Accurate point-cloud segmentation of cotton organs is essential for precise phenotypic characterization. However, reliable instance segmentation of cotton bolls in field-derived point clouds remains challenging because foliage occlusion, contact between adjacent bolls and incomplete reconstruction obscure instance boundaries. Here we present RQ-PointNeXt, an end-to-end framework that directly maps input point clouds to boll instance masks within a unified trainable network. Built on PointNeXt, it incorporates relative-elevation geometric channel attention in the shallow encoder to fuse global channel context with elevation and surface-normal cues. Its Query–mask branch integrates semantic guidance, center-seeded queries and a center-aware mask prior to suppress background responses, localize instances and constrain mask extent. Hungarian matching and multitask optimization establish one-to-one query–instance assignments, whereas query-based decoding produces instance masks without external geometric clustering. We evaluated the framework on 226 field-grown cotton plants containing 720 annotated boll instances reconstructed from UAV multi-view imagery using neural radiance fields. On the held-out test set, overall accuracy, mean class accuracy and mean intersection over union reached 0.8942, 0.8980 and 0.8076, respectively. AP25, AP50 and AP75 were 0.7359, 0.5585 and 0.2777, yielding an mAP25/50/75 of 0.5240. The framework provides instance-level outputs for boll counting and spatial analysis in high-throughput field phenotyping.
Why it matches plant phenotyping methods綿花ボールの点群インスタンス分割を開発・評価し、計数や空間解析に利用可能な植物器官表現型を抽出する方法が中心である。
abstractHere we present RQ-PointNeXt, an end-to-end framework that directly maps input point clouds to boll instance masks within a unified trainable network.
Reproduction assets foundThe paper's own field cotton point-cloud dataset (226 plants, 720 annotated bolls) is only available upon request. However, the authors directly used the public UGA-BSAIL Cotton Plants with Foliage point-cloud dataset (with their added boll instance annotations) as an evaluation benchmark for RQ-PointNeXt, and it is公开发Dataset · publict to the pointwise overlap between
predicted and ground-truth instances.
To further evaluate the proposed method under conditions of relatively high point-
cloud completeness, experiments were conducted using the public UGA-BSAIL Cot-
ton Plants with Foliage dataset. The point-cloud data are publicly available through
Figshare (https://figshare.com/projects/Cotton_plant_with_foliage/258065, accessed on
8 September 2026), while the associated code and documentation are hosted on GitHub
(https://github.com/UGA-BSAIL/Cotton_plants_with_foliage, accessed on 8 September
2026). The dataset contains relatively complete cotton plant point clouds, surface-normal
attributes, and semantic labels distinOpen asset ↗Figshare · Cotton_plant_with_foliage/258065pdf-raw-page:16 lines:1-52Code / dataset availability confirmedCrossref · checked 15 Sept 2026
Published11 Sept 2026Journal of the Nigerian Society of Physical Sciences
Field / plotLeafClassificationStress / disease detectionDisease symptoms / severity
Plant diseases threaten agricultural productivity, and automated image analysis can support early identification of visible disease symptoms. This study introduces HybOptic-CNN, a convolutional neural network (CNN) whose learning rate and batch size are selected using a hybrid Whale Optimization Algorithm--Grey Wolf Optimizer (WOA-GWO). Nine disease classes were selected from the 22-class CCMT field-image dataset, and 152 local farm leaf images were collected in Enugu State, Nigeria. Of the local images, 122 (80.3%) were added to the model-development data for training and validation, whereas 30 (19.7%) formed an independent Nigerian hold-out set excluded from augmentation, class balancing, early stopping, validation, and hyperparameter selection. Across 10 model-development runs, the optimized model achieved 96.8 ± 0.4% mean validation accuracy, 95.2 ± 0.5% macro-precision, 94.9 ± 0.6% macro-recall, and 95.0 ± 0.5% macro-F1, compared with 90.3 ± 0.9% validation accuracy and 86.3 ± 1.2% macro-F1 for the baseline. The optimized model improved mean validation accuracy by 6.5 percentage points and converged 14.6 epochs earlier. On the independent 30-image Nigerian hold-out, HybOptic-CNN achieved 93.3% accuracy and 93.1% macro-F1 across four represented disease classes. A web application integrating the trained classifier was also demonstrated. These results support improved model-development performance through hybrid hyperparameter selection and motivate broader multi-location field evaluation.
Why it matches plant phenotyping methods植物の可視病徴を画像から分類するCNN手法を開発・検証しており、病害状態のフェノタイピング手法が中心である。
abstractautomated image analysis can support early identification of visible disease symptoms
Reproduction assets foundThe paper's Data availability statement points to two public sources: a Mendeley dataset (the locally collected Nigerian field images) and the Kaggle CCMT plant disease dataset used as the principal image source. Only the Kaggle URL matches an allowed URL; the Mendeley URL is not in the allowed list, so only the CCMT/KDataset · publicnt and independent field-test data and should pub-
lish the class-wise split manifest, random seeds, WOA-GWO
numerical settings, and evaluation code so that the reported pro-
cedure can be reproduced and extended.
Data availability
The data used in this study are available at https://
data.mendeley.com/datasets/bwh3zbpkpv/1 and https://www.kaggle.com/datasets/rahimanshu/ccmt-plant-disease-dataset.Declaration of competing interest
The authors declare that they have no known competing fi-
nancial interests or personal relationships that could have ap-
peared to influence the work reported in this manuscript.
Funding
The authors received no specific funding from any public,
commercial, or not-fOpen asset ↗Kaggle · rahimanshu/ccmt-plant-disease-datasetpdf-raw-page:12 lines:1-78Code / dataset availability confirmedEurope PMC · checked 15 Sept 2026
Abstract Tomato leaf diseases (TLDs) such as Early Blight (EB), Late Blight (LB), and Leaf Mold (LM) have a negative impact on crop yield and quality, result-ing in economic losses in agriculture. Traditional diagnosis methods depend on the visual recognition of a disease, which are time-consuming, subjective and may be difficult to reach in rural settings. Keeping these drawbacks in mind, the present work introduces a Transfer Learning model for tomato leaf disease classification based on EfficientNetB3 network. A pretrained Ef-ficientNetB3 network, trained on ImageNet, is used to obtain discriminative features like lesion boundaries, discoloration, fungal textures, and infection spots. Images are cropped to 224 × 224 pixels and split into training, validation and test set. The proposed architecture employs Global Average Pooling, a dense layer with ReLU activation, drop out regularization and Softmax classifier for classification of tomato leaf images into four classes: Early Blight, Late Blight, Leaf Mold and Healthy. Experimental results show the high classification accuracy and low training, validation and test-ing losses. Inter-class misclassifications of the confusion matrix show very few, which supports good generalization. Moreover, Grad-CAM visualiza-tions can generate interpretable heat maps that point to the regions of the image affected by the disease, and multi-class ROC analysis gives high AUC values, which means that it has excellent class separability. The proposed framework provides a precise, reliable, and interpretable approach for auto-mated tomato leaf disease diagnosis, contributing to precision agriculture by assisting in early detection and prompt management of tomato diseases.
Why it matches plant phenotyping methodsトマト葉画像から病害状態を推定する深層学習手法が研究の中心であり、Grad-CAMによる病変領域の解釈と性能評価も行っているため、植物表現型計測手法として採択。
abstractthe present work introduces a Transfer Learning model for tomato leaf disease classification based on EfficientNetB3 network
Reproduction assets foundThe paper's tomato leaf disease classification uses a publicly available Kaggle dataset (PlantVillage-derived tomato leaf images, 4000 images across 4 classes), explicitly declared in the Data Availability statement with a public URL. No author code, trained models, or other paper-specific assets are disclosed.Dataset · publicitted in accordance with the Journal policies.
Permission to use third-party material
Images or figures are never published previously and did not take from any
internet resources.
Data Availability
The dataset used in this study is publicly available from the PlantVillage
tomato leaf disease dataset on Kaggle’s following link:
https://www.kaggle.com/datasets/kaustubhb999/tomatoleaf
Acknowledgements
The authors would like to thank SR University, Warangal, Telangana,
INDIA and Sharda University, Greater Noida, Uttar Pradesh, INDIA for
providing research facilities and computational resources to carry out this
work.Open asset ↗Kaggle · kaustubhb999/tomatoleafpdf-raw-page:20 lines:1-18Code / dataset availability confirmedEurope PMC · checked 15 Sept 2026
Abstract Maize plant plays crucial role not only in the field of agriculture but also in global economy, since it is the third most cultivated crop across the globe. However, these plants are usually affected by various types of diseases such as blight, common rust, gray leaf spot, etc., protecting the plants from these disease is very important. This research proposes a new deep learning model for disease detection to perform well than other models. The hybrid model uses MobileNetV3 as the backbone architecture integrated with attention, fusion and head. The framework includes data preprocessing, feature extraction, classification and interpretation. We will compare the performance of this model with other models such as VGG16, ResNet50, DenseNet121, ALEXNET, etc. criteria for the final evaluation includes Accuracy, Precision, Recall, F1score, Specificity, Logloss, AUC-ROC curve. Through this proposed model we have achieved an accuracy of 98% which is high than the other models compared. The lightweight nature of MobileNetV3 enables us to implement the model in the mobile and IoT devices also. The present study contributes to the development of deep learning model in the field of agriculture, offering a efficient solution for early maize leaf disease detection.
Why it matches plant phenotyping methodsトウモロコシ葉の病徴を画像から検出・分類する深層学習手法の開発と比較が中心であり、植物病害状態の画像ベース表現型計測に該当する。
abstractThis research proposes a new deep learning model for disease detection to perform well than other models.
Reproduction assets foundThe paper's maize leaf disease detection model (MAFH) was trained and evaluated entirely on a public Kaggle image dataset, which the authors explicitly declare in the Data Availability statement. No author code, trained model checkpoints, or other paper-specific assets are stated as publicly available.Dataset · publicig and real-
time datasets and in all the environmental situations.
Funding: This research received no external funding.
Disclosure statement: The authors declare no conflict of interest.
Data Availability
The datasets generated and/or analyzed during the current study are available in the CORN OR
MAIZE LEAF DATASET repository,
https://www.kaggle.com/datasets/smaranjitghose/corn-or-maize-leaf-disease-datasetOpen asset ↗Kaggle · corn-or-maize-leaf-disease-datasetpdf-raw-page:27 lines:1-34Code / dataset availability confirmedEurope PMC · Crossref · checked 15 Sept 2026
Published4 Sept 2026Springer Science and Business Media LLC
Abstract Plant diseases substantially reduce global crop yields, and cotton production is particularly vulnerable to field-acquired variability in symptom appearance, background clutter, and illumination changes that limit the reliability and scalability of expert visual inspection. This study aimed to develop an accurate, computationally efficient, and explainable framework for real-time cotton leaf disease recognition that is suitable for deployment on resource-constrained edge devices. Using the SAR-CLD-2024 dataset (322 RGB images captured under natural agricultural conditions across seven categories, including healthy and diseased leaves), images were preprocessed via resizing and normalization and augmented online in the training set (random rotations, flips, brightness/contrast adjustments, and random cropping). An EfficientNet-B3 backbone initialized with ImageNet-pretrained weights was fine-tuned using categorical cross-entropy loss and Adam optimization, with early stopping, checkpointing, regularization, and a fixed-seed 70/15/15 train–validation–test partition to enhance reproducibility and reduce leakage. Performance was evaluated on an independent test set using accuracy, precision, recall, F1-score, MCC, balanced accuracy, Cohen’s kappa, confusion matrix, multi-class ROC/AUC, and precision–recall analysis, alongside computational benchmarking (parameters, FLOPs, memory, and inference latency) and comparative experiments against contemporary CNN, lightweight, and transformer-based models. The model showed stable convergence over 30 epochs with a small training–validation gap, predominantly correct predictions with limited confusion among visually similar classes, consistently high precision–recall behavior under moderate class imbalance, and stable performance across repeated runs with low variability and a tight confidence interval. Grad-CAM heatmaps localized necrotic lesions, discoloration, and infected tissues while largely ignoring background, and failure cases were associated with early-stage symptoms, occlusion, shadows, and inter-class similarity. Overall, the framework provides a reproducible, interpretable, and efficient solution for cotton leaf disease classification with practical implications for trustworthy, low-latency, on-device decision support in precision agriculture.
Why it matches plant phenotyping methods綿葉の病徴を画像から分類する深層学習手法の開発が中心で、独立テスト、比較評価、計算性能評価、Grad-CAMによる病徴局在化を実施しているため、植物病害フェノタイピング手法に該当する。
abstractThis study aimed to develop an accurate, computationally efficient, and explainable framework for real-time cotton leaf disease recognition
Reproduction assets foundThe paper's Data Availability statement explicitly names the SAR-CLD-2024 cotton leaf dataset used for all experiments as publicly available on Kaggle with a direct URL. No author analysis code or trained model checkpoint is deposited.Dataset · publicntribute to the development of fully automated, scalable, and real-time smart agriculture
systems.
Declaration
Funding
Datta Meghe Institute of Higher Education and Research Wardha, Maharashtra, India
Data Availability: The SAR-CLD-2024 cotton leaf dataset used in this study is publicly
available through the Kaggle platform at: https://www.kaggle.com/datasets/pantho12/sar-cld-2024-dataset-for-cotton
This dataset includes annotated images of various cotton leaf diseases collected under diverse
environmental conditions. All data utilized in this work are freely accessible, and the data
processing methodology has been described in detail to facilitate reproducibility.
Conflict of interest The aOpen asset ↗Kaggle · SAR-CLD-2024pdf-raw-page:32 lines:1-38Code / dataset availability confirmedEurope PMC · checked 15 Sept 2026
Abstract Maize is the staple crop for millions of people in Sub-Saharan Africa, particularly for Zambia. Unfortunately, maize crops are exposed to several serious threats due to their susceptibility to foliar diseases like Maize Rust, Leaf Blight, Leaf Spot, Maize Streak Virus, and Maize Lethal Necrosis that may lead to great yield losses. Conventional methods of crop disease identification consist of field surveys that are not only subjective but also difficult to conduct for smallholder farmers. This paper presents the design and evaluation of a highly optimized version of the EfficientNet-B0 Convolutional Neural Network for the automatic detection of maize leaf diseases using maize leaf images obtained from real-world scenarios. The proposed model utilized the concept of transfer learning with ImageNet pre-trained weights and was trained on the Mendeley Maize Crop Disease (Leaf) Dataset which consists of 30,120 images in nine maize disease classes. The developed fine-tuned EfficientNet-B0 yielded 97.57% classification accuracy, macro precision of 97.61%, macro recall of 97.64%, and macro F1-score of 97.61%. From these results, it is evident that transfer learning and fine-tuning greatly boost maize disease classification accuracy while ensuring high computational efficiency. This study makes a significant contribution to precision agriculture as it offers an accurate and computationally efficient AI-based maize disease classification model, which could help smallholder farmers in early maize disease classification.
Why it matches plant phenotyping methodsトウモロコシ葉画像から病害状態を推定する深層学習モデルを開発・評価しており、植物病害表現型の取得・分類手法が中心的な研究です。
abstractThis paper presents the design and evaluation of a highly optimized version of the EfficientNet-B0 Convolutional Neural Network for the automatic detection of maize leaf diseases using maize leaf images obtained from real-world scenarios.
Reproduction assets foundThe paper's sole qualifying asset is the public Mendeley Maize Crop Disease (Leaf) Dataset of maize leaf images used for all phenotyping/classification measurements, explicitly declared publicly available with a URL. No author analysis code, trained model checkpoints, or other paper-specific assets are disclosed.Dataset · publiconflicts of interest to publish the paper.
Consent to Publish
All authors have read and approved the final version of the manuscript and agree to its
submission to Discover Networks.
Consent to Participate
Not applicable
Data Availability
The Mendeley Maize Crop Disease (Leaf) Dataset used in this study is publicly available at
https://data.mendeley.com/datasets/6w6gsvghfw
Clinical Trial Number
Not applicable.
Ethics Declaration:
Not applicable.
Competing interests
All authors declare no competing interests.Open asset ↗Mendeley · 6w6gsvghfwpdf-raw-page:55 lines:1-22Code / dataset availability confirmedEurope PMC · checked 15 Sept 2026
Background Olive ( Olea europaea L.) breeding initiatives rely heavily on the extensive and correct characterisation of genetic resources to successfully achieve their goals, such as addressing climate change and emerging diseases challenges. However, the historical lack of standardised phenotyping protocols across multi-environment trials has severely hindered data interoperability and large-scale comparative analyses. Methods Within the Horizon 2020 GEN4OLIVE project, five international olive germplasm banks established a consensus-based methodological framework to systematically evaluate over 500 olive cultivars. We harmonised 14 evaluation protocols covering six fundamental dimensions: phenological and agronomic traits, abiotic stress resilience, biotic stress resilience, olive oil yield and chemical quality, table olive quality assessment, and morphological characterisation and photography. While most protocols were adapted from previously published literature to ensure ease of implementation across different facilities, novel methodologies for frost tolerance and standardised photography were developed de novo. Results The implementation of these consensus methods across five countries proved highly successful. This methodological framework enabled the generation of the largest harmonised, publicly available dataset on olive genetic resources to date, effectively making possible the correct comparation and ranking of the olive cultivars based on their specific characteristics. Conclusions This compendium of methods provides a robust, highly replicable reference point for the standardisation of olive germplasm characterisation and use of shared benchmark cultivars as an effective way for data normalization and comparation. It facilitates future global pre-breeding efforts, ensures international data interoperability, and supports the discovery of resilient cultivars to secure the future of the olive sector.
Why it matches plant phenotyping methodsオリーブ遺伝資源の標準化フェノタイピングプロトコルを体系化し、複数機関で実装・検証して大規模データセットを生成した方法論中心の研究である。
abstractthe historical lack of standardised phenotyping protocols across multi-environment trials has severely hindered data interoperability and large-scale comparative analyses.
Reproduction assets foundThe article declares two paper-specific public assets: the GEN4OLIVE phenotypic dataset from evaluating over 500 olive accessions across five germplasm banks, hosted on the project's Olive Varieties Database, and a Zenodo-deposited methodological handbook (Extended Data) containing the 14 protocols, visual assessment, Dataset · publicData and software availability
The phenotypic dataset generated from the evaluation of over 500 olive varieties across the five Mediterranean
germplasm banks using this compendium of protocols and methodologies, is publicly available via the GEN4OLIVE
project repository.
• Repository: GEN4OLIVE Olive Varieties Database.
• Link: https://www.uco.es/ucolivo/gen4olive/olivevarieties (GEN4OLIVE Database, 2025).
Page 8 of 15
Open Research Europe 2026, 6:322 Last updated: 14 SEP 2026Open asset ↗GEN4OLIVE Olive Varieties Databasepdf-raw-page:8 lines:1-44Code / dataset availability confirmedCrossref · checked 14 Sept 2026
Rice panicle blast detection is an important task in plant disease phenotyping. Field-based detection remains challenging because infected spike regions are often small, sparse, elongated, and affected by overlapping panicles, complex backgrounds, and variable illumination. In this study, we propose RPB-YOLO11, a lightweight YOLO11-based detector designed for rice panicle blast detection. The model uses a Lightweight Ghost Backbone (LGB) to reduce redundant computation. It uses Anisotropic Axial Stripe Attention (A2SA) to represent elongated panicle structures. It also uses Focal Multi-Scale Attention (FMSA) for multi-scale feature refinement and Adaptive Geometric Shape IoU (AGS-IoU) for geometry-aware localization. The model was trained and evaluated on a rice panicle image dataset containing 1,055 training images, 69 validation images, and 169 test images. On the test set, RPB-YOLO11 achieved 76.09% mAP50, 45.44% mAP50-95, 73.98% precision, and 72.75% recall with 6.21 GFLOPs. Compared with the YOLO11n baseline, it improved mAP50, mAP50-95, precision, and recall by 2.73, 2.12, 1.64, and 2.11 percentage points, respectively. An Android-oriented inference application supports local image inference, detection visualization, class counting, and diseased-panicle incidence estimation. These results suggest that RPB-YOLO11 provides a practical approach for image-based rice panicle blast survey.
Why it matches plant phenotyping methodsイネ穂いもちの画像検出モデルを開発・比較検証し、罹病穂率を推定する実用アプリまで構築しており、植物病害状態の画像ベース表現型取得が中心である。
abstractIn this study, we propose RPB-YOLO11, a lightweight YOLO11-based detector designed for rice panicle blast detection.
Reproduction assets foundThe paper links a public Hugging Face dataset used to establish the rice panicle blast detection dataset and a public GitHub release (data availability statement) containing the study's datasets/models.Dataset · publicsites, cultivars, growth stages, imaging conditions, and disease severities are still needed to evaluate generalization more fully.
Statements
Data availability statement
The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: https://github.com/XuzheYang2Doc/RPB-YOLO11/releases/tag/rpb-yolo11 .
Author contributions
XY: Data curation, Formal analysis, Investigation, Methodology, Software, Validation, Visualization, Writing – original draft, Writing – review & editing. XZ: Conceptualization, Methodology, Visualization, Writing – original draft, Writing – review & editing. CX: Formal analysisOpen asset ↗XuzheYang2Doc/RPB-YOLO11 · rpb-yolo11lines:639-658Code / dataset availability confirmedCrossref · checked 15 Sept 2026
Automated plant disease classification from leaf images demands models that jointly achieve high accuracy and efficient training convergence. Standard deep learning approaches process images through a single feature pathway, limiting their ability to capture diverse visual manifestations such as color changes, texture patterns, and spatial distributions. This paper introduces DMCNNA-FBVL, a framework integrating two complementary innovations: (1) a Deep Multi-Component Neural Network Architecture (DMCNNA) employing three specialized pathways processing color-space statistics, texture descriptors, and raw image features before fusing them through SoftMax-weighted aggregation; and (2) Feedback-Based Validation Learning (FBVL), a training strategy that periodically blends validation-set gradients into weight updates to accelerate convergence. Experiments on the New Plant Diseases Dataset (87,000 images, 38 classes) show that DMCNNA-FBVL achieves 98.7% accuracy, 98.8% precision, 98.6% recall, and 98.7% F1-score, outperforming ResNet-50 by 3.2 percentage points ( 𝑝 < 0 . 0 0 1 ). The primary reported metrics are computed exclusively on an independent 10% hold-out test set, whereas the separate 10% validation partition is used during training for FBVL gradient blending and does not contribute to final test evaluation. Five-fold cross-validation confirms stability (98.7% ± 0.15%). Ablation experiments confirm additive gains, while FBVL reduces wall-clock training time by 15% through faster convergence.
Why it matches plant phenotyping methods葉画像から植物病害を分類するニューラルネットワークと学習戦略の開発・検証が研究の中心であり、植物の病害状態を直接推定している。
abstractAutomated plant disease classification from leaf images demands models that jointly achieve high accuracy and efficient training convergence.
Reproduction assets foundThe paper's plant disease classification experiments use the New Plant Diseases Dataset, which the authors state is publicly available on Kaggle. The authors' code and trained models are only promised 'upon acceptance' (no public URL), so they do not qualify as public assets.Dataset · publicral
monitoring systems.
Declaration of competing interest
The authors declare that they have no known competing financial interests or personal relationships that could have
appeared to influence the work reported in this paper.
Data availability
The New Plant Diseases Dataset used in this study is publicly available on Kaggle (https://www.kaggle.com/datasets/vipoooool/new-plant-diseases-dataset). Code and trained models will be made available upon
acceptance.
Funding
This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit
sectors.
Acknowledgments
[Removed for double-blind review.]
CRediT authorship contribution statement
[Removed fOpen asset ↗Kaggle · new-plant-diseases-datasetpdf-raw-page:19 lines:1-59Code / dataset availability confirmedEurope PMC · checked 14 Sept 2026
Southern corn leaf blight (SCLB) is caused by the fungal pathogen Bipolaris maydis (syn. Cochliobolus heterostrophus Drechsler) and is a common disease of fall crops of sweet corn. Phenotyping for SCLB resistance is performed through visual scoring, which is subjective and may limit genetic gain for this quantitative trait. As an alternative, we integrated computer vision (CV)-based phenotyping, genome-wide association studies (GWASs), and predictive breeding approaches to dissect the genetic basis of SCLB resistance. We utilized a sweet corn diversity panel with 693 genotypes, for which whole-genome resequencing produced a high-density single-nucleotide polymorphism (SNP) dataset. Broad-sense heritability for visual scoring ranged from 0.44 to 0.73, while CV-based phenotyping produced estimates ranging from 0.56 to 0.73 in multi-environment resistance trials conducted across 5 years and three locations. We performed GWAS using 16,755,210 SNPs and identified 41 associated SNPs. Genomic selection (GS) models on visual scoring phenotypes achieved moderate prediction accuracies under cross-validation of untested genotypes across characterized environments (0.22-0.47) and high prediction accuracies when predicting tested genotypes in uncharacterized environments (0.49-0.68). Using CV-based phenotypes for GS, we observed prediction accuracies of 0.45-0.47 under the untested genotypes in the characterized environments cross-validation scheme and 0.59-0.62 under the tested genotypes in the uncharacterized environments scheme. GS demonstrated reliability for ranking the individuals across a gradient of environments. These findings identify candidate loci and predictive breeding strategies to accelerate the development of resistant sweet corn cultivars.
Why it matches plant phenotyping methodsCVベースの病害抵抗性表現型測定を視覚評定と比較し、多環境・多年次試験で妥当性を評価しており、フェノタイピング手法が研究の中心である。
abstractPhenotyping for SCLB resistance is performed through visual scoring, which is subjective and may limit genetic gain for this quantitative trait.
Reproduction assets foundThe authors state that all datasets (phenotype data) and analysis code (CV phenotyping script, customized GAPIT script) are publicly available in their GitHub repository, which is listed in allowed_urls.Code · publiche images taken for each plot were saved in JPG format and analyzed using a CV method. Here, we refer to the CV method as a custom Python script written using the OpenCV library version 4.5.0, a set of tools for CV (Bradski, 2000 ). The Python script used for leaf CV image analysis is available in our public GitHub repository ( https://github.com/Resende‐Lab/SCLB‐Disease ).
FIGURE 1
Leaf imaging set up with QR‐coded plot IDs (bottom right) and color checker for computer vision phenotyping of southern corn leaf blight disease severity in sweet corn.
In the CT19 environment, a black cloth attached to a wooden board was used as the background. A wooden frame was used to clamp the leaves down toOpen asset ↗Resende‐Lab/SCLB‐Diseaselines:199-209Dataset · publicBLUP and BayesB model implemented in BGLR.
ACKNOWLEDGMENTS
This work was supported by the National Institute of Food and Agriculture USDA‐NIFA2018‐51181‐28419, USDA‐NIFA2019–05410, and USDA‐NIFA 2022–51181‐38333.
DATA AVAILABILITY STATEMENT
All the datasets and codes used in this study are available in the following repository: https://github.com/Resende‐Lab/SCLB‐Disease
REFERENCES
Amadeu , R. R.
,
Cellon , C.
,
Olmstead , J. W.
,
Garcia , A. A. F.
,
Resende , M. F. R.
, &
Muñoz , P. R.
( 2016 ).Open asset ↗Resende‐Lab/SCLB‐Diseaselines:566-596Code / dataset availability confirmedOpenAlex · Europe PMC · Crossref · checked 14 Sept 2026
Grain yield is a central target in wheat breeding, yet accurately predicting it remains challenging because it depends on many genes and responds strongly to environmental variation. Genomic selection (GS) has improved breeding efficiency by enabling genome-based prediction of genetic merit, but predictability (PA) for grain yield is often limited under stress environments. At the same time, advances in high-throughput phenotyping (HTP) using unmanned aerial vehicles (UAVs) provide phenomic data that capture environment-responsive plant performance and may complement genomic information. In this study, we evaluated genomic and phenomic models for predicting grain yield in elite bread wheat lines across irrigated, drought, and heat-stress environments. Using a sparse phenotyping framework, we compared parametric and non-parametric models. PA was evaluated within environments and under cross-environment sparse phenotyping scenarios. Genomic models provided a stable baseline and enabled effective information sharing across environments when phenotypic data were incomplete. Phenomics-only models captured environment-specific plant responses but were more sensitive to environmental context. Multiomics models that integrated genomic and phenomic information consistently achieved the highest PA, with the largest gains observed under stress conditions. Overall, our results demonstrate that integrating genomics and UAV-based phenomics within sparse phenotyping designs offers a practical and scalable approach to improve grain yield prediction in wheat.
Why it matches plant phenotyping methodsUAV由来のフェノミクスを用いた疎な表現型取得と予測モデルを中心に、環境横断で評価しており、収量という植物形質の推定手法が主要な貢献である。
abstractadvances in high-throughput phenotyping (HTP) using unmanned aerial vehicles (UAVs) provide phenomic data that capture environment-responsive plant performance
Reproduction assets foundThe paper's grain yield BLUEs, spectral wavelength BLUEs, and genotypic data are publicly deposited in the CIMMYT data repository (https://doi.org/10.71682/10549399), directly reproducing this paper's phenotyping measurements. No author analysis code with a public URL is stated; other URLs are generic tools/services.Dataset · publicok.com.
Paolo Vitale, Email: p.vitale@cgiar.org.
DATA AVAILABILITY STATEMENT
The datasets generated and analyzed during this study, including best linear unbiased estimates (BLUEs) for grain yield and spectral wavelengths, as well as the corresponding genotypic information, are publicly available in the CIMMYT data repository ( https://doi.org/10.71682/10549399 ).
REFERENCES
Araus, J. L.
,
Kefauver, S. C.
,
Zaman‐Allah, M.
,
Olsen, M. S.
, &
Cairns, J. E.
(2018). Translating high‐throughput phenotyping into genetic gain. Trends in Plant Science, 23(5), 451–466. 10.1016/j.tplants.2018.02.001
Brault, C.
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Lazerges, J.
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Doligez, A.
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Thomas, M.
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Ecarnot, M.
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Roumet, P.
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Bertrand, Y.Open asset ↗CIMMYT data repository · 10.71682/10549399lines:280-433Code / dataset availability confirmedEurope PMC · checked 15 Sept 2026
Surface phenotyping underpins plant science, preclinical animal research and entomology, yet across all three the measurement is almost always a photograph, which records a projection and not the surface itself. Here we present the Gentschinator3000 , an open structured-light platform that brings high-end metric surface measurement within reach of laboratories with no optics expertise, combining documented open hardware, open reconstruction software and analysis workflows for under 4000 Euro in components. It resolves a planar reference to 45 µm local flatness, registers full rotations to a loop closure of 156 µm, and performs stably across acquisition ranges that we define. Applying one workflow to a leaf before and after desiccation, to murine anatomy and to a spread lepidopteran, we find that projection underestimates surface area by 11 to 41 %. That error grows with the condition under study, with the evaluation scale and with the direction of view, so it can confound phenotype comparisons dramatically. In murine limbs a 15-degree change of viewing direction shifts a projected inter-segment angle by up to 23.2 degrees, while the three-dimensional angle does not move. Projection geometry can therefore contribute as much to a measured phenotype as the biology it is meant to quantify.
Why it matches plant phenotyping methods植物表面の三次元形状を測定するオープンな構造化光プラットフォームと再構成・解析ワークフローを開発し、葉で投影バイアスを評価しており、表現型取得手法が中心である。
abstractHere we present the Gentschinator3000 , an open structured-light platform that brings high-end metric surface measurement within reach of laboratories with no optics expertise, combining documented open hardware, open reconstruction software and analysis workflows for under 4000 Euro in components.
Reproduction assets foundThe paper explicitly deposits three public Zenodo records: reconstructed 3D surfaces of all specimens (including the leaf and hop cone phenotyping measurements), the authors' analysis notebooks with derived and per-panel source data, and the reconstruction software with build documentation and working examples. All areDataset · publicData availability
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hardware design files under CERN-OHL-P v2. The visible-light platform described
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hereOpen asset ↗Zenodo · 10.5281/zenodo.22167598pdf-raw-page:35 lines:1-52Code / dataset availability confirmedCrossref · checked 11 Sept 2026
Rice leaf diseases pose a significant threat to global food security by reducing crop productivity and causing substantial economic losses. The traditional diagnosis method is manual method, which is low in efficiency, subjective and not suitable for large-scale agricultural monitoring. Despite the advances in automated disease detection using deep learning methods like CNNs, GANs, and transfer learning models, these techniques remain highly computational, not very flexible, and struggle to perform well in different imaging scenarios. Considering these drawbacks, this paper introduces an Explainable Deep Q-Learning based CNN framework which employs CNN-based feature extraction and Deep Q-learning-based adaptive policy optimization for rice leaf disease classification. The proposed model continuously refines the classification actions through reward-based learning, which makes the model more robust in various agricultural imaging environments, in contrast to traditional supervised CNN models that have static classification decisions. The proposed model achieved 98.5% accuracy, 98.52% precision, 98.50% recall, and a 98.51% F1-score, outperforming existing CNN, GAN, reinforcement learning, and transformer-based methods. It also offers a high computational efficiency of 14.2 GFLOPs, 248 MB memory consumption, ~ 48 min of training time, and 6.8 ms inference time per image suitable for resource constrained applications in agriculture. The results demonstrate the effectiveness, scalability, and practical applicability of the proposed framework. The proposed framework performs well on benchmark datasets but more research in the deployment of the edge-devices under different real-world agricultural settings will be investigated in future work.
Why it matches plant phenotyping methodsイネ葉の病害状態を画像から分類する深層学習手法の開発・評価が研究の中心であり、植物の病害表現型を直接推定しているため。
abstractthis paper introduces an Explainable Deep Q-Learning based CNN framework which employs CNN-based feature extraction and Deep Q-learning-based adaptive policy optimization for rice leaf disease classification.
Reproduction assets foundThe paper trains its Deep Q-CNN rice leaf disease classifier on public Kaggle rice leaf image datasets, which are cited with explicit public URLs and qualify as paper-specific phenotyping image inputs. The authors' own derived data/analysis artifacts are only available upon request, so no authors' code or trained modelDataset · publicSoni Gautam. Rice Leaf Bacterial and Fungal Disease Dataset. Kaggle. Available:Open asset ↗Kagglepdf-page:24 lines:1-94Code / dataset availability confirmedCrossref · checked 15 Sept 2026
Plant diseases are still posing a challenge to the productivity, quality of crops, and food security, especially in locations where field diagnosis is based on manual visual inspec-tion. This paper assesses deep learning network-based automated classification of plant leaf diseases on public RGB leaf-image datasets, such as the Kaggle New Plant Diseases Dataset (Augmented) and PlantVillage images. They investigated four archi-tectures: EfficientNetV2B0, ResNet152V2, DenseNet201, and one hybrid Vision Trans-former (ViT)-based model. The steps of the experiment involved loading the dataset, exploratory analysis, preprocessing, resizing, normalizing, augmentation, transfer learning, independent model training, and evaluation metrics such as accuracy, preci-sion, recall, F1-score, training curves, testing results, and confusion matrices. The hy-brid ViT-based model was reported to have the best accuracy of 99.5%. On the smaller seven class subset of PlantVillage, EfficientNetV2B0 scored 98.11%. On the 38-class dataset, DenseNet201 improved test accuracy (97.34) and validation classification ac-curacy (around 98). ResNet152V2 scored 97.01 on the 38-class test set. The results demonstrate that CNN and transformer-based models can help to recognize plant diseases accurately whereas hybrid attention-based structures provide a promising path to enhance fine-grained classification. Since the model notebooks had varying class settings and splits, the comparison is seen as a model-structured assessment as opposed to a precisely identical benchmark across all architectures.
Why it matches plant phenotyping methods植物葉画像から病害状態を分類する深層学習手法を複数モデルで比較・評価しており、病害表現型の取得・抽出と技術検証が研究の中心である。
abstractThis paper assesses deep learning network-based automated classification of plant leaf diseases on public RGB leaf-image datasets
Reproduction assets foundThe paper's phenotyping inputs are two public plant leaf-image datasets explicitly named in the Data Availability statement: the Kaggle New Plant Diseases Dataset (Augmented) and the PlantVillage dataset, both with public URLs. No author code, models, or supplementary materials are deposited (supplementary materials: 'Dataset · publicy available. Plant leaf images were
obtained from the Kaggle New Plant Diseases Dataset (Augmented) and PlantVillage
datasets. The datasets contain publicly accessible RGB images of healthy and diseased
plant leaves used for supervised image classification research.
DATASET SOURCES
Kaggle New Plant Diseases Dataset (Augmented):
https://www.kaggle.com/datasets/vipoooool/new-plant-diseases-dataset
PlantVillage Dataset: https://plantvillage.psu.edu/All processed data, experimental configurations, and model implementation details are
described within the manuscript. Additional materials may be made available from the
corresponding author upon reasonable request.
ACKNOWLEDGMENTS
The author acknowOpen asset ↗Kaggle · new-plant-diseases-datasetpdf-raw-page:24 lines:1-23Dataset · publicgmented) and PlantVillage
datasets. The datasets contain publicly accessible RGB images of healthy and diseased
plant leaves used for supervised image classification research.
DATASET SOURCES
Kaggle New Plant Diseases Dataset (Augmented):
https://www.kaggle.com/datasets/vipoooool/new-plant-diseases-dataset
PlantVillage Dataset: https://plantvillage.psu.edu/All processed data, experimental configurations, and model implementation details are
described within the manuscript. Additional materials may be made available from the
corresponding author upon reasonable request.
ACKNOWLEDGMENTS
The author acknowledges Istanbul Aydin University for academic support and research
guidance duringOpen asset ↗PlantVillagepdf-raw-page:24 lines:1-23Code / dataset availability confirmedCrossref · checked 15 Sept 2026
Precision agriculture is becoming more and more of a challenge that requires the use of intelligent systems that are able to predict stress and prevent yield loss before it is too late. Traditional methods of agricultural surveillance are predominantly reactive with irrigation demands being based on thresholds or individual yield forecasts models that do not represent the intricate spatio-temporal interactions that exist between crop physiology, soil status, and environmental stresses. Besides, the majority of the current practices do not have an autonomous decision-making approach to preventive intervention which leads to inefficient use of water and slows down the response to stress. This paper suggests a cognitive UAV-assisted agro-surveillance system to predict yield vulnerability caused by crop stress and optimize adaptive irrigation with the help of spatio-temporal deep and reinforcement learning. The framework combines UAV-obtained RGB and multispectral and thermal imagery with measurements of soil sensors and meteorological data obtained with the Crop Health and Environmental Stress Dataset. A new GeoSpatio-TRiNet model is used to acquire long-range spatial relationship, time stress development, and diffusion of stresses across agricultural regions. The model predicts the vulnerability trajectories of the stress instead of the direct yield regression, and this allows early detection of yield risk. Such predictions serve to generate a cognitive environmental state of a Soft ActorCritic (SAC) reinforcement learning agent that autonomously computes zone-based irrigation behaviors to reduce the recurrence of stress at the minimum water usage cost. As shown by the results of the experiment, the proposed framework has a stress forecasting accuracy of 96.3% and performs much better than the traditional machine learning, CNN-based, and transformer-based baselines. The system also decreases the predicted yield vulnerability by 46.6 and enhances water-use efficiency by 41.1 as compared to irrigation strategies based on rules. The results confirm the usefulness of spatio-temporal intelligence with predictive control in terms of effectiveness, and the proposed framework is a scalable and sustainable solution to precision agriculture of the next generation.
Why it matches plant phenotyping methodsUAV画像とセンサーデータから作物ストレスの時系列状態および収量脆弱性を推定する計算・センシング手法が研究の中心であり、灌漑制御への応用も技術評価の一部として記述されている。
abstractThe framework combines UAV-obtained RGB and multispectral and thermal imagery with measurements of soil sensors and meteorological data
Reproduction assets foundThe paper uses the public Kaggle Crop Health and Environmental Stress Dataset (UAV RGB/multispectral/thermal imagery plus soil/weather measurements and stress labels) as its phenotyping data source, and the authors provide an explicit public GitHub repository for the analysis code.Dataset · publicThe current research is based on the Crop Health and Environmental Stress Dataset, which is a publicly available
dataset on Kaggle, specially created to help perform a spatio-temporal analysis of crop health in response to changing
environmental and water-stress factors [26].Open asset ↗pdf-raw-page:10 lines:1-62Code · publicturn: Final zone-wise stress predictions 𝐶
𝑡
𝑧, Yield vulnerability trajectories 𝑉𝑡
𝑧, Optimal adaptive irrigation policy
𝜋∗
End Algorithm
Code availability:
The data used to support the findings of this study are included in the article.
Code availability:
The code used in this research work is available in the following link.
https://github.com/replyvenugopal/Cognitive-UAV-Driven-Agro-Surveillance
4. Result and Discussion
The architectural agro-surveillance solution, which is proposed to be executed by UAVs, is executed through a
modular and scalable software framework to guarantee reproducibility and extensibility. The experiments are all
performed in Python as a main programming languageOpen asset ↗github.com/replyvenugopal/Cognitive-UAV-Driven-Agro-Surveillancepdf-raw-page:24 lines:1-55Code / dataset availability confirmedOpenAlex · Europe PMC · bioRxiv · checked 14 Sept 2026
Abstract Background and aims Plant volatile organic compounds (VOCs) change dynamically with plant development and in response to environmental conditions. However, their potential as non-invasive indicators of phenological progression remains poorly explored. In this study, we developed a framework integrating automated VOC sampling, time-resolved VOC profiling, and machine-learning analysis for the non-invasive assessment of plant phenology. Using soybean ( Glycine max (L.) Merr.), we investigated whether development-associated temporal variation in VOC emissions could delineate and predict developmental phases. Methods We collected VOCs daily under controlled environmental conditions from 16 to 43 days after sowing, spanning the transition from vegetative to reproductive stages, using an automated sampling system coupled with thermal desorption-gas chromatograph-mass spectrometer (TD- GC-MS). To characterise temporal changes in VOC profiles associated with phenological progression, we analysed the daily VOC data using a multi-step pipeline combining statistical filtering and similarity-based network analysis. We defined VOC-derived developmental phases from similarity patterns in the VOC profiles, then developed and evaluated machine-learning models to predict these phases. Key results Seven VOCs exhibited distinct phase-dependent dynamics, including green leaf volatiles and monoterpenes showing characteristic temporal changes during phenological progression. Network-based clustering of VOC profiles resolved five developmental phases closely aligned with conventional developmental stages. A machine-learning model predicted these phases from the VOC profiles with high predictive accuracy on independent test data, demonstrating that phenological progression could be quantitatively inferred from VOC emission patterns. Conclusions Our findings support VOC profiling as a reliable and non-invasive approach for assessing phenological progression in soybean. By extracting temporally structured VOC signals, this framework captures developmental information that may be difficult to obtain through visual observation alone, particularly after canopy closure. VOC profiling offers a practical tool for monitoring crop developmental dynamics and has broader potential for plant phenotyping and precision crop management.
Why it matches plant phenotyping methods自動VOCサンプリング、時系列VOCプロファイリング、機械学習を統合し、VOCから植物の発育段階を非破壊推定する方法を開発・評価しており、フェノタイピング手法が中心である。
abstractwe developed a framework integrating automated VOC sampling, time-resolved VOC profiling, and machine-learning analysis for the non-invasive assessment of plant phenology.
Reproduction assets found保存済みの本文根拠を更新済みルールで再検証し、公開資産1件を確認しました。Supplement · publicThe peak area matrix obtained from the MS- DIAL analysis (Supplementary Dataset S1) was filtered to remove unreliable features.Open asset ↗lines:66-69Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Abstract Technological advances have expanded the adoption of digital technologies in agriculture, helping to reduce labour effort, increase profitability, improve crop efficiency and productivity, enhance product quality, mitigate environmental impacts, and promote human health. This context also extends to soybean farming, a sector of major economic importance in Brazil. Most importantly, Brazil has the global leadership in soybean production with biological nitrogen fixation (BNF) replacing chemical fertilisers. The research and evaluation of BNF is limited by manual counting of nodules, a time-consuming procedure. This study presents SoyNodules, designed for the automatic identification of soybean nodules, consisting of a dataset of images. The dataset includes 1,701 images acquired under controlled conditions: 1,662 images of soybean roots with nodules and 39 images of isolated nodules without roots. A total of 49,210 nodule instances are manually annotated with bounding boxes. SoyNodules was designed to promote reuse and interoperability in alignment with the FAIR principles (Findable, Accessible, Interoperable, Reusable) and to support the development, training, and evaluation of computer vision and deep learning methods for precision agriculture.
Why it matches plant phenotyping methods大豆根粒を自動識別する画像データセットであり、手作業計数の代替となる植物器官形質の抽出・評価を支援する方法論的データセット。
abstractThis study presents SoyNodules, designed for the automatic identification of soybean nodules, consisting of a dataset of images.
Reproduction assets foundThe paper is a data descriptor for SoyNodules, an annotated dataset of 1,701 soybean root/nodule images with 49,210 bounding-box annotations, publicly deposited on Zenodo with a DOI. The same repository also hosts the authors' annotation-format conversion script (AnyLabeling to Pascal VOC/COCO), per the Code AvailabilDataset · publicThe SoyNodules dataset, released as version 1.0, is publicly available on Zenodo [28]
at https://doi.org/10.5281/zenodo.22081914.Open asset ↗Zenodo · 10.5281/zenodo.22081914pdf-page:9 lines:1-43Code / dataset availability confirmedEurope PMC · Crossref · checked 14 Sept 2026
Abstract Deep convolutional networks now classify leaf images on curated benchmarks such as PlantVillage with accuracies close to the measurement ceiling of those datasets, which has shifted the open questions away from raw accuracy toward two under-reported issues: which components of a composite pipeline actually cause the result, and whether the components that matter on laboratory images are the same ones that matter on field photographs. We address both with a classification framework evaluated under a protocol that fixes every development decision before the independent test data are read. A Mask R-CNN stage localizes the dominant leaf, the accepted box is expanded by a validation-selected 5% margin and resized to a shared 224 by 224 input, and the same localized image is passed to ResNet50, InceptionV3, and MobileNetV2 together with an extractor that produces eighteen colour and shape descriptors. The forty-five class probabilities and eighteen descriptors form a sixty-three-dimensional input to a neural meta-classifier developed by three repetitions of stratified five-fold cross-validation. On a locked 3,101-image PlantVillage test partition of fifteen classes the framework reached 99.77% accuracy and 99.75% macro F1 with seven misclassifications, and a one-component-at-a-time ablation confirmed that every stage contributed. The same design was then trained and evaluated entirely within a separate thirteen-class PlantDoc field-image dataset, where it reached 90.03% accuracy and 89.40% macro F1. This is a within-PlantDoc experiment and not a controlled-to-field transfer test, so the figure measures how the pipeline behaves on field imagery rather than how a PlantVillage-trained model survives a domain shift. The central finding comes from running the identical ablation on both datasets: on clean images the ensemble breadth and descriptors provide the incremental gains, but under field conditions the ordering changes, and leaf localization and learned fusion become the decisive components. Removing localization cost 2.83 accuracy points and replacing the neural fusion with soft voting cost a further 2.08 points, the two largest effects on PlantDoc. The contribution is a controlled and transparent account of where each component of a localization-aware plant disease classifier earns its place, and of how that ordering shifts between laboratory and field acquisition.
Why it matches plant phenotyping methods葉画像から植物病害状態を推定する分類パイプラインの開発・アブレーション検証が中心であり、単なる病害実験や routine measurement ではない。
titleA Localization-Aware Heterogeneous CNN Ensemble with Neural Meta- Fusion for Plant Disease Classification, with a Component Analysis on Laboratory and Field Images
Reproduction assets found保存済みの本文根拠を更新済みルールで再検証し、公開資産1件を確認しました。Dataset · publicThe classification subset used here (20,638 images spanning fifteen pepper-bell, potato, and tomato classes) was obtained from PlantVillage, which is openly accessible at https://www.kaggle.com/datasets/emmarex/plantdisease.Open asset ↗Kaggle · emmarex/plantdiseaselines:314-336Code / dataset availability confirmedCrossref · checked 11 Sept 2026
Abstract. In the face of escalating global food demand and increasing climate variability, precise and granular crop yield monitoring is indispensable for maintaining regional agricultural stability. However, current deep learning approaches for yield estimation are severely constrained by their heavy reliance on massive in situ labeled data, which limits their application in data-scarce regions. Furthermore, these models often overlook the essential temporal evolution logic of yield formation and lack a systematic discussion regarding the contribution patterns of different feature dimensions, resulting in a black-box nature of the underlying model mechanisms. To address these challenges, this study proposes a field-label-free training framework for maize yield estimation that couples mechanistic model with deep learning. The framework's core strength lies in a physiologically complete simulation database, using the WOFOST model to exhaustively cover 30 years of climate variability and habitat combinations across Northeast China (1.24 × 106 km2). A Gated Recurrent Unit (GRU) network was then introduced for end-to-end modeling, accurately capturing the energy accumulation trajectory from vegetative to reproductive growth. Validation against 458 independent ground points (2022–2024) demonstrated robust generalization with an R2 of 0.69, an RMSE of 1.21 t ha−1, and an RRMSE of 13.73 %, despite using no ground data for training. Our analysis revealed that integrating photosynthetic intensity (LAImean), duration (LAD) and peak features (LAImax) across growth stages is critical for accuracy, while omitting early-stage features significantly impairs the model's ability to capture cumulative growth effects. Furthermore, the model successfully captured the spatiotemporal yield anomalies caused by the 2023 typhoon and flooding events. Ultimately, this study generated a 10 m resolution maize yield dataset (2019–2024) for Northeast China. The dataset exhibits consistent interannual stability, with the RRMSE ranging from 7.98 % to 12.92 % and the R2 remaining above 0.44 at the city level. By deeply coupling mechanistic simulation with data mining, this dataset provides detailed support for optimizing agricultural production and guiding farming practices. The Northeast China Maize Yield 10 m dataset is openly available at https://doi.org/10.5281/zenodo.19547014 (Hu et al., 2026).
Why it matches plant phenotyping methodsトウモロコシ収量という植物・作物群落の形質を推定する計算フレームワークを開発し、独立地点で性能検証したうえで再利用可能な10 m解像度データセットを生成しており、単なる農業実験の routine measurement ではない。
abstractthis study proposes a field-label-free training framework for maize yield estimation that couples mechanistic model with deep learning.
Reproduction assets foundThe paper's core output, the NortheastChinaMaizeYield10m maize yield dataset (2019–2024) with accompanying uncertainty layers, is openly deposited on Zenodo with an explicit availability statement and DOI. No author analysis code or trained model checkpoints are stated as publicly available.Dataset · publicThe Northeast China Maize Yield 10 m dataset is openly available at https://doi.org/10.5281/zenodo.19547014 (Hu et al., 2026).Open asset ↗Zenodo · 10.5281/zenodo.19547014lines:158-191Code / dataset availability confirmedOpenAlex · Europe PMC · bioRxiv · Crossref · checked 5 Sept 2026
Reliable and objective phenotyping is essential for plant breeding programs to characterize genetic variation and accelerate crop improvement. Conventional disease assessment relies on expert visual scoring, which is labor-intensive, subjective, and prone to inter- and intra-rater variability. Although image-based phenotyping methods have been proposed, many require manual intervention, specialized imaging setups, or single time-point measurements, limiting their ability to capture disease progression over time. Here, we present a pipeline for longitudinal plant disease phenotyping that quantifies wheat stripe rust and leaf rust progression from time-series images. The pipeline performs semi-automated leaf and automated pustule segmentation from images acquired in situ , enabling objective disease severity estimation with minimal user intervention and without requiring solid backgrounds or manual leaf manipulation or detachment. By extracting temporal traits, including disease severity trajectories and standardized area under the disease progress curve, the method provides a comprehensive characterization of disease development throughout infection. Association between automated and expert assessments was moderate for stripe rust ( R 2 = 0.58) and strong for leaf rust ( R 2 = 0.85), while expert inter-rater reliability was moderate for both diseases (ICC = 0.675 and 0.800, respectively). The proposed approach establishes a scalable and reproducible framework for longitudinal disease phenotyping in controlled environments, with broad applications in disease resistance screening and crop breeding.
Why it matches plant phenotyping methods画像時系列から植物病害の進展と重症度を抽出する半自動・自動解析パイプラインを開発し、専門家評価との比較で検証しており、表現型取得手法が研究の中心です。
abstractHere, we present a pipeline for longitudinal plant disease phenotyping that quantifies wheat stripe rust and leaf rust progression from time-series images.
Reproduction assets foundThe paper's Code and Data Availability section explicitly states that software and datasets (the phenotyping pipeline and imaging datasets) are publicly available at the authors' GitHub repository and project website, both of which are in the allowed URL list.Code · publicSoftware and datasets are available at:
https://github.com/USask-BINFO/greenskeye_analysis and https://greenskeye.usask.ca/speedbreeding/ .Open asset ↗USask-BINFO/greenskeye_analysislines:195-225Dataset · publicSoftware and datasets are available at:
https://github.com/USask-BINFO/greenskeye_analysis and https://greenskeye.usask.ca/speedbreeding/ .Open asset ↗lines:195-225Code / dataset availability confirmedEurope PMC · checked 6 Sept 2026
Abstract Satellite-based prediction of grain protein concentration (GPC) in wheat typically composites spectral observations over fixed calendar windows, implicitly assuming phenological synchrony across fields. We present a systematic evaluation of whether aligning multi-source remote sensing time series to field-specific, spectral-peak-relative windows improves field-level GPC prediction, for a quality trait whose physiology, senescence-linked nitrogen remobilization, contrasts with the season-integrating behavior of yield. Integrating Sentinel-2 imagery (31 vegetation indices, 10 spectral bands), ERA5-Land reanalysis, gSSURGO soil properties, and USGS 3DEP topography across 228 commercial winter wheat fields in western Kansas (2024–2025), we compared six temporal strategies (peakrelative vs. calendar × monthly, biweekly, growth-stage) using three ensemble tree models under nested cross-validation with Boruta feature selection. A single 30-day post-peak window (peak + [16,45] days) was the top-performing and most consistently selected window, chosen in 4 of 5 outer folds, reproducing prior accuracy under random cross-validation (R2 ≈ 0.28); though its advantage over the best calendar window was not statistically significant (paired bootstrap p = 0.08). Under leave-county spatial cross-validation, however, this skill did not transfer across counties (Sentinel-2–only R2 ≈ 0.01; per-county median R 2 = −0.23), indicating the satellite signal supports within-region interpolation but not spatial extrapolation to unseen counties; ablation shows that neither the spectral nor the static features transfer across counties on their own, and the residual crosscounty skill emerges only from their combination. A near-real-time application at ∼3 weeks before harvest retains most within-region skill at a modest accuracy cost. The results delineate where spectral-peak-relative alignment helps, concentrating a senescence-linked signal within region, and where it does not, providing an honest operational baseline for satellite-based grain-quality monitoring.
Why it matches plant phenotyping methods小麦の穀粒タンパク質濃度という植物形質を対象に、衛星時系列のスペクトルピーク相対アラインメントを開発・比較評価し、交差検証で性能と空間移 transfer 性を検証しているため、方法が中心的である。
abstractWe present a systematic evaluation of whether aligning multi-source remote sensing time series to field-specific, spectral-peak-relative windows improves field-level GPC prediction
Reproduction assets foundThe preprint explicitly releases the authors' analysis code (data-acquisition pipeline, feature engineering, cross-validation/modeling, figure scripts) at a public GitHub repository, and a de-identified field-level GPC dataset released alongside the code repository. Both are paper-specific, public, and actionable. The Code · publicthe figure-generation scripts is available at https://github.com/Ciampitti-Lab/Open asset ↗Ciampitti-Labpdf-page:48 lines:1-55Dataset · publica de-identified version of the dataset is released alongside the code repositoryOpen asset ↗pdf-page:48 lines:1-55Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Introduction Accurate classification of unsound wheat kernels is important for automated grain quality assessment, but improved recognition performance often comes at the cost of increased model complexity. Methods This study presents ECA-ModNet, a parameter-efficient convolutional network derived from EfficientNetV2-S. The architecture replaces two early-stage Fused-MBConv blocks with Mod-FusedMBConv blocks to introduce input-dependent local contextual modulation and replaces the squeeze-and-excitation modules in later stages with efficient channel attention to model local cross-channel interactions using fewer attention-related parameters. Experiments were conducted on the seven-class G600 wheat subset of the GrainSpace dataset. Results Across three independent runs, ECA-ModNet achieved an accuracy of 90.17 ± 0.21% and a macro-F1 score of 90.23 ± 0.21%, improving upon EfficientNetV2-S by 3.80 and 3.84 percentage points, respectively. The parameter count decreased from 20.19M to 16.49M, while FLOPs increased marginally from 2.90G to 2.95G. ECA-ModNet achieved accuracy statistically comparable to that of ConvNeXt-Tiny and InceptionNeXt-T while using substantially fewer parameters, and obtained 3.03-4.55 percentage points higher mean accuracy than six lightweight baselines. Discussion Ablation experiments identified two Stage 1 Mod-FusedMBConv blocks with a 3×3 context kernel as the configuration with the highest mean accuracy among those evaluated. These results indicate that ECA-ModNet offers a favorable accuracy-parameter trade-off for image-based classification of unsound wheat kernels.
Why it matches plant phenotyping methods小麦粒の状態（unsound kernel）を画像から分類するためのCNNを開発・比較・アブレーション評価しており、植物器官の状態推定手法が研究の中心である。
abstractThis study presents ECA-ModNet, a parameter-efficient convolutional network derived from EfficientNetV2-S.
Reproduction assets foundThe paper analyzes the public GrainSpace dataset (G600 seven-class unsound wheat kernel subset) and provides an explicit data availability statement with a public GitHub URL. No author analysis code or trained model deposit is stated.Dataset · publicPublicly available datasets were analyzed in this study. This data can be found here: https://github.com/hellodfan/GrainSpace .Open asset ↗hellodfan/GrainSpacelines:1035-1076Code / dataset availability confirmedOpenAlex · checked 5 Sept 2026
Published18 Aug 2026Journal of King Saud University - Computer and Information SciencesCited by 0 · OpenAlex ↗
Plant phenotyping is essential for modern crop breeding, yet traditional static image analysis fails to capture the nonlinear dynamics of plant growth. Existing time-series forecasting models exhibit notable limitations when processing multimodal data: global pooling operations may compress local 2D spatial topology of plants, and shallow feature concatenation may be insufficient for effective cross-modal semantic alignment. Moreover, current methods typically regress absolute morphological states, which may contribute to temporal lag during nonlinear growth spurts. In this paper, we propose ST-CrossGro-Former, a cross-modal residual forecasting framework for plant dynamic growth. The network removes the final global pooling and classification layers to preserve spatial topology and incorporates a scalar-guided cross-modal attention module based on the standard query-key-value formulation. This module utilizes 1D morphological features as queries to dynamically weight local visual regions, promoting multimodal feature alignment. Concurrently, a residual incremental forecasting strategy is introduced to predict short-term growth increments rather than absolute states, aiming to improve tracking sensitivity to sudden growth events. Evaluations on the UNL-CPPD maize dataset and supplementary validation on the FIP1 wheat field dataset show that the proposed model achieves competitive single-step forecasting accuracy and favorable temporal trajectory alignment compared with adapted spatiotemporal attention, graph-based, and physics-informed baselines under the evaluated settings. In particular, the FIP1 results suggest that ST-CrossGro-Former can maintain favorable height trajectory alignment under a field-acquired wheat setting, indicating its potential for helping mitigate temporal misalignment in dynamic growth forecasting.
Why it matches plant phenotyping methods植物の動的形態成長を予測する新規クロスモーダル手法を開発し、トウモロコシ・コムギデータセットで評価しており、表現型の抽出・予測手法が中心である。
abstractwe propose ST-CrossGro-Former, a cross-modal residual forecasting framework for plant dynamic growth.
Reproduction assets foundThe paper evaluates its ST-CrossGro-Former model on two public plant phenotyping datasets: the UNL-CPPD maize dataset (explicitly stated as publicly available with a repository URL) and the FIP1 wheat field dataset (public dataset from ETH Zürich, with its GigaScience dataset publication DOI). No author analysis code, Dataset · publicThe UNL-CPPD dataset used in this research was acquired from the UNL Plant Phenotyping Datasets repository, accessible at https://plantvision.unl.edu/datasets.Open asset ↗UNL Plant Phenotyping Datasets · UNL-CPPDlines:266-273Code / dataset availability confirmedOpenAlex · Crossref · checked 15 Sept 2026
Abstract Heat stress causes ultrastructural damage in pollen grains, leading to reduced pollen germination, pollen size and shortened pollen tube length, ultimately lowering seed set and yield. This study presents a high-throughput phenotyping framework that integrates controlled-environment pollen germination assays with deep learning–based object detection for rapid, accurate, and scalable evaluation of reproductive heat tolerance in soybean breeding programs. Sixteen soybean genotypes were grown under controlled environments at optimal (28/18°C; day/night) and high temperature (38/28°C; day/night) regimes during flowering. In vitro pollen germination was quantified using six YOLO (You Only Look Once) object-detection architectures (YOLOv7–YOLOv12) to identify the best-performing model for automated analysis. Among the tested object-detection architectures, YOLOv9 achieved the best overall performance for detecting germinated and non-germinated pollen grains in complex images. High temperature significantly reduced mean pollen germination from an average of 40% under optimal conditions to an average of 21% under heat stress (P < 0.05), with a significant genotype × growth temperature interaction. Invitro incubation temperatures ranging from 10 °C to 45 °C produced a clear thermal response; however, no significant genotype × incubation temperature interaction was detected within either growth temperature regime. Although photosynthetic and physiological traits were measured exploring their relationship with pollen germination, their transient and complex response limited their reliability for predicting reproductive performance. The automated pipeline substantially reduced the time required to evaluate pollen germination. The pipeline processed nearly 5,000 images in approximately one hour, substantially increasing throughput and reducing reliance on manual counting. The findings demonstrate that pollen germination is a promising proxy trait for screening reproductive heat tolerance in soybean. Combining controlled environment phenotyping with YOLO-based object detection enabled efficient, accurate, and scalable pollen analysis, and represents the central methodological advance of this study. YOLOv9 performed best among the tested architectures, although discrepancies from manual counts in some images indicate that additional validation is needed. The weak associations with vegetative physiological traits further support the value of direct pollen-based phenotyping.
Why it matches plant phenotyping methods深層学習による花粉画像解析を中心に、花粉発芽という生殖形質を高速・自動測定するハイスループット表現型解析フレームワークを開発・比較・検証している。
abstractThis study presents a high-throughput phenotyping framework that integrates controlled-environment pollen germination assays with deep learning–based object detection for rapid, accurate, and scalable evaluation of reproductive heat tolerance in soybean breeding programs.
Reproduction assets foundThe authors state that all data supporting the study, including annotated pollen germination images, computational and statistical codes, and analysis tools, were deposited in Zenodo with a public DOI. This is a paper-specific, publicly actionable asset. LabelMe and Ultralytics YOLO are generic third-party tools, not作者Dataset · publicCommission.
Data availability
All data supporting the findings of this study, including annotated images, computational and
statistical codes, and analysis tools, have been deposited in the Zenodo data repository. Additional
data will be made available upon reasonable request following acceptance of the manuscript.
Repository: https://doi.org/10.5281/zenodo.21685593
Ethics approval and consent to participate
Not applicable
Consent for publication
Not applicable
Competing Interests
Authors declared no competing interests
References
1. FAOSTAT: Crops and livestock products: soybean production data. https://www.fao.org/faostat/
(2022). Accessed 15 Feb 2026.
2. Patel D, Franklin KA. TemperaturOpen asset ↗Zenodo · 10.5281/zenodo.21685593pdf-raw-page:28 lines:1-34Code / dataset availability confirmedOpenAlex · Europe PMC · checked 15 Sept 2026
Boll-opening concentration is critical for mechanical cotton harvesting, yet it is still assessed mainly by manual records and single time-point indicators that miss temporal dynamics. To bridge the lack of a unified workflow linking vision foundation models, multi-temporal boll-opening monitoring, and harvest decision-making, we developed a cross-scale UAV high-throughput phenotyping framework centered on DINO-BollGX. DINO-BollGX couples a DINO v3 backbone, a RetinaNet detection head, and an adaptive refinement-and-suppression module for robust open-boll detection under complex field conditions. Using multi-temporal UAV imagery collected over two years for 383 cultivars, we reconstructed plot-scale time series of open-boll counts, derived dynamic features describing progression and intensity changes, and proposed a Cotton Boll-Opening Temporal Stability Index (CTSI) to quantify boll-opening rhythm and concentration; CTSI was further integrated with a time-based risk function to generate harvest decision curves. Under unified data and training settings, DINO-BollGX achieved precision = 0.91, F1 = 0.88, and AP@0.50 = 0.80, and provided accurate boll-count estimation (R 2 =0.98; MAE=3.10), outperforming YOLOv11, YOLOv12, YOLOv13, and RT-DETR. On an independent cross-year dataset acquired at 5 m altitude, it obtained precision = 0.98 and F1 = 0.87. An internal consistency analysis showed that CTSI had the expected negative association with Window_days (r = −0.83) and positive associations with Max_count (r = 0.78) and the boll-opening efficiency index (r = 0.92), reflecting the co-occurrence of temporal compactness and main-phase opening intensity in the cultivar population. CTSI ranged from −2.72 to 4.69 across cultivars, enabling identification of highly synchronized boll-opening. Harvest decision curves indicated that the relative net income index peaked at day 67 after the first observation and a compact optimal harvest window near the end of monitoring; on a fixed harvest date, Kuche 130292 (CTSI=4.69) produced 486 open bolls versus 182 for Xinluzao 36 (CTSI=0.53) and 90 for Andizhan-60 (CTSI=-2.72). Overall, the framework integrates dynamic boll-opening phenotyping with harvest timing optimization, supporting scalable cultivar screening and mechanization-ready deployment, with potential extension to harvest decision scenarios in other crops.
Why it matches plant phenotyping methodsUAV画像と基盤モデルを用いて綿花の開絮を検出・定量し、時系列表現型指標を構築・検証する方法が研究の中心であるため。
abstractwe developed a cross-scale UAV high-throughput phenotyping framework centered on DINO-BollGX.
Reproduction assets foundThe paper publicly releases its cotton boll-opening UAV image dataset (3638 patches, 94,774 YOLO-format bounding-box annotations) on GitHub, directly supporting the paper's phenotyping analysis. No author analysis code or trained model checkpoints are explicitly deposited.Dataset · publicentary information for evaluating cross-scale detection performance and characterizing macroscopic spatial patterns. The 5 m imagery acquired on 18 Sept 2024 is used exclusively for cross-year generalization assessment. All cropped images and the corresponding YOLO-format annotation files have been publicly released on GitHub ( https://github.com/mianchen0529/cotton-boll-dataset/tree/main ) to facilitate further research on cotton phenotyping, agricultural remote sensing, and intelligent analytics.
2.3.
Model construction
2.3.1.
Overall architecture of the DINO-BollGX network
The proposed DINO-BollGX network consists of four stages: image preprocessing, feature extraction, object prediction,Open asset ↗mianchen0529/cotton-boll-datasetlines:63-74Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Published18 Aug 2026TAG. Theoretical and applied genetics. Theoretische und angewandte GenetikCited by 0 · OpenAlex ↗
Key message Our scalable two-step method estimates genotypic performance and genetic parameters from ranking data, producing reliable results comparable to quantitative analyses, enabling the integration of ranking data into breeding pipelines. Plant breeding research has chiefly relied on on-station experiments to evaluate varietal performance. Nevertheless, these trials often fail to represent on-farm growing conditions and farmers' preferences, potentially leading to poorly defined breeding targets. Recent work has demonstrated the potential of using on-farm verification trials combined with ranking data to support farmers in evaluating varieties while providing information that is representative of farmers' needs. Despite this potential, scalable methods for quantifying genetic differences and assessing the strength of the genetic signal in such trials remain limited. Here, we present a two-step procedure for analyzing trials based on ranking data, allowing the estimation of genetic parameters. The approach follows a common strategy in quantitative genetics, in which parameters are estimated from tables of genotypic means and their variances. In our framework, these estimates are obtained from Thurstonian and/or Plackett-Luce models, which treat rankings as observations of an underlying continuous trait associated with genotypic performance. Using simulated data, we showed that genotypic mean estimates derived from ranking analyses are linearly related to those obtained from quantitative trait analyses and that their variances adequately capture estimation uncertainty. We further demonstrated that incorporating these estimates and their variances into a second-step mixed-effects model yields accurate estimates of variance components. Analyses of groundnut, maize, and sweetpotato datasets confirmed the applicability of the approach and showed that ranking data can provide reliable estimates of genetic parameters. We argue that this framework can be scaled to obtain genotypic performance estimates from multi-trial on-farm data.
Why it matches plant phenotyping methods作物品種の遺伝型性能をランキングデータから推定する統計的方法そのものが研究の中心であり、育種に再利用可能な植物性能の推定手法を開発・検証している。
abstractHere, we present a two-step procedure for analyzing trials based on ranking data, allowing the estimation of genetic parameters.
Reproduction assets foundThe paper's Data availability statement provides public access to the observed groundnut and sweetpotato ranking/trial datasets (Zenodo 17112492), the authors' R functions and simulation workflow (GitHub hdorado/tricot-ranking-analysis, archived Zenodo 17942919), and supplementary material with methods and figures (ZenDataset · publicThe observed data for groundnut and sweetpotato used in this study are publicly available and can be accessed at: Global multi-crop agricultural trial data supported by citizen science, Zenodo [ https://doi.org/10.5281/zenodo.17112492 ]Open asset ↗Zenodo · 10.5281/zenodo.17112492lines:205-225Code · publicThe R functions and simulation workflow used in this study are publicly available at: - Source code available from: [ https://github.com/hdorado/tricot-ranking-analysis ]Open asset ↗GitHub · hdorado/tricot-ranking-analysislines:205-225Code · public- Archived software available from: [ https://doi.org/10.5281/zenodo.17942919 ] - License: [MIT License]Open asset ↗Zenodo · 10.5281/zenodo.17942919lines:205-225Code / dataset availability confirmedEurope PMC · checked 15 Sept 2026
Introduction Applying general-purpose vision-language models (VLMs) to crop disease diagnosis presents three critical bottlenecks: reliance on large-scale annotated data, the high computational cost of full finetuning, and existing adaptation methods designed mainly for discriminative classification without sufficient visual-linguistic interaction for generative diagnosis. Methods We propose BLAP, an adaptive multi-scale visual prompt fine-tuning framework built upon BLIP-2. BLAP introduces an adaptive visual prompt fusion module (APFM) with learnable prompt vectors and a gating mechanism, together with a multi-scale pyramid feature fusion module (PFM). All BLIP-2 backbone parameters are frozen, and only 0.11% of the model parameters are optimized. Results On a few-shot dataset comprising 990 images from 11 crops and 33 disease categories, BLAP achieved 92.78% recognition accuracy, outperforming the BLIP-2+LoRA baseline by 21.67 percentage points. BLEU-4 and ROUGE-L scores reached 0.6507 and 0.7184, respectively, while inference latency increased by only 2.15%. Discussion BLAP provides a lightweight solution that balances accuracy, efficiency, and interpretability for crop disease diagnosis in resource-constrained settings. The proposed dynamic prompt fusion and multiscale pyramid adaptation strategy may also be extended to parameter-efficient fine-tuning of visionlanguage models in other domain-specific applications.
Why it matches plant phenotyping methods作物病害画像から病徴・病害状態を推定する視覚モデル適応手法BLAPの開発と評価が中心であり、植物病害フェノタイピング手法に該当する。
abstractWe propose BLAP, an adaptive multi-scale visual prompt fine-tuning framework built upon BLIP-2.
Reproduction assets foundThe paper's few-shot crop disease dataset (990 images, 11 crops, 33 classes) is compiled entirely from four public Mendeley Data image repositories, each cited in Table 1 as the data source for specific crop/disease classes. These are the plant image inputs directly used for this paper's phenotyping/analysis. No authorDataset · publicncluding laboratory and field environments (Approximately 45% of them were captured in field environments), to enhance sample representativeness and model robustness.
Table 1
The number of collected diseases or healthy image data for each crop.
Crop
Disease
No. of images
Collection conditions
Data source
Apple
Apple scab
30
Lab
https://data.mendeley.com/datasets/tywbtsjrjv/1
Cedar apple rust
30
Lab
https://data.mendeley.com/datasets/tywbtsjrjv/1
Healthy
30
Lab
https://data.mendeley.com/datasets/tywbtsjrjv/1
Cashew
Healthy
30
Lab
https://data.mendeley.com/datasets/8fr7grr73p/1
Leaf miner
30
Lab
https://data.mendeley.com/datasets/8fr7grr73p/1
Red rust
30
Lab
https://data.mendeley.com/datasets/Open asset ↗lines:37-116Code / dataset availability confirmedCrossref · checked 15 Sept 2026
Published17 Aug 2026International Journal of Drug Delivery TechnologyCited by 0 · OpenAlex ↗
Why it matches plant phenotyping methodsトマト葉の病害を画像と深層学習で検出する手法が題名上の中心であり、植物の病害状態を観察的に推定するフェノタイピング研究に該当する。
titleDetection of Tomato Leaf Disease in Leaves with Deep Learning MobileNetV2 with Gaussian and Gabor Preprocessing
Reproduction assets foundThe paper's phenotyping analysis is based on the publicly available PlantVillage plant leaf disease image dataset hosted on Kaggle (54,303 labeled leaf images across 38 classes), which the authors explicitly state was sourced from a publicly available Kaggle dataset. No author-specific code, models, or derived datasetsDataset · publicThe research incorporated PlantVillage dataset(24)
accessible on Kaggle that contains 54,303 plant leaf
images showing both healthy and diseased
conditions spanning across 38 specific categories.Open asset ↗Kagglepdf-raw-page:2 lines:1-105Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Stomatal traits are key microscopic phenotypes for evaluating plant physiology, stress responses, and crop breeding potential. However, in vivo high-magnification microscopy often suffers from a shallow depth of field, causing noticeable defocus blur across different spatial locations and making it difficult to capture clear and complete stomatal structures in a single image. Multi-focus image fusion offers a practical solution, yet existing methods typically rely on supervised training, paired data, or hand-crafted rules, limiting their use in real agricultural microscopy scenarios. In this study, we propose an unsupervised multi-focus fusion framework for reconstructing fully focused stomatal microscopic images. The method integrates two-dimensional feature extraction with three-dimensional cross-focal-plane modeling to capture both spatial details and complementary information across focal planes. A max-response-guided spatial gating module is introduced to enhance focused regions while suppressing defocused responses. Additionally, dual sharpness priors based on perceptual features and wavelet high-frequency information enable pixel-wise pseudo-supervised learning without requiring all-in-focus ground-truth images. The model also predicts a probabilistic focal-plane volume for interpretable all-in-focus reconstruction. Experiments on a maize multi-focus image dataset demonstrate that the proposed method achieves superior or competitive performance across multiple fusion metrics, with entropy (EN), edge information preservation ( Q AB∕F ), Chen-Blum contrast metric ( Q CB ), and visual information fidelity for fusion (VIFF) reaching 7.43, 0.21, 0.41, and 1.01, respectively. Ablation studies confirm the effectiveness of the 3D modeling, spatial gating, and dual-prior sharpness supervision. More importantly, when the fused images serve as input to a YOLO-based stomatal instance segmentation model, the proposed method yields the best segmentation accuracy, with mAP50 and mAP50-95 reaching 0.9937 and 0.9121, respectively. Phenotypic measurements derived from the segmentation masks show high consistency with manual annotations, with the highest coefficient of determination R 2 = 0.97 achieved for stomatal count. These results indicate that the framework can act as an effective front-end module for automated microscopic stomatal phenotyping in agriculture.
Why it matches plant phenotyping methods植物の気孔表現型を対象に、マルチフォーカス画像融合、セグメンテーション、形質測定までを中核的に開発・検証しているため。
abstractwe propose an unsupervised multi-focus fusion framework for reconstructing fully focused stomatal microscopic images.
Reproduction assets foundThe authors state their data and code are publicly available on GitHub, covering the multi-focus stomatal microscopy dataset and the UMF-stomata fusion/phenotyping code.Code · publicOur data and code are available at: https://github.com/Longer-S/UMF-Stomata.Open asset ↗Longer-S/UMF-Stomatahtml-lines:640-655Dataset · publicOur data and code are available at: https://github.com/Longer-S/UMF-Stomata.Open asset ↗Longer-S/UMF-Stomatahtml-lines:683-756Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Abstract The classification of banana leaf disease has a large impact on agricultural output and relies heavily on timely early detection, with reliability as a fundamental component of effective crop management. The framework proposed in this study comprises a Hamiltonian Full Node Coverage Graph Attention Network (HFNC-GAT) and Fuzzy C-Means super pixel graph learning to explain the classification of banana leaf diseases. The HFNC-GAT allows for the representation of segmented leaf areas as the nodes in a graph. This framework also makes optimal use of an attention learning model to represent the spatial dependence of diseased leaf regions, allowing it to leverage both local and global spatial dependencies. The HFNC-GAT was demonstrated through observed experiments to achieve high performance with 96.11 and 94.19 accuracy, 0.9111 Cohen's Kappa, 0.9111 MCC, 0.9344 F2-score, and 0.9939 ROC-AUC compared to the performance of conventional CNN, GCN, and baseline GAT models.
Why it matches plant phenotyping methodsバナナ葉の病斑領域を画像から抽出・分類するグラフ学習手法が研究の中心であり、植物の病害状態を直接推定するため、植物フェノタイピング手法として適格です。
abstractThe framework proposed in this study comprises a Hamiltonian Full Node Coverage Graph Attention Network (HFNC-GAT) and Fuzzy C-Means super pixel graph learning to explain the classification of banana leaf diseases.
Reproduction assets foundThe paper's Dataset Availability statement explicitly declares two public Kaggle banana leaf image datasets used for the phenotyping/classification experiments: Banana Leaf Disease Dataset V4 and BananaLSD. No author analysis code or trained model is reported as publicly available.Dataset · publicThe Banana Leaf Disease
Dataset V4 is available at https://www.kaggle.com/datasets/rayhanarlistya/banana-leaf-disease-dataset-v4.Open asset ↗Kaggle · banana-leaf-disease-dataset-v4pdf-page:19 lines:1-55Dataset · publicThe Banana Leaf Spot Diseases (BananaLSD) dataset is available at
https://www.kaggle.com/datasets/shifatearman/bananalsdOpen asset ↗Kaggle · bananalsdpdf-page:19 lines:1-55Code / dataset availability confirmedOpenAlex · Europe PMC · checked 5 Sept 2026
The inflorescence is a key yield-determining organ, yet its complex morphology makes manual pixel-level annotation time-consuming, leading to a scarcity of high-quality segmentation datasets. To address this bottleneck, we propose ZCAT (Zero-shot Cross-crop Annotation Transfer), a novel paradigm for zero-annotation cross-crop pseudo-mask screening. ZCAT completely eliminates pixel-level manual annotation of the target crop, requiring only holistic quality assessment of model-generated pseudo-masks (5-10 s per image). Specifically, we train a SegFormer model on public rice panicle datasets (CVRP and RiceSEG) and transfer it across crops to the wheat spike segmentation task. The key innovation is the introduction of a human-defined quality function Q, which circumvents the fundamental challenge in self-learning algorithms: the inability of computers to autonomously distinguish good masks from bad ones. Through iterative human-in-the-loop pseudo-label screening with a curriculum learning strategy, each round adds only a few high-quality pseudo-masks to the training set, continuously improving model performance. After four iterations, ZCAT produces pseudo-masks with an average Spike IoU of 0.7003, evaluated against the GWFSS manual annotations as ground truth. Moreover, the pseudo-mask dataset exhibited higher benchmark performance than the GWFSS manual annotations (Spike IoU 0.7612 vs. 0.7027; mIoU 0.8627 vs. 0.8247), suggesting stronger self-consistency. A generalization test on a strictly held-out set of 100 manually annotated wheat spike images showed that the model trained on ZCAT-generated pseudo-masks achieved marginally better performance than that trained on the GWFSS manual annotations (Spike IoU: 0.5112 vs. 0.4927; mIoU: 0.5627 vs. 0.5247). The time budget of the ZCAT pipeline was substantially lower than that of manual annotation. ZCAT opens a new pathway for rapid annotation of plant reproductive structures or other organs and significantly reduces data preparation costs in plant phenomics. The generated wheat spike pseudo-mask dataset and the mask quality screening tool (Mask Quality Screener) are open-sourced.
Why it matches plant phenotyping methods植物器官セグメンテーションのためのゼロショット転移、擬似マスク品質評価、反復学習パイプラインを開発・検証しており、表現型取得基盤が中心である。
abstractThe key innovation is the introduction of a human-defined quality function Q
Reproduction assets foundThe paper explicitly open-sources two paper-specific assets: the ZCAT-generated wheat spike pseudo-mask dataset and the Mask Quality Screener tool, both with public GitHub URLs in the Data availability statement.Dataset · publicThe wheat spike pseudo-mask dataset and Mask Quality Screener are available at https://github.com/zyxyes1/MaskQualityScreener and https://github.com/zyxyes1/Wheat-Spike-Semantic-Segmentation , respectively.Open asset ↗Wheat-Spike-Semantic-Segmentationlines:415-440Code / dataset availability confirmedCrossref · Europe PMC · checked 5 Sept 2026
Sustainable wheat farming is challenging. Real-time information on crop health, disease transmission, and anticipated yields is essential for farmers. However, they frequently use slow, expensive, or non-communicative tools. This project develops a workable solution. There is no need for massive server farms because the entire system operates on a single graphics card. It incorporates images of wheat fields, Indian farming notes, greenhouse records, harvest statistics, and NASA meteorological data. Consider them as various “eyes” for crop photo analysis, and we tried several lightweight computer vision models. ConvNeXt-Tiny was slower but could operate on older equipment with 75% accuracy; EfficientNetB0 recognised wheat heads with 92% accuracy; and AgroMark, a hybrid solution that merged photo analysis with agricultural metadata (soil type, rainfall, increased to 87%, etc. Combining picture analysis with attention mechanisms (CBAM) allowed us to anticipate the amount of wheat that a field will yield based on these photo insights, and the results showed that our predictions were accurate, with an R 2 score of 0.97. Additionally, we developed a versatile detector that simultaneously detects disease, stress, head count, and pests. It is adjusted to deal with training data that is unbalanced (some diseases are common, while others are rare). As we packed everything into a 16-GB graphics card, we spent real time determining which strategies smaller training sets, removing weak features, and adjusting loss functions, work. We encounter real-world obstacles along the road, such as photographs from different locations not always match, mislabeled photographs from different locations not always match, mislabeled diseases, and neglected rare pests. Our step-by-step instructions, charts, and code are available.
Why it matches plant phenotyping methods小麦画像から病害・ストレス・穂数・収量などの植物形質・状態を推定するマルチモーダル手法を開発し、複数モデルの精度比較と実装上の検証を行っており、表現型取得・推定が研究の中心である。
abstractThis project develops a workable solution.
Reproduction assets foundThe paper builds its multimodal wheat phenotyping analysis on several explicitly cited public data assets: the Kaggle Wheat Plant Diseases image dataset (used for disease classification, Tables 2 and 9), the Global Wheat Head Detection dataset (used for head detection, Tables 1 and 6), FAOSTAT and India Open GovernmentDataset · publicAvailable online at: https://www.fao.org/faostat/ . FAOSTAT statistical database.Open asset ↗lines:1110-1162Code / dataset availability confirmedOpenAlex · Europe PMC · checked 5 Sept 2026
Thermal imaging enables non-invasive assessment of canopy temperature, an essential indicator of plant stress, yet the lack of color cues and strong shadow interference make plant segmentation in thermal images difficult. Recent advances in foundation models have demonstrated improved performance and generalizability across applications, showing promise for domain-specific applications with limited annotated datasets such as plant segmentation in thermal images. This study investigates large multimodal models (LMMs) for thermal image segmentation in plant phenotyping. Building upon the SAM-CLIP framework, we design a unified pipeline spanning zero-shot inference, few-shot and low-shot fine-tuning, and active learning to maximize accuracy with minimal supervision. Evaluations on two thermal datasets, LadyBird Brassica and UGA Brassica, demonstrate robust performance after minimal adaptation across both datasets and superior performance compared with baselines, achieving mIoU D values of 97.54% on the LadyBird dataset and 76.94 % on the UGA dataset. We also release the resulting thermal segmentation annotations to support community benchmarking and reproducible research, highlighting the potential of LMMs to enable scalable, high-quality dataset construction for field phenotyping. The released datasets can be found at: https://cornell.box.com/s/dh69xf84464yrc1vlws92l1tflx7qa89
Why it matches plant phenotyping methods熱画像から植物を分割する手法を開発・評価し、植物フェノタイピング用データセットとアノテーションも公開しているため、フェノタイピング手法が中心的である。
abstractThis study investigates large multimodal models (LMMs) for thermal image segmentation in plant phenotyping.
Reproduction assets foundThe authors publicly released the paper-specific thermal segmentation annotations (20,538 LadyBird masks and 37,790 UGA masks) via a Cornell Box link stated in the abstract, results, and data availability statement. No author analysis code or trained model checkpoints are explicitly released; the mmsegmentation GitHub/Dataset · publicwe generated and publicly released segmentation annotations for the complete LadyBird and UGA thermal image datasets using the best-performing SAM-CLIP model. Specifically, the final model obtained through the multi-round training process was used to generate 20,538 masks for the LadyBird dataset and 37,790 masks for the UGA dataset. Details of the generated annotations are provided in Supplementary Fig. S1 , and both annotated datasets are publicly available at: https://cornell.box.com/s/dh69xf84464yrc1vlws92l1tflx7qa89Open asset ↗lines:220-232Code / dataset availability confirmedEurope PMC · checked 14 Sept 2026
Abstract Sustainable agriculture has substantial share on improvement of food security and optimization of resources utilization particularly for high value crops like rice leaf. Rice varieties should be properly classified in order to benefit the harvest management, reduced loss after harvest and improved agriculture methods. The traditional classification method usually brings the low precision and the traditional classification method is also subjected to human error, which is difficult to bring about reliable output. This study introduces an optimized multi-class rice leaf disease classification system utilizing “Rice Feature Selection” (RiceFS) and ensemble machine learning approaches. RiceFS is realized based on a feature selection mechanism based on Recursive Feature Elimination. Selected classifiers such as KNN, Random Forest, Gradient Boosting, Ensemble Learning and Optimized SVM are analyzed based on the extracted subset of features and the proposed system is used to classify the seven classes of rice leaf disease. The experimental results show that the Optimized SVM has the best classification results among the different classifiers with accuracy of 92.10%, Precision of 92.20%, balanced Recall and F1 Score, which shows that Optimized SVM is very effective in multi-class rice leaf disease classification. The performance can be improved by feature reduction, generalization capability and computational complexity reduction, which are realized with the help of RiceFS. The proposed framework is designed to provide an intelligent decision support system for timely intervention, loss minimization and sustainable agriculture. Results indicate that these algorithms are applicable for rice leaf disease classification since they are accurate, reliable and scalable.
Why it matches plant phenotyping methodsイネ葉の病害状態を観察データから分類する計算手法が研究の中心であり、RiceFSと複数の機械学習器を用いた分類フレームワークを開発・評価しているため。
abstractThis study introduces an optimized multi-class rice leaf disease classification system utilizing “Rice Feature Selection” (RiceFS) and ensemble machine learning approaches.
Reproduction assets foundThe paper's RiceFS phenotyping/classification experiments are built on two public Kaggle rice leaf disease image datasets, explicitly cited with URLs and a data availability statement. No author code or models are deposited.Dataset · publicThe RiceFS framework proposed initially
performs a feature selection, followed by training
several classifiers: K-Nearest Neighbors (KNN),
Random Forest (RF), Gradient Boosting (GB),
Ensemble Learning, and Optimized Support
Vector Machine (Optimized SVM). The data is
published on the Kaggle website. The data is
open-source at:
https://www.kaggle.com/datasets/vbookshelf/rice-leaf-diseases [44].
This data consists of 120 jpgs of disease infected
rice leaves. The photos are divided into 3
categories according to the kind of disease. There
are 40 images in each class.
Classes
• Leaf smut
• Brown spot
• Bacterial leaf blight
The datasets are preprocessed by eliminating
redundant information, normOpen asset ↗Kaggle · vbookshelf/rice-leaf-diseasespdf-raw-page:11 lines:1-103Code / dataset availability confirmedCrossref · checked 14 Sept 2026
Published11 Aug 2026Engineering, Technology & Applied Science ResearchCited by 0 · OpenAlex ↗
Corn is a staple crop of global significance; however, foliar diseases may lead to 30–60% yield loss if not detected at an early stage. Conventional visual inspection is time-consuming, subjective, and difficult to scale for smallholder farmers worldwide. To overcome these issues, we present Corn Transfer Learning Network (CTL-Net), an end-to-end hybrid deep learning model for corn leaf disease identification. CTL-Net, which combines Inception-ResNet-v2 as the backbone and MobileNetV3 as a feature extractor in parallel convolutional streams, simultaneously learns diverse scales of texture information from low-level textures, mid-level structural patterns, and high-level disease semantics of RGB leaf images. Adaptive feature fusion is formulated through learnable weighting coefficients and bi-directional spatial–channel attention mechanisms, which further enhance feature discriminability and robustness. The proposed approach is tested on an extensive dataset of 12,456 images from 10 corn diseases, including Northern Leaf Blight, Common Rust, Gray Leaf Spot, and Cercospora Leaf Spot, acquired under controlled and real-field conditions. CTL-Net attains the highest classification accuracy of 99.42%, outperforming DenseNet121 (97.92%), EfficientNetB3 (97.35%), and general stacking models (97.89%). Robustness experiments demonstrate the effectiveness of the proposed method against illumination variations, additive noise, and partial occlusions. CTL-Net enables real-time inference with a latency of 42 ms on an NVIDIA RTX 3090 GPU. Gradient-weighted Class Activation Mapping++ (Grad-CAM++)-based interpretability analysis results in a mean Intersection over Union (IoU) of 87.6% with expert-annotated disease regions. Five-fold cross-validation, ablation studies, and statistical significance testing (p
Why it matches plant phenotyping methodsトウモロコシ葉画像から病徴・病害状態を推定する深層学習手法を開発し、複数モデルとの比較、頑健性評価、交差検証、アブレーションを行っており、植物フェノタイピング手法が中心である。
abstractwe present Corn Transfer Learning Network (CTL-Net), an end-to-end hybrid deep learning model for corn leaf disease identification.
Reproduction assets foundThe paper states its final curated corn leaf disease dataset (12,456 images, 10 classes) is publicly available via the authors' GitHub repository vishruthkp/maizedataset (reference [30] and Data Availability statement). The Kaggle PlantVillage and Corn or Maize Leaf Disease datasets are cited source inputs, not paper-Dataset · public"Prediction of Crop Yield using Machine Learning," International Available: https://github.com/vishruthkp/maizedataset.Open asset ↗vishruthkp/maizedatasetpdf-page:7 lines:1-53Code / dataset availability confirmedCrossref · checked 14 Sept 2026
Published11 Aug 2026Engineering, Technology & Applied Science ResearchCited by 0 · OpenAlex ↗
In recent years, areca nut plants have been vulnerable to different diseases that appear as distinct colors on leaves, caused by bacteria or fungi. These symptoms disrupt photosynthesis and reduce yield, affecting productivity and crop health. Therefore, accurate plant disease classification is essential for detecting distinct disease shapes and sizes. Existing Deep Learning (DL) models have several limitations that prevent them from distinguishing between various plant diseases due to similar characteristics. To overcome this limitation, a Dynamic elastic boundary strategy Sailfish Optimization Algorithm and Convolution Neural Network (DSFO-CNN) method is proposed to identify and accurately classify arecanut plant diseases. The Visual Geometry Graph-19 (VGG-19) model extracts features that have significant information about disease in arecanut plants. The proposed arecanut plant disease classification model employed feature selection and drop cyclic learning rate, which adjusts the CNN learning rate to efficiently learn the subtle information about various leaf and nut diseases to enhance classification. The experimental results of the DSFO-CNN demonstrate superior performance compared to existing approaches.
Why it matches plant phenotyping methodsアレカヤシの葉・果実に現れる病徴を画像から分類するCNNベース手法を提案・評価しており、植物病害状態の取得・推定が中心的な方法論的貢献である。
abstractTherefore, accurate plant disease classification is essential for detecting distinct disease shapes and sizes.
Reproduction assets foundThe paper's phenotyping inputs are two public image datasets: the collected Arecanut dataset (Kaggle) and the PlantVillage dataset (Kaggle), both explicitly cited and declared openly available. No author analysis code or trained model is released.Dataset · publicDATA AVAILABILITY
The data used in this study are openly available at [19] and
[20].Open asset ↗pdf-page:7 lines:1-63Code / dataset availability confirmedCrossref · Europe PMC · checked 5 Sept 2026
Abstract Crop diseases pose significant challenges to productivity in resource-constrained settings, often remaining undiagnosed when diagnostic tools and infrastructure are either non-existent or inadequate. Current crop disease diagnosis relies on manual inspection methods that are labor-intensive, prone to error, and incapable of delivering real-time or region-specific insights in the process. Such limitations call for developing advanced diagnostic systems that are scalable and efficient in resource-constrained settings. This research introduced a comprehensive multi-spectral imaging and machine learning framework that can easily revolutionize the disease diagnosis and management inside the low-resource farming communities. Built within its core is the 3D Spectral-Spatial Convolutional Neural Network (3D SSCNN) that extracts high-resolution spectral-spatial features from hyperspectral image cubes. The accuracy achieved is around ~ 95% within 0.3 s per sample. Fed-DiagNet has provided support for distributed training that enables scalability and also data privacy to enhance the accuracy of regional models at approximately 92% as well as reduces training by almost 40%. Temporal disease progression modeling is enabled by Temporal Progression LSTM that provides dynamic trends with 90% accuracy up to a horizon of 10 days. This means that in addition to integrating disparate data sources-including hyperspectral imagery, environmental data, and pest observations-MTAN achieves an almost ~ 93% stress identification accuracy. Lastly, an RL-FO system tailors its treatment recommendations to local conditions so as to optimize for yield improvement and cost-effectiveness. With the proposed system, diagnostic precision increases to ~ 94%, and it is manifested in real-time efficiency while supporting scalability with actionable insights to empower farmers to mitigate crop losses and augment food security across several scenarios.
Why it matches plant phenotyping methods植物病害の状態をマルチスペクトル画像から推定する画像・機械学習フレームワークの開発が研究の中心であり、植物フェノタイピング手法に該当する。
abstractThis research introduced a comprehensive multi-spectral imaging and machine learning framework that can easily revolutionize the disease diagnosis and management inside the low-resource farming communities.
Reproduction assets foundThe paper's Data Availability statement points to two public repositories containing the data analyzed: a Kaggle PlantVillage dataset and a GitHub hyperspectral datasets repository. No author code or models are explicitly deposited.Dataset · publicAll data analyzed during this study are available in the Kaggle and Github repository, in the links https://www.kaggle.com/datasets/rohithaaiswarya/plant-village and https://github.com/antmedellin/HyperspectralDatasets .Open asset ↗Kaggle · rohithaaiswarya/plant-villagelines:563-583Dataset · publicAll data analyzed during this study are available in the Kaggle and Github repository, in the links https://www.kaggle.com/datasets/rohithaaiswarya/plant-village and https://github.com/antmedellin/HyperspectralDatasets .Open asset ↗GitHub · antmedellin/HyperspectralDatasetslines:563-583Code / dataset availability confirmedCrossref · Europe PMC · checked 5 Sept 2026
Identifying plant health conditions is an emerging precision-agriculture and food-security challenge, intensified by deploying deep-learning models on memory- and power-constrained edge devices. We present a TinyMLOps pipeline spanning model design, optimization, quantization, and deployment across diverse edge devices, evaluated under controlled laboratory conditions. Using a dataset derived from the PlantVillage benchmark, 39 fine-grained classes are aggregated into three superclasses: healthy leaf, unhealthy leaf, and no leaves. The resulting system therefore performs plant health-status classification and background filtering rather than diagnosing specific diseases. We train a MobileNet-based convolutional neural network jointly optimized for classification accuracy and computational efficiency, adopting state-of-the-art hyperparameter optimization (HPO) tools. Five models are selected, four from the Pareto Front and one as the biggest evaluated model during HPO, converted to LiteRT and ONNX, and evaluated at float32 and post-training int8 precision on a Raspberry Pi Zero 2 W and an STM32H743ZI microcontroller. At float32, LiteRT is 1.87–2.65× faster than ONNX Runtime on the Raspberry Pi across all five models. Relative to their float32 LiteRT counterparts, the int8 LiteRT models are 2.83–3.67× smaller on disk and 21.3–31.2% faster on the same board, at a cost in F1-score of between 0.0010 and 0.0068. On the microcontroller, only the two smallest models deploy at both precisions; for these, the fully quantized int8 variants are 4.3× faster and 3.85× smaller in MCU flash footprint than the float32 counterparts. The mid-range model fits the 2 MB flash and 1 MB RAM budget only when quantized, while the two largest models exceed it in every configuration tested.
Why it matches plant phenotyping methods葉画像から植物の健康状態を推定する分類手法と、エッジデバイス向けの最適化・量子化・展開パイプラインが研究の中心であり、植物状態の画像ベースフェノタイピングに該当する。
abstractWe present a TinyMLOps pipeline spanning model design, optimization, quantization, and deployment across diverse edge devices, evaluated under controlled laboratory conditions.
Reproduction assets foundThe paper's plant-phenotyping measurements are based on a derived PlantVillage dataset (39 classes aggregated into three superclasses) that the authors explicitly state is openly available in their own GitHub repository, also catalogued in the AgrifoodTEF Data Space. No author analysis code or trained model checkpointsDataset · publicThe data used in this study are derived from the openly available GitHub repository available at https://github.com/FBK-OpenIoT/PlantVillage-AugNoLeaves , accessed on 1 July 2026.Open asset ↗FBK-OpenIoT/PlantVillage-AugNoLeaveslines:1355-1403Dataset · publicPlantVillage-AugNoLeaves—AgrifoodTEF Data Space Catalogue. 2025. [(accessed on 1 July 2026)]. Available online: https://dataspace.agrifoodtef.eu/asset/did:op:3091fdcf83a05784416e585e4e45ea24afaf8c925a891921a3949acd98426f65Open asset ↗did:op:3091fdcf83a05784416e585e4e45ea24afaf8c925a891921a3949acd98426f65lines:1424-1474Code / dataset availability confirmedEurope PMC · checked 15 Sept 2026
Precise and reliable diagnosis of leaf diseases in tomato is essential for enhancing crop cultivation and minimizing agricultural losses. While deep learning models have performed well on benchmark datasets, the majority of present techniques rely on flat multi-class classification, which predicts all disease categories simultaneously. Such formulations promotes inter-class confusion, particularly when biologically different diseases with similar visual symptoms are learned within a same model. To overcome this constraint, we propose a biologically structured hierarchical deep learning framework in this study. Instead of directly classifying 10 disease classes, the proposed method first classifies leaf images into meaningful biological groups such as bacterial, fungal, pest-associated and healthy using a vision transformer (ViT) model. Then, specialized convolutional neural network (CNN) experts perform fine-grained classification within each category. The proposed hierarchical model shows an overall accuracy of 97.8%, when validated on PlantVillage tomato dataset. A flat ViT model trained with class-weighted loss obtained 96.3% accuracy, whereas a flat CNN model reached 99.3% under clean conditions but decreased sharply to 41% under Gaussian perturbation ( σ = 0.05). On the other hand, the hierarchical model performed steadily under noise with 97.4% accuracy at the same perturbation level. These results indicate that adding biological structure to model design reduces confusion, helps prevent imbalance effects and increases robustness, providing a more trustworthy and interpretable solution for real-world agricultural disease diagnosis.
Why it matches plant phenotyping methodsトマト葉画像から病害状態を分類する深層学習手法を開発し、既存モデルとの比較およびノイズ下での技術検証を行っており、植物表現型（病害状態）の取得・推定が中心である。
abstractwe propose a biologically structured hierarchical deep learning framework in this study.
Reproduction assets foundThe paper's phenotyping/classification measurements are based on the public PlantVillage tomato leaf image dataset, which the authors explicitly state was analyzed and provide a public Kaggle URL. No author analysis code, trained models, or paper-specific supplementary assets are described with availability language.Dataset · publicIsabel Luna-Maldonado , Autonomous University of Nuevo León, Mexico
Reviewed by: Noredine Hajraoui , Moulay Ismail University, Morocco
Tri Handhika , Universitas Gunadarma Pusat Studi Komputasi Matematika, Indonesia
Data availability statement
Publicly available datasets were analyzed in this study. This data can be found here: https://www.kaggle.com/datasets/charuchaudhry/plantvillage-tomato-leaf-dataset .
Author contributions
HG: Conceptualization, Formal analysis, Methodology, Writing – original draft, Writing – review & editing. SR: Supervision, Validation, Writing – review & editing. BL: Supervision, Validation, Writing – review & editing.
Conflict of interest
The author(s) declared thaOpen asset ↗Kaggle · charuchaudhry/plantvillage-tomato-leaf-datasetlines:588-616Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
TomatoLiDAR / point cloudLeafMorphology / geometry measurementSegmentationLeaf traits
Leaf parameters are crucial indicators reflecting the growing status of plants. Monitoring and analysis of leaf parameters significantly contributes to the improvement of crop yield and food quality. This study focused on three tomato plant varieties commonly grown in the Netherlands and proposed a fully automatic pipeline for leaf phenotyping. Three-dimensional (3D) point clouds of target plants were acquired with a specially designed imaging unit naming Maxi-Marvin. A semantic segmentation of plant organs was performed with PointNet++ model. To mitigate point cloud resolution decrement, the down-sampling operation in the baseline model was replaced with a distributed segmentation strategy. Leaf instances were further identified with Density-Based Spatial Clustering of Applications with Noise (DBSCAN), followed by a morphological phenotypic trait quantification based on 3D geometrical analysis. Target phenotypic traits including leaf length, leaf width, and leaf area. The evaluation results indicated that the distributed segmentation strategy achieved the best F 1 scores of 0.98 with block size set to 30,000. The Mean Average Errors (MAE) of leaf length, leaf width, and leaf area estimation were 2.09 cm, 1.78 cm and 8.98 cm 2 respectively. The estimation accuracies for leaf length, leaf width, and leaf area were 91.98%, 92.66%, and 89.67%, respectively.
Why it matches plant phenotyping methodsトマト葉の3D画像取得、器官セグメンテーション、葉インスタンス識別、形態形質推定を統合した自動フェノタイピング手法を開発・評価しており、方法が研究の中心です。
abstractproposed a fully automatic pipeline for leaf phenotyping
Reproduction assets foundThe paper's tomato point cloud dataset (with semantic and leaf instance annotations used for the phenotyping pipeline) is publicly available on Kaggle via a footnote. NPEC website is a facility page, and Open3D is a generic library, so neither qualifies.Dataset · public2. ^ The dataset used in this study is available at: https://www.kaggle.com/datasets/xinbolai/vtc-tomatoOpen asset ↗Kaggle · xinbolai/vtc-tomatolines:545-624Code / dataset availability confirmedEurope PMC · checked 14 Sept 2026
Introduction This study evaluates the applicability of digital morphometric analysis to images of archaeological carbonized olive endocarps as a proof-of-concept initial approach for archaeobotanical investigations. Conventional morphometric analyses of olive endocarps largely rely on manual measurements, limiting reproducibility and quantitative comparison. Methods Ten archaeological endocarps were selected from previously published archaeological assemblages based on the integrity of their outlines, apex-base morphology and overall preservation quality. Quantitative descriptors describing endocarp size, symmetry, curvature and contour geometry were extracted using the OliveID software and compared with a modern morphometric reference database comprising Greek and international olive cultivars. Results Reliable contour extraction and quantitative descriptor computation were successfully achieved for all archaeological specimens despite carbonization. Preliminary comparison of representative morphometric descriptors showed that the archaeological specimens were positioned within the morphometric variation observed among the modern reference collection. Hierarchical clustering consistently associated the archaeological endocarps with the modern Throumbolia morphotype, while distinguishing them from elongated, globular and mucro-bearing cultivars. Discussion These findings demonstrate the feasibility of applying digital image-based morphometric analysis to sufficiently preserved archaeological carbonized olive endocarps and indicate a similar morphometric affinity between the analyzed archaeological material and the modern Throumbolia cultivar. This proof-of-concept study highlights the potential of digital morphometric approaches for quantitative archaeobotanical investigations of archaeological olive remains, while emphasizing the need for larger archaeological datasets and standardized image acquisition to further validate the observed morphometric similarity.
Why it matches plant phenotyping methodsOliveIDを用いて炭化オリーブ内果皮の輪郭からサイズ、対称性、曲率、形状記述子を抽出し、デジタル画像形態計測の適用可能性と再現性を評価している。植物器官の形質抽出法が研究の中心である。
abstractThis study evaluates the applicability of digital morphometric analysis to images of archaeological carbonized olive endocarps as a proof-of-concept initial approach for archaeobotanical investigations.
Reproduction assets found保存済みの本文根拠を更新済みルールで再検証し、公開資産1件を確認しました。Supplement · publicThe quantitative measurements of the archaeological specimens are presented in Supplementary Table 2 , whereas the corresponding mean values and standard errors for the modern cultivars are provided in Supplementary Table 3 .Open asset ↗lines:311-320Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
The simultaneous diagnosis of diseases and evaluation of age quality grades in tea leaves are critical for precision agriculture and the economic valuation of tea products. Although deep learning has shown promise in agricultural vision tasks, current multi-task models often suffer from performance degradation due to feature conflicts: tea leaf disease recognition relies heavily on macro-structural lesions, whereas tea leaf-age quality grading depends on micro-textural features such as trichome density and color uniformity. To address this discrepancy, we propose a novel dual branch fusion network. Our architecture fundamentally decouples the feature extraction process by utilizing a dual branch mechanism. The first branch employs global average pooling to capture first-order spatial statistics; it can retain the global structural layout necessary for macro-lesion detection. The second branch introduces a dimensionality-reduced self-bilinear pooling module to compute second-order covariance matrices; it can effectively capture the fine-grained textural patterns essential for micro-grade classification. These decoupled features are subsequently fused and optimized through a weighted multi-task loss function. Experimental results on a comprehensive tea leaf dataset demonstrate that the proposed dual fusion framework significantly outperforms baseline models. The proposed network can rescue the disease classification accuracy drop observed in standard bilinear models while maintaining exceptional grading performance. Furthermore, the proposed network maintains a compact parameter footprint and low computational complexity. This balance renders it suitable for deployment on agricultural Internet of Things edge devices where inference speed is critical.
Why it matches plant phenotyping methods茶葉の病害状態と葉齢品質を画像から推定する深層学習手法を開発し、データセット上でベースラインと比較評価しており、表現型取得・推定法が中心である。
abstractwe propose a novel dual branch fusion network
Reproduction assets foundThe paper's Data Availability Statement publicly releases the two tea leaf image datasets used for its phenotyping tasks (disease recognition and leaf-age quality grading) via Mendeley Data. The authors' analysis code and trained models are only promised 'upon acceptance' with no public URL, so they do not qualify.Dataset · publicThe tea leaf disease recognition dataset analyzed in this study is available from https://data.mendeley.com/datasets/744vznw5k2/3 (accessed on 11 February 2026)Open asset ↗744vznw5k2/3lines:514-565Dataset · publicthe tea leaf grading dataset is available from https://data.mendeley.com/datasets/7t964jmmy3/1 (accessed on 11 February 2026)Open asset ↗7t964jmmy3/1lines:514-565Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Phenotyping high-biomass perennial crops is laborious and the rate of genetic gain in conventional perennial crop breeding programs is typically low. So, it is especially important to identify methods that produce efficiency gains in the breeding process. Miscanthus is a C4 perennial grass with favorable characteristics for producing biomass as a feedstock for biofuels and diverse bio-based products. Increasing biomass yield will increase profitability and environmental benefits, so it is a key target for Miscanthus breeding. In addition, the identification of well-adapted genotypes across a wide range of environmental conditions requires the establishment of multi-environment trials (METs). Sparse testing is a genomic prediction-based strategy that reduces the phenotyping costs in METs by selecting a subset of genotypes to evaluate in a subset of environments and then predicts the performance of the unobserved genotype-environment combinations. A Miscanthus sacchariflorus (MSA) population comprising 336 genotypes observed across three environments was analyzed implementing sparse testing designs. Three prediction models considering main effects (environments, genotypes, genomic) and interaction effects (genotype-by-environment; G×E interaction) were implemented for forecasting dry biomass yield (YDY), total culm (TCM), average internode length (AIL), and culm node number (CNN). Multiple calibration sets based on different compositions and sizes were considered to evaluate performance in terms of the predictive ability (PA) and the mean square error (MSE) for a fixed testing set size. The training set size ranged from 52 to 112 to predict a fixed set of 224 unobserved genotypes across all three environments. The results showed that the model accounting for G×E interaction consistently presented the highest PA and the lowest MSE: for CNN (PA: ~0.77, MSE: ~0.5) and YDY (PA: ~0.70, MSE: ~1.3) while for TCM and AIL these ranged from ~0.28 to 0.41 and ~1.3 to 4.3, respectively. Overall, varying training sets and allocation strategies did not affect PA and MSE, with 52 non-overlapping and 0 overlapping genotypes per environment as the optimal cost-effective allocation framework. This suggests that implementing sparse testing designs could significantly reduce phenotyping costs by fivefold, without compromising PA in breeding programs for perennial crops such as Miscanthus .
Why it matches plant phenotyping methodsスパーステスト設計とゲノム予測を用いて、複数環境での植物形質予測と表現型測定コスト削減を評価しており、表現型取得・予測手法が研究の中心である。
abstractSparse testing is a genomic prediction-based strategy that reduces the phenotyping costs in METs by selecting a subset of genotypes to evaluate in a subset of environments and then predicts the performance of the unobserved genotype-environment combinations.
Reproduction assets foundThe paper's data availability statement points to a public figshare deposit (DOI 10.6084/m9.figshare.31796794) containing the datasets analyzed in this Miscanthus sparse-testing genomic prediction study, including the phenotypic and genotypic data used for the models.Dataset · publicThe datasets analyzed for this study can be found in the figshare repository at https://doi.org/10.6084/m9.figshare.31796794 .Open asset ↗figshare · 10.6084/m9.figshare.31796794lines:603-621Code / dataset availability confirmedEurope PMC · checked 14 Sept 2026
Reliable traits are needed for identification of tea ( Camellia sinensis ) cultivars, yet the stability of leaf morphology and color across leaf positions remains unclear. This study evaluated inter-cultivar variation and positional stability in leaf morphological, RGB color, and SPAD traits in six predominant cultivars. One-year-old shoots were sampled in a completely randomized design, and five fully expanded leaves below the apical bud were analyzed. SPAD values were measured with a chlorophyll meter, and scanned images were used to extract contour and RGB traits. Data were analyzed using ANOVA, correlation analysis, PCA, and discriminant analysis. Leaf morphology differed among cultivars and leaf positions, with significant cultivar-by-position interactions; however, the width-to-length ratio differed among cultivars but remained stable across positions in these cultivars. SPAD values increased with leaf position and were strongly associated with RGB components, being negatively correlated with R and G and positively correlated with B. Morphological traits explained 52.988% of total variance in PCA and yielded 64.6% overall classification accuracy, with LaoHan showing the highest accuracy (83.3%). Misclassification was concentrated among genetically similar cultivars. These findings suggest that stable leaf shape proportions and SPAD-RGB relationships provide useful descriptors, whereas genetic relatedness limits morphology-based cultivar identification under the present conditions.
Why it matches plant phenotyping methods茶品種識別のため、葉の形態・RGB・SPAD特性の取得と安定性、分類性能を中心に評価しており、画像由来形質抽出を含む実質的な表現型解析である。
abstractscanned images were used to extract contour and RGB traits
Reproduction assets found保存済みの本文根拠を更新済みルールで再検証し、公開資産1件を確認しました。Dataset · publicThe following supporting information can be downloaded at https://www.mdpi.com/article/10.3390/biology15151283/s1 , Table S1: Original data of leaf morphological traits, RGB values, and SPAD values from six tea cultivars in this study.Open asset ↗lines:368-409Code / dataset availability confirmedarXiv · OpenAlex · checked 15 Sept 2026
Accurate 3D crop monitoring underpins data-driven precision agriculture by enabling field-scale analysis of plant structure, growth dynamics, and management response. Modern 3D reconstruction methods perform strongly on generic benchmarks, but rendered appearance may not translate into metrically and agronomically useful geometry in crop fields. We introduce UAV3DCrop, a public benchmark of repeated multi-angle unmanned aerial vehicle (UAV) crop surveys. It contains 88,830 RGB images at $5280 \times 3956$ pixels, with a ground sampling distance of 3.6-5.8 mm, from 91 scenes spanning corn, soybean, wheat, and oat. Track A evaluates seven scene-optimized methods -- Neural Radiance Field (NeRF) and 3D Gaussian Splatting (3DGS) variants -- on held-out views, photogrammetry-referenced depth, and canopy-height recovery. Track B tests four pretrained feed-forward models on zero-shot camera-pose and geometry estimation. The scene-optimized methods rank differently across the three targets: Splatfacto-big leads appearance, whereas Scaffold-GS leads depth and is statistically tied with Splatfacto for canopy height. Among feed-forward models, MapAnything leads on seven of the eight metrics, while the remaining models vary more across crops and fail severely on absolute scale in a way that alignment conceals. Repeated acquisitions reveal further sensitivities that differ by output type and by model, associated with position within the acquisition sequence and with tie-point multiplicity. Current 3D reconstruction methods are therefore not yet interchangeable for agronomic use: no single method wins on appearance, geometry, and canopy height at once, and only one of four feed-forward models recovers usable metric scale. The dataset is publicly available at https://link-dev.github.io/UAV3DCrop/
Why it matches plant phenotyping methods植物キャノピー高さという明示的な形質を対象に、UAV 3D再構成手法をベンチマークし、公開データセットとして提供しているため、フェノタイピング手法が中心である。
abstractWe introduce UAV3DCrop, a public benchmark of repeated multi-angle unmanned aerial vehicle (UAV) crop surveys.
Reproduction assets foundThe paper introduces UAV3DCrop, a public benchmark of repeated multi-angle UAV crop surveys (88,830 RGB images, 91 scenes, four crops) with refined poses, photogrammetric depth references, and linked canopy-height and effective-LAI field measurements. The dataset is explicitly stated to be publicly available under CC BDataset · publiche acquisition sequence and with tie-point multiplicity. Current 3D reconstruction methods are therefore not yet interchangeable for agronomic use: no single method wins on appearance, geometry, and canopy height at once, and only one of four feed-forward models recovers usable metric scale. The dataset is publicly available at https://link-dev.github.io/UAV3DCrop/ .
Keywords:
UAV imagery; agricultural datasets; crop-field reconstruction; neural radiance fields;
Gaussian splatting; feed-forward geometry.
1 IntroductionOpen asset ↗UAV3DCroplines:1-90Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Idesia polycarpa Maxim. is a premier woody oil species in Guizhou Province, China, whose fruit yield and oil quality largely depend on effective pollination and fertilization. However, limited research on pollen viability and germination has hindered industrial progress. To address this gap, a comprehensive evaluation framework for elite I. polycarpa germplasm was developed, integrating micromorphological analysis, optimized staining protocols, and in vitro germination assay. Scanning electron microscopy (SEM) revealed that I. polycarpa pollen, while genetically conserved at the genus level-characterized by prolate shapes, tricolporate apertures, and reticulate exine ornamentation-exhibits notable micromorphological variation among genotypes. Of the nine staining protocols tested (2,3,5-triphenyl tetrazolium chloride [TTC], carbol fuchsin, acetocarmine, methylene blue, Alexander, peroxidase, 2,5-diphenylmonotetrazolium bromide [MTT], I2-KI, and red ink), TTC and red ink were the most effective, offering clear chromatic distinction between viable and non-viable pollen. Through orthogonal experimental designs, genotype-specific optimal media for in vitro germination were identified: 0.40 g/L H3BO3, 0.01 g/L KNO3, 0.02 g/L Ca(NO3)2·4H2O, and 0.20 g/L KH2PO4 for STZ-6; and 0.20 g/L H3BO3, 0.02 g/L KNO3, 0.02 g/L Ca(NO3)2·4H2O, and 0.10 g/L KH2PO4 for STZ-9. Regression analysis confirmed a highly significant positive correlation (P < 0.01) between in vitro germination rates and the staining results from both TTC and red ink across various concentrations. Notably, 5% TTC and 30% red ink exhibited the highest coefficients of determination. A hierarchical evaluation strategy is thus proposed: the 5% TTC method is recommended for precise laboratory quantification due to its stability, while the 30% red ink method, due to its ease of use, is suited for rapid field-based screening. This study provides valuable insights into the morphological characteristics of I. polycarpa pollen and establishes a standardized evaluation framework, supporting germplasm innovation and optimizing pollination management.
Why it matches plant phenotyping methods花粉の生存性・発芽という植物の生殖形質を対象に、染色法とin vitro発芽法を最適化・検証し、標準化した評価フレームワークを開発しているため、方法論が中心である。
abstracta comprehensive evaluation framework for elite I. polycarpa germplasm was developed, integrating micromorphological analysis, optimized staining protocols, and in vitro germination assay.
Reproduction assets foundThe article's Data Availability statement points to a public Biostudies deposit containing the study's data (pollen morphology measurements, staining viability counts, and in vitro germination results). No author analysis code or trained models are mentioned.Dataset · publicData Availability: The data that support the findings of this study are openly available in Biostudies at https://doi.org/10.6019/S-BSST3125 .Open asset ↗Biostudies · S-BSST3125lines:176-186Code / dataset availability confirmedEurope PMC · Crossref · checked 5 Sept 2026
Accurate tracking and measurement of pollen dispersal in the atmosphere are essential for assessing cross-pollination risks, particularly in the case of genetically engineered (GE) crops. We conducted a series of unique release-recapture field studies with GE switchgrass in Oliver Springs, TN, USA. Two hundred transgenic switchgrass plants (Panicum virgatum L. "Performer") were planted at the center of a clear-cut field, with one block of 100 plants expressing orange fluorescent protein (OFP) under a switchgrass ubiquitin promoter (PvUBI1) and another block of 100 plants expressing OFP driven by a maize pollen-specific promoter (Zm13). Pollen was sampled from the atmosphere using fixed (ground-based) and mobile (drone-based) sampling devices at different distances from the source field, with Lagrangian stochastic dispersal simulations run for sampling periods using high-resolution wind measurements. The pollen emission rate was estimated by combining simulated and measured pollen concentrations, and strong diurnal trends were observed. Diurnal emission rate trends were positively correlated with wind speed, temperature, and vapor pressure deficit, while negatively correlated with relative humidity. In low-wind meandering conditions, incorporating changing wind direction into the dispersal modeling improved pollen emission rate estimation and model-measurement comparisons. This study assesses the effectiveness of high- and low-volume pollen samplers in relation to source strength up to 1 km from the source, enhancing understanding of pollen measurement techniques. Additionally, it is a proof-of-concept for drone-based pollen sampling and GMO pollen tracking using fluorescence measurements. Results from our experiments have significant implications for cross-pollination risk assessment, prediction, and management of airborne allergens.
Why it matches plant phenotyping methods固定・ドローン搭載サンプラー、蛍光測定、風況モデルを組み合わせて植物由来の花粉放出率を推定し、花粉測定技術を評価することが中心であるため、植物の生殖状態・放出特性に関するフェノタイピング手法として採用。
abstractPollen was sampled from the atmosphere using fixed (ground-based) and mobile (drone-based) sampling devices
Reproduction assets foundThe paper's Data Availability statement deposits all sampling data, modeling code, and simulation results on the Virginia Tech Data Repository (DOI 10.7294/25733604), which is an allowed URL. This directly covers the paper's pollen concentration measurements and Lagrangian stochastic dispersal modeling. Other URLs (e.gDataset · publicAll sampling data, modeling code, and simulation results underlying this manuscript are made available on the Virginia Tech Data Repository at https://doi.org/10.7294/25733604 .Open asset ↗Virginia Tech Data Repository · 10.7294/25733604lines:201-219Code / dataset availability confirmedCrossref · checked 15 Sept 2026
Published1 Aug 2026International Journal of Advances in Data and Information SystemsCited by 0 · OpenAlex ↗
Plant diseases have continued to threaten agricultural productivity, while manual inspection methods have remained inefficient and prone to subjectivity. This study proposed and assessed a hybrid framework integrating a Convolutional Neural Network (CNN) with a Large Language Model (LLM) to perform image-based plant leaf disease classification accompanied by interpretable diagnostic explanations. EfficientNetV2-M was employed as the visual backbone and trained on 11 selected classes of apple, grape, and potato leaf images derived from the PlantVillage dataset. A structured data splitting strategy was applied to ensure reliable model validation and unbiased testing. The classification capability of the CNN component was examined through standard multi-class evaluation indicators, including class-wise predictive consistency and error distribution analysis. Experimental results indicated that the model delivered highly consistent predictions, reaching a peak test accuracy of 99.79%, reflecting its robustness in distinguishing visually similar disease patterns. To overcome the black-box limitation, prediction outputs were transformed into structured prompts and processed by GPT-4o to generate contextual explanations. The generated narratives systematically described observable symptoms, highlighted distinguishing characteristics, and suggested initial management actions. Overall, the proposed hybrid system demonstrated that combining high-performance visual recognition with language-based reasoning enhanced both diagnostic reliability and interpretability in digital agriculture applications.
Why it matches plant phenotyping methods植物葉の画像から病害状態を推定するCNN・LLM統合手法を開発・評価しており、病害分類と説明生成が研究の中心であるため。
abstractThis study proposed and assessed a hybrid framework integrating a Convolutional Neural Network (CNN) with a Large Language Model (LLM) to perform image-based plant leaf disease classification accompanied by interpretable diagnostic explanations.
Reproduction assets foundThe paper uses the public PlantVillage color dataset (11 apple/grape/potato classes, 9,385 images) and explicitly points to it in the DATA AVAILABILITY statement as the replication package data. The authors also provide a public Streamlit demonstration of their hybrid CNN–LLM system. No author analysis code or trained-Dataset · publicaper. The research was conducted for academic purposes, and no financial, commercial, or
personal relationships influenced the study design, data analysis, interpretation of results, or
preparation of the manuscript.
DATA AVAILABILITY
The data associated with this study are publicly available online in the replication package.
[https://github.com/spMohanty/PlantVillage-Dataset/tree/master/raw/color]
AUTHOR CONTRIBUTIONS
Frenky Riski Gilang Pratama: Conceptualization; Programming and coding
implementation; Methodology; Writing-Original Draft. Sugiarto Surono: Conceptualization;
Methodology; Supervision; Writing-Review & Editing. Aris Thobirin: Proofreading Paper;
Writing-Review & Editing; FunOpen asset ↗https://github.com/spMohanty/PlantVillage-Dataset/tree/master/raw/colorpdf-raw-page:10 lines:1-52Code / dataset availability confirmedOpenAlex · checked 14 Sept 2026
Background: Tropism, an adaptive growth mechanism often completely overlooked in tree phenotyping studies, is a crucial aspect of tree growth that allows them to reconfigure geometrically in relation to their immediate environment. This study introduces an integrated method to quantify tropic behaviour in plant phenotyping studies. Methods: The methodology combines cost-effective three-dimensional (3D) photogrammetric data capture from video, stem delineation techniques and 3D mathematical modelling of posture control for model-assisted identification of tropism traits. The proposed method was tested on a Pinus radiata D.Don. seedling subjected to a gravitational stimulus for 75 days. Stem posture was repeatedly measured using both 3D photogrammetry and fixed photography to create multitemporal 3D datasets and two-dimensional (2D) reference curves. Results: Individual 3D stem curves reconstructed with the proposed methodology introduced an error on spatial coordinates with a normalised RMSD ranging from 1.6 to 4.3% depending on time of capture, when compared with the 2D reference. The error for local tilt angle was higher than the error on spatial coordinates, with RMSD ranging between 5.6–12.2°, as expected for a first-order derivative. The gravitropic coefficient, capturing the sensing of and the reaction to local inclination by the plant, was underestimated by 2% if compared to the reference methodology. No contribution of autotropism (tendency to remain straight) was identified using the new methodology, but that contribution was found to be small using the 2D-approach and likely a key aspect of the gravitropic signature in the studied species. The major challenge with the proposed point cloud-based methodology arose from automated stem delineation. With dedicated algorithm enhancements to address stem occlusion in juvenile conifers and with more regular captures during plant motion, the proposed method could, however, perform identically to the 2D reference methodology. Overall, recovery of tropism traits performed equivalently whether using 2D or 3D data to fit the model of posture control. The minor discrepancies with experimental behaviour originated from fitting a simple kinematic model to complex real-world behaviour rather than data capture and digitising procedures. Conclusions: Overall, the proposed methodology, in its current form, offers a viable alternative to traditional 2D imagery methods at the cost of a small reduction in accuracy and capture time. The advantage of the 3D methodology is that it has the potential to track motion in multiple planes, whilst also measuring plant structure. With refinement, this methodology could be streamlined and adapted for deployment in field and operational environments at scale for phenotyping studies.
Why it matches plant phenotyping methods3Dフォトグラメトリ、茎の自動抽出、点群解析、姿勢モデルを統合し、植物の屈性形質を定量化・検証する方法が研究の中心である。
abstractThis study introduces an integrated method to quantify tropic behaviour in plant phenotyping studies.
Reproduction assets foundThe paper's data availability statement explicitly deposits the raw photogrammetric point clouds and derived stem curves on Figshare and the R stem-extraction pipeline code on GitHub, both with public URLs.Dataset · publicthe
Ministry of Business Innovation & Employment (MBIE)
New Zealand as part of the Tree Interactions Programme
(Catalyst Fund C09X1923).
Supplementary materials and data availability
The raw photogrammetric point clouds and the stem
curves derived from both photogrammetry and 2D
imagery can be found at the following repository:
https://doi.org/10.6084/m9.figshare.32248617. The
R code for the stem extraction pipeline is available
at https://github.com/Robin-hartley/tropism-stem-curves-3d
Hartley et al. New Zealand Journal of Forestry Science (2026) 56:11 Page 14Open asset ↗figshare · 10.6084/m9.figshare.32248617pdf-raw-page:14 lines:97-113Code · publicamme
(Catalyst Fund C09X1923).
Supplementary materials and data availability
The raw photogrammetric point clouds and the stem
curves derived from both photogrammetry and 2D
imagery can be found at the following repository:
https://doi.org/10.6084/m9.figshare.32248617. The
R code for the stem extraction pipeline is available
at https://github.com/Robin-hartley/tropism-stem-curves-3d
Hartley et al. New Zealand Journal of Forestry Science (2026) 56:11 Page 14Open asset ↗github · Robin-hartley/tropism-stem-curves-3dpdf-raw-page:14 lines:97-113Code / dataset availability confirmedCrossref · checked 14 Sept 2026
Sugarcane plant diseases pose a significant threat to agricultural productivity, yet early and accurate identification remains challenging for farmers due to the limitations of manual inspection. This study proposes a sugarcane leaf disease classification system using ConvNeXt V2 Tiny, a modern convolutional architecture with a Global Response Normalization (GRN) mechanism, combined with an ensemble Stratified K-Fold Cross Validation strategy (K=6) to improve generalization on real-world field data. A dataset of 2,948 leaf images spanning five classes (Red Rot, Mosaic, Rust, Yellow Leaf, and Healthy) was used, with field-collected images held out as a fixed test set. The ensemble model achieved a mean validation accuracy of 98.49% ± 0.58% across six folds and a test accuracy of 98.39% on 427 unseen field images, with macro-average precision, recall, and F1-score each reaching 98%. ConvNeXt V2 Tiny substantially outperformed ResNet-50 (87.35%) and EfficientNetV2-S (83.37%) under identical experimental settings, demonstrating superior generalization across the domain gap between curated and field data. The primary contribution of this study is the first application of ConvNeXt V2 Tiny with ensemble K-Fold strategy for sugarcane disease classification, offering high accuracy with moderate computational complexity (28.6M parameters) and practical deployability, as demonstrated through the SugarScan web application.
Why it matches plant phenotyping methodsサトウキビ葉画像から病害状態を推定する画像ベースの表現型解析手法が研究の中心であり、モデル性能の検証・比較も実施しているため含める。
abstractThis study proposes a sugarcane leaf disease classification system using ConvNeXt V2 Tiny
Reproduction assets foundThe paper's phenotyping inputs include a public Kaggle dataset (Sugarcane Leaf Disease Dataset, SLD) of sugarcane leaf disease images used for training/validation, plus field-collected images. Only the Kaggle dataset qualifies as a paper-specific public asset with an authors' URL; no author analysis code, trained modelDataset · publicsecondary data from the Sugarcane Leaf Disease Dataset (SLD)
available publicly on Kaggle (https://www.kaggle.com/datasets/pritpal2873/sug arcane-leaf-disease-dataset)Open asset ↗Kaggle · pritpal2873/sugpdf-page:2 lines:54-60Code / dataset availability confirmedOpenAlex · checked 14 Sept 2026
Introduction: Habitat restoration is necessary for the conservation and management of plant and animal species, especially in rare ecosystems. Drones may be well-suited to monitor changes in plant and animal communities in response to restoration efforts. The objective of the study was to examine whether drone imagery can detect differences in vegetation across multiple contexts. Materials and methods: Using a commercially available drone, I captured and processed aerial imagery with an open-source photogrammetric processing program. Point cloud data were processed to generate a vegetation density index, which was quantified across four cover types and compared between disturbance histories. In addition, using automated radio tracking, I compared vegetation density between used and available locations for Eastern Whip-poor-wills during the day and at night. Results: In August 2024, a drone flight covering a 3.05 km2 area of pine barrens captured 3372 images. Vegetation density differed by cover type (p = 0.001) and was greater in recently disturbed sites (p = 0.002). Scrub oak and recently burned sites had ~30% and ~12% greater vegetation density than deciduous forests and plots > 2 years post-disturbance, respectively. Vegetation density was lower at Eastern Whip-poor-will used locations than at available locations (151.0 vs. 159.7 points/m2, p < 0.001). Conclusions: Analysis of fine-scale differences in vegetation structure was important in discriminating subtle differences in habitat selection for Eastern Whip-poor-wills. This study demonstrated that drones and relatively simple image processing can be practical tools for restoration when quantifying and monitoring vegetation differences in dynamic ecosystems.
Why it matches plant phenotyping methodsドローン画像と点群処理により植生密度・植生構造を定量化する手法を中心に、異なる植生条件での適用性を評価しているため、植物表現型計測の方法適用研究に該当する。
abstractPoint cloud data were processed to generate a vegetation density index, which was quantified across four cover types and compared between disturbance histories.
Reproduction assets foundThe paper's data availability statement points to a public Zenodo deposit containing the study's drone-derived vegetation density data and related measurements.Dataset · publicThe data supporting the findings of this publication has been made available within a publicly accessible
repository at https://doi.org/10.5281/zenodo.20398090.Open asset ↗Zenodo · 10.5281/zenodo.20398090pdf-page:11 lines:1-49Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Camera-based visual sensing provides a non-destructive and scalable approach for monitoring strawberry diseases and pests in greenhouse environments. However, greenhouse images acquired under practical cultivation conditions often contain early-stage tiny lesions, complex leaf backgrounds, uneven target scales, illumination variations, and partial occlusions, making accurate and efficient visual detection challenging. To address these issues, this study proposes YOLOv8n-DSLW (YOLOv8n enhanced by Dense reuse, Shuffle attention, LSKA-LAMP lightweight modeling, and Wise-IoU optimization), an AI-enabled vision-sensing detection model based on YOLOv8n for tiny strawberry disease and pest detection. Specifically, Shrink Residual Dense Block (ShrinkRDB) dense connection blocks and the C2f with Shuffle Attention (C2fSA) module are introduced to preserve weak lesion textures and suppress background interference in greenhouse visual data. A high-resolution P2 detection layer combined with Wise-IoU (WioU) dynamic regression loss is further incorporated to enhance tiny-target perception and localization. In addition, the Spatial Pyramid Pooling-Fast with Large Separable Kernel Attention (SPPF-LSKA) module strengthens contextual modeling under occlusion and clutter, while Layer-Adaptive Magnitude-based Pruning (LAMP) is adopted to mitigate model redundancy and improve the accuracy-efficiency balance. Experiments on a self-collected greenhouse strawberry disease and pest dataset show that YOLOv8n-DSLW achieves a mean Average Precision at 0.5 IoU threshold (mAP@0.5) of 94.3% and a mAP@0.5:0.95 of 77.5%, outperforming the YOLOv8n baseline. The final model has a parameter count of 4.386 M and a computational cost of 27.6 GFLOPs, achieving a frame rate of 45 FPS on the test workstation. It shows application potential for real-time visual monitoring in greenhouses under controlled data acquisition conditions. The results demonstrate that the proposed method improves tiny lesion detection under dense targets, complex backgrounds, and leaf occlusions, providing an AI-enabled vision-sensing framework for automated strawberry health monitoring in greenhouses. Nevertheless, due to limitations associated with imaging equipment, dataset representativeness, and the inherent constraints of the algorithm, further optimization and validation are required to support large-scale field deployment.
Why it matches plant phenotyping methodsイチゴ葉の病斑を画像から検出・局在化する新規YOLOモデルを開発し、データセット上で性能評価しており、植物病害状態の画像ベース表現型取得が中心である。
abstractthis study proposes YOLOv8n-DSLW (YOLOv8n enhanced by Dense reuse, Shuffle attention, LSKA-LAMP lightweight modeling, and Wise-IoU optimization), an AI-enabled vision-sensing detection model based on YOLOv8n for tiny strawberry disease and pest detection.
Reproduction assets foundThe paper's self-collected greenhouse strawberry disease/pest image dataset (with COCO annotations and train/test splits) is explicitly stated as publicly deposited on GitHub at the allowed URL. No author analysis code or trained model checkpoint is mentioned as publicly available.Dataset · publicThe dataset used in this study, including the training and independent test subsets, has been uploaded to a GitHub repository for dataset verification and is available at: https://github.com/dataset-review-2026/strawberry-dataset (accessed on 26 July 2026).Open asset ↗dataset-review-2026/strawberry-datasetlines:111-131Code / dataset availability confirmedCrossref · Europe PMC · checked 5 Sept 2026
Introduction Timely and accurate detection of plant diseases is essential for ensuring global food security and supporting sustainable agriculture. Conventional diagnostic approaches, such as manual inspection and laboratory testing, are often time-consuming, labor-intensive, and impractical for large-scale or remote agricultural environments. Although deep learning models, particularly Convolutional Neural Networks (CNNs), have significantly improved automated plant disease classification, they often lack interpretability and struggle to generalize under diverse field conditions. Methods This study proposes AgriX-SENet, an explainable deep learning framework that integrates Squeeze-and-Excitation (SE) blocks with a DenseNet121 backbone to enhance disease classification performance. The SE blocks recalibrate channel-wise feature responses to emphasize disease-relevant information while suppressing background noise. To improve model transparency, Grad-CAM, SHAP, and LIME were incorporated to provide visual and feature-level explanations of the model’s predictions. The framework was trained and evaluated using the Plant Pathology 2020 dataset containing four classes: healthy, rust, scab, and multiple diseases. Results AgriX-SENet achieved a training accuracy of 97.47% and a validation accuracy of 95.07%, outperforming fourteen state-of-the-art deep learning models. The classification report demonstrated high precision and recall across most disease categories, although the scab class exhibited comparatively lower recall, indicating an opportunity for further improvement. The explainability analyses consistently showed that the model focused on pathologically relevant regions of leaf images, validating the reliability of its predictions. Discussion The proposed AgriX-SENet framework effectively combines high classification performance with model interpretability, addressing a key limitation of existing CNN-based plant disease detection systems. Its ability to provide accurate and explainable predictions makes it a promising solution for scalable agricultural diagnostics. Future work will focus on improving classification performance for challenging disease categories and optimizing the framework for deployment on mobile and edge computing devices to enable real-time field applications.
Why it matches plant phenotyping methods葉画像から植物病害状態を推定する説明可能な深層学習フレームワークを開発・評価しており、植物表現型取得・判定手法が中心である。
abstractThis study proposes AgriX-SENet, an explainable deep learning framework that integrates Squeeze-and-Excitation (SE) blocks with a DenseNet121 backbone to enhance disease classification performance.
Reproduction assets foundThe paper trains and evaluates AgriX-SENet on the public Plant Pathology 2020 (FGVC7) Kaggle image dataset, which is the paper-specific plant image input for its disease-classification measurements. No author analysis code, trained model checkpoints, or supplementary code/data deposit is mentioned; the data statement (Dataset · publicPlant Pathology 2020 - Fgvc7 . Available online at: https://www.kaggle.com/competitions/plant-pathology-2020-fgvc7/data .Open asset ↗Kaggle · plant-pathology-2020-fgvc7lines:895-974Code / dataset availability confirmedCrossref · Europe PMC · checked 5 Sept 2026
Rice stem internal structure is a critical micro-phenotype influencing lodging resistance and yield; however, its analysis remains constrained by labor-intensive manual methods. Here, we present a publicly available dataset of 686 rice stem cross-sections, with 21,027 large vascular bundles (LVBs) and 19,342 small vascular bundles (SVBs) manually annotated. Five deep learning architectures were systematically evaluated, among which UNet-VGG16 achieved the best performance with a mean intersection over union (mIoU) of 87.4% (82.49% for LVBs and 74.41% for SVBs). An improved model, UNet-ECA-Bio, further raised mIoU to 89.32% and SVB IoU to 78.97% by integrating Efficient Channel Attention (ECA) and biologically informed class weighting using an image-level dataset. Leveraging these high-accuracy phenotypic predictions, genome-wide association studies (GWAS) indicated concordance between annotated and predicted traits, with SNP overlap rates of 96% (LVB count: 1,217/1,262), 43% (SVB count: 6/14), 98% (stem area: 122/124), and 100% (cavity area: 3/3) at −log10(p) ≥ 6. Meanwhile, compared with manual annotation (estimated 10–30 minutes per image), the proposed approach processed all 686 images within 10 minutes, representing a >600-fold increase in throughput. We further developed a user-friendly software tool, “Rice_Stem_Pre_V1.1.exe,” for automated phenotyping of 14 stem traits, providing a cost-effective platform for genetic studies of lodging resistance and yield improvement.
Why it matches plant phenotyping methodsイネ茎維管束の画像から複数の表現型形質を自動抽出する深層学習モデル、データセット、検証、ソフトウェアを中心的に開発しており、明確な植物フェノタイピング手法研究である。
abstractwe present a publicly available dataset of 686 rice stem cross-sections, with 21,027 large vascular bundles (LVBs) and 19,342 small vascular bundles (SVBs) manually annotated.
Reproduction assets found本文中に内容が明示された植物フェノタイピング関連の補足表と、その公開リンクを確認しました。Supplement · publicSupplementary Table 6
Description of annotated and predicted stem internal structural traits.Open asset ↗lines:510-582Code / dataset availability confirmedCrossref · Europe PMC · checked 5 Sept 2026
Plants encounter multiple abiotic stresses. Among them, heat and drought stress play a substantial role in reducing the agricultural productivity of commercial plants. Hence, wild and underutilized plants can be a potential alternative as they are naturally tolerant to extreme climatic conditions and are a rich source of nutrition. Manual stress and disease detection is a laborious and expensive process, and hence automation in this field is required to reduce agricultural losses. This study evaluates the prediction and detection of abiotic stress in Acacia senegal bipinnate leaves, exploring various stress-induced changes using machine learning (ML) algorithms and biochemical analysis. A. senegal , an underutilized edible desert legume, was grown under controlled greenhouse conditions. After 2 months, these plants were segregated into groups and subjected to heat and drought treatments. Image acquisition was performed to obtain a dataset of 3,454 images of A. senegal leaves. Physiological parameters, such as fresh and dry leaf weight, shoot length, number of leaves, and biochemical assays like antioxidant assay (DPPH), total phenolic content (TPC), and total flavonoid content (TFC), were determined. LC-MS/MS analysis was conducted to identify over 50 phytochemical compounds. A hybrid model was developed consisting of a fine-tuned EfficientNet-based Convolutional Neural Network (CNN) followed by a Support Vector Machine (SVM) for the binary classification of A. senegal leaves. The model distinguishes between healthy and stress-affected unhealthy leaves and achieved an accuracy score of 86.6%. This report provides a significant lead toward stress phenotyping and prediction of a bipinnate leaf plant using ML algorithms. The overall study is useful to understand how the stress encountered by arid plants alters the nutritional quality.
Why it matches plant phenotyping methods画像データと機械学習モデルを用いて、アカシア葉の健全・ストレス状態を自動分類する手法を開発・評価しており、植物表現型取得が中心です。
abstractThis study evaluates the prediction and detection of abiotic stress in Acacia senegal bipinnate leaves
Reproduction assets foundThe paper's data availability statement explicitly makes the 3,454-image A. senegal leaf imaging dataset public on Zenodo and the ML implementation source code public on GitHub; both are paper-specific, public, and actionable.Dataset · publicThe plant leaf imaging data used in the work is publicly available at https://doi.org/10.5281/zenodo.16531486.Open asset ↗zenodo · 10.5281/zenodo.16531486html-lines:480-497Code · publicThe source code of the implementation is available at https://github.com/softwareinnovationslabBITS/CDRF_ASenegal_MLImagingOpen asset ↗github · softwareinnovationslabBITS/CDRF_ASenegal_MLImaginghtml-lines:480-497Code / dataset availability confirmedCrossref · Europe PMC · checked 5 Sept 2026
Early and accurate identification of plant diseases is essential for improving crop productivity and ensuring food security. Many existing deep learning-based plant disease classification methods rely solely on leaf images collected from a controlled environment, which limits their applicability in real-world agricultural conditions where symptoms may be visually unclear and influenced by environmental factors. To address these challenges, this study discusses AgriFusionNet, a context-aware multimodal deep learning framework that integrates leaf images, textual symptom descriptions, and environmental data for robust plant disease classification. The proposed architecture employs EfficientNet-B0 for visual feature extraction, BERT for semantic representation of symptom descriptions, and a lightweight multilayer perceptron for modeling environmental factors such as temperature, humidity, rainfall, and soil moisture. Features from all three modalities are fused into a unified representation to train the CNN model. The model is trained and tested upon the Context-Aware Multimodal Augmented PlantVillage dataset covering 38 plant diseases and healthy classes. Experimental results show that AgriFusionNet gives an overall accuracy of 98.94% on the dataset Context-Aware Multimodal Augmented PlantVillage, with competitive precision and recall and F1-score. The multimodal framework facilitates the co-learning of visual, semantic, and contextual environmental representations and the analyses of the confusion matrix and feature interactions give insights into cross-modal relationships. The proposed approach aims to explore context-aware multimodal representation learning for agricultural AI applications, with emphasis on integrating complementary visual, semantic, and contextual information.
Why it matches plant phenotyping methods葉画像を中心に、症状記述と環境情報を統合して植物病害状態を分類する手法を開発・評価しており、植物フェノタイピング手法が中心である。
abstractthis study discusses AgriFusionNet, a context-aware multimodal deep learning framework that integrates leaf images, textual symptom descriptions, and environmental data for robust plant disease classification.
Reproduction assets foundThe paper's data availability statement points to the Context-Aware Multimodal Augmented PlantVillage dataset (leaf images, symptom text, environmental data used for the phenotyping/classification analysis) deposited publicly on IEEE Dataport with a DOI matching an allowed URL.Dataset · publicPublicly available datasets were analyzed in this study. This data can be found here: Dataset. IEEE Dataport. https://dx.doi.org/10.21227/9jat-r836 [Accessed on August 2025].Open asset ↗IEEE Dataport · 10.21227/9jat-r836lines:1029-1047Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Background Covered smut in barley caused by Ustilago hordei leads to yield reduction and quality loss of stored grains and is especially challenging in organic production. However, screening for resistance remains challenging. The goal of our research was to evaluate protocols for screening covered smut in barley under normal and speed breeding conditions that could be scaled up for breeding purposes. We considered favorable pathogen growth conditions, a sufficient sample size to detect differences among genotypes through a power analysis, sources of disease escape or avoidance, and the infection effect on agronomic traits. Results In the first experiment, twenty genotypes treated with various inoculum concentrations were screened for disease incidence under a speed breeding system. Generally, low infection levels were found, likely due to disease escape or avoidance. Based on a power analysis, we modified the protocol to include more plants and improved pathogen growth conditions under a normal greenhouse system. With the modified protocol, the incidence of covered smut was significantly different among genotypes. The protocol also reduced the number of plants required to detect at least one infected plant. Artificial inoculation significantly decreased germination rates while head emergence, days to heading, and plant height were affected by disease infection in the most susceptible genotypes. We also found that covered smut incidence varied with tiller emergence order. The genotypes 'DH160779' (RES check), PI 270630', 'CIho15270', and 'MTV-color-158' presented potential resistance to covered smut. Conclusion The protocol has a high power to differentiate moderately resistant barley genotypes and we confirmed that specific agronomic traits were affected by disease incidence in susceptible genotypes.
Why it matches plant phenotyping methodsオオムギ病害の抵抗性スクリーニングプロトコルを評価・改良し、検出力と遺伝子型間の識別性能を検証しているため、植物病害表現型の取得法が研究の中心です。
abstractThe goal of our research was to evaluate protocols for screening covered smut in barley under normal and speed breeding conditions that could be scaled up for breeding purposes.
Reproduction assets foundThe paper's disease-screening and agronomic-trait measurement data are publicly deposited on Zenodo, as stated in the Availability of data and materials section. No author analysis code or trained models are explicitly deposited.Dataset · publicThe data used and/or analyzed in the current study are available through the Zenodo, which is available at Gopinathan, G. (2025). Optimization of a protocol for covered smut in barley [Dataset]. Zenodo. [ 47 ] (https:/doi.org/ https://doi.org/10.5281/zenodo.17906264 ).Open asset ↗Zenodo · 10.5281/zenodo.17906264lines:190-223Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
This dataset contains images of Manalagi apple diseases from Indonesia. Data collection was conducted from August 2024 to June 2026. Data were collected in apple orchards. All images were captured under natural environmental conditions. A total of 1168 unique Manalagi apple specimens were successfully documented. The specimens consisted of both healthy and diseased fruit. This dataset comprises four classes: Healthy, Anthracnose, Black Pox, and Powdery Mildew. Each specimen was observed and photographed directly. The documentation process yielded approximately 5100 raw images. The images were captured using various smartphone cameras and DSLR cameras. Each device has different camera specifications. The image size depends on the device used. Images that passed quality inspection were selected for the next stage. Each fruit specimen is cropped from the selected raw image. Each image was then labeled according to its disease class. The image size was standardized to 1024 × 1024 pixels. All images were saved in JPEG format. The curation process yielded 482 images. Each image represents a distinct fruit specimen.
Why it matches plant phenotyping methodsリンゴ果実の健全・病害状態を画像で記録し、分類用データセットとして構築・キュレーションした研究であり、植物病害表現型の取得方法と再利用可能なデータセットが中心です。
titleImage dataset of manalagi apple fruits for multi-class disease classification using deep learning.
Reproduction assets foundThe paper is a Data in Brief article describing a public Mendeley Data repository of Manalagi apple fruit disease images (raw, curated, and augmented), directly usable for plant disease phenotyping/classification.Dataset · publicRepository name: Mendeley Data
Data identification number: DOI: 10.17632/9zgkwwv9j8.6
Direct URL to data: https://data.mendeley.com/datasets/9zgkwwv9j8/6Open asset ↗Mendeley Data · 10.17632/9zgkwwv9j8.6html-lines:97-124Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
The intelligent identification of tea diseases is crucial for ensuring tea quality and reducing economic losses in the tea industry. However, the deployment of deep learning models on edge devices remains challenging due to the conflict between detection accuracy and computational overhead. To address this, we propose CA-YOLOv8n, a lightweight object detection model tailored for tea disease diagnosis. Specifically, we introduce a Path-Decoupling strategy to streamline the network structure and integrate the Coordinate Attention (CA) mechanism to enhance the model's spatial awareness of subtle pathological features. Experimental results demonstrate that the proposed model achieves a mean Average Precision (mAP@50) of 98.89% while reducing the parameter count by 32.6% and FLOPs by 24.1% compared to the baseline YOLOv8n. The model was integrated into a diagnostic platform with an automated reporting interface, demonstrating that real-time tea disease identification is feasible on commodity CPU hardware in resource-constrained agricultural environments.
Why it matches plant phenotyping methods茶葉の病害を画像から検出する軽量深層学習モデルを開発・評価し、植物の病害状態を直接推定する方法が研究の中心である。
titleSpatial-aware lightweight network for real-time tea disease detection: A coordinate attention-enhanced YOLOv8n approach with path-decoupling strategy.
Reproduction assets foundThe paper's tea-leaf disease image dataset (9,591 images, YOLO format) is publicly deposited on figshare under CC BY 4.0, as stated in the Data Availability statement and dataset description. No author analysis code or trained model checkpoints are explicitly deposited.Dataset · publicAll data underlying the findings of this study are publicly available on figshare at https://doi.org/10.6084/m9.figshare.32253357 (CC BY 4.0).Open asset ↗figshare · 10.6084/m9.figshare.32253357lines:1-122Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Field / plotLeafClassificationDisease symptoms / severity
Early and reliable diagnosis of hibiscus leaf diseases is critical to protect horticultural yield. Yet, it remains challenging under real-time field conditions where uncontrolled lighting, clutter, and the non-contiguous nature of pathological symptoms blur diagnostic cues. To address these challenges, we introduce CNN-FusionViT-GNN. This explainable hybrid multi-branch framework synergizes the fine-grained texture extraction of a DenseNet201 backbone, the global contextual modeling of a Vision Transformer (ViT), and the relational reasoning of a Graph Neural Network (GNN). The model is trained and validated on 'Hibiscus,' a curated field dataset of 1165 images from Bangladesh, which is strategically augmented to 8000 samples for robust training following a strict train-validation-test split. The proposed framework achieves a state-of-the-art accuracy of 98.33% with a macro F1-score of 0.98. The framework's generalization is confirmed through high performance on external datasets: 98.78% accuracy on the 52-class Plant City dataset and 83.88% on the 10-class Tomato Leaf Disease dataset, while maintaining a rapid inference time of 10-45 ms. Furthermore, a multi-faceted Explainable AI (XAI) audit using LIME, Grad-CAM++, ViT Attention Maps, and Occlusion Sensitivity validates that the model's decisions are driven by biologically meaningful symptom patterns rather than background artifacts. This study establishes a computationally efficient, transparent, and robust pathway for automated disease diagnosis in precision agriculture.
Why it matches plant phenotyping methodsハイビスカス葉の病徴を画像から分類するCNN-ViT-GNN手法を開発し、複数データセットで性能検証しているため、植物病害表現型の取得・推定が中心である。
abstractwe introduce CNN-FusionViT-GNN. This explainable hybrid multi-branch framework synergizes the fine-grained texture extraction of a DenseNet201 backbone, the global contextual modeling of a Vision Transformer (ViT), and the relational reasoning of a Graph Neural Network (GNN).
Reproduction assets foundThe paper's primary Hibiscus leaf disease image dataset is publicly deposited on Mendeley Data, and the external Tomato Leaf Disease dataset used for validation is also publicly available on Mendeley Data. No author analysis code or trained model checkpoints are reported.Dataset · publicThe primary dataset generated and analyzed during the current study,“Hibiscus Leaf Diseases Classification Dataset,”is publicly available in Mendeley Data 7 .Open asset ↗Mendeley Datalines:307-347Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Premise Accurate species identification is crucial for ecological restoration and can be especially challenging for understudied non-model species. Quercus garryana is the only native oak species in the Pacific Northwest and is an important component of the endangered oak savanna ecosystem. Quercus robur is an imported ornamental species from Europe and has been found to be mistakenly planted as Q. garryana in habitat restoration projects. Methods We measured leaf morphological traits sampled from herbarium collections in their native ranges using the digital morphometric tools MorphoLeaf and Tomato Analyzer. We then used Lasso logistic analysis to generate a predictive model and tested it on leaves from Portland, Oregon. To streamline this species detection process, we developed Garryanalyzer, an ImageJ plug-in that automatically measures leaf traits and outputs species predictions. Results Garryanalyzer demonstrated 95% accuracy in predicting the species identity of herbarium specimens of oaks. Garryanalyzer correctly identified all Q. robur individuals sampled in Portland but showed lower accuracy for Q. garryana . Discussion Many existing morphometric software are not open source, which makes them unable to be customized to specific study systems. Garryanalyzer is built upon the widely used open-source ImageJ platform. This study also demonstrates a viable workflow for developing similar tools for other ecologically important non-model plant species.
Why it matches plant phenotyping methods葉の形態形質を自動測定し、種予測まで行うImageJプラグインとワークフローの開発・評価が中心であり、植物フェノタイピング手法として適格です。
abstractTo streamline this species detection process, we developed Garryanalyzer, an ImageJ plug-in that automatically measures leaf traits and outputs species predictions.
Reproduction assets foundThe paper's authors publicly released the Garryanalyzer ImageJ plug-in source code on GitHub, all original and modified leaf images used in the morphometric analyses on Zenodo, and the full leaf morphometric measurement dataset plus R Lasso analysis code in a second Zenodo repository. All are paper-specific, public,可直接Code · publicThe source code and installation instructions for Garryanalyzer can be accessed on GitHub at https://github.com/zxie8561/Garryanalyzer.Open asset ↗https://github.com/zxie8561/Garryanalyzer · zxie8561/Garryanalyzerhtml-lines:210-274Dataset · publicAll images used in the morphometric analyses, both original and modified, are available on Zenodo (https://doi.org/10.5281/zenodo.17462266).Open asset ↗https://doi.org/10.5281/zenodo.17462266 · 10.5281/zenodo.17462266html-lines:210-274Dataset · publicThe full dataset of leaf morphometric measurements of both GBIF and Portland samples, R code for Lasso analysis, and other miscellaneous files are available on a separate Zenodo repository (https://doi.org/10.5281/zenodo.17546152).Open asset ↗https://doi.org/10.5281/zenodo.17546152 · 10.5281/zenodo.17546152html-lines:210-274Code / dataset availability confirmedCrossref · checked 14 Sept 2026
Published23 Jul 2026Journal of Intelligent Decision Making and Information ScienceCited by 0 · OpenAlex ↗
The early and effective diagnosis of tomato leaf diseases is very important to enhance crop yield and reduce economic loss in precision agriculture. The conventional image-based methods are typically based on single architecture model, which cannot capture fine-grained lesion details and global contextual patterns simultaneously in the real-field. To this end, we introduce a deep hybrid Convolutional Neural Network (CNN) –Transformer architecture by combining ConvNeXt Large (ConvNeXt-L) (as local feature extractor) and Swin Transformer (as global context encoder). The concatenated features vector is then fed to a shallow classifier to predict the disease. The model was tested on two datasets, namely a field dataset in agriculture areas from Madhya Pradesh (India) and a benchmark tomato leaf dataset. Experimental results revealed that the proposed scheme achieved accuracy of 92.83% on a primary dataset, and performance was significantly high with an accuracy of up to 95.65% in terms of generalization rate for computing technique models from various environmental conditions.
Why it matches plant phenotyping methodsトマト葉の病害状態を画像から推定するCNN–Transformer手法を提案し、複数データセットで性能検証しており、植物フェノタイピング手法が中心である。
abstractwe introduce a deep hybrid Convolutional Neural Network (CNN) –Transformer architecture by combining ConvNeXt Large (ConvNeXt-L) (as local feature extractor) and Swin Transformer (as global context encoder).
Reproduction assets foundThe paper uses a public Tomato Leaves Dataset from GTS AI as its secondary/external validation dataset for tomato leaf disease classification. The primary field dataset from Madhya Pradesh is not stated as publicly available, and no author analysis code or trained model is reported as deposited.Dataset · publicSecondary Dataset: The Secondary dataset was extracted from the public Tomato Leaves Dataset
available at GTS AI platform. It involves various disease classes, such as bacterial spot, early blight,
late blight, leaf mold, powdery mildew, septoria leaf spot and spider mites (Figure 1) target spots are
present in tomato mosaic virus leaves yellow curl virus of tomato. This data set was employed as an
external validation to evaluate the generalization of proposed model in different conditions and
diseases types.
Source : https://gts.ai/dataset-download/tomato-leaves-dataset/Open asset ↗GTS AIpdf-page:20 lines:1-23Code / dataset availability confirmedCrossref · checked 14 Sept 2026
Published23 Jul 2026Journal of Intelligent Decision Making and Information ScienceCited by 0 · OpenAlex ↗
- Enhancing agricultural productivity and attaining sustainable crop management depend on the early and precise identification of leaf disease. Using state-of-the-art technologies in precision agriculture like machine learning (ML) and image processing greatly increases the effectiveness of disease detection and facilitates well-informed decision-making. But conventional manual inspection techniques are still tedious, unpredictable, and prone to errors. In order to overcome these constraints, this research offers YOLOv12-CropNet, an innovative deep learning-based system for multi-crop leaf disease diagnosis in real time. The proposed YOLOv12-CropNet approach makes use of the Convolutional Block Attention Module (CBAM) for adaptive attention, the Content-Aware Reassembly of Features (CARAFE) up-sampling module to preserve fine-grained disease characteristics, the YOLOv12 architecture improved with Ghost Convolution for effective feature extraction, and Involution layers to capture spatially specific patterns. Inspection techniques are still laborious, arbitrary, and prone to mistakes. A substantial set of data of 38 classes of both healthy and sick leaves from a variety of crops, including tomato, potato, apple, grape, corn, mango and sugarcane, was put together for training and evaluation. Experimental results show that YOLOv12-CropNet finds a suitable balance between computational speed and accurate detection. Accuracy, F1-score, recall, and precision are important performance metrics that verify the model's resilience in challenging environmental and visual circumstances. The suggested technique provides a scalable and field-deployable way to assist effective identification of diseases and precision agricultural decision-making. The proposed YOLOv12-CropNet model exhibits better performance than the other evaluated models, attaining a 98.45% peak accuracy, 98.10% precision ,98.20 % sensitivity and a 98.18% F1 score, thereby highlighting its efficacy in multi-crop leaf disease detection.
Why it matches plant phenotyping methods複数作物の葉の病徴を画像から検出・分類する深層学習手法を開発し、データセットと性能評価を伴うため、植物病害状態のフェノタイピング手法が中心である。
abstractthis research offers YOLOv12-CropNet, an innovative deep learning-based system for multi-crop leaf disease diagnosis in real time.
Reproduction assets foundThe paper uses public Kaggle datasets as its phenotyping image inputs: the PlantVillage dataset (38 crop-disease classes) and the Sugarcane Leaf Disease dataset, both cited with explicit public URLs. No author code, models, or checkpoints are reported as publicly available.Dataset · public[37] PlantVillage Dataset. Available online: https://www.kaggle.com/datasets/abdallahalidev/plantvillage-datasetOpen asset ↗pdf-page:22 lines:1-61Dataset · public[39] Sugarcane leaf Disease Dataset available online: https://www.kaggle.com/datasets/nirmalsankalana/sugarcane-Open asset ↗pdf-page:22 lines:1-61Code / dataset availability confirmedEurope PMC · checked 14 Sept 2026
Farmers must be able to estimate their crop yields at various growth stages for effective management of their farms and to enable them to interact with cooperatives or traders as early as possible. Here we developed an AI-based cocoa pod detection method using low resolution colour images of cocoa trees on farms in Côte d'Ivoire. We compared nano and extra-large architectures of six neural networks, including Faster RCNN, Baidu's Real-Time Detection Transformer (RTDetr), Detr-ResNet Vision Transformer (ViT), YOLOv5, YOLOv8 and YOLOv11. These networks were trained with 7,850 annotated cocoa pods on 400 low resolution images, and validated in two independent datasets: a 42 low resolution images containing 990 annotated pods, and a 100 low resolution images containing 2,400 annotated pods. The performances of the nano YOLOv8 and YOLOv11 networks were 2% higher than that of the RTDetr networks and 5% higher than that of the YOLOv5, ViT and Faster RCNN networks with an F1-score of 77% on all images and up to 90% on foreground trees. The dominance of nano architectures suggests that the extra-large architectures, which contain 20-30-times more neurons, may not have been fully trained. The study of learning performance curves showed that extra-large networks were unable to outperform nano networks, which contradicts the theory. After review, the annotated dataset was found to contain inconsistencies. The inconsistency of the training and validation data and their limited quantity restricted the objectivity of comparisons between network architectures. Finally, although the average detection performance of RTDetr for cocoa pods was only 2% lower than that of the YOLOv8 network, it was definitively excluded from the candidate models because its per-image processing time was 15-20% higher than that of YOLOv8 and YOLOv11. However, with a performance sensitivity to data of less than 0.5%, YOLOv8 Nano became the best option.
Why it matches plant phenotyping methodsカカオ果実を画像から検出・定量するAI手法を開発し、複数モデルと独立データセットで性能比較・検証しており、植物フェノタイピング手法が中心である。
abstractHere we developed an AI-based cocoa pod detection method using low resolution colour images of cocoa trees on farms in Côte d'Ivoire.
Reproduction assets found保存済みの本文根拠を更新済みルールで再検証し、公開資産1件を確認しました。Dataset · publicData Availability: The data used in the study can be downloaded from CIRAD’s data verse at https://doi.org/10.18167/DVN1/8COJBB .Open asset ↗10.18167/DVN1/8COJBBlines:129-140Code / dataset availability confirmedOpenAlex · checked 5 Sept 2026
Accurate identification of individual plants from unmanned aerial vehicle (UAV) imagery is essential for high-throughput phenotyping and data-driven decision-making in plant breeding. This study presents MatchPlant, a modular, open-source Python pipeline with a graphical user interface for UAV-based single-plant detection and geospatial trait extraction. The pipeline integrates UAV image processing, user-guided annotation of selected undistorted images, convolutional neural network–based object-detection training, forward projection of bounding boxes onto an orthomosaic, and shapefile generation for spatial phenotypic analysis. This workflow preserves native image geometry during detection while maintaining coordinate traceability from source imagery to georeferenced outputs. Across five independent training runs using early-season maize imagery, MatchPlant achieved source-image-level detection performance of AP@0.5 = 90.3 ± 1.1% and mAP@0.5:0.95 = 43.4 ± 2.9%. Orthomosaic-level evaluation after forward projection showed AP@0.5 = 89.7 ± 0.8% and recall = 93.7 ± 1.2%, demonstrating the workflow’s ability to transfer plant detections into georeferenced outputs. Plant-level traits, including plant height derived from canopy height models and NDVI derived from vegetation index rasters, showed strong agreement with manual annotations ( r = 0.87–0.97). Detection outputs were reused across time points with minimal additional annotation, supporting temporal phenotyping during early growth. The framework was validated using maize imagery from a single site and growing season, where plant separation remained clear. By combining modular design, reproducibility, and coordinate traceability, MatchPlant provides an open-source workflow for UAV-based plant-level analysis, with broader applications requiring validation across additional crops, sensors, growth stages, GSDs, and field conditions.
Why it matches plant phenotyping methodsUAV画像から個体検出と植物形質（草高・NDVI）を抽出する、オープンソースの再利用可能なワークフローを開発・検証しており、植物フェノタイピング手法が中心である。
abstractThis study presents MatchPlant, a modular, open-source Python pipeline with a graphical user interface for UAV-based single-plant detection and geospatial trait extraction.
Reproduction assets foundThe paper's MatchPlant analysis pipeline is publicly available on GitHub, and the maize case-study training dataset and pre-trained model are publicly available on Zenodo; both are paper-specific, public, and actionable.Dataset · publicThe public datasets supporting the case study are available on Zenodo at https://doi.org/10.5281/zenodo.14856123 (accessed on February 14, 2025).Open asset ↗Zenodo · 10.5281/zenodo.14856123lines:169-250Model / weights · publicThe training dataset and pre-trained model used in the maize case study presented in Section 3 are also publicly available via Zenodo ( Sangjan et al., 2025a ) at https://doi.org/10.5281/zenodo.14856123 (accessed on February 14, 2025).Open asset ↗Zenodo · 10.5281/zenodo.14856123lines:70-82Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
This study compiles and releases the first standardized rapeseed phenology observation dataset spanning forty-four years (1981-2024) over the core winter rapeseed production region of the Middle and Lower Yangtze River Plain in China. The data originate from systematic observations at 50 national-level agrometeorological stations across six provinces: Jiangsu, Zhejiang, Anhui, Jiangxi, Hubei, and Hunan. The dataset provides complete records of the specific dates for each phenology stage from sowing to maturity, including eight key phenology periods: Sowing (SO), Emergence (EM), Five-leaf (FV), Bud Formation (BF), Stem Elongation (SE), Flowering (FL), Green Ripening (GR), and Maturity (MA), along with the calculated durations of six distinct growth lengths. We implemented a multi-level quality control protocol encompassing internal logical checks, statistical outlier detection, climatological validation, time series homogenization, and expert arbitration. This protocol effectively constrained data uncertainty and corrected non-climatic discontinuities. Univariate linear regression was further employed to quantify the decadal change trends of each phenology period and growth length, supplemented by Kernel Density Estimation (KDE) to characterize their probability distribution features. The final dataset is presented as structured tables (in xlsx format) and high-resolution diagnostic plots (including trend and density plots), with a total volume of approximately 470 MB, systematically organized by province and station. This dataset fills a critical gap in long-term, standardized rapeseed phenology data for the region. The integrated analysis of phenology dates, growth stage durations, and their trends across the entire network provides an indispensable, high-quality empirical foundation. It is designed to support in-depth investigations into the nonlinear response mechanisms of overwintering crops to climate warming, improve crop model parameterization and validation, and inform regional adaptive management strategies.
Why it matches plant phenotyping methods44年間のナタネの生育段階日を標準化・品質管理して公開するデータセット研究であり、植物状態（フェノロジー）の測定データ整備が中心です。
abstractThis study compiles and releases the first standardized rapeseed phenology observation dataset spanning forty-four years (1981-2024)
Reproduction assets foundThe paper's rapeseed phenology dataset (1981–2024, 50 stations) is openly deposited in Science Data Bank under DOI 10.57760/sciencedb.34086, containing structured xlsx tables and diagnostic plots. No custom code was created per the authors.Dataset · publicThe dataset described in this work has been deposited in the Science Data Bank (ScienceDB) under
accession code https://doi.org/10.57760/sciencedb.34086 [27].Open asset ↗Science Data Bank · 10.57760/sciencedb.34086pdf-page:12 lines:1-68Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
With climate change and global population growth, accelerating the breeding of superior crop varieties is essential for food security. Genomic prediction, which uses genome-wide genetic markers to predict crop traits, plays an important role in intelligent crop breeding. However, existing methods often lack stable and accurate performance across crops and traits. Here, we propose GEG2P, a genetic algorithm-based ensemble learning method for genotype-to-phenotype prediction, integrates 20 base learners, dynamically selects their combinations through an iterative optimization strategy, and optimizes their weights using the genetic algorithm. Compared with the best-performing single base learners, GEG2P improves prediction accuracy by 4.02% on average across maize, wheat, rice, chickpea, and soybean. We use SHAP to quantify the contribution of SNPs to phenotype prediction and find that SNPs with large effects captured by different base learners are functionally complementary. This study provides a robust and accurate genomic prediction method for crop breeding.
Why it matches plant phenotyping methods作物形質の遺伝子型から表現型を予測するアンサンブル計算法を開発し、複数作物で精度比較・検証しており、表現型推定手法が研究の中心である。
abstractHere, we propose GEG2P, a genetic algorithm-based ensemble learning method for genotype-to-phenotype prediction, integrates 20 base learners, dynamically selects their combinations through an iterative optimization strategy, and optimizes their weights using the genetic algorithm.
Reproduction assets foundThe paper provides public author code (GitHub GEG2P repository and Docker Hub image), a Zenodo deposit of significant SNP interaction pairs generated in this study, and a Figshare link with the wheat genotypic and phenotypic data used in the analyses. These are paper-specific, publicly available, and actionable.Code · publicScripts used in this study are available at GitHub [ https://github.com/Deep-Breeding/GEG2P ] 89 .Open asset ↗GitHub · Deep-Breeding/GEG2Plines:236-266Dataset · publicThe genotypic and phenotypic data of wheat are available at Figshare [ https://figshare.com/s/287c2c7f1623008487a5 ] 68 .Open asset ↗Figsharelines:236-266Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Accurate identification of rice diseases from field images is critical for crop health monitoring and sustainable agriculture, particularly in low-resource environments. However, most deep learning approaches depend on large-scale labeled datasets and pretrained backbones, limiting their applicability to rare or emerging diseases. In this work, we formulate a domain-specific prototype-based few-shot framework that avoids pretrained visual backbones and treats rice disease recognition as structured matching over a pathogen-aware class graph. The individual components, including wavelet-scattering features, optimal transport, semantic prototype fusion, and transductive refinement, are established techniques; the contribution lies in their coupled use within a disease-taxonomy-guided few-shot matching process. This design combines fixed visual descriptors, root-to-leaf prototype matching, class symptom descriptors, and confidence-gated refinement to support rice disease recognition under limited labeled data. We evaluate the model on two publicly available rice disease datasets-the Philippines Rice Diseases and Roboflow Rice-under 1-shot and 5-shot classification settings. In in-domain experiments, our approach achieves up to 95.8% accuracy and 94.9% macro-F1 on the Philippines dataset, consistently outperforming a diverse set of baselines including CNN-from-scratch, ResNet-18-from-scratch, Matching Networks, MAML, ProtoNet, RelationNet, SimpleShot, FEAT, and a flat optimal-transport variant. In cross-domain evaluation, the model demonstrates strong generalization capability, attaining up to 91.7% accuracy and 90.6% macro-F1 when transferring across datasets. An ablation study further confirms the consistent contribution of hierarchical structure, semantic fusion, and transductive refinement to performance gains. These results demonstrate that the proposed framework delivers highly accurate, robust, and data-efficient disease recognition, making it well-suited for real-world agricultural deployment under limited supervision.
Why it matches plant phenotyping methodsイネの病害を圃場画像から認識する手法を開発・評価しており、植物の病害状態を画像から推定する方法が研究の中心である。
abstractwe formulate a domain-specific prototype-based few-shot framework
Reproduction assets foundThe paper evaluates its few-shot rice disease recognition framework on two publicly available rice disease image datasets, with explicit public URLs in the Data Availability statement and dataset description sections. No author analysis code or trained model checkpoints are disclosed.Dataset · publicThe datasets used in this study are publicly available: Philippines Rice Diseases dataset (https://www.kaggle.com/
datasets/shrupyag001/philippines-rice-diseases)Open asset ↗Kaggle · shrupyag001/philippines-rice-diseasespdf-page:19 lines:1-81Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Plant diseases significantly affect agricultural productivity and global food security, while accurate disease identification remains challenging because of uncertain and overlapping visual symptoms in leaf images. Existing deep learning approaches often require large annotated datasets and suffer from limited interpretability in practical agricultural environments. This study presents a multi-parameter improved fuzzy soft set-based framework for plant disease classification using tomato leaf images from the PlantVillage dataset. The objective is to develop an interpretable and reliable classification model capable of handling uncertainty in plant disease patterns through feature-driven fuzzy similarity analysis. The methodology integrates image preprocessing, color and texture feature extraction, variance-based feature weighting, prototype generation using K-means clustering, and fuzzy similarity computation using Mahalanobis distance and Gaussian membership functions. RGB, HSV, and Gray-Level Co-occurrence Matrix (GLCM) features are extracted from standardized leaf images and evaluated within an improved fuzzy soft classification framework. Performance comparison is carried out using machine learning models including Support Vector Machine (SVM), Random Forest (RF), Linear Discriminant Analysis (LDA), and Naive Bayes (NB) implemented in Python using Scikit-learn libraries. Experimental simulation results demonstrate that the proposed framework achieves competitive classification performance while preserving interpretability and robustness under uncertain feature distributions. Performance evaluation is conducted through accuracy analysis, ROC-AUC curves, confusion matrices, ablation studies, and Wilcoxon Signed-Rank statistical testing. The proposed Improved Fuzzy Soft model achieved an accuracy of 88.57% which is less than LDA (94.92%), Random Forest (97.78%) and SVM (97.94%) classifiers. However, in the cross data set validation, the proposed Improved Fuzzy Soft model achieved an accuracy of 67.35% which is greater than LDA (51.02%), Random Forest (51.02%) and SVM (55.10%) classifiers. Statistical validation using the Wilcoxon Signed-Rank Test produced a p-value of [Formula: see text], confirming that the performance difference between the Improved Fuzzy Soft framework and the Random Forest classifier is statistically significant under the current experimental setting.
Why it matches plant phenotyping methodsトマト葉画像から植物病害状態を推定する解釈可能な画像解析・分類フレームワークを開発し、複数モデル、交差データセット検証、アブレーション、統計検定で評価しており、病害表現型の取得・抽出手法が中心である。
abstractThis study presents a multi-parameter improved fuzzy soft set-based framework for plant disease classification using tomato leaf images from the PlantVillage dataset.
Reproduction assets foundThe paper uses public tomato leaf image datasets (PlantVillage and PlantDoc from Kaggle) as phenotyping inputs and states the authors' Improved Fuzzy Soft Framework implementation is publicly available on Zenodo with source code and reproduction instructions.Dataset · publicThe dataset analyzed during the current study are available in the repository:
https://www.kaggle.com/datasets/abdallahalidev/plantvillage-datasetOpen asset ↗kaggle.com/datasets/abdallahalidev/plantvillage-datasetpdf-page:24 lines:1-75Code · publicThe implementation of the proposed Improved Fuzzy Soft Framework is publicly available through the Zenodo repository:
https://doi.org/10.5281/zenodo.20570546
The repository contains the source code, documentation, and instructions required to reproduce the experiments reported in
this study.Open asset ↗zenodo · 10.5281/zenodo.20570546pdf-page:25 lines:1-74Code / dataset availability confirmedEurope PMC · bioRxiv · checked 11 Sept 2026
Solitary bee species that use artificial trap nests are important for agricultural crop production and as indicators of habitat quality. Quantifying cavity-nesting solitary bee foraging and nesting behavior is essential for real-time analysis of population numbers and pollination activity, as well as understanding how environmental conditions shape reproductive success and population dynamics. However, manual observation is labor-intensive, prone to observer bias, and unable to deliver continuous data. Existing automated systems either require individual bee marking or detect presence without resolving nest-tube-level entry and exit events. We developed BeeMonitor, an integrated hardware and computer-vision pipeline that detects nest entry and exit events in cavity-nesting solitary bees from continuous video, using Osmia cornifrons (the horn-faced mason bee) as a model system. A low-cost Raspberry Pi handles solar-powered field recording, while the software combines object detection (YOLOv26), a custom multiple-object tracker (BeeTrack), and a Random Forest classifier trained on trajectory-derived features to distinguish genuine events from incidental detections. Over a 29-day deployment, hardware reliability averaged 97.5% recording coverage. The pipeline achieved 91.3% precision and 87.3% recall (F1 = 0.893), generalizing robustly under leave-one-video-out cross-validation (mean F1 = 0.904). Detected foraging trips correlated strongly with brood cell counts (R2 = 0.849, p < 0.001, n = 19), and a Random Forest model (AUC = 0.820) identified solar radiation as the dominant driver of foraging activity, followed by temperature. BeeMonitor demonstrates that automated computer vision can reliably extract ecologically relevant behavioral data from continuous video, enabling real-time analysis of pollinator behavior and abundance at a temporal and spatial resolution unattainable through manual observation. Its modular design supports adaptation to other species and monitoring contexts.
Why it matches plant phenotyping methods植物ではなく昆虫を対象とするが、映像から採餌・営巣行動を抽出する技術開発として中心的であり、指定スコープの植物表現型ではないため除外。
abstractWe developed BeeMonitor, an integrated hardware and computer-vision pipeline that detects nest entry and exit events in cavity-nesting solitary bees from continuous video
Reproduction assets foundThe paper explicitly states that source code, 3D STL files, and validation datasets/code are publicly available on the authors' GitHub repository and ScholarSphere. These directly support reproducing the paper's behavioral-event detection pipeline and its evaluation (annotated videos, classifier training/LOVO cross-vaCode · publicSource code for
software and 3D stl files can be found on the official GitHub repository here
https://github.com/Team-Insect-Net/BeeMonitor.Open asset ↗Team-Insect-Net/BeeMonitorpdf-page:2 lines:1-57Dataset · publicValidation datasets and code are available on
Scholars Sphere here
https://scholarsphere.psu.edu/resources/55f1f34b-959f-4c60-8dd3-9b33fb09357f.Open asset ↗Scholars Sphere · 55f1f34b-959f-4c60-8dd3-9b33fb09357fpdf-page:2 lines:1-57Code / dataset availability confirmedCrossref · Europe PMC · checked 5 Sept 2026
Plant disease detection under complex climatic conditions and cross-crop scenarios remains a critical challenge. To address this, we propose a novel SimAM-Inception-StyleRandomization (SIS)-YOLOv11 algorithm based on YOLOv11n for early/late blight detection on potato and tomato leaves. Our core innovations are: 1) A C3k2-SSI module integrating Style Randomization, Inception architecture, and SimAM attention to enhance cross-crop generalization; 2) A Fusion-InceptionConv module for fine-grained feature extraction under rainfall/haze noise; 3) SPPF-Inception and C2PSA-IS modules to optimize multi-scale feature fusion; 4) DepGraph pruning to reduce 47.82% parameters while improving performance. Experiments show that the pruned SIS-YOLOv11 outperforms YOLOv11n by 3.7% in precision, 6.6% in recall, 5.4% in mAP50, and 7.9% in mAP50-95, and surpasses mainstream models (Faster R-CNN, SSD, etc.). This study provides a robust, lightweight solution for automated cross-crop disease detection in complex agricultural environments.
Why it matches plant phenotyping methodsジャガイモとトマト葉の病害状態を画像から検出する新規アルゴリズムを開発し、性能比較・軽量化まで行っており、植物フェノタイピング手法が中心である。
abstractwe propose a novel SimAM-Inception-StyleRandomization (SIS)-YOLOv11 algorithm based on YOLOv11n for early/late blight detection on potato and tomato leaves.
Reproduction assets foundThe paper's image dataset (potato/tomato leaf disease images with annotations and climate-noise augmentation) is explicitly declared publicly available on Baidu AI Studio. No author code or trained model deposit is stated.Dataset · publicData Availability: All image datasets used and analyzed in this study are publicly available from the Baidu AI Studio dataset repository at the URL: https://aistudio.baidu.com/datasetdetail/245434 .Open asset ↗Baidu AI Studio · 245434lines:1-133Code / dataset availability confirmedOpenAlex · Europe PMC · checked 14 Sept 2026
Yellow rust (YR) is a major threat to both bread and durum wheat production, often causing substantial yield losses. Conventional visual scoring of YR severity, while widely adopted, is labor-intensive, time-consuming, and prone to human error. In this study, we evaluated the predictability (PA), defined as the correlation between predicted and observed values, using genomic and phenomic data for YR severity under multiple prediction scenarios in two biparental wheat populations (bread and durum). YR scoring was conducted on two dates, with YR severity visually assessed while unmanned aerial vehicle (UAV)-based high-throughput phenotyping (HTP) data were collected using a multispectral camera. HTP data were processed to extract spectral wavelengths and vegetation indices (VIs), and all lines were also genotyped using SNP arrays. We tested a diverse set of models, including parametric, machine learning, and deep learning approaches. PA increased markedly when HTP-derived data were used compared with genomic markers alone. For example, support vector regression (SVR) improved from 0.35 (markers only) to 0.87 (wavelengths only). However, integrating genomic and phenomic data did not yield further improvements, as models often plateaued when using HTP-derived features alone. Cross-crop prediction demonstrated promising generalization across bread and durum wheat, achieving PA values up to 0.83. For this last task, best linear unbiased prediction (BLUP) and multilayer perception (MLP) consistently provided robust performance across scenarios. These findings highlight the strong potential of UAV-based HTP for rapid, scalable, and accurate prediction of YR severity in wheat. While genomics retains broad utility for breeding, the practical integration of phenomics and AI-driven prediction pipelines will ultimately depend on breeding program strategies, resources, and objectives.
Why it matches plant phenotyping methodsUAV multispectral HTPによる小麦黄さび病重症度の推定と、複数の予測モデルの比較・検証が研究の中心であり、植物病害状態を直接推定する実質的なフェノタイピング手法研究である。
abstractHTP data were processed to extract spectral wavelengths and vegetation indices (VIs)
Reproduction assets foundThe article's Data Availability statement deposits the datasets generated and analyzed in this study (yellow rust phenotyping with UAV spectral data and genomic markers in bread and durum wheat) in the CIMMYT repository under DOI 10.71682/10549375, which is an allowed URL. No author analysis code or trained model is avDataset · publicand scalable strategy for YR assessment in wheat breeding.
Funding
The authors gratefully acknowledge financial support from the Government of Mexico through
the “MasAgro – Cultivos para México” initiative.
Data Availability
The datasets generated and/or analyzed during the current study are available in the CIMMYT
repository: https://doi.org/10.71682/10549375.Acknowledgements
We are deeply grateful to Julio Huerta-Espino for his guidance and support throughout all stages
of this manuscript. We also thank Hedilberto Velásquez Miranda for his valuable assistance with
rust visual score phenotyping, and Neftalí Cruz Pérez for his dedicated support in trial sowing and
field management.
Conflict Open asset ↗10.71682/10549375pdf-raw-page:30 lines:1-37Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Detecting cotton leaf diseases in open-field environments is challenging due to cluttered backgrounds, scale variation, and irregular lesion morphology. Conventional detectors rely on isotropic receptive fields and coupled box-regression losses, which limit their ability to localize elongated lesions with poorly defined boundaries. We present an anisotropic boundary-aware detection framework that propagates high-frequency boundary information across four successive pipeline stages. In the backbone, an Anisotropic Morphological Contrast Aggregation module (AMCA) enhances direction-aware representation and lesion-background contrast via re-parameterizable strip convolutions and high-frequency residual extraction. A Dynamic Semantic Boundary Transfer mechanism (DSBT) then captures boundary priors from shallow layers before they are lost to downsampling and injects them into the neck. A Morphological-Spectral Synergistic Feature Pyramid Network (MFS-FPN) preserves these cues during multi-scale fusion through spatial-domain operations compatible with edge hardware. Finally, an Anisotropic Boundary-Decoupled IoU loss (ABD-IoU) independently penalizes each of the four box boundaries and sustains optimization signals in high-IoU regimes via a logarithmic modulation factor. On the self-constructed Complex Cotton Leaf Disease dataset (CCLD; 6,856 images, 6 classes), the method achieves 78.50% mAP@50 and 65.00% mAP@50:95, improving the YOLOv11n baseline by 4.80% and 2.70% with only 2.73 M parameters at 202 FPS. Cross-domain evaluations on PlantDoc and RWD confirm consistent improvements. The framework runs in real time on NVIDIA Jetson edge platforms with INT8 quantization.
Why it matches plant phenotyping methods綿花葉の病斑・病害状態を画像から検出する手法を開発し、複数データセットとベースラインで性能検証しているため、植物表現型取得が中心である。
abstractWe present an anisotropic boundary-aware detection framework that propagates high-frequency boundary information across four successive pipeline stages.
Reproduction assets foundThe authors explicitly state that their source code, trained models, and implementation details are publicly available, and the data availability statement points to the same repository, which hosts the self-constructed CCLD cotton leaf disease dataset (6,856 images, 6 classes) used for the paper's phenotyping/disease-Code · publicFurthermore, to facilitate future research, our source code, trained models, and implementation details have been made publicly available at https://github.com/DynaVLA/ABAD-CLD .Open asset ↗DynaVLA/ABAD-CLDlines:331-343Dataset · publicThe datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: https://github.com/DynaVLA/ABAD-CLD .Open asset ↗DynaVLA/ABAD-CLDlines:1278-1317Code / dataset availability confirmedEurope PMC · checked 15 Sept 2026
Eggplant (Solanum melongena) is a major cash crop, yet field detection of its pests and diseases remains difficult because disease evidence is simultaneously occluded by foliage, blurred at lesion boundaries, and highly variable in scale. Fruit rot is especially challenging: the waxy epidermis and purple anthocyanin-rich surface reduce chromatic contrast, while infection spreads gradually from water-soaked tissue to necrotic tissue, producing diffuse borders between diseased and healthy regions. In this work, we reframe eggplant disease detection through a context-boundary-scale coupling principle, which states that accurate field detection should jointly model incomplete contextual cues, ambiguous lesion boundaries, and scale-varying symptom morphology rather than optimize these cues independently. ISA-YOLO is proposed as an implementation of this principle on top of YOLOv13 through coordinated context modeling, boundary-aware aggregation, and progressive multi-scale fusion. Experiments on two public datasets show that ISA-YOLO achieves 78.1 and 77.7% mAP at 30.66 and 31.74 FPS, outperforming mainstream detectors in overall trade-off between accuracy and speed. After pruning and quantization, inference speed increases to about 75 FPS while maintaining strong accuracy. These results indicate that the proposed principle provides an effective pathway for accurate and deployable eggplant pest and disease detection in smart agriculture.
Why it matches plant phenotyping methodsナスの病害・害虫を画像から検出するISA-YOLOモデルの開発と性能評価が研究の中心であり、植物の病害状態を直接推定するフェノタイピング手法に該当する。
titleA high-performance detection model ISA-YOLO for eggplant pests and diseases.
Reproduction assets foundThe paper uses four public Roboflow image datasets (BISU, UTM, Papaya, Tomato) and states that supporting data and code are publicly available on Zenodo, all with explicit URLs in the Data availability section.Dataset · publicwas supported by National Natural Science Foundation of China grants (62472269, 62072291).
Data availability
This research relies entirely on four publicly available detection datasets: Papaya ( https://universe.roboflow.com/hm-xsfz9/papaya-eswlk-r2ydy ), Tomato ( https://universe.roboflow.com/test-fqgof/tomato-rotten ), BISU ( https://universe.roboflow.com/bohol-island-state-university-vgjlb/eggplant-disease-detection ), and UTM ( https://universe.roboflow.com/utm-xpfqs/eggplant-disease-detection-5fuqv ). The authors believe that the creators of these public datasets complied with relevant institutional, national, and international guidelines and legislation when collecting the data. No newOpen asset ↗eggplant-disease-detectionlines:1509-1560Dataset · publicty
This research relies entirely on four publicly available detection datasets: Papaya ( https://universe.roboflow.com/hm-xsfz9/papaya-eswlk-r2ydy ), Tomato ( https://universe.roboflow.com/test-fqgof/tomato-rotten ), BISU ( https://universe.roboflow.com/bohol-island-state-university-vgjlb/eggplant-disease-detection ), and UTM ( https://universe.roboflow.com/utm-xpfqs/eggplant-disease-detection-5fuqv ). The authors believe that the creators of these public datasets complied with relevant institutional, national, and international guidelines and legislation when collecting the data. No new data collection was performed for this research. The authors confirm that the use of these datasets in thOpen asset ↗eggplant-disease-detection-5fuqvlines:1509-1560Dataset · publicof the outcomes of the Provincial Undergraduate Training Program on Innovation and Entrepreneurship (Number: S202510108100). This work was supported by National Natural Science Foundation of China grants (62472269, 62072291).
Data availability
This research relies entirely on four publicly available detection datasets: Papaya ( https://universe.roboflow.com/hm-xsfz9/papaya-eswlk-r2ydy ), Tomato ( https://universe.roboflow.com/test-fqgof/tomato-rotten ), BISU ( https://universe.roboflow.com/bohol-island-state-university-vgjlb/eggplant-disease-detection ), and UTM ( https://universe.roboflow.com/utm-xpfqs/eggplant-disease-detection-5fuqv ). The authors believe that the creators of these publicOpen asset ↗papaya-eswlk-r2ydylines:1509-1560Dataset · publicnovation and Entrepreneurship (Number: S202510108100). This work was supported by National Natural Science Foundation of China grants (62472269, 62072291).
Data availability
This research relies entirely on four publicly available detection datasets: Papaya ( https://universe.roboflow.com/hm-xsfz9/papaya-eswlk-r2ydy ), Tomato ( https://universe.roboflow.com/test-fqgof/tomato-rotten ), BISU ( https://universe.roboflow.com/bohol-island-state-university-vgjlb/eggplant-disease-detection ), and UTM ( https://universe.roboflow.com/utm-xpfqs/eggplant-disease-detection-5fuqv ). The authors believe that the creators of these public datasets complied with relevant institutional, national, and internatOpen asset ↗tomato-rottenlines:1509-1560Code · publicarch. The authors confirm that the use of these datasets in this study is fully compliant with their original licenses and ethical guidelines. The final images presented in the article accurately reflect the original data and meet community standards. The data and code supporting the conclusions of this article are available at https://zenodo.org/records/19425300 .
Declarations
Ethics approval and consent to participateOpen asset ↗Zenodo · 19425300lines:1509-1560Code / dataset availability confirmedEurope PMC · checked 15 Sept 2026
To address this challenge, we propose StyleGAN3-T, the translation-equivariant alias-free variant of StyleGAN3, as a generative framework for producing high-fidelity synthetic plant disease images, integrated with a hybrid Swin Transformer-ResNet50 classifier for precise recognition. Accurate detection of plant leaf diseases is essential for sustainable agriculture and early intervention. However, deep learning models often struggle with small, imbalanced datasets that limit generalization and robustness. To address this challenge, we propose StyleGAN3-T, a novel alias-free generative framework for producing high-fidelity synthetic plant disease images, integrated with a hybrid Swin Transformer-ResNet50 classifier for precise recognition. The proposed approach ensures translation-equivariant, artifact-free image synthesis and enhanced feature diversity. A balanced dataset of 18,000 images was developed by combining real and StyleGAN3-T-generated samples. In pooled GAN benchmarking, StyleGAN2-ADA achieved the strongest generative-quality metrics, whereas StyleGAN3-T was selected as the preferred augmentation model because its alias-free synthesis and spatial consistency yielded superior downstream classification performance in the proposed pipeline.
Why it matches plant phenotyping methods植物病害画像を合成・認識する画像解析手法が研究の中心であり、植物の病害状態を画像から推定するフェノタイピング手法に該当する。
abstractwe propose StyleGAN3-T, a novel alias-free generative framework for producing high-fidelity synthetic plant disease images, integrated with a hybrid Swin Transformer-ResNet50 classifier for precise recognition.
Reproduction assets foundThe paper's grape leaf disease image inputs are two publicly available Kaggle datasets explicitly named in the Data Availability statement. No author code, models, or synthetic dataset deposit is provided; other processed data is request-only.Dataset · publictechnical guidance. Y.L. and A.W. supervised the study, provided critical revisions, and contributed to the interpretation of results. All authors reviewed and approved the final manuscript.
Data availability
The datasets analyzed during the current study are publicly available from Kaggle: Grapevine Disease Dataset (Original) (https://www.kaggle.com/datasets/rm1000/grape-disease-dataset-original; accessed 13 March 2026; license: MIT) and Grape Leaf Disease 4 Class (https://www.kaggle.com/datasets/jawadulkarim117/grape-leaf-disease-4-class; accessed 13 March 2026; license: CC0: Public Domain). Additional processed metadata, label-harmonization records, dataset split definitions, and other daOpen asset ↗Kaggle · rm1000/grape-disease-dataset-originallines:549-576Dataset · publicthors reviewed and approved the final manuscript.
Data availability
The datasets analyzed during the current study are publicly available from Kaggle: Grapevine Disease Dataset (Original) (https://www.kaggle.com/datasets/rm1000/grape-disease-dataset-original; accessed 13 March 2026; license: MIT) and Grape Leaf Disease 4 Class (https://www.kaggle.com/datasets/jawadulkarim117/grape-leaf-disease-4-class; accessed 13 March 2026; license: CC0: Public Domain). Additional processed metadata, label-harmonization records, dataset split definitions, and other data used and/or analyzed during the current study are available from the corresponding author on reasonable request.
Declarations
Competing inOpen asset ↗Kaggle · jawadulkarim117/grape-leaf-disease-4-classlines:549-576Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
The genetic identity of coffee cultivars is fundamental to the specialty coffee sector, where premium prices are paid under the assumption that the purchased planting material corresponds to the declared variety. However, many producing countries lack the certification infrastructure necessary to guarantee this identity in their informal seed systems, exposing producers to undetected varietal non-conformity. In this study, we examine a case from a specialty coffee ( Coffea arabica L.) farm in southern Ecuador where seeds labeled as Sidra (USD 100/kg) and Gesha (USD 500/kg) were purchased without genetic or phytosanitary certification. Using a combination of SSR-based DNA fingerprinting and quantitative morphological characterization, including plant architecture, leaf functional traits, and fruit characteristics, we documented varietal identity and assessed the discriminant capacity of morphological traits across the four resulting morphotypes. Using eleven microsatellite markers for SSR fingerprinting, we found that two of the four morphotypes did not match their declared commercial identity. One plant sold as Sidra was identified as compatible with Batian, a composite variety of Kenyan origin that is genetically unrelated to Ethiopian landraces. The plants acquired as Gesha corresponded to a pure Ethiopian landrace that is genetically similar to, but not identical to, the Panamanian Geisha reference accession T.02722. Only two morphotypes were confirmed as Sidra. Furthermore, the placement of Sidra within the Core Ethiopia genetic group is consistent with prior population-level analyses and with its likely status as a selected Ethiopian landrace rather than a variety of hybrid origin. Morphological linear discriminant analysis achieved 82.4% overall classification accuracy under leave-one-out cross-validation (LOOCV), with internode length dominating the first discriminant function (LD1 = 66.6%). These results demonstrate that varietal nonconformity in the specialty coffee seed sector can extend to the inadvertent introduction of genetically unrelated material and underscore the urgent need for accessible seed certification.
Why it matches plant phenotyping methodsコーヒー品種識別のための形態形質測定と判別分析が研究の中心であり、形態形質の識別性能をLOOCVで検証しているため、植物フェノタイピング手法の適用・検証に該当する。
abstractquantitative morphological characterization, including plant architecture, leaf functional traits, and fruit characteristics
Reproduction assets foundThe paper's morphological/functional trait dataset (used for the phenotyping and LDA analysis) is explicitly stated to be publicly available on Figshare (10.6084/m9.figshare.32841344). No author analysis code repository is stated; other URLs in the text are generic libraries or cited prior work.Dataset · publicThe morphological and functional trait dataset generated and analyzed in this study is publicly available in the Figshare repository at 10.6084/m9.figshare.32841344 .Open asset ↗Figshare · 10.6084/m9.figshare.32841344lines:526-568Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Timely identification of crop diseases is imperative in precision agriculture to intervene at the right time and maximise yield sustainability. Despite achieving high accuracy, deep learning models are ineffective for rare plant disease classes, mainly due to severe data imbalance and insufficient training samples. Currently, most generative augmentation methods are designed to enhance either visual realism or data diversity, while ignoring methods that are sensitive to early-stage diseases or that control disease progression. In this paper, we propose RareAgriDetectAI, which comprises RareSimGAN, a generative deep learning framework for synthesising images of rare diseases, and a latent traversal mechanism that collaboratively visualises disease progression with increasing severity. We introduce a pipeline for synthesising realistic crop images for data augmentation. We augment the representation of rare classes using synthetic samples in a ResNet50-based classification pipeline. A strong experimental setup, relying on controlled baselines and synthetic-aided training scenarios, was employed. Evaluation on a real dataset shows significant improvement for the rare class ToLCNDV, with recall increasing from 0.42 in the baseline to 0.81 after synthetic augmentation. In contrast, the performance on other common disease classes remains stable. SSIM, Inception Score, and FID metrics were shown to validate generative quality. At the same time, an ablation study identified a suitable augmentation threshold at which sufficient performance is achieved without excessive synthetic data generation. The results further indicate improvements in feature diversity, which translate into earlier disease recognition (before full disease onset) and improved classification robustness with RareSimGAN. The post-framework combines generative modelling and latent space exploration to deliver a low-cost, scalable, and data-efficient solution for agricultural AI systems. RareAgriDetectAI utility can assist in the proactive monitoring of crop health and simulate rare disease scenarios to drive learning that can aid reliable, interpretable deep learning applications in precision agriculture.
Why it matches plant phenotyping methods希少作物病害の画像合成、病徴進行の可視化、早期病害認識を中心とする画像ベースの植物病害フェノタイピング手法であり、生成品質と分類性能も検証している。
abstractwe propose RareAgriDetectAI, which comprises RareSimGAN, a generative deep learning framework for synthesising images of rare diseases, and a latent traversal mechanism that collaboratively visualises disease progression with increasing severity.
Reproduction assets foundThe paper's data availability statement lists the public plant-disease image datasets used (PlantVillage, AI Challenger mirror, PlantDoc, Tomato Leaf Disease), and the code availability statement provides an authors' GitHub repository containing the RareSimGAN implementation, preprocessing, classifier training, andGradDataset · publicThe datasets analysed during the current study are publicly available from the following sources:
•PlantVillage dataset:
https://www.kaggle.com/datasets/emmarex/plantdiseaseOpen asset ↗pdf-page:36 lines:1-66Code / dataset availability confirmedCrossref · checked 14 Sept 2026
Plant diseases threaten global agriculture, causing 20–40% yield losses and food insecurity. Current diagnostic methods are costly and lack scalability. While deep learning advances plant disease detection, there remains a need for CNNs with simpler architectures, better generalizability, and lower computational cost. This study presents a novel CNN for multi-class classification of 38 diseases. Trained on a public dataset of over 87,000 RGB images, the architecture comprises five convolutional blocks (filters 32–512) with max pooling and dropout (0.25, 0.4), followed by a 1,500-unit dense layer and SoftMax output. Optimized with Adam (lr=0.0001) and categorical cross-entropy, the model achieved 98% training and 96% validation accuracy with approximately 28.7 million parameters significantly fewer than transfer learning architectures. These results demonstrate an effective balance between predictive performance and computational efficiency, positioning the model as a promising tool for real-world agricultural deployment.
Why it matches plant phenotyping methods葉画像から植物病害を分類するCNNの開発と性能評価が研究の中心であり、植物の病害状態を直接推定するため、植物フェノタイピング手法に該当します。
titleLeaf-by-Leaf Diagnosis: A Custom CNN with Pyramidal Feature Extraction for Plant Disease Classification
Reproduction assets foundThe paper's sole qualifying asset is the plant disease image dataset used for all its CNN training/validation measurements: the publicly available New Plant Diseases Dataset (Augmented) on Kaggle, explicitly declared in the Data availability statement. No author code, trained model checkpoints, or other paper-specific Dataset · publict to disclose.
Acknowledgment:
The authors are sincerely grateful to their institutions for their continued support and trust, which greatly contributed to
the completion of this research.
Data availability
The dataset used and analyzed during the current study, “New Plant Diseases Dataset”, is publicly available on Kaggle at:
(https://www.kaggle.com/datasets/vipoooool/new-plant-diseases-dataset?select=New+Plant+Diseases+Dataset%28Augmented%29)
References
[1] P. Arputharaj and K. Karunanithy, "A review on machine learning and deep learning techniques for plant leaf disease
detection and classification with IoT in agriculture industry," Journal of Industrial Information Integration, vol. 50, Open asset ↗Kaggle · vipoooool/new-plant-diseases-datasetpdf-raw-page:11 lines:1-49Dataset · publict to disclose.
Acknowledgment:
The authors are sincerely grateful to their institutions for their continued support and trust, which greatly contributed to
the completion of this research.
Data availability
The dataset used and analyzed during the current study, “New Plant Diseases Dataset”, is publicly available on Kaggle at:
(https://www.kaggle.com/datasets/vipoooool/new-plant-diseases-dataset?select=New+Plant+Diseases+Dataset%28Augmented%29)
References
[1] P. Arputharaj and K. Karunanithy, "A review on machine learning and deep learning techniques for plant leaf disease
detection and classification with IoT in agriculture industry," Journal of Industrial Information Integration, vol. 50, Open asset ↗Kaggle · vipoooool/new-plant-diseases-datasetpdf-raw-page:11 lines:1-49Code / dataset availability confirmedOpenAlex · Europe PMC · Crossref · checked 5 Sept 2026
Sweet potato virus disease (SPVD) is one of the most destructive diseases affecting sweet potato production worldwide, causing severe yield losses and posing a significant threat to food security. Vision-based intelligent diagnosis has emerged as a promising solution for large-scale SPVD monitoring due to its low cost and scalability. However, existing publicly available datasets for SPVD are extremely limited and typically focus on a single task, such as disease classification or lesion segmentation, under constrained imaging conditions. This lack of comprehensive, task-oriented datasets significantly restricts the development, evaluation, and fair comparison of advanced computer vision methods for SPVD analysis. In this study, we present SPVD-Field, a task-oriented multi-task visual dataset suite composed of two independently collected sub-datasets optimized for different computer vision tasks. Rather than constructing a single homogeneous dataset, SPVD-Field is deliberately organized into two complementary task-oriented sub-datasets: SPVD-DET, designed for disease detection with bounding-box annotations, and SPVD-SEG, designed for fine-grained lesion segmentation with pixel-level masks. The two sub-datasets were independently collected using different acquisition protocols optimized for their respective tasks, while sharing a unified semantic definition of SPVD symptoms, crop growth stages, and field environments. SPVD-Field captures substantial real-world variability in imaging scale, viewpoint, illumination, background complexity, and symptom manifestation, reflecting the inherent challenges of fieldbased disease diagnosis. We provide detailed documentation of data acquisition, annotation strategies, and quality control procedures, along with baseline benchmark results for both detection and segmentation tasks to demonstrate the usability and difficulty of the dataset. By offering a structured dataset suite rather than a single-task collection, SPVD-Field aims to support diverse research directions, including detection, segmentation, multi-task learning, and disease severity analysis, and to facilitate reproducible and comparable research in SPVD-related plant phenotyping.
Why it matches plant phenotyping methodsサツマイモの病徴を対象とする画像データセットで、検出・病斑セグメンテーション、データ取得・アノテーション・品質管理、ベンチマークを中心的に提供しており、植物病害状態の画像フェノタイピング手法・データ基盤に該当する。
abstractIn this study, we present SPVD-Field, a task-oriented multi-task visual dataset suite composed of two independently collected sub-datasets optimized for different computer vision tasks.
Reproduction assets foundThe paper's core asset is the SPVD-Field dataset (SPVD-DET detection images with bounding-box annotations and SPVD-SEG segmentation images with pixel-level masks), explicitly deposited in a public repository via the data availability statement with a DOI link.Dataset · publicThe datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: https://dx.doi.org/10.21227/hq1q-jp43 .Open asset ↗10.21227/hq1q-jp43lines:664-703Code / dataset availability confirmedEurope PMC · bioRxiv · checked 15 Sept 2026
Accurate segmentation of plant disease symptoms is essential for crop monitoring and phenotyping, yet it typically requires costly pixel-level annotations. Weakly supervised semantic segmentation (WSSS) alleviates this burden using image-level labels, but its performance depends on the quality of spatial priors such as class activation maps (CAMs). We investigate whether text-guided segmentation with the Segment Anything Model 3 (SAM3) can serve as an alternative weak supervision signal. Three pseudo-mask generation strategies are compared: (i) CAMs refined with SAM or SAM3, (ii) zero-shot text-guided SAM3, and (iii) a hybrid approach combining weak spatial cues with text prompts. The resulting pseudo-masks are used to train a DeepLabV3 model. Text guidance alone matches or outperforms conventional WSSS, achieving up to 0.46 IoU without spatial supervision and 0.61 IoU on a public dataset, although performance is sensitive to text prompt formulation. The hybrid strategy improves robustness, reaching 0.50 IoU on the primary dataset and 0.58 IoU on the additional dataset while reducing prompt sensitivity. Overall, text guidance is a promising alternative to conventional weak supervision, while hybrid approaches provide a more robust solution for plant disease segmentation.
Why it matches plant phenotyping methods植物病害症状の画像セグメンテーション手法を開発・比較し、病斑の疑似マスク生成とセグメンテーション性能を評価しているため、植物フェノタイピング手法が中心です。
abstractAccurate segmentation of plant disease symptoms is essential for crop monitoring and phenotyping
Reproduction assets foundThe paper's own oilseed rape leaf disease image dataset (2,540 RGB images, 601 pixel-level annotations) is explicitly made publicly available on Recherche Data Gouv under DOI 10.57745/R3HZOQ, which is an allowed URL. A companion dataset describing the foliar pathogens (DOI 10.57745/UCEKI8) is also public. The pixel-annDataset · publicAn original dataset of 2,540 RGB images of oilseed rape leaves affected by
7 fungal and bacterial diseases (Table 1) was built to develop and evaluate
the proposed pipelines, and is made publicly available [25].Open asset ↗pdf-raw-page:5 lines:1-43Code / dataset availability confirmedCrossref · checked 15 Sept 2026
Accurate estimation of evapotranspiration (ET) is critical for irrigation management in water-scarce regions such as the Middle East and North Africa (MENA). This study compares sensible heat flux (H), latent heat flux (LE), and ET derived from eddy covariance (EC) and a boundary-layer scintillometer (BLS) operated with an aperture reducer, deployed simultaneously over an irrigated late-season potato field (1.8 ha) in the Beqaa Valley, Lebanon. Satellite NDVI observations indicate that the BLS–EC overlap period (13 October–27 November 2021) sampled the crop from peak canopy (NDVI ≈ 0.85–0.90) through the onset of senescence (NDVI ≈ 0.79). The BLS (Scintec BLS900) operated along a 140 m path. The EC system showed incomplete daytime energy-balance closure, with a regression slope of ≈0.69 and a seasonal Bowen-ratio-preserving correction factor of CF = 1.24 (a ~19% closure deficit) was used. Across the matched period, daily H from the BLS was strongly correlated with EC (r ≈ 0.82) but systematically lower, with a regression slope of ≈0.63 that persisted across timescales; this scale-invariant amplitude compression reflects the path-averaged, similarity-based nature of the scintillometer retrieval rather than the EC closure deficit, which instead governs the mean bias. BLS-derived daily ET showed a systematic positive bias relative to uncorrected EC (mean bias error, MBE = +0.30 mm d−1; +16% cumulative). Applying the Bowen-ratio-preserving correction (CF = 1.24) to EC reduced this to MBE = −0.14 mm d−1 (−6%), and the residual-to-LE correction yielded MBE = −0.15 mm d−1 (−6.4%); the latter comparison is only partly independent, as both methods share the same Rn and G. The Bowen-ratio-preserving method is therefore recommended for this dataset. Overall, the BLS captured the temporal variability of crop water use well, but residual-based ET estimates require careful treatment of the energy-balance-closure gap and are sensitive to the high BLS gap fraction (61.6% of 15 min records over the overlap, exceeding 90% at night). Once EC is closure-corrected to serve as the reference, the BLS offers a cost-effective alternative for field-scale ET monitoring in the MENA region, subject to the conditional agreement documented here.
Why it matches plant phenotyping methodsジャガイモ圃場の作物蒸発散量（ET）という生理・水利用状態を対象に、ECとBLSを比較検証し、補正法や測定誤差も評価している。センサー測定法の技術的妥当性が中心であり、単なる routine measurement ではない。
abstractThis study compares sensible heat flux (H), latent heat flux (LE), and ET derived from eddy covariance (EC) and a boundary-layer scintillometer (BLS) operated with an aperture reducer
Reproduction assets foundThe paper's flux/ET datasets are only available on request from the corresponding author, so they do not qualify as public assets. However, the Supplementary Information file (available at the MDPI supplementary URL) explicitly contains experiment sensor documentation and field/canopy images (Figures S1–S4: study site,Supplement · publicmeasurements along the beam. Because these results derive from a single crop, season, and phenological window, their generalization awaits multi-site, multi-season replication spanning the full-canopy cycle—the priority for subsequent campaigns.
Supplementary Materials
The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/s26144398/s1 , Figure S1: Study site and potato canopy—Beqaa Valley, Lebanon; Figure S2: Eddy covariance system—full tower view (peak canopy); Figure S3: EC sensor suite close-up and soil sensor installation; Figure S4: BLS900 scintillometer—transmitter, receiver, and meteorological station.
Author Contributions
Conceptualization, HOpen asset ↗lines:251-268Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Agricultural leaf disease detection is crucial for early intervention and yield protection in precision agriculture. Among representative economic crops, such as apples, leaf lesions are typically small and appear in complex backgrounds, making accurate detection performed on resource-constrained embedded devices challenging. To address this, we propose a lightweight small-object detection models, namely the dynamic Differential Compensation Lightweight-YOLO (DCL-YOLO) model and its pruned version (DCL-YOLO-P), based on YOLO11n. A novel Dual-Aspect Feature Complementary Mapping (DAFCM) module type is embedded in their backbone to recover lost semantic and spatial information, while the original YOLO11n's neck is replaced by an Efficient Enhanced Cross-Scale Feature Fusion (EE-CSFF) module, which incorporates Gated Differential Convolutional Fusion (GDCF) modules to strengthen cross-scale information flow and small-object representation. Experimental results obtained on the ALDSOD dataset show that, compared with the YOLO11n baseline, DCL-YOLO improves recall from 81.9% to 84.6%, mAP50 from 86.8% to 88.4%, and mAP50:95 from 47.0% to 47.8%, while also reducing the parameter count from 2.58 M to 1.91 M and Giga Floating-Point Operations (GFLOPs) from 6.3 to 5.5. After applying Layer-Adaptive Magnitude-based Pruning (LAMP), the parameter count and GFLOPs are further reduced to 0.75 M and 2.7, respectively, with mAP50 and mAP50:95 still exceeding the baseline by 1.2 and 0.5 percentage points, respectively. When deployed on an embedded device, the pruned model achieved 15.2 FPS and 139 msec per image, confirming its applicability in real-time scenarios. Furthermore, cross-domain validation, performed on the Global Wheat Head Detection (GWHD) dataset, indicates the stable generalization capabilities of the proposed models across environmental domain shifts. The DCL-YOLO's source code is publicly available at: https://github.com/q123-code/dcl-yolo.
Why it matches plant phenotyping methodsリンゴ葉の病斑を画像から検出する軽量モデルを開発し、データセットで性能比較・クロスドメイン検証・組込み機器での実装評価を行っており、植物の病害状態推定手法が研究の中心です。
abstractTo address this, we propose a lightweight small-object detection models, namely the dynamic Differential Compensation Lightweight-YOLO (DCL-YOLO) model and its pruned version (DCL-YOLO-P), based on YOLO11n.
Reproduction assets foundThe paper's constructed ALDSOD apple-leaf disease detection dataset is publicly available via Zenodo DOI, and the authors' DCL-YOLO source code is publicly available on GitHub. Both are paper-specific, public, and actionable.Dataset · publicData Availability: The constructed ALDSOD dataset used in this study is available for download from the following DOI: https://doi.org/10.5281/zenodo.17198053 .Open asset ↗zenodo · 10.5281/zenodo.17198053lines:148-159Code · publicThe DCL-YOLO’s source code is publicly available at: https://github.com/q123-code/dcl-yolo .Open asset ↗github · q123-code/dcl-yololines:148-159Code / dataset availability confirmedEurope PMC · Crossref · checked 5 Sept 2026
Abstract Plant diseases affecting leaves and fruits cause substantial yield and economic losses worldwide, particularly in horticultural crops cultivated under diverse agro-climatic conditions. Early and accurate disease diagnosis is essential for effective crop management; however, manual inspection is time-consuming, subjective, and often infeasible at large scale. In this work, we present the Tomato–Chilli–Papaya (TCP) Fruit and Leaf Disease Dataset, a comprehensive multi-crop image dataset designed to support deep learning-based plant disease recognition. The dataset comprises labeled RGB images of healthy and diseased leaves and fruits from three economically important crops—tomato, chilli, and papaya—captured under real-field and semi-controlled environments, reflecting significant variability in illumination, background complexity, and disease severity. To demonstrate the applicability of the dataset, several commonly used convolutional neural network (CNN) architectures, including VGG, ResNet, DenseNet, MobileNet, and EfficientNet models, were trained and evaluated on the TCP dataset using transfer learning. Experimental results show that deep CNN models can effectively learn discriminative visual features corresponding to disease-specific patterns such as leaf spots, lesions, discoloration, curling, and fruit surface abnormalities. Lightweight models such as MobileNet achieve competitive performance with reduced computational cost, while deeper architectures provide improved accuracy at the expense of higher complexity. The results highlight the importance of dataset diversity for robust model generalization across multiple crops and plant organs. The TCP dataset provides a challenging benchmark for single-crop and multi-crop disease classification and supports the development of advanced deep learning, attention-based, and explainable AI models for precision agriculture. By enabling reproducible research and realistic performance evaluation, this dataset contributes toward scalable and practical AI-driven plant disease diagnosis systems aimed at reducing yield losses and supporting sustainable agriculture.
Why it matches plant phenotyping methods植物の葉・果実の病徴を画像から評価する大規模データセットとベンチマークを中心に扱っており、植物病害状態の画像ベース表現型解析に該当する。
abstractwe present the Tomato–Chilli–Papaya (TCP) Fruit and Leaf Disease Dataset, a comprehensive multi-crop image dataset designed to support deep learning-based plant disease recognition.
Reproduction assets foundThe paper introduces the TCP (Tomato-Chilli-Papaya) fruit and leaf disease image dataset and reports CNN experiments on it. The dataset is publicly deposited on Mendeley Data, and the authors state that analysis code is available on GitHub. Both are paper-specific, public, and actionable.Dataset · publicData is available on Mendeley:1Open asset ↗pdf-page:27 lines:1-51Code · publicCode availability: Code is available on GitHub 2Open asset ↗GitHubpdf-page:27 lines:1-51Code / dataset availability confirmedCrossref · Europe PMC · checked 15 Sept 2026
Accurate lesion segmentation is essential for automated plant disease analysis in precision agriculture. Although the Segment Anything Model (SAM) exhibits strong generalization ability, its direct application to plant disease images in natural field environments remains challenging due to cluttered backgrounds, dense leaf veins, uneven illumination, and frequent occlusions. In particular, SAM mainly relies on global structural cues and is often insufficiently sensitive to subtle lesion textures and weak local details, which can result in missed small or early-stage lesions and inaccurate boundary delineation. To address these limitations, we enhance SAM with a disease-specific detail compensation module for plant disease lesion segmentation. A ResNet-50based branch is employed to extract fine-grained local texture features that are difficult for SAM to capture. These fine-grained features are fused with SAM encoder representations and then injected into the SAM decoder, enabling more accurate lesion prediction while preserving SAM’s strong global modeling capability. More importantly, we propose a reliability-guided variational fusion framework to further improve the interaction between heterogeneous features. Specifically, instead of conventional similarity or addition-based fusion, we introduce an uncertainty-aware variational fusion strategy that explicitly quantifies the confidence of each feature stream. An uncertainty encoder models feature distributions probabilistically, and a variational fusion module dynamically assigns higher weights to more reliable features while suppressing uncertain or interfering responses. In addition, Kullback-Leibler divergence regularization is introduced to stabilize cross-feature alignment and improve fusion robustness. Extensive experiments on PlantSeg, PlantDoc-Seg, and ATLDSD demonstrate that the proposed method outperforms state-of-theart approaches, achieving DSC scores of 81.05%, 91.12%, and 88.27%, respectively. The proposed method addresses SAM’s weakness in fine-grained disease feature extraction, accurately identifies early and small lesions, and delivers reliable segmentation for field plant disease automatic diagnosis.
Why it matches plant phenotyping methods植物病斑を対象とする画像セグメンテーション手法を開発し、複数データセットで性能検証しているため、病害状態のフェノタイピング手法が中心である。
abstractwe enhance SAM with a disease-specific detail compensation module for plant disease lesion segmentation.
Reproduction assets foundThe paper evaluates ReLeaf-SAM on three public plant disease segmentation datasets. One of them, PlantDoc-Seg, is explicitly a community-provided Kaggle dataset with a verbatim URL matching an allowed URL; it is a public plant image/mask dataset directly used for this paper's segmentation measurements. PlantSeg and ATLDataset · publicTherefore, we used a community-provided segmentation subset from Kaggle 1 , which we refer to as PlantDoc-Seg in this study. This subset is derived from PlantDoc and contains 588 diseased leaf images with corresponding binary masks, enabling supervised leaf disease segmentation.Open asset ↗Kagglelines:48-115Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Agriculture is significant in world food production and global economic stability, but leaf disease and pest infection can cause a threat to crop quantity and quality. Thus, it became crucial to have timely and accurate identification of plant leaf disease to prevent loss in agriculture on a large scale and to have sustainable crop management. This paper introduces LeafLiteX, a lightweight mobile-based deep learning application for real-time detection and classification of leaf diseases. This application uses U-Net segmentation to precisely find leaf regions and MobileNetV3-Large to quickly classify diseases with less computation on the computer. The application performs end-to-end processing, from image acquisition to segmentation and disease prediction on mobile devices. An experiment was performed on publicly available crop disease datasets containing various leaf images having different disease types. The model obtained an accuracy of 98.85% showing improved generalization with minimal latency. The design of the model was such that it was suitable for inference on-device while still being robust enough despite changes in lighting conditions, background noise, and camera resolution. LeafLiteX is a low-cost, easy to use, offline-capable, and in-the-moment decision-making supportive diagnostic application that supports farmers and agrarians who require early detection. This paper demonstrates the capabilities that can be achieved using edge-optimized machine learning and computer vision to support the development of smart agriculture technologies. While traditional methods rely solely on classification, this research focuses more on practical implementation by incorporating segmentation, lightweight classification, and explainability to develop a mobile-friendly model.
Why it matches plant phenotyping methods葉画像から病害状態をセグメンテーション・分類する手法とモバイルアプリ自体が研究の中心であり、植物病害の表現型推定に該当する。
abstractThis paper introduces LeafLiteX, a lightweight mobile-based deep learning application for real-time detection and classification of leaf diseases.
Reproduction assets foundThe paper's Data availability statement explicitly links the public PlantVillage (Mendeley) and PlantDoc (GitHub) leaf-image datasets used for its experiments, and provides the authors' LeafLiteX source code on GitHub.Dataset · publicThe dataset used in this study is publicly available from the repository:
https://data.mendeley.com/datasets/tywbtsjrjv/1Open asset ↗data.mendeley.com · tywbtsjrjv/1pdf-page:29 lines:1-74Code · publicThe source code is available on the following link: https://github.com/phdpawan/LeafLiteX.Open asset ↗github.com/phdpawan/LeafLiteXpdf-page:29 lines:1-74Code / dataset availability confirmedCrossref · Europe PMC · checked 5 Sept 2026
Field-based phenotyping of water-related traits for precision irrigation in tropical agroecosystems poses a persistent methodological challenge, driven by high climatic variability and the complex water-use physiology of Crassulacean Acid Metabolism (CAM) crops such as pineapple (Ananas comosus var. MD2). We developed and validated a Physics-Informed Machine Learning (PIML) framework that integrates high-resolution UAV multispectral imagery, IoT-based microclimatic records, and a mechanistic soil water balance based on the FAO-56 Penman–Monteith standard to predict plot-scale soil moisture depletion as a proxy of plant water status. A six-month field campaign (March–August 2022) across 25 georeferenced commercial pineapple plots in the Colombian Orinoquia piedmont yielded a spatiotemporally balanced dataset of N=150 observations. Soil-adjusted vegetation indices (OSAVI, MSAVI) outperformed standard NDVI for capturing water-related canopy traits, effectively decoupling spectral responses from substrate noise. A Gradient Boosting regressor achieved R2=0.842 and RMSE=0.0705 on a normalized target scale, corresponding to a 7.05% error over the prediction range, while the traffic-light Decision Support System (DSS) for irrigation scheduling reached 91.1% accuracy (Cohen’s Kappa =0.91). Incorporating daily soil moisture depletion as a mechanistic feature improved predictive accuracy over a spectral-only baseline (ΔR2=+0.052) and anchored predictions within a physically consistent framework based on the FAO-56 water balance, with no false negatives observed for water deficit detection in the hold-out validation set. This framework advances high-throughput, population-scale phenotyping of water-related traits in open-canopy CAM crops, establishing a transferable methodology for operational precision irrigation under tropical savanna conditions.
Why it matches plant phenotyping methodsUAVマルチスペクトル画像と機械学習を用いて植物の水関連形質・水状態を推定する枠組みを開発・検証しており、表現型取得と予測手法が研究の中心である。
abstractWe developed and validated a Physics-Informed Machine Learning (PIML) framework that integrates high-resolution UAV multispectral imagery, IoT-based microclimatic records, and a mechanistic soil water balance based on the FAO-56 Penman–Monteith standard to predict plot-scale soil moisture depletion as a proxy of plant water status.
Reproduction assets foundThe paper's Data Availability Statement explicitly deposits the complete dataset and source code (raw UAV multispectral imagery, Python scripts, IoT sensor logs, CROPWAT 8.0 files, and XGBoost model code) in a public Mendeley Data repository, which directly reproduces this paper's phenotyping measurements and analysis.Dataset · publicThe complete dataset and source code supporting this study are publicly available at Mendeley Data: https://data.mendeley.com/datasets/9xwdvzf3bf/1 (accessed on 20 May 2026). The repository includes: (1) raw multispectral UAV imagery with calibration panel captures; (2) Python scripts for DN-to-reflectance conversion and spectral index extraction; (3) IoT sensor logs (soil moisture, temperature, relative humidity); (4) CROPWAT 8.0 project files for FAO-56 soil water balance simulation; and (5) XGBoost model source code with hyperparameter optimization routines.Open asset ↗Mendeley Data · 9xwdvzf3bf/1lines:193-228Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Introduction Wheat is one of the most widely planted staple crops worldwide and underpins global food security. Fungal diseases severely threaten wheat growth and trigger massive yield losses during cultivation. Traditional manual diagnosis is time-consuming and highly subjective, while existing deep learning models often struggle to achieve high accuracy and robustness in complex field environments. Accurate identification of these fungal diseases is therefore vital to secure grain production. Methods This paper constructs a lightweight convolutional neural network named ShuffleNetV2_SSM_MLCA for wheat fungal disease classification. First, the original basic blocks of ShuffleNetV2 are substituted with SS-Conv-SSM modules to strengthen the extraction of fine-grained lesion features amid visually analogous fungal disease samples; half convolution is embedded to cut down model computational overhead. Second, a Mixed Local Channel Attention (MLCA) unit is attached to the convolution branch of each SS-Conv-SSM module, which adaptively highlights discriminative disease features and filters irrelevant background noise. Standard training configurations and five-fold cross-validation are adopted for fair model evaluation. Results Comparative experiments reveal that the presented network reaches a classification accuracy of 91.35%, which surpasses the original ShuffleNetV2 baseline by 1.16 percentage points. Controlled ablation tests verify the independent performance gain of each core component: the SS-Conv-SSM module raises overall accuracy by 0.89%, and the MLCA mechanism brings an extra 0.27% accuracy increment. Discussion The proposed ShuffleNetV2_SSM_MLCA architecture strikes a favorable trade-off between model lightweight property and classification performance. It delivers a low-computation, high-precision recognition scheme for wheat fungal diseases and lays a solid technical foundation for real-time disease monitoring in intelligent agricultural scenarios.
Why it matches plant phenotyping methods小麦葉片の病斑特徴を画像から抽出し、植物の真菌病状態を分類する軽量深層学習手法を開発・検証しており、病害表現型の取得・推定が研究の中心である。
abstractThis paper constructs a lightweight convolutional neural network named ShuffleNetV2_SSM_MLCA for wheat fungal disease classification.
Reproduction assets foundThe paper's plant-image measurements are based entirely on publicly available wheat disease image datasets: a primary Kaggle dataset (Wheat Plant Diseases by Kushagra Agarwal) used for model development, and two additional public datasets (Alibaba Cloud Developer Community and CSDN Modelers) used for generalization andDataset · publicThe dataset is publicly available at https://www.kaggle.com/datasets/kushagra3204/wheat-plant-diseases and was accessed on September 5, 2025.Open asset ↗Kaggle · kushagra3204/wheat-plant-diseaseslines:322-374Dataset · publicThe second dataset was contributed by blogger DL data set and released on December 25, 2025 via the CSDN Modelers platform ( https://modelers.csdn.net/69a67f4c7bbde9200b9c3240.html )Open asset ↗CSDN Modelerslines:644-669Code / dataset availability confirmedOpenAlex · Europe PMC · checked 5 Sept 2026
Abstract Background Stomata and pavement cells are fundamental components of the leaf epidermis, jointly regulating gas exchange, water loss, and leaf surface expansion. Stomata size, aperture, density, and pavement cell morphology are critical parameters for assessing plant transpiration efficiency, epidermal growth dynamics, and adaptive responses to environmental constraints. Despite their biological importance, quantifying stomatal and pavement-cell traits remains seldom not generalized, simple, and fast enough . Manual or semi-automated approaches limit large-scale phenotyping and restrict the integration of epidermal morphology into crop-improvement pipelines aimed at developing climate-resilient varieties with optimised stomatal patterning. To address such limitations, we developed Stomatalia , a deep learning-based platform designed to automate and standardise the quantification of stomatal and pavement cell traits. The algorithm was trained on epidermal images of cultivated and wild potato and tomato genotypes grown under optimal and abiotic-stress conditions. Stomatalia automatically detects stomata and pavement cells and extracts a broad range of morphological and integrative epidermal parameters, enabling high-throughput phenotyping within a unified workflow. Results Prior to platform development, we optimised a rapid, minimally-destructive leaf-printing protocol that generates negative impressions of the leaf surface within 40–100 s. Transparent positive prints were subsequently produced and imaged under a light microscope at scale settings ranging from 20 to 200 μm. The resulting images are analysed using Stomatalia’s user-friendly web-based interface, which runs an instance-segmentation deep learning algorithm to detect, count, and calculate stomatal and pavement cell parameters. The platform outputs structured files containing raw measurements, derived integrative traits, and associated metadata, facilitating downstream statistical and physiological analyses. Algorithm evaluation on independent datasets demonstrated high performance within the validated dicot imaging domain, with F 1 -scores ranging from 0.86 to 0.94 depending on image scale, species, and resolution, and high segmentation overlap for both stomata and pavement cells. The generality of stomatal detection was also tested on spring onion, chickpea, balsam poplar, and wheat in cross-species feasibility tests, although performance was more variable in monocots, and pavement-cell segmentation remained species- and architecture-dependent. Benchmarking against another publicly available app further showed that, under the tested web interface settings and image types, Stomatalia exhibited closer agreement with manual counts and substantially faster processing times. The practical performance of Stomatalia was further tested in a proof-of-concept trial with potato plants subjected to optimal irrigation and a long, gradual drought. The platform reliably quantified epidermal traits despite variations in leaf morphology and image quality, supporting the integrated interpretation of stomatal and pavement-cell responses under stress. Conclusions We developed Stomatalia as a robust, user-friendly deep learning platform for automated, high-throughput analysis of bright-field leaf epidermal images across varying magnifications and resolutions. Stomatalia facilitates rapid, reproducible, and coordinated phenotyping of stomatal and pavement cells by integrating methodological standardisation, computational automation, and multi-trait extraction in a single analytical workflow. Its strongest current application is the analysis of high-quality dicot leaf-print images, particularly in species and imaging conditions similar to those used for model training and validation. Cross-species and benchmark analyses further define its current scope: stomatal detection can be transferred to some additional epidermal architectures, whereas robust pavement-cell segmentation in monocots or highly divergent species will require further annotation and model retraining. Within these defined boundaries, Stomatalia provides a flexible and extensible framework for studying stomatal and pavement cell morphology and environmental plasticity, while also supporting broader efforts to dissect and optimise plant responses to abiotic stress.
Why it matches plant phenotyping methods気孔・舗装細胞の形態形質を画像から自動抽出する深層学習プラットフォームを開発し、独立データで性能評価・比較検証しているため、植物フェノタイピング手法が中心である。
abstractwe developed Stomatalia , a deep learning-based platform designed to automate and standardise the quantification of stomatal and pavement cell traits.
Reproduction assets foundThe authors publicly deposited the paper's test image datasets (raw/input leaf-print images, detection outputs, manual ground-truth counts, exported datasets) and the model file on Figshare, and provide a public Google Colab demo for running the Stomatalia algorithm. Both are paper-specific, public, and actionable.Dataset · publicThe test datasets and model file used in this work are available through the following link:
https://doi.org/10.6084/m9.figshare.32532672. The test_sets.zip archive contains the test image datasets
(cross-species and benchmark analysis), including raw/input images, detection output images, manual
ground-truth counts and exported datasets.Open asset ↗Figshare · 10.6084/m9.figshare.32532672pdf-page:25 lines:1-75Code / dataset availability confirmedEurope PMC · checked 14 Sept 2026
Traditional manual grading of fresh chili peppers suffers from inconsistent quality control and low efficiency. To meet the demand for accurate fruit shape recognition during the post-harvest stage, this study proposes an intelligent recognition method based on an improved DenseNet-121 network. This approach facilitates the application of machine vision in agricultural sorting equipment. DenseNet-121 serves as the backbone network. The Convolutional Block Attention Module (CBAM) is introduced to enhance feature focus on fruit shapes. A regularization strategy (Dropout = 0.3, weight decay = 1 × 10 -4 ) and a cross-entropy loss function with label smoothing (LS = 0.1) are integrated to optimize decision boundaries. These configurations prevent the model from overfitting to hard training labels and yield a robust classification architecture. Experimental results demonstrate that the proposed model achieves a precision of 90.09%, a recall of 89.60%, an F1-score (the harmonic mean of precision and recall) of 89.53%, and an overall accuracy of 89.74%. The model contains 7.09 M parameters and requires a single-frame inference time of 7.35 ms. Comprehensive evaluations indicate that the proposed model achieves an optimal balance among environmental noise robustness, prediction accuracy, and computational efficiency. Consequently, by maintaining high fine-grained classification accuracy alongside a low memory footprint and rapid inference speed, the model demonstrates strong potential for real-time deployment on resource-constrained edge devices within actual agricultural optical sorting equipment.
Why it matches plant phenotyping methodsチリペッパー果実の形状という植物器官形質を画像から分類する深層学習手法の開発・評価が中心であり、単なる品質測定ではない。
abstractExperimental results demonstrate that the proposed model achieves a precision of 90.09%, a recall of 89.60%, an F1-score (the harmonic mean of precision and recall) of 89.53%, and an overall accuracy of 89.74%.
Reproduction assets found保存済みの本文根拠を更新済みルールで再検証し、公開資産1件を確認しました。Dataset · publicThe original image dataset is provided as Supplementary Materials .Open asset ↗lines:30-40Code / dataset availability confirmedEurope PMC · checked 15 Sept 2026
Cotton leaf diseases present a major threat to global cotton production, significantly impacting both yield and fiber quality. Traditional diagnostic methods are labor-intensive, time-consuming, and demand highly skilled professionals, making them inefficient for large-scale agricultural applications. Although earlier deep learning -based approaches have shown promising results in identifying cotton leaf diseases such as Bacterial Blight, Fusarium Wilt, and Curl Virus Disease, their performance is often limited by complex preprocessing requirements and insufficient generalization to real-world field conditions. To address these challenges, this study proposes and optimized transfer learning-based model, CLDP-CNN, designed to enhance feature extraction and classification efficiency using pre-trained deep neural networks. This study demonstrates the development of Cotton Leaf Disease Prediction Convolutional Neural Network (CLDP-CNN) automatically, utilizing Transfer Learning (TL) which operates on meticulously prepared datasets. Two distinct datasets were used to train the model: the first consisted of field images from cotton farms, while the second was sourced from Kaggle. The main goal of this research examines how the model performs on real-world field datasets. The CLDP-CNN model has proven highly accurate by attaining 99.78% detection success rates for cotton leaf diseases when processing primary dataset which surpasses its secondary dataset accuracy rate of 99.62%. Both the primary dataset and secondary dataset resulted in high accuracy values for the VGG16 pre-trained model which achieved 99.56% accuracy on the primary dataset and 98.82% on the secondary dataset. A web-based application enhances the capabilities of the CLDP-CNN model by providing real-time updates on the health status of cotton plants. This technology empowers farmers with valuable information, enabling them to take timely protective actions to prevent potential severe yield losses in their cotton crops.
Why it matches plant phenotyping methods綿花葉の画像から病害状態を推定する深層学習モデルを開発・評価しており、植物フェノタイピング手法が研究の中心です。
abstractThe main goal of this research examines how the model performs on real-world field datasets.
Reproduction assets foundThe paper's cotton leaf disease image datasets are publicly available: the authors' primary field-collected dataset on the first author's GitHub repository, and the secondary Kaggle dataset used for comparison. No analysis code or trained model checkpoints are explicitly deposited.Dataset · publicbia.
Funding: This work was supported by Princess Nourah bint Abdulrahman
University Researchers Supporting Project number (PNURSP2026R760),
Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia.
Data and code availability
The data that support the findings of this study are openly available in Github and
Kaggle at. https://github.com/mnaeem303/Cotton-Leaf_Disease-Dataset),
and https://www.kaggle.com/datasets/seroshkarim/cotton-leaf-disease-dataset/data
Author Contributions
All the authors (Muhammad Naeem, Muhammad Ibrahim, Nadeem Sarwar, Oumaima
Saidani, Asma Irshad, Muhammad Shadab Alam Hashmi, Muhammad Tayyab
Qammar) contributed equally to this work in their respective meaningOpen asset ↗https://github.com/mnaeem303/Cotton-Leaf_Disease-Datasetpdf-raw-page:29 lines:1-54Dataset · publicbdulrahman
University Researchers Supporting Project number (PNURSP2026R760),
Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia.
Data and code availability
The data that support the findings of this study are openly available in Github and
Kaggle at. https://github.com/mnaeem303/Cotton-Leaf_Disease-Dataset),
and https://www.kaggle.com/datasets/seroshkarim/cotton-leaf-disease-dataset/data
Author Contributions
All the authors (Muhammad Naeem, Muhammad Ibrahim, Nadeem Sarwar, Oumaima
Saidani, Asma Irshad, Muhammad Shadab Alam Hashmi, Muhammad Tayyab
Qammar) contributed equally to this work in their respective meaningful ways. All the
authors have read and approved the final manuOpen asset ↗pdf-raw-page:29 lines:1-54Code / dataset availability confirmedEurope PMC · checked 14 Sept 2026
Food productivity, quantity and quality are at stake when plant diseases such as rice diseases undermine the food security. Rice leaf disease treatment necessitates accurate and timely diagnosing. This study describes a deep learning model for categorizing and forecasting rice plant diseases. Using the remora optimization algorithm (ROA) on a rice leaf dataset demonstrates its potential for plant disease classification. The ROA-DM method detects rice leaf diseases using the ROA algorithm, a deep maxout network (DMN), and a deep autoencoder (DAE). ROA is applied to the learning parameters of deep model in order to achieve better convergence and avoiding local minima, which usually happens with conventional gradient-based optimizers. Experiments show that the suggested framework is accurate and precise across illness categories. The confusion matrices display the training and validation accuracy, losses of this model. The performance of our optimal learning method with respect to other methods indicated its potential for identifying leaf diseases. The accuracy of the ROA-DM method is 98.5%.
Why it matches plant phenotyping methodsイネ葉の観察画像から病害状態を分類・検出する深層学習手法が研究の中心であり、植物病害フェノタイピング手法に該当する。
abstractThis study describes a deep learning model for categorizing and forecasting rice plant diseases.
Reproduction assets found保存済みの本文根拠を更新済みルールで再検証し、公開資産1件を確認しました。Dataset · publicThe dataset collected from https://www.kaggle.com/datasets/emmarex/plantdisease (PlantVillage dataset) for algorithm testing in plant disease diagnosis 35 . The selected rice leaf disease samples from PlantVillage dataset consisting of 3050 colour leaf images across four classes.Open asset ↗Kaggle · emmarex/plantdiseaselines:85-97Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Brinjal (eggplant) is a critical crop in South Asia, especially in Bangladesh, but its production is drastically affected by numerous diseases that inhibit yield and quality. Manual diagnosis of disease is time-consuming, subjective, and prone to errors, necessitating automated, scalable technology. To address these issues, this paper proposes PD-ViCo, a lightweight, efficient transformer-based model for brinjal fruit disease classification using Simple Vision Transformer (ViT) with Patch Dropout and Contrastive Captioner (CoCa) methods. One new dataset of 1,823 field-harvested brinjal images encompassing five disease classes including Phomopsis Blight, Fruit and Shoot Borer, Fruit Cracking, Wet Rot, and Healthy samples were prepared through real-world agricultural data collection from Bangladesh. The approach includes extensive preprocessing, class balancing (under-sampling/oversampling), and resilient augmentation methods. The PD-ViCo model significantly improves classification performance under data imbalance with patch dropout regularization and CoCa-style aggregation, resulting in better generalization and robustness. On a range of imbalanced, under-sampled, and oversampled datasets, PD-ViCo achieved a classification accuracy of 99.12% and F1-score of 97.76%, outperforming both ViT and Swin Transformer across all key evaluation metrics. Explainability was also applied using Grad-CAM and Grad-CAM + + , generating visual explanations of model decisions and maintaining conformity to disease-affected regions in the images. These visualizations ensure the credibility of the model and its usability for real agricultural conditions. This study demonstrates that PD-ViCo is a highly accurate, interpretable, and lightweight model for multi-class brinjal disease diagnosis. Not only does it advance state-of-the-art in agricultural AI, but it also provides a valuable dataset and an understandable decision-making protocol that can be applied directly by farmers, agronomists, and agricultural technologists.
Why it matches plant phenotyping methods植物画像から病害状態を分類するモデル、データセット、説明可能性評価を中心に開発・検証しており、植物フェノタイピング手法として適格。
abstractthis paper proposes PD-ViCo, a lightweight, efficient transformer-based model for brinjal fruit disease classification
Reproduction assets foundThe paper's own field-harvested brinjal disease image dataset (1,823 images, five classes) is publicly deposited on Mendeley Data, with an explicit availability statement and URL matching an allowed entry. No code or model checkpoint deposit is stated.Dataset · publicThe data utilized in this study is publicly accessible on Mendeley Data Repository at the following link: [ https://data.mendeley.com/datasets/ngc58fsxgd/1 ].Open asset ↗Mendeley Data · ngc58fsxgd/1lines:226-251Code / dataset availability confirmedOpenAlex · Crossref · checked 14 Sept 2026
Abstract Fruit size, shape, color, and percent fruit rot are important quality traits for breeding cranberry ( Vaccinium macrocarpon Ait.). Image analysis can be used to measure these traits, but affordable hardware for standardized image capture and integrated user‐friendly software pipelines are lacking. Additionally, no image‐based method exists to estimate percent fruit rot, an otherwise tediously and subjectively measured trait. We created the BerryBox, a simple and inexpensive lightbox, camera mount, and accompanying software pipeline to standardize the capture and analysis of postharvest fruit images. Trained deep neural network models were highly accurate for segmenting sound fruit (F1 score: 99.4%) and detecting rotten fruit (F1 score: 98.5%). We applied the BerryBox to images of cranberries harvested across 3 years from a 156‐clone breeding population. Narrow‐sense heritability estimates of image‐based fruit color, shape, size, and percent fruit rot ranged from 0.37 to 0.95. Random subsampling showed that 25–30 berries per genotype were sufficient to describe the variation in the full dataset. We demonstrated the utility of BerryBox traits in a small‐scale genetic linkage mapping analysis, detecting significant marker–trait associations that coincided with those of traditionally measured traits. The BerryBox software was able to accurately segment fruit from images of blueberries without model retraining, showing its applicability to other similarly shaped fruits. The software pipeline and BerryBox materials and assembly instructions are publicly available for others to adopt for low‐cost image‐based phenotyping.
Why it matches plant phenotyping methodsクランベリー等の果実形質と腐敗率を画像から抽出する低コスト撮像装置・ソフトウェアパイプラインを開発し、精度検証と他果実への適用性評価を行った、中心的な植物フェノタイピング手法研究である。
abstractWe created the BerryBox, a simple and inexpensive lightbox, camera mount, and accompanying software pipeline to standardize the capture and analysis of postharvest fruit images.
Reproduction assets foundThe paper explicitly states public availability of the annotated image datasets (USDA Ag Data Commons DOI), R analysis scripts, the BerryBox Python software package with pre-trained models, and the model training code, all with author-provided public URLs.Dataset · publics (LOD)
score at a particular marker exceeded that computed at the
α = 0.05 level under null models generated via 1000 random
permutations.
2.8 Data, software, and equipment
instruction availability
The image datasets, along with annotations, are publicly
available through the USDA National Agricultural Library
Ag Data Commons (https://doi.org/10.15482/USDA.ADC/29853332). All analyses in this study were performed in R (v.
4.5.0; R Core Team, 2025). Scripts to replicate the analyses,
along with a list of materials for recreating the Berry-
Box, are available from the GitHub repository https://github.com/neyhartj/BerryBox_FruitPhenotyping. Software for run-
ning the image capture and analysis Open asset ↗10.15482/USDA.ADC/29853332pdf-raw-page:8 lines:1-125Code · publicable through the USDA National Agricultural Library
Ag Data Commons (https://doi.org/10.15482/USDA.ADC/29853332). All analyses in this study were performed in R (v.
4.5.0; R Core Team, 2025). Scripts to replicate the analyses,
along with a list of materials for recreating the Berry-
Box, are available from the GitHub repository https://github.com/neyhartj/BerryBox_FruitPhenotyping. Software for run-
ning the image capture and analysis software pipeline is
available as a Python package from the GitHub reposi-
tory https://github.com/NeyhartLab/berryboxai. The package
includes pre-trained models for berry segmentation and fruit
rot detection, and the code is available from https://github.com/NOpen asset ↗github.com/neyhartj/BerryBox_FruitPhenotypingpdf-raw-page:8 lines:1-125Code · public). Scripts to replicate the analyses,
along with a list of materials for recreating the Berry-
Box, are available from the GitHub repository https://github.com/neyhartj/BerryBox_FruitPhenotyping. Software for run-
ning the image capture and analysis software pipeline is
available as a Python package from the GitHub reposi-
tory https://github.com/NeyhartLab/berryboxai. The package
includes pre-trained models for berry segmentation and fruit
rot detection, and the code is available from https://github.com/NeyhartLab/berryboxai_training_public for training a
custom model using high-performance computing resources
or the widely available Google Colab environment (Rippner
et al., 2022).
3 RESULTOpen asset ↗github.com/NeyhartLab/berryboxaipdf-raw-page:8 lines:1-125Code · publiceyhartj/BerryBox_FruitPhenotyping. Software for run-
ning the image capture and analysis software pipeline is
available as a Python package from the GitHub reposi-
tory https://github.com/NeyhartLab/berryboxai. The package
includes pre-trained models for berry segmentation and fruit
rot detection, and the code is available from https://github.com/NeyhartLab/berryboxai_training_public for training a
custom model using high-performance computing resources
or the widely available Google Colab environment (Rippner
et al., 2022).
3 RESULTS
3.1 Deep learning model training
The trained berry segmentation model achieved an overall
accuracy of 98.9% and an F1 score of 99.4%. The fruit rot
detection mOpen asset ↗github.com/NeyhartLab/berryboxai_training_publicpdf-raw-page:8 lines:1-125Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Rice leaf diseases pose a major challenge to crop health and agricultural productivity, particularly when timely and accurate diagnosis is required under natural field conditions. The development of automated disease recognition systems depends heavily on the availability of large, well-annotated image datasets. However, many existing rice leaf disease datasets are limited in terms of environmental variability, disease representation, and real-field imaging conditions. To address this gap, this paper presents BanglaRiceLeaf, an original rice leaf image dataset collected and curated by the authors from the experimental fields of the Bangladesh Rice Research Institute (BRRI), Gazipur, Bangladesh, between July 2023 and July 2024. The dataset contains 4152 images belonging to five classes: Bacterial Leaf Blight, Bacterial Leaf Streak, Sheath Blight, Leaf Blast, and Healthy Leaf. The images were acquired from two rice varieties, BR11 and BRRI dhan34, under natural field conditions across varying illumination environments in order to reflect practical disease recognition scenarios. All images were manually annotated by trained annotators under expert supervision. The dataset is systematically organized and publicly released to support reproducible research in rice disease classification. In addition to dataset presentation, benchmark experiments using Xception, NASNetMobile, and InceptionV3 are provided to demonstrate its applicability for deep learning-based disease recognition. BanglaRiceLeaf is expected to serve as a useful resource for plant disease analysis, comparative model evaluation, and future research in precision agriculture and agricultural computer vision.
Why it matches plant phenotyping methodsイネ葉の病徴・健全状態を画像で分類する公開ベンチマークデータセットであり、データ収集・注釈・ベンチマーク評価が中心です。
abstractthis paper presents BanglaRiceLeaf, an original rice leaf image dataset collected and curated by the authors
Reproduction assets foundThe paper's core asset is the BanglaRiceLeaf rice leaf disease image dataset (4152 field images, five classes), publicly released on Harvard Dataverse with DOI 10.7910/DVN/XAOBYW. No author analysis code or trained model checkpoints are stated as publicly available.Dataset · publicData Identification Number: https://doi.org/10.7910/DVN/XAOBYW
Direct URL to Data: https://dataverse.harvard.edu/dataset.xhtml?persistentId=doi:10.7910/DVN/XAOBYW
Access Instructions: This dataset is publicly available on the Harvard Dataverse repository and can be accessed for academic, research, and instructional purposes.Open asset ↗Harvard Dataverse · doi:10.7910/DVN/XAOBYWhtml-lines:100-131Code / dataset availability confirmedEurope PMC · OpenAlex · checked 5 Sept 2026
The co-evolutionary arms race between crops and their parasites requires continuous identification of new resistance mechanisms. Broomrape (Orobanche cumana), a root parasitic plant, poses a severe threat to sunflower (Helianthus annuus) production, yet the genetic architecture underlying host resistance remains poorly understood. To address this, we established a high-throughput phenotyping platform to quantify root infestation across a diverse sunflower association mapping (SAM) population. Combining this phenotypic resource with a dual genome-wide association study (GWAS) strategy based on both single nucleotide polymorphisms (SNPs) and k-mers, we highlight the genetic basis of broomrape resistance at unprecedented resolution. Our analyses revealed quantitative trait loci (QTLs) and identified novel candidate genes, including putative leucine-rich repeat receptor kinases potentially involved in parasite recognition and defense activation. Importantly, the k-mer approach circumvented reference genome bias and uncovered key genomic introgressions from wild Helianthus relatives that contribute substantially to resistance. These findings demonstrate the utility of integrating high-resolution phenotyping with advanced association mapping to dissect complex host-parasite interactions. Moreover, they emphasize the enduring value of wild germplasm as a reservoir of adaptive variation, providing crop breeders with crucial tools to counter the rapid evolutionary dynamics of parasitic plants.
Why it matches plant phenotyping methods根部の寄生程度を定量する高スループット表現型解析プラットフォームの確立が明示され、遺伝解析の基盤として方法が実質的に扱われている。
abstractwe established a high-throughput phenotyping platform to quantify root infestation across a diverse sunflower association mapping (SAM) population.
Reproduction assets foundThe paper's Data availability statement explicitly deposits the paper-specific raw phenotyping images on Zenodo, the k-mer genotype data on the sunflower genome database, and the authors' analysis code on the Hübner lab GitHub repository, all with public URLs.Dataset · publicAll phenotypes raw images for Gadot and Yavor are available through the Zenodo repository ( https://doi.org/10.5281/zenodo.18961268 ).Open asset ↗Zenodo · 10.5281/zenodo.18961268lines:238-238Code · publicCode is accessible through the Hübner lab github: https://github.com/hubner-lab/Sunflower-Broomrape-paper .Open asset ↗Hübner lab github · hubner-lab/Sunflower-Broomrape-paperlines:238-238Code / dataset availability confirmedCrossref · checked 14 Sept 2026
Published1 Jul 2026International Journal of IoT, Embedded Systems and Industrial AutomationCited by 0 · OpenAlex ↗
Modern agriculture is rapidly adopting Artificial Intelligence (AI) and Internet of Things (IoT) technologies to improve crop monitoring and decision-making. Many existing systems focus either on water stress detection or pest detection separately. The proposed system integrates both functions into a single platform. It uses a camera module and environmental sensors connected to a Raspberry Pi (5/4) as the main controller. A Convolutional Neural Network (CNN) model processes leaf images captured by the AI camera, while a soil moisture sensor supports water stress analysis. The system classifies crops into three categories: healthy, water-stressed, and pest-infected. Based on the output, it provides real-time recommendations for irrigation and pesticide application. This reduces manual inspection, prevents unnecessary chemical usage, saves water, and improves crop productivity.
Why it matches plant phenotyping methods植物の葉画像と土壌水分センサーを用いて、健康・水ストレス・害虫感染という植物の状態を自動分類する統合センシング基盤を開発しており、表現型取得・判定が中心的です。
abstractThe proposed system integrates both functions into a single platform.
Reproduction assets foundThe paper's CNN phenotyping/classification analysis is built directly on two public Kaggle image datasets (PlantVillage plant disease and Crop Water Stress), explicitly cited with URLs. No author code or trained model is deposited.Dataset · publicThe PlantVillage Dataset was used for
plant disease detection, and it is available at https://www.kaggle.com/datasets/emmarex/plantdisease.Open asset ↗Kaggle · emmarex/plantdiseasepdf-page:7 lines:1-57Dataset · publicThe Crop Water Stress Dataset was used for crop water stress analysis, and it can be accessed at
https://www.kaggle.com/datasets/harshilsharma/crop-water-stress.Open asset ↗Kaggle · harshilsharma/crop-water-stresspdf-page:7 lines:1-57Code / dataset availability confirmedCrossref · checked 15 Sept 2026
Published30 Jun 2026International Journal for Research in Applied Science and Engineering TechnologyCited by 0 · OpenAlex ↗
The research trains and evaluates multiple CNN architectures, including Basic CNN, AlexNet, VGG16, and EfficientNet B0, to enhance the accuracy of plant disease identification. Each model was tested using the New Plant Diseases Dataset from Kaggle, which includes various plant species and diseases, in order to assess performance, accuracy, and efficiency. The trained models were subsequently integrated into a Marathi language chatbot to facilitate real-time disease detection and provide agricultural guidance. This study provides valuable insights into the strengths and limitations of different models for precision agriculture, especially in applications that support regional languages to encourage accessible and sustainable farming practices. Additionally, a Marathi language chatbot is incorporated, enabling users to obtain plant disease information instantly through a user-friendly web application
Why it matches plant phenotyping methods植物病害状態を画像から識別するCNN群を訓練・評価し、リアルタイム検出システムへ統合しており、病害フェノタイプの取得・推定手法が中心である。
abstractThe research trains and evaluates multiple CNN architectures, including Basic CNN, AlexNet, VGG16, and EfficientNet B0, to enhance the accuracy of plant disease identification.
Reproduction assets foundThe paper's plant-phenotyping input is the public New Plant Diseases Dataset from Kaggle (healthy/diseased leaf images of tomato, potato, corn) used to train and evaluate the CNN ensemble. No author analysis code, trained model checkpoints, or supplementary data deposit is mentioned with an availability statement orURLDataset · publicInitially, the dataset was collected from the New Plant Diseases Dataset available
on Kaggle, which contains images of healthy and diseased plant leaves from various crops such as tomato, potato, and corn.Open asset ↗Kaggle · New Plant Diseases Datasetpdf-raw-page:3 lines:1-44Code / dataset availability confirmedCrossref · checked 14 Sept 2026
Wild-relative introgression broadens wheat diversity, as exemplified by the Multiple Synthetic Derivatives (MSD) population, a unique hexaploid wheat resource capturing extensive genetic diversity from Aegilops tauschii. However, root system architecture (RSA), a key determinant of resource acquisition and stress adaptation, remains poorly characterized in this population. Here, we established a practical two-dimensional root phenotyping framework that enables continuous imaging to track RSA traits and their responses to heat stress. Using this framework we evaluated MSD417 as a representative genotype against its recurrent parent, Norin 61 (N61). Under control conditions, MSD417 displayed greater total root length, root system width, and convex hull area than N61 (p < 0.001), indicating enhanced early root vigor. MSD417 also exhibited larger second pair seminal root angle (p < 0.001) and length (p < 0.01) across both conditions, suggesting enhanced horizontal root exploration while maintaining similar rooting depth to N61 (p = 0.981). Heat stress reduced overall root growth and narrowed genotypic differences, limiting RSA expression. Microscopic observations revealed a lower coleorhiza height-to-width ratio in MSD417. These findings demonstrate the effectiveness of the two-dimensional platform for early-stage RSA phenotyping and highlight Aegilops tauschii-derived germplasm as a source of favorable root traits in wheat breeding.
Why it matches plant phenotyping methods二次元画像による根系構造フェノタイピング基盤を構築し、連続撮像で根形質を追跡する方法が研究の中心であるため含める。
abstractHere, we established a practical two-dimensional root phenotyping framework that enables continuous imaging to track RSA traits and their responses to heat stress.
Reproduction assets foundThe paper's data availability statement deposits the paper-specific phenotyping inputs publicly on Zenodo: root images of wheat N61 and MSD417 (the two genotypes measured for RSA traits) and microscopic coleorhiza images. These are public, paper-specific image datasets directly underlying the study's measurements. No作者Dataset · publical development in arid regions.
ORCID
Sultan Md Monwarul Islam http://orcid.org/0009-0002-7219-2104
Izzat Sidahmed Ali Tahir http://orcid.org/0000-0002-1711-6961
Kinya Akashi http://orcid.org/0000-0002-9991-5766
Data availability statement
The root images of wheat N61 and MSD417 are deposited in the Zenodo data repository under https://doi.org/10.5281/zenodo.18080159 and https://doi.org/10.5281/zenodo.18079748, respectively. The microscopic images of
coleorhiza are deposited under https://doi.org/10.5281/zenodo.18091131. The other original contributions presented
in the study are included in the article and/or supplementary material.
References
Alahmad, S., El Hassouni, K., Bassi, F. M., DiOpen asset ↗Zenodo · 10.5281/zenodo.18080159pdf-raw-page:14 lines:1-49Dataset · publicMd Monwarul Islam http://orcid.org/0009-0002-7219-2104
Izzat Sidahmed Ali Tahir http://orcid.org/0000-0002-1711-6961
Kinya Akashi http://orcid.org/0000-0002-9991-5766
Data availability statement
The root images of wheat N61 and MSD417 are deposited in the Zenodo data repository under https://doi.org/10.5281/zenodo.18080159 and https://doi.org/10.5281/zenodo.18079748, respectively. The microscopic images of
coleorhiza are deposited under https://doi.org/10.5281/zenodo.18091131. The other original contributions presented
in the study are included in the article and/or supplementary material.
References
Alahmad, S., El Hassouni, K., Bassi, F. M., Dinglasan, E., Youssef, C., Quarry, G., Aksoy,Open asset ↗Zenodo · 10.5281/zenodo.18079748pdf-raw-page:14 lines:1-49Dataset · public-6961
Kinya Akashi http://orcid.org/0000-0002-9991-5766
Data availability statement
The root images of wheat N61 and MSD417 are deposited in the Zenodo data repository under https://doi.org/10.5281/zenodo.18080159 and https://doi.org/10.5281/zenodo.18079748, respectively. The microscopic images of
coleorhiza are deposited under https://doi.org/10.5281/zenodo.18091131. The other original contributions presented
in the study are included in the article and/or supplementary material.
References
Alahmad, S., El Hassouni, K., Bassi, F. M., Dinglasan, E., Youssef, C., Quarry, G., Aksoy, A., Mazzucotelli, E., Juhász, A.,
Able, J. A., Christopher, J., Voss-Fels, K. P., & Hickey, L. T. (2019). A majOpen asset ↗Zenodo · 10.5281/zenodo.18091131pdf-raw-page:14 lines:1-49Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Paddy leaf disease (PLD) detection has grown more difficult, yet early detection might prevent significant losses due to decreased crop yield. However, existing models struggle to accurately classify diseases under difficult circumstances like intricate backgrounds, fluctuating lighting, and overlapping leaves. Additionally, existing models do not incorporate efficient optimization strategies, leading to suboptimal accuracy and poor generalization on unseen data. To address these challenges, a novel deep learning-based YOLO-LEAFNET method for PLD detection utilizing IGT-YOLO, integrating the YOLOv8 disease detection with the Improved Gorilla Troops (IGT) optimization. The input paddy leaf images are pre-processed using Bilateral Contrast Limited Adaptive Histogram Equalization (B-CLAHE) to enhance image quality and improve local contrast while preserving disease boundaries. YOLOv8 model is utilized to detect and classify paddy leaf diseases by accurately localizing affected regions with bounding boxes. Then, the IGT algorithm boosts the disease detection accuracy by optimizing YOLOv8 through effective hyperparameter tuning. The proposed YOLO-LEAFNET method effectiveness was evaluated using recall, F1 score, specificity, accuracy, and precision. B-CLAHE enhanced noise-free images improve contrast and detection accuracy, while the IGT-YOLO model ensures scalable, efficient early diagnosis of paddy leaf diseases with 99.07% accuracy. The YOLO-LEAFNET enhanced the total accuracy by 3.21%, 5.25%, and 1.98% related to CNN, DeepRice, and FasterR-CNN, respectively.
Why it matches plant phenotyping methodsイネ葉の病害状態を画像から検出・分類するYOLOベース手法を提案し、前処理・最適化・性能評価を中心に扱っているため、植物フェノタイピング手法として該当する。
abstractTo address these challenges, a novel deep learning-based YOLO-LEAFNET method for PLD detection utilizing IGT-YOLO, integrating the YOLOv8 disease detection with the Improved Gorilla Troops (IGT) optimization.
Reproduction assets foundThe paper's phenotyping input is the public UCI Rice Leaf Diseases dataset (paddy leaf images of bacterial leaf blight, leaf smut, brown spot), also mirrored on Kaggle. No author analysis code, trained model, or supplementary assets are disclosed.Dataset · publicThe dataset is publicly available
at: https://archive.ics.uci.edu/dataset/486/rice+leaf+diseases. The dataset is distributed
under the Creative Commons Attribution 4.0 (CC BY 4.0) license.Open asset ↗rice+leaf+diseasespdf-page:7 lines:1-33Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Low temperature stress severely restricts the cultivation and distribution of pear ( Pyrus L.) germplasms, frequently resulting in frost injury and yield reduction. To accurately evaluate the cold resistance of pear germplasm resources, this study investigates the physiological and biochemical responses of one-year-old branches to different degrees of low-temperature stress, as well as differences in the tissue structure of these pear germplasms after low-temperature stress. In this study, 122 pear germplasms were classified into high (HR), medium (MR), and low (LR) cold-tolerance categories based on their semi-lethal temperature (LT 50 ). Further analysis of pear germplasms with different levels of cold resistance revealed that, with decreasing temperature, HR germplasms exhibited smaller increases in relative electrolyte conductivity (REC) and malondialdehyde (MDA) content and higher accumulation of proline (Pro), soluble proteins (SP), soluble sugars (SS), and peroxidase activity compared with LR germplasms. In addition, the peak values of these indicators generally occurred at lower temperatures in HR germplasms. A correlation analysis and principal component analysis indicated that physiological indices, including REC, bound water/free water ratio, SS, and MDA, as well as branch anatomical traits related to xylem and cortex proportions, were closely associated with variation in LT 50 . An integrated assessment using membership function analysis produced rankings consistent with LT 50 -based clustering, supporting the reliability of the multivariate evaluation framework. Overall, this study establishes an integrated, indicator-based approach for evaluating cold resistance in pear germplasm by integrating physiological, biochemical, and anatomical characteristics. These results provide a theoretical basis and methodological reference for screening cold resistance germplasms.
Why it matches plant phenotyping methods生理・生化学・解剖学的形質を統合し、LT50と多変量評価によってナシ遺伝資源の耐寒性を分類・スクリーニングする評価フレームワークが研究の中心である。
abstractTo accurately evaluate the cold resistance of pear germplasm resources, this study investigates the physiological and biochemical responses of one-year-old branches to different degrees of low-temperature stress, as well as differences in the tissue structure of these pear germplasms after low-temperature stress.
Reproduction assets foundThe article's Data Availability statement links a public Zenodo deposit containing the paper's raw phenotyping data (LT50, physiological/biochemical and anatomical measurements for pear germplasms). Supplemental files also contain germplasm characteristics and LT50 comparisons, but the Zenodo raw-data deposit is the明确,Dataset · publicThe data is available at Zenodo: liu186253. (2025). liu186253/Data: raw data (Version V11). Zenodo. https://doi.org/10.5281/zenodo.17524773 .Open asset ↗Zenodo · 10.5281/zenodo.17524773lines:636-710Code / dataset availability confirmedEurope PMC · checked 15 Sept 2026
This paper presents a deep learning model to detect cotton plant pests and classify diseases, which must overcome limited datasets, class imbalance, and feature redundancy. At the preprocessing phase, the Gaussian blur filtering and Contrast Limited Adaptive Histogram Equalization (CLAHE) are used to sharpen images by improving their clarity and contrast. To increase and diversify the data, Spa-GAN-based data augmentation is used to produce realistic synthetic samples. To obtain an accurate Region of Interest (RoI), an Attention-Guided Multi-Scale Residual U-Net (AGMS-U-Net) is considered to segment local and global structural information. The proposed framework makes three major contributions: (i) a new attention-based feature extractor, TriAttnNet, that incorporates spatial, channel, and contextual attention to represent diseases on a fine-grained level (ii) a new optimization strategy, Hybrid Mongoose Ray Chaotic Optimization (HMRCO), which includes chaotic strategies to better tune the parameters and explore the feature space and (iii) classification layer with focal loss for final decision. Experimental analyses prove that the suggested method is much more effective than the current state-of-the-art models, providing a powerful and understandable solution to precision agriculture and sustainable cotton crop health monitoring. Experimental results show that TriAttnNet achieves 98.66% accuracy, 98.71% recall, and 98.81% F1-score, which is better than the state-of-the-art algorithms, such as EfficientNetB1-CBAM (96.38%) and BERT-ResNet-PSO (95.69%). The proposed system is computationally feasible and interpretable, and it is interpretable to provide a practical solution to precision agriculture and sustainable monitoring of the health of cotton crops.
Why it matches plant phenotyping methods綿花植物の画像から病害を分類する深層学習手法を開発・評価しており、植物の病害状態を直接推定する方法が研究の中心である。
abstractThis paper presents a deep learning model to detect cotton plant pests and classify diseases
Reproduction assets foundThe paper's plant-phenotyping input is the public Kaggle Cotton Plant Disease Dataset (Dhamodharan R), explicitly cited as the study's data source with a matching public URL. The authors' model/code is not publicly deposited (available only upon request), so no qualifying code asset exists.Dataset · publicThe dataset of this study is taken from the publicly available Kaggle repository, Cotton Plant Disease Dataset 43Open asset ↗Kagglelines:48-58Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Objective This study presents an integrated, multi-scale approach for the non-destructive estimation of phenological stages and carotenoid content in carrots by combining spectral techniques, colorimetry, and artificial intelligence. Methods Six commercial varieties, including orange, yellow, white, and purple genotypes, were evaluated under field and laboratory conditions using multispectral drone imagery, high-resolution spectroradiometric signatures, red green blue (RGB) images, and CIELAB color measurements. A hierarchical modeling framework was developed across two phases: (i) spectral modeling using uncrewed aerial vehicle (UAV)-based multispectral indices, textural and geometric metrics, and laboratory-generated hyperspectral signatures; and (ii) a colorimetric index from RGB images. Results Using UAV-based multispectral field data, phenological prediction indices achieved high classification performance (F1-scores > 0.90) when modeled with a Random Forest classifier, supported by distinct spectral signatures associated with canopy development and senescence. In parallel, carotenoid content estimation using a Random Forest regression model demonstrated strong predictive accuracy ( R 2 = 0.897; RMSE = 0.584), with the Plant Senescence Reflectance Index (PSRI) and Carotenoid Reflectance Index (CRI) identified as the most influential predictors. A complementary laboratory-based Random Forest regression model using high-resolution spectral signatures achieved near-perfect predictive performance ( R 2 = 0.987). SHapley Additive exPlanations (SHAP) analysis identified physiologically relevant wavelengths in the green (540-550 nm) and red-edge (∼700 nm) regions as the primary drivers of carotenoid concentration. Likewise, a novel colorimetric index (ICarot), derived from CIELAB parameters, enabled accurate image-based carotenoid estimation ( R 2 = 0.85). Conclusion This study introduces an innovative multi-sensor framework for precision agriculture and automated postharvest quality control, enabling rapid, objective, and scalable phenotyping in carrot production systems. Through the integration of spectral, colorimetric, and AI-based approaches, the proposed methodology effectively captures both internal nutritional attributes and external quality traits within a unified, non-destructive assessment pipeline.
Why it matches plant phenotyping methods複数センサー画像・分光計測とAIを統合し、ニンジンの生育段階およびカロテノイド含量を非破壊推定する手法を開発・評価しており、表現型取得が研究の中心である。
abstractThis study presents an integrated, multi-scale approach for the non-destructive estimation of phenological stages and carotenoid content in carrots by combining spectral techniques, colorimetry, and artificial intelligence.
Reproduction assets foundThe paper's Data Availability section explicitly deposits the study's data (and project materials) on GitHub and Zenodo, both with authors' public URLs matching allowed_urls. These qualify as paper-specific public assets for the carrot phenotyping measurements and analysis.Dataset · publicThe data is available at GitHub and Zenodo:
- https://github.com/agrocompuepidemlab/Carrot-value-chain-proyect/tree/mainOpen asset ↗github.com/agrocompuepidemlab/Carrot-value-chain-proyectlines:184-307Code / dataset availability confirmedCrossref · checked 14 Sept 2026
Abstract. As key components of agricultural management, planting and harvesting schedules have strongly influenced crop production by defining the length of the crop growing season and shaping the environmental conditions crops experience. Accurate knowledge of these management data is crucial for enhancing crop yield estimates by capturing the timing of crop development relative to weather and soil conditions, assessing climate adaptation by tracking shifts in farming practices over time, and supporting agricultural carbon accounting. Yet, existing planting and harvesting date datasets are largely based on state-level statistics or rule-based calendars that overlook intra-regional variability and the influence of human decision-making. The absence of long-term, high-resolution planting and harvesting date information hinders our ability to reconstruct historical agricultural practices and assess their agronomic and environmental consequences. In this study, we introduce CropPlantHarvest, the first dataset of annual corn and soybean planting and harvesting dates across the U.S. Midwest at 500 m resolution from 2001 to 2024. Planting dates are estimated using CropSow, an integrative remotely sensed crop modeling system that aligns simulated crop growth trajectories with satellite observations to retrieve field-level planting dates. Harvesting dates are retrieved using the Normalized Harvest Phenology Index (NHPI), a novel index that integrates Normalized Difference Vegetation Index (NDVI) and near-infrared (NIR) reflectance to detect harvesting events by capturing the distinct spectral transition from senescent crops to exposed crop residues. Validation against USDA crop progress reports and field-level dataset demonstrates high accuracy of CropPlantHarvest, with a mean absolute error of approximately 5 d for both crop species. This large spatial and temporal dataset captures management-driven variability in crop season timing and duration, supporting improved modeling of crop yields, greenhouse gas emissions, and resource use. It could also serve as a benchmark for refining remote-sensing phenology products and evaluating the agro-environmental impacts of evolving crop management decisions. CropPlantHarvest is available at https://doi.org/10.5281/zenodo.16967482 (Liu and Diao, 2025).
Why it matches plant phenotyping methods衛星観測と作物モデルによる圃場レベルの作付・収穫時期推定手法を開発し、NHPIを提案して独立データで検証した大規模データセット研究であり、植物の生育・収穫状態の取得が中心的です。
abstractPlanting dates are estimated using CropSow, an integrative remotely sensed crop modeling system that aligns simulated crop growth trajectories with satellite observations to retrieve field-level planting dates.
Reproduction assets found保存済みの本文根拠を更新済みルールで再検証し、公開資産1件を確認しました。Dataset · publicOur CropPlantHarvest dataset, which provides planting and harvesting dates for corn and soybean fields at 500 m spatial resolution across the U.S. Midwest from 2001 to 2024, can be accessed via Zenodo: https://doi.org/10.5281/zenodo.16967482 (Liu and Diao, 2025).Open asset ↗Zenodo · 10.5281/zenodo.16967482lines:322-333Code / dataset availability confirmedCrossref · checked 14 Sept 2026
This study addresses the need for efficient and accessible plant disease identification systems in the era of Agriculture 4.0, where advances in artificial intelligence (AI) and machine learning (ML) support data-driven agricultural practices. The increasing popularity of home gardening highlights challenges faced by users in identifying plant diseases due to limited knowledge and diagnostic tools. Therefore, this research aims to develop a web plant disease detection system using the Django framework and convolutional neural networks (CNNs). The model was trained on a controlled dataset consisting of 57,320 leaf images collected from the PlantVillage and Turmeric Plant Disease datasets. Image preprocessing was applied, including resizing, normalization, and data augmentation such as image rotation, zooming, image inversion and brightness adjustmen. Class imbalance during training was handled using class weighting. The dataset is divided into a training set and a validation set for model development and evaluation. The CNN model achieved an accuracy of 92% on the labeled validation dataset, with a mean F1 score of 0.79 and a weighted mean F1 score of 0.92. For generalization testing, an uncontrolled (wild) dataset consisting of 223 images collected from online sources was used, resulting in an accuracy of 11%, indicating limited real-world generalization due to domain differences. Despite this limitation, the proposed system demonstrates the feasibility of CNN-based plant disease classification in a web application.
Why it matches plant phenotyping methodsCNNによる葉画像からの植物病害識別システムを開発し、検証データと野外データで性能評価しているため、植物の病害状態を推定する画像ベースのフェノタイピング手法が中心である。
abstractthis research aims to develop a web plant disease detection system using the Django framework and convolutional neural networks (CNNs).
Reproduction assets foundThe paper's CNN plant-disease model was trained primarily on the public Kaggle 'New Plant Diseases Dataset' (PlantVillage-derived, 54,528 images), which is a paper-specific, publicly available image dataset directly used for the study's phenotyping measurements. The Turmeric Plant Disease Dataset (Mendeley DOI 10.17632Dataset · public[23] Samir Bhattarai, “New Plant Diseases Dataset,” San Francisco, CA, USA, 2018. Accessed: Jun. 16, 2025.
[Online]. Available: https://www.kaggle.com/datasets/vipoooool/new-plant-diseases-datasetOpen asset ↗Kaggle · vipoooool/new-plant-diseases-datasetpdf-page:15 lines:1-45Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Global food security is largely based on the accurate and timely diagnosis of crop diseases, where paddy rice is an extremely essential staple of more than half of the world population. The conventional disease identification techniques tend to be laborious, time consuming and demand a great deal of domain knowledge, which becomes a bottleneck in the efficient management of the farms. Although deep learning [and especially Convolutional Neural Networks (CNNs)] have demonstrated a spectacular performance in automated classification of diseases based on leaf images, they tend to overlook important contextual features that are implicitly processed by agronomic experts. The visual defects of a disease might be unclear and this can greatly differ depending on factors like the genetic variety of the plant and the stage of development. We overcome this shortcoming by proposing a new multi-modal deep learning framework, Multi-Modal Factorized Bilinear Pooling (MFBP) model which is capable of a more holistic and precise paddy health measurement. The proposed method is the only one that combines high-level visual information obtained using leaf images and related tabular information, namely the paddy type and number of days. The MFBP model uses Factorized Bilinear Pooling (FBP) rather than the simple feature concatenation which commonly loses the complex relationship between different data types. This systematic method efficiently encodes all the complex interactions between all components of the visual and tabular features vectors in such a way that helps the model to pick up subtle, context-specific patterns. As an example, it will only be possible to educate the model that a specific visual blemish is predictive of a given disease through a specific species at a specific age. We test our model on the Paddy Doctor: Paddy Disease Classification dataset, which is a detailed public dataset comprising of more than 10,000 labeled images and containing relevant metadata, and thus it forms a perfect testing bed to conduct multi-modal research. Through our detailed experiments, we have shown that the proposed MFBP model is much better than a baseline model based on concatenation fusion, which proves that deep, multiplicative interactions can be best modeled in this task. The findings highlight the massive possibilities of multi-modes AI in the development of more robust, more accurate, and more context-aware diagnostic instruments and precision agriculture to enable more sustainable and productive agricultural activities.
Why it matches plant phenotyping methods葉画像とメタデータを統合してイネの健康状態・病害を推定する新規深層学習手法を提案し、ベースライン比較で検証しているため、植物フェノタイピング手法が中心である。
abstractWe overcome this shortcoming by proposing a new multi-modal deep learning framework, Multi-Modal Factorized Bilinear Pooling (MFBP) model which is capable of a more holistic and precise paddy health measurement.
Reproduction assets foundThe paper's phenotyping inputs are the public Kaggle 'Paddy Doctor: Paddy Disease Classification' dataset (10,407 leaf images with tabular metadata for variety and age), explicitly named in the Data Availability statement with a persistent public URL. No author analysis code, trained models, or checkpoints are reportedDataset · publicThe datasets used and/or analysed during the current study are publicly available in the
“Paddy-doctor: paddy disease classification” repository at the following persistent
URL: https://www.kaggle.com/datasets/vbookshelf/paddy-disease-classification.Open asset ↗Kaggle · vbookshelf/paddy-disease-classificationpdf-page:20 lines:1-74Code / dataset availability confirmedCrossref · Europe PMC · checked 15 Sept 2026
Image processing plays a vital role in precision agriculture by enabling automated disease detection and crop health monitoring. This research presents a novel Hybrid Vision Transformer with Dense Attention Capsule Network (HVT-DACapNet) model for accurate cotton plant disease detection. The proposed framework integrates Adaptive Wavelet Transform Filtering (AWTF) for noise removal while preserving disease-related features. A Hybrid Vision Transformer (HVT) is employed to extract both local spatial patterns and global contextual dependencies, and the Dense Attention Capsule Network (DACapNet) captures hierarchical spatial relationships with an attention mechanism that emphasizes infected regions. In addition, a hybrid optimization strategy combining Mayfly and Aquila Optimization (HMAO) is used to fine-tune model hyperparameters for improved convergence. The model is evaluated on a publicly available Kaggle cotton leaf disease dataset containing healthy leaves and multiple disease categories including Target Spot, Powdery Mildew, Bacterial Blight, Army Worm, and Aphids, using a 70:15:15 train-validation-test split under the simulation setup and hyperparameter configuration described in the manuscript. The proposed HVT-DACapNet achieves an F1-score of 99.68%, sensitivity of 99.68%, specificity of 98.89%, and an overall accuracy of 99.79%, outperforming existing models such as ConvLSTM-ZOA, GOA, SFO, Inception-V3, and VGG-16.
Why it matches plant phenotyping methods綿花葉の画像から病害状態を推定する深層学習手法を新規開発し、公開データセットで性能評価しているため、植物フェノタイピング手法が中心である。
abstractThis research presents a novel Hybrid Vision Transformer with Dense Attention Capsule Network (HVT-DACapNet) model for accurate cotton plant disease detection.
Reproduction assets foundThe paper's only qualifying asset is the public Kaggle Cotton Plant Disease Dataset used as the input image dataset for all experiments. The authors' code is explicitly not publicly available (institutional restrictions), with only a supplementary algorithm document and on-request implementation details.Dataset · publicthodological workflow of the proposed model. Additional
implementation details may be made available from the corresponding
author upon reasonable request for academic and non-commercial
research purposes.
Data Availability-The datasets generated and/or analysed during the
current study are available in the Kaggle repository,
https://www.kaggle.com/datasets/dhamur/cotton-plant-disease
Author’s contribution – G.Neelavathi– Research proposal –
construction of the workflow and model – Final Drafting– Survey of
Existing works – Improvisation of the proposed model;
Dr.K.Venkatasalam – Initial Drafting of the paper – Collection of
datasets and choice of their suitability – Formulation of pseudOpen asset ↗Kaggle · dhamur/cotton-plant-diseasepdf-raw-page:39 lines:1-42Code / dataset availability confirmedCrossref · Europe PMC · checked 5 Sept 2026
Crop leaf diseases cause 10–40% annual yield losses, yet timely field diagnosis remains difficult. Vision-language models (VLMs) lift recognition accuracy with rich textual descriptions, but multimodal pipelines are too slow for real-time field use because they require text processing at inference. We present MTL-AWL, a framework built on a training–inference asymmetry: VLM text serves as privileged training-time supervision, and two coupled mechanisms—one retaining VLM semantics in the image encoder and one exploiting them—enable image-only deployment at multimodal accuracy. A modal-dropout strategy (p=0.6) intermittently masks the VLM text sequence during training, forcing the image encoder to retain cross-modal representations independently. An adaptive multi-task loss jointly optimizes InfoNCE contrastive alignment, attention diversity, and modality consistency under learnable softmax weights, consistently converging to a dominant contrastive weight (55% on soybean, 68% on PlantDoc)—identifying cross-modal alignment as the primary mechanism of VLM knowledge transfer. At inference, the model reaches 818 FPS (3.7× faster than multimodal methods) at only 0.41% accuracy cost, attaining 99.30%/98.89% (multimodal/image-only) on soybean and 72.65%/68.80% on PlantDoc—compact enough for real-time, offline field screening.
Why it matches plant phenotyping methods葉画像から植物病害状態を推定する画像ベース手法を開発し、複数データセットで精度・速度を評価しており、フェノタイピング手法が中心である。
abstractWe present MTL-AWL, a framework built on a training–inference asymmetry: VLM text serves as privileged training-time supervision, and two coupled mechanisms—one retaining VLM semantics in the image encoder and one exploiting them—enable image-only deployment at multimodal accuracy.
Reproduction assets foundThe paper's Data Availability Statement links a public Dryad DOI for the soybean leaf disease image dataset used in the study's phenotyping/recognition experiments. No author code or model release is stated.Dataset · publicThe datasets utilized in this study are openly accessible. The soybean dataset is available at https://doi.org/10.5061/dryad.41ns1rnj3 .Open asset ↗Dryad · 10.5061/dryad.41ns1rnj3lines:441-459Code / dataset availability confirmedarXiv · OpenAlex · checked 11 Sept 2026
Tomographic microscopy enables three-dimensional internal imaging but often requires expensive optical or X-ray instrumentation. Here we present an ultra-low-cost continuous-wave diffusive tomography (CWDT) system for biological samples. The system uses a smartphone microscope, a white LED coupled into an optical fiber, 3D-printed micropositioners, and a physics-based forward model optimized with machine learning. We demonstrate full-color volumetric reconstructions from a tartrazine-cleared poplar section, a scattering phantom, fungal mycelium near an Arabidopsis root, and thick poplar branch imaging with an inserted side-emitting fiber. The current results are qualitative and exploratory, but they show that scanned fiber illumination and inexpensive hardware can produce useful three-dimensional reconstruction outputs for low-cost microscopy experiments.
Why it matches plant phenotyping methods低コスト三次元断層イメージング法そのものを開発し、ポプラ組織・枝やシロイヌナズナ根近傍を対象に植物の内部構造を可視化しているため、植物形態の取得法として中心的です。
abstractHere we present an ultra-low-cost continuous-wave diffusive tomography (CWDT) system for biological samples.
Reproduction assets foundThe paper's raw imaging inputs, configurations, and reconstruction outputs for Figures 2–5 are publicly deposited on Kaggle. The analysis code repository is only 'prepared for release' (no confirmed public deposit yet), so it is listed as request-only. Hardware CAD mirrors are public but are instrument designs, not theDataset · publicFigure-level raw inputs, model configurations, selected outputs, and manifests are available through the Kaggle dataset https://www.kaggle.com/datasets/alingold/continuous-wave-diffusive-tomography .Open asset ↗continuous-wave-diffusive-tomographylines:108-129Code / dataset availability confirmedEurope PMC · checked 15 Sept 2026
Pearl millet is an important crop in arid regions, but its yield is reduced by foliar diseases like Downy Mildew and Rust. Traditional and deep learning methods struggle with accurate lesion detection, severity estimation, and robustness under complex field conditions, and often lack interpretability for practical agricultural deployment. To address these challenges, this study proposes the Adaptive Severity-Aware Swin Attention Network (ASA-SAN), an integrated framework designed for disease segmentation, classification, and severity estimation in pearl millet leaves. The proposed architecture combines a Swin Transformer encoder for hierarchical feature extraction with a ResUNet++ decoder for accurate lesion segmentation. This is further enhanced using Adaptive Channel Attention to improve feature discrimination and a dual-stream classification network to jointly capture local lesion characteristics and global contextual information. Additionally, an Adaptive Disease Severity Index (ADSI) is introduced to quantitatively assess disease progression based on lesion area ratio, color degradation, edge irregularity, and texture variations. Experimental evaluations conducted on a pearl millet leaf dataset demonstrate that the proposed method achieves a Dice score of 97.8%, IoU of 95.6%, classification accuracy of 98.3%, and F1-score of 98.2%, outperforming several state-of-the-art methods. Furthermore, Grad-CAM visualizations enhance model interpretability by highlighting disease-relevant regions. Overall, the ASA-SAN framework provides a robust, interpretable, and severity-aware solution for automated pearl millet disease analysis, enabling early detection and supporting precision agriculture practices for improved crop protection and yield optimization.
Why it matches plant phenotyping methods真珠粟葉の病斑を画像から分割・分類し、病害重症度を定量推定する手法を中心に開発・評価しているため、植物表現型計測手法として含める。
abstractAdditionally, an Adaptive Disease Severity Index (ADSI) is introduced to quantitatively assess disease progression based on lesion area ratio, color degradation, edge irregularity, and texture variations.
Reproduction assets foundThe paper's phenotyping inputs are drawn from a public, open-access image dataset: the Pearl Millet Leaf Disease dataset (Version 2) hosted on Roboflow Universe, containing annotated images of Downy Mildew, Rust, and healthy pearl millet leaves. This is a paper-specific, publicly available asset directly used for the作者Dataset · publicThe dataset used in this research was taken from the publicly available open-access Pearl
Millet Leaf Disease dataset hosted on Roboflow Universe, which has images of Downy
Mildew, Rust and healthy pearl millet leaves annotated publicly available [26]. To ensure
experimental consistency and reproducibility, all experiments were conducted with Version
2 of the open access dataset.Open asset ↗Roboflow Universepdf-raw-page:10 lines:1-28Code / dataset availability confirmedOpenAlex · Crossref · checked 15 Sept 2026
LeafScans-Orchard is a curated, multi-year RGB image dataset of orchard plant leaves designed to support research in computer vision, machine learning, and plant phenotyping. The dataset comprises 9708 high-quality leaf scans acquired during collection campaigns conducted between 2015 and 2025, covering seven orchard crop species: apple, pear, sweet cherry, sour cherry, plum, peach, and apricot. In total, the dataset includes 67 cultivar labels. All samples were acquired using flatbed scanning under controlled conditions on a uniform background, ensuring high visual consistency and minimal background variability. The original scans were captured at 1200 dpi and subsequently converted into a public release format at 300 dpi, stored as lossless TIFF images to preserve morphological and textural details. Each image corresponds to a single leaf and is organized in a hierarchical directory structure by species, cultivar, and acquisition year, accompanied by image-level metadata and aggregated species–cultivar–year counts. LeafScans-Orchard is suitable for plant species classification, cultivar recognition, leaf morphology analysis, texture analysis, and general visual feature extraction. In addition to the main release, a representative subset of 300 original 1200 dpi scans is provided to support high-resolution analyses. The dataset is particularly suited for fine-grained classification, morphology-driven analysis, and methodological studies under controlled imaging conditions.
Why it matches plant phenotyping methods果樹葉のRGBスキャン画像を収録した公開データセットで、植物フェノタイピングおよび葉形態解析を目的とする。標準化された画像取得と再利用可能なデータ構成が中心であり、フェノタイピング用データセットとして適格。
abstractLeafScans-Orchard is a curated, multi-year RGB image dataset of orchard plant leaves designed to support research in computer vision, machine learning, and plant phenotyping.
Reproduction assets foundThe paper's core asset is the LeafScans-Orchard dataset itself (9708 RGB leaf scans, 300 dpi TIFF release plus 1200 dpi subset, image-level metadata and summary counts), openly deposited on Zenodo with an explicit DOI and CC BY 4.0 license. This is a paper-specific, public, actionable phenotyping image dataset. No codeDataset · publicthe published version of the manuscript.
Funding: This research received no external funding.
Institutional Review Board Statement: Not applicable.
Informed Consent Statement: Not applicable.
Data Availability Statement: The dataset described in this article is openly available in Zenodo
as LeafScans-Orchard Dataset (v1.0.0) at https://doi.org/10.5281/zenodo.20187966 (accessed on
10 May 2026). The repository includes the 300 dpi image release, the 1200 dpi high-resolution subset,
image-level metadata, aggregated species–cultivar–year counts, and supporting documentation. The
complete archive of original 1200 dpi scans is retained locally by the authors but is not included in
the current pubOpen asset ↗Zenodo · 10.5281/zenodo.20187966pdf-raw-page:12 lines:1-46Code / dataset availability confirmedCrossref · checked 14 Sept 2026
Published23 Jun 2026International Journal of Innovative Research and Scientific StudiesCited by 0 · OpenAlex ↗
Plant health plays a critical role in agriculture, climate balance, and economic stability. However, plant diseases caused by bacteria, fungi, and viruses can significantly reduce crop productivity if not detected early. Traditional manual inspection methods are time-consuming, labor-intensive, and prone to human error, especially in large-scale farming. To address these challenges, this study proposes an automated and accurate plant disease detection system using deep learning-based object detection models for early disease diagnosis in agriculture. A publicly available dataset containing 38 different plant leaf diseases annotated in You Only Look Once (YOLO) format is used, along with a standardized preprocessing pipeline to ensure data quality and consistency. Three modern architectures: YOLOv8, YOLOv11, and YOLOv26 were trained and evaluated under identical conditions using the Ultralytics framework on Google Colab. Experimental results show that YOLOv11 achieves the highest accuracy in terms of precision, recall, and mean Average Precision (mAP), while YOLOv8 provides the fastest inference speed with lower computational complexity. Based on the results, the study concludes that YOLO-based models show great potential for plant disease detection, with YOLOv11 offering superior detection accuracy among the evaluated models. The practical implications of these findings lie in the potential for precision agriculture to monitor diseases in real-time, minimize crop losses, and aid in timely decision-making for farmers and agricultural stakeholders.
Why it matches plant phenotyping methods植物葉の病害状態を画像から検出するYOLOベース手法を提案し、複数モデルを同一条件で評価しているため、病害表現型の取得・抽出が中心である。
abstractthis study proposes an automated and accurate plant disease detection system using deep learning-based object detection models
Reproduction assets found保存済みの本文根拠を更新済みルールで再検証し、公開資産1件を確認しました。Dataset · publicFor this study, we obtained a publicly accessible dataset (plant disease detection dataset) from Kaggle [30]. The
dataset comprises 2569 images of 13 different plant species, as shown in Figure 2.Open asset ↗Kagglepdf-page:6 lines:1-41Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
The robust Dutch rose, also known as the Rosa hybrida is distinguished by its vibrant colors, superior product quality, and extended vase life. These rose varieties, originating from Netherlands, have proven highly successful in Indian agricultural conditions and the international export industry. The dataset consists of a total of 1,995 high resolution petal image collected during this research, encompassing petal color categories, such as red, yellow, white, pink, purple, orange, bi-color, and multi-color, as well as health statuses including fresh, dry, and diseased petals. The primary purpose of this dataset is to support machine learning activities in agriculture and specifically for tasks such as automatic petal health evaluation and rose variety categorization. Although the rose flower is scientifically rich and has a wide range of industrial uses, it has not been given much attention in machine learning, especially when compared to other plant-based datasets. This study adds to the accuracy of quality assessment through the use of modern computer vision and machine learning methods, thus helping the agriculture sector, rose-based edible product making, and flavor development industries.
Why it matches plant phenotyping methodsバラ花弁画像データセットの構築と、花弁の健康状態・色分類による植物状態評価が研究の中心であり、画像ベースの表現型計測データセットに該当する。
abstractThe dataset consists of a total of 1,995 high resolution petal image collected during this research, encompassing petal color categories, such as red, yellow, white, pink, purple, orange, bi-color, and multi-color, as well as health statuses including fresh, dry, and diseased petals.
Reproduction assets foundThe paper's own rose petal image dataset is publicly deposited on Mendeley Data, and the authors' validation/metadata scripts are publicly available on GitHub. Both are paper-specific, public, and actionable.Dataset · publicThe RoseVisuals dataset is publicly available on Mendeley Data at Direct URL to data: https://data.mendeley.com/datasets/f44jwtbfjg/5. Data Identification Number: 10.17632/f44jwtbfjg.5. Repository Name: RoseVisuals.Open asset ↗Mendeley Data · 10.17632/f44jwtbfjg.5html-lines:246-284Code · publicThe RoseVisuals codebase, comprising all validation scripts, is publicly available on GitHub Repository at https://github.com/Arya-S14/RoseVisuals-Validation-Doc.Open asset ↗GitHubhtml-lines:246-284Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Plant diseases cause 20-40% annual crop losses worldwide, yet conventional detection methods remain slow, subjective, and inaccessible to smallholder farmers. This work presents GreenAid, an end-to-end plant disease detection and management system that bridges the gap between laboratory-level deep learning performance and practical agricultural deployment. The system integrates a confidence-weighted ensemble of three CNN architectures (VGG16, ResNet50, InceptionV3), fused through per-class F1-score reliability weights, with a cross-platform mobile application supporting offline inference via TensorFlow Lite, a web-based analytics dashboard, and an NLP-powered chatbot. On the PlantVillage benchmark (87,000 images, 38 classes, 14 species), the ensemble achieves 98.74% accuracy and 98.48% F1-score. Systematic comparison of six fusion strategies confirms that per-class F1 weighting outperforms alternatives including majority voting, simple averaging, and stacking. The INT8-quantised deployment model (78 MB, 127 ms on a mid-range smartphone) retains 98.43% accuracy with per-class analysis confirming disproportionate impact on the five most challenging categories. All pairwise model comparisons are validated by McNemar's test ([Formula: see text]). The primary contribution is the complete, reproducible integration of competitive classification, edge deployment, and an end-to-end agricultural delivery pipeline (mobile application, web dashboard, and NLP chatbot) rather than the ensemble mechanism itself.
Why it matches plant phenotyping methods植物画像から病害状態を推定する深層学習手法の開発・比較検証と、モバイル実装が中心であり、植物病害フェノタイピング手法として適格。
abstractThis work presents GreenAid, an end-to-end plant disease detection and management system
Reproduction assets foundThe paper's plant-disease phenotyping analysis is built on the public PlantVillage dataset (87,000 leaf images, 38 classes), which the authors explicitly state is publicly accessible via Kaggle. No authors' analysis code, trained models, or checkpoints are released with an explicit public URL in the supplied blocks.Dataset · publicThe dataset used in this study is the publicly available PlantVillage dataset, accessible via Kaggle at:Open asset ↗Kagglelines:270-340Code / dataset availability confirmedEurope PMC · checked 14 Sept 2026
Sapodilla (Manilkara zapota), or chickoo, is a key tropical fruit, very popular in India, Mexico, and Thailand, as it is nutritionally and economically valuable. Nonetheless, the production of sapodillas is often affected by several diseases, which reduce fruit quality and quantity. The dataset used in this paper is a sapodilla fruit image dataset, comprising 1,518 images, gathered in the field under the practicing conditions on 18 February 2025, 22 February 2025, in Rahu village, Pune district, Maharashtra, India, with the use of smartphone cameras. The data is sorted into four categories, namely: Anthracnose, Bacterial rot, Healthy, and Sap bleeding. The photographs were taken in different backgrounds and in different lighting conditions to represent real-life cultivation conditions. The data is expected to be useful in machine learning-based plant disease detection, classification, and analysis, and spur the creation of intelligent and sustainable agricultural systems.
Why it matches plant phenotyping methodsサポディラ果実の病害・健全状態を画像で記録したデータセット自体が中心で、植物病害の画像ベース表現型解析に利用できる。
titleA curated image dataset for sapodilla fruit (Manilkara zapota) disease and fruit quality analysis.
Wheat (Triticum aestivum L.) is a staple crop of paramount importance to global food security; however, its productivity is significantly compromised by foliar diseases. Conventional diagnostic approaches, relying on manual observation or laboratory analyses, are often labor-intensive and susceptible to inaccuracies. While recent advancements in deep learning present promising avenues for automated disease detection, persistent challenges such as limited annotated datasets, environmental heterogeneity, and model generalization continue to hinder optimal performance. This study proposes a novel hybrid deep learning model called HybridViT, which combines ConvNeXt and Vision Transformer (ViT) architectures with the Convolutional Block Attention Module (CBAM) to improve the classification of wheat leaf diseases. While ConvNeXt ensures local feature extraction and ViT provides global contextual understanding, CBAM dynamically highlights the most discriminative features. Additionally, the Contrast Limited Adaptive Histogram Equalization (CLAHE) method is employed to enhance the visibility of disease symptoms in low-contrast leaf images. Unlike conventional hybrid CNN-Transformer approaches that rely on static feature concatenation, the proposed model employs an adaptive gated fusion mechanism to dynamically balance local and global feature representations. The fused features are further refined using a lightweight CBAM module to enhance discriminative capability. Additionally, Contrast Limited Adaptive Histogram Equalization (CLAHE) is applied to improve feature visibility under varying illumination conditions. Evaluated on three different datasets obtained under both controlled and field conditions, HybridViT achieved 100% accuracy on balanced datasets and 99.10% accuracy on complex images captured in real-world conditions, surpassing existing methods. Furthermore, a 5-fold cross-validation strategy yielded an average accuracy of 99.04% ± 0.22, demonstrating the model's robustness and stability across different data splits. The results demonstrate the model's robustness against environmental noise, lighting variations, and class imbalance. This approach, which enables early and accurate disease diagnosis, supports sustainable agricultural practices, reduces pesticide use, and contributes to global food security.
Why it matches plant phenotyping methods小麦葉の病徴を画像から分類する深層学習手法を開発・検証しており、植物病害状態の取得・推定が研究の中心です。
abstractThis study proposes a novel hybrid deep learning model called HybridViT, which combines ConvNeXt and Vision Transformer (ViT) architectures with the Convolutional Block Attention Module (CBAM) to improve the classification of wheat leaf diseases.
Reproduction assets foundThe paper evaluates HybridViT on three public wheat leaf disease image datasets from Kaggle, cited in the reference list with explicit URLs. These are the paper-specific image inputs used for its disease-classification measurements. No author analysis code, trained model checkpoints, or supplementary code deposit is披露dDataset · publicAvailable: https://www.kaggle.com/datasets/olyadgetch/wheat-leaf-datasetOpen asset ↗Kaggle · olyadgetch/wheat-leaf-datasetpdf-page:51 lines:1-64Dataset · public[78] J. Jayaprakash, “Wheat Leaf Disease,” Kaggle. Accessed: May 1, 2026.
[Online]. Available:
https://www.kaggle.com/datasets/jayaprakashpondy/wheat-leaf-diseaseOpen asset ↗Kaggle · jayaprakashpondy/wheat-leaf-diseasepdf-page:51 lines:1-64Dataset · public[79] S. Kumar, “Multiple Plant Diseases Dataset,” Kaggle. Accessed: May 1, 2026.
[Online]. Available:
https://www.kaggle.com/datasets/samareshkumar/multipleplantdiseasesOpen asset ↗Kaggle · samareshkumar/multipleplantdiseasespdf-page:51 lines:1-64Code / dataset availability confirmedEurope PMC · checked 14 Sept 2026
Introduction Wheat stem rust (Puccinia graminis f. sp. tritici) remains a major threat to wheat production worldwide. Detecting the disease at the pre-symptomatic stage is important for earlier warning and more timely management. Methods We evaluated hyperspectral imaging and deep learning for pre-symptomatic wheat stem rust detection using a time-series dataset collected at 4-9 days post inoculation (DPI 4-9). Seven representative deep learning models were compared across DPI stages. A weighted cross-entropy strategy was then applied to the three strongest models, and model interpretability was examined using input gradient analysis, SHAP attribution, and vegetation-index screening. Results The weighted optimization increased overall F1-scores by 10.0%-18.4%. At the pre-symptomatic stage, the best model achieved an F1-score of 0.94 at DPI 4 and 0.99 at DPI 5, enabling detection before visible symptom development at DPI 6-7. Across the interpretability analyses, the 480-550 nm blue-green region emerged as the main source of information for pre-symptomatic detection, whereas the 750-870 nm near-infrared region contributed more general information on disease presence. Discussion These results show that hyperspectral imaging paired with deep learning can support accurate pre-symptomatic detection of wheat stem rust under controlled experimental conditions and provide useful evidence for future field-scale studies of early disease warning.
Why it matches plant phenotyping methods小麦の病害状態をハイパースペクトル画像と深層学習で検出する方法が研究の中心であり、時系列評価・モデル比較・性能改善・解釈性分析を含むため、植物フェノタイピング手法として含める。
abstractWe evaluated hyperspectral imaging and deep learning for pre-symptomatic wheat stem rust detection using a time-series dataset collected at 4-9 days post inoculation (DPI 4-9).
Reproduction assets found保存済みの本文根拠を更新済みルールで再検証し、公開資産1件を確認しました。Dataset · publicThe data can be accessed at: https://drive.google.com/drive/folders/1vpKPlPw5uK5AnKctaE2oYCuOaRFX4-yN .Open asset ↗lines:787-847Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Accurate and timely identification of plant diseases along with their severity is critical for effective crop management and minimizing agricultural losses. While recent advances in deep learning have demonstrated high performance in plant disease classification, limited attention has been given to quantifying disease severity, which is essential for informed agronomic decision-making. To address this gap, this study proposes TomatoMTL, a unified multi-task learning framework for simultaneous disease classification and severity estimation of tomato leaf diseases from a single image. The proposed architecture employs a shared ResNet50-based convolutional backbone augmented with CBAM-based feature refinement, followed by task-specific branches for disease classification and severity prediction. Furthermore, a cross-task attention mechanism is introduced to enable interaction between disease-specific and severity-related features, thereby enhancing the robustness of severity estimation. To effectively leverage partially labeled data, a masking strategy is incorporated during training. Experimental evaluation on a publicly available tomato leaf disease severity dataset demonstrates that the proposed model achieves 97.85% disease classification accuracy and 77.66% severity prediction accuracy, outperforming state-of-the-art single-task classifiers including EfficientNetV2-S, ViT-B/16, and ConvNeXt-Tiny as well as existing multi-task learning baselines including Cross-Stitch Networks and MTAN. Comprehensive ablation studies confirm the individual contributions of CBAM, MixUp and CutMix augmentation, and the cross-task attention mechanism. Statistical significance analysis across five independent runs yields p-values less than 0.001 and Cohen's d greater than 14, establishing the reliability of the reported improvements. Quantitative localization analysis reveals that the model achieves 89.4% Pointing Game accuracy, confirming that attention maps focus on biologically meaningful disease regions. The proposed framework represents a complete and effective approach for integrated plant disease analysis with strong potential for real-world precision agriculture applications.
Why it matches plant phenotyping methodsトマト葉画像から病害の重症度という植物状態を推定するマルチタスク画像解析手法を開発・評価しており、表現型取得・推定が研究の中心である。
abstractthis study proposes TomatoMTL, a unified multi-task learning framework for simultaneous disease classification and severity estimation of tomato leaf diseases from a single image.
Reproduction assets foundThe paper's Data availability and Code availability statements explicitly link a public Kaggle tomato leaf disease severity dataset (the phenotyping image data used) and the authors' public GitHub repository containing the TomatoMTL implementation scripts and documentation.Dataset · publicThe datasets analysed during the current study are publicly available in the kaggle Data repository at: https://www.kaggle.com/datasets/janiruwalisingha/tomato-leaf-disease-severity-dataset .Open asset ↗kaggle Data repository · tomato-leaf-disease-severity-datasetlines:354-386Code · publicThe implementation, along with relevant scripts and documentation, can be accessed through the following GitHub repository: https://github.com/Parnika798/tomato_leaf_disease .Open asset ↗GitHub repository · Parnika798/tomato_leaf_diseaselines:354-386Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Accurate and efficient identification of cucumber leaf diseases is a critical step in preventing losses and facilitating timely intervention in agricultural activi-ties. However, most state-of-the-art plant disease recognition models, including those employing deep learning, often fail to identify spatial dependencies among symptomatic leaf feature regions, require high computational resources, and lack robustness in their predictions. To overcome these challenges, this paper pro-poses MobileGraph, a graph-aided deep learning model that jointly reasons local texture patterns and spatial dependencies among CNN-derived cucumber leaf feature regions using MobileNetV3 as a lightweight feature extractor. Experi-ments on a publicly available cucumber leaf disease dataset containing 5 classes and 4,000 images show that the proposed model achieves 99.75% accuracy, 99.75% macro F1-score, and 99.69% MCC, outperforming several state-of-the-art models including ResNet-152, EfficientNet-B7, DenseNet-201, ConvNeXt, and VGG16, while having a significantly lower computational cost of 0.465 GFLOPs. Explainability results from Grad-CAM and LIME indicate that the model is focused on biologically important regions of plant lesions. Furthermore, a proto-type mobile application illustrates the feasibility of real-time cucumber disease diagnosis for practical agricultural monitoring. These results indicate that Mobi-leGraph provides an efficient and interpretable solution for intelligent crop health surveillance.
Why it matches plant phenotyping methodsキュウリ葉の病斑という植物状態を画像から診断する深層学習手法を開発し、複数モデルとの性能比較・検証まで行っており、病害表現型の取得・推定が研究の中心である。
abstractExplainability results from Grad-CAM and LIME indicate that the model is focused on biologically important regions of plant lesions.
Reproduction assets foundThe paper's experiments use the publicly available Cucumber Disease Recognition Dataset (4,000 images, 5 classes) hosted on Mendeley Data, which is a paper-specific public phenotype/image asset. The MobileGraph source code is only available upon request, so it does not qualify as a public asset.Dataset · publicThe dataset analysed of this study, titled ”Cucumber Disease Recognition
Dataset” is publicly available in the Mendeley Data repository at
(https://data.mendeley.com/datasets/y6d3z6f8z9/1).Open asset ↗Mendeley Data · y6d3z6f8z9pdf-page:36 lines:1-71Code / dataset availability confirmedCrossref · Europe PMC · checked 5 Sept 2026
Agricultural disease monitoring remains a critical challenge in precision farming, particularly when deploying computer vision systems on resource-constrained platforms. This study presents a rigorous comparative evaluation of four deep learning architectures—ResNet50, DenseNet121, a Binarized Neural Network (BNN), and YOLOv8-cls—for multi-class plant disease classification using the PlantVillage dataset (15 classes). Unlike prior benchmarking studies, we incorporate statistical validation through repeated stratified experiments (5 runs) and report mean ± standard deviation for accuracy, precision, recall, and F1-score. Results show that while DenseNet121 achieves high classification accuracy (99.48)% ± 0.12), it exhibits significantly higher inference latency. The BNN achieves minimal latency but suffers substantial performance degradation (88.31% ± 0.45). YOLOv8-cls provides the best trade-off, achieving 99.64% ± 0.09 accuracy with low latency (3.3 ms ± 0.2). Statistical comparison using paired t-tests confirms that YOLOv8 significantly outperforms ResNet50 p
Why it matches plant phenotyping methods植物病害を画像から分類する深層学習モデルを比較・反復実験・統計検証しており、植物の病害状態を推定する画像ベース表現型手法の技術評価が中心です。
abstractThis study presents a rigorous comparative evaluation of four deep learning architectures—ResNet50, DenseNet121, a Binarized Neural Network (BNN), and YOLOv8-cls—for multi-class plant disease classification using the PlantVillage dataset (15 classes).
Reproduction assets foundThe authors' Data Availability statement points to a public Zenodo deposit containing the dataset, source code, and models used for this paper's plant disease classification experiments. The PlantDoc Kaggle dataset and Ultralytics GitHub repositories are cited third-party resources, not paper-specific assets.Dataset · publicThe complete dataset is available at [Dataset, Source Code, and Models for: Deep Learning-based Plant Disease Detection using YOLOv8] via [https://doi.org/10.5281/zenodo.18895667].Open asset ↗zenodo · 10.5281/zenodo.18895667html-lines:284-295Code / dataset availability confirmedEurope PMC · checked 15 Sept 2026
Abstract Rice and potatoes are major crops in Bangladesh, frequently affected by major disease outbreaks that challenge food security. Inaccurate disease identification often contributes to yield losses. Recently, machine learning garnered much attention in identifying crop diseases. The present study was conducted to develop a deep learning model-based image‑analysis system that automatically identifies key diseases of Bangladeshi rice and potato, and integrates it into a web app to provide farmers with rapid, accurate diagnoses. The system employs a convolutional neural network (CNN) implemented with TensorFlow’s Sequential API, featuring ReLU-activated hidden layers and a Softmax output layer. A dataset of 4,809 images, comprising both healthy and diseased, was collected and processed through pre-processing, feature extraction, and classification. A web-based application was deployed utilizing the Python Streamlit framework. This application integrates the proposed model to predict 2 rice diseases viz. blast ( Magnaporthe oryzae ), bacterial leaf blight ( Xanthomonas campestris ), and 2 potato diseases viz. Early blight (Alternaria solani) and Late blight ( Phytophthora infestans ) from uploaded images, providing a confidence score for the predictions with approximately 92.84% for all detected diseases. The proposed model achieved a training accuracy of 0.9357, a validation accuracy of 0.8983, and a test accuracy of 0.9333. The developed web application indicates strong diagnostic performance for four major diseases, offering Bangladeshi farmers an accessible tool to make timely management decisions.
Why it matches plant phenotyping methodsイネ・ジャガイモ葉の病徴を画像から分類するCNNと実用Webアプリを開発・評価しており、植物の病害状態推定が中心的な方法論的貢献である。
abstractdevelop a deep learning model-based image‑analysis system that automatically identifies key diseases of Bangladeshi rice and potato
Reproduction assets foundThe paper's rice/potato leaf disease image dataset partially comes from Kaggle, and the data availability statement points to PlantVillage for additional image data; both are public image assets used for the paper's CNN phenotyping/disease-classification analysis. No author analysis code, trained model checkpoints, or专Dataset · publicch, M.Y.H. analyzed the data, A.A.J.,
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M.Y.H. and M.S. wrote this manuscript, M.R.I., F.M.A. and S.O.N. reviewed and edited the
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manuscript. All authors have read and agreed to the published version of the manuscript.
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Data availability statement
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Some of the datasets used in this study was obtained from Kaggle
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(https://www.kaggle.com/datasets). Additional datasets used and/or analyzed during the current
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study are available from the corresponding author upon reasonable request. More image data can
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be found at https://www.plantvillage.org/en/plant_images
459Open asset ↗Kagglepdf-raw-page:24 lines:1-57Dataset · publiche manuscript.
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Data availability statement
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Some of the datasets used in this study was obtained from Kaggle
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(https://www.kaggle.com/datasets). Additional datasets used and/or analyzed during the current
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study are available from the corresponding author upon reasonable request. More image data can
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be found at https://www.plantvillage.org/en/plant_images
459Open asset ↗PlantVillagepdf-raw-page:24 lines:1-57Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Abstract Mild stress is often difficult to distinguish from non-stress signals that may even mask the detection of stress; therefore, early diagnosis and precision grading of plant/microbial stress severity are essential for sustainable precision agriculture toward achieving optimized yields. We propose an interpretable hybrid deep learning–fuzzy decision framework combining EfficientNet B7 and Inception-ResNet-v2 with multiscale feature aggregation integrating Sparse Pyramid Pool (SPP) and Atrous Spatial Pyramid Pooling (ASPP). A Gaussian-based fuzzy inference system is incorporated to derive severity reasoning in a linguistically interpretable manner to address uncertainty and overlapping stress stages. Unlike conventional approaches evaluated only on controlled datasets, the proposed framework is validated through stringent cross-dataset generalization between the PlantVillage and PlantDoc datasets. The model demonstrates robustness under environmental disturbances and passes statistical significance tests. On the PlantVillage benchmark, the framework achieves an exact-match accuracy of $97.82\%$, a macro F1-score of $97.60\%$, and an AUC of $0.979$. When evaluated across a different domain, the performance decreases by only $4.8\%$, indicating strong generalization capability. The integration of fuzzy logic reduces adjacent-class error by $3.4\%$ and improves probability calibration with an Expected Calibration Error (ECE) of $0.021$. Grad-CAM visualizations and saliency analyses further confirm that the model focuses on biologically relevant diseased regions. These results demonstrate that combining multiscale deep feature learning with structured fuzzy reasoning enhances robustness, interpretability, and decision stability, thereby supporting human-centered agricultural monitoring systems.
Why it matches plant phenotyping methods植物のストレス重症度を画像から推定する深層学習・ファジー推論手法を開発し、異なるデータセット間で検証しているため、植物フェノタイピング手法が中心である。
abstractWe propose an interpretable hybrid deep learning–fuzzy decision framework
Reproduction assets foundThe paper's plant-phenotyping measurements rely on two public leaf-image datasets, PlantVillage and PlantDoc, both cited with explicit public URLs in the supplied text. No author analysis code, trained models, or code deposit is mentioned.Dataset · publicthe proposed model was validated
on the PlantDoc dataset1 , a publicly available real-field plant disease dataset
that reflects practical agricultural variability.Open asset ↗pdf-page:19 lines:1-53Code / dataset availability confirmedOpenAlex · arXiv · checked 5 Sept 2026
The Vines-DB dataset contains 1,218 original high-resolution RGB images of seven ornamental vine species collected under field conditions at the Utah Agricultural Experiment Station's Greenville Research Farm in Logan, Utah, USA. The dataset was generated from 168 individual vine plants that were transplanted in 2022 and photographed repeatedly across multiple months during the 2023 and 2024 growing seasons (July-October). Images were captured with an iPhone 16 Pro equipped with a 48 MP camera between 10:00 AM and 12:00 PM under daylight. Vines were grown on 1.2m x 2.4m trellises and photographed from a distance of 1m against black or white Styrofoam backdrops to improve contrast and reduce background noise. The dataset includes Akebia quinata, Campsis radicans, Hydrangea anomala petiolaris, Lonicera x heckrottii, Campsis x tagliabuana 'Madame Galen', Parthenocissus quinquefolia, and Wisteria floribunda. All original images were manually annotated in Roboflow by trained annotators to produce polygon-based instance segmentation masks for eight classes, including seven species and background. After preprocessing and data augmentation, the working dataset was expanded to 2,307 images for model development and evaluation. The augmented dataset was divided into 2,019 training images, 192 validation images, and 96 test images using stratified sampling to maintain balanced representation. Vines-DB supports the development and evaluation of deep learning models for multi-class instance segmentation in precision horticulture and urban ecology. The dataset enables applications such as automated canopy cover estimation, species identification, and scalable field phenotyping. In addition, repeated monthly imaging of the plants captures temporal variation in canopy development and plant appearance, increasing the dataset's utility for segmentation benchmarking under realistic field conditions.
Why it matches plant phenotyping methods植物のRGB画像とポリゴン注釈から成るデータセットを構築し、セグメンテーション評価およびキャノピー被覆推定などの植物フェノタイピングを支援することが中心であるため。
abstractVines-DB supports the development and evaluation of deep learning models for multi-class instance segmentation in precision horticulture and urban ecology.
Reproduction assets foundThe paper's core asset is the Vines-DB RGB image dataset with instance segmentation annotations, publicly deposited on OSF with an explicit DOI and URL matching an allowed URL.Dataset · publicData accessibility Repository name: Vines-DB
Data identification number: 10.17605/OSF.IO/YJHCK
Direct URL to data: https://osf.io/yjhck/overviewOpen asset ↗OSF · 10.17605/OSF.IO/YJHCKpdf-page:2 lines:1-49Code / dataset availability confirmedCrossref · Europe PMC · checked 5 Sept 2026
Early and accurate disease detection is important for increasing the agricultural output, decreasing the financial costs, and ensuring food security. Traditional diagnostic procedures take much time and effort, involve the necessity of having deep expertise, and are not always suitable for large scale farming disease detection. For this purpose, the current research suggests developing an explainable lightweight CNN-based model for crop disease identification based on RGB leaf images. The model utilizes several innovative architectural solutions such as depth-wise separable convolution, SE blocks, skip connections, and guided attention-based feature learning that allow enhancing the effectiveness of features extraction and decreasing computation load. Moreover, Grad-CAM is used to visualize affected areas on a map and thus increase the interpretability of the model. The suggested solution was implemented and tested on the PlantVillage dataset containing 54,305 images for 38 crop diseases out of 14 crops. The results show that the training, validation, and testing accuracies equal 97.6%, 88.3%, and 97.63%, correspondingly, along with the Macro-F1 measure of 0.867 and Micro-ROC-AUC equal to 0.99. A comparative study reveals that the presented model performs comparably well in terms of classification with lightweight structure and built-in interpretability capabilities to be applied in the mobile and edge-enabled agriculture environment. The results show that the presented approach is capable of being used as an effective and interpretable tool for diagnosing plant diseases in real-time.
Why it matches plant phenotyping methods葉画像から植物病害を推定するCNN手法の開発・評価が研究の中心であり、植物の病害状態を直接推定するため、植物フェノタイピング手法として含める。
abstractthe current research suggests developing an explainable lightweight CNN-based model for crop disease identification based on RGB leaf images.
Reproduction assets foundThe paper's plant-phenotyping input is the public PlantVillage leaf-image dataset (54,305 RGB images, 38 crop-disease classes), explicitly declared in the Data availability statement with a Kaggle URL. No author code, trained model, or checkpoint is deposited.Dataset · publicThe data set analyzed during current study are available in https://www.kaggle.com/datasets/emmarex/plantdisease.Open asset ↗Kaggle · emmarex/plantdiseaselines:366-390Code / dataset availability confirmedCrossref · checked 15 Sept 2026
Crop diseases play a significant role in food production globally; therefore, there is an urgent need to develop quick and accurate diagnostic techniques that are more effective than manual inspection methods. The proposed hybrid multimodal learning framework in this research provides a solution that integrates adaptive therapy suggestion, market price prediction, and image-based disease detection. This study also proposes a framework for pesticide recommendation and the treatment of plants. This study experiment on tomato and cotton crop leaf data for disease detection. Experimental results on a tomato crop disease detection dataset show that the proposed model shows high performance. EfficientNetB0 provides more stability and generalization capabilities in different scenarios compared to other models, such as YOLOv8, ResNet50, and a custom CNN model. The use of a knowledge-based decision support system provides sustainable pesticide recommendations based on environmental and symptom-specific parameters. Forecasting of pesticide prices through LSTM methods yields forecasts within 3.2% and 4.1% MAE, enabling improved decision-making by providing instant points of reference for potential price movements. Research uses SHAP and LIME to provide explainability to users, thus improving user buy-in through transparency. Overall, this modular system provides a data-driven decision-making model to improve the efficiency of managing crops.
Why it matches plant phenotyping methods植物葉画像から病害状態を推定する画像ベース手法を、複数モデルで比較評価しており、植物病害フェノタイピングがシステムの主要構成要素です。価格予測や農薬推薦も含みますが、病害検出の技術評価が明示されています。
abstractThe proposed hybrid multimodal learning framework in this research provides a solution that integrates adaptive therapy suggestion, market price prediction, and image-based disease detection.
Reproduction assets foundThe paper's disease-detection experiments use publicly available cotton and tomato leaf image datasets (Kaggle, IEEE DataPort, Roboflow), all cited with explicit public URLs in the references. No author analysis code or trained model checkpoints are stated as publicly available; the supplementary material is referencedDataset · publiccholar
View reference in article
19
Muppala C. Guruviah V. ( 2020 ). Machine vision detection of pests, diseases, and weeds: a review . J. Phytol. 12 , 9 – 19 . doi: 10.25081/jp.2020.v12.6145
CrossRef
Google Scholar
View reference in article
20
National College of Ireland ( 2025 ). “Cotton Disease Dataset.” Available online at: https://www.kaggle.com/datasets/janmejaybhoi/cotton-disease-dataset (Accessed May 19, 2025).
Google Scholar
View reference in article
21
Naveed Gul and Kaggle ( 2026 ). Tomato Leaf Disease . Kaggle. Available online at: https://www.kaggle.com/datasets/naveedgull/tomato-leaf-disease (Accessed March 29, 2026).
Google Scholar
View reference in article
22
Ngugi H. N. EzugOpen asset ↗Kagglelines:554-633Dataset · publicreference in article
20
National College of Ireland ( 2025 ). “Cotton Disease Dataset.” Available online at: https://www.kaggle.com/datasets/janmejaybhoi/cotton-disease-dataset (Accessed May 19, 2025).
Google Scholar
View reference in article
21
Naveed Gul and Kaggle ( 2026 ). Tomato Leaf Disease . Kaggle. Available online at: https://www.kaggle.com/datasets/naveedgull/tomato-leaf-disease (Accessed March 29, 2026).
Google Scholar
View reference in article
22
Ngugi H. N. Ezugwu A. E. Akinyelu A. A. Abualigah L. ( 2024 ). Revolutionizing crop disease detection with computational deep learning: a comprehensive review . Environ. Monit. Assess. 196 : 302 . doi: 10.1007/s10661-024-12454-z
Pubmed AOpen asset ↗Kagglelines:554-633Dataset · publicComputer Vision and Pattern Recognition (CVPR) ( Las Vegas, NV : IEEE ), 779 – 788 . doi: 10.1109/CVPR.2016.91
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Roboflow ( 2026a ). A Comprehensive Dataset of Cotton Plant Diseases for National Disease Identification and Treatment Guidance | IEEE DataPort. Available online at: https://ieee-dataport.org/documents/comprehensive-dataset-cotton-plant-diseases-national-disease-identification-and-treatment (Accessed March 29, 2026).
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Roboflow ( 2026b ). Cotton Plant Disease Prediction Object Detection Model by National College of Ireland . Available online at: https://universe.roboflow.com/national-colleOpen asset ↗IEEE DataPortlines:554-633Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
In-season estimation of wheat grain yield potential is critical for crop management and advancing breeding efforts. Spike and spikelet counts serve as key indicators directly linked to yield potential, yet their assessment still relies on manual counting which is both labor-intensive and error-prone. High-resolution digital (RGB) imagery combined with deep learning-based object detection methods has substantially advanced automatic wheat spike detection and counting. However, precise spikelet-level phenotyping remains largely underexplored. This study evaluates two recent YOLO variants, YOLOv11 and YOLOv12, for wheat spike and spikelet detection and counting using oriented bounding boxes (OBB), and introduces a new large-scale benchmark dataset comprising 48,521 spike and 60,404 spikelet instances with OBB annotations. For spike detection, the pre-trained YOLOv11 achieved superior accuracy (mAP@0.5 = 95.8%, Pearson r = 0.993) with shorter training and inference times compared to YOLOv12. For spikelet detection, the non-pretrained YOLOv11 demonstrated higher accuracy (mAP@0.5 = 99.0%), while counting performance was comparable across models. These results establish OBB-based YOLO detection as a robust and scalable approach for AI-driven wheat phenotyping.
Why it matches plant phenotyping methods小麦の穂・小穂という収量関連形質の画像ベース検出・計数手法を比較評価し、大規模ベンチマークデータセットも構築しているため、フェノタイピング手法が中心である。
abstractThis study evaluates two recent YOLO variants, YOLOv11 and YOLOv12, for wheat spike and spikelet detection and counting using oriented bounding boxes (OBB), and introduces a new large-scale benchmark dataset comprising 48,521 spike and 60,404 spikelet instances with OBB annotations.
Reproduction assets foundThe paper openly states its supporting data (spike/spikelet imagery with OBB annotations) is available on Zenodo, and the underlying models are deployed on the authors' public WheatAI cloud platform.Dataset · publicData availability
The data supporting the findings of this study are openly available at: https://doi.org/10.5281/zenodo.20215489 .Open asset ↗zenodo · 10.5281/zenodo.20215489lines:219-266Code / dataset availability confirmedEurope PMC · checked 14 Sept 2026
Accurate assessment of leaf chlorophyll is essential for understanding plant physiological responses to environmental variation. While solvent extraction provides precise chlorophyll measurements, it is destructive and temporally limited, whereas portable optical meters such as the CCM-300 enable rapid, non-destructive measurement of the chlorophyll fluorescence ratio (CFR) but require species- and season-specific calibration. This study evaluates the performance of CCM-300 measurements and reconstructs seasonal chlorophyll dynamics in field maple (Acer campestre) across two contrasting summers in the United Kingdom. Paired CFR and acetone-extracted chlorophyll data collected in 2023 were used to develop calibration models. RF regression achieved the highest predictive performance within the calibration dataset, although substantial uncertainty remained at the leaf level; a simple linear model was therefore adopted for cross-year projection due to its stability under extrapolation. Applying this calibration to daily 2022 CFR measurements generated a continuous "virtual acetone" trajectory, enabling qualitative comparison with weekly destructive extractions in 2023. Both years exhibited mid-season chlorophyll plateaus followed by late-summer declines; however, senescence, defined as the initiation of sustained post-peak decline, occurred earlier during the warmer and drier 2022 season. Mixed-effects modelling identified positive effects of temperature and wind speed on CFR in 2022, while generalised additive modelling of the 2023 dataset revealed a non-linear seasonal decline under comparatively mild conditions. Because cross-year projections rely on a low-fit linear calibration, interannual differences are interpreted primarily in terms of relative seasonal trajectory shape and timing rather than absolute chlorophyll magnitude.
Why it matches plant phenotyping methodsCCM-300による葉クロロフィル測定を破壊的測定と比較し、校正モデルの開発・性能評価と季節軌跡の再構築を行っており、植物表現型取得法が研究の中心である。
abstractThis study evaluates the performance of CCM-300 measurements and reconstructs seasonal chlorophyll dynamics in field maple (Acer campestre) across two contrasting summers in the United Kingdom.
Reproduction assets found保存済みの本文根拠を更新済みルールで再検証し、公開資産1件を確認しました。Dataset · publicData Availability: Data used in the study can be accessed via https://zenodo.org/records/17475985.Open asset ↗zenodo · 17475985pdf-page:11 lines:1-44Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Early and accurate detection of apple leaf diseases is critical for sustainable agriculture, yet manual diagnosis remains time-consuming and error-prone. This study introduces a novel deep learning framework centered on a custom ContinuousLayer, a spatially adaptive convolutional layer designed to overcome the limitations of standard CNNs. This architecture automates the classification of apple leaf diseases Black rot, rust, scab, and healthy leaves with high precision. The model addresses dataset imbalance through strategic resampling, achieving uniform class distribution. The ContinuousLayer introduces spatial feature modulation using trainable Gaussian basis functions, enhancing feature extraction while penalising kernel irregularities through a hybrid composite loss function. Trained on a dataset of 3,164 images balanced via bicubic up-sampling, and evaluated on a held-out test set of 10% of the data, the model attains a 98.63% test accuracy, with F1-scores ranging from 0.98 to 1.00 across classes. Visual analysis of the confusion matrix reveals minimal misclassification, predominantly between rust and scab. Comparative evaluation against baseline architectures demonstrates the efficacy of the ContinuousLayer in capturing disease-specific spatial patterns. These results underscore the potential of integrating mathematically inspired layers into CNNs for plant pathology applications, offering a highly accurate tool for precision agriculture in controlled environments.
Why it matches plant phenotyping methodsリンゴ葉の病徴を画像から分類する新規深層学習層と解析手法を開発・比較評価しており、植物病害状態の表現型抽出が中心である。
abstractThis study introduces a novel deep learning framework centered on a custom ContinuousLayer, a spatially adaptive convolutional layer designed to overcome the limitations of standard CNNs.
Reproduction assets foundThe paper's apple leaf disease image dataset (3,164 images) is explicitly stated to be publicly available on Kaggle, matching an allowed URL. No author code or model checkpoints are reported as available.Dataset · publicThe datasets analysed during the current study is publicly available in the Kaggle repository at https://www.kaggle.com/datasets/mhantor/apple-leaf-diseases.Open asset ↗Kaggle · mhantor/apple-leaf-diseaseslines:595-613Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Field / plotClassificationDisease symptoms / severity
This research discusses the incorporation of IoT with blockchain technique to enhance the efficiency of smart farming systems, particularly focusing on plant disease classification, pest detection, and smart irrigation. The study aims to develop a secure and effective IoT-based smart farming framework using the Ethereum blockchain to store and transmit data, and a Hybrid Convolution Adaptive Recurrent MobileNet (HC-ARMNet) model for predictive analytics, optimized by the Improved Secretary Bird Optimization (ISBO) algorithm. The research employs IoT sensors to acquire real-time data, which is then stored in the Ethereum blockchain to ensure security. The HC-ARMNet model, combining 1D/2D convolutions with recurrent connections, processes this data for pest detection and irrigation management. The ISBO algorithm is leveraged to fine-tune the technique's parameters. Datasets used: The proposed system utilizes three standard datasets for evaluation. The PlantifyDr Dataset is used for classifying plant disease, and the Pest Detection Dataset is used for recognizing pests. Also, for the smart irrigation process, the significant field images are collected manually. The accuracy, precision, and FNR rates of the ISBO-HC-ARMNet-aided plant disease classification are 94.16%, 94.2% and 5.87%. At the same time, the ISBO-HC-ARMNet-based pest detection process's accuracy, sensitivity, and specificity are 93.78%, 93.79% and 93.76%, respectively. In addition, the ISBO-HC-ARMNet-based smart irrigation task's MSE is 3.21, SMAPE is 0.03, and MASE is 30.23. Thus, the designed system showcases promising performance over classical approaches in terms of accuracy and error rates for plant disease classification, pest detection, and smart irrigation. The research concludes that the IoT-aided smart farming framework with blockchain and the HC-ARMNet model provides a robust solution for secure and efficient agricultural management. The system's predictive capabilities provide accurate and timely data analysis, facilitating to the improvement of precision agriculture. Future work will focus on improving the system with advanced feature extraction strategies to reduce processing time.
Why it matches plant phenotyping methods植物画像に基づく病害分類モデルの開発・評価が研究の中心的技術貢献であり、感染植物の状態を直接推定しているため含める。
abstractThe study aims to develop a secure and effective IoT-based smart farming framework using the Ethereum blockchain to store and transmit data, and a Hybrid Convolution Adaptive Recurrent MobileNet (HC-ARMNet) model for predictive analytics
Reproduction assets foundThe paper explicitly states that implementation code, trained models, and experimental configurations are publicly available in an authors' GitHub repository, and that the PlantifyDr plant disease dataset and IP02 pest detection dataset used in the study are available on Kaggle. These are paper-specific, public, and可直接Code · publicThe implementation code, trained models, and experimental configurations used are publicly available in: “ https://github.com/sumanthvmani/-Pest-Detection-and-Smart-Irrigation ”. The repository contains all necessary instructions and dependencies required to reproduce the reported experimental results.Open asset ↗https://github.com/sumanthvmani/-Pest-Detection-and-Smart-Irrigationlines:253-302Dataset · publicThe datasets generated and/or analyzed during the current study are available in the [PlantifyDr Dataset and Pest detection dataset] repository“ https://www.kaggle.com/datasets/lavaman151/plantifydr-dataset ”Open asset ↗https://www.kaggle.com/datasets/lavaman151/plantifydr-datasetlines:400-436Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Abstract Aegle marmelos (bael) is a medicinally important tropical crop that remains severely underrepresented in computational plant pathology research. This study proposes AMnet, a deep learning framework integrating an InceptionV3 backbone with a fixed graph convolutional network to capture both within-region disease texture and between-region spatial propagation patterns for automated four-class classification of Aegle marmelos leaf diseases: Cercospora leaf, healthy leaf, leaf curl, and leaf spot. The graph module constructs a 25-node spatial graph directly from CNN feature maps, enabling end-to-end training without external preprocessing. Compared against MobileNetV2, InceptionV3, VGG19, and DenseNet201, AMnet achieved the best overall performance with 98.83% accuracy, 98.84% F1-score, 99.95% PR-AUC, and 98.45% MCC, alongside the fastest inference time of 1.83 ms. Robustness was confirmed through bootstrap confidence interval estimation and four-fold cross-validation. PCA-based clustering analysis with silhouette scoring and Davies–Bouldin indexing demonstrated clear class separability in the learned embeddings. Grad-CAM and LIME visualizations confirmed that predictions were grounded in biologically meaningful leaf regions rather than background artifacts. A Gradio-based prototype further demonstrated practical deployment potential. Although broader field validation remains necessary, AMnet provides an accurate, interpretable, and reproducible framework for diagnosing Aegle marmelos leaf disease.
Why it matches plant phenotyping methods葉画像から植物の病害状態を分類する説明可能な深層学習手法を開発・比較・検証しており、植物表現型（病徴・病害状態）の取得・推定が中心的です。
abstractThis study proposes AMnet, a deep learning framework integrating an InceptionV3 backbone with a fixed graph convolutional network to capture both within-region disease texture and between-region spatial propagation patterns for automated four-class classification of Aegle marmelos leaf diseases: Cercospora leaf, healthy leaf, leaf curl, and leaf spot.
Reproduction assets foundThe paper analyses a publicly available Aegle marmelos leaf disease image dataset deposited on Mendeley Data, explicitly linked in the Data availability statement and reference [36]. No author analysis code or trained model checkpoint is reported as publicly available.Dataset · publicThe dataset analysed of this study is publicly available in the Mendeley Data repository at
(https://data.mendeley.com/datasets/54r883j5zr/1).Open asset ↗Mendeley Datapdf-page:29 lines:1-43Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Introduction Nutrient deficiencies in coffee plants significantly impact bean quality and yield, making timely detection crucial for successful cultivation. Current assessment methods rely on manual inspection, which is labor-intensive and time-consuming, posing challenges for large-scale field management. This approach often results in inconsistent evaluations and delayed interventions. Methods This study presents CoNutriNet, an automated deep learning architecture that integrates DenseNet121 with a novel Graph-Enhanced Attention Feature Network (GEAFNet) for classifying nutrient deficiencies in coffee leaves. DenseNet121 provides deep hierarchical and regional feature representation, while GEAFNet captures local, fine-grained spatial features through Inception, Ghost, and Efficient Channel Attention (ECA) modules. Furthermore, a Graph Convolutional Network (GCN) is included to model spatial dependencies and structural variations between leaf regions. Feature representations from both pathways are concatenated and refined using a Coordinate Attention (CA) module to enhance discriminative capability. Results Evaluation on the CoLeaf dataset demonstrates that CoNutriNet achieves an accuracy of 94.5%. The integration of lightweight attention mechanisms, dense connectivity, and graph-based modeling improves both performance and computational efficiency. Conclusion These results indicate that CoNutriNet achieves and efficient performance in nutrient deficiency detection in coffee crops, highlighting its potential for deployment in agricultural environments to support precision farming and optimize yield.
Why it matches plant phenotyping methodsコーヒー葉の栄養欠乏という植物状態を画像から分類する深層学習手法を開発し、データセットで性能評価しており、表現型取得・推定が研究の中心である。
abstractThis study presents CoNutriNet, an automated deep learning architecture that integrates DenseNet121 with a novel Graph-Enhanced Attention Feature Network (GEAFNet) for classifying nutrient deficiencies in coffee leaves.
Reproduction assets foundThe paper's phenotyping analysis (coffee nutrient deficiency classification) is performed on publicly available leaf image datasets. The data availability statement links a Mendeley Data repository containing the analyzed data, which is an allowed URL. No author analysis code or trained model checkpoints are explicitlyDataset · publicPublicly available datasets were analyzed in this study. This data can be found here: https://data.mendeley.com/datasets/brfgw46wzb/1Open asset ↗brfgw46wzb/1lines:866-910Code / dataset availability confirmedOpenAlex · Europe PMC · checked 15 Sept 2026
The number of petals in an inflorescence is an important phenotypic indicator for quality evaluation and cultivar identification of cut chrysanthemums ( Chrysanthemum morifolium Ramat.). Current manual measurement methods are time-consuming, error-prone, and poorly suited to the complex geometry of chrysanthemum flowers, which limits their utility for large-scale phenotyping and breeding programs. Although image-based phenotyping has advanced rapidly, automated and reliable methods for petal counting in densely packed or partially obscured inflorescences remain underdeveloped. Here, we developed a deep learning-based framework for automatic extraction of petal number in cut chrysanthemums. Images from multiple varieties were collected to construct a representative dataset, and petal density maps were generated through manual annotation with Gaussian kernel function. We employed a Congested Scene Recognition Network (CSRNet) enhanced with a Squeeze-and-Excitation (SE) channel attention mechanism (SE-CSRNet) for petal density estimation. Spearman correlation analysis revealed strong agreement between visible and actual petal counts (Spearman’s r=0.953, p<0.0001). Compared with the original CSRNet, SE-CSRNet reduced mean absolute error (MAE) and root mean squared error (RMSE) by 5.2% and 7.4%, respectively. Further optimization using regression fitting revealed that random forest achieved the best performance (MAE = 4.24, RMSE = 5.06, R 2 = 0.967), indicating reliable stability and satisfactory generalization under the conditions evaluated in this work. Application of the optimized model to two cut chrysanthemum varieties confirmed its practicality by successfully detecting reductions in petal number under high-temperature stress. Our results demonstrate that integrating dataset construction, deep learning–based density estimation, and machine learning optimization enables efficient and accurate prediction of petal number in cut chrysanthemums.
Why it matches plant phenotyping methods花弁数という植物形質を画像から自動抽出する深層学習手法を開発し、データセット構築、性能比較、検証、実用適用まで行っており、表現型取得手法が研究の中心である。
abstractHere, we developed a deep learning-based framework for automatic extraction of petal number in cut chrysanthemums.
Reproduction assets foundThe article states that some data (the chrysanthemum petal-counting dataset and related materials) will be available at the authors' public GitHub repository (qwsdfgz/petalscount), with other data available from the corresponding author upon reasonable request. The repository URL is explicitly provided by the authors,但Dataset · publicnctional components of bud-leaves and flowers in edible chrysanthemum (Chrysanthemum morifolium Ramat)
Horticulturae 11 5 2025 448
10.3390/horticulturae11050448
Appendix A
Supplementary data
The following is the Supplementary data to this article.
Multimedia component 1
Data availability
Some data will be available at this URL: https://github.com/qwsdfgz/petalscount . Other data are openly available from the corresponding author upon reasonable request.
Appendix A
Supplementary data to this article can be found online at https://doi.org/10.1016/j.plaphe.2026.100238 .Open asset ↗qwsdfgz/petalscountlines:602-636Code / dataset availability confirmedEurope PMC · checked 14 Sept 2026
Common beanLeafClassificationStress / disease detectionDisease symptoms / severity
Introduction Accurate disease diagnosis is crucial for enhancing agricultural productivity and reducing postharvest losses, directly impacting food quality and safety. Traditional detection methods often rely on extensive feature modeling and perform poorly in complex field environments. Methods This study proposes a deep learning model called ZDAM, based on an improved ZFNet integrated with a dual attention mechanism. The classical ZFNet is first optimized to improve feature extraction efficiency. A combined channel and spatial attention mechanism is then incorporated to refine feature representation for disease identification in key crops. Finally, a residual module is added to boost accuracy. Results Evaluated on a dataset of 11,903 bean leaf images covering healthy leaves and four disease types, including leaf mould, rust, mosaic, and white spot, the model achieves an average recognition accuracy of 99.02%, outperforming MobileMamba, Vision Transformer, and Chest- OMD. Discussion This approach offers a scalable solution for automated disease monitoring, supporting postharvest quality preservation and sustainable crop production.
Why it matches plant phenotyping methods豆葉の病害状態を画像から推定する深層学習モデルを開発し、複数モデルとの性能比較も行っており、植物フェノタイピング手法が研究の中心である。
abstractThis study proposes a deep learning model called ZDAM, based on an improved ZFNet integrated with a dual attention mechanism.
Reproduction assets found保存済みの本文根拠を更新済みルールで再検証し、公開資産1件を確認しました。Dataset · publictomato leaf disease data from the open-source dataset New Plant Disease Dataset ( https://www.kaggle.com/vipoooool/new-plant-diseases-dataset ) were also utilized. Both datasets include healthy samples and four disease categories: rust disease, mosaic disease, leaf mold disease, and white spot disease. ( https://pan.baidu.com/s/197Lyn2TGdIjLCE2gylsiHA?pwd=krpw )Open asset ↗pan.baidu.comlines:405-484Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Traditional apple maturity assessment methods are destructive and time- and labour-intensive, yielding only population-level approximations. Hyperspectral imaging provides a non-destructive alternative to assess individual fruit, but progress has been constrained by the lack of large, diverse datasets that support robust model generalisation. This study presents a multi-cultivar, multi-season, multi-country hyperspectral apple dataset to enable generalisable prediction of soluble solids content (Brix) and firmness. Using this dataset, we adopt an iterative modelling framework to evaluate deep learning architectures, image resolutions, cultivar encoding, seasonal effects, and feature-specific models. Wavelength and spatial region importance were also analysed. The best predictive performance was achieved using Vision Transformer (ViT) models trained on edge-cropped 40 × 40 pixel images with explicit cultivar encoding, with Brix and firmness modelled independently. Although seasonal specificity was observed, models trained across all three seasons achieved the strongest overall performance. A 50% reduction in spectral wavebands did not compromise prediction accuracy. Key wavelength ranges contributing to Brix and firmness prediction were identified across the visible-near-infrared spectrum. Spatial regions were unimportant for Brix prediction but showed relevance for firmness. The optimised ViT model achieved firmness prediction performance comparable to previous studies (RMSE = 0.76 kgf, R[Formula: see text] = 0.63), while Brix prediction accuracy was lower (RMSE = 0.91 [Formula: see text]Brix, R[Formula: see text] = 0.75), likely reflecting increased biological and environmental variability captured in the dataset. Overall, this work demonstrates that hyperspectral imaging combined with deep learning and large, diverse datasets enables robust, non-destructive prediction of apple quality attributes across production conditions.
Why it matches plant phenotyping methodsリンゴ果実の硬度とBrixという植物器官形質を、ハイパースペクトル画像と深層学習で非破壊推定するデータセット・モデル・汎化性能評価が研究の中心である。
abstractThis study presents a multi-cultivar, multi-season, multi-country hyperspectral apple dataset to enable generalisable prediction of soluble solids content (Brix) and firmness.
Reproduction assets foundThe paper explicitly states that the hyperspectral apple dataset (5756 apples, firmness/Brix/starch measurements) is deposited in the University of Essex research data repository and that the data cleaning, model training, and analysis code is on GitHub, both with public URLs.Dataset · publicThe datasets generated during and analysed during the current study are available in the University of Essex repository ( https://researchdata.essex.ac.uk/228/ )Open asset ↗researchdata.essex.ac.uk · 228lines:192-220Code · publicthe code used for data cleaning, model training and analysis are available on GitHub: ( https://github.com/EIS-Ressearch-Lab/Apple_maturity_hyperspectral_imaging.git )Open asset ↗github.com/EIS-Ressearch-Lab/Apple_maturity_hyperspectral_imaginglines:192-220Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Introduction Rubber tree powdery mildew is a major foliar disease that threatens the yield and quality of natural rubber. Its lesions are typically small, irregular, and embedded in complex backgrounds, making accurate automated detection difficult. Methods To address this challenge, we propose RubberFormer, an end-to-end detection framework based on a refined Transformer architecture for detecting small powdery mildew lesions in complex scenarios. RubberFormer adopts MobileNetV4 as a lightweight backbone, introduces the Hierarchical Attention with Local-global Optimization (HALO) module for multiscale local-global feature fusion, incorporates the Unified Cross-Attention Network (UCAN) to enhance multidimensional feature interaction, and applies Normalized Wasserstein Distance (NWD) Loss to improve small-object localization. Results Extensive experiments were conducted on PM-Dataset-Plus, which contains 9,765 images, and PD-40, a large-scale plant disease dataset containing 80,369 images across 40 disease categories and 8 crops. RubberFormer achieved superior detection accuracy and generalization performance compared with existing methods, while maintaining computational efficiency suitable for practical agricultural monitoring. Discussion These results demonstrate that RubberFormer is effective for detecting small and irregular rubber tree powdery mildew lesions under complex conditions. The framework has practical value for rubber tree disease monitoring and provides a transferable design strategy for agricultural vision tasks involving small objects and complex backgrounds.
Why it matches plant phenotyping methodsゴム樹の病斑という植物の病害状態を画像から検出するTransformer手法を開発し、複数データセットで性能検証しており、植物表現型取得が中心である。
abstractwe propose RubberFormer, an end-to-end detection framework based on a refined Transformer architecture for detecting small powdery mildew lesions in complex scenarios.
Reproduction assets foundThe paper's authors publicly release both plant disease image datasets used in this study: PM-Dataset-Plus (9,765 rubber tree powdery mildew images) and PD-40 (80,369 images, 40 categories, 8 crops), each with an explicit availability statement and GitHub URL matching the allowed URLs. No analysis code or trained modelDataset · publicPM-Dataset-Plus is available at https://github.com/wfcyliyuheng-dev/PM-Dataset-PlusOpen asset ↗wfcyliyuheng-dev/PM-Dataset-Pluslines:1199-1255Dataset · publicPD-40 is available at https://github.com/wfcyliyuheng-dev/PD40-DatasetOpen asset ↗wfcyliyuheng-dev/PD40-Datasetlines:1199-1255Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Clubroot disease, caused by Plasmodiophora brassicae , is one of the major constraints in rapeseed production. Breeding disease-resistant cultivars is the best way to control this devastating disease. However, breeding reliable resistant germplasm and genes is limited. Inactivation of susceptible genes has been shown to be a new and effective strategy for developing resistant crops. Therefore, we aimed to screen key candidate susceptible genes in this study. Firstly, we established a stable, high-throughput visualization method for identifying gall formation at the early stage of P.brassicae infection. At 14 days post-inoculation (dpi), the earliest time point with a clear record of scorable root swelling, remarkable variations in the speed of gall formation were observed among 85 genotypes. Secondly, genome-wide association studies (GWAS) were performed to identify genes involved in gall development. Three and two consecutive significant peaks were detected at 14 and 21 dpi, respectively. Thirdly, comparative transcriptomic analysis was conducted between 2AF195 and 2AF058 at 7 and 14 dpi; these two materials exhibit contrasting speeds of gall development. Gene clustering analysis revealed two opposite expression patterns at 14 dpi. One pattern comprised 1,383 genes downregulated in 2AF195 but upregulated in 2AF058, which were significantly enriched in 10 KEGG pathways, including Environmental Information Processing and Plant-pathogen interaction, and involved core repressors JAZ8/10 in the jasmonic acid (JA) signaling pathway, as well as nucleotide-binding site (NBS) protein-encoding genes. The opposite pattern consisted of 79 genes upregulated in 2AF195 but downregulated in 2AF058, which were enriched in an additional 10 KEGG pathways, predominantly related to Carbohydrate Metabolism and the Ubiquitin System. These genes were functionally annotated mainly as pectin methylesterases, xyloglucan endotransglucosylase/hydrolases (XTHs), and lignin biosynthesis-related enzymes. These findings demonstrated that distinct regulatory networks exist in different susceptible rapeseed genotypes. Finally, through the combined analysis of haplotype and transcriptome data, we co-localized and identified the candidate gene BnaC08g46100D , a nodulin-related gene belonging to the MtN21 transporter family. These results provide a theoretical basis for developing novel disease-resistant materials by editing the key susceptibility genes involved in root gall formation. The candidate genes identified in this study are the most promising targets for this purpose.
Why it matches plant phenotyping methods根こぶ形成を高スループットに可視化・判定する方法の確立が明示され、感染植物の病徴を測定する手法として研究の主要な技術要素になっている。
abstractwe established a stable, high-throughput visualization method for identifying gall formation at the early stage of P.brassicae infection.
Reproduction assets found本文中に内容が明示された植物フェノタイピング関連の補足表と、その公開リンクを確認しました。Supplement · publicSupplementary Table 2
Disease incidence data of 85 rapeseed accessions at various time points following inoculation with the Xinmin strain.Open asset ↗lines:502-594Code / dataset availability confirmedOpenAlex · Europe PMC · checked 15 Sept 2026
Plant phenotyping based on unmanned aerial vehicles still faces challenges regarding the direct correlation between spectral information with field-collected variables, due to the influence of environmental factors and the considerable variation among maize phenological stages. Therefore, the objectives of this research were: I) to evaluate the interaction of nitrogen doses and evaluation environments (phenological stages and growing seasons) and variance components for field variables and vegetation indices; II) to identify the most suitable indices according to the evaluation environments; and III) to predict field variables based on relevant vegetation indices identified through the proposed methodology. The study was conducted using a randomized complete block design with four repetitions, in which treatments consisted of six nitrogen (N) topdressing doses (0, 50, 100, 200, 300, and 400 kg ha−1) during the 2022/2023 and 2023/2024 growing seasons. Evaluations of agronomic variables and image acquisition were performed in five distinct phenological stages throughout the maize crop cycle. The data were analyzed using deviance analysis and variance components, principal component analysis (PCA), and multivariate linear modeling for the prediction of field variables. Our results demonstrated that all indices were affected by the interaction between N doses and evaluation environments (phenological stages and growing seasons). Additionally, the most reliable were EXGRaw, TGI, GNDVI, NDRE, CIRE, GVI, CVI, BNDVI, PanNDVI, SRNIRRe, SFDVI, RGBindex, NDVI, SAVI, MSAVI, and OSAVI, which showed clustering patterns according to growing season condition and phenological stage. Finally, the variables predicted using the proposed methodology achieved coefficients of determination above 0.80, except for shoot biomass and 100-grain weight. Therefore, it can be concluded that vegetation indices are influenced by the evaluated environment; however, the proposed framework based on the deduction of fixed and random effects enables the prediction of field variables with high accuracy using relatively simple models.
Why it matches plant phenotyping methodsUAVマルチスペクトル画像から植生指数を選定し、農業形質を予測する方法論の開発・評価が研究の中心であり、植物形質の取得・推定に直接関与している。
titleMethodology for Selecting Stable UAV-Based Vegetation Indices for Prediction of Agronomic Variables in Maize Using a Multispectral Sensor.
Reproduction assets foundThe paper's supplementary file contains the REML-BLUP adjusted values for all vegetation indices and field variables, which directly reproduce the paper's phenotyping measurements and underpin its computational analysis. The raw UAV imagery and field data are only available on request, and the EstimateBreed R package (Dataset · publicdual author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to people or property resulting from any ideas, methods, instructions or products referred to in the content.
Supplementary Materials
The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/plants15121782/s1 , Table_Supplementary_1. This table contains all vegetation indices and field variables with values adjusted using the RELM-BLUP methodology.
Author Contributions
C.d.S.L.: Conceptualization, methodology, validation, visualization, writing—original draft, writing—review and editing. A.J.T.S.: Data collection and iOpen asset ↗lines:76-146Code / dataset availability confirmedEurope PMC · checked 15 Sept 2026
Single-molecule fluorescence in situ hybridization (smFISH) has emerged as a powerful tool for studying gene expression dynamics with unparalleled precision and spatial resolution in a variety of biological systems. Recent advancements have expanded its application to encompass plant studies, yet there remains a need for a simple and robust smFISH method adapted to plant tissue sections. Here, we present an optimized smFISH protocol, termed cryo-smFISH, for visualizing and quantifying single mRNA molecules in plant tissue cryosections. This method exhibits remarkable sensitivity, enabling the detection of low-expression transcripts, including long non-coding RNAs. By integrating a deep learning-based algorithm into our image analysis pipeline, our method enables precise assignment of RNA abundance in nuclear and cytoplasmic compartments. The method also enables robust integration with immunofluorescence, as cryosectioning enhances antibody penetration. This allows for the sequential visualization and quantification of both RNAs and endogenous proteins within the same cells. Finally, this study demonstrates the use of smFISH to validate single-cell RNA sequencing (scRNA-seq) expression patterns in plant tissues. By extending smFISH to plant cryosections, plant scientists will be able to exploit the full potential of quantitative transcript analysis at cellular and subcellular resolution.
Why it matches plant phenotyping methods植物組織向けcryo-smFISHプロトコルと画像解析法を開発し、RNA量を細胞・細胞内区画で定量する手法が研究の中心である。分子測定ではあるが、植物組織の状態を定量する方法として技術的貢献が明確。
abstractHere, we present an optimized smFISH protocol, termed cryo-smFISH, for visualizing and quantifying single mRNA molecules in plant tissue cryosections.
Reproduction assets foundThe authors deposit all data underlying graphs/heatmaps plus custom R/Python scripts and Cellpose segmentation models in a public GitHub repository specific to this paper. Third-party tools (FISH-quant, DeconvolutionLab2, Stellaris Designer) are generic and excluded.Code · publicAll custom code, including R/Python scripts and Cellpose segmentation models, is available at https://github.com/xuezhang911/zhang_et_al_smFISH_cyrosections .
Funding
This work was supported by Vetenskapsrådet (2023-03895), the Novo Nordisk Foundation (NFF24OC0093553 and NNF25OC0100533), and the Carl Tryggers Stiftelse (CTS 18- 325).
Acknowledgments
We thank A. Menkis for initial technical support with cryostat operation and Alexandre Berr for scientific feedback. We also thank memOpen asset ↗zhang_et_al_smFISH_cyrosectionslines:122-152Dataset · publictic ( Bolger et al., 2014 ). The raw gene-count matrix was obtained using the pseudoalignment software Kallisto ( Bray et al., 2016 ). RNA-seq reads were normalized as transcripts per million (TPM).
Data and code availability
The supplemental information and all data underlying the graphs and heatmaps presented are available at https://github.com/xuezhang911/zhang_et_al_smFISH_cyrosections .Open asset ↗zhang_et_al_smFISH_cyrosectionslines:106-121Code · publicech.com/stellaris-designer . For mRNA detection, the coding sequence of the target gene was entered into the program, which automatically generated a set of probes complementary to the target mRNA.
The sequences of the probes were then subjected to quality control using an automated local blast R script, available on GitHub at: https://github.com/xuezhang911/zhang_et_al_smFISH_cyrosections/tree/main/smFISHprobes . The smFISH probes used in this study and their respective fluorophores are shown in Supplemental Table 3 . The probes were diluted in Tris-EDTA buffer to a final stock concentration of 25 μM.
Cryo-smFISH
Sample preparationOpen asset ↗zhang_et_al_smFISH_cyrosectionslines:75-85Code / dataset availability confirmedCrossref · checked 15 Sept 2026
Published8 Jun 2026International Journal of Engineering and ManufacturingCited by 0 · OpenAlex ↗
Plant disease detection is vital for agricultural sustainability and food security. While Convolutional Neural Networks (CNNs) and Vision Transformers (ViTs) have achieved high accuracy in this domain, CNNs often require millions of parameters and substantial computation. ViTs suffer from the quadratic time and space complexity of self-attention (SA), limiting their use on resource-constrained devices. Although SA is capable of modelling long-range dependencies when symptoms are dispersed, many plant diseases exhibit small, localized lesions or texture changes; therefore, Neighborhood Attention (NA) offers a more efficient and targeted alternative by focusing on nearby regions rather than the entire image. This work proposes a custom Localized NA block implemented in TensorFlow/Keras that operates directly on CNN feature maps, bypassing patch embedding and transformer modules. A lightweight CNN is then developed by combining depth-wise separable convolutions with the proposed localized NA block. In addition, a 100-category plant disease dataset covering 16 crops is presented. The dataset is curated, class-balanced, and made publicly available to support reproducibility and encourage further research. The proposed 9-layer CNN, with just 1.7M parameters and a size of 6.74 MB, achieved a favorable balance between accuracy, model size, and computational efficiency, compared with MobileNetV1, MobileNetV2, DenseNet121, InceptionV3, MobileViT-XXS, and EfficientViT-M0, achieving 98.97%± 0.33% accuracy on PlantVillage and 93.36%± 0.28% on the proposed dataset. The ablation study showed that the NA block improved test accuracy by approximately 2–3%, while Grad-CAM visualizations indicated more precise targeting of diseased areas in the leaf image.
Why it matches plant phenotyping methods植物葉画像から病徴を推定する軽量CNNと注意機構を開発し、複数データセットで比較評価・アブレーションを行い、さらに100カテゴリの公開データセットを提示しているため、植物フェノタイピング手法が中心である。
abstractThis work proposes a custom Localized NA block implemented in TensorFlow/Keras that operates directly on CNN feature maps
Reproduction assets foundThe paper's authors curated a 100-category plant disease dataset and explicitly state it is publicly available on Kaggle in both augmented-train and raw split forms. These are paper-specific, public, actionable phenotype image datasets. The PlantVillage benchmark is a third-party dataset, not a paper-specific asset, soDataset · publicrs declare no conflict of interest
Funding Declaration
This research work was supported by KLE Technological University, Hubbali, India under the Ph.D. Fellowship
Program.
Data Availability Statement
The newly curated 100-category Plant Disease Dataset used in this study is publicly available on Kaggle.
Augmented Train Dataset: https://www.kaggle.com/datasets/rithambararajput/augmented-train
Raw Dataset: https://www.kaggle.com/datasets/rithambararajput/100-class-split-raw-dataset
The Plant Village dataset, used as a benchmark for comparative evaluation, is also publicly accessible at:
https://www.kaggle.com/datasets/vipoooool/new-plant-diseases-dataset.Ethical Declarations
This study does noOpen asset ↗Kaggle · rithambararajput/augmented-trainpdf-raw-page:19 lines:1-51Dataset · publicsupported by KLE Technological University, Hubbali, India under the Ph.D. Fellowship
Program.
Data Availability Statement
The newly curated 100-category Plant Disease Dataset used in this study is publicly available on Kaggle.
Augmented Train Dataset: https://www.kaggle.com/datasets/rithambararajput/augmented-train
Raw Dataset: https://www.kaggle.com/datasets/rithambararajput/100-class-split-raw-dataset
The Plant Village dataset, used as a benchmark for comparative evaluation, is also publicly accessible at:
https://www.kaggle.com/datasets/vipoooool/new-plant-diseases-dataset.Ethical Declarations
This study does not involve human participants or animals. Therefore, ethical approval was not rOpen asset ↗Kaggle · rithambararajput/100-class-split-raw-datasetpdf-raw-page:19 lines:1-51Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Apple leaf disease segmentation is critical for yield and quality preservation in what is globally one of the most economically significant fruit crops. Despite recent advances in deep learning, real-world orchard environments present three primary challenges: (1) low contrast between lesions and background textures, which hinders accurate localization; (2) leaf overlap and occlusion, leading to incomplete feature representation and increased false negatives; and (3) the inherent limitations of unimodal RGB imagery in capturing subtle pathological features, which constrains generalization and accuracy. To address these issues, we proposed Language-Infused Visual Mamba (LViM), a dual-path U-Net architecture that integrates Mamba and Transformer modules for semantic-visual feature fusion. LViM achieves robust segmentation in complex environments through three core innovations: (1) A U-shaped Multimodal Transformer (MTT) branch integrated with AMBERT, which leverages inter-modal semantic relationships to enhance textual feature extraction and provide high-level semantic cues, thereby improving lesion-background discriminability; (2) a U-shaped Visual State Space (VMamba) branch that employs 2D Selective Scanning (SS2D) and Visual State Space (VSS) blocks to capture global context and fine-grained details, mitigating the impact of occlusion; and (3) Cross-Attention Gate Fusion (CAGF) and Linguistic Cross-Nested (LCN) modules that facilitate efficient cross-modal alignment and hierarchical feature modeling to better identify subtle lesions. Experimental results demonstrate that LViM consistently outperforms the VM-UNet baseline, yielding improvements of 4.05% in Precision, 4.25% in Dice coefficient, 4.49% in mIoU, and 4.23% in Recall.
Why it matches plant phenotyping methodsリンゴ葉の病斑を画像から分割する手法を開発し、複雑な環境での性能を評価しており、植物病害状態の取得・推定が研究の中心である。
abstractApple leaf disease segmentation is critical for yield and quality preservation
Reproduction assets foundThe paper's curated multimodal apple leaf disease dataset (image-text pairs with pixel-level annotations for four disease types) is explicitly stated as publicly released in the authors' LViM GitHub repository. Code/models are only promised 'upon acceptance,' so the dataset asset qualifies as public, while the code is.Dataset · publicThe curated multimodal apple leaf disease dataset constructed in this study has been publicly released at https://github.com/csuft1906ll/LViMOpen asset ↗csuft1906ll/LViMlines:273-283Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Litchi is an important economic fruit in southern China, and its precision management relies on the rapid and accurate estimation of the Soil and Plant Analyzer Development (SPAD) values in leaves. Addressing the limitations of existing SPAD detection methods, such as limited rapid coverage, inadequate modeling of dynamic environmental interference, and shallow fusion of multi-source data, this study constructed an Internet of Things (IoT) system to collect real-time environmental data from a litchi orchard, combined with unmanned aerial vehicle (UAV) multispectral imagery to obtain canopy vegetation index and texture features. A Long Short-Term Memory (LSTM) network model integrated with a feature level attention mechanism (MLSTM) was proposed to fuse IoT time-series data, vegetation index, and high dimensional texture features for dynamic SPAD value prediction. The results indicate that multi-source feature fusion significantly improves SPAD estimation accuracy. The MLSTM model achieved optimal performance under the all-features situation, with a coefficient of determination (R²) of 0.897 and a root mean square error (RMSE) of 2.638, outperforming other comparative models. The attention mechanism effectively enhanced the model's focus on key features, improving feature utilization efficiency and model interpretability. The multi-source data fusion method and MLSTM model proposed in this study enable high precision, dynamic estimation of SPAD values in litchi leaves, providing reliable data support for precision fertilization, stress diagnosis, and yield prediction in litchi orchards, as well as theoretical support for promoting the practical application of this technology in smart agriculture.
Why it matches plant phenotyping methodsIoT・UAVマルチスペクトル画像から葉のSPAD値を推定するデータ融合システムとMLSTMモデルを開発・評価しており、植物形質取得手法が研究の中心です。
abstractthis study constructed an Internet of Things (IoT) system to collect real-time environmental data from a litchi orchard, combined with unmanned aerial vehicle (UAV) multispectral imagery to obtain canopy vegetation index and texture features.
Reproduction assets foundThe paper's data availability statement points to a public Zenodo repository containing the study's multi-source SPAD/IoT/multispectral dataset.Dataset · publicThe datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: https://zenodo.org/records/18308090 .Open asset ↗zenodo · 18308090lines:427-441Code / dataset availability confirmedEurope PMC · checked 14 Sept 2026
Advancing wheat breeding requires reliable digital traits that capture genotype × environment interactions and improve yield prediction across diverse growing conditions. Although vegetation indices such as the normalized difference vegetation index (NDVI) are widely used, their performance relative to yield variability and environmental stress remains underexplored in multi-environment trials. This study utilized unmanned aerial vehicle multispectral imagery to derive NDVI and assess its relationship with grain yield in 34 spring and winter wheat variety trials. These trials included data across seven Washington State locations in different precipitation zones, five years (2019 to 2023), and some irrigated trials. Environments were grouped into high-, moderate-, and low-stress clusters based primarily on precipitation and temperature. Variability was quantified using the coefficient of variation, and correlations between grain yield and NDVI were evaluated within and between varieties across environments based on market classes (hard and soft spring and winter wheat). Across all environments and varieties, NDVI strongly correlated with grain yield ( r = 0.79-0.82, p r = 0.72 in hard spring, r = 0.53 in soft spring). These conditions also improved discrimination between varieties. Although heritability patterns were not clearly differentiated by stress clusters, environments with higher genetic control of yield also tended to show stronger NDVI heritability. Overall, NDVI reliably captured wheat grain yield, which is governed by the genotype × environment driven variability, with its predictive value strongest in stress-prone conditions. These findings underline NDVI's usability as a practical digital trait for improving variety testing and guiding breeding decisions in challenging environments.
Why it matches plant phenotyping methodsUAVマルチスペクトル画像からNDVIを抽出し、複数環境・品種で収量との関係、予測性、遺伝率を評価しており、デジタル植物形質の測定・検証が中心である。
abstractThis study utilized unmanned aerial vehicle multispectral imagery to derive NDVI and assess its relationship with grain yield in 34 spring and winter wheat variety trials.
Reproduction assets found保存済みの本文根拠を更新済みルールで再検証し、公開資産1件を確認しました。Dataset · publicTrial data, including grain yield, variety, and market class information, were obtained from the Washington State University Extension Cereal Variety Selection and Testing Program ( https://smallgrains.wsu.edu/variety/ ).Open asset ↗lines:38-48Code / dataset availability confirmedOpenAlex · Europe PMC · bioRxiv · Crossref · checked 15 Sept 2026
BarleyCommon beanCowpeaGrowth chamberMesh / voxelLiDAR / point cloudMultispectral / hyperspectralLeafWhole plant / canopy / plot / fieldAnnotation / quality control
Abstract High-throughput 3D multispectral plant phenotyping platforms generate large volumes of point cloud files, but trait extraction is typically performed by sensor-bundled software whose internal algorithms are not publicly documented, which limits reproducibility and integration into custom research pipelines. Here we present PhytoScan3D, an open-source Python pipeline that extracts morphological and spectral phenotypic traits, spanning plant height, 3D leaf area, digital biomass, convex hull volume, leaf inclination, canopy geometry, NDVI, hue, and vegetation indices, from both PLY and PCD point cloud files generated by Phenospex PlantEye F500 and F600 sensors, and is portable to point clouds from any acquisition platform. PhytoScan3D was validated against HortControl (PhenoSpex) ground-truth measurements on 936 barley ( Hordeum vulgare ) pot-date observations from the growth chamber trial (20 Norwegian cultivars, 12 scan dates, Septemenr 2025 to January 2026), achieving Pearson r = 0.913 to 0.999 and ratio approximately 1.000 for Plant Height Max, 3D Leaf Area, and NDVI Average. A vectorised mesh face filtering implementation achieved a 120x speed improvement, increasing valid 3D Leaf Area coverage from 0.6% to 100% of files. Cross-format validation on 223 PlantEye F600 PCD files from the ICRISAT LeasyScan platform (four legume species: mungbean, cowpea, lima bean, and common bean; 1,523 plant observations) yielded r = 0.884 against independent cuboid annotation heights. The systematic positive bias (mean +27.2 mm, ratio = 1.44) is attributable to PhytoScan3D computing height from raw point cloud Z-range while cuboid annotations are fitted to segmented plant points only, with the offset consistent across all four species (per-species r = 0.880 to 0.888). Cross-dataset processing of 1,180 PLY files from the Crops3D benchmark (8 species, 3 acquisition methods) confirmed zero extraction errors. PhytoScan3D is available at “github.com/kovimallik/phytoscan3d” under the MIT licence and processes 1,651 files across three independent datasets in under 12 minutes on GPU hardware. Highlights PhytoScan3D is the first open-source Python pipeline for batch extraction of phenotypic traits, including plant height, 3D leaf area, digital biomass, convex hull volume, leaf inclination, NDVI, and excess green index, from both PLY and PCD point cloud files generated by Phenospex PlantEye sensors. Primary validation against HortControl ground-truth measurements on 936 barley pot-date observations achieved Pearson r = 0.913-0.999 for Plant Height Max, 3D Leaf Area, and NDVI Average. A 120x computational speedup in mesh face filtering (vectorised NumPy vs. set-based loop) increased the coverage of valid 3D Leaf Area extraction from 0.6% to 100% of files. Cross-format validation on 223 PlantEye F600 PCD files from ICRISAT LeasyScan (four legume species, 1,523 plants) achieved r = 0.884 against independent cuboid annotation heights. The systematic +27.2 mm bias reflects a methodological difference (raw Z-range vs. soil-segmented annotations), is consistent and predictable across all four species (per-species r = 0.880-0.888), and is correctable by a single linear factor. Cross-dataset processing of 1,180 PLY files from the Crops3D benchmark (8 species, 3 acquisition methods) confirmed zero extraction errors. Significant scan-unit variation was detected for Plant Height Max (F = 5.71, p < 0.001, η 2 = 0.138) and Canopy Width X (F = 6.32, p < 0.001, η 2 = 0.150), demonstrating the biological utility of extracted traits.
Why it matches plant phenotyping methods植物の3D点群・マルチスペクトルデータから形態・スペクトル形質を抽出するオープンソース手法を開発し、複数データセットで技術検証・ベンチマークしているため、植物フェノタイピング手法が中心である。
abstractHere we present PhytoScan3D, an open-source Python pipeline that extracts morphological and spectral phenotypic traits
Reproduction assets foundThe paper's own analysis code (PhytoScan3D pipeline) is publicly released on GitHub under the MIT licence, and the two external 3D point cloud datasets used for validation (Crops3D and ICRISAT LeasyScan) are publicly available on figshare. The primary barley PLY dataset is not yet public (to be deposited in NVA upon).Code · publicditing, Funding acquisition.
Declaration of Competing Interest
The authors declare that they have no known competing financial interests or personal
relationships that could have appeared to influence the work reported in this paper.
Data Availability
PhytoScan3D source code, documentation, and example datasets are available at
https://github.com/kovimallik/phytoscan3d under the MIT licence. The barley PLY dataset
will be deposited in the Norwegian Research Information Repository (NVA) upon acceptance.
The Crops3D benchmark dataset is publicly available at
https://doi.org/10.6084/m9.figshare.27313272 (Zhu et al. 2024). The ICRISAT LeasyScan
dataset is publicly available at https://doi.org/10Open asset ↗github.com/kovimallik/phytoscan3dpdf-raw-page:15 lines:1-36Dataset · publicData Availability
PhytoScan3D source code, documentation, and example datasets are available at
https://github.com/kovimallik/phytoscan3d under the MIT licence. The barley PLY dataset
will be deposited in the Norwegian Research Information Repository (NVA) upon acceptance.
The Crops3D benchmark dataset is publicly available at
https://doi.org/10.6084/m9.figshare.27313272 (Zhu et al. 2024). The ICRISAT LeasyScan
dataset is publicly available at https://doi.org/10.6084/m9.figshare.28270742 (Galba et al.
2025).
Acknowledgements
This work was supported by the PheNo, DLT-Farming and Soil2Milk from Research Council
of Norway and TWIN-NUE from Norwegian University of Life Sciences (NMBU). The
authoOpen asset ↗figshare · 10.6084/m9.figshare.27313272pdf-raw-page:15 lines:1-36Dataset · publicimallik/phytoscan3d under the MIT licence. The barley PLY dataset
will be deposited in the Norwegian Research Information Repository (NVA) upon acceptance.
The Crops3D benchmark dataset is publicly available at
https://doi.org/10.6084/m9.figshare.27313272 (Zhu et al. 2024). The ICRISAT LeasyScan
dataset is publicly available at https://doi.org/10.6084/m9.figshare.28270742 (Galba et al.
2025).
Acknowledgements
This work was supported by the PheNo, DLT-Farming and Soil2Milk from Research Council
of Norway and TWIN-NUE from Norwegian University of Life Sciences (NMBU). The
authors thank Sara Catarina Costa Laranjeira, Min Lin and other NMBU growth facility staff
for plant care and scanning operOpen asset ↗figshare · 10.6084/m9.figshare.28270742pdf-raw-page:15 lines:1-36Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
ToBRFV is a major threat to tomato and pepper crops because it spreads quickly and survives for a long time in the environment. Since there are few ways to control it after infection, early detection before symptoms are visible is crucial. Yet, only limited public datasets are available for this research. We present one of the first openly accessible, longitudinal multispectral image dataset dedicated to ToBRFV detection. In this study, two tomato cultivars and two pepper cultivars, all of which are commercially important and widely cultivated in greenhouses, were selected. Using these plants ensures that the dataset reflects real-world agricultural practices and captures variability across commercially grown types. Both healthy and ToBRFV-inoculated plants from each cultivar were included in the imaging process. All plants were cultivated under fully controlled greenhouse conditions in Adana Province, Türkiye. Healthy and infected tomato plants were grown in two separate greenhouses to prevent cross-contamination. Imaging was conducted over a 29-day period using Red-Green-Blue (RGB) and Visible Near Infrared (VNIR) cameras, including narrowband captures at 800 nm and 1000 nm, from multiple viewing angles. Infection status was confirmed via Reverse Transcription quantitative Polymerase Chain Reaction (RT-qPCR) analysis at multiple time points. The dataset is organized into four clean, labelled subsets and released under a CC BY 4.0 license. This resource provides unique opportunities for developing and benchmarking computer vision and machine learning approaches for pre-symptomatic plant disease detection, spectral feature analysis, and integration into precision agriculture systems. By combining controlled experimental design, spectral diversity, and open access, it establishes a robust foundation for cross-disciplinary research in plant pathology, agricultural engineering, and artificial intelligence.
Why it matches plant phenotyping methods植物病害状態を対象にした縦断マルチスペクトル画像データセットであり、公開データセットとして開発・ベンチマーク利用を目的とするため、表現型取得が中心です。
abstractWe present one of the first openly accessible, longitudinal multispectral image dataset dedicated to ToBRFV detection.
Reproduction assets foundThe article is a Data in Brief describing the authors' own openly released longitudinal multispectral plant image dataset (ToBRFV-LMID) for tomato and pepper disease detection, deposited on Zenodo under CC BY 4.0 with a direct DOI URL. This is a paper-specific, public, directly actionable phenotype/image asset. No codeDataset · publicData accessibility
Repository name: ZENODO
Data identification number: 10.5281/zenodo.17244968
Direct URL to data: https://doi.org/10.5281/zenodo.17244968Open asset ↗ZENODO · 10.5281/zenodo.17244968html-lines:98-126Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Monitoring and precisely localizing rice diseases is essential for agricultural productivity and food security. Existing detection methods face challenges such as high computational complexity, semantic information loss, difficulty detecting small targets, and limited robustness. To address these issues, this study proposes ECL-RTDETR, an enhanced RT-DETR-based rice disease detection model. First, a lightweight EfficientViT backbone is employed for feature extraction, incorporating a streamlined multi-head self-attention module to improve inference speed, reduce computational cost, and strengthen local feature extraction. Second, the CARAFE upsampling operator is introduced to better preserve detailed feature information without added computational burden, enhancing fine-grained representation. Finally, standard convolution in the neck network is replaced with LDConv (lightweight dynamic convolution) to enable adaptive feature learning under complex conditions, addressing variations caused by illumination, occlusion, and disease diversity. Experimental results show that ECL-RTDETR improves mAP@0.5 by 0.7%, increases detection speed by 22.2 FPS, and reduces computational cost by 81.8 GFLOPs and parameters by 22.12M compared with the baseline RT-DETR. Overall, ECL-RTDETR delivers superior accuracy, speed, and efficiency, offering a robust solution for intelligent rice disease detection and localization, and advancing smart agriculture and sustainable food security.
Why it matches plant phenotyping methodsイネ病害の検出・局在化を目的とする画像解析モデルを開発し、精度・速度・計算量を実験的に比較検証しており、植物の病害状態を推定する方法が研究の中心である。
titleResearch on an improved RT-DETR-based model for rice disease detection.
Reproduction assets foundThe paper's rice disease image dataset (drone-collected, annotated, augmented) is explicitly stated to be publicly available on figshare. No author analysis code or trained model checkpoint is explicitly deposited; the Ultralytics repository is a generic third-party library, not a paper-specific asset.Dataset · publicData Availability: All relevant data for this study are publicly available from the figshare repository ( https://figshare.com/s/b491aeb44611dea9c481 ).Open asset ↗figsharelines:1-123Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Abstract Potatoes are one of the major crops eaten in developing countries; however, their production is falling due to various diseases. Early identification and detection of potato leaf diseases play a vital role in improving potato quality and quantity. Existing methods are either computationally resource intensive or lack trust in their decision-making process, which makes them difficult to deploy for real-time potato disease classification and limits its accessibility. To mitigate these limitations, this study proposed an attention-enhanced MobileNetV2 with a squeeze-and-excitation architecture, which balances high accuracy with low computational resources. This method incorporates the strength of MobileNetV2 and Squeeze-and-excitation networks. A total of 2152 images of early blight, late blight, and healthy leafs were obtained from the Kaggle public repository, which are partitioned into 70% training, 20% validation, and 10% testing and were utilized to train, validate, and test the proposed model. The MobileNetV2 backbone is utilized for feature extraction, and then a squeeze-and-attention block is used to recalibrate the feature maps by focusing on important features and suppressing irrelevant ones. Gradient-weighted Class Activation Mapping (Grad-CAM) was implemented to visualize the most relevant region of the leaf for decision-making, which increases model interpretability and user trust. The proposed model achieves a remarkable performance of 99% testing accuracy with 9.41 MB total parameters. The proposed model is suitable for real-time potato leaf disease detection and classification, which can be easily accessible to agricultural stakeholders, including farmers, and contributes to food security.
Why it matches plant phenotyping methodsジャガイモ葉の病害状態を画像から分類する深層学習手法を提案・評価しており、植物表現型（病害状態）の取得・推定が中心である。
abstractthis study proposed an attention-enhanced MobileNetV2 with a squeeze-and-excitation architecture, which balances high accuracy with low computational resources.
Reproduction assets foundThe paper's phenotyping inputs are 2152 potato leaf images (early blight, late blight, healthy) obtained from a public Kaggle repository, explicitly stated as publicly available in the Declarations. No author analysis code is shared (Code Availability: Not applicable), and no trained model checkpoints are released.Dataset · publicAvailability of Data: The datasets generated during and/or analyzed during the current study are
publicly available at https://www.kaggle.com/datasets/faysalmiah1721758/potato-dataset.Open asset ↗Kaggle · faysalmiah1721758/potato-datasetpdf-page:23 lines:1-35Code / dataset availability confirmedCrossref · checked 15 Sept 2026
Published1 Jun 2026International Journal of Electrical and Computer Engineering (IJECE)Cited by 0 · OpenAlex ↗
Plant diseases remain a critical challenge in agriculture, causing substantial yield losses and threatening food security. In this work, we propose a hybrid deep feature engineering framework that integrates deep learning-based feature extraction with classical machine learning for accurate plant disease detection. A pretrained vision transformer (ViT) model is employed to extract discriminative features from leaf images, effectively capturing complex spatial relationships. To address the curse of dimensionality, principal component analysis (PCA) is applied, retaining 98% of the variance while reducing feature space complexity. The refined features are then classified using a support vector machine (SVM) optimized through hyperparameter tuning. Experimental results on the bean leaf lesions dataset demonstrate strong performance, achieving 92% accuracy and a weighted F1-score of 0.92. The proposed ViT–PCA–SVM pipeline effectively balances accuracy, computational efficiency, and generalization, making it a promising solution for real-time smart farming applications.
Why it matches plant phenotyping methods葉画像から植物病害状態を推定するViT–PCA–SVM解析パイプラインが研究の中心であり、植物表現型（病斑・病害状態）の画像ベース推定手法に該当する。
titleTransformer-based hybrid classification for plant leaf disease detection using vision transformer, principal component analysis, and support vector machine
Reproduction assets foundThe paper's only qualifying asset is the public Bean Leaf Lesions dataset (leaf images used as phenotyping input for disease classification), explicitly declared in the DATA AVAILABILITY section with a Kaggle URL. No author analysis code, trained models, or checkpoints are released.Dataset · publicI R D O E Vi Su P Fu
Vijayalakshmi S. Abbigeri ✓ ✓ ✓ ✓ ✓ ✓ ✓ ✓ ✓ ✓ ✓ ✓ ✓
Geetha D. Devanagavi ✓ ✓
CONFLICT OF INTEREST STATEMENT
All authors declare that they have no conflicts of interest.
DATA AVAILABILITY
The data that support the findings of this study are openly available in Kaggle, "Bean leaf lesions
dataset," [Online] at https://www.kaggle.com/datasets/advayprasad/bean-leaf-lesions-dataset.
REFERENCES
[1] Food and Agriculture Organization (FAO), “Climate change fans spread of pests and threatens plants and crops, new FAO study,”
Food and Agriculture Organization (FAO), 2021. https://www.fao.org/newsroom/detail/Climate-change-fans-spread-of-pests-
and-threatens-plants-and-crops-new-FAOOpen asset ↗Kagglepdf-layout-page:7 lines:1-70Code / dataset availability confirmedCrossref · OpenAlex · Europe PMC · checked 5 Sept 2026
Ear density ( ) and ear surface area in cereals are important traits for adaptation to low inputs and climate change. Here we propose a high-throughput field phenotyping method to estimate these traits using nadir and 45° RGB images acquired by the Phenomobile ground robot. First, the YOLOv5 ear detection algorithm is applied to nadir RGB images to estimate . Second, an ear segmentation algorithm is applied to nadir and 45° RGB images to compute the ear gap fraction at different viewing angles. The Beer-Lambert law is then inverted to compute the ear area index (EAI) from the observed ear gap fraction. is finally derived as the ratio between EAI and . We applied the methodology to a panel of 10 commercial bread wheat varieties how both traits vary across 12 environments. The relative error obtained for awnless varieties is 12% (56 ears m -2 ) for and 18% (1.3 cm 2 ) for . For awned varieties, ground-truth observations of were shown to be biased due to an overestimation of awns contribution, leading to an error of 41% (3.6 cm 2 ). was strongly correlated with grain dry mass per ear at harvest ( r 2 = 0.80 across genotypes and environments, r 2 per genotype ranged between 0.80 and 0.95) and was strongly correlated with grain yield ( r 2 = 0.83). These results indicate that both EAI and can be interesting non-destructive proxies for yield and grain dry mass per ear.
Why it matches plant phenotyping methodsRGB画像と地上ロボット、物体検出・セグメンテーション・Beer–Lambert法を組み合わせ、コムギ穂の密度と表面積を推定・検証する手法が研究の中心であるため。
abstractHere we propose a high-throughput field phenotyping method to estimate these traits using nadir and 45° RGB images acquired by the Phenomobile ground robot.
Reproduction assets foundThe authors publicly release their ear surface area estimation algorithm with an example dataset on an INRAE forge repository, and the Phenomobile-derived ear density/ear surface area estimations used in the multi-environment analysis are included as supplemental material with the open-access article. The YOLOv5 GWC_SoDataset · publicThe algorithm developed to estimate the EAI and the average ear surface using binary images from ear segmentation are publicly available in the repository https://forge.inrae.fr/raul.lopez-lozano/wheat-ear-surface , jointly with an example dataset from the Mauguio 2023 trial (4 treatments, 1 replicate). The Phenomobile estimations of ear surface area and ear density used in the multi-environmental mixed model presented in Section 2.5 are included as supplemental material.Open asset ↗lines:614-652Code / dataset availability confirmedCrossref · checked 15 Sept 2026
Manual quantification of specialty crop traits, such as flowers and fruits, is often labor-intensive, time-consuming, and inconsistent, limiting scalability and precision. We present PhenoSnap, an artificial intelligence (AI)-powered web application that provides an intuitive and efficient interface for automated specialty crop trait extraction from images. PhenoSnap bridges the gap between advanced computer vision technologies and practical agricultural applications by eliminating the need for programming expertise. This ready-to-use solution can enable growers, breeders, and Extension faculty to accelerate field work and enhance decision-making related to strawberry and tomato yield estimation for breeding selections and strawberry runner management. Written by Santhi Daggubati, Xu Wang, Xue Zhou, Shubham Singh, and Jessica Chitwood-Brown, and published by the UF/IFAS Department of Agricultural and Biological Engineering, June 2026.
Why it matches plant phenotyping methods画像から花・果実などの植物形質を自動抽出するAIウェブアプリケーションの開発・提供が中心であり、植物フェノタイピング手法およびソフトウェアとして適格。
abstractWe present PhenoSnap, an artificial intelligence (AI)-powered web application that provides an intuitive and efficient interface for automated specialty crop trait extraction from images.
Reproduction assets foundThe article describes PhenoSnap, a publicly accessible AI web application for specialty crop trait extraction, and cites a publicly released Dryad imagery dataset (Zhou et al. 2025b) that is a subset of the training data for the Strawberry Runner model. Both are paper-specific, public, and actionable. No author code orDataset · publicDataset preparation
and the training process are detailed in Zhou et al. (2025a),
and a subset of the dataset has been publicly released on
Dryad (Zhou et al. 2025b).Open asset ↗Dryadpdf-raw-page:5 lines:1-55Code / dataset availability confirmedCrossref · Europe PMC · checked 5 Sept 2026
Three-dimensional (3D) point-cloud phenotyping enables non-destructive and repeatable characterization of plant architecture, supporting the measurement of traits such as internode length, branching topology, and organ orientation. This article presents TomatoPGT (Tomato Plant Graph Twin) , a 3D tomato dataset designed for research on semantic/instance segmentation, graph-based structural representation, and graph-derived phenotypic trait extraction. The dataset contains 42 scans from three greenhouse-grown tomato plants acquired across early to mid-vegetative development using a rotational multi-view imaging system. Each scan consists of 60-70 overlapping RGB images captured under uniform illumination and reconstructed into a metrically scaled dense colored point cloud using Structure-from-Motion and multi-view stereo. TomatoPGT provides: (i) multi-view RGB images, (ii) dense colored point clouds, (iii) manually curated semantic and instance annotations at organ level, (iv) graph representations encoding plant topology and geometry, and (v) tabulated phenotypic traits computed deterministically from the graphs (internode length, insertion angles, and phyllotactic angles). TomatoPGT supports reproducible development and evaluation of 3D phenotyping pipelines, including learning-based segmentation and graph-based modeling of plant architecture.
Why it matches plant phenotyping methods植物の3D形態表現型抽出を目的としたデータセットで、画像・点群・器官アノテーション・グラフ・形質値を提供し、再現可能なフェノタイピング手法の開発と評価を直接支援している。
abstractThis article presents TomatoPGT (Tomato Plant Graph Twin) , a 3D tomato dataset designed for research on semantic/instance segmentation, graph-based structural representation, and graph-derived phenotypic trait extraction.
Reproduction assets foundThe paper's own TomatoPGT dataset (multi-view RGB images, dense point clouds, semantic/instance annotations, graph representations, and CSV phenotypic traits) is publicly deposited on Mendeley Data, and the authors' Cloud-Seg/Cloud-Graph software tools plus supplementary materials (camera calibrations, example datasetsDataset · publicRepository name 1: Mendeley[2].
Data identification number: DOI: 10.17632/72md54c7n7.1
Direct URL to data: https://data.mendeley.com/datasets/72md54c7n7/1Open asset ↗Mendeley · 10.17632/72md54c7n7.1html-lines:105-178Code · public6. Code and documentation: CloudSeg and CloudGraph software tools, environment specifications, and example usage instructions are hosted on Zenodo[3].Open asset ↗Zenodohtml-lines:264-308Code / dataset availability confirmedEurope PMC · OpenAlex · Crossref · checked 5 Sept 2026
Urochloa grasses are among the most widely used forage grasses across the tropics. Spittlebugs (Hemiptera: Cercopidae) are major pests of tropical Urochloa (syn. Brachiaria) grass pastures, severely reducing forage productivity and quality. Understanding the genetic basis of host-plant resistance is essential for developing durable resistant cultivars. Here, we combined high-throughput image-based phenotyping and genome-wide association studies (GWAS) to dissect the genetic architecture of response to Aeneolamia varia nymphs in 339 interspecific F1 hybrids derived from crosses between resistant sexual and susceptible apomictic Urochloa parents. Digital image analysis using both unsupervised (DQU) and supervised (DTR) quantification pipelines enabled accurate estimation of plant damage, yielding moderate to high broad-sense heritability estimates (H2 = 0.49 to 0.66). In contrast, insect survival (NTS) exhibited low to moderate correlations with all damage traits and lower heritability estimates (H2 = 0.42). Using 57,051 high-quality SNPs aligned to the genome of the hybrid cultivar Basilisk, GWAS models identified 18 quantitative trait loci (QTLs) for plant damage traits, but none for insect survival (antibiosis). Six robust QTLs on chromosomes 1, 6, 7, 27, 29, and 36 were consistently detected across models and phenotyping methods, explaining up to 21.5% of phenotypic variance. Candidate gene analysis revealed proteins involved in hormone signaling, oxidative stress response, and cell wall modification, suggesting multifaceted plant-insect interaction mechanisms. These results provide a foundational set of molecular markers associated with spittlebug response in Urochloa grasses, useful for marker-assisted and genomic selection in the forage breeding program.
Why it matches plant phenotyping methods高スループット画像表現型解析と、植物損傷を推定する2つの画像解析パイプラインが研究の中心であり、異なる手法間の比較と形質推定性能も評価している。
abstractHere, we combined high-throughput image-based phenotyping and genome-wide association studies (GWAS) to dissect the genetic architecture of response to Aeneolamia varia nymphs
Reproduction assets foundThe paper's digital plant-damage images are publicly deposited in Harvard Dataverse (paper-specific phenotyping input). The RAD-Seq accession PRJEB109285 is a sequencing/omics deposit and is excluded per criteria. No author analysis code repository with explicit availability URL is stated.Dataset · publicThe digital images used for plant damage quantification are available in the Harvard Dataverse repository at the following identifier: https://dataverse.harvard.edu/dataset.xhtml?persistentId=doi:10.7910/DVN/EGUVHA .Open asset ↗Harvard Dataverse · doi:10.7910/DVN/EGUVHAlines:387-414Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Plant leaf diseases must be detected and treated early to improve crop yield and reduce agricultural losses. However, pixel-level representations and the inability to be read limit the applicability of existing deep learning approaches to the agricultural sector. A graph neural network termed the Attention-Enhanced Graph Neural Network (AE-GNN) may explain and diagnose multi-plant leaf disease. The proposed framework models leaf pictures as a graph with nodes representing discriminative leaf areas and edges representing their spatial connection. Before creating the global context vector and classification, graph features are aggregated, and an attention weighting method is applied to refocus on disease-relevant nodes obscured by less informative background characteristics. Final disease prediction uses a multilayer perceptron classifier. A curated dataset of half-spinach and curry leaf pictures is used to assess the proposed method for fifteen illnesses and their healthy classifications. Grad-CAM-based explainable AI methods make the model predictions' most important areas clearer. The dataset and source code from this work are available on GitHub for reproducibility and openness. Experimental results reveal that the proposed AE-GNN outperforms convolutional neural networks and graph-based models in classification. Graph-structured learning, attention enhancement, and explainability create a robust and interpretable framework for multi-plant leaf disease diagnosis.
Why it matches plant phenotyping methods葉画像から植物病害状態を分類・診断する画像解析手法を提案し、既存モデルとの比較評価と説明可能性解析を行っているため、植物フェノタイピング手法が中心である。
abstractA graph neural network termed the Attention-Enhanced Graph Neural Network (AE-GNN) may explain and diagnose multi-plant leaf disease.
Reproduction assets foundThe paper's Data availability section explicitly links a public GitHub repository containing the paper's spinach/curry leaf fungal disease image dataset used for the AE-GNN phenotyping/classification analysis.Dataset · publicData availability
The dataset is available at the link below. https://github.com/MeganathanE1990/FINAL-DISEASE-DATA-SET/tree/mainOpen asset ↗MeganathanE1990/FINAL-DISEASE-DATA-SETlines:413-463Code / dataset availability confirmedEurope PMC · checked 6 Sept 2026
As the demand for plant-based nutrition increases, improving the protein profile of legumes like cowpea has become a breeding priority. Cowpea, a multiuse legume and staple in many low-income regions, provides important dietary protein that can help meet the demand in our growing population. Our research used genome-wide association studies (GWAS) and phenomic tools to investigate the genetic architecture of seed protein content in cowpea and integrated 4 cohorts of undergraduate researchers through a USDA-AFRI REEU program. Using wet chemistry and near-infrared spectroscopy (NIRS), we assessed crude protein (CP) within the University of California Riverside Minicore collection, developed and validated a custoMED-made NIRS calibration equation for CP (R2 = 0.86), and performed GWAS with ∼41k single-nucleotide polymorphisms (SNPs). Significant SNPs associated with protein content were identified on chromosomes 1, 3, 7, 10, and 11, and candidate genes were linked to functions including nutrient transport, stress response, and seed storage protein regulation. These results provide a foundation for future marker validation and functional studies, and demonstrate the value of pairing trait discovery with undergraduate training.
Why it matches plant phenotyping methods種子タンパク質含量という植物形質の取得に用いるNIRS校正式を開発・検証しており、表現型測定法が研究の主要な技術的要素である。
abstractdeveloped and validated a custoMED-made NIRS calibration equation for CP (R2 = 0.86)
Reproduction assets foundThe paper's Data Availability statement deposits the phenotypic data (wet chemistry CP, NIRS-derived CP phenotypes used for calibration and GWAS) in Dryad. No author analysis code or trained NIRS model files are explicitly deposited; other URLs are generic tools or citations.Dataset · publicThe phenotypic data collected and used in this research are available in the Dryad Digital Repository under DOI: https://doi.org/10.5061/dryad.8cz8w9h72 .Open asset ↗Dryad Digital Repository · 10.5061/dryad.8cz8w9h72lines:305-345Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
This article presents a multispectral imaging dataset dedicated to training a machine learning algorithm for the in situ detection of Huanglongbing (HLB). HLB, also known as citrus greening disease, is a major pathology caused by the bacterial pathogen Candidatus Liberibacter asiaticus , particularly in species of the citrus genus. The dataset is constituted of terrestrial images acquired in a commercial sweet orange orchard of the variety Pera Rio ( Citrus sinensis (L.) Osbeck). The images describe large portions of canopy, with healthy leaves and sections infected by HLB as well as some confounding factors naturally present in orchards. Multispectral images were acquired with a multi-lens camera within the visible-near-infrared domain, resulting in 14 narrow spectral bands. The image acquisition was conducted during two field campaigns in 2023 and 2024. In total, the dataset contains 2,978 images divided into two classes HLB (1,681) and non-HLB (1,297). Originally, data are stored in TIFF format as 14 monochromatic images, organised by spectra band. Additionally, an HDF5-format version is provided, where images are stored as 3D arrays with spectral bands in ascending order. This format is compatible with various programming languages, enables efficient data handling, and is optimised for machine learning and image processing applications, supporting reproducible and portable analysis. This dataset is a valuable resource for the development and benchmarking of classification models, including deep learning approaches, aimed at the detection of HLB. Phytopathology imaging datasets are scarce yet essential for advancing digital agriculture and the development of robust tools for crop disease detection worldwide.
Why it matches plant phenotyping methods柑橘葉・樹冠のマルチスペクトル画像からHLB感染状態を推定するデータセットであり、植物病害状態の表現型取得と機械学習ベンチマークを中心とする。
abstractThis article presents a multispectral imaging dataset dedicated to training a machine learning algorithm for the in situ detection of Huanglongbing (HLB).
Reproduction assets foundThe article is a Data in Brief describing a public multispectral HLB citrus image dataset deposited on Data INRAE (Recherche Data Gouv, DOI 10.57745/054NAB), plus an authors' GitHub repository with preprocessing, registration, and model training scripts. Both are paper-specific, public, and directly actionable.Dataset · publicData accessibility
Repository name: Data INRAE
Data access link: https://doi.org/10.57745/054NABOpen asset ↗Data INRAE · 10.57745/054NABhtml-lines:89-123Code / dataset availability confirmedEurope PMC · bioRxiv · checked 14 Sept 2026
Hyperspectral imaging is an imaging technique that allows for acquisition of high-resolution spectral information beyond that of the visible spectrum. When applied to plants, it effectively enables non-invasive characterization of physiological status and has been widely used in agricultural settings. Marchantia is a model bryophyte species whose flat morphology and visually distinct stress-response phenotypes makes it an ideal candidate for imaging studies. Here, we provide a comprehensive protocol for hyperspectral imaging for Marchantia plants, which encompasses hardware configuration, data acquisition, and computations processing. This protocol features a streamlined data processing pipeline hosted on a web-based development platform that automates 1) the segmentation of plant area into spatially distinct regions for localized analysis of intra-specimen physiological gradients, and 2) classification of plant pixels based on their spectral signatures. All results are exported as structured CSV files for ease of further analysis as desired by the user.
Why it matches plant phenotyping methodsマーチャンティアを対象としたハイパースペクトル撮像プロトコルと、植物領域のセグメンテーション・スペクトル分類を含む処理パイプラインを開発しており、植物の生理状態取得が中心的な方法論的貢献である。
abstractHere, we provide a comprehensive protocol for hyperspectral imaging for Marchantia plants, which encompasses hardware configuration, data acquisition, and computations processing.
Reproduction assets found保存済みの本文根拠を更新済みルールで再検証し、公開資産1件を確認しました。Dataset · publicExample images used in this protocol have previously been published by Krishnamoorthi et al. (2024) 4 and can be downloaded from https://github.com/dr-daisuke-urano/PlantHyperspectralSVDOpen asset ↗PlantHyperspectralSVDlines:47-85Code / dataset availability confirmedEurope PMC · checked 15 Sept 2026
MaizeTomatoLeafPhysiological trait estimationCalibration / preprocessingWater status / transpiration
Within the soil-plant-atmosphere continuum, water movement is driven by the water potential gradients between these three domains. To have a comprehensive understanding of such water relations, an examination of how plants respond to variations in soil water availability is required. The methodologies employed for measuring water potential in leaf (Ψ leaf ) and soil (Ψ soil ) have undergone a significant evolution; transitioning from qualitative assessments to the use of high-precision digital sensors over the past few decades. The present protocol aims to provide a comprehensive, step-by-step guide from the germination phase of maize and tomato plants to the installation of two sensors that continuously monitor water potential in the leaf (PSY1 psychrometer) and in the soil (TEROS 21 matric potential sensor). Additionally, we present the code for processing the raw data files in RStudio.
Why it matches plant phenotyping methods葉の水ポテンシャルを連続測定するセンサー設置、データ処理コード、手順を中心とした植物生理形質の測定プロトコルであり、方法論的貢献が明確。
abstractThe present protocol aims to provide a comprehensive, step-by-step guide from the germination phase of maize and tomato plants to the installation of two sensors that continuously monitor water potential in the leaf (PSY1 psychrometer) and in the soil (TEROS 21 matric potential sensor).
Reproduction assets foundThe paper deposits its authors' R analysis notebook with an example water-potential dataset, the CR800 datalogger program, and an installation video on Zenodo, all publicly accessible.Code · publicthat were missing, zero, or otherwise aberrant. It was also programmed to identify and remove inverted day-night cycle patterns, as well as values that were statistically insignificant.
Figure 9 shows applications of data cleaning on the example dataset. For more details, please check codes that have been deposited on Zenodo (
https://doi.org/10.5281/zenodo.20080750 ,
D’Agostino, 2026 ).
Figure 9.
Example of data cleaning using the algorithm.
Green is kept data and red is discarded data.
Conclusion
In summary, the present protocol is not confined to the descriptive monitoring of Ψ
soil
and Ψ
leafOpen asset ↗Zenodo · 10.5281/zenodo.20080750lines:452-504Code · public(1) the address of each Teros 21; (2) the data transporting port (“C1” or “C3”); (3) the creation of dataset files to store the recorded soil matric potential and temperature, as well as the voltage of the battery for power supply; (4) the time interval for the data recording.
An example of the program was deposited on Zenodo (
https://doi.org/10.5281/zenodo.17158115 ), with the document name of “Program-CR800”). Before starting, install the software of “Device Configuration Utility” and “PC400” from Campbell Scientific (
https://www.campbellsci.com/devconfig ;
https://www.campbellsci.com/pc400 ). “CRBasic Editor” is integrated inside PC400. For more details about the programming, please reOpen asset ↗Zenodo · 10.5281/zenodo.17158115lines:321-378Dataset · publiculic limitation, soil-root disconnection, and recovery. Consequently, this linkage of the protocol to mechanistic analyses of water transport in the SPAC is more direct.
Ethics and consent
Ethical approval and consent were not required.
Data availability
The datasets and codes to analyze the data have been deposited on Zenodo (
https://doi.org/10.5281/zenodo.20080750 ,
D’Agostino (2026) ).
Data are available under the terms of the Creative Commons Zero v1.0 Universal.
An additional explicative video for the psychrometer installation on leaves is available on Zenodo (
https://doi.org/10.5281/zenodo.17510720 ,
Degand
et al. (2025) ).
The author(s) declare that this video is released under theOpen asset ↗Zenodo · 10.5281/zenodo.20080750lines:505-651Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Plant leaf disease detection is a critical task in precision agriculture, where reliable diagnosis under real-world conditions is essential for reducing crop losses and supporting timely intervention. Although deep learning models have achieved high classification accuracy, their performance often degrades under domain shift between controlled laboratory datasets and real-field environments, while predictive uncertainty and confidence calibration remain largely unaddressed.This study presents an uncertainty-aware cross-domain evaluation framework based on a Hierarchical Vision Transformer (HViT) for plant leaf disease classification. The framework integrates multi-scale feature learning with Monte Carlo Dropout-based predictive uncertainty estimation and temperature-based calibration to systematically analyze model behavior in terms of accuracy, reliability, and robustness. Experiments were conducted on two complementary datasets: the New Plant Diseases Dataset (controlled conditions) and the PlantDoc dataset (field conditions), enabling bidirectional cross-domain evaluation. Results demonstrate that the proposed framework achieves superior performance, attaining 97.8% accuracy on controlled data and 93.6% on field data, while significantly improving calibration with lower Expected Calibration Error (ECE = 0.032 / 0.041), reduced Negative Log-Likelihood, and lower Brier score compared to baseline CNN and transformer models. Furthermore, the framework exhibits improved robustness under domain shift, with reduced performance degradation and stable uncertainty behavior. Overall, this study highlights the importance of integrating uncertainty estimation and calibration within a hierarchical transformer-based framework, providing a more reliable and deployment-ready solution for real-world agricultural disease diagnosis.
Why it matches plant phenotyping methods植物葉の病害状態を直接推定する不確実性-aware分類フレームワークの開発・評価が中心であり、異なる条件のデータセット間で精度、校正、頑健性を検証している。
abstractThis study presents an uncertainty-aware cross-domain evaluation framework based on a Hierarchical Vision Transformer (HViT) for plant leaf disease classification.
Reproduction assets foundThe paper's Data availability statement explicitly links the two public image datasets used for its cross-domain plant leaf disease classification experiments: the New Plant Diseases Dataset on Kaggle and the PlantDoc dataset on Dataset Ninja. No author analysis code, models, or checkpoints are reported as available.Dataset · publicThe New Plant Diseases Dataset can be obtained from Kaggle at [https://www.kaggle.com/datasets/vipoooool/new-plant-diseases-dataset]Open asset ↗Kaggle · vipoooool/new-plant-diseases-datasetlines:360-398Dataset · publicThe PlantDoc dataset is available for download at [https://datasetninja.com/plantdoc#download]Open asset ↗plantdoclines:360-398Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Cotton production is highly vulnerable to foliar diseases and pest-induced damage, which significantly reduce yield and compromise fiber quality. Rapid, reliable, and automated disease identification is therefore essential for supporting sustainable crop management. In this study, we propose a hybrid deep learning framework integrating a ResNet50 backbone with Squeeze-and-Excitation (SE) channel attention modules to enhance discriminative feature representation for cotton leaf disease classification. The model is trained on a publicly available disease dataset comprising six classes and optimized using Weighted CrossEntropyLoss, Adam optimization, ReduceLROnPlateau scheduling, and Early Stopping to ensure stable convergence and robust generalization. Experimental results demonstrate outstanding performance, achieving 99.72% training accuracy and 99.31% validation accuracy, with convergence at the 14th epoch. Visualization through Grad-CAM reveals that the model focuses on biologically relevant symptom regions, thereby enhancing interpretability and supporting expert validation. Comparative analysis with state-of-the-art methods shows that the proposed model surpasses existing CNN, transfer learning, and hybrid architectures in both accuracy and model transparency. These results indicate that the proposed SE-ResNet50 framework offers a highly accurate, interpretable, and computationally efficient solution suitable for real-world cotton disease monitoring and precision agriculture applications.Clinical trial registrationThis study is not a clinical trial; therefore, clinical trial registration is not applicable.
Why it matches plant phenotyping methods綿花葉の病徴を画像から分類する深層学習フレームワークの開発が中心であり、植物の病害状態を直接推定するため、植物フェノタイピング手法として適格です。
titleA hybrid SE-ResNet50 deep learning framework for high-accuracy and explainable cotton leaf disease classification.
Reproduction assets foundThe paper's Data Availability statement points to the public Kaggle cotton plant disease dataset used for training the SE-ResNet50 model. No author analysis code or trained model checkpoint is explicitly deposited.Dataset · public“Cotton plant disease.” Accessed: Nov. 21, 2025. [Online]. Available: https://www.kaggle.com/datasets/dhamur/cotton-plant-disease.Open asset ↗Kaggle · dhamur/cotton-plant-diseasehtml-lines:458-493Code / dataset availability confirmedEurope PMC · Crossref · checked 5 Sept 2026
Plant diseases pose a major threat to global food security, significantly reducing agricultural yields. Therefore, timely diagnosis of plant diseases can help prevent food losses and support economic stability. This study explores the use of eight Convolutional Neural Networks and two Vision Transformers for apple leaf disease diagnosis. The feature extraction layers of each model were modified to incorporate DropBlock layers, while preserving pretrained weights from the ImageNet dataset. Images from the Plant Pathology 2021 dataset were used to fine-tune the models for multi-label classification, targeting five disease categories and a healthy label. Three experiments were conducted to evaluate model performance on the test set. First, the ResNet50 model was used to determine optimal Dropout and DropBlock probabilities. Second, these parameters were applied across all models to identify those with the best performance. Finally, twenty-three Swarm Optimization Algorithms were used to optimize classifier thresholds, improving accuracy and F1-scores. A DropBlock probability of 0.05 and a Dropout probability of 0.2 yielded superior results. Among the models, SwinV2T attained an accuracy of 90.7%, while SwinV2S achieved the highest F1-score of 91.7%, slightly outperforming the ConvNeXtT and ConvNeXtS architectures. The results demonstrated the effectiveness of DropBlock regularization and optimized classifier thresholds, highlighting the superior performance of recent architectures and optimization algorithms over their older counterparts. These findings suggest that such networks hold substantial promise for accurately identifying and diagnosing apple leaf diseases.
Why it matches plant phenotyping methodsリンゴ葉画像から病害状態を分類・診断する深層学習手法を比較評価し、正則化や閾値最適化による性能改善も検証しており、植物フェノタイピング手法が研究の中心である。
abstractThis study explores the use of eight Convolutional Neural Networks and two Vision Transformers for apple leaf disease diagnosis.
Reproduction assets foundThe paper's apple leaf disease phenotyping is based on the public Plant Pathology 2021 (FGVC8) Kaggle image dataset and an authors' reorganized multi-label version publicly deposited on GitHub; both are explicitly linked in the Data availability statement. No author analysis code or trained model checkpoints are statedDataset · publicFor this research, the dataset was reorganized and extended into a multi-label format. The complete modified dataset is publicly available at: https://github.com/soroushtou/Plant-Pathology-2021---MultiLabel-Dataset.Open asset ↗Plant-Pathology-2021---MultiLabel-Datasetlines:239-262Dataset · publicThe original dataset used in this study is the publicly available Plant Pathology 2021 dataset from the FGVC8 competition available at: https://www.kaggle.com/competitions/plant-pathology-2021-fgvc8.Open asset ↗lines:239-262Code / dataset availability confirmedOpenAlex · Crossref · checked 15 Sept 2026
A comprehensive description of plant phenotypes of certain taxa is an important task when describing genera and species, as well as when setting their natural taxonomies. The development of modern technologies of effective phenotyping makes it possible to obtain a large amount of data with a quantitative and/or qualitative description of various traits in plants, mainly based on the analysis of their digital images. The study compared the results of the F2 hybrids assessment - visually and using machine learning methods - of two endemic tetraploid (2n = 4x = 28) wheat species which are Ethiopian wheat (Triticum aethiopicum Jakubz.) and Kartalian or Dika wheat (T. carthlicum Nevski). In the latter case, it is proposed to use the method of a mixture of Gaussian (normal) distributions in plant morphometry in order to identify groups that differ in character values. Most taxonomically important (species-specific) traits are controlled oligogenically and have a clear phenotypic manifestation, so hybridological analysis was an indispensable and basic type of analysis for subsequent detailed phenotyping of wheat spikes using machine-learning methods. According to a number of criteria, the estimates of patterns of inheritance obtained by different methods coincide. Based on the conducted research, we can state that the trait "tetraaristatum" (the presence of awns on both flower and spike glumes) is species-specific (taxonomically important) for T. carthlicum and it can be effectively used for taxonomic purposes both in carrying out hybridological analysis and in experiments using machine learning. Such a species-specific character is the "character (type) of awnedness" for T. aethiopicum. Our study demonstrates that a combination of automatic phenotyping methods and a model of a mixture of Gaussian distributions can, in principle, lead to an automatic analysis of the allocation of classes in F2 hybrids. It allows, in turn, to detect the presence of genes associated with species-specific traits of wheat plants. Further, the improvement of the applied artificial intelligence (AI) algorithms is required.
Why it matches plant phenotyping methodsコムギ穂の形態形質を対象に、画像に基づく機械学習フェノタイピングとガウス混合モデルを提案・適用しており、表現型の自動抽出・分類が研究の中心である。
abstractThe study compared the results of the F2 hybrids assessment - visually and using machine learning methods
Reproduction assets foundThe paper's supplementary materials (Supplementary Tables S1–S3 and Figure S1) contain the paper-specific phenotyping data: species-specific trait descriptions, the 19 spike morphometric characters per projection, and the Gaussian mixture model splitting results (means, variances, group sizes, χ² values). The full textSupplement · publicof these traits
are controlled by oligogenes and have a clear phenotypic
manifestation, the hybridological method was an indispensable
and primary type of analysis for subsequent detailed
phenotyping spikes of wheat species using machine learning
methods.
Supplementary Materials are available in the online version of the paper:
https://vavilov.elpub.ru/jour/manager/files/Suppl_Kruch_Engl_30_3.pdf
Plant material. The object of study was interspecific
hybrids obtained by crossing two endemic tetraploid
wheat species ♀T. aethiopicum Jakubz. (k-19301/2) with
♂T. carthlicum
Nevski (k-32496). The experiment was produced
in spring sowing in the greenhouses of the Breeding
and Genetics Complex (BGC)Open asset ↗lines:111-200Code / dataset availability confirmedEurope PMC · OpenAlex · checked 13 Sept 2026
Among carnivorous plants, the Venus flytrap (Dionaea muscipula) is known for its rapid (<1 s) trap closure. Although buckling instability, hydrostatic pressure, and hydroelastic coupling have all been proposed to be involved, the nature of this process and the relationship between trap size and curvature remain elusive. Here, we monitored the closure of Venus flytraps and performed micro-CT scanning and 3D reconstruction, revealing that increasing angular velocity was correlated with higher values of a non-dimensional shape index. Based on these experimental data, we constructed a geometric model of the trap that takes leaf orientation into account. We found that leaf curvature is dependent on leaf size, a relationship we denote as a size-curvature constraint. We further propose a curvature design derived from differential deformations of a two-layer model of the leaf, which could be a powerful tool to control the curvatures of soft and bending surface structures in the field of biomimetics.
Why it matches plant phenotyping methodsマイクロCTと3D再構成で葉の閉鎖運動・曲率を定量化し、幾何モデルでサイズ–曲率関係を推定することが研究の中心であり、植物形態・運動状態のフェノタイピング手法に該当する。
abstractHere, we monitored the closure of Venus flytraps and performed micro-CT scanning and 3D reconstruction, revealing that increasing angular velocity was correlated with higher values of a non-dimensional shape index.
Reproduction assets foundThe paper's Data Availability statement points to an authors' GitHub page hosting all data files and related rendering files for the Venus flytrap closure measurements and 3D reconstructions, matching an allowed URL.Dataset · publicAll data files and related rendering files are available from the github ( https://satorutsugawa.github.io/flytrap_geometric_model_datashare/) .Open asset ↗githublines:105-144Code / dataset availability confirmedEurope PMC · OpenAlex · checked 5 Sept 2026
The vertical heterogeneity of rice canopy structure limits the accuracy of inverting leaf physicochemical parameters using traditional radiative transfer models, while LiDAR-based 3D reconstruction remains costly for large-scale applications. To address these challenges, this study proposes a method for constructing 3D rice canopy scenes using "Precision Mode" and "Rapid Mode" strategies. The Precision Mode builds detailed structural models based on measured morphological parameters, validated via the LESS 3D radiative transfer model. To overcome the limitations of obtaining detailed morphology via UAV remote sensing, the Rapid Mode employs machine learning algorithms-specifically Support Vector Machine (SVM), Random Forest (RF), and XGBoost-to map easily accessible parameters (LAI, Above-ground Biomass, Plant Height, and Transplanting Date) to detailed 3D structural parameters. Results indicate that XGBoost achieves the highest accuracy in the Rapid Mode. Furthermore, simulated spectra under both modes showed high consistency with measured spectra, yielding average RMSE values of 0.0104 (R 2 = 0.9965) for the Precision Mode and 0.0307 (R 2 = 0.9694) for the Rapid Mode. Although the spectral accuracy of the Rapid Mode is slightly lower, its modeling efficiency is significantly enhanced, retaining a strong capability to reproduce spectral response characteristics across growth stages. This approach provides an effective tool for analyzing vertical spectral response mechanisms and offers an efficient data simulation scheme for UAV remote sensing parameter inversion based on 3D radiative transfer models.
Why it matches plant phenotyping methodsイネ群落の3D構造を構築・推定する手法を開発し、放射伝達モデルと実測スペクトルで検証しており、植物形質の取得・再現が研究の中心です。
abstractthis study proposes a method for constructing 3D rice canopy scenes using "Precision Mode" and "Rapid Mode" strategies.
Reproduction assets foundThe paper's Data Availability statement says the collected phenotype/structural/spectral data are publicly available on the authors' GitHub repository (allowed URL), while the analysis code is only available from the corresponding author upon request (request_only, no public URL).Dataset · publicThe data collected and used in this study are publicly available at: https://github.com/baijc4095-code/2024data . The code used for analysis can be obtained from the corresponding author upon reasonable request.Open asset ↗baijc4095-code/2024datalines:240-256Code / dataset availability confirmedCrossref · checked 14 Sept 2026
Published23 May 2026Informatika: Jurnal Teknik Informatika dan MultimediaCited by 1 · OpenAlex ↗
Early identification of Rice leaf diseases remains a challenge in agricultural practices, as detection is commonly performed through manual visual observation that is time-consuming and prone to misclassification. Diseases such as blast, Bacterial Leaf Blight, tungro, and Brown Spot often exhibit similar visual characteristics, particularly at early stages. To address this problem, an Android-based application was developed to classify Rice leaf diseases using a Convolutional Neural Network (CNN) with a transfer learning approach based on the MobileNetV3 architecture. The model was trained using a labeled Rice leaf image Dataset obtained from Hugging Face, with preprocessing and data augmentation applied to improve generalization performance. The trained model was deployed through Hugging Face Space using an API-based architecture, allowing image classification to be performed without heavy computational requirements on mobile devices. Experimental results demonstrate that the proposed model achieved an accuracy of approximately 90% on the testing Dataset, exceeding the predefined minimum target accuracy of 85%, with precision and recall values above 80% across all disease classes based on confusion matrix evaluation. These results indicate that the MobileNetV3-based transfer learning approach provides reliable classification performance with good computational efficiency, making it suitable for mobile-based Rice leaf disease detection applications.
Why it matches plant phenotyping methodsイネ葉の画像から病害状態を分類するCNN手法を開発・評価し、モバイル実装まで行っているため、植物病害フェノタイピング手法が中心です。
abstractan Android-based application was developed to classify Rice leaf diseases using a Convolutional Neural Network (CNN) with a transfer learning approach based on the MobileNetV3 architecture
Reproduction assets foundThe paper's plant-phenotyping input is a public labeled rice leaf disease image dataset obtained from Hugging Face (girish787/riceLeafDataset), used to train the MobileNetV3 classifier. No author analysis code or trained model checkpoint is explicitly deposited.Dataset · public[12] G. Kumar, “riceLeafDataset.” Apr. 25, 2024. Accessed: Oct. 20, 2025. [Online]. Available:
https://huggingface.co/Datasets/girish787/riceLeafDatasetOpen asset ↗huggingface.co/Datasets/girish787/riceLeafDataset · girish787/riceLeafDatasetpdf-page:10 lines:1-44Code / dataset availability confirmedEurope PMC · Crossref · checked 5 Sept 2026
Abstract Chlorophyll estimation is fundamental in plant physiology, crop management, and ecological studies; however, destructive and non-destructive methods are often interpreted interchangeably despite differing measurement principles. The present study compared four chlorophyll estimation approaches—two non-destructive (SPAD meter and GreenSeeker) and two destructive (80% acetone and DMSO extraction)—across eight crop species under uniform field conditions. Significant interspecific variation was observed for all methods. Correlation and regression analyses revealed generally weak relationships among methods, particularly between leaf-level (SPAD, solvent extraction) and canopy-level (GreenSeeker) measurements, reflecting scale-dependent behavior and methodological differences. Moderate associations were observed between SPAD and acetone-extracted chlorophyll for certain traits, whereas GreenSeeker showed poor agreement with solvent-based estimates. Differences between DMSO and acetone extraction further highlighted solvent-specific extraction efficiency. The results demonstrate that chlorophyll estimation methods are not directly interchangeable and should be selected based on study objectives, biological scale, and leaf anatomical characteristics. Species-specific calibration and integration of canopy structural parameters are required to improve cross-method interpretability.
Why it matches plant phenotyping methods複数の葉・キャノピーのクロロフィル推定法を作物種間で比較し、相関、回帰、スケール依存性、互換性を評価しており、植物表現型測定法の技術的検証が中心である。
abstractThe present study compared four chlorophyll estimation approaches—two non-destructive (SPAD meter and GreenSeeker) and two destructive (80% acetone and DMSO extraction)—across eight crop species under uniform field conditions.
Reproduction assets foundThe preprint declares that the datasets generated in this chlorophyll-method comparison study (SPAD, GreenSeeker, acetone and DMSO measurements across eight crop species) are publicly deposited in Figshare under DOI 10.6084/m9.figshare.31817989. This is a paper-specific, publicly actionable phenotype dataset. No authorDataset · publicThe datasets generated during the current study are available in the Figshare repository, https://doi.org/10.6084/m9.figshare.31817989Open asset ↗Figshare · 10.6084/m9.figshare.31817989lines:163-185Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
The increasing global food insecurity driven by climate-induced natural hazards and soil degradation has made the resilience of alternative agricultural systems a critical focus in risk management. This study presents a geospatially integrated monitoring framework, the Optimized Multi-Scale Adaptive Graph Neural Network (OMSA-GNN), designed to mitigate risks associated with nutrient instability in hydroponic and aeroponic environments. The proposed system leverages a Raspberry Pi-based IoT network to monitor complex interactions among microclimatic variables, plant physiological health, and nutrient concentrations, treating them as localized geospatial data points. To enhance decision-making under environmental uncertainty, an Improved Sparrow Search Algorithm (ISSA) is employed to optimize the predictive performance of the GNN. The OMSA-GNN model incorporates visual plant indices as a proximal remote sensing approach to enable early detection of physiological stress that may lead to crop failure. Evaluated using a lettuce growth dataset, the framework demonstrates superior performance in forecasting growth trajectories and managing resource-related risks compared to conventional static models. The results highlight a scalable approach for improving the reliability of urban food systems, where traditional land-based agriculture is increasingly vulnerable to natural hazards.
Why it matches plant phenotyping methods植物の生理的ストレスと成長軌跡を、視覚的植物指数およびIoTセンサーデータから推定するGNNベースの監視・解析手法が研究の中心であり、植物表現型取得と予測に該当する。
abstractThe OMSA-GNN model incorporates visual plant indices as a proximal remote sensing approach to enable early detection of physiological stress that may lead to crop failure.
Reproduction assets foundThe paper's Data Availability statement points to a public Kaggle lettuce growth dataset used for evaluation, matching an allowed URL. No author code or model checkpoints are disclosed.Dataset · publicThe datasets used and/or analyzed during the current study are available in the Kaggle repository, https://www.kaggle.com/datasets/jurijsruko/lettuce/data.Open asset ↗Kaggle · jurijsruko/lettucehtml-lines:469-500Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Tomato diseases pose a significant threat to global agricultural production, often leading to substantial yield loss and major economic damage. Traditional disease detection methods rely on manual inspection, which is not only time-consuming and labor-intensive but also difficult to implement for real-time monitoring. While deep learning-based object detection techniques offer a potential alternative to manual inspection, existing models still face challenges in extracting subtle disease features, suppressing complex background interference, and in handling multi-scale disease representations in complex agricultural environments, limiting detection performance. To address these limitations, this paper proposes a novel TDD-YOLO model for precise tomato-disease detection (TDD) in complex agricultural settings. The proposed model is based on YOLOv11 with the following three main improvements: (1) a feature enhancement module is added to improve the backbone's ability to extract disease spot textures; (2) a joint attention mechanism is introduced to explicitly model cross-dimensional dependencies, effectively suppressing background interference; and (3) a feature fusion module is added to retain disease information across different scales while reducing computational costs. Experimental results, obtained on the Tomato-Village dataset (containing field-acquired images of tomato leaves with six diseases, collected in real agricultural environments, featuring complex backgrounds and varying illumination conditions) and Tomato-Disease dataset (emphasizing a greater diversity in tomato disease types along with healthy leaf samples), demonstrate that the proposed TDD-YOLO model outperforms the baseline in detection of tomato diseases (e.g., by improving mAP@50 and mAP@50:95, averaged across disease categories, by 4.1% and 6.0% on Tomato-Village and by 3.6% and 3.9% on Tomato-Disease, respectively) and state-of-the-art models (e.g., by improving the average mAP@50 and mAP@50:95, compared to the first runner-up, by 3.2% and 4.7% on Tomato-Village and by 2.4% and 2.1% on Tomato-Disease, respectively), while maintaining good parameter count and computational complexity, confirming its effectiveness and potential for practical usage in complex agricultural environments. The author-generated code and weight files are publicly available at https://github.com/LingShaQ/TDD-YOLOCode.
Why it matches plant phenotyping methodsトマト葉の病斑・病害状態を画像から検出するYOLOモデルを開発し、複数データセットでベースラインおよび既存モデルと比較検証しており、植物病害フェノタイピング手法が中心である。
abstractExperimental results, obtained on the Tomato-Village dataset
Reproduction assets foundThe paper's tomato-disease detection experiments rely on two public image/annotation datasets (Tomato-Village on GitHub, Tomato-Disease on Zenodo), and the authors explicitly state their generated code and weight files are publicly available on GitHub. The Ultralytics YOLO repositories are generic third-party librariesCode · publicThe author-generated code and weight files are publicly available at https://github.com/LingShaQ/TDD-YOLOCode.Open asset ↗LingShaQ/TDD-YOLOCodehtml-lines:110-113Dataset · publicAll data used in this article are obtained from the publicly available Tomato-Village dataset (https://github.com/mamta-joshi-gehlot/Tomato-Village)Open asset ↗mamta-joshi-gehlot/Tomato-Villagehtml-lines:1159-1171Dataset · publicthe publicly available Tomato-Disease dataset (https://zenodo.org/records/15868289).Open asset ↗html-lines:1159-1171Code / dataset availability confirmedCrossref · Europe PMC · checked 5 Sept 2026
Introduction Confidence calibration, selective prediction, out-of-distribution scoring, and deep ensembles are mature techniques in machine learning, yet their efficacy under the severe domain shift encountered when plant disease classifiers move from controlled laboratory imagery to heterogeneous field photographs has not been systematically benchmarked. Methods Models trained on PlantVillage were evaluated on PlantDoc leaf-level crop images under a parent-image-aware split protocol, and a suite of standard mitigation techniques was applied to characterize the reliability gap. Analyses included temperature scaling and selective prediction for a fine-tuned ResNet-50, quantitative image-level shift analysis, Grad-CAM visualization, simple target-aware adaptation baselines, frozen-feature backbone comparisons, and ensemble baselines. Results In the primary case study, a fine-tuned ResNet-50 suffered a 67.7-percentage-point accuracy collapse upon cross-domain transfer, while mean predicted confidence remained at 79.76%. Post-hoc temperature scaling reduced calibrated ECE to 0.3645 but left selective risk at 80% coverage at 64.30%. Quantitative image-level shift analysis confirmed large-effect-size differences in saturation ( d = 3.90), border edge density ( d = 3.33), and foreground-occupancy proxy ( d = 2.48) between the two domains, while Grad-CAM visualizations showed that the model shifts attention from lesion-centered regions in PlantVillage to background-dominated areas in PlantDoc. Simple target-aware mitigations, including adaptive batch normalization and feature moment matching, improved accuracy from 0.321 to 0.343 and 0.366, respectively, whereas DANN-style adversarial adaptation degraded performance to 0.252. A frozen-feature backbone comparison across five backbones showed that, within the energy-scoring frozen-backbone comparison, DINOv2-S/14 achieved the highest unknown-detection AUROC (0.764) and the lowest selective risk at 80% coverage (0.520), with paired Wilcoxon tests confirming statistically significant accuracy and macro-F1 differences across backbones. Two ensemble baselines were evaluated: a warm-start end-to-end ResNet-50 ensemble reduced calibrated ECE to 0.063 but achieved only 0.666 AUROC, while a lightweight DINOv2 linear-probe ensemble achieved 0.779 AUROC after calibration but under limited epistemic diversity. Discussion Neither ensemble established deployment-grade reliability: the best selective risk at 80% coverage across all configurations remained above 0.51. The principal contribution is a reproducible, deployment-oriented reliability characterization showing that standard post-hoc and lightweight adaptation techniques reduce but do not eliminate the severe reliability gap under controlled-to-field transfer in agricultural computer vision.
Why it matches plant phenotyping methods植物病害画像分類の信頼性・ドメインシフト・校正・選択的予測を体系的にベンチマークしており、病害状態を画像から推定する方法の技術評価が中心である。
abstracttheir efficacy under the severe domain shift encountered when plant disease classifiers move from controlled laboratory imagery to heterogeneous field photographs has not been systematically benchmarked.
Reproduction assets found本文中に内容が明示された植物フェノタイピング関連の補足表と、その公開リンクを確認しました。Supplement · publicSupplementary Table 1 ) was therefore constructed by normalizing all labels to a canonical Crop_Disease format and retaining only those categories for which an unambiguous semantic match existed in both datasets.Open asset ↗lines:335-337Code / dataset availability confirmedCrossref · checked 15 Sept 2026
Published22 May 2026JITK (Jurnal Ilmu Pengetahuan dan Teknologi Komputer)Cited by 0 · OpenAlex ↗
Plant leaf diseases are a major factor in reducing agricultural productivity, particularly for local commodities that often lack adequate artificial intelligence-based disease detection systems. This study aims to optimize the performance of a Convolutional Neural Network (CNN) model using the Inception V3 architecture through the application of multi-stage data augmentation to improve the classification accuracy of local plant leaf diseases. The dataset used is PlantifyDR from Kaggle, which has limited data volume and visual variation, requiring an effective augmentation strategy to improve the model's generalization ability. The proposed multi-stage augmentation approach consists of three stages—geometric, photometric, and texture-noise augmentation—that systematically enrich the diversity of training images. Evaluation results show that the proposed model provides significant performance improvements compared to the baseline model. The Inception V3 model with multi-stage augmentation achieved an accuracy of 0.762, an F1-score of 0.727, and a perfect AUC (1.00) across all classes, while the baseline model only achieved an accuracy of 0.595 and an average AUC of 0.877. Accuracy, loss, ROC curve, and confusion matrix analyses confirmed that multi-stage augmentation reduced overfitting and enhanced the model's ability to differentiate disease symptoms across leaf types. Therefore, this study concludes that multi-stage data augmentation is an effective approach for optimizing deep learning models on small and complex datasets, while also providing a significant contribution to the development of more accurate and reliable AI-based plant disease detection systems.
Why it matches plant phenotyping methods葉画像から植物病害症状を分類するCNNと、性能改善のための多段階データ拡張を開発・評価しており、植物の病害状態を推定する画像ベースのフェノタイピング手法が中心です。
abstractThis study aims to optimize the performance of a Convolutional Neural Network (CNN) model using the Inception V3 architecture through the application of multi-stage data augmentation to improve the classification accuracy of local plant leaf diseases.
Reproduction assets foundThe paper's plant leaf disease classification experiments use the publicly available PlantifyDR Kaggle dataset (Apple, Berry, Guava leaf images), which is the image input for the study's phenotyping measurements. No author analysis code or trained model checkpoints are reported as publicly deposited.Dataset · publice: (Research Results, 2025)
Figure 1. Sample Image from the Research Dataset
Figure 1 shows a sample of the research data.
The dataset used in this study was obtained from
the open dataset platform Kaggle under the title
"PlantifyDR Dataset," provided by Lavaman151.
The dataset is publicly accessible through the
following link:
https://www.kaggle.com/datasets/lavaman151/pl
antifydr-dataset. This dataset is a collection of plant
leaf images from several species, including Apple,
Berry, and Guava, categorized based on leaf health,
making it relevant for plant disease classification
research.
Comparison of the Baseline Model with the
Proposed Model (Multi-Stage Data
Augmentation)
This subsectioOpen asset ↗lavaman151pdf-raw-page:4 lines:1-150Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
The research proposes Cross Disease Similarity Awareness Learning (CDSAL), a robust multiclass tomato leaf disease detection framework based on high-quality and explainable deep learning. The approach solves the problem of superimposed patterns of disease especially Leaf Miner, Tomato Spotted Wilt Virus (TSWV), and nutrient deficiencies through the combination of multi-domain feature learning and inter-disease similarity modeling. In contrast to conventional metric learning or contrastive learning methods that function on pairwise or triplet sample associations, CDSAL develops a class-level Cross Disease Similarity Matrix that represents structured inter-disease proximity within the embedding space. Moreover, rather than employing episodic prototype construction typical of few-shot learning, the proposed system persistently updates centroid representations throughout supervised training and incorporates similarity-aware regularization directly into the loss function. This facilitates structural embedding reshaping specifically designed for visually overlapping illness categories, beyond traditional prototype-based learning methodologies. The input images are processed through HSV based green masking, morphological cleaning, extraction of leaf contours and resizing, and using a large amount of geometric and color-space augmentation to reduce the imbalance among the classes. DenseNet121 and EfficientNet-B0 are used to obtain feature representations and class-separated centroid of latent embedding's to form a Cross Disease Similarity Matrix, where similarity-aware optimization is possible during training. Grad-CAM on the target layers offers decipherable disease-specific activation signatures. The findings of the experiments show that classification accuracy at unseen samples is 99.77% with high resilience to visual confounding. The predictions, proximity of diseases that are similar and explainable features are provided by CDSAL, thereby facilitating reliable decision-making in agricultural diagnostics.
Why it matches plant phenotyping methodsトマト葉の病害状態を画像から推定する深層学習手法を提案し、前処理・特徴抽出・類似度学習・説明可能性を技術的中心として評価しているため。
abstractThe research proposes Cross Disease Similarity Awareness Learning (CDSAL), a robust multiclass tomato leaf disease detection framework based on high-quality and explainable deep learning.
Reproduction assets foundThe paper's plant-phenotyping inputs are two publicly available Kaggle image datasets explicitly named in the Data Availability statement: PlantVillage (emmarex/plantdisease) used as the main dataset and TomatoVillage (mamtag/tomato-village) used for ablation/field-condition experiments. No author analysis code, modelsDataset · publicThe datasets analyzed during the current study are available in the Kaggle repository. [https://www.kaggle.com/datasets/emmarex/plantdisease]Open asset ↗Kaggle · emmarex/plantdiseasehtml-lines:605-624Code / dataset availability confirmedCrossref · checked 15 Sept 2026
Accurately estimating leaf area index (LAI) is vital for evaluating crop growth and predicting yields. Conventional approaches, however, often struggle due to the limited representativeness of available data and the complex structure of plant canopies, which reduce their reliability across diverse canopy architectures and observation conditions. To overcome these challenges, this work introduces an LAI retrieval framework that combines a three-dimensional radiative transfer model (3D RTM) with deep learning techniques. Representative 3D maize canopy scenarios were generated using the LESS model, producing synthetic LiDAR point clouds constrained by realistic structural parameters. A deep learning model based on PointNet++ was trained, and transfer learning (TL) was employed to facilitate knowledge transfer from simulated to actual measured data. The TL-enhanced model demonstrated significant improvement, with R2 rising from 0.537 to 0.842 and RMSE dropping from 0.541 to 0.288 m2·m−2. Moreover, retrieval performance was notably affected by scanning mode, angle, and stem diameter, achieving optimal results under TLS acquisition, moderate scanning angles, and intermediate stem widths. These findings suggest that integrating 3D RTM-generated synthetic point clouds with transfer learning is an effective strategy for enhancing the robustness and generalization of LiDAR-based LAI retrieval.
Why it matches plant phenotyping methodsLiDAR点群からトウモロコシのLAIを推定する手法を、3D放射伝達モデル、PointNet++、転移学習で開発・検証しており、植物形態形質の取得・推定が研究の中心です。
abstractthis work introduces an LAI retrieval framework that combines a three-dimensional radiative transfer model (3D RTM) with deep learning techniques.
Reproduction assets foundThe paper's field-measured LiDAR point cloud and LAI data (Yingke Oasis and Huazhaizi sites) come from a publicly accessible TPDC dataset with an explicit URL in the Data Availability Statement. No author analysis code, trained models, or synthetic dataset deposit is stated.Dataset · public2024WX06.
Data Availability Statement: The dataset used in this study was obtained from the National Tibetan
Plateau Data Center (TPDC, https://www.tpdc.ac.cn/ (accessed on 6 September 2025)), a publicly
accessible scientific data platform providing multi-source geoscientific datasets. The specific dataset
can be accessed via: https://www.tpdc.ac.cn/zh-hans/data/4d60d570-0aa9-417b-8a9d-c32b73b564
(accessed on 6 September 2025). The TPDC database integrates long-term observational and remote
sensing data with standardized quality control, ensuring the reliability and consistency of the datasets
for scientific research.
Acknowledgments: The authors would like to acknowledge the National TibetaOpen asset ↗4d60d570-0aa9-417b-8a9d-c32b73b564pdf-raw-page:19 lines:1-51Code / dataset availability confirmedEurope PMC · checked 8 Sept 2026
Field / plotMultimodalWhole plant / canopy / plot / fieldClassificationCountingGrowth / development / phenology
Phenological monitoring of Actinidia chinensis is critical for optimising operational costs and yield prediction. However, current manual assessment methods are time-consuming, making them impractical for large-scale precision agriculture applications. Most existing phenological datasets focus exclusively on image data without spatial validation. The Multi-Modal Actinidia chinensis Phenology Dataset is composed of (i) 1 665 annotated images of phenological stages from bud to fruit set and (ii) georeferenced videos with systematic manual ground truth of spatial stage distributions. The dataset employs an adapted 17-class BBCH system that consolidates visually similar stages, excludes problematic categories, and introduces generic structural classes to address practical annotation difficulties. Additionally, the data is organised hierarchically across various plant structures, genders, and phenological stages. The annotated images offer versatility for a range of applications, including training data for computer vision models to detect phenological stages. Furthermore, the georeferenced videos facilitate the validation of automated counting algorithms. This combined approach enables plant-level detection accuracy and provides an illustrative methodology for spatial validation that users can extend to additional orchards, promoting the development and benchmarking of automated phenological monitoring systems for precision agriculture applications in kiwifruit production.
Why it matches plant phenotyping methodsキウイフルーツの生育段階を対象とした注釈画像・地理参照動画データセットであり、自動フェノロジー検出と空間検証のためのベンチマーク基盤が中心である。
abstractThe Multi-Modal Actinidia chinensis Phenology Dataset is composed of (i) 1 665 annotated images of phenological stages from bud to fruit set and (ii) georeferenced videos with systematic manual ground truth of spatial stage distributions.
Reproduction assets foundThe paper describes a public multi-modal Actinidia chinensis phenology dataset (annotated images, georeferenced videos, ground-truth counts) deposited on Zenodo, plus authors' MIT-licensed preprocessing scripts on GitHub. CVAT and FiftyOne are generic third-party tools and excluded.Dataset · publicThe Multi-Modal Actinidia chinensis Phenology Dataset described in this Data Descriptor is publicly available
at Zenodo: https://doi.org/10.5281/zenodo.17371025.Open asset ↗Zenodo · 10.5281/zenodo.17371025pdf-page:12 lines:1-92Code · publicCustom scripts for dataset preparation are publicly available under the MIT License at https://github.com/Open asset ↗GitHubpdf-page:12 lines:1-92Code / dataset availability confirmedCrossref · checked 14 Sept 2026
Chili peppers (Capsicum annuum L.) are a strategic horticultural commodity in Indonesia, but their productivity is often hampered by pathogen infections that cause leaf diseases such as anthracnose, leaf spot, and yellow virus. Early detection by farmers is still dominated by subjective visual observation and prone to misdiagnosis due to the similarity of symptoms between diseases. Although Deep Learning technology through Convolutional Neural Networks (CNN) offers an automated solution, implementation in real-world conditions still faces significant challenges such as lighting variations, complex backgrounds, and limited local datasets. This often leads to a drastic decrease in model performance compared to testing in a controlled environment. To address these issues, this study proposes an optimization of the transfer learning strategy on the MobileNetV2 architecture by integrating progressive layer-wise fine-tuning and adaptive data augmentation techniques. The fine-tuning method is carried out gradually on the pre-trained model layers, while adaptive augmentation dynamically manipulates images based on environmental characteristics to improve model robustness. The results of this study, which include multi-class classification on cross-location image data, are projected to be able to boost the accuracy and generalization ability of the model in heterogeneous field conditions. Practically, this research provides a framework for a more precise and robust disease detection system to accelerate the implementation of precision agriculture in the future.
Why it matches plant phenotyping methods植物葉の病徴を画像から分類するCNN手法の改良が研究の中心であり、病害状態の表現型推定に該当する。転移学習のファインチューニングと適応的画像拡張、異なる圃場条件での頑健性評価を扱っている。
abstractThe results of this study, which include multi-class classification on cross-location image data, are projected to be able to boost the accuracy and generalization ability of the model in heterogeneous field conditions.
Reproduction assets foundThe paper states its chili leaf image dataset was supplemented with data from a supporting repository, cited as a public Mendeley Data deposit (reference [2]). This is a public plant-image dataset directly used for the paper's disease-classification phenotyping. No authors' analysis code or trained model checkpoint is,Dataset · public[2] F. Wajidi and N. Arifin, “Deteksi Penyakit Daun Cabai Menggunakan Kombinasi GLCM dan HSV dengan
Klasifikasi SVM,” vol. 11, no. 02, 2025. [Online]. Available:
https://data.mendeley.com/datasets/w9mr3vf56s/1Open asset ↗w9mr3vf56s/1pdf-page:9 lines:1-56Code / dataset availability confirmedCrossref · Europe PMC · checked 15 Sept 2026
Abstract Plant diseases are a serious danger to the world’s food security, because they lower agricultural output and increase economic losses. Due to subjectivity, fluctuating lighting, and environmental unpredictability, traditional visual examination techniques are frequently incorrect. The Excess Green (ExG) vegetation index and pseudo-thermal representations produced from RGB pictures are two synthetically developed complementary representations that are integrated with RGB imagery in this study’s lightweight multimodal deep learning system to address these issues. Histogram shifting and pseudo-infrared color mapping are used in a reproducible picture alteration pipeline to create the pseudo-thermal modality, which allows for extra visual signals without the need for specific thermal sensors. In order to classify plant diseases while preserving computational efficiency, the suggested framework uses MobileNetV3-Small backbones to extract modality-specific characteristics. This is followed by feature-level fusion. The publicly accessible Ginger Leaf Dataset, which includes RGB pictures of ginger leaves in four different conditions—Damage-Pest, Dehydrated, Healthy, and Leaf-blight—was used for the experiments. For training, validation, and testing, the dataset was split using a stratified 70:15:15 split. Python-based preprocessing procedures were used to create the extra modalities (ExG and pseudo-thermal representations) from the original RGB images. The experimental results show that the combination of the representations with RGB images can enhance the classification performance compared with the unimodal RGB-based models. Ablation experiments are also conducted to examine the contributions of different modalities to the overall categorization accuracy. The experimental results show that plant disease recognition can be improved with the help of efficient computing by combining lightweight convolutional neural networks with computationally generated visual representations.
Why it matches plant phenotyping methodsRGB画像からExG・疑似熱画像を生成し、植物葉の病害状態を分類するマルチモーダル手法が研究の中心であり、アブレーション評価も実施している。
titleHybrid deep learning-based multimodal framework for plant leaf disease classification using RGB, Excess Green (ExG), and pseudo-thermal representations with MobileNetV2
Reproduction assets foundThe paper's phenotyping experiments use the publicly available Ginger Leaf Dataset (RGB leaf images of four ginger leaf conditions), with a public GitHub repository and dataset website. The authors' derived ExG/pseudo-thermal representations and preprocessing scripts are only available upon request, so they do not yetDataset · publicor multispectral images
IEEE Geosci. Remote Sens. Lett. 2025
10.1109/LGRS.2025.XXXXXXX
Ulku, I., Tanriover, O. O. & Akagündüz, E. Cross-band correlation-aware interactive fusion for multispectral images. IEEE Geosci. Remote Sens. Lett.
10.1109/LGRS.2025.XXXXXXX
(2025).
10. Wong, J. Ginger Leaf Dataset. GitHub Repository (2023). https://github.com/wongjay1941/Ginger-Leaf-Dataset
11.
Bhakta I
A novel plant disease prediction model based on thermal images using modified deep convolutional neural network
Precis. Agric. 2023 24 23 39
10.1007/s11119-022-09927-x
Bhakta, I. et al. A novel plant disease prediction model based on thermal images using modified deep convolutional neural network. Precis.Open asset ↗https://github.com/wongjay1941/Ginger-Leaf-Datasetlines:580-681Code / dataset availability confirmedCrossref · Europe PMC · checked 5 Sept 2026
Three-dimensional (3D) procedural plant architecture models have emerged as an important tool for simulation-based studies of plant structure and function, extracting plant architectural parameters from field measurements, and for generating realistic plants in computer graphics. However, measuring the architectural parameters for these models at the field and population scales remains prohibitively labor-intensive. We present a novel algorithm that generates the 3D plant architecture from an image, to create a functional structural plant model from an image that reflects organ-level geometric and topological parameters, providing a more comprehensive representation of the plant’s architecture. Instead of using 3D sensors or processing multi-view images with computer vision to obtain the 3D structure of plants, we propose a method that generates token sequences containing a procedural definition of the plant architecture. This work uses only synthetic images for training and testing, where “exact” architectural parameters were known, which allowed for testing of the hypothesis that organ-level architectural parameters could be extracted from imagery data using a vision language model (VLM). A synthetic dataset of cowpea plant images was generated using the Helios 3D plant simulator, with the detailed plant architecture encoded in XML files. We developed a plant architecture tokenizer for the XML file defining plant architecture, converting it into a token sequence that a language model can predict. Then, a VLM was trained to predict plant architecture token sequences from images. Our results demonstrate that the model can predict plant architecture tokens with an F1 score of 0.73 in a teacher-forcing method. Evaluation of the model was performed through autoregressive generation, achieving a BLEU-4 score of 94.00% and a ROUGE-L score of 0.5182. Our model achieves lower MAPE than feature regression-based methods in estimating bulk plant-level traits that require understanding of the occluded 3D structure of the plant, such as leaf count and leaf area. We conclude that generating plant architecture and parameter extraction from synthetic imagery are feasible using a VLM approach, supporting future extension to real imagery.
Why it matches plant phenotyping methods画像から器官レベルの植物構造と形態形質を抽出するVLM手法の開発・評価が中心であり、植物フェノタイピング手法に該当する。
abstractWe present a novel algorithm that generates the 3D plant architecture from an image, to create a functional structural plant model from an image that reflects organ-level geometric and topological parameters
Reproduction assets foundThe paper's footnotes explicitly state that the authors' code is available on GitHub and the synthetic cowpea image/XML dataset is available on Hugging Face, both paper-specific and publicly actionable. The Helios URL is a generic third-party simulator library, not a paper-specific asset.Code · public1. ^ Code is available at: https://github.com/GEMINI-Breeding/Image2PlantArchitecture .Open asset ↗GEMINI-Breeding/Image2PlantArchitecturelines:600-676Dataset · public2. ^ Dataset is available at: https://huggingface.co/datasets/heesup/Cowpea-Architecture-XML .Open asset ↗heesup/Cowpea-Architecture-XMLlines:600-676Code / dataset availability confirmedEurope PMC · checked 14 Sept 2026
Many countries greatly rely on agriculture as a means of livelihood and economic growth. Even the most industrialized countries need food, medicine, clothing, and shelter produced by crops. Rice is one of the most significant and widely grown crops worldwide. Nonetheless, the severely impacted crops in rice production are those of bacteria, fungi, and viruses, which decrease yield and quality. Manual disease detection is hectic, challenging, and, in most cases, inaccurate. Recent advances in deep learning and computer vision have demonstrated significant potential to improve the detection and classification of diseases. This study proposes a deep learning hybrid model for the automated detection and classification of rice leaf diseases. This method consists of five key stages: image preprocessing, segmentation, augmentation, multi-feature extraction via adaptive fusion, and classification. There are five rice leaf diseases to discuss and recognize: Blight, brown spot, sheath blight, tungro, and leaf blast. The first step is global contrast enhancement, which improves image quality. After that, the segmentation is performed using Otsu's Thresholding to extract the leaf area. Then, the modified VGG16 and modified ResNet50 networks are used in parallel to extract features using a transfer-learning approach. The adaptive fusion technique combines these features to obtain a dominant, proper feature representation. Lastly, the classification is done using an adaptive fusion score technique. Experimental results show excellent performance, with class-wise Precision in the range of 95.5-100%, class-wise recall in the range of 97.4-100%, and overall test accuracy of 98.5%.
Why it matches plant phenotyping methodsイネ葉の病害状態を画像から自動検出・分類する深層学習ワークフローが研究の中心であり、葉領域抽出、特徴抽出、分類性能まで評価しているため、植物病害フェノタイピング手法に該当する。
abstractThis study proposes a deep learning hybrid model for the automated detection and classification of rice leaf diseases.
Reproduction assets found保存済みの本文根拠を更新済みルールで再検証し、公開資産1件を確認しました。Dataset · publicThe dataset employed in this study is accessible online at https://www.kaggle.com/datasets/rajeshbhattacharjee/rice-diseases-using-cnn-and-svm.Open asset ↗Kaggle · rajeshbhattacharjee/rice-diseases-using-cnn-and-svmhtml-lines:929-951Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Introduction Under small-sample conditions, hyperspectral leaf chlorophyll estimation is affected by high-dimensional collinearity, measurement noise, and cross-source acquisition discrepancies. Existing studies often treat training-distribution expansion and model-error complementarity separately. This study proposed a physically constrained composite spectral augmentation-weighted ensemble framework for reproducible small-sample chlorophyll estimation. Methods Using 1,113 valid spectrum-label pairs from the leaf subset of the GreenHySpectra dataset in the 400-1000 nm range, spectra and chlorophyll reference values were matched by sample identifiers and divided into training and validation sets. Low-magnitude Gaussian noise and smooth wavelength warping were applied only to the training set. XGBoost, partial least squares regression, and ridge regression were optimized with Optuna using a CMA-ES sampler, and ensemble weights were calibrated by Bayesian optimization. An independent external set of 90 tomato leaf samples was used to evaluate transferability. Results Composite augmentation improved model stability and reduced validation error relative to the non-augmented baseline. The weighted ensemble model achieved the best internal performance, with R² = 0.6392 and RMSE = 8.8883. On the external samples, the model achieved R² = 0.498 and RMSE = 9.801. Discussion The proposed workflow integrates physically plausible augmentation, heterogeneous learner complementarity, and independent external validation. The external results indicate partial cross-source transferability while highlighting distributional and measurement-chain discrepancies that still limit absolute generalization.
Why it matches plant phenotyping methods葉のクロロフィル量という植物形質をハイパースペクトルから推定する手法を開発し、外部データで転移性を検証しており、表現型取得・推定が研究の中心である。
titleHyperspectral estimation of leaf chlorophyll under small-sample conditions via spectral augmentation and weighted ensemble learning.
Reproduction assets foundThe paper's phenotyping analysis is built on the public GreenHySpectra hyperspectral dataset (leaf subset, 1,113 spectrum–chlorophyll pairs), which is a paper-specific, publicly available input with an authors' cited URL matching the allowed list. No author analysis code, trained models, or public deposit of the 90-solDataset · publicAvatarr05 ( 2023 ). GreenHySpectra/GreenHyperSpectra dataset (Hugging Face Datasets) [WWW document] . Available online at: https://huggingface.co/datasets/Avatarr05/GreenHySpectra (Accessed May 15, 2026).Open asset ↗Hugging Face Datasets · Avatarr05/GreenHySpectralines:749-785Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
The citrus diseases are affecting the fruit production worldwide thereby posing an economical burden. Major research is moving towards finding solutions using Artificial Intelligence (AI) and Image processing methods. Due to factors like illumination variations, leaf form, and disease symptoms, image data has intrinsic uncertainties that are typically difficult for traditional machine learning techniques to handle. In this paper, the interpretability of fuzzy logic is combined with the resilience of deep learning to propose a novel Fuzzy Convolutional Neural Network (Fuzzy-CNN) architecture for the automated diagnosis of citrus leaf diseases. The hybrid method uses a Convolutional Neural Network (CNN) to obtain complex features of citrus images, and a Fuzzy Inference System (FIS) to improve the classification results. The proposed approach encodes accurate data into fuzzy sets and applies linguistic concepts to determine the severity of a disease, which will contribute to the further development of the decision. In order to test and verify the proposed approach, several experiments were carried out, which proved that Fuzzy-CNN is more effective than regular CNN models with the approximate accuracy difference approximately 1.8, and especially in cases when the symptoms of disease are not clear. To strengthen experimental validation, the proposed method is evaluated on two independent datasets, including an external benchmark dataset, imbalance-aware evaluation metrics are employed to ensure robustness and generalizability. Experimental results demonstrate consistent and statistically significant improvements over existing neuro-fuzzy and machine learning approaches. This research contributes to early detection by collaborating the potential of fuzzy neural networks and offering a flexible solution for real-time disease detection in citrus crops.
Why it matches plant phenotyping methods柑橘葉画像から病害および重症度を推定するFuzzy-CNN手法を開発し、独立データセットとベンチマークで検証しており、植物フェノタイピング手法が中心である。
abstractpropose a novel Fuzzy Convolutional Neural Network (Fuzzy-CNN) architecture for the automated diagnosis of citrus leaf diseases.
Reproduction assets foundThe paper's Data Availability statement links two public image datasets used for the citrus disease phenotyping/classification experiments (a Mendeley citrus leaves dataset and a Kaggle orange fruit dataset), and a third public Kaggle citrus disease dataset is cited as the external benchmark dataset used for validationDataset · publicThe data used in the current study is publicly available from the following links. [https://data.mendeley.com/datasets/3f83gxmv57/2]Open asset ↗data.mendeley.com · 3f83gxmv57/2html-lines:525-539Dataset · publicThe data used in the current study is publicly available from the following links. [https://data.mendeley.com/datasets/3f83gxmv57/2] [https://www.kaggle.com/datasets/sgandhi2003/orange-fruit-dataset]Open asset ↗www.kaggle.com · sgandhi2003/orange-fruit-datasethtml-lines:525-539Code / dataset availability confirmedOpenAlex · arXiv · checked 15 Sept 2026
Accurate estimation of wheat spike volume is important for yield component analysis and stress resilience assessment, yet field-based measurement remains challenging. Active 3D sensing methods such as Light Detection and Ranging (LiDAR) or time-of-flight (ToF) are sensitive to plant motion or poorly suited to outdoor conditions, while 3D reconstructions are computationally expensive. Direct 2D image processing would offer computational advantages, but image-based models lack explicit geometric information. We therefore propose a hybrid 2D-3D approach with knowledge distillation during training while enabling efficient image-only inference. First, we train a rigid-invariant point cloud network using distance-based histogram features to obtain pose-robust geometric representations. We then combine the 3D model with a proposed multi-view image-based regulated Transformer (RT) in an ensemble architecture. Finally, we distill the ensemble knowledge into a purely image-based student model using either feature-based or label-based distillation. The two distilled RTs reduce the mean absolute error (MAE) from 654.31 mm$^3$ of the non-distilled RT to 639.93 mm$^3$ and 644.62 mm$^3$, and increase correlation from 0.76 to 0.77 and 0.82, respectively. At the same time, inference time is reduced from 160 ms to 1.4 ms per spike. Distillation further mitigates volume-dependent bias and reshapes the latent representation of the image model toward a geometry-aware shape. Our results demonstrate that 3D-informed training of a 2D Transformer allows for scalable and efficient spike volume estimation for high-throughput field phenotyping.
Why it matches plant phenotyping methods小麦穂の体積を画像・3D再構成・知識蒸留で推定する手法の開発と性能評価が中心であり、高スループット植物フェノタイピングへの応用も明示されている。
abstractWe therefore propose a hybrid 2D-3D approach with knowledge distillation during training while enabling efficient image-only inference.
Reproduction assets foundThe paper explicitly states that links to its wheat spike dataset (multi-view images and 3D scans) and its analysis code are available via the authors' project webpage, which is an allowed URL. Other URLs (pyrender, CORDIS projects) are generic libraries or unrelated funding projects, not paper-specific assets.Dataset · publictance of around 2.5 m with a ground sampling distance of 0.3 mm (Fig. S1 a). The tagged and imaged spikes (Fig. S1 b) were sampled and ground truth volumes were acquired with a 3D light scanner (Shining 3D Einscan-SE V2, SHINING3D, Hangzhou, China) following the protocol of [ 76 ] . Links to the dataset and code can be found at https://oliviazum.github.io/3DKD-wheat/ . Detailed information about the dataset can be found in Sec. A .
3.3 Data Pre-Processing
Field images contained approximately 300-500 spikes per genotype within a plot of about 1.5 m 2 m^{2} . To reduce background inference, spike detection was first performed, and all subsequent processing was restricted to the detected regioOpen asset ↗lines:91-104Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Introduction Colorimetric analysis of food using the CIELab/Ch colour space (i.e., from digital images of samples) is an accessible, non-destructive method for carotenoid and anthocyanin content prediction. Literature presents very well-fit, but rudimentary, models for pigment estimation (e.g., single/multiple linear regressions). However, standardised methods that statistically account for the high multicollinearity between CIELab/Ch colour parameters, varying light conditions and colour calibration, and samples with high genotypic variability are lacking. Methods An image analysis optimisation was developed for the prediction of carotenoid and anthocyanin content of 16 carrot genotypes of different colours. Samples were photographed under six light conditions with a digital camera and image colour was calibrated before analysis with the CIELab/Ch colour space. Total pigment contents and individual carotenoid contents were analysed chemically via spectrophotometry and high-performance liquid chromatography, respectively. Partial least squares (PLS) regressions were used to assess the colour-pigment relationships to correct for high multicollinearity amongst the independent variables (CIELab/Ch colour parameters). Results/discussion The PLS models achieved satisfactory accuracy for the prediction of total carotenoid content ( ca. R 2 = 0.77) and total anthocyanin content ( ca. R 2 = 0.81) under all light conditions. The two models are suggested as robust approaches to total pigment prediction with multi-dimensional colour spaces, varying light conditions, and for a sample group of high genotypic variability. The carrot samples proved to have very high genetic diversity within each cultivar, resulting in unsatisfactory models for prediction of individual carotenoids ( ca. R 2 = 0.45) under the default light condition. However, all the results can be used to expand databases (towards artificial intelligence) and aid breeding programmes in search for higher concentrations of these interesting antioxidants for human health.
Why it matches plant phenotyping methodsニンジン試料の画像色解析を最適化し、化学分析値を用いてカロテノイド・アントシアニン含量を予測する手法を開発・検証しており、植物形質取得が研究の中心である。
abstractThe PLS models achieved satisfactory accuracy for the prediction of total carotenoid content ( ca. R 2 = 0.77) and total anthocyanin content ( ca. R 2 = 0.81) under all light conditions.
Reproduction assets foundThe authors deposited the paper's data and protocols in public repositories (DOI links in the Data availability statement). The anthocyanin quantification protocol is explicitly linked (10.34894/BTPTSV), and the other two DOIs (10.34894/P37WCL, 10.34894/OUURRH) are stated to hold the paper's data. No separate author's'Dataset · publicData and protocols are available in the following links: https://doi.org/10.34894/P37WCL , https://doi.org/10.34894/OUURRH , https://doi.org/10.34894/BTPTSV .Open asset ↗10.34894/P37WCLlines:641-686Dataset · publicData and protocols are available in the following links: https://doi.org/10.34894/P37WCL , https://doi.org/10.34894/OUURRH , https://doi.org/10.34894/BTPTSV .Open asset ↗10.34894/OUURRHlines:641-686Code / dataset availability confirmedCrossref · checked 5 Sept 2026
Early disease diagnosis plays a key role in grape production for minimizing crop risk and maximizing yield. Downy Mildew, Powdery Mildew, and Bacterial Leaf Spot are some of the major diseases that threaten productivity and require timely and accurate diagnosis. This research introduces a new multi-model framework that integrates AI-based image segmentation triggered by Environmental Susceptibility Conditions to inform precision grape farming. The proposed method combines a soft-voting ensemble of the DeepLabV3+, U-Net, and FCN-8’s models for segmentation of diseased and healthy leaf areas with high accuracy, by understanding environment data to evaluate the risk of disease propagation. Major contributions of the study are the understanding of environmental conditions for context-aware disease propagation, an efficient ensemble segmentation method for accurate leaf disease segmentation and severity analysis, performed on a self-collected dataset from a grape farm in Nashik, Maharashtra, India. The system enables early warning and decision support mechanisms to promote sustainable disease management in grape cultivation, with potential implications for reducing unnecessary pesticide usage. Experimental results show the efficacy of the proposed method, with segmentation accuracy of 96.81% and precision of 99.09%, with a Dice score of 0.95 and a mean Intersection over Union (mIoU) of 0.91, demonstrating excellent robustness under noise conditions. Unlike existing studies either image or sensor-approaches, this work introduces the integration of image data and knowledge of environmental insights offers a scalable, reliable, and real-time disease monitoring solution aligned with the goals of smart and sustainable farming.
Why it matches plant phenotyping methodsブドウ葉の病斑領域を画像分割し、病害の重症度を推定する手法を開発・評価しており、植物の病害状態の取得が研究の中心です。
abstractThe proposed method combines a soft-voting ensemble of the DeepLabV3+, U-Net, and FCN-8’s models for segmentation of diseased and healthy leaf areas with high accuracy
Reproduction assets foundThe paper's grape leaf disease image dataset (NGLDD/NGLD) used for segmentation phenotyping is publicly deposited on Mendeley Data by the authors. No code or model checkpoints are reported as publicly available.Dataset · publicThe dataset used in this study is publicly available in the Mendeley Data repository as the Niphad Grape Leaf Disease
Dataset (NGLD) (DOI: https://doi.org/10.17632/8nnd2ypcv3.5).Open asset ↗Mendeley Data · 10.17632/8nnd2ypcv3.5pdf-page:25 lines:1-65Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Genomic selection (GS) can accelerate crop breeding and enhance selection efficiency. However, accurately predicting genomic estimated breeding values (GEBVs) for complex traits and applying GS in diverse environments remains challenging. To address these issues, we developed a novel hybrid method capable of modelling gene-gene and gene-environment interactions. This method offers precise predictions of phenotypic performance for complex traits, identifies haplotypes associated with desirable phenotypes, and enables prediction of optimal haplotypes tailored to specific environments. We evaluated the approach using a dataset of 855 barley lines, with phenotypic data for grain yield and flowering time collected across multiple environments. The model incorporated 30,543 SNPs, nine soil parameters, and six daily environmental variables, achieving high prediction accuracies, with correlation coefficients of 0.93 for flowering time and 0.82 for grain yield. Our method identified 10 haplotype blocks significantly associated with flowering time and 13 blocks with grain yield, collectively accounting for over 90% of the total genetic variance. Additionally, we predicted the phenotypic effects of each haplotype and identified elite varieties carrying the most favourable haplotypes for crossing design and selection. The method also allows prediction of untested genotype × environment combinations, enabling selection of optimal genotypes for targeted environments. To facilitate its application, we developed a web-based interface (accessible at [https://penghaowang.shinyapps.io/shinygui/]), which enables breeders to identify optimal haplotypes and the varieties that carry them, streamlining the process of haplotype-based, environment-informed breeding. We note that the reverse prediction framework is currently applied on a single-trait basis and does not resolve multi-trait trade-offs such as between flowering time and yield, which remains a topic for future extensions.
Why it matches plant phenotyping methods複雑形質の表現型性能を遺伝子型・環境情報から予測する新規計算手法を開発し、オオムギの収量・開花期で評価している。ウェブインターフェースも提供され、形質推定ワークフローが中心である。
abstractwe developed a novel hybrid method capable of modelling gene-gene and gene-environment interactions.
Reproduction assets foundThe paper deposits its barley genotype, phenotype, and environmental datasets at three DOI repositories, and its analysis source code on GitHub, plus a public Shiny web tool.Dataset · publicDetailed information on all experimental lines, including their genotypes, phenotypic, and environmental data, is available at https://doi.org/10.60867/00000010 , https://doi.org/10.60867/00000003 , and https://doi.org/10.60867/00000011 , respectively.Open asset ↗10.60867 · 10.60867/00000010lines:31-42Dataset · publicDetailed information on all experimental lines, including their genotypes, phenotypic, and environmental data, is available at https://doi.org/10.60867/00000010 , https://doi.org/10.60867/00000003 , and https://doi.org/10.60867/00000011 , respectively.Open asset ↗10.60867 · 10.60867/00000003lines:31-42Dataset · publicDetailed information on all experimental lines, including their genotypes, phenotypic, and environmental data, is available at https://doi.org/10.60867/00000010 , https://doi.org/10.60867/00000003 , and https://doi.org/10.60867/00000011 , respectively.Open asset ↗10.60867 · 10.60867/00000011lines:31-42Code · publicAll the data and source codes have been uploaded to GitHub and can be accessed under the GNU Open License at: https://github.com/pwang2019/GxE_Model .Open asset ↗github.com/pwang2019/GxE_Modellines:196-205Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
This paper explores the use of optimized convolutional neural networks (CNNs) to classify diseases affecting potato leaves using TensorFlow-2. The dataset, sourced from Kaggle's Plant Village repository, includes 152 images of healthy potato leaves and 1000 images each of early and late blight. The methodology covers data preparation, model architecture design, training, evaluation, and deployment. During data preparation, the data set was split into training sets (80%) and testing sets (20%), with images resized to 128x128 pixels. The Deep Learning (DL) models built using CNN with 4 different optimizers (ADAM, SGD, RMSPROP, and ADAMAX) and trained using a sparse categorical cross-entropy loss function, include multiple convolutional and pooling layers for feature extraction, and fully connected layers for classification. Early stopping was used to prevent overfitting. Model performance was assessed using accuracy, loss curves, confusion matrix, ROC curve, precision recall curve, classification report, and F1 score. In addition, we have used data augmentation to balance the dataset by increasing healthy potato leaves 6 times and the use of Ensemble Deep Learning (EDL). EDL10 which contains DL1 (CNN + ADAM), DL2 (CNN + SGD), DL3 (CNN + RMSPROP) and DL4 (CNN + ADAMX) performs best with a accuracy score of 97.0%. This highlights the importance of data balancing and the use of the ensemble classification approach for the detection of blight in Potato Leaves.
Why it matches plant phenotyping methodsジャガイモ葉の病害状態を画像から分類するCNN・アンサンブル手法の設計、評価、データ拡張が研究の中心であり、植物病害フェノタイピング手法に該当する。
abstractThis paper explores the use of optimized convolutional neural networks (CNNs) to classify diseases affecting potato leaves using TensorFlow-2.
Reproduction assets foundThe paper uses the public Kaggle PlantVillage potato leaf image dataset and archives its complete analysis source code on Zenodo with explicit availability statements and URLs.Code · publicThe complete source code is hosted in a DOI-minting repository and has been archived on Zenodo to ensure long-term accessibility and reproducibility. The code is released under an open-source license. The archived version corresponding to this publication is available at : https://doi.org/10.5281/zenodo.19624017Open asset ↗Zenodo · 10.5281/zenodo.19624017lines:252-314Dataset · publicThe datasets generated and/or analysed during the current study are available at : PlantVillage Dataset, accessed from https://www.kaggle.com/datasets/abdallahalidev/plantvillage-dataset.Open asset ↗Kaggle · plantvillage-datasetlines:252-314Code / dataset availability confirmedEurope PMC · bioRxiv · Crossref · checked 15 Sept 2026
Plant disease detection using deep learning is essential for precision agriculture, enabling early and automated crop health monitoring. This study proposes an end-to-end transfer learning pipeline, LeafyVGG-16, for multi-class classification of plant diseases and nutrient deficiencies using a tomato leaf dataset. The framework integrates data preprocessing, augmentation, and a VGG-16 backbone with a two-stage fine-tuning strategy. The proposed model is evaluated against CNN, DenseNet-121, Inception-V3, EfficientNetB0, and ResNet-50, achieving an accuracy of 0.93 with precision, recall, and F1-scores of 0.93, 0.90, and 0.92, respectively. These results demonstrate the effectiveness of transfer learning for fine-grained plant disease recognition. We further evaluate model robustness under adversarial cyber attacks to assess deployment reliability in agricultural systems. Under Fast Gradient Sign Method (FGSM) attacks ( ϵ = 0.01– 0.05), the model shows an accuracy drop of 1%–7.5%, while Projected Gradient Descent (PGD) attacks ( ϵ = 0.05, step size = 0.005, 10 iterations) produce similar degradation, highlighting the model’s vulnerability to adversarial perturbations. These findings highlight potential security and reliability risks in AI-based agricultural decision-making systems. Future work will focus on improving robustness and cyber-resilience and extending this framework to other crops for secure and context-aware deployment in resource-constrained environments.
Why it matches plant phenotyping methods植物葉の画像から病害・栄養欠乏状態を分類する深層学習パイプラインが研究の中心であり、複数モデルとの比較評価と敵対的攻撃下での頑健性検証も実施しているため。
abstractThis study proposes an end-to-end transfer learning pipeline, LeafyVGG-16, for multi-class classification of plant diseases and nutrient deficiencies using a tomato leaf dataset.
Reproduction assets foundThe paper's plant-phenotyping input is the publicly available Tomato-Village Variant-a dataset (4,525 tomato leaf images across 8 disease/deficiency classes), which the authors explicitly cite with a public Kaggle URL. No author analysis code, trained model checkpoints, or supplementary data deposits are mentioned. TheDataset · publicThis study uses the publicly available Tomato-Village
dataset [18], which is designed for real-world tomato disease
detection in agricultural environments.Open asset ↗pdf-raw-page:3 lines:1-59Code / dataset availability confirmedOpenAlex · Europe PMC · checked 5 Sept 2026
Introduction: Wheat kernel hardness, vitreousness, and creaseness are key determinants of milling performance, yet they reflect different physical scales of grain structure and are not necessarily coupled. Methods: We developed a digital phenotyping framework based on hyperspectral imaging and spectral unmixing to quantify these traits at both kernel and cultivar levels in a diverse panel of common wheat. Pixel-level spectral unmixing resolved glassy, intermediate, and mealy endosperm components within individual kernels, enabling vitreousness to be expressed as a continuous spatial index. Results: The hyperspectral-derived vitreousness index showed moderate associations with kernel protein content and the protein-to-starch ratio, consistent with variation in endosperm packing density, but weak relationships with kernel hardness and crease geometry. Kernel hardness, primarily determined by puroindoline genotype, showed limited association with bulk protein and starch composition. Crease geometry, quantified using composite indices from RGB images, captured macroscopic grain features largely independent of both hardness and vitreousness. Discussion: These results demonstrate that hardness, vitreousness, and creaseness represent complementary but largely independent dimensions of grain quality, corresponding to molecular-scale adhesion, mesoscale packing, and macroscopic geometry, respectively. The proposed framework provides a scalable, non-destructive approach for resolving intra-kernel heterogeneity, enabling improved digital phenotyping for wheat breeding and quality assessment.
Why it matches plant phenotyping methodsハイパースペクトル画像とスペクトルアンミキシングを用いて小麦粒の硝子質を定量するデジタル表現型解析フレームワークを開発しており、形質取得手法が中心的である。
abstractWe developed a digital phenotyping framework based on hyperspectral imaging and spectral unmixing to quantify these traits at both kernel and cultivar levels in a diverse panel of common wheat.
Reproduction assets foundThe paper's data availability statement deposits full hyperspectral image cubes and RGB image datasets on Figshare, and the supplementary material includes Python analysis scripts (Supplementary Code S1–S2) and processed feature tables (Supplementary Table S3) directly reproducing the paper's phenotyping measurements.Dataset · publicfull hyperspectral image cubes and associated RGB imagedatasets are available via Research Datas 1 – 3 at Figshare: https://doi.org/10.6084/m9.figshare.31259530Open asset ↗Figshare · 10.6084/m9.figshare.31259530lines:151-201Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
This study developed a model to predict zeaxanthin content in peppers using multispectral imaging and chemical data. A one-dimensional convolutional neural network (1D CNN) model was identified as the optimal single-modal model after comparing four machine learning algorithms. On the prediction dataset, the model achieved a determination coefficient ( Rp 2 ) of 0.7639. Building upon the 1D CNN framework, a multimodal feature fusion model (MCSF) was constructed by integrating the chemical measurements of capsanthin and total carotenoid contents using a multilayer perceptron. This enhanced model demonstrated excellent predictive accuracy and robustness, with Rp 2 values of 0.9318 and 0.9211 across different spectral ranges. For high-throughput detection purposes, a simplified model that replaced measured capsanthin with a comprehensive red index still performed well, with an Rp 2 of 0.8912 and an RPD of 3.11. This strategy provides a new solution for the efficient spectral detection of plant chemicals affected by multicollinearity in their absorption spectra.
Why it matches plant phenotyping methodsマルチスペクトル画像と機械学習を用いて、トウガラシ果皮のゼアキサンチン含量という植物器官の形質を非破壊・高スループット推定する手法を開発・評価しており、フェノタイピング手法が中心である。
abstractThis study developed a model to predict zeaxanthin content in peppers using multispectral imaging and chemical data.
Reproduction assets foundThe paper's data availability statement explicitly states that the datasets (multispectral imaging and chemical trait measurements) and the main model code are publicly available in the authors' GitHub repository, which is an allowed URL.Dataset · publicThe datasets and the main model code are available online at https://github.com/liang-wei-tian/Chili-Peppers-Zeaxanthin.Open asset ↗liang-wei-tian/Chili-Peppers-Zeaxanthinhtml-lines:303-325Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Crop diseases pose a significant threat to agricultural productivity and global food security. Timely and accurate detection of such diseases is crucial for improving both crop yield and quality. While numerous deep learning approaches rely solely on image data for disease identification, they often overlook the complementary value of textual information in enhancing visual analysis. To address this limitation and effectively fuse features from different modalities, we propose a Cross-Model fusion framework based on a vision-language model that integrates cross-attention and gated fusion mechanisms for crop disease recognition. Our approach utilizes the Zhipu.ai multi-modal model to generate comprehensive textual descriptions of diseased crop leaves, including global description, local lesion description, and color-texture description. These textual descriptions are then encoded into feature embeddings, while visual features are extracted using the ShuffleNet-v2 model as the image encoder. Subsequently, a cross-attention module aligns and fuses the two modalities, and a gated fusion module enables dynamic feature selection during the fusion process. Extensive evaluations on the Soybean Disease and PlantVillage datasets demonstrate that our method outperforms existing image-based models in terms of accuracy. Specifically, our model achieves recognition accuracies of 99.04% and 99.12% on the respective datasets, surpassing the ShuffleNet-V2 model by 1.09% and 2.53%, respectively. These results highlight the effectiveness of Cross-Model learning in integrating visual and textual cues for accurate and efficient disease recognition, offering a scalable solution for crop disease diagnosis.
Why it matches plant phenotyping methods植物葉の病徴を画像と言語情報から認識する融合フレームワークを開発し、複数データセットで既存手法と比較評価しているため、植物フェノタイピング手法が中心である。
abstractwe propose a Cross-Model fusion framework based on a vision-language model that integrates cross-attention and gated fusion mechanisms for crop disease recognition.
Reproduction assets foundThe paper's crop disease recognition experiments use two openly available image datasets, both with explicit public availability statements in the Data Availability section: the Soybean Disease dataset (Dryad DOI) and the PlantVillage dataset (Kaggle). No author analysis code, trained models, or generated text-annotaitDataset · publicThe datasets utilized in this study are openly accessible. The soybean dataset is available at https://doi.org/10.5061/dryad.41ns1rnj3.Open asset ↗Dryad · 10.5061/dryad.41ns1rnj3html-lines:403-424Dataset · publicThe plantvillage dataset is available at https://www.kaggle.com/datasets/abdallahalidev/plantvillage-dataset.Open asset ↗Kaggle · plantvillage-datasethtml-lines:403-424Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
AppleField / plotRGB / grayscaleFruitClassificationObject detectionSegmentationGrowth / development / phenology
This article presents a comprehensive dataset of 1406 RGB images of apples ( Malus domestica ), covering three key growth stages-immature (green), semi-mature (color transition), and mature (red). The dataset serves as a resource for detecting and segmenting apples across different developmental phases. Each image includes pixel-level instance segmentation masks annotated in JSON format using the VGG Image Annotator (VIA), ensuring compatibility with deep learning frameworks. The dataset's real-world variability-spanning lighting conditions, occlusions, and clustered fruit arrangements-enhances its utility for training generalizable computer vision models in precision agriculture. It supports tasks such as fruit detection, segmentation and growth-stage classification, addressing the scarcity of annotated data for transitional maturity phases. With 2574 annotated apple instances, this dataset facilitates research on maturity grading and transfer learning for agricultural robotics. By standardizing annotations and incorporating diverse field conditions, this dataset reduces preprocessing overhead and accelerates the development of deployable AI solutions for orchard management. It is particularly valuable for improving model robustness in heterogeneous environments, thereby advancing data-driven horticultural practices.
Why it matches plant phenotyping methodsリンゴ果実の発育段階・成熟度という植物器官の状態を対象に、画素単位アノテーション付き画像データセットを構築しており、観測・抽出手法の再利用可能な基盤が中心である。
abstractThis article presents a comprehensive dataset of 1406 RGB images of apples ( Malus domestica ), covering three key growth stages-immature (green), semi-mature (color transition), and mature (red).
Reproduction assets foundThe paper is a data descriptor for a public apple image dataset (1406 RGB images, pixel-level instance segmentation masks in JSON) deposited on Mendeley Data with a direct URL and DOI, matching the allowed URL exactly.Dataset · publicRepository name: Wang, Dandan; Wang, Bo (2026), “A Multi-Stage, Pixel-Level Annotated Apple Dataset for Precision Agriculture Research”, Mendeley Data, V4
Data identification number: 10.17632/gfcmdbvw65.4
Direct URL to data:https://data.mendeley.com/datasets/gfcmdbvw65/4Open asset ↗Mendeley Data · 10.17632/gfcmdbvw65.4html-lines:1-97Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Machine learning has become an increasingly important tool for overcoming agricultural challenges by enabling efficient and consistent classification of crop-related data. Training such supervised models requires high quality labeled datasets. This work presents a dataset consisting of raw and preprocessed hyperspectral imaging (HSI) files capturing reflectance in the visible to near-infrared range (400-1000 nm) from two problematic weed species on California's Central Coast: annual sowthistle ( Sonchus oleraceus ) and little mallow ( Malva parviflora ). Hyperspectral imaging provides rich spectral-spatial data cubes that can support the development of deep learning models and autonomous technology for precision weed management. Plants were grown in a greenhouse under five conditions: standard, drought, overwatering, excess fertilizer, and no fertilizer. Custom MATLAB scripts were utilized for preprocessing, including k-means clustering to define regions of interest (ROIs), and extraction of spectral metrics. Data visualization was performed using Wolfram language and MATLAB. The dataset includes both raw and ENVI-formatted hyperspectral cubes and pre-processed MATLAB outputs, supporting spectral feature engineering, benchmark development, and exploratory machine learning workflows for controlled environment stress classification.
Why it matches plant phenotyping methods植物のストレス状態を対象とするハイパースペクトル画像データセットで、ROI抽出・スペクトル指標化と機械学習ベンチマークを中心的に提供しているため、植物フェノタイピング手法・データセットとして適格。
abstractThis work presents a dataset consisting of raw and preprocessed hyperspectral imaging (HSI) files capturing reflectance in the visible to near-infrared range (400-1000 nm) from two problematic weed species
Reproduction assets foundThe paper is a Data in Brief article describing its own hyperspectral imaging dataset of annual sowthistle and little mallow under five abiotic stress treatments, deposited publicly on Zenodo (record 17398082). The dataset includes raw ENVI-format hyperspectral cubes, preprocessed MATLAB outputs (ROI masks, extracted植被Dataset · publicData accessibility
Repository name: Zenodo
Data identification number: zenodo.17398082
Direct URL to data: https://doi.org/10.5281/zenodo.17398082Open asset ↗Zenodo · zenodo.17398082html-lines:92-120Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Tea (Camellia sinensis) is the world's second most consumed beverage, enjoyed daily by more than two billion people. In Bangladesh, it serves as a cornerstone agricultural export and a major sector of the domestic economy. However, commercial tea cultivation remains highly vulnerable to fungal and pest-related diseases such as Blight, Red Rust, and Helopeltis which severely reduce crop yield and compromise leaf quality. While early detection is critical to preventing widespread outbreaks, traditional manual inspection is slow, subjective, and highly error-prone. Deep learning provides a scalable alternative, yet single-branch networks often struggle to capture both minute disease lesions and broader structural degradation simultaneously. To address this, we propose a Hybrid Feature Fusion architecture that runs two highly efficient feature extractors in parallel: EfficientNetV2-Small to isolate fine-grained local textures, and MobileNetV3-Small to capture the global structural context of the leaf. The models were trained and evaluated on a real-world dataset of 2,000 annotated images, evenly distributed across the four target classes (Blight, Red Rust, Helopeltis, and Healthy). Before training, the images underwent a standardized preprocessing pipeline including resizing to 224 × 224 pixels and normalization, supplemented by a dynamic augmentation strategy featuring random rotations, horizontal flips, and brightness adjustments to improve model robustness. The proposed hybrid framework achieved an outstanding peak classification accuracy of 96.80% alongside a macro Area Under the Curve (AUC) of 0.9980. To rigorously validate its performance, the hybrid model was benchmarked against six diverse architectures: a Vision Transformer (ViT-B16 at 76.40%), a Custom CNN (89.60%), MobileNetV3 (94.40%), ResNet50 (95.60%), DenseNet121 (96.40%), and EfficientNetV2-B3 (97.60%). Although EfficientNetV2-B3 achieved a marginally higher raw accuracy, the proposed dual-branch framework delivered a superior precision-recall balance and faster convergence stability. These findings demonstrate that the proposed hybrid methodology is highly reliable and computationally balanced, making it an ideal candidate for integration into Internet of Things (IoT) edge devices for real-time disease monitoring in precision agriculture.
Why it matches plant phenotyping methods茶葉の病徴を画像から分類する深層学習手法の開発と、注釈付きデータセットおよび複数モデルとのベンチマーク検証が中心であり、植物病害状態の表現型推定に該当する。
abstractwe propose a Hybrid Feature Fusion architecture
Reproduction assets foundThe paper's Data Availability statement explicitly deposits the curated 2000-image tea leaf dataset on Mendeley Data and the analysis code on GitHub, both with public URLs matching allowed_urls.Dataset · publicThe dataset comprising 2000 annotated tea leaf images was curated under real-world field conditions. It has been made available at https://data.mendeley.com/datasets/3x42rbj8yv/1.Open asset ↗3x42rbj8yv/1html-lines:465-480Code · publicThe computational code supporting the findings of this study is publicly accessible on GitHub: https://github.com/rayhankhan2192/Tea_Leaf_Disease_Model.Open asset ↗GitHub · rayhankhan2192/Tea_Leaf_Disease_Modelhtml-lines:465-480Code / dataset availability confirmedOpenAlex · Europe PMC · checked 5 Sept 2026
Quantifying the kinetics of net CO2 assimilation (A) and stomatal conductance (gs) under fluctuating light typically relies on gas exchange measurements, which are slow and thus unsuited for high-throughput phenotyping. As a result, faster, non-invasive phenotyping methods are needed to further evaluate these traits at a larger scale. However, first the relationship between non-steady-state parameters must be examined in greater detail. In this study, we aimed to determine whether variations in non-steady-state values of chlorophyll fluorescence and leaf temperature reflect differences in key gas exchange traits under fluctuating light conditions. Here, the correlations between the times required for a change in non-steady-state A, gs, operating efficiency of PSII (ΦPSII), and leaf temperature (Tleaf) during stepwise changes in light intensity were evaluated across nine plant species. Both steady-state and non-steady-state photosynthetic traits varied significantly among species. Overall, we found significant positive correlations between non-steady-state A and ΦPSII for time to 50% and 90% of final steady-state values (t50; r2 = 0.70) and (t90; r2 = 0.33). The t90 of gs and that of Tleaf were also significantly correlated after both increases (r2 = 0.45) and decreases (r2 = 0.61) in light intensity. Our findings suggest that the times required for a change in ΦPSII (particularly t50) and Tleaf (particularly t90) can be used as indicators of dynamic A and gs, respectively, facilitating faster phenotyping of the complex processes of photosynthesis and stomatal conductance kinetics in the future.
Why it matches plant phenotyping methods非定常クロロフィル蛍光と葉温を用いて光合成・気孔コンダクタンス動態を推定する高速フェノタイピング手法を評価しており、相関検証が研究の中心である。
abstractfaster, non-invasive phenotyping methods are needed to further evaluate these traits at a larger scale.
Reproduction assets foundThe paper's primary gas exchange, chlorophyll fluorescence, and leaf temperature phenotyping data are explicitly deposited in the WUR data repository (DOI 10.17887/WUR01-TMWYJN), stated in the Data availability section. No author analysis code repository is stated; the agricolae R package is a generic library, not a论文-Dataset · publicThe primary data and associated metadata are publicly available through the WUR data repository at https://doi.org/10.17887/WUR01-TMWYJN .Open asset ↗WUR data repository · 10.17887/WUR01-TMWYJNlines:406-446Code / dataset availability confirmedCrossref · Europe PMC · checked 14 Sept 2026
LiDAR / point cloudFlowerLeafStem / branchSegmentationGrowth / development / phenology
The segmentation of 3D point clouds of plant organs, such as leaves and stems, helps to monitor plant growth and is a key step in plant growth phenotype analysis. Compared to point cloud segmentation tasks in other fields, plant point cloud segmentation is more challenging due to the interwoven distribution of various parts such as stems, leaves, and flowers. In this paper, we propose a universal point cloud segmentation network PlantEFRSegnet that can be used for multi-species of plants. The proposed PlantEFRSegnet utilizes a newly designed edge point preservation downsampling module to identify and preserve the points at the edges of plant organs during the downsampling process, in order to assist the segmentation network in learning the contours of various plant organs. PlantEFRSegnet performs supervised feature repair on the point cloud features obtained through downsampling to mitigate the impact of feature loss on segmentation performance during feature embedding. The encoder of the segmentation network is composed of four local feature extraction modules. These four modules can not only extract features but also enhance the features corresponding to points with high contributions in local regions based on point attention mechanism. We evaluated the proposed PlantEFRSegnet on a laser-scanned plant point cloud dataset. Compared with the state-of-the-art approaches, the proposed PlantEFRSegnet achieved better segmentation results.
Why it matches plant phenotyping methods植物器官の3D点群を対象に、器官分割と植物成長フェノタイプ解析を行う新規ネットワークを開発・評価しており、フェノタイプ取得の計算手法が中心である。
abstractThe segmentation of 3D point clouds of plant organs, such as leaves and stems, helps to monitor plant growth and is a key step in plant growth phenotype analysis.
Reproduction assets found保存済みの本文根拠を更新済みルールで再検証し、公開資産1件を確認しました。Dataset · publicThe experimental dataset used in this paper can be obtained through the following link: https://github.com/dllab23/PlantPointCloud (accessed on 11 May 2026).Open asset ↗dllab23/PlantPointCloudhtml-lines:785-806Code / dataset availability confirmedEurope PMC · checked 15 Sept 2026
Background High-throughput automated image analysis holds great promise for plant breeding by enabling faster, more accurate assessment of traits relevant to crop improvement. Imaging-based systems, such as the CropReporter, allow automated quantification of photosynthetic parameters like PSII efficiency under ambient light from a top-down 2D perspective. However, standard analysis tools average values across the 2D top view, overrepresenting upper leaves and underrepresenting those in the lower canopy. Upper leaves may occlude lower ones, and due to the pinhole projection of the camera, lower leaves of the same size appear smaller in the image. Consequently, vertical heterogeneity in PSII efficiency within the canopy cannot be resolved using a single 2D image. Results To address these issues, we integrated top-view PSII efficiency data (by CropReporter) with 3D structural data from RGB point clouds (by MaxiMarvin). Alignment accuracy between MaxiMarvin and CropReporter was high, with R² ≥ 0.98 for the x-axis and R² ≥ 0.99 for the y-axis. The method was tested using Chenopodium quinoa, Glycine max, and Solanum tuberosum, exposed to salinity, waterlogging and drought stress respectively. In Chenopodium quinoa, it allowed precise determination of when senescence began in the lower leaves. In Solanum tuberosum, the reduction in PSII efficiency by drought was the same for all leaf layers, while in Glycine max, waterlogging stress most strongly affected the middle layer of the canopy. Conclusions This framework enables the 3D mapping of PSII efficiency across the vertical plant profile by combining top-view chlorophyll fluorescence imaging (CropReporter) with 3D structural data (MaxiMarvin). It reveals vertical variation in photosynthetic activity across canopy layers. With standard 2D chlorophyll fluorescence imaging it is difficult to distinguish between non-photosynthetic tissues like flower heads and lower layers of leaves, that might have the same PSII values. Using height-based filtering, taking data from the 3D mapping, such distinction can be made with the method presented in this paper. This allows estimating the PSII efficiencies of leaves only. By capturing layer-specific responses to abiotic stress and developmental changes, the method provides physiologically relevant input for crop growth modelling and highlights the importance of accounting for canopy structure in photosynthetic analyses.
Why it matches plant phenotyping methods2Dクロロフィル蛍光によるPSII効率を3D植物構造へ投影し、群落層別の葉の生理形質を推定する手法の開発・検証が中心である。
abstractTo address these issues, we integrated top-view PSII efficiency data (by CropReporter) with 3D structural data from RGB point clouds (by MaxiMarvin).
Reproduction assets foundThe authors state that the analysis scripts (2D–3D alignment pipeline) and the phenotyping data used in the study are included with the publication as supplementary material, accessible via the article DOI. This is a paper-specific, publicly available asset containing the authors' analysis code and data.Dataset · publicThe scripts and the data that were used in the current study are available and added to this publication.Open asset ↗lines:143-180Code / dataset availability confirmedCrossref · checked 14 Sept 2026
Given the increasing frequency, severity, and socioecological impacts of wildfires, there is an urgent need for robust frameworks to better characterize fire behavior and flammability patterns across ecosystems to support early warning, mitigation, and management strategies. However, flammability remains difficult to quantify and scale, as it involves multiple interacting components that are typically measured at the bench scale. This study aimed to establish empirical links between spectral information, plant traits, and flammability metrics, and to scale these relationships to satellite imagery to translate these metrics into a spatial context. We combined laboratory spectroscopy, plant trait measurements including leaf mass per area, carbon, and cellulose, and combustion experiments using a simple and reproducible burning device. In total, 84 samples were collected and analysed, allowing us to characterise how spectral signatures relate to vegetation traits and fire behaviour. Spectral indices were developed to estimate plant traits, which were subsequently used as predictors in flammability models. These models were then transferred to Environmental Mapping and Analysis Program (EnMAP) hyperspectral imagery to derive spatial estimates across eucalypt forests and grasslands of the Australian Capital Territory (ACT). Spectral information distinguished fuel types and captured variability of the plant traits, while these traits showed associations with combustion behaviour. Based on these links, the best-performing model predicted the rate of temperature increase, a combustibility metric, in eucalypt forests (R2 = 0.70; Root Mean Square Error = 32.48 °C/s). In contrast, grassland models showed limited predictive performance, likely due to weaker relationships between plant traits and flammability metrics. Overall, this study demonstrates a practical and scalable approach for deriving flammability maps from hyperspectral and in situ data, highlighting the potential of plant-trait-based remote sensing. The resulting maps should not be interpreted as standalone fire risk products, but rather as a characterization of the structural and biochemical drivers of flammability. The main constraint of this work is the limited sample size. Future research should expand spatial and temporal coverage to better capture vegetation variability and enable the inclusion of independent validation datasets. Exploring alternative combustion protocols and testing more advanced spectral modelling approaches for trait estimation would provide additional insights.
Why it matches plant phenotyping methods植物形質を分光情報から推定し、ハイパースペクトル画像へ展開して可燃性関連の植物状態を評価する手法が研究の中心であり、モデル性能も検証しているため。
abstractSpectral indices were developed to estimate plant traits, which were subsequently used as predictors in flammability models.
Reproduction assets foundThe paper's supplementary materials (hosted publicly by MDPI) contain the paper-specific plant phenotype measurements: sampled species lists, fractional cover, and measured vegetation traits across dates and plots, plus combustion replicate variability and trait–flammability relationship data. The raw underlying data,谱Supplement · publicbroader environmental coverage, improved plant trait retrieval meth-
ods, and independent validation. Future work should also explore non-linear modelling
frameworks to better capture the complexity of vegetation flammability across ecosystems.
Supplementary Materials: The following supporting information can be downloaded at:
https://www.mdpi.com/article/10.3390/rs18101546/s1, Supplementary Table S1 provides the list of
sampled plant species and their percentage cover across sites, paddocks, plots, and fuel types; Table
S2 presents the fractional cover of each species and litter component; Figure S1 shows the study-site
vegetation map; Figures S2–S6 show the measured vegetation traits acrosOpen asset ↗pdf-raw-page:22 lines:1-49Code / dataset availability confirmedCrossref · Europe PMC · checked 5 Sept 2026
Introduction Plant diseases pose a major challenge to sustainable agriculture, particularly in regions that heavily depend on farming. Early and accurate identification of plant diseases is crucial for ensuring food production and minimizing crop losses. The rapid advancement of deep learning, particularly in convolutional neural networks (CNNs), has significantly enhanced plant disease classification performance. However, many models often struggle to generalize effectively in real-world scenarios due to challenges such as low-intensity visuals, low contrast between the background and foreground of the suspected sample, noise, and chrominance variation. Methods To address the challenges mentioned above, we introduce ConvGem-NeXt, an end-to-end deep learning architecture specifically designed for fine-grained plant disease classification, built on the ConvNeXt baseline model featuring enhanced generalization capabilities. More precisely, our method incorporates a learnable Generalized Mean pooling layer and ReLU activation in the ConvNeXt model to enhance spatial feature representation, and a custom classifier head that integrates batch normalization, ReLU activation, and dropout to mitigate overfitting and improve classification accuracy. Results We tested the presented model on two large-scale and diverse databases, PlantVillage and the PlantDoc. The model achieved 99.65% accuracy on the PlantVillage dataset and 94.69% accuracy on the real-world PlantDoc dataset, demonstrating the efficacy of our method for reliably classifying plant diseases. Discussion This work contributes to the rapidly growing field of agricultural automation by providing a reliable framework for timely disease diagnosis and supporting the enhancement of crop productivity.
Why it matches plant phenotyping methods植物病害を画像から分類する深層学習アーキテクチャを開発し、複数データセットで性能検証しており、植物の病害状態の取得・推定が研究の中心である。
abstractwe introduce ConvGem-NeXt, an end-to-end deep learning architecture specifically designed for fine-grained plant disease classification
Reproduction assets foundThe paper's plant disease classification experiments were performed on two public image datasets, PlantVillage and PlantDoc, both explicitly linked in the data availability statement. No author code or model checkpoints are released.Dataset · publicPublicly available datasets were analyzed in this study. This data can be found here: https://www.kaggle.com/datasets/abdallahalidev/plantvillage-datasetOpen asset ↗kaggle.com/datasets/abdallahalidev/plantvillage-datasetlines:1466-1516Code / dataset availability confirmedCrossref · checked 15 Sept 2026
Published12 May 2026Journal of Advanced College of Engineering and ManagementCited by 0 · OpenAlex ↗
Apple cultivation is a crucial agricultural activity in various mountainous regions, playing a vital role in supporting the local economy and sustaining the livelihoods of farmers. Several prominent mountain districts are known for leading apple production. However, apple orchards in these areas are often threatened by numerous diseases that reduce fruit yield and quality. In this research, we suggest a machine learning-based technique to automate the detection and classification of common apple diseases based on images of apple leaves collected from various regions. Through the use of Convolutional Neural Networks (CNN), the system can classify diseases with 97.36% precision. For post hoc explainability, Grad-CAM is used, which highlights the important regions that influenced CNN’s decision. The automated disease detection tool provides farmers in Nepal’s rural mountain areas with an affordable real time solution to monitor orchard health, minimize crop loss, and improve apple production. The dataset used in this study is originally derived from the United States based PlantVillage dataset, which is widely used for apple leaf disease classification research. Although the dataset is not collected from Nepal, the visual characteristics of apple leaf diseases remain largely consistent across regions due to similar biological infection patterns. Therefore, the model trained on this dataset is applicable to Nepali apple cultivation environments as well. At present, a publicly available or annotated Nepali specific apple leaf disease dataset is not available, which limits region-specific training and evaluation.
Why it matches plant phenotyping methodsリンゴ葉画像から病害状態を分類するCNNベースの手法とGrad-CAMによる解釈を中心に扱うため、植物病害フェノタイピング手法として該当する。
abstractwe suggest a machine learning-based technique to automate the detection and classification of common apple diseases based on images of apple leaves collected from various regions.
Reproduction assets foundThe paper's apple leaf disease image dataset (9,696 images, four classes) is publicly available on Kaggle and explicitly cited by the authors as the dataset used for training and evaluation. No author code, trained model, or other paper-specific assets are reported.Dataset · publicIn this study, the dataset used for apple leaf disease classification was obtained from
Kaggle [20]. The dataset contains a total of 9,696 images of apple leaves, which include
both diseased and healthy samples.Open asset ↗Kagglepdf-raw-page:4 lines:1-39Code / dataset availability confirmedCrossref · checked 14 Sept 2026
Common beanRiceWheatLeafClassificationDisease symptoms / severity
In Bangladesh, crop leaf diseases create a serious risk to food security and production from agriculture. Timely identification of leaf diseases in rice, wheat, and bean crops is considered crucial for the implementation of effective disease detection and classification strategies. To address this challenge, a MobilenetV2-based disease identification and classification system is proposed in this research. Previous studies focus on classifying diseases of a single species, leaving the need to train models separately for each species. This research focuses on forming a single standard model to perform leaf disease classification for multiple crop species including rice, wheat, and beans. The approach makes use of transfer learning with the MobilenetV2 model, which is fine-tuned using a dataset of annotated crop leaf images specific to Bangladesh. Following a comprehensive evaluation, an overall accuracy of 97.87% was achieved in the classification of crop leaf diseases, which surpasses the accuracy of a number of previous studies focusing on leaf disease detection of a single crop. The system demonstrates the capability to rapidly diagnose diseases in real time by enabling the users to prompt intervention to mitigate potential crop losses, ultimately leading to amplified crop yield and food security. Overall, the research highlights the promise of AI-powered solutions in tackling crop leaf disease detection, which in turn encourages greater research and technology adoption to support sustainable farming methods especially in the crop disease classification domain in Bangladesh and throughout the world. Received: 24 May 2025 | Revised: 9 March 2026 | Accepted: 14 April 2026 Conflicts of Interest The authors declare that they have no conflicts of interest to this work. Data Availability Statement The data that support the findings of this study are openly available in the Bangladeshi Crops Disease Dataset at https://www.kaggle.com/datasets/nafishamoin/bangladeshi-crops-disease-dataset and the Bean Disease Dataset at https://www.kaggle.com/datasets/therealoise/bean-disease-dataset. Author Contribution Statement Md. Mahmudul Hasan: Conceptualization, Methodology, Visualization, Supervision. Md. Omar Faruq: Software, Validation, Writing – original draft. Mahadi Hasan Musa: Formal analysis, Investigation. Mohammad Mamunur Rashid: Resources, Data curation, Writing – review & editing. Khandaker Mohammad Mohi Uddin: Writing – review & editing, Project administration, Supervision.
Why it matches plant phenotyping methods葉画像から作物の病害状態を推定する深層学習手法を開発・評価しており、植物病害フェノタイピングが中心的な技術貢献である。
abstracta MobilenetV2-based disease identification and classification system is proposed in this research.
Reproduction assets foundThe paper's Data Availability Statement openly provides the Bean Disease Dataset on Kaggle, which is one of the two public image datasets used to train the multi-crop leaf disease classification model. The Bangladeshi Crops Disease Dataset URL is not among the allowed URLs, so only the bean dataset is reported. No codeDataset · publict
The authors declare that they have no conflicts of interest to
this work.
Data Availability Statement
The data that support the findings of this study are openly
available in the Bangladeshi Crops Disease Dataset at https://
www.kaggle.com/datasets/nafishamoin/bangladeshi-crops-disease-
dataset and the Bean Disease Dataset at https://www.kaggle.com/datasets/therealoise/bean-disease-dataset.Author Contribution Statement
Md. Mahmudul Hasan: Conceptualization, Methodology,
Visualization, Supervision. Md. Omar Faruq: Software, Valida-
tion, Writing – original draft. Mahadi Hasan Musa: Formal
analysis, Investigation. Mohammad Mamunur Rashid: Resources,
Data curation, Writing – review & editing.Open asset ↗Kaggle · therealoise/bean-disease-datasetpdf-raw-page:11 lines:1-83Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Tomato leaf diseases pose significant threats to crop yield and food security. However, in real-world cultivation environments, factors such as fluctuating illumination, varying leaf occlusion, and ambiguous lesion morphology often compromise detection accuracy. This paper presents the Gradient-aware Bidirectional Retentive Detection Transformer (GBR-DETR), a model designed for high-precision, real-time disease detection. This model is composed of two network structures and a retentive feature aggregation module: (1) a Multi-scale Gradient-Aware Transfer Network (MGAT-Net) is designed to encode gradient information through the Sobel operator, thereby enhancing the localization stability for small and blurry lesions; (2) a Bidirectional Context Pyramid Network (BCPN) is proposed to enable bidirectional interactions among multi-level features through a top-down and a bottom-up pathway, thereby generating multi-scale lesion features and bridging cross-scale semantic gaps; and (3) a Retentive Feature Aggregation Module (RFAM) is used to suppress background noise and establish global feature correlations, thereby enhancing the overall representation capability for lesion recognition. Experiments on the Multi-scenario Tomato Leaf Disease (M-TLD) dataset show that GBR-DETR yields gains of 3.12, 4.88, and 3.41 percentage points in mAP 50-95 , mAP 50 , and mAP 75 , respectively, over the baseline RT-DETR, while also outperforming representative DETR-based and CNN-based detectors. The model demonstrates robust generalization on the PlantDoc cross-domain benchmark, achieving a 2.11% improvement in mAP 50 over the baseline. Deployed on the NVIDIA Jetson Orin Nano with TensorRT FP16, it achieves 54 ms latency, enabling real-time disease monitoring on edge devices. This solution provides effective technical support for real-time disease monitoring in smart agriculture.
Why it matches plant phenotyping methodsトマト葉の病斑・病害状態を画像から検出するモデルを開発し、複数データセットで比較検証、エッジデバイス実装まで評価しており、植物病害表現型の取得手法が中心である。
abstractThis paper presents the Gradient-aware Bidirectional Retentive Detection Transformer (GBR-DETR), a model designed for high-precision, real-time disease detection.
Reproduction assets foundThe paper's M-TLD tomato leaf disease dataset (2212 images, 6581 annotations) and the GBR-DETR implementation/training code are explicitly stated to be publicly available at the authors' GitHub repository.Dataset · publicThe M-TLD dataset and all annotation files are publicly available at https://github.com/zhuojiaxiong6/DETR (accessed on 29 April 2026) to facilitate reproducibility and future research.Open asset ↗zhuojiaxiong6/DETRlines:38-108Code · publicThe code and dataset used in this study are publicly available at the following GitHub repository: https://github.com/zhuojiaxiong6/DETR (accessed on 29 April 2026). This repository contains the implementation of GBR-DETR, a Detection Transformer variant developed for detecting tomato leaf diseases and pests. All relevant training scripts, configuration files, and instructions for dataset usage are provided in the repository.Open asset ↗zhuojiaxiong6/DETRlines:673-675Code / dataset availability confirmedCrossref · Europe PMC · checked 5 Sept 2026
Accurate plant disease segmentation is often constrained by the availability of large, finely annotated datasets, particularly for rare diseases. This work presents a synthetic data generation pipeline that combines 3D leaf modelling with diffusion-based disease synthesis to address this limitation. Procedurally-generated leaf geometries are built in the 3D modelling package Blender to provide exact ground-truth masks, after which style-transfer is applied using Stable Diffusion, fine-tuned with Low-Rank Adaptation (LoRA) and guided by ControlNet conditioning to both preserve leaf structure and enforce correct lesion placement. The approach is evaluated on apple leaf diseases using a deliberately restricted subset of the PlantVillage dataset, simulating a controlled low-data-resource environment. Downstream task effectiveness is measured through leaf disease segmentation. The results show that combining data from the pipeline with limited real data leads to consistent improvements in segmentation performance.
Why it matches plant phenotyping methods植物病斑の画像セグメンテーション性能向上を目的に、3D葉モデルと拡散モデルによる合成データ生成パイプラインを開発・評価しており、植物病害状態の画像ベース推定が中心である。
abstractThis work presents a synthetic data generation pipeline that combines 3D leaf modelling with diffusion-based disease synthesis to address this limitation.
Reproduction assets foundThe authors publicly deposited the paper's annotated PlantVillage subset (75 images with segmentation masks) plus 300 synthetic images with ground-truth masks on Zenodo, directly reproducing this paper's phenotyping/segmentation data.Dataset · publicThis annotated subset of PlantVillage is available at https://doi.org/10.5281/zenodo.18659728 . The repository contains the 75 images from the restricted dataset with the corresponding segmentation masks along with 100 synthetic images per disease generated using Blender and Stable Diffusion, each with corresponding ground truth masks.Open asset ↗zenodo · 10.5281/zenodo.18659728lines:314-325Code / dataset availability confirmedEurope PMC · checked 15 Sept 2026
Accurate and real-time detection of maize foliar diseases is important for field disease monitoring and yield protection. However, in complex natural field environments, different diseases often exhibit high visual similarity, and early weak lesions are easily confused with background elements such as dry leaves, soil, and shadows, leading to false positives and missed detections in existing models. To address these challenges, this study proposes an improved lightweight maize foliar disease detection model based on YOLO11, termed CKM-YOLO11. First, a mixed local channel attention mechanism is introduced and adapted to the task in the backbone to construct the C3k2-MLCA module, thereby enhancing joint modeling of local lesion textures, edge details, and global contextual information. Second, a lightweight residual attention module, named MLCA-HeadLite, is designed at the P5 layer of the neck/head to alleviate the suppression of weak lesion responses during deep feature fusion. Experimental results demonstrate that the proposed model achieves an mAP@50 of 81.5% on a self-constructed maize disease dataset with complex field backgrounds, improving mAP@50 and mAP@50-95 by 3.2 and 3.4 percentage points, respectively, compared with the baseline YOLO11, while maintaining a low parameter count and computational cost. Further analyses based on the confusion matrix, comparisons of detection results, and Grad-CAM visualizations indicate that the proposed model performs better in background suppression, retention of weak lesion responses, and robustness in complex scenes. This study provides a reference for the lightweight design of maize foliar disease detection models in complex field environments and their deployment on agricultural edge devices.
Why it matches plant phenotyping methodsトウモロコシ葉の病斑・病害状態を画像から検出する軽量モデルを開発し、データセット上で性能評価しているため、植物病害表現型の取得手法が中心である。
abstractthis study proposes an improved lightweight maize foliar disease detection model based on YOLO11, termed CKM-YOLO11.
Reproduction assets foundThe paper's maize foliar disease detection dataset is built from public image sources (CD&S Dataset from OpenDataLab and PlantDoc-Dataset corn rust leaf folders) that are explicitly cited with public URLs, qualifying as paper-specific public phenotype image inputs. The self-collected images and the authors' code/tranedDataset · publict was constructed using three public-data components together with a small number of self-collected maize leaf images. First, field-acquired maize disease images were obtained from the Corn Disease and Severity (CD&S) Dataset downloaded from OpenDataLab, and only the Dataset_Original folder in the raw dataset package was used ( https://opendatalab.com/OpenDataLab/CD_and_S/tree/main , accessed on 3 May 2026). Second, to supplement the leaf rust category, additional images were collected from the train/Corn rust leaf folder of the PlantDoc-Dataset GitHub repository ( https://github.com/pratikkayal/PlantDoc-Dataset/tree/master/train/Corn%20rust%20leaf , accessed on 3 May 2026). Third, leaf rustOpen asset ↗OpenDataLab/CD_and_Slines:38-47Dataset · publicOpenDataLab, and only the Dataset_Original folder in the raw dataset package was used ( https://opendatalab.com/OpenDataLab/CD_and_S/tree/main , accessed on 3 May 2026). Second, to supplement the leaf rust category, additional images were collected from the train/Corn rust leaf folder of the PlantDoc-Dataset GitHub repository ( https://github.com/pratikkayal/PlantDoc-Dataset/tree/master/train/Corn%20rust%20leaf , accessed on 3 May 2026). Third, leaf rust images from the test folder of the same PlantDoc-Dataset repository were also used ( https://github.com/pratikkayal/PlantDoc-Dataset/tree/master/test , accessed on 3 May 2026). In addition, a small number of self-collected maize leaf images Open asset ↗pratikkayal/PlantDoc-Datasetlines:38-47Dataset · public, additional images were collected from the train/Corn rust leaf folder of the PlantDoc-Dataset GitHub repository ( https://github.com/pratikkayal/PlantDoc-Dataset/tree/master/train/Corn%20rust%20leaf , accessed on 3 May 2026). Third, leaf rust images from the test folder of the same PlantDoc-Dataset repository were also used ( https://github.com/pratikkayal/PlantDoc-Dataset/tree/master/test , accessed on 3 May 2026). In addition, a small number of self-collected maize leaf images were included as negative samples and field-background supplements. Considering that the present study focuses on object detection under complex backgrounds rather than image-level classification under simple-backgOpen asset ↗pratikkayal/PlantDoc-Datasetlines:38-47Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Protein content is an important quality trait in sorghum that influences breeding approaches, end-use applications, and market value. Influenced by genetic, agronomic, and environmental variability, sorghum is characterized by its wide variation in composition, which may also be evident in kernels from the same sample. This study developed and evaluated a method for a non-destructive and rapid prediction of protein content in individual sorghum kernels using single-kernel near-infrared spectroscopy (SKNIR). Applying different pre-processing techniques to the spectra collected from intact kernels, the calibration models were developed using partial least squares regression and the reference protein content values obtained from the LECO combustion method. The best model was obtained using multiplicative scatter correction as pre-processing, resulting in a standard error of prediction of 0.83% and a relative predictive determinant of 3.40. These were indicative of the good predictive ability of the model and the instrument to be applied in quality control and sorting applications. These results highlight the potential of SKNIR to capture the inter-kernel variability in sorghum protein content and enhance screening for grain quality in breeding and grain processing.
Why it matches plant phenotyping methods単一穀粒NIRによるソルガム種子のタンパク質含量推定法を開発・評価しており、植物器官の形質取得が研究の中心である。
abstractThis study developed and evaluated a method for a non-destructive and rapid prediction of protein content in individual sorghum kernels using single-kernel near-infrared spectroscopy (SKNIR).
Reproduction assets foundThe paper's Data Availability Statement deposits the original single-kernel NIR spectra and reference protein data openly in Ag Data Commons, a paper-specific public dataset directly reproducing this study's measurements.Dataset · publicThe original data presented in the study is openly available in Ag Data Commons [https://doi.org/10.15482/USDA.ADC/31316725].Open asset ↗Ag Data Commons · 10.15482/USDA.ADC/31316725html-lines:226-278Code / dataset availability confirmedOpenAlex · Crossref · Europe PMC · checked 5 Sept 2026
Latest imaging technologies play a vital role in the extraction of plant phenotypic traits in high ranges. Most existing analytical methods treat these traits as independent features, overlooking the complex interaction patterns that focus on plant responses to environmental stress. Proposed Perceptual Graph Kernel (PGK) framework model address the limitation in terms of image-derived phenotypic traits plat information graph structured interaction networks leverages perceptual similarity learning to capture higher-order phenotypic patterns. In the PGK framework, traits extracted from RGB (Red, Green, Blue) and multispectral imagery are encoded as nodes, and biologically meaningful relationships amongst trait pairs are represented as weighted edges. Extracted trait values are continuously transformed into perceptual states to enhance biological interpretability, and a graph kernel is employed to measure similarity between trait graphs. Experiments performed in an agricultural field with a precision agriculture dataset for plant stress phenotyping demonstrated that the proposed PGK achieved 93.8% classification accuracy, improving performance by 5.3 percentage points over the CNN baseline. The outcome results clearly highlight the effectiveness of the perceptual graph model for plant phenotyping and provide a robust, interpretable computational framework for sustainable crop monitoring and decision-support in precision agriculture.
Why it matches plant phenotyping methods画像由来の植物形質を抽出・関係グラフ化し、ストレス表現型分類を行う計算手法が研究の中心であるため。
abstractProposed Perceptual Graph Kernel (PGK) framework model address the limitation in terms of image-derived phenotypic traits
Reproduction assets foundThe paper's Data Availability Statement points to a public GitHub repository (marathonengineer/Agriproject) containing the datasets used in this plant stress phenotyping study. The other allowed URL (PlantCV) is a generic phenotyping library, not a paper-specific asset.Dataset · publicThe datasets used in this study are available in publicly accessible online repositories. The repository can be accessed at: https://github.com/marathonengineer/Agriproject.Open asset ↗marathonengineer/Agriprojecthtml-lines:589-657Code / dataset availability confirmedOpenAlex · Europe PMC · Crossref · checked 15 Sept 2026
Climate change threatens global Chinese cabbage ( Brassica rapa L. ssp. pekinensis ) production, a cool-season crop essential for Asian markets. With optimal growth at 18-20°C and severe disruption above 25°C, developing heat-resilient varieties is critical. This study integrated high-throughput 3D multispectral phenotyping with multivariate analysis to characterize temporal heat stress responses in 18 Chinese cabbage genotypes. Seedlings were subjected to heat stress (setpoint 40/35°C day/night; measured 35.7/31.5°C day/night air temperature) or controls (setpoint 25/20°C day/night; measured 25.0/17.7°C day/night air temperature) for 14 days, with continuous non-destructive monitoring of 14 morphological and spectral parameters using PlantEye F600 multispectral 3D scanner. Principal component analysis of temporal phenotyping data explained 62-68% of variance, enabling quantitative assessment of phenotypic stability through Euclidean distance measurements in PC space. Temporal analysis revealed crop-specific response patterns with maximum treatment separation at 3 days after treatment (DAT) (ΔC=3.27), reflecting Chinese cabbage’s rapid heat sensitivity as a cool-season crop, followed by progressive acclimation by 14 DAT (ΔC=1.41). Early responses (3-5 DAT) were dominated by morphological parameters, transitioning to physiological adjustments (10-14 DAT) characterized by spectral indices. Under heat stress, plants prioritized evaporative cooling through increased transpiration (four-fold increase) over carbon assimilation. A critical finding was the disproportionately greater reduction in root biomass relative to shoot biomass under to heat stress, with root biomass declining 38-47% versus 20% in shoots. Strong correlations (r>0.8) between 3D imaging parameters and destructive biomass measurements validated the non-destructive approach’s reliability. Notably, image-based root surface area analysis correlated strongly with actual root biomass (R 2 =0.698, p<0.001), enabling practical assessment of root area without conventional destructive processing. Based on integration of phenotypic stability (Euclidean distances in PC space) and biomass production under heat stress, this approach identified four distinct heat tolerance strategies: stable-productive genotypes (ideal breeding targets combining phenotypic stability with high heat-stress biomass production), stable-conservative genotypes (phenotypic stability with lower production), plastic-productive genotypes (substantial phenotypic changes yet high biomass production), and plastic-sensitive genotypes (phenotypically unstable and poor biomass production). This validated framework accelerates heat-tolerant Chinese cabbage breeding through efficient high-throughput phenotyping, enabling targeted genotype selection for diverse production environments facing climate warming.
Why it matches plant phenotyping methods3Dマルチスペクトルスキャナによる非破壊・時系列表現型取得と、その解析・検証が研究の中心であり、熱ストレス下の形態・生理形質を定量化する実質的なハイスループット表現型解析研究である。
abstractThis study integrated high-throughput 3D multispectral phenotyping with multivariate analysis to characterize temporal heat stress responses in 18 Chinese cabbage genotypes.
Reproduction assets foundThe paper states its collected phenotyping data are available in the supplementary material hosted with the article (open access under CC BY-NC-ND), making the paper-specific phenotype dataset publicly actionable via the article DOI. The analysis code, however, is only available from the corresponding author uponReasonDataset · publichrough field phenotyping.) between RDA and the World Vegetable Center (WorldVeg)” and by the long-term strategic donors to the WorldVeg: Taiwan, the United States, Australia, the United Kingdom, Germany, Thailand, South Korea, Philippines, and Japan.
Footnotes
Appendix A
Supplementary data to this article can be found online at https://doi.org/10.1016/j.plaphe.2026.100221 .
Appendix A.
Supplementary data
The following is the Supplementary data to this article.
Multimedia component 1
Data availability
The data collected and used in this study are available in the supplementary material. The code used for analysis can be obtained from the corresponding author upon reasonable request.
ReferenceOpen asset ↗lines:486-514Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Pakistan is the fourth-largest rice producer and the fifth-largest exporter worldwide. Timely disease detection remains challenging due to the scale of cultivation and reliance on manual monitoring. Developing reliable, ongoing computerized systems for plant health management is essential for efficient disease control. A deep learning approach is used as the core method to identify diseases in rice leaves. This methodology employs a range of advanced deep learning architectures to achieve top-tier feature extraction and classification. The publicly available rice leaf disease dataset on Zenodo supports research reproducibility and data transparency. We systematically process a balanced dataset of 1914 image samples using Python with TensorFlow and a GPU to enable high-speed computation for large-scale image processing. This study conducts a systematic comparative evaluation of five deep transfer learning architectures (InceptionV3, DenseNet201, ResNet152V2, EfficientNetV2L and MobileNetV2) trained independently. The base backbone models are then integrated with guided GrabCut segmentation with contour-detection method for interpretable disease localization. In this work, the methods of segmentation by GrabCut and contour detection are introduced to make the results of the study easier to interpret and explain the disease areas, but the final classification outcomes are obtained only on the basis of the underlying deep transfer learning models. As a result, infected leaf areas can be identified more effectively, allowing for better understanding and explainable of the disease.To enhance interpretability, GrabCut segmentation and contour detection are applied as post-hoc visualization techniques to highlight diseased regions corresponding to CNN predictions. These techniques do not influence the classification training process. All five models InceptionV3, DenseNet201,ResNet152V2,EfficientNetV2L and MobileNetV2 demonstrated their effectiveness in detecting rice diseases during training, validation, and testing phases, with models trained over 30 epochs. The training methods and accuracy rates of the models were compared during validation and final testing. InceptionV3 demonstrated the most moderate performance of 98.80% training, 98.44% validation, and 98.43% test accuracy, which means that it has strong generalization and consistent learning behavior. The performance of very high-density networks such as DenseNet201 (98.72% train, 98.43% val, 98.43% test), ResNet152V2 (99.02% train, 99.22% val, 97.39% test), EfficientNetV2L model accuracies (39.01% train, 48.70% val, 44.50% test) also showed competitive results, which validated the effectiveness of deep transfer learning in the classification of rice leaf disease, while MobileNetV2 model accuracies (98.09% train, 98.18% val, 96.87% test) indicate that a lightweight model can still achieve reliable classification performance with lower computational complexity. In general, the comparative analysis defines InceptionV3 as the most stable and efficient model in the framework proposed. These results illustrate InceptionV3 superior generalization ability, supported by explainable methods for improved feature localization, confirming the viability of transfer learning for accurate and practical rice disease detection using GrabCut segmentation and contour detection technique. The complete implementation code and data used for the research experimentation is publicly available at https://github.com/ummershakeel03/Rice-Leaf-Diseases-Classification for reproducibility and reuse.
Why it matches plant phenotyping methodsイネ葉の病徴領域を画像から分類・局在化する深層学習ワークフローが研究の中心であり、GrabCut・輪郭検出と複数モデルの比較評価を含むため、植物病害状態の画像ベース表現型計測として採用。
abstractA deep learning approach is used as the core method to identify diseases in rice leaves.
Reproduction assets foundThe paper explicitly states that the complete implementation code and the rice leaf disease image dataset (1914 samples) used in this study are publicly available: code on the authors' GitHub repository and the dataset on Zenodo (DOI 10.5281/zenodo.15817084). Both are paper-specific, public, and actionable.Code · publicThe complete implementation code and data used for the research experimentation is publicly available at https://github.com/ummershakeel03/Rice-Leaf-Diseases-Classification for reproducibility and reuse.Open asset ↗ummershakeel03/Rice-Leaf-Diseases-Classificationhtml-lines:1357-1368Dataset · publicThe dataset for this research study is available at: https://doi.org/10.5281/zenodo.15817084.Open asset ↗10.5281/zenodo.15817084html-lines:1357-1368Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Image analysis of pits and grains provide alternative routes for overcoming the invasive approach of genomic tools in the investigation of archaeological or modern plant material, which is only seldom a viable option due to the complex and laborious methodologies required. Nevertheless, any investigation of pit morphology and cultivar interpretation requires a high quality, comprehensive dataset for comparison. Such a benchmark dataset for the morphology of olive (Olea europaea) pits is presented in this paper, designed to facilitate similar research and establish a base for future investigations. The dataset was established by image analysis of pits of 18 olive cultivars that were photographed in both lateral and dorsal positions. A dedicated MATLAB® code was developed to extract the silhouettes of each pit and to calculate 16 morphometric traits of each view of the pit. Altogether, a total of 1008 photos of 504 pits of the 18 cultivars, together with their detailed morphometric description and statistical analysis are available here. These were used to test the accuracy of the dataset and the new approach in representing the different cultivars.
Why it matches plant phenotyping methodsオリーブ核の画像から形態形質を抽出する専用コードと、検証用ベンチマークデータセットを開発・提示しており、植物形質取得法が中心である。
abstractSuch a benchmark dataset for the morphology of olive (Olea europaea) pits is presented in this paper, designed to facilitate similar research and establish a base for future investigations.
Reproduction assets foundThe paper's olive pit images (1008 photos of 504 pits) and morphometric trait data (16 parameters per view) are openly deposited on Zenodo, along with the authors' MATLAB 'PitAnalyzer' software used for silhouette extraction and trait calculation. Both are paper-specific, public, and directly actionable via the Zenodo.Dataset · publicAll the images are available on a dedicated Zenodo repository17. The file name of each image comprises an abbreviation of the cultivar name (Table 1), tree number (a, b or c), pit number (1–30) and the pit position (VD VL for dorsal and lateral, respectively).Open asset ↗Zenodohtml-lines:220-292Code · publicThe code that was used in this work is compiled as a stand-alone software based on MATLAB “PitAnalyzer”. The software is available to download at the following repository, where any use of it should be attributed appropriately to this publication (https://zenodo.org/records/18789307).Open asset ↗Zenodohtml-lines:381-404Code / dataset availability confirmedCrossref · checked 15 Sept 2026
Plant disease is a serious threat to agricultural productivity and food security worldwide. Traditional diagnostic methods such as manual observation and laboratory testing are time-consuming, labor-intensive and error prone. The emergence of artificial intelligence (AI) and deep learning (DL) offer scalable solutions for precision agriculture in plant disease detection using advanced computational techniques to process large datasets. Hybrid deep learning architecture integrates Convolutional Neural Networks (CNNs) along with Artificial Neural Networks (ANNs) can leverage both visual and contextual data to improve detection performance. The hybrid CNN-ANN model was developed to analyze visual data (plant images) and contextual data (environmental and soil metrics). The CNN module extracted spatial and textural features from plant images, while the ANN module processed environmental parameters. These outputs were fused into a unified feature vector for disease classification. A total of 15 plant species and their associated diseases were analyzed using 200-270 training samples and 150-190 testing samples for each disease across a total of 1000 images. The model was judged by metrics such as detection accuracy, AUC, sensitivity etc. Data augmentation, pre-trained architectures (e.g., ResNet50) and early stopping techniques were utilized to improvise model performance. The hybrid model saliently achieved detection accuracy consistently above 87% with majority of diseases surpassing 90%. Highperforming cases like Rice Blast (92.5%), Tomato Early Blight (93.8%), and Coffee Rust (93.0%), with AUC values of 0.93 or higher, sensitivity exceeding 94% and specifically above 90%. Diseases of Sugarcane Red Rot and Tea Blister Blight exhibited sensitivities of 92.4% and 92.1% and specificities of 91.1% and 90.5% respectively. Moderate accuracy for Coconut Bud Rot (87.5%) and Mustard Alternaria Blight (87.8%) was due to smaller training sample sizes.
Why it matches plant phenotyping methods植物画像から病害状態を分類するハイブリッドCNN-ANN手法を開発し、精度・AUC・感度などで評価しており、病害フェノタイピング手法が研究の中心である。
abstractThe hybrid CNN-ANN model was developed to analyze visual data (plant images) and contextual data (environmental and soil metrics).
Reproduction assets foundThe paper's plant disease detection model was trained on public plant image datasets: the PlantSeg dataset (Zenodo record 13958858, DOI 10.5281/zenodo.13293891) and the UCI Machine Learning Repository Plants dataset. Both are cited in Materials and Methods as sources of the visual data used for the CNN module. No code,Dataset · publicebao (ZiranKexueBan)/Journal of
Huazhong University of Science and Technology
(Natural Science Edition). 2021;49(8).
37. Ma C, Mu X, Sha D. Multi-Layers Feature Fusion of
Convolutional Neural Network for Scene
Classification of Remote Sensing. IEEE Access.
2019;7.
38. Hämäläinen W.Plants Dataset[Internet]. 2024.
Available from:
https://archive.ics.uci.edu/dataset/180/plants
39. WeiT. PlantSeg: A Large-Scale In-the-wild Dataset
for Plant Disease Segmentation [Internet]. 2018.
Available from: https://zenodo.org/records/13958858Open asset ↗180pdf-raw-page:15 lines:1-48Code / dataset availability confirmedCrossref · Europe PMC · checked 5 Sept 2026
Background Recently, plant disease detection and classification have become major concerns in agriculture. Early detection of plant diseases supports farmers to take precautionary actions to prevent the spread of infections across different parts of the plant. However, detecting and classifying plant leaf diseases remain challenging tasks due to the overlapping characteristics of different diseases. Methods To mitigate these limitations, this research developed a Multi-FusNet–convolutional neural network (Multi-FusNet–CNN) with an improved Huber loss function to classify multiple classes of plant leaf diseases. Here, a multipath residual network (Multi-RG) with cross-filtering fusion is integrated, and the pixel shuffling fusion method is developed for fusing low-level to up-sampled features. An improved Huber loss function is incorporated into the Multi-FusNet–CNN to effectively handle outliers and enhance the model’s generalization capability during training. Results The developed Multi-FusNet–CNN with improved Huber loss function achieved 99.95% accuracy, 99.13% F1-score, 99.87% recall, 99.27% precision, and 99.93% specificity, thereby outperforming existing conventional techniques. Conclusion The proposed Multi-FusNet–CNN model improved the generalization capability of the method during the training process on plant leaf disease detection and classification.
Why it matches plant phenotyping methods植物葉の病徴を画像から検出・分類するCNN手法の開発と性能評価が研究の中心であり、植物の病害状態を推定するフェノタイピング手法に該当する。
abstractthis research developed a Multi-FusNet–convolutional neural network (Multi-FusNet–CNN) with an improved Huber loss function to classify multiple classes of plant leaf diseases.
Reproduction assets foundThe paper uses two public plant leaf image datasets directly in its analysis: the Plant Village dataset (Kaggle) as the primary training/classification dataset and the RoCoLe dataset (datasetninja) for coffee leaf disease samples. Both have explicit public URLs in the references. No author code, models, or checkpoints,Dataset · public26
Plant village dataset . Available online at: https://www.kaggle.com/datasets/emmarex/plantdisease (Accessed February 03, 2026 ).Open asset ↗Kaggle · emmarex/plantdiseaselines:1010-1131Dataset · public31
RoCoLe dataset . Available online at: https://datasetninja.com/rocoleing (Accessed February 03, 2026 ).Open asset ↗datasetninja · rocoleinglines:1010-1131Code / dataset availability confirmedEurope PMC · checked 15 Sept 2026
Apple surface diseases are crucial factors affecting the quality and yield of apples. Traditional manual inspection methods suffer from low efficiency and poor real-time performance. To address these issues, this paper proposes an apple surface disease detection method based on an improved YOLOv11s. Firstly, three groups of GAM attention mechanisms are integrated into the neck structure of the YOLOv11s to enhance the efficiency of feature fusion and the capability of semantic information transmission. Secondly, the original convolutional downsampling in the backbone network is replaced with a Haar-based feature downsampling module, enabling the model to retain more high-frequency detail information during the downsampling process. In addition, the WFU module is introduced to realize the dynamic allocation of feature weights, enhancing the model's ability to recognize multi-scale defect features. Finally, the PIOUv2 loss function is adopted to optimize bounding box regression, improving the model's detection performance for tiny defect spots. In addition, various data augmentation methods for small datasets are employed to improve the model training performance and effectively avoid the problem of data overfitting. The experimental results demonstrate that the F1-score of the proposed model is increased by 4.2%, and the mAP@50:95 is boosted by 2.4%. The detection performance outperforms various comparative models, which verifies the effectiveness and superiority of the proposed method.
Why it matches plant phenotyping methodsリンゴ表面の病斑・欠陥を画像から検出する改良YOLO手法の開発と比較検証が研究の中心であり、植物の病害状態を直接推定するフェノタイピング手法に該当する。
abstractthis paper proposes an apple surface disease detection method based on an improved YOLOv11s.
Reproduction assets foundThe paper uses a hybrid apple disease image dataset whose public portion is explicitly cited as reference [27] with a public Baidu Netdisk URL (the only allowed URL), matching the paper's apple surface disease detection dataset. The self-built portion and raw data are available only on request, and no author analysis代码Dataset · public3390/foods12061352.
26. Liu J., Zhao G., Liu S., Liu Y., Yang H., Sun J., Yan Y., Fan G., Wang J., Zhang H. New progress in intelligent picking: Online detection of apple maturity and fruit diameter based on machine vision. Agronomy. 2024;14:721. doi: 10.3390/agronomy14040721.
27. [(accessed on 4 April 2026)]. Available online: https://pan.baidu.com/s/1pfsr3yPczEJywNwwDUFliw?pwd=98te .
28. Géron A. Hands-on Machine Learning with Scikit-Learn, Keras, and TensorFlow. O’Reilly Media, Inc.; Sebastopol, CA, USA: 2022.
29. Apicella A., Isgrò F., Prevete R. Don’t push the button! exploring data leakage risks in machine learning and transfer learning. Artif. Intell. Rev. 2025;58:339. doi: 10.1007/s1Open asset ↗lines:424-433Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Field / plotLeafClassificationSegmentationStress / disease detectionDisease symptoms / severity
Early and accurate detection of plant leaf diseases is an essential requirement for precision agriculture, given their severe impact on global food security. While much has been done recently, many deep learning-based approaches will still fail in real-world tests because of challenges such as background clutter, differences in illumination, occlusion, or the fact that visual symptoms for these diseases can be very subtle early on. Traditional CNN- and Transformer-based architectures generally lack accurate lesion localisation and interpretability, hindering their practical deployment in agricultural decision-support tools. To address these issues, we present LDDHybridNet, a region-based, explanation-friendly deep learning framework that can identify leaf disease at an early, accurate stage. It then applies preprocessing steps guided by ROI, based on leaf segmentation from the U-Net, followed by a compact CNN-based spatial feature-extraction framework. We arrange spatial feature embeddings extracted from lesion regions into an ordered sequence and employ a Bi-LSTM with attention to model structured contextual dependencies, allowing progression-aware feature learning without requiring actual temporal image sequences. Lastly, Grad-CAM-based post-hoc explainability is employed to interpret model decisions, enabling transparent visualisation of disease-relevant regions. We conduct extensive experiments on the PlantVillage benchmark and the FieldPlant dataset and show that LDDHybridNet consistently outperforms representative CNN, transformer, and hybrid baselines across multiple evaluation metrics. Although the near-ceiling performance on PlantVillage reveals the dataset's artificial nature, the proposed framework achieves 95.37% accuracy under real-world field conditions and 92.84% on weak-lesion early-stage samples, demonstrating the method's robustness and early-stage detection potential. The performance boosts are statistically significant (P < 0.01). In general, LDDHybridNet is an interpretable and robust deep learning framework for leaf disease detection, which can support data-driven crop protection and precision agriculture applications.
Why it matches plant phenotyping methods葉の病害症状を画像から検出・局在化する深層学習手法の開発とベンチマーク評価が中心であり、植物の病害状態を直接推定するため、植物フェノタイピング手法として収録する。
abstractwe present LDDHybridNet, a region-based, explanation-friendly deep learning framework that can identify leaf disease at an early, accurate stage.
Reproduction assets foundThe paper's phenotyping measurements are leaf disease detection experiments on two public image datasets: PlantVillage (Kaggle) and FieldPlant (IEEE Dataport), both cited with explicit public URLs. The authors' code, trained weights, and scripts are not publicly released and are available only on request, so no code/模型Dataset · public43.Hughes, D. P. & Mohanty, S. P. PlantVillage Dataset. [online] (2015). Available at: https://www.kaggle.com/datasets/emmarex/plantdiseaseOpen asset ↗PlantVillage Datasethtml-lines:657-726Dataset · public44.Moupojou, R. K., Bouachir, W., Ahamed, T. & Taki, A. H. FieldPlant: A Real-World Dataset for Leaf Disease Detection in Field Conditions. IEEE Dataport. [online] (2021). Available at: https://ieee-dataport.org/documents/fieldplant-datasetOpen asset ↗FieldPlanthtml-lines:657-726Code / dataset availability confirmedEurope PMC · checked 15 Sept 2026
Multispectral / hyperspectralLeafRootMorphology / geometry measurementLeaf traitsRoot system architecture
Premise Selective breeding over thousands of years has prioritized aboveground yield, with little regard for changes belowground. Roots underpin plant growth and resilience, but our knowledge of these critical structures lags behind that of aboveground structures. Accurately phenotyping root traits is labor-intensive, expensive, and often destructive. High-throughput, nondestructive methods are required to advance understanding of the fundamental biology of root systems and to integrate hard-to-measure root traits into breeding programs. Methods We used American licorice (Glycyrrhiza lepidota Pursh.), a perennial legume with a rich ethnobotanical history, as a model to investigate root system phenotypes. We assessed root traits across multiple populations, analyzed relationships between above- and belowground phenotypes, and tested the use of multidimensional leaf traits, including spectral reflectance, in predicting root traits. Results Root traits of American licorice varied significantly across source populations. Root traits were strongly intercorrelated and each root trait correlated with an aboveground phenotype. Leaf spectral reflectance and elemental composition predicted belowground traits; however, interpretation of some trait-specific signals were complicated by isometric scaling between plant size and root traits. Conclusions These findings demonstrate the use of high-dimensional leaf traits as a proxy for root traits, with potential applications for understanding foundational questions in plant biology and in breeding programs targeting belowground structures of perennial herbaceous species. Further optimization and larger studies are needed to improve predictive models.
Why it matches plant phenotyping methods葉の高次元形質とスペクトル反射を用いて、測定困難な根形質を非破壊・高スループットに推定する方法が研究の中心である。
abstractHigh-throughput, nondestructive methods are required to advance understanding of the fundamental biology of root systems and to integrate hard-to-measure root traits into breeding programs.
Reproduction assets foundThe paper's data availability statement points to two public, paper-specific assets: raw root scans on Zenodo and a Figshare deposit containing RhizoVision Explorer output features, CropReporter data and metadata, spectral reflectance data, elemental composition data, and all R code needed to reproduce the analyses. NoDataset · publich Center Bioanalytical Chemistry Facility (RRID:SCR_001047). Finally, we thank the reviewers for their careful evaluation of our manuscript and constructive comments, which helped us clarify the conceptual framing and strengthen the overall quality of the work.
DATA AVAILABILITY STATEMENT
Raw root scans can be found on Zenodo ( https://zenodo.org/records/18852041 ). RhizoVision Explorer output features, CropReporter and associated metadata, spectral reflectance data, elemental composition data, and all R code needed to reproduce the analyses presented in this manuscript can be found on Figshare ( https://doi.org/10.6084/m9.figshare.28742870 ).
REFERENCES
Alahmad , S.
,
D.
Smith
,
C.
KatOpen asset ↗Zenodo · 18852041lines:173-419Dataset · publicILITY STATEMENT
Raw root scans can be found on Zenodo ( https://zenodo.org/records/18852041 ). RhizoVision Explorer output features, CropReporter and associated metadata, spectral reflectance data, elemental composition data, and all R code needed to reproduce the analyses presented in this manuscript can be found on Figshare ( https://doi.org/10.6084/m9.figshare.28742870 ).
REFERENCES
Alahmad , S.
,
D.
Smith
,
C.
Katsikis
,
Z.
Aldiss
,
S. M.
Brunner
,
S. V.
Meer
,
L.
Meijer
, et al. 2025 .
Phenotyping the hidden half: combining UAV phenotyping and machine learning to predict barley root traits in the field
. Journal of Experimental Botany
76 : 5161 ‐ 5178 .
40580084
10.1093/jxb/eraf268
PMC1Open asset ↗Figshare · 10.6084/m9.figshare.28742870lines:173-419Code / dataset availability confirmedOpenAlex · Europe PMC · checked 15 Sept 2026
Accurate plant segmentation in thermal imagery remains a significant challenge for high throughput field phenotyping, particularly in outdoor environments where low contrast between plants and weeds and frequent occlusions hinder performance. To address this, we present a framework that leverages synthetic RGB imagery, a limited set of real annotations, and GAN-based cross-modality alignment to enhance semantic segmentation in thermal images. We trained models on 1128 synthetic images containing complex mixtures of crop and weed plants in order to generate image segmentation masks for crop and weed plants. We additionally evaluated the benefit of integrating as few as 20 real, manually segmented field images within the training process using various sampling strategies. When combining all the synthetic images with a few labeled real images, we observed a maximum relative improvement of the mean IoU score of 25% compared to the synthetic-only baseline. Cross-modal alignment was enabled by translating RGB to thermal using CycleGAN-Turbo, allowing robust template matching without calibration. Results demonstrated that combining synthetic data with limited manual annotations and cross-domain translation via generative models can significantly boost segmentation performance in complex field environments for multi-model imagery.
Why it matches plant phenotyping methods熱画像における作物・雑草の分割を対象とし、合成データ、少数の実画像、GANによるモダリティ間整合を用いた高スループット圃場フェノタイピング手法を開発・評価しているため。
abstractAccurate plant segmentation in thermal imagery remains a significant challenge for high throughput field phenotyping
Reproduction assets foundThe paper's real annotated cowpea segmentation images and its synthetic Helios-generated training imagery are both publicly available on Hugging Face per the Data Availability statement. No author analysis code repository with explicit deposit language is provided (Helios and AgML are generic third-party tools, not theDataset · publicendix A
Supplementary data to this article can be found online at https://doi.org/10.1016/j.plaphe.2026.100214 .
Appendix A.
Supplementary data
The following is the Supplementary data to this article:
Multimedia component 1
Data availability
Data can currently be accessed through Huggingface [ 75 ]. The real data is found here: https://huggingface.co/datasets/earlranario/cowpea-segmentation . The synthetic data is found here: https://huggingface.co/datasets/earlranario/cowpea-synthetic-segmentation .Open asset ↗earlranario/cowpea-segmentationlines:341-366Code / dataset availability confirmedOpenAlex · arXiv · checked 5 Sept 2026
Purpose: Fast detection of plant stress is key to plant phenotyping, precision agriculture, and automated crop management. In particular, efficient irrigation management requires early identification of water stress to optimize resource use while maintaining crop performance. Direct physiological sensing offers the potential to detect stress responses before visible symptoms appear. Methods: In this study, we recorded electrophysiological signals from greenhouse-grown tomato plants subjected to water stress and developed a framework based on machine learning for online stress detection. The recorded time-series data were processed using a processing pipeline that includes statistical feature extraction and selection, automated machine learning or alternatively deep learning, and probability calibration. Results: Across multiple input time horizons, we found that a 30-minute look-back window strikes the best balance between rapid decision-making and classification performance. Using automated machine learning, the framework achieved classification accuracies of up to 92%, outperforming deep learning approaches. Sequential backward selection reduced the feature set while maintaining performance. Importantly, the framework detects transitions from healthy to stressed states in recordings that were not included in the training set. Conclusion: Overall, we provide a decision-support tool for farmers and establish a foundation for biofeedback-driven irrigation control to improve resource efficiency in (semi-)autonomous crop production systems.
Why it matches plant phenotyping methodsトマトの電気生理シグナルから水ストレス状態を推定するセンシング・機械学習パイプラインを開発し、未学習データで性能検証しているため、植物フェノタイピング手法が中心である。
abstractDirect physiological sensing offers the potential to detect stress responses before visible symptoms appear.
Reproduction assets foundThe paper's electrophysiological time-series and soil moisture measurements from the water-stress tomato experiment are explicitly stated to be publicly available online via a Zenodo deposit (Buss et al. 2026a), referenced in both the Methods and Data availability sections.Dataset · publicAll recorded and
processed data are available online (Buss et al. 2026a).Open asset ↗pdf-page:5 lines:1-37Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Accurate detection of cocoa pod diseases is vital to reducing yield losses and supporting sustainable agriculture. Although deep learning models have shown promise in plant disease classification, their performance often varies between datasets due to limitations in feature extraction and generalisation. This study introduces a Learnable Gated Fusion Convolutional Block Attention Module (LGF-CBAM) integrated with a ResNetV2-101 backbone to improve discriminative feature learning and improve robustness in cocoa disease classification. Unlike the standard CBAM, which processes attention modules sequentially, LGF-CBAM adaptively balances the importance of spatial and channel cues through trainable gating parameters normalized with a softmax function. Incorporating LGF-CBAM provided outstanding results on the Cocoa_Pod_Disease_Gh dataset, achieving 98.95% accuracy along with F1 and PPV scores of 99.11%. The cross-dataset evaluation confirmed robustness, with accuracies of 98.53% on Cocoa Diseases (YOLOv4), 97.96% on Black and Borer Pod Rot, and 96.19% on Cacao Diseases in Davao. Although greater variability in the Coffee and Cocoa dataset reduced accuracy to 94.00%, the model still maintained strong adaptability under diverse conditions. These findings establish LGF-CBAM as a state-of-the-art framework that outperforms all other referenced systems, offering high accuracy, stability, and generalization. In general, this research contributes to a novel attention-based deep learning framework that can support early and reliable identification of cocoa pod diseases, providing a scalable solution for precision agriculture.
Why it matches plant phenotyping methodsカカオ果実の病害状態を画像から分類する深層学習手法を開発し、複数データセットで性能・頑健性を評価しており、植物フェノタイピング手法が研究の中心である。
abstractThis study introduces a Learnable Gated Fusion Convolutional Block Attention Module (LGF-CBAM) integrated with a ResNetV2-101 backbone to improve discriminative feature learning and improve robustness in cocoa disease classification.
Reproduction assets foundThe authors' primary plant-phenotyping asset is the Cocoa_Pod_Disease_Gh image dataset, publicly deposited on Figshare with an explicit Data Availability statement and DOI. The Kaggle/Roboflow datasets are cited prior external datasets used for cross-dataset evaluation, not paper-specific deposits, so they are excludedDataset · publicThe data that support the findings of this study is available at https://figshare.com/articles/dataset/Cocoa_Disease_Datasets/31294003. https://doi.org/10.6084/m9.figshare.31294003.Open asset ↗figshare · 10.6084/m9.figshare.31294003html-lines:1039-1062Code / dataset availability confirmedCrossref · Europe PMC · checked 5 Sept 2026
This paper addresses the problem of automated segmentation of plant green biomass in field crop images aimed at improving the accuracy of crop and weed identification. To construct a training dataset for neural network models, an automatic annotation algorithm is proposed, enabling the generation of polygonal object masks without human intervention. The method is based on adaptive analysis of color characteristics of plant fragments with iterative narrowing of the hue range in the HSV color space, combined with an integral quality metric that accounts for the dynamics of contour area and shape. The proposed method achieved an IoU of 93.22% and a DSC of 96.30%, demonstrating a high level of agreement between automatic and manual annotations. The generated masks are used to train segmentation models of the YOLO11-seg family. Models of different scales (n, s, m, l, x) were trained and evaluated using standard metrics, including Intersection over Union (IoU), mAP@0.5, mAP@0.5–0.95, F1-score, and Precision–Recall (PR) curves. Experimental results demonstrate that models trained on automatically generated annotations achieve stable segmentation performance of plant green biomass. The best results were obtained with the YOLO11m-seg model, achieving an F1-score of 0. 772. The results confirm the effectiveness of the proposed approach and demonstrate acceptable segmentation quality, supported by both quantitative metrics and visual analysis. The developed automatic annotation algorithm can be used to expand training datasets in computer vision tasks for agricultural applications.
Why it matches plant phenotyping methods植物の緑色バイオマスを画像から自動抽出するポリゴン注釈法を開発し、手動注釈との一致度で検証しているため、植物表現型取得・抽出法が中心である。
abstractan automatic annotation algorithm is proposed, enabling the generation of polygonal object masks without human intervention
Reproduction assets foundThe authors publicly released the paper-specific generated dataset of polygonal segmentation annotations (masks and supporting materials) on Hugging Face. CVAT is only a generic annotation tool, and no author analysis code or trained model checkpoints are explicitly deposited.Dataset · publicThe generated dataset with polygonal segmentation annotations of crop and weed plants, produced using the proposed algorithm and based on the LincolnBeet Dataset, is publicly available on Hugging Face at: https://huggingface.co/datasets/ivliev123/polygonal_marking_plant_objectsOpen asset ↗Hugging Face · ivliev123/polygonal_marking_plant_objectshtml-lines:438-462Code / dataset availability confirmedCrossref · checked 5 Sept 2026
Disease prevention and water management are important to all the crops, particularly rice and sugarcane production in India. The article proposes a reinforcement learning (RL) based intelligent irrigation management system that is capable of optimising water consumption and crop nutrition in response to the changing agricultural climatic conditions. Decentralised reinforcement learning (RL) is used in a network of irrigation agents that utilise soil and microclimate sensor networks to set the terms of water allocation, water use efficiency (WUE) and crop health. At the same time, deep convolutional networks can be used to differentiate between plant stress/disease and leaf images and take applicable proactive actions. It is a framework that incorporates satellite-derived indices (NDVI, EVI, land surface temperature) with local sensor measurements and image-based health measurements through multimodal deep learning. Far-reaching simulations (including Indian climate and crop calendars) demonstrate that the multi-agent system lowers water consumption and preserves the yields and properly notifies stressed plants. The scores of disease detection with plantvillage-based fine-tuned on rice (120 (3 disease types) and 3829 (5 disease types) and sugarcane (2569 images for all disease types, Convolutional Neural Network (CNN) yield results of >98 % accuracy. Crop mapping (rice/sugarcane) Satellite/LSTM-based crop mapping (with Sentinel-1 / Sentinel-2) achieves more than 97 % accuracy. The suggested structure provides a data-driven, scalable system for precision agriculture to enhance the management of irrigation periods and crop health. Simulation experiments show that the RL-based controller can reduce water consumption while preserving optimal soil moisture levels when compared to rule-based irrigation strategies.
Why it matches plant phenotyping methods画像・衛星・センサーを統合して植物ストレス／病害状態を推定するマルチモーダル基盤が提案され、病害検出性能も評価されているため、植物表現型推定が実質的な構成要素である。
abstractdeep convolutional networks can be used to differentiate between plant stress/disease and leaf images
Reproduction assets foundThe paper reports simulation-based experiments using public leaf-image datasets. The only paper-specific public asset explicitly identified is the Kaggle rice leaf diseases dataset (vbookshelf/rice-leaf-diseases) cited as a data source for the rice disease fine-tuning set. No authors' code, trained models, or data dépDataset · publicConflict of interest: Authors do not have any conflict of interest 2026 Mar 31). Available from: https://www.kaggle.com/datasets/Open asset ↗Kagglepdf-page:16 lines:1-58Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Common beanLeafClassificationStress / disease detectionDisease symptoms / severity
Context Plant diseases are a serious danger to the world's food security since they drastically lower crop output. Traditional manual plant leaf inspection is time-consuming, labor-intensive, and frequently subjective. Recent developments in deep learning provide effective and scalable methods for image-based analysis-based automated plant disease identification. Techniques Three deep learning architectures-a proprietary Convolutional Neural Network (CNN), ResNet18, and Vision Transformer (ViT)-are used in this study to examine automated bean leaf disease identification. The Augmented iBean dataset, which has three classes-angular leaf spot, bean rust, and healthy leaves-was used to train and assess the models. Every model was trained using the same preprocessing and training settings to provide fair benchmarking. Receiver Operating Characteristic (ROC) curves, accuracy, precision, and confusion matrices were used to assess the model's performance. Outcomes ResNet18 fared better than CNN and Vision Transformer models, according to a comparative analysis. ResNet18 maintained a high level of computing efficiency while achieving 99% accuracy and 99.01% precision. Its better categorisation capacity across all disease categories was validated using confusion matrix and ROC analysis. In conclusion The study shows that ResNet18 offers the optimal trade-off between accuracy and efficiency and creates a standard benchmarking framework for bean leaf disease identification. The results demonstrate its applicability for real-time deployment in precision agricultural systems for better crop management and early disease identification.
Why it matches plant phenotyping methods豆葉の病徴を画像から認識する深層学習手法を比較・ベンチマークしており、植物病害状態の取得手法が研究の中心である。
abstractThree deep learning architectures-a proprietary Convolutional Neural Network (CNN), ResNet18, and Vision Transformer (ViT)-are used in this study to examine automated bean leaf disease identification.
Reproduction assets foundThe paper's data availability statement points to the Augmented iBean dataset on IEEE DataPort, the public bean leaf image dataset used for all phenotyping/classification experiments in this study. No author analysis code or trained model checkpoints are shared.Dataset · publicPublicly available datasets were analyzed in this study. This data can be found here: https://ieee-dataport.org/documents/bean-leaf-disease-augmented-ibean-dataset.Open asset ↗ieee-dataport · bean-leaf-disease-augmented-ibean-datasethtml-lines:446-496Code / dataset availability confirmedCrossref · Europe PMC · checked 15 Sept 2026
Proper diagnosis of crop diseases and accurate measurement of fruit ripeness is essential in enhancing agricultural productivity, but conventional methods of diagnosis are time-consuming, error-prone, and inefficient. With the rapid development of AI, deep learning (DL), and IoT, there is increasing demand for combined solutions that jointly address plant health monitoring and harvest optimization in a reproducible and deployment-oriented manner. This study develops a new bi-phasic DL framework, AgroDualNet, that predicts crop diseases and identifies fruit ripeness stages to optimize yield quality and minimize agricultural losses. The work explicitly targets improved classification reliability, broader class evaluation, rigorous validation and generation of decision-ready outputs for precision agriculture. AgroDualNet comprises two modules. The crop-disease prediction module integrates ResNet50 with a Convolutional Block Attention Module (CBAM), and a Sequential Minimal Optimization (SMO)-based SVM classifier to enhance feature learning and classification performance Several different architectural designs are benchmarked and the resultant model is tested on both a dedicated 3-class subset and a large multi-class model of the PlantVillage dataset with leakage safe protocol(augmentation applied only on training data), cross-validation, statistical significance testing as well as ablation. The fruit-ripeness module employs YOLOv8 for real-time fruit localization and MobileNetV2 for lightweight ripeness classification suitable for edge deployment and a prototype decision-support layer maps predictions to actionable recommendations. That is able to run on the edge. Experiments show that the hybrid CBAM + ResNet50 + SMO model achieves 99.6% accuracy for crop disease classification on a three-class configuration of the PlantVillage dataset and maintains consistently higher accuracy than strong baseline in a 38-class setting, with statistically significant results confirmed by McNemar's test (p < 0.001) outperforming baseline and intermediate architectures in accuracy, precision, Recall and F1-Score The fruit ripeness pipeline achieves 98.88% classification accuracy across four ripeness stages (unripe, semi-ripe, ripe, over-ripe) on a combined Kaggle and real-field apple dataset with low inference time, confirming its suitability for near real-time deployment on edge devices. Cross-validation, Statistical significance tests and ablation studies collectively validate the robustness and significance of these gains and the decision-support layer demonstrates the feasibility of converting raw predictions into interpretable, recommendation-oriented outputs. AgroDualNet provides an efficient and unified system for monitoring plant diseases and evaluating fruit ripeness, with statically validated performance across both focused and full multi-class settings, addressing two critical challenges in precision agriculture with a single extensible framework. The dual-module design of AgroDualNet, which combines disease prediction with ripeness analysis and a preliminary decision-support prototype offers a more comprehensive and practically relevant AI-driven monitoring solution than conventional single-task models. By emphasizing multi-class validation on PlantVillage, leakage-aware experimentation, statistical verification, and system-level integration, this works supports real-time, precise and automated guidance to reduce crop losses, improve harvest timing, and enable smarter farm-level decision making.
Why it matches plant phenotyping methods植物病害状態と果実成熟度を画像から推定する深層学習パイプラインの開発・比較検証が中心であり、PlantVillageおよび実圃場データで交差検証、アブレーション、統計検定を実施しているため、植物フェノタイピング手法として含める。
abstractThis study develops a new bi-phasic DL framework, AgroDualNet, that predicts crop diseases and identifies fruit ripeness stages
Reproduction assets foundThe paper's Data availability statement names two public datasets used directly in the phenotyping experiments: the PlantVillage crop-disease dataset and a Kaggle apple fruit-ripeness dataset, both with explicit Kaggle URLs matching allowed_urls. The statement also mentions implementation files, trained weights, and a Dataset · public. and V.V. wrote the main manuscript text, and K.N. prepared figures. All authors reviewed the manuscript.
Funding
There is no funding received from any organization for this work.
Data availability
The datasets that have been used and analysed in this study are publicly available. PlantVillage crop disease data are on kaggle ( https://www.kaggle.com/datasets/abdallahalidev/plantvillage-dataset ) accessed March 2026). The dataset on the ripeness of apple fruits can be found in Kaggle ( https://www.kaggle.com/datasets/mdsagorahmed/fruit-image-dataset-22-classes ) accessed March 2026). The files used to run the implementation, trained model weights, class definitions and split metadata are opeOpen asset ↗Kaggle · plantvillage-datasetlines:583-665Dataset · publiction for this work.
Data availability
The datasets that have been used and analysed in this study are publicly available. PlantVillage crop disease data are on kaggle ( https://www.kaggle.com/datasets/abdallahalidev/plantvillage-dataset ) accessed March 2026). The dataset on the ripeness of apple fruits can be found in Kaggle ( https://www.kaggle.com/datasets/mdsagorahmed/fruit-image-dataset-22-classes ) accessed March 2026). The files used to run the implementation, trained model weights, class definitions and split metadata are openly available at: 10.5281/zenodo.19051520.
Declarations
Competing interests
The authors declare no competing interests.
References
1.
George R Thuseethan S RagelOpen asset ↗Kaggle · fruit-image-dataset-22-classeslines:583-665Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Plant diseases threaten global agriculture, and deep learning-based disease recognition has become crucial for addressing this challenge. While DenseNet excels in plant disease classification due to its dense connectivity, its large size limits deployment on resource-constrained edge devices. This paper proposes Connection-Aware DenseNet Pruning (CADP), achieving efficient compression through three collaborative modules. First, the EdgePrune module explicitly models inter-channel feature flows via an edge weight network, using dual-channel importance scoring that fuses activation correlation and gradient information to remove redundant connections while preserving critical propagation paths. Second, connection-guided CP decomposition leverages EdgePrune's importance information, adaptively assigning differentiated ranks through the Connection Importance Index (CII) to balance preservation of critical layers with deep compression of secondary layers. Third, dual-stream knowledge distillation integrates throughout post-pruning and post-decomposition fine-tuning, combining output-level soft labels and intermediate spatial attention transfer to recover compression losses. CADP achieves 88% parameter reduction and 89% computational savings on DenseNet-121, maintaining 99.67% and 99.66% accuracy on PlantVillage and RiceLeaf datasets, achieving competitive accuracy with significantly fewer parameters. This provides a promising approach for resource-constrained deployment with potential generalizability and practical value.
Why it matches plant phenotyping methods植物画像から病害状態を推定する分類モデルの軽量化手法を開発し、PlantVillageおよびRiceLeafで性能を評価しているため、病害フェノタイピング手法が中心である。
titleCADP: Connection-Aware DenseNet Pruning for lightweight plant disease classification.
Reproduction assets foundThe paper uses two publicly available plant image datasets (PlantVillage and Rice Leaf Disease) hosted on Mendeley Data, explicitly linked in the Data Availability statement. No author analysis code, models, or checkpoints are shared.Dataset · publicThe datasets used in this study are publicly available. The PlantVillage dataset can be accessed at https://data.mendeley.com/datasets/tywbtsjrjv, and the Rice Leaf Disease dataset is available at https://data.mendeley.com/datasets/fwcj7stb8r/1.Open asset ↗fwcj7stb8rhtml-lines:698-748Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
This study proposes RoViT-KAN, a multi-task deep learning framework for plant disease classification, severity estimation, and uncertainty quantification. The architecture integrates a DeiT-Tiny Vision Transformer backbone with task-specific heads for disease classification, ordinal severity prediction, and heteroscedastic uncertainty estimation. To enhance interpretability, a Kolmogorov–Arnold Network (KAN) module is introduced to model continuous disease severity through learnable spline-based transformations. A four-stage curriculum learning strategy is employed to stabilize multi-task optimization by progressively activating prediction objectives. The model is evaluated on a rose leaf disease dataset comprising 3,113 original images and 10,000 augmented samples across four classes: healthy leaf, leaf holes, black spot disease, and dry leaf condition. Experimental results demonstrate a classification accuracy of 99.70%, with calibrated uncertainty estimates (Brier score = 0.0914) and reliable severity prediction. Ablation studies validate the contribution of each architectural component. The model highlights the potential of combining transformer-based architectures with uncertainty-aware learning and interpretable neural representations for robust plant disease analysis.
Why it matches plant phenotyping methodsバラ葉の画像から病害分類と病害重症度を推定する手法を開発・評価しており、植物の病態を対象とした画像ベース表現型解析が研究の中心である。
abstractThis study proposes RoViT-KAN, a multi-task deep learning framework for plant disease classification, severity estimation, and uncertainty quantification.
Reproduction assets foundThe paper's rose leaf disease dataset (RoseLeafSet) is publicly deposited on Mendeley Data, and the authors' RoViT-KAN implementation code is publicly available on GitHub, both with explicit availability statements and URLs matching allowed entries.Dataset · publicThe datasets analyzed during the current study are publicly available in the Mendeley Data repository at: https://data.mendeley.com/datasets/9g668bfhy5/3.Open asset ↗Mendeley Datahtml-lines:716-742Code · publicThe code used to develop and evaluate the model in this study is publicly available to support transparency and reproducibility of the research. The implementation, along with relevant scripts and documentation, can be accessed through the following GitHub repository: https://github.com/nishitbohra/RoViT-KAN-Interpretable-Vision-Transformer-for-Rose-Disease-Severity-Estimation.Open asset ↗GitHubhtml-lines:716-742Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Introduction Early detection of plant diseases is essential for maintaining crop health and ensuring sustainable agricultural productivity. Guava fruit and leaf diseases, if not identified at an early stage, can lead to significant yield losses. Recent advances in deep learning offer promising solutions; however, challenges remain in achieving both high accuracy and model interpretability for practical agricultural deployment. Methods This study proposes an explainable deep learning-based framework for the classification of guava fruit and leaf diseases. A real-world dataset consisting of 527 annotated images across five classes-Disease Free, Phytophthora, Red Rust, Scab, and Styler and Root Rot-was utilized. Six hybrid model architectures were developed by integrating transfer learning backbones (VGG16, MobileNetV2, InceptionV3, and ResNet50) with custom convolutional neural network (CNN) classifiers. Model performance was evaluated using accuracy, precision, recall, F1-score, and class-wise metrics. To enhance transparency, Gradient-weighted Class Activation Mapping (Grad-CAM) was employed to visualize disease-relevant regions. Results Among all evaluated models, the proposed VGG16 + MobileNetV2 hybrid architecture achieved the best performance, attaining an accuracy of 96%, an F1-score of 0.96, and strong generalization across all disease classes. Comparative analyses using confusion matrices, ROC-AUC curves, precision-recall curves, and radar plots confirmed the superior and consistent performance of the proposed model over other hybrid configurations. Discussion The results demonstrate that combining deep feature extractors with lightweight architectures enhances both classification accuracy and computational efficiency. The integration of Grad-CAM provides meaningful visual explanations, increasing trust and interpretability in AI-assisted disease diagnosis. This framework shows strong potential for deployment in real-time smart farming systems and mobile-based diagnostic applications, particularly in resource-constrained agricultural environments.
Why it matches plant phenotyping methodsグアバの葉・果実画像から病害状態を推定する深層学習手法が研究の中心であり、複数モデルの比較評価とGrad-CAMによる説明可能性検証も行っているため、植物フェノタイピング方法論として採用する。
abstractThis study proposes an explainable deep learning-based framework for the classification of guava fruit and leaf diseases.
Reproduction assets foundThe paper's plant image dataset (527 annotated guava fruit/leaf disease images) is a public Kaggle deposit explicitly cited by the authors with a URL, making it a paper-specific, publicly actionable asset. No author analysis code or trained model checkpoints are stated as publicly available; the data availability only指Dataset · publicKaggle ). Available online at: https://www.kaggle.com/datasets/noamaanabdulazeem/guava-dataset (Accessed January 10, 2024 ).Open asset ↗Kagglelines:550-617Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Objectives Nutritional deficiency in coffee is a major problem that compromises plant health, crop yield, and bean quality, directly threatening the economies of coffee-dependent regions. Traditional detection methods are primarily manual, time-consuming, and relied upon expert availability. Methods This study introduces a novel Deep Learning (DL)-based dual-track architecture designed for the efficient classification of nutritional deficiencies in coffee leaf. The first track utilizes a MobileNetV3 backbone integrated with a Multi-Convolutional Shape-Aware Kernel (MCSK) block to capture spatially adaptive features from leaf textures and vein patterns. The second track employs a Hierarchical Shuffled Group Attention Network (HSGAN), utilizing Efficient Channel Attention (ECA) and Local Group Attention (LGA) modules to balance fine-grained local variations with broad spatial dependencies. Finally, a Multidimensional Collaborative Attention (MCA) mechanism is applied to the fused features to enhance cross-channel interactions and feature extraction. Results The proposed model was evaluated using the CoLeaf dataset, where it achieved an accuracy score of 96.04%. This performance demonstrates an improvement over existing research and current state-of-the-art models, highlighting the architecture's ability to identify complex nutrient-related patterns in coffee leaves. Conclusion The performance of the proposed DL approach offer a solution for the automated monitoring of coffee plants. By providing a reliable alternative to manual inspection, this method presents the potential to help coffee production and support the agricultural regions worldwide.
Why it matches plant phenotyping methodsコーヒー葉の栄養欠乏という植物状態を画像から分類する深層学習手法を開発・評価しており、表現型取得・推定が研究の中心であるため。
abstractThis study introduces a novel Deep Learning (DL)-based dual-track architecture designed for the efficient classification of nutritional deficiencies in coffee leaf.
Reproduction assets foundThe paper's primary phenotyping asset is the CoLeaf coffee leaf nutrient-deficiency image dataset, which the authors state is publicly available via a Mendeley Data URL matching an allowed URL. No author analysis code or trained model checkpoints are disclosed.Dataset · publicPublicly available datasets were analyzed in this study. This data can be found here: https://data.mendeley.com/datasets/brfgw46wzb/1 .Open asset ↗brfgw46wzb/1lines:733-764Code / dataset availability confirmedCrossref · checked 14 Sept 2026
The decline in environmental quality caused by industrial pollution and climate change has weakened the natural resistance of rice plants (Oryza sativa), increasing their susceptibility to various diseases. Conventional disease identification methods that rely on manual observation are often limited by subjectivity and human visual constraints. This study proposes a deep learning–based system for automatic rice leaf disease classification using the You Only Look Once version 8 (YOLOv8) architecture. The model was trained using a publicly available rice leaf image dataset consisting of 6,889 images categorized into eight classes: Bacterial Leaf Blight, Brown Spot, Leaf Blast, Leaf Scald, Sheath Blight, Narrow Brown Leaf Spot, Rice Hispa, and Healthy Rice Leaf. The research methodology includes image pre-processing, data augmentation, dataset splitting, and training using the YOLOv8n-cls model for 50 epochs. Experimental results demonstrate high classification performance with an accuracy of 99.5%, precision of 99%, recall of 98%, and an F1-score of 0.99. The trained model was then deployed into a web-based application that allows users to upload rice leaf images and obtain real-time disease classification results. The proposed system provides a practical tool to support early detection of rice plant diseases and assist farmers in improving crop management in modern agriculture.
Why it matches plant phenotyping methodsイネ葉画像から病害状態を推定するYOLOv8画像解析手法の開発と性能評価が中心であり、植物病害フェノタイピングに該当する。
abstractThis study proposes a deep learning–based system for automatic rice leaf disease classification using the You Only Look Once version 8 (YOLOv8) architecture.
Reproduction assets foundThe paper's rice leaf disease image dataset (6,889 images, eight classes) used for YOLOv8n-cls training is a publicly available Kaggle dataset cited by the authors with an explicit URL. No author code, trained model, or other paper-specific assets are reported.Dataset · publicThe primary dataset was obtained from a
publicly available dataset on Kaggle [16], which provides a
comprehensive collection of rice leaf disease images for
machine learning research.Open asset ↗Kagglepdf-raw-page:3 lines:1-102Code / dataset availability confirmedOpenAlex · Crossref · checked 5 Sept 2026
Abstract 3D models are used in plant phenotyping for non-destructive quantification and analysis of morphological characteristics. Analyzing plant structure allows breeders to select for desirable traits, associated with e.g. drought tolerance or increased productivity. In sugar beet, morphological parameters depict an essential element of the variety approval for distinguishing between genotypes. However, only a limited number of measured or scored parameters are considered at a single time point. In contrast, 4D data adds a temporal component and can depict the dynamic development of 3D parameters. To explore the potential of spatio-temporal 4D phenotyping for automated crop genotype differentiation, a greenhouse experiment was conducted by us covering twelve sugar beet genotypes. High-resolution 3D models were generated twice a week over the course of two months and both common and novel 3D morphological parameters were extracted. The importance of these parameters was assessed by us, and the dataset was analyzed using unsupervised pointwise clustering and time series clustering. Varying importance of parameters depending on the time point and significantly higher importance of plant parameters compared to leaf parameters are demonstrated by our results. Moreover, increased and more stable genotype differentiation is archived using time series clustering compared to pointwise clustering. Furthermore, taproot formation of sugar beet was found to have a crucial impact on morphological development. Substantial variations in the dynamic development of 3D morphological parameters underline the importance of 4D data for plant genotype differentiation. Thus, a novel foundation for genotype differentiation in plant phenotyping is provided by our findings.
Why it matches plant phenotyping methods3Dモデルから植物形態形質を抽出し、時系列クラスタリングで遺伝型識別を評価する4Dフェノタイピング手法が研究の中心である。
titleSpatio-temporal 4D phenotyping for automated morphological genotype differentiation of sugar beet
Reproduction assets foundThe paper publicly deposits its generated sugar beet point cloud dataset under CC BY 4.0 at a Dataverse DOI, directly reproducing the paper's phenotyping measurements. Supplementary Python codes and extracted parameter values are stated to be included with the article, but no authors' public URL for the code is presentDataset · publicThe generated point cloud dataset is available at https://doi.org/10.60507/FK2/IS8YBZ under CC BY 4.0 license.Open asset ↗10.60507/FK2/IS8YBZlines:277-363Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Plant disease diagnosis based on visual symptoms is crucial for preventing yield loss; however, deployment in practical settings remains challenging due to inter-class similarity, background noise, and limited computational resources. This study presents a plant disease classification framework evaluated on a curated multi-crop dataset aggregated from multiple publicly available repositories, comprising 51 disease and healthy classes. The dataset includes approximately 45,000 original images that were expanded through controlled augmentation during training to improve generalization. We benchmark eight ImageNet-pretrained tiny vision transformer architectures trained for up to 50 epochs. Among these, CAFormer-s18 achieved strong validation performance but with increased computational overhead. To enable efficient and computationally lightweight solutions, we design two fully customized convolutional neural networks: PlantaNetLite (1.28M parameters) and PlantaNet (2.58M parameters). After hyperparameter optimization and full 100-epoch training, PlantaNet achieved 99.37% validation accuracy and 99.66% test accuracy with a compact model size (9.85 MB) and moderate computational cost, while PlantaNetLite achieved a best validation accuracy of 99.22% under further parameter reduction. Qualitative Grad-CAM and Grad-CAM++ analyses provide insight into the regions influencing model predictions. Overall, the proposed models demonstrate competitive accuracy while maintaining computational efficiency, highlighting their potential suitability for resource-constrained deployment scenarios.
Why it matches plant phenotyping methods植物の視覚症状から病害状態を推定する画像ベースの表現型解析手法を開発・比較し、データセット上で性能評価しているため、方法が中心的である。
abstractThis study presents a plant disease classification framework evaluated on a curated multi-crop dataset aggregated from multiple publicly available repositories
Reproduction assets foundThe paper's Data Availability Statement explicitly states the curated multi-crop plant disease image dataset used for all classification experiments is publicly available on Kaggle at the authors' URL. No author analysis code, trained model checkpoints, or code repository is disclosed in the supplied blocks.Dataset · publicThe dataset used in this study is publicly available at https://www.kaggle.com/datasets/alimransonet/plant-disease-dataset.Open asset ↗Kaggle · alimransonet/plant-disease-datasethtml-lines:727-758Code / dataset availability confirmedCrossref · checked 15 Sept 2026
Phenotyping plant traits using UAV-based multispectral imaging offers a robust and unbiased approach to assessing crop status. With approximately 70% of smallholder farmers in East and Southern Africa cultivating common beans as a key source of food and income, there is a critical need for accurate and timely measurements of crop health and yield to support data-driven management decisions and disease mitigation. Traditional phenotyping methods are labor-intensive, and existing remote sensing and machine learning approaches remain limited. This study presents a comprehensive framework for plot-level assessment of common bean health and yield using time-series RGB and multispectral imagery. Data collected over three growing seasons (2022–2024) were used to extract canopy variables and vegetation indices (VIs) across phenological stages. For yield prediction, traditional machine learning models achieved a root mean squared error (RMSE) of 242.33 kg ha⁻¹ and an R² of 0.66 using an Extra Trees Regressor. A novel BY-GRU architecture improved performance, achieving an RMSE of 242.40 kg ha⁻¹ and an R² of 0.79. The analysis also identified 45–60 days after sowing as the optimal window for prediction. To address limitations in conventional plant health assessments, this study introduces a novel Health Index. Comparative analysis demonstrated its robustness across genotypes and stronger correlation with yield. Machine learning and deep learning models, including MaxViT, were applied to estimate the Health Index, achieving improved predictive performance. Overall, this work integrates UAV sensing and modelling to provide scalable tools for phenomics, crop management, and breeding.
Why it matches plant phenotyping methodsUAVのRGB・マルチスペクトル画像から作物の健康状態、収量、キャノピー形質を推定するセンシング・機械学習フレームワークが研究の中心であり、植物フェノタイピング手法として適格です。
abstractThis study presents a comprehensive framework for plot-level assessment of common bean health and yield using time-series RGB and multispectral imagery.
Reproduction assets foundThe preprint's DATA AVAILABILITY section states that all processed data required to reproduce the results are publicly available in a Google Drive repository, which qualifies as a paper-specific public phenotype dataset asset. No author analysis code or trained model checkpoints are explicitly deposited.Dataset · publicCommon Bean Breeding Program for
facilitating field trials. We also thank the Phenomics team for their valuable assistance with UAV-based
data collection.
CONFLICT OF INTEREST
The authors declare no conflict of interest.
DATA AVAILABILITY
The datasets generated and/or analyzed during the current study are publicly available at:
https://drive.google.com/drive/folders/1fN3Q9n3bK_YoXFK8VFKZ3uEb13y9iRWj?usp=sharing. This
repository includes all processed data required to reproduce the results presented in this study.
SUPPLEMENTAL MATERIAL
Supp. Figure 1. Drone-based field view of the bean trial site at CIAT Palmira Research Station: A) RGB
image and B) NDVI image.
Supp. Figure 2. Drone Features Open asset ↗pdf-raw-page:40 lines:1-46Code / dataset availability confirmedCrossref · checked 15 Sept 2026
Published23 Apr 2026International Journal of Drug Delivery TechnologyCited by 0 · OpenAlex ↗
The currently growing effects that plant diseases have on global agriculture require the creation of highly intelligent and accurate detection systems. Convolutional Neural Networks (CNNs), as deep learning, have proved effective in the detection of plant diseases based on images. The CNN performance, however, is very sensitive to hyperparameter tuning, which usually requires manual, sub-optimal tuning. The study suggests a new method to detect plant diseases with an optimized CNN architecture optimized by the Bacterial Colony Optimization (BCO). The BCO algorithm replicates the adaptive foraging behavior of bacterial colonies to automatically determine optimal CNN hyperparameters, such as the number of filters, kernel size, pooling methods, learning rate, and dropout probability of the CNN. The experiment conducted on the PlantVillage dataset demonstrated that the proposed BCO-CNN achieved an accuracy of 96.68% with a false alarm rate (FAR) of 4.05% outperforming other heuristic-fitted models such as particle swarm optimization (PSO) - CNN, CNN with support vector machine (SVM), and CNN, VGG16 in accuracy, precision, recall, and F1-score. The given work offers an automated, scalable approach to the accurate, early detection of the diseases of the plant, contributing to better yields of crops and sustainable agriculture.
Why it matches plant phenotyping methods植物葉画像から病害状態を推定するCNNのハイパーパラメータ最適化手法を開発・評価しており、植物フェノタイピング手法が研究の中心である。
abstractThe study suggests a new method to detect plant diseases with an optimized CNN architecture optimized by the Bacterial Colony Optimization (BCO).
Reproduction assets foundThe paper's plant-phenotyping experiments (CNN/BCO leaf disease detection) were run on the public Kaggle Plant Disease (PlantVillage) dataset, explicitly cited with its public URL. No author code or models are reported as available.Dataset · publictectural and hyperparameter changes. A
comparison of the results also indicates the success of data
augmentation, which indicates whether the model has a better
generalization when the data is more diverse. The MATLAB
2022b was used to implement the proposed method. The
tomato dataset was collected from Plant Disease datasets
(“https://www.kaggle.com/datasets/emmarex/plantdisease").
The average values of 30 independent runs with varying
random seeds are used to report the obtained results. This will
minimize the effects of the chance and provide a fair
representation of the strength of the model. Also, 80 % of the
data is employed in the training and the rest 20 % in the test
purposes. TableOpen asset ↗Kaggle · emmarex/plantdiseasepdf-raw-page:6 lines:1-115Code / dataset availability confirmedOpenAlex · Crossref · Europe PMC · checked 5 Sept 2026
Effective high-throughput phenotyping is crucial for modern plant breeding, yet the optimal image acquisition parameters for UAV-based systems in forage crops remain poorly defined. We optimized UAV-based phenotyping methods for a Megathyrsus maximus biparental population, examining how ground sampling distance (GSD), environment, and harvest date affect the accuracy of RGB-derived digital traits in predicting yield and canopy height. Machine learning algorithms and mixed model analyses were applied to evaluate predictive power and heritability. Pixel count and Haralick's entropy showed strong correlations with conventional yield measurements, particularly in Environment 2, while most vegetative indices were poor predictors. Integrating machine learning substantially enhanced predictive power for green and dry matter yield (r > 0.80). For canopy height, machine learning models achieved correlations of 0.71 with ground truth measurements despite weak pairwise correlations. Mixed model analysis revealed high broad-sense heritability (0.7 < H 2 < 0.87) for yield traits, pixel count, and entropy, while vegetative indices and canopy height showed greater environmental susceptibility. Moderate GSD resolutions (0.5–1.0 cm) consistently outperformed both very high (0.27 cm) and very low (1.5 cm) resolutions. Coincidence index analysis demonstrated 80% correspondence between top genotypes ranked by pixel count and conventionally measured dry matter yield. This study provides an optimized framework for UAV-based phenotyping in M. maximus , demonstrating that combining advanced digital traits with machine learning accurately predicts key agronomic traits and significantly enhances genotype selection efficiency in forage breeding programs.
Why it matches plant phenotyping methodsUAV画像取得条件、RGBデジタル形質、機械学習による収量・草高推定を最適化・検証する研究であり、植物表現型取得法が中心的です。
abstractWe optimized UAV-based phenotyping methods for a Megathyrsus maximus biparental population, examining how ground sampling distance (GSD), environment, and harvest date affect the accuracy of RGB-derived digital traits in predicting yield and canopy height.
Reproduction assets foundThe paper's data availability statement points to a public Mendeley Data repository containing the study's UAV-derived digital phenotyping and conventional trait datasets. No author analysis code repository is explicitly deposited.Dataset · publicThe datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: https://data.mendeley.com/datasets/jrrb76x82h/1 .Open asset ↗jrrb76x82h/1lines:435-487Code / dataset availability confirmedOpenAlex · Europe PMC · checked 5 Sept 2026
Introduction Herbicide dose-response assays are routinely implemented to compare herbicide resistance among weed biotypes, which requires plant biomass to estimate the dose that reduces growth by 50% relative to untreated plants (GR 50 ). The Phenospex TraitFinder is a high-throughput, non-destructive, digital phenotyping system that collects data from 7 spectral parameters and 13 morphological parameters, including Digital Biomass (DB), which offers the opportunity for researchers to eliminate the time and labor associated with manual biomass collection. However, DB is the product of 3D Leaf Area and Plant Height (PH) Mean, making it a measurement of plant volume and an indirect indicator of biomass. While DB is highly correlated with true biomass, digitally collected plant volume data has not been implemented for dose-response assays or assessed for accuracy relative to true biomass data. Additionally, inaccurate PH measurements could impact the accuracy of DB measurements. Methods This study sought to assess the accuracy and utility of DB and the 19 remaining parameters in dose-response assays by comparing dose-response curves and GR 50 estimates generated from digital data and fresh biomass (FB) data. Accuracy of PH measurements were also assessed by comparing digital and manual measurements with the paired t-test. Pre-emergence dose-response assays using fomesafen and atrazine were implemented with common lambsquarters ( Chenopodium album L.). At 21 days after treatment, manual measurements of FB and PH were collected following digital data collection. Results Consistently strong correlations ( r = 0.97, P < 0.05) were observed between digitally collected data and their equivalent manual measurements. Comparisons of the dose-response curves indicated that only 3D Leaf Area, DB, Convex Hull Area, Projected Leaf Area, and Voxel Volume Total generated highly similar curves and GR 50 estimates relative to FB data, indicating that any one or all of these parameters could be utilized instead of FB. Small differences (approximately 1.06 to 1.77 mm) between manual and digital PH measurements were identified with the paired t-test, but since DB consistently produced similar dose-response curves and GR 50 estimates relative to FB, these differences did not impact the accuracy of DB measurements. Discussion Without requiring manual biomass collection, turnaround time for dose-response and other phenotyping assays decreases and allows faster sharing of research. Furthermore, herbicide-resistant plants can be preserved for phenotyping at later growth stages, tissue collection, and to produce progeny for future experiments.
Why it matches plant phenotyping methodsデジタル表現型システムで植物体積・草丈などを取得し、手作業の生体重測定との精度比較および除草剤用量反応曲線への有用性を検証しており、表現型取得法が中心です。
abstractThe Phenospex TraitFinder is a high-throughput, non-destructive, digital phenotyping system that collects data from 7 spectral parameters and 13 morphological parameters
Reproduction assets foundThe paper's digital phenotyping dose-response datasets are publicly deposited: the data availability statement names Ag Data Commons DOI 10.15482/USDA.ADC/29815082 and a figshare link, both paper-specific. No author analysis code repository is explicitly stated.Dataset · publicThe datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: 10.15482/USDA.ADC/29815082 or https://figshare.com/s/64d1bbac59a95c4721f1 .Open asset ↗figshare · 10.15482/USDA.ADC/29815082lines:548-573Code / dataset availability confirmedEurope PMC · Crossref · checked 15 Sept 2026
Abstract Current phytopathological diagnostic systems rely on manual inspections or laboratory analyses, which delay early detection and limit in-field responsiveness. Phytopathogenic fungal diseases pose a persistent threat to food security, directly affecting the productivity of essential crops such as potato ( Solanum tuberosum ) and tomato ( Solanum lycopersicum ) [1]–[5]. Among these diseases, Phytophthora infestans , the causal agent of late blight, is characterized by its high virulence and rapid spread, capable of generating significant losses in short periods when detection occurs too late [3], [4]. To address this issue, a computer vision and deep learning–based system for multistage detection of fungal infections in potato and tomato crops is proposed. The system comprises a convolutional neural network optimized for edge processing and a mobile robotic platform equipped with a manipulator arm for localized treatment application. The developed model was deployed on a Raspberry Pi 4 connected to a 12-MP Raspberry Pi Camera Module 3 NoIR, responsible for acquiring RGB images in the field. The proposed network was compared with reference architectures—ResNet-50, VGG16, MobileNetV2, and Inception-v3—within a four-stage detection pipeline: crop identification, health-state classification, infection diagnosis, and foliar severity estimation. A dataset of 18,200 images obtained from publicly accessible online sources, under diverse lighting and background conditions, was used, partitioned into 70% for training, 20% for validation, and 10% for testing. Preliminary results show an average accuracy in the range of 0.90–0.92, with inference latencies below 60 ms per image, ensuring smooth performance on the Raspberry Pi 4 without requiring cloud connectivity. Additionally, the network demonstrated higher sensitivity to visual variations compared to the baseline models.
Why it matches plant phenotyping methods植物病害の健康状態・感染・葉面重症度を画像から推定するコンピュータビジョン手法を開発・比較検証しており、植物表現型取得が中心である。
abstracta computer vision and deep learning–based system for multistage detection of fungal infections in potato and tomato crops is proposed
Reproduction assets foundThe paper's CNN training data are two publicly available third-party plant-disease image datasets (Mendeley Data and Kaggle Plant Village) with explicit URLs in the Data Availability Statement. The authors' field-test images and experimental records are only available on request, and no analysis code or trained model/сDataset · public10
Network, DOI: 10.17632/tywbtsjrjv.1, available at
https://data.mendeley.com/datasets/tywbtsjrjv/1, and the
Kaggle Plant Village dataset, available at
https://www.kaggle.com/datasets/emmarex/plantdisease.The field-test images and experimental records generated during
the current study during the real-world evaluation of the
embedded-vision system are available from the corresponding
author on reasonable request.
IX. REFERENCOpen asset ↗10.17632/tywbtsjrjv.1pdf-raw-page:11 lines:1-98Dataset · public10
Network, DOI: 10.17632/tywbtsjrjv.1, available at
https://data.mendeley.com/datasets/tywbtsjrjv/1, and the
Kaggle Plant Village dataset, available at
https://www.kaggle.com/datasets/emmarex/plantdisease.The field-test images and experimental records generated during
the current study during the real-world evaluation of the
embedded-vision system are available from the corresponding
author on reasonable request.
IX. REFERENCES
[1] P. W. Crous, A. Y. Rossman, M. C. Aime, W. C. Allen, T.
Burgess, J. Z. Groenewald y L. A. CastlebuOpen asset ↗Kagglepdf-raw-page:11 lines:1-98Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Introduction Rapid population growth and climate change have intensified the need for sustainable agricultural productivity. Plant leaf diseases significantly impact the crop yield, quality, and food safety, necessitating accurate and automated detection methods. Methods This study proposes a deep learning (DL)-based framework for automated detection and classification of tomato and soybean leaf diseases. The proposed framework is trained and evaluated over a large-scale datasets comprising 16,012 tomato leaf images and 6,410 soybean leaf images. Multiple convolutional neural network (CNN) models, including DenseNet121, MobileNetV2, and InceptionV3, are employed for classification. Object detection is performed using YOLOv12. To enhance interpretability, Gradient-Weighted Class Activation Mapping (Grad-CAM) is integrated. Furthermore, a novel Hybrid Attention-Based Stacking Ensemble Model is developed using ResNet152V2, VGG19, and EfficientNetB0, combined with Convolution Block Attention Module (CBAM) and spatial attention mechanisms. Results The CNN models achieved classification accuracies of 97% for DenseNet121, 98% for MobileNetV2, and 99.94% for InceptionV3. YOLOv12 attained a mean average precision (mAP) of 99.5%. The proposed hybrid ensemble model achieved an accuracy of 99.18%, demonstrating improved feature learning through combined channel and spatial attention. Grad-CAM visualizations confirmed that the model effectively identifies the disease-relevant regions. Discussion The results indicate that the proposed framework has attained a high accuracy, robustness, and interpretability for plant disease detection. The integration of attention mechanisms and explainable AI enhances model reliability and transparency. This framework shows a strong potential for the real-time agricultural monitoring, although further validation across diverse crops and real-world field conditions is required.
Why it matches plant phenotyping methods植物葉の病害状態を画像から自動検出・分類する深層学習フレームワークの開発であり、病害表現型の取得・推定が研究の中心。
abstractThis study proposes a deep learning (DL)-based framework for automated detection and classification of tomato and soybean leaf diseases.
Reproduction assets foundThe paper's leaf-disease classification/detection experiments are built on two public Kaggle image datasets cited by the authors as the study's data sources: a soybean leaf dataset (Patil 2024) and a tomato leaf disease dataset (Rex 2019). No authors' analysis code, trained model checkpoints, or paper-specific phenotypDataset · publicPatil A. ( 2024 ). Soyabean-Latest Dataset (
Kaggle ). Available online at: https://www.kaggle.com/datasets/adityapatil1205/soyabean-latestOpen asset ↗Kagglelines:1523-1646Dataset · publicRex E. ( 2019 ). Plant Disease Dataset (Tomato Leaf Diseases) (
Kaggle ). Available online at: https://www.kaggle.com/datasets/emmarex/plantdisease197Open asset ↗Kagglelines:1523-1646Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
The quality of forest reproductive material is crucial for successful reforestation and afforestation. While physical seed properties like mass are known indicators of quality, the potential of non-destructive, rapid color analysis for predicting germination in coniferous species requires further exploration. This study investigates the relationship between the seed coat color of individual Pinus sylvestris seeds, quantified in RGB (Red, Green, Blue) space using a flatbed scanner, and their subsequent germination in container nurseries. The resulting images were processed using ImageJ software to measure the mean pixel intensity (0–255) for the Red (R), Green (G), and Blue (B) channels from the segmented seed area, following the «seed–culture» passport methodology [Forestry Engineering Journal 14 | 55 (2024), 37–60]. From a population of individually tracked seeds, we compared the RGB values of germinated (N = 942) and non-germinated (N = 258) seeds after 30 days. Results from the Kolmogorov-Smirnov test showed that non-germinated seeds had significantly lower individual mass (p = 0.0045) and significantly higher pixel brightness values in the R-, G-, and B-channels (p < 0.0001) compared to germinated seeds. Normalized RGB indices also showed significant differences between groups. Our findings demonstrate that seeds with a lighter, more reflective epidermis – indicative of higher RGB brightness – are statistically associated with a lower probability of successful germination under container nursery conditions. This non-destructive, low-cost method shows significant promise for the rapid pre-sorting of Scots pine seeds. It offers a practical tool to improve the efficiency and predictability of seedling production in forest nurseries by increasing the proportion of viable seeds in sowing batches.
Why it matches plant phenotyping methods個別種子のRGB画像から種皮色を定量抽出し、発芽予測・事前選別に用いる非破壊的な表現型計測法が研究の中心である。
abstractthe potential of non-destructive, rapid color analysis for predicting germination in coniferous species requires further exploration
Reproduction assets foundThe paper openly deposits its three core phenotyping datasets in Mendeley Data: morphometric seed data (Dataset 1), the raw VIS/RGB scanner images of individual Pinus sylvestris seeds (Dataset 2), and germination outcome data (Dataset 3). All three DOIs are listed in the Data Availability statement and match allowed URDataset · publicThe original morphometric data—Dataset 1—of Pinus sylvestris L. are openly available in Mendeley Data at DOI: https://doi.org/10.17632/8g258nbgmf.1Open asset ↗Mendeley Data · 10.17632/8g258nbgmf.1lines:133-160Dataset · publicThe original VIS image data of Pinus sylvestris L. are openly available in Mendeley Data at DOI: https://doi.org/10.17632/dt78jhyw2j.2Open asset ↗Mendeley Data · 10.17632/dt78jhyw2j.2lines:133-160Dataset · publicThe original germination data—Dataset 3—are openly available in Mendeley Data at DOI : https://doi.org/10.17632/hrs3fgc8tt.1Open asset ↗Mendeley Data · 10.17632/hrs3fgc8tt.1lines:133-160Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Grain number estimation plays a crucial role in agriculture, serving as a key indicator for crop yield and quality assessment. With advances in computer vision, automatic grain detection has become a significant research area, where deep learning methods have shown remarkable promise. This study proposes a vision transformer model called Swin Transformer, which leverages hierarchical attention mechanisms across shifted windows to effectively capture both local and global features of grains in complex imagery. The model achieves the highest accuracy of 98%, outperforming baseline traditional CNN (ResNet-50) and DINO models in grain counting tasks. To support and validate model performance, explainable AI (XAI) techniques such as Grad-CAM and LIME are employed, highlighting the interpretability and focus of the model on relevant grain regions. Furthermore, a comprehensive empirical analysis is conducted using multiple statistical tests to evaluate the model's robustness and generalizability across various grain morphological parameters, establishing the Swin Transformer as a powerful and interpretable solution for intelligent grain counting in agricultural data analytics.
Why it matches plant phenotyping methods画像から穀粒数を推定する深層学習手法の開発・比較検証が研究の中心であり、植物の収量関連形質を測定するため、植物フェノタイピング手法として収録する。
abstractThis study proposes a vision transformer model called Swin Transformer
Reproduction assets foundThe paper's Data availability statement names a public Kaggle dataset of wheat grain counting images used for the study's grain counting experiments. No author analysis code or trained model checkpoints are disclosed.Dataset · publicThe dataset used and/or analyzed during the current study is publicly available at: https://kaggle.com/datasets/ociule/wheat-grain-counting-100-images.Open asset ↗kaggle · ociule/wheat-grain-counting-100-imageslines:1190-1253Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
FruitClassificationGrowth / development / phenology
Introduction Cashew apple is a nutrient-rich fruit containing abundant minerals, vitamins, and energy. However, its fleshy texture and delicate skin significantly limit its storage life and market value. Accurate maturity grading is therefore essential for improving post-harvest management and transportation efficiency. Methods This study proposes a lightweight vision transformer (ViT) student model trained using multi-granular knowledge distillation (KD) from a stronger data-efficient image transformer (DeiT)-Base teacher. The distillation framework integrates response-based soft-label supervision, attention transfer, and token-level feature regression to enhance representation learning under limited data conditions. Auxiliary lightweight architectures, including MobileNet, ConvNeXt, and EdgeNeXt, were trained independently to provide complementary predictions, and a weighted fusion strategy was employed for ensemble evaluation. Results The proposed ensemble ViT-KD with EdgeNeXt achieved 90% accuracy under the evaluated test split. To ensure statistical reliability and address potential partition bias, a stratified fivefold cross-validation was conducted on the dataset, yielding a mean accuracy of 86.89% ± 2.89% with consistent F1 scores and recall. The relatively low variance across the folds indicates stable internal generalization. Comparative experiments with conventional convolutional neural network (CNN) baselines and lightweight CNN baselines such as MobileViT-S and ShuffleNetV2 were performed, with the proposed ensemble framework achieving improved accuracy while maintaining computational efficiency. Computational analysis indicates that the stand-alone distilled ViT maintains a real-time inference capability of 8.79 ms per image, which supports suitability for edge-oriented agricultural applications. Discussion These results highlight the effectiveness of knowledge-distilled lightweight transformers for data-efficient maturity grading of cashew apples.
Why it matches plant phenotyping methodsカシューナッツ果実の成熟度という植物器官の状態を画像から推定する手法を開発し、交差検証・比較実験・推論速度評価まで行っており、フェノタイピング手法が中心である。
abstractThis study proposes a lightweight vision transformer (ViT) student model trained using multi-granular knowledge distillation (KD) from a stronger data-efficient image transformer (DeiT)-Base teacher.
Reproduction assets foundThe paper's cashew apple maturity grading experiments use a public image dataset from IEEE Dataport (Sawant, 2025), explicitly linked in the data availability statement. No author code or models are shared.Dataset · publicPublicly available datasets were analyzed in this study. This data can be found here: https://ieee-dataport.org/documents/goa-cashew-apple-maturity-grading .Open asset ↗goa-cashew-apple-maturity-gradinglines:837-851Code / dataset availability confirmedEurope PMC · checked 14 Sept 2026
Wood apple (Feronia limonia L.) is an underutilized perennial fruit tree with substantial ecological, nutritional, and economic potential, yet its phenotypic diversity and trait organization remain poorly characterized. Here, we applied a mixed-scale multivariate framework to resolve phenotypic structure in 62 wood apple genotypes using 31 ordinal and categorical vegetative, leaf, floral, fruit, and seed descriptors. Trait interrelationships were examined through the complementary use of Spearman’s rank correlation and Cramér’s V association analyses, capturing both directional rank-based dependencies and scale-independent categorical linkages. Hierarchical clustering based on Gower distance separated the genotypes into three distinct phenotypic clusters, with inter-cluster dissimilarities (0.92–1.18) consistently exceeding intra-cluster variation (0.42–0.55), indicating well-supported phenotypic stratification based on cluster validation. Multiple Correspondence Analysis (MCA) explained 23.30% of total inertia across the first two dimensions, with tree growth habit, branch angle, tree shape, and fruit color emerging as the principal drivers of phenotypic differentiation. Vegetative and leaf traits formed a tightly integrated module, whereas fruit-related traits displayed weaker monotonic but persistent categorical associations, reflecting partial phenotypic independence. The strong concordance among association analyses, clustering, and MCA indicates structured patterns of coordinated and partially independent trait associations in wood apple. Overall, this study demonstrates the effectiveness of mixed-scale multivariate approaches for resolving complex trait architecture in underutilized perennial fruit crops and provides a quantitative phenotypic framework to support germplasm conservation, parent selection, and ideotype-oriented improvement of wood apple.
Why it matches plant phenotyping methods混合尺度の多変量解析を用いて植物遺伝資源の表現型構造を定量化する手法が研究の中心であり、単なる生物学的実験の routine 測定ではない。
abstractHere, we applied a mixed-scale multivariate framework to resolve phenotypic structure in 62 wood apple genotypes using 31 ordinal and categorical vegetative, leaf, floral, fruit, and seed descriptors.
Reproduction assets found保存済みの本文根拠を更新済みルールで再検証し、公開資産1件を確認しました。Supplement · publicAll data generated or analyzed during this study are available in the article and the accompanying Supplementary Table S1.Open asset ↗lines:137-161Code / dataset availability confirmedOpenAlex · Europe PMC · checked 5 Sept 2026
RootMorphology / geometry measurementSegmentationRoot system architecture
BACKGROUND: Root segmentation is a fundamental yet challenging task in image-based plant phenotyping. Accurate segmentation is a prerequisite for extracting root traits relevant to plant physiology, breeding, and agronomy. While U-Net and other convolutional neural network (ConvNet) architectures have been applied to root segmentation, no systematic comparison of multiple Transformer and ConvNet architectures has been conducted across diverse root imaging conditions. RESULTS: We evaluated 21 segmentation architectures across nine diverse root image datasets, training 1511 models to assess all combinations of architecture, dataset, pre-training strategy, and learning rate, producing over 3 million segmentations for evaluation. Transformer-based models significantly outperformed ConvNets for Dice (mean Dice 0.679 vs 0.659; [Formula: see text]). Root-diameter and root-length correlation were also higher for Transformers, but the differences were not statistically significant ([Formula: see text] and [Formula: see text] respectively). Pre-training significantly improved mean Dice from 0.623 to 0.666 ([Formula: see text]), with Transformers benefiting more from pre-training than ConvNets (Dice improvement + 0.072 vs + 0.021; [Formula: see text]), supporting the hypothesis that fine-tuned Transformers transfer more effectively across large domain gaps. MobileSAM achieved the highest Dice score (0.693) while maintaining computational efficiency. Both architecture families underestimated thin root length compared to manual annotations. Dataset choice explained 70.9% of performance variance, far exceeding model architecture (6.7%). PURPOSE: Transformer architectures significantly outperform ConvNets for root segmentation accuracy, and pre-training significantly improves performance, particularly for Transformers. Pre-trained MobileSAM offers the best accuracy at competitive computational cost. Dataset choice dominates performance variance, suggesting practitioners should prioritize data curation over architecture selection.
Why it matches plant phenotyping methods根の画像セグメンテーション手法を複数データセットで体系的に比較・検証し、根長・根径などの形質抽出性能も評価しているため、植物フェノタイピング手法が中心である。
abstractRoot segmentation is a fundamental yet challenging task in image-based plant phenotyping.
Reproduction assets foundThe paper's root image datasets (DeepRootLab, Grassland, Chicory, PRMI) are publicly available, and the authors' training code and modified RhizoVision Explorer trait-extraction fork are on GitHub with explicit availability statements.Dataset · publicImages are available from https://zenodo.org/records/15213661 .Open asset ↗Zenodo · 15213661lines:872-982Dataset · publicImages are available from https://figshare.com/ndownloader/articles/20440497/versions/2 .Open asset ↗Figshare · 20440497lines:872-982Dataset · publicImages are available from https://zenodo.org/records/3527713 .Open asset ↗Zenodo · 3527713lines:872-982Dataset · publicImages are available from https://gatorsense.github.io/PRMI/ .Open asset ↗lines:872-982Code · publicTraining code is available at https://github.com/sotlampr/seg .Open asset ↗GitHub · sotlampr/seglines:1183-1225Code · publicAll nine root image datasets used in this study are publicly available. DeepRootLab images are available from Zenodo (https://zenodo.org/records/15213661). Grassland images are available from Figshare (https://figshare.com/ndownloader/articles/20440497/versions/2). Chicory images are available from Zenodo (https://zenodo.org/records/3527713). The six PRMI datasets (Papaya, Peanut, Sesame, Sunflower, Cotton, Switchgrass) are available from https://gatorsense.github.io/PRMI/. Training code is available at https://github.com/sotlampr/seg. The modified RhizoVision Explorer fork used for trait extraction is available at https://github.com/sotlampr/RhizoVisionExplorer.Open asset ↗GitHub · sotlampr/RhizoVisionExplorerlines:1294-1347Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Background Accurate segmentation of foliar diseases under field conditions is essential for large-scale phenotyping, as breeding programs rely on reliable severity estimates to identify genotypes with improved resistance. However, most deep learning approaches have been developed as pathogen-specific models, which limits scalability in field-grown barley where multiple diseases naturally co-occur and exhibit substantial visual similarity. Results We evaluated whether a multiclass segmentation model can simultaneously detect and distinguish two fungal diseases of barley, Puccinia hordei and Ramularia collo-cygni, and compared its performance with two disease-specific binary models. Using 336 high-resolution leaf scans collected in the field with naturally occurring co-infections, the multiclass model achieved higher Dice scores for brown rust (0.59 vs 0.40; +47.5% relative improvement) and ramularia (0.60 vs 0.53; +13.2% relative improvement). It also captured a greater proportion of individual lesions across both classes. At the genotype level, the model-predicted disease area percentages were highly consistent with those from ground truth annotations ([Formula: see text]). Conclusions A unified multiclass framework can more effectively segment visually similar foliar diseases than separate binary models, while simplifying the computational workflow. This provides a scalable basis for automated resistance assessment within breeding pipelines. Code and data are publicly available at https://github.com/grimmlab/BarleyDiseaseSegmentation, with Mendeley Data dataset DOI 10.17632/4ny92p2r8f.1.
Why it matches plant phenotyping methods圃場画像から葉面病害面積をセグメンテーションし、遺伝子型レベルの病害重症度を推定する手法を開発・比較・検証しており、植物フェノタイピングが中心です。
abstractAccurate segmentation of foliar diseases under field conditions is essential for large-scale phenotyping
Reproduction assets foundThe paper's annotated barley leaf disease segmentation dataset (Mendeley Data DOI 10.17632/4ny92p2r8f.1) and the authors' analysis/segmentation code (GitHub grimmlab/BarleyDiseaseSegmentation) are explicitly declared publicly available, directly reproducing this paper's phenotyping measurements and computational modelsDataset · publicThe annotated dataset and the code implementing our machine learning–based model are publicly available on Mendeley Data (https://doi.org/10.17632/4ny92p2r8f.1) and GitHub (https://github.com/grimmlab/BarleyDiseaseSegmentation).Open asset ↗Mendeley Data · 10.17632/4ny92p2r8f.1lines:133-140Code · publicCode and data are publicly available at https://github.com/grimmlab/BarleyDiseaseSegmentation, with Mendeley Data dataset DOI 10.17632/4ny92p2r8f.1.Open asset ↗GitHub · grimmlab/BarleyDiseaseSegmentationlines:1-70Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Plant diseases are a major problem for farmers around the world, reducing crop yields. The absence of expertise makes plant disease detection difficult and complicated. Plant disease detection is made easier by deep learning algorithms; however, they are computationally demanding and need huge training datasets. This research work proposes a novel Conv-7 DCNN model with modified ParNet attention layer to classify plant leaves into distinct categories with improved accuracy. Because of its architecture, the proposed network can identify leaf diseases with more accuracy by extracting the wider range of features from the images. The proposed Conv-7 DCNN model classifies the leaf diseases of three plants such as tomato, potato, and pepper-bell into fifteen categories. The CNN model is trained using publicly accessible Kaggle dataset, utilising image augmentation techniques. It is evident from the simulation results that the proposed model outperforms several pre-trained, and other trending deep learning models. Proposed model achieves 99.18% classification accuracy with an average precision of 99.17% and area under the curve (AUC) of 1, making this model highly effective in leaf diseases detection. Additionally, Conv-7 DCNN achieved high FPS of 112.49, low inference time of 18.34 s, and low GFLOPS of 13.98, making it suitable for real-time applications in smart agriculture systems.
Why it matches plant phenotyping methods植物葉画像から病害状態を推定する深層学習モデルを開発・比較しており、病害表現型の取得・分類手法が研究の中心である。
abstractThis research work proposes a novel Conv-7 DCNN model with modified ParNet attention layer to classify plant leaves into distinct categories with improved accuracy.
Reproduction assets foundThe paper's plant-phenotyping measurements (leaf disease classification of tomato, potato, and pepper-bell) are based on a publicly available Kaggle dataset explicitly named in the Data Availability statement. No author analysis code, trained model checkpoints, or other paper-specific assets are disclosed.Dataset · publicThe dataset is available online at https://www.kaggle.com/datasets/emmarex/plantdisease.Open asset ↗Kaggle · emmarex/plantdiseasehtml-lines:824-854Code / dataset availability confirmedCrossref · Europe PMC · OpenAlex · checked 5 Sept 2026
Automated quantification of plant-level development from multi-plant greenhouse scenes requires separating individual plants from shared scene-level reconstructions and quantifying organ-level development, a challenge that single-plant acquisition workflows do not directly address. This study presents an end-to-end phenotyping pipeline built on 3D Gaussian Splatting (3DGS) and a post-reconstruction extraction framework, LCR-GS, designed to isolate plant instances from full greenhouse scenes without scene-specific model retraining. LCR-GS integrates zero-shot 2D cues with multi-view lifting, geometric clustering, and chromatic refinement to convert large scene-level reconstructions (~2M Gaussians) into compact per-plant subsets (~16K Gaussians). Experiments on greenhouse-grown muskmelon at the early vegetative stage demonstrate high plant-extraction precision (0.933) and strong organ-level instance segmentation (mean AP50 = 0.924). Plant height and leaf count are validated against manual measurements (height R² = 0.98, RMSE = 1.88 cm; leaf count R² = 0.86), whereas additional morphological traits, including leaf area, leaf area index, mean internode length, and stem node count, are reported as pipeline-derived descriptors for within-cohort comparison. By decoupling semantic inference from reconstruction, the pipeline reduces scene-scale data by over 99% and provides a practical route to derive compact per-plant 3D representations from multi-plant greenhouse imagery for downstream organ-level analysis.
Why it matches plant phenotyping methods3DGS画像から個体・器官を抽出し、植物形質を定量化するフェノタイピング手法の開発と検証が中心である。
abstractThis study presents an end-to-end phenotyping pipeline built on 3D Gaussian Splatting (3DGS) and a post-reconstruction extraction framework, LCR-GS, designed to isolate plant instances from full greenhouse scenes without scene-specific model retraining.
Reproduction assets foundThe paper's Data Availability Statement points to a public GitHub repository containing the muskmelon 3DGS phenotyping dataset (scenes, Gaussian-level plant/background annotations, and point-level organ labels) used in this study.Dataset · publicThe datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: https://github.com/bblabNTU/3dgs-muskmelon-phenotyping-dataset.Open asset ↗bblabNTU/3dgs-muskmelon-phenotyping-datasethtml-lines:485-547Code / dataset availability confirmedEurope PMC · Crossref · checked 5 Sept 2026
Accurate and efficient grain quality assessment is critical for making informed decisions throughout the grain value chain. Early detection of disease enables actions to mitigate spread and further damage, and optimal batch mixing to fulfill specified quality requirements allows for maximizing value and minimizing scrapping. Vision based machine learning and deep learning approaches are gaining attention in the agricultural sector and are useful for the development of automated grain quality assessment. These techniques can reduce the current manual inspection load and are key for objective and precise analysis. Yet, the majority of prior studies are constrained to small or controlled and curated datasets. Practical challenges associated with real-world deployment and reliability are rarely addressed. That is the focus of this work. We present and demonstrate a structured approach for investigating convolutional neural networks (CNNs) and key factors influencing performance for wheat kernel classification. The objective is to determine a CNN model that ensures high and robust classification accuracy, while elucidating and explaining how different image dataset characteristics and training parameters affect performance and reliability. We use a commercial mirror-based imaging system that captures over 90% of each kernel's surface and contrast and compare model architectures, robustness, the effect on pre-processing and image resolution. Our results show similar and high overall performance for ResNet50V2 and EfficientNetV2B0 ([Formula: see text]% accuracy), but per-class analysis indicate that the smaller classes suffer from lack of representative examples, and that most classes benefit from pre-processing including downsampling whereas others benefit from higher resolution. Interactive visualizations reveal that another contributing factor is dubious annotation and multi-class belongingness. Thus, our step-by-step analysis of CNN performance underscores the need for representative data, proper pre-processing, and class-aware evaluation to ensure trustworthy deployment in wheat grain quality assessment.
Why it matches plant phenotyping methods小麦粒画像から品質・病害クラスを推定するCNN画像解析手法の性能、頑健性、前処理、解像度、データ特性を体系的に評価しており、フェノタイピング手法が中心的である。
abstractWe present and demonstrate a structured approach for investigating convolutional neural networks (CNNs) and key factors influencing performance for wheat kernel classification.
Reproduction assets foundThe paper's wheat grain image dataset has a publicly available subset deposited on Zenodo (DOI 10.5281/zenodo.17397123), explicitly stated in the Data Availability statement. The full dataset is proprietary; code is only available upon request, so no qualifying code asset.Dataset · publicA publicly available subset of the segmented wheat grain images used in this study has been deposited in Zenodo to support transparency and reproducibility. The dataset includes representative samples per class collected from instrument and can be accessed at https://doi.org/10.5281/zenodo.17397123.Open asset ↗Zenodo · 10.5281/zenodo.17397123html-lines:337-368Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
RGB / grayscaleFlowerClassificationGrowth / development / phenology
This study presents a comprehensive BDFlower growth stage dataset designed to support research in precision agriculture and floriculture. The dataset encompasses eight common flower species found in Bangladesh: Bush Allamanda, Red Hibiscus, Yellow Bell, Pinwheel Flower, Pink Periwinkle, White Madagascar Periwinkle, Marvel of Peru, and White Hibiscus. Each species is represented across three growth stages-Early, Mid, and Full-resulting in 24 distinct classes. A total of 23,334 colour images are included, comprising 3889 original photographs and 19,445 augmented samples generated with five augmentation techniques. Bush Allamanda contains 499 images, Red Hibiscus contains 489 images, Yellow Bell contains 483 images, Pinwheel Flower contains 497 images, Pink Periwinkle contains 452 images, White Madagascar Periwinkle contains 472 images, Marvel of Peru contains 468 images and White Hibiscus contains 529 images. Each image was collected using smartphone camera at three-time intervals per day, spaced eight hours apart, to capture natural variations in lighting and appearance. The dataset is further organized into training, validation, and testing splits, enabling direct application to machine learning workflows. This is a publicly available dataset specifically curated for flower growth stage classification. In addition to dataset collection, we also conducted a simple experiment using a CNN model to evaluate its performance on this dataset. It is intended to facilitate the development of robust computer vision models that can monitor flower development, with potential applications in automated plant phenotyping, crop monitoring, and digital floriculture systems.
Why it matches plant phenotyping methods花の生育段階を画像で分類する公開データセットを構築し、CNN評価も行っており、植物表現型取得・解析が研究の中心である。
abstractThis is a publicly available dataset specifically curated for flower growth stage classification.
Reproduction assets foundThe paper's own flower growth-stage image dataset (BDFlower) is publicly deposited on Mendeley Data with an explicit direct URL and DOI, directly reproducing the paper's phenotyping (flower growth stage) image measurements. No author analysis code or trained model checkpoints are explicitly deposited.Dataset · publicRepository name: Data Mendeley
Data identification number: 10.17632/m8g2wynwyr.2
Direct URL to data: https://data.mendeley.com/datasets/m8g2wynwyr/2Open asset ↗10.17632/m8g2wynwyr.2html-lines:94-129Code / dataset availability confirmedEurope PMC · checked 14 Sept 2026
We introduce ``Primitive Indian Paddy Panicle Images,'' a benchmark image dataset of 22 primitive Indian rice panicle varieties (Sethy, Prabira; Pamerelli, Ranjith, 2026; Mendeley Data, V1, doi:10.17632/khfd7pzskd.1) and present an identification approach based on deep residual transfer learning. Using a transfer-learned ResNet-50 with image augmentation and an 80/10/10 train/validation/test split, the model attains 100.0% validation accuracy and 98.74% accuracy on the held-out test set. Per-class one-vs-rest AUCs on validation are 1.000 for all 22 classes; test AUCs range from 0.9924 to 1.000 (mean ≈ 0.999), with separate confusion matrices and ROC curves provided for validation and test partitions. These results demonstrate that deep residual transfer learning can robustly discriminate closely related panicle morphotypes when trained on a carefully curated dataset. We release the dataset to support reproducible research in germplasm identification, varietal purity assessment, and automated phenotyping.
Why it matches plant phenotyping methodsイネ穂画像のベンチマークデータセットと、深層学習による穂形態の自動識別手法が研究の中心であり、再現可能な植物表現型解析基盤として明示されている。
abstractWe introduce ``Primitive Indian Paddy Panicle Images,'' a benchmark image dataset of 22 primitive Indian rice panicle varieties
LeafStem / branchPhysiological trait estimationLeaf traitsWater status / transpiration
Leaf and hydraulic traits are key determinants of growth rates, and hence potentially exhibit significant associations with wood density (WD) and its intraspecific variation (ITV). However, the extent to which functional traits could improve WD prediction accuracy, and how ITV in WD correlates with functional traits remain incompletely understood. We investigated WD and its ITV across 10,218 plant species, mapped the global distribution of WD, and analyzed the association of ITV in WD with niche breadth and functional traits. Plant species with an acquisitive resource-use strategy, characterized by higher specific leaf area (SLA), leaf nitrogen concentration (LN), and leaf maximum stomatal conductance (g max ), exhibited lower WD. Associations of WD with hydraulic traits indicated species with greater hydraulic safety exhibited higher WD. Moreover, the integration of leaf traits (i.e., SLA and LN) and hydraulic traits with environmental factors substantially enhanced WD prediction accuracy in a random forest model, raising the explained variance from 55% to 95%. Furthermore, resource-acquisitive species demonstrated higher ITV for WD. ITV was positively related to relative niche breadth concerning both climatic factors and soil properties. Overall, functional traits significantly improve WD prediction accuracy, and plant species with an acquisitive resource-use strategy exhibit lower WD but greater intraspecific variation.
Why it matches plant phenotyping methods木材密度という植物形質の予測モデルを構築し、機能形質・環境因子の統合による予測精度を検証しており、形質推定手法が中心的です。
abstractthe integration of leaf traits (i.e., SLA and LN) and hydraulic traits with environmental factors substantially enhanced WD prediction accuracy in a random forest model, raising the explained variance from 55% to 95%.
Reproduction assets foundThe paper's Data Availability Statement points to a public Zenodo deposit containing the authors' global wood density distribution data, which directly reproduces this paper's measurements. The TRY Plant Trait Database is a generic third-party database, not a paper-specific asset, and no author analysis code is stated.Dataset · publicData for the global distribution of wood density is available on Zenodo Repository https://sandbox.zenodo.org/records/425279.Open asset ↗Zenodo · 425279html-lines:405-429Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Purpose/significance Sugarcane is a vital global crop, critical for sugar and energy production. The accurate and timely identification of its leaf diseases is paramount for sustaining the health and stability of the sugarcane industry. While deep learning models offer promising solutions, their deployment on mobile or edge devices is often hindered by substantial model size and high computational demands. Conversely, existing lightweight models frequently compromise on feature extraction capabilities and recognition accuracy. To bridge this gap, this study develops an architecturally improved lightweight model designed to achieve both high accuracy and computational efficiency. Methods We propose the ReMA-MobileViT model, which significantly enhances feature representation by incorporating a newly designed Residual Multi-head Attention (ReMA) module. This module ingeniously leverages a multi-head attention mechanism to capture richer contextual information from diverse subspaces, while its residual connection structure effectively mitigates network degradation and facilitates robust gradient flow. The proposed model underwent rigorous training and evaluation on a comprehensive Mendeley Data repository for classification tasks. Results Experimental evaluations demonstrate that the ReMA-MobileViT model achieves an outstanding classification accuracy of 99.02% on the sugarcane leaf disease dataset, substantially surpassing existing state-of-the-art methods. An ablation study confirms the module's efficacy, showing that the ReMA-MobileViT model, integrated with the ReMA module, improved accuracy, recall, and F1-Score by 1.58, 1.76, and 1.58 percentage points, respectively, over the baseline MobileViT. Comparative analyses further illustrate ReMA-MobileViT's superior overall performance; it exceeds classic lightweight MobileNetV2 by 15.77 percentage points and the mainstream Vision Transformer by 2.96 percentage points in accuracy. Critically, ReMA-MobileViT achieves this with significantly fewer model parameters and reduced computational complexity compared to Vision Transformer, establishing a superior balance between accuracy and efficiency. Conclusion The proposed ReMA-MobileViT model offers an effective and lightweight solution for improving sugarcane leaf disease recognition accuracy, particularly in challenging complex backgrounds. Its ability to balance high accuracy with computational efficiency presents a promising technical avenue and a deployable solution for high-precision crop disease diagnosis systems on resource-constrained mobile or edge platforms.
Why it matches plant phenotyping methodsサトウキビ葉の病害状態を画像から認識する軽量深層学習モデルを開発し、精度・計算量・アブレーションを評価しており、植物表現型取得・判定手法が中心である。
abstractWe propose the ReMA-MobileViT model, which significantly enhances feature representation by incorporating a newly designed Residual Multi-head Attention (ReMA) module.
Reproduction assets foundThe paper's sugarcane leaf disease image dataset (2022 Sugarcane Leaf Disease Dataset, Thite et al.) is publicly available on Mendeley Data and directly constitutes the image inputs used for the paper's disease recognition experiments. No author analysis code or trained model checkpoints are reported.Dataset · publicPublicly available datasets were analyzed in this study. This data can be found here: https://data.mendeley.com/datasets/9424skmnrk/1 .Open asset ↗9424skmnrklines:757-778Code / dataset availability confirmedCrossref · Europe PMC · checked 5 Sept 2026
Introduction Accurate plant disease identification is of great importance for ensuring agricultural productivity and food security. However, complex illumination variations, leaf occlusion, and diverse disease spot scales throughout plant growth stages significantly increase the difficulty of real-time detection, leading to limited accuracy and robustness in existing approaches. Methods To address these challenges, we propose an improved RT-DETRv2-based plant disease detection model, termed AF-RT-DETR. A Bidirectional Cross Gate (BCG) module is introduced in the feature extraction stage to reduce channel redundancy and enhance discriminative feature representation through multi-level feature interactions. The original RepVGG structure is replaced with a Dynamic Channel Shift (DCS) module, effectively enlarging the receptive field and strengthening contextual feature fusion without additional computational overhead. Additionally, an improved Scale-aware Multi-level Loss (SML) emphasizes low-quality feature maps to improve detector robustness. Results The model achieves mAP50 and mAP50:95 of 93.6% and 67.2% on the Plant-Disease dataset, surpassing the baseline by 5.1% and 4.5%. Furthermore, the model was evaluated on multiple crops and growth stages under diverse field conditions, demonstrating robust performance and adaptability. Discussion These results indicate that AF-RT-DETR effectively enables real-time plant disease detection in complex field environments.
Why it matches plant phenotyping methods植物の病徴を画像から検出するモデルの開発と、複数作物・生育段階・圃場条件での性能評価が中心であり、植物病害状態の表現型計測手法に該当する。
Reproduction assets foundThe paper evaluates AF-RT-DETR on three public Roboflow plant-disease image datasets, each cited with an explicit public URL. No author analysis code or trained model release is mentioned. The Ultralytics YOLOv8 repository is a generic third-party library, not a paper-specific asset.Dataset · publicRoboflow Detecting rice crop diseases object detection dataset . Available online at: https://universe.roboflow.com/crop-diseases-l2qhk/detecting-rice-crop-diseases/dataset/21Open asset ↗lines:816-932Dataset · publicRoboflow Disease detection object detection dataset . Available online at: https://universe.roboflow.com/projects-h0apg/disease-detection-0slunOpen asset ↗lines:816-932Dataset · publicRoboflow Plant Disease v2 512×512 . Available online at: https://universe.roboflow.com/sangeeth-mathew-john-nl43i/plant-disease-czcfe/dataset/2Open asset ↗lines:933-1045Code / dataset availability confirmedOpenAlex · checked 5 Sept 2026
Abstract Modern agriculture faces the dual challenge of sustainably increasing food production while mitigating the environmental impact of intensive monocultures. Mixed cropping, which is the cultivation of multiple species or varieties, may provide ecological benefits that address productivity and environmental sustainability challenges. However, evaluating its multifunctionality in conventional agricultural field experiments is costly and labour-intensive, and small sample sizes and high spatial variability often make it difficult to detect the statistical significance of mixed cropping effects. This study aims to introduce and validate a high-throughput field phenotyping (HTP) framework that integrates aerial imagery obtained from unmanned aerial vehicles (UAVs) to efficiently assess the multifunctionality of mixed cropping systems. We conducted a field experiment comparing monocultures of oat, rye, and barley; intraspecific mixed cropping combining three oat varieties; and interspecific mixed cropping combining oat, rye, and barley. Using UAV-derived data across the entire field, including vegetation cover, plant height, and the normalised difference vegetation index, we evaluated five multifunctionalities (biomass production, spatial variability in biomass production, early canopy closure, lodging resistance, and lodging resilience). This framework reveals that mixed cropping outperforms monocropping in several key ecological functions. The proposed UAV-based HTP approach enables cost-effective, robust, and scalable evaluation of mixed cropping systems, facilitating their optimisation for multifunctionality and contributing to the advancement of sustainable agriculture.
Why it matches plant phenotyping methodsUAV画像を用いた高スループット圃場フェノタイピング枠組みを導入・検証し、植生被覆、草丈、NDVIから複数の植物形質・状態を抽出しており、フェノタイピング手法が中心的です。
abstractThis study aims to introduce and validate a high-throughput field phenotyping (HTP) framework that integrates aerial imagery obtained from unmanned aerial vehicles (UAVs)
Reproduction assets foundThe paper's Data availability statement explicitly deposits the datasets generated and analysed (UAV-derived phenotyping measurements) in a public Zenodo repository with a DOI matching an allowed URL.Dataset · publicThe datasets generated and analysed during the current study are available in the Zenodo repository, https://doi.org/10.5281/zenodo.17042273.Open asset ↗Zenodo · 10.5281/zenodo.17042273lines:197-235Code / dataset availability confirmedCrossref · checked 5 Sept 2026
Abstract. Large-scale mapping of plant biophysical and biochemical traits is essential for ecological and environmental applications. Given their finer spectral resolution and unprecedented data availability, hyperspectral data, in concert with machine and particularly deep learning models, have emerged as a promising, non-destructive tool for accurately retrieving these traits. However, when deploying these methods on a large scale, reliably quantifying the associated uncertainty remains a critical challenge, especially when models encounter out-of-domain (OOD) data, i.e., samples that differ substantially from those of the training data, such as unseen geographical regions, species, biomes, data acquisition modalities, or scene components (e.g., clouds and water bodies). Traditional uncertainty quantification methods for deep learning models, including deep ensembles (deterministic and probabilistic) and Monte Carlo dropout, rely on the variance of predictions but often fail to capture uncertainty in OOD scenarios, leading to overly optimistic and possibly misleading uncertainty estimates. To address this limitation, we propose a distance-based uncertainty estimation method (Dis_UN) that quantifies prediction uncertainty by measuring the dissimilarity in the predictor space (spectral inputs) and embedding space (features learned by the deep model) between the training and test data. Dis_UN leverages residuals as a proxy for uncertainty and employs dissimilarity indices in data manifolds to estimate worst-case errors via 95-quantile regression. We evaluate Dis_UN using a pretrained deep learning model to predict multiple plant traits from hyperspectral images, analyzing its performance across OOD data, such as pixels containing spectral variations from urban surfaces, bare ground, water, clouds, or open surface waters. In this study, we target six leaf and canopy traits: leaf mass per area, chlorophylls, carotenoids, nitrogen content, equivalent water thickness, and leaf area index. Compared to scaled variance-based methods, Dis_UN provides (1) a superior estimation of uncertainty in OOD scenarios, achieving 36 % higher contrast (KS distances: 0.648 vs. 0.475) between non-vegetation pixels, particularly under mixed-pixel conditions at medium resolution (30 m); (2) uncertainty quantification without requiring normality or symmetry assumptions, accommodating asymmetric error patterns; (3) enhanced interpretability of uncertainty sources, as uncertainty is directly linked to sample dissimilarity from the training data; and (4) computational efficiency at inference (2.6–7.7× faster), requiring only a single forward pass compared to multiple passes for ensemble-based methods. Challenges remain for traits that are affected by spectral saturation. These findings highlight the advantages of distance-aware uncertainty quantification methods and underscore the necessity of diverse training datasets to minimize sampling biases and enhance model robustness. The proposed framework improves the reliability of uncertainty estimation in vegetation monitoring and offers a promising approach for broader applications.
Why it matches plant phenotyping methods植物形質をハイパースペクトル画像から推定する深層学習について、OOD条件での不確実性推定手法Dis_UNを開発・評価しており、表現型取得・推定手法が中心である。
abstractwe propose a distance-based uncertainty estimation method (Dis_UN) that quantifies prediction uncertainty
Reproduction assets foundThe paper's authors publicly released their uncertainty-analysis code (two GitHub repositories) and the study data (Hugging Face dataset) with explicit availability statements and URLs. The EnMAP and NEON hyperspectral scenes are third-party public data sources, not paper-specific deposits, and the supplement is not anCode · publicThe code for this study is available at: https://github.com/echerif18/Multi_trait_Uncertainty/ (last access: 8 March 2026).Open asset ↗echerif18/Multi_trait_Uncertaintylines:449-456Dataset · publicThe data used in this study are available on Hugging Face: https://doi.org/10.57967/hf/7838 (Cherif et al., 2026).Open asset ↗Hugging Face · 10.57967/hf/7838lines:457-483Code / dataset availability confirmedEurope PMC · checked 14 Sept 2026
Abstract Purpose Accurate estimation of crop transpiration is essential for optimizing irrigation management and improving water-use efficiency in precision agriculture. However, direct measurement of transpiration is often invasive, costly, and difficult to maintain at large scales. This study proposes a data-driven framework to estimate maize ( Zea mays L.) sap flow driven by transpiration using widely available climatic and soil moisture data combined with machine learning techniques. Methods Field experiments were conducted during the 2023 and 2024 growing seasons in central Italy under irrigated silage maize. Meteorological variables, soil water content, and crop growth indicators were used as inputs, while sap flow measurements served as reference outputs. Several machine learning models were evaluated, including Linear Regression, Support Vector Regression (SVR), Decision Tree Regressor, and Multi-Layer Perceptron Regressor (MLPR), using both Point Estimation and Temporal Estimation strategies. Temporal approaches incorporated short-term historical information through feature concatenation and previous-average windows. Results Results demonstrate that non-linear models, particularly MLPR and SVR, consistently outperform linear and tree-based approaches. The inclusion of short temporal windows (45 minutes to 2 hours) significantly improves predictive accuracy, enhancing reconstruction of the diurnal transpiration pattern. Feature concatenation proved more effective than averaging strategies in capturing soil–plant–atmosphere interactions. Model performance remained robust across two contrasting growing seasons, confirming good generalization capability under interannual variability and data discontinuities. Conclusion The proposed framework provides a reliable and minimally invasive solution for real-time estimation of maize transpiration, supporting precision irrigation management. These findings highlight the potential of machine learning models as practical decision-support tools for sustainable agricultural water management.
Why it matches plant phenotyping methodsトウモロコシの蒸散・樹液流という生理形質を、気象・土壌水分データと機械学習で推定する手法を開発・比較し、複数年で性能検証しているため、植物フェノタイピング手法が中心である。
abstractThis study proposes a data-driven framework to estimate maize ( Zea mays L.) sap flow driven by transpiration using widely available climatic and soil moisture data combined with machine learning techniques.
Reproduction assets foundThe paper's Data Availability statement says part of the datasets generated and analyzed (maize sap flow, climate, and soil moisture measurements) are publicly available on the authors' GitHub, while the analysis source code is only promised upon acceptance.Dataset · publicon; Datacuration; Formal
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Funding This work was carried out within the framework of the project Agritech National ROpen asset ↗isarlab-department-690pdf-raw-page:31 lines:1-67Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Abstract The global issue of water scarcity and climate change requires highly efficient and intelligent irrigation systems that are capable of optimizing water consumption with high crop productivity. The paper aims to provide a holistic machine learning framework for crop water stress prediction and efficient irrigation scheduling using multi-parametric agronomic data. The paper analyzes 55,450 soybean data with 13 physiological and biochemical parameters to implement and compare six regression models for predicting the water stress index. After eliminating tautology by removing the direct water content parameter from the prediction model, LightGBM and XGBoost ensemble tree models achieved near-perfect accuracy for predicting crop water stress using regular plant parameters alone, with R² = 1.0 and RMSE = 1.57×10⁻⁸ to 5.04×10⁻⁵. The Random Forest classifier, which was implemented without any direct stress indicators, achieved perfect discrimination between low, moderate, and high stress classes with precision/recall equal to 1.0, and 5-fold cross-validation and noise tests confirmed its robustness. SHAP analysis of the results showed protein percentage (PPE) and seed yield per unit area (SYUA) to be key drivers of water stress, providing valuable insights for precision agriculture. The model for determining irrigation requirements based on crop evapotranspiration and stress level achieved R² = 1.0 with zero error, making it possible to translate trait values directly into irrigation requirements. The framework presented in this paper brings together machine learning and agronomic knowledge to provide real-time data-driven solutions for irrigation systems, which have 30–50% water savings potential while maintaining healthy crops. It lays the ground for the development of AI-assisted irrigation systems that are applicable to different crops and climatic conditions, particularly in water-scarce countries such as Iraq.
Why it matches plant phenotyping methods作物の水ストレス状態を生理・農学データから機械学習で推定し、複数モデルの比較、交差検証、ノイズ試験、解釈分析まで行う計算的フェノタイピング手法が中心である。灌漑最適化への応用を含むが、単なる日常的測定ではない。
abstractThe paper aims to provide a holistic machine learning framework for crop water stress prediction and efficient irrigation scheduling using multi-parametric agronomic data.
Reproduction assets foundThe paper's soybean phenotyping dataset (55,450 records, 13 physiological/biochemical traits) is publicly available on Kaggle; the Data Availability statement points to it, though it ambiguously labels it as the code implementation location. No separate verified code repository is provided.Dataset · publicThe dataset used in this study (Advanced Soybean Agricultural Dataset) is available from the corresponding author upon reasonable request. The code implementation for all analyses is available at: https://www.kaggle.com/datasets/wisam1985/advanced-soybean-agricultural-dataset-2025 .Open asset ↗kaggle · wisam1985/advanced-soybean-agricultural-dataset-2025lines:372-406Code / dataset availability confirmedOpenAlex · Crossref · Europe PMC · checked 5 Sept 2026
Plant phenotyping increasingly relies on (semi-)automated image-based analysis workflows to improve its accuracy and scalability. However, many existing solutions remain overly complex, difficult to reimplement and maintain, and pose high barriers for users without substantial computational expertise. To address these challenges, we introduce PhenoAssistant: a pioneering AI-driven system that streamlines plant phenotyping via intuitive natural language interaction. PhenoAssistant leverages a large language model to orchestrate a curated toolkit supporting tasks including automated phenotype extraction, data visualisation and automated model training. We validate PhenoAssistant through several representative case studies and a set of evaluation tasks. By lowering technical hurdles, PhenoAssistant underscores the promise of AI-driven methodologies to democratising AI adoption in plant biology.
Why it matches plant phenotyping methods植物表現型抽出を自然言語で自動化するAIシステムの開発であり、ツールとワークフローが研究の中心です。代表的ケーススタディと評価タスクによる検証も行っています。
abstractwe introduce PhenoAssistant: a pioneering AI-driven system that streamlines plant phenotyping via intuitive natural language interaction.
Reproduction assets foundThe paper deposits its PhenoAssistant analysis code (with chat logs and generated outputs) on GitHub, and uses public phenotyping datasets: the CVPPP2017 leaf segmentation challenge data (case study 1 training/evaluation) and the CVPPA@ICCV'23 WW2020 winter wheat nutrient-deficiency dataset (case study 3), both on CodaCode · publicThe code for this research, as well as the chat logs and generated outputs of the case studies and evaluations, are available at Github [ https://github.com/vios-s/PhenoAssistant/ ] 78 .Open asset ↗vios-s/PhenoAssistantlines:224-268Dataset · publicThe data used for training and evaluating the computer vision model used in case study 1 are publicly available from the CVPPP2017 Leaf Segmentation Challenge dataset (A1 and A4 subsets) at CodaLab [ https://codalab.lisn.upsaclay.fr/competitions/8970 ].Open asset ↗CodaLab · CVPPP2017lines:224-268Dataset · publicThe winter wheat data used in case study 3 are publicly available from the CVPPA@ICCV'23: image classification of nutrient deficiencies in winter wheat and winter rye dataset (WW2020 subset) at CodaLab [ https://codalab.lisn.upsaclay.fr/competitions/13833 ].Open asset ↗CodaLab · WW2020lines:224-268Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
This dataset consists of a collection of high-resolution RGB images of grapevine leaves, designed to support research in plant pathology, precision viticulture, and computer vision. The images were collected in situ from experimental and commercial vineyards in the north of Portugal, covering different vineyard conditions and management practices. The dataset includes healthy leaves from three grapevine Portuguese cultivars Loureiro, Viosinho and Malvasia Fina, photographed under natural lighting conditions without artificial adjustments. It is organized into five categories: healthy leaves and leaves showing symptoms of downy mildew ( Plasmopara viticola ), powdery mildew ( Erysiphe necator ), Esca complex and Erineum Mite ( Colomerus vitis ). Images are provided in JPEG format with a resolution of 3000 × 3000 pixels and 1024 × 1024 pixels and arranged in folders by health status and disease type. This dataset can be used for machine learning and deep learning applications in disease detection/classification, cultivar identification, and can support other precision agriculture applications, as well as being used for agricultural robotics and educational purposes. An evaluation on three deep learning architectures demonstrated the suitability of the dataset into separating the five classes.
Why it matches plant phenotyping methodsブドウ葉の病徴を画像化した再利用可能なデータセットで、植物の健康状態・病害状態の画像ベース推定を支えることが中心です。深層学習による5クラス分類評価も記載されています。
abstractThis dataset consists of a collection of high-resolution RGB images of grapevine leaves, designed to support research in plant pathology, precision viticulture, and computer vision.
Reproduction assets foundThe paper is a Data in Brief article describing a public Zenodo repository of RGB grapevine leaf images (healthy plus downy mildew, powdery mildew, Esca complex, erineum mite) collected for plant disease/phenotyping research, with explicit data accessibility details. No author analysis code or trained model checkpointsDataset · publicData accessibility
Repository name: Zenodo
Data identification number: https://doi.org/10.5281/zenodo.17343473
Direct URL to data: https://zenodo.org/records/17343473Open asset ↗Zenodo · 10.5281/zenodo.17343473html-lines:93-144Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Proper detection and treatment of plant leaf diseases are essential factors for achieving good crop yields and ensuring food security. Convolutional Neural Networks (CNNs) have shown significant potential for classifying diseases from leaf images. Instead, most current work focuses on image-level prediction and ignores the relationship between infected leaves. This limitation somewhat constrains their use in modelling disease spread. Also, it makes them less efficient in typical field situations where disease is transmitted from plant to plant by physical contact. Moreover, existing CNN architectures do not access inter-lobar contextual information, an essential factor for early detection and control. To tackle this, we propose AdjLeafGNN, an innovative hybrid deep learning and graph neural network model that performs multi-class leaf disease classification and probabilistic prediction of adjacent-leaf disease spread in a single pass. The method uses the enhanced CNN model (LDDNet), with Atrous Spatial Pyramid Pooling (ASPP) and a Channel-Spatial Attention Module (CSAM), to achieve a more precise representation across multiple scales. These embeddings are then used to construct a similarity graph, enabling a GNN to infer likely disease transmission paths among leaves. We evaluate the PlantVillage dataset on the proposed model, and the results show that it outperforms state-of-the-art CNN-based methods, achieving 98.88% classification accuracy and 98.71% F1 Score. Additionally, we were able to predict disease spread with a high AUC-ROC of 0.942 and an MCC of 0.884 using our framework. These results confirm that AdjLeafGNN can accurately model both local and relational patterns. The approach we propose is scalable and interpretable, facilitating real-time monitoring and control of diseases in precision agriculture.
Why it matches plant phenotyping methods葉画像から植物病害を分類し、隣接葉間の病害拡大を推定する深層学習・GNN手法を提案・評価しており、植物の病害状態の取得・推定が研究の中心である。
abstractwe propose AdjLeafGNN, an innovative hybrid deep learning and graph neural network model that performs multi-class leaf disease classification and probabilistic prediction of adjacent-leaf disease spread in a single pass.
Reproduction assets foundThe paper uses the public Kaggle PlantVillage leaf-image dataset as its phenotyping input and releases the complete AdjLeafGNN implementation (model, preprocessing, training, evaluation) on GitHub with a Zenodo-archived DOI.Dataset · publicthe dataset was obtained from the publicly available Kaggle distribution of the PlantVillage dataset: https://www.kaggle.com/datasets/mohitsingh1804/plantvillageTheOpen asset ↗html-lines:584-607Code · publicThe complete source code of the proposed AdjLeafGNN framework, including model implementation, training scripts, and evaluation pipeline, is publicly available. GitHub repository: https://github.com/surekhareddy123/AdjLeafGNN. A permanent archived version of the repository has been deposited in Zenodo and assigned the following DOI: 10.5281/zenodo.18862439.Open asset ↗https://github.com/surekhareddy123/AdjLeafGNN · 10.5281/zenodo.18862439html-lines:584-607Code / dataset availability confirmedOpenAlex · checked 15 Sept 2026
ABSTRACT 3D reconstruction has matured into a robust technology. However, small, flexible objects such as conifer seedlings remain challenging due to their fine‐scale structures, and susceptibility to movement. This study investigates and evaluates methods for reconstructing spruce ( Picea abies ) and pine ( Pinus sylvestris ) seedlings, with the aim of establishing a workflow capable of capturing geometry and texture for applications in machine learning and virtual testing environments. Two acquisition approaches were tested: photogrammetry using a RGB camera and a 3D scanner, both mounted on a robotic arm. While the scanner produced incomplete results, the photogrammetry approach successfully generated point clouds (pcl) with color information. Three different photogrammetry software were tested before relying on Agisoft Metashape and Meshroom for image processing and dense pcl generation, followed by pcl filtering in CloudCompare and meshing in Blender. Six seedlings were reconstructed to textured meshes and quantitatively evaluated using the metrics precision, recall, F1‐score, mask intersection‐over‐union (IoU), and boundary IoU. Results showed an average mask IoU of 75.7% and F1‐score of 86.1%. Pine seedlings yielded higher recall and F1‐scores, whereas spruce reconstructions demonstrated higher precision. The proposed semi‐automated workflow demonstrates the feasibility of reconstructing small and slender structured flexible objects, specifically conifer seedlings.
Why it matches plant phenotyping methods針葉樹苗の形状・テクスチャを取得する3D画像再構成ワークフローを開発・比較・定量評価しており、植物フェノタイピング手法が中心である。
abstractThis study investigates and evaluates methods for reconstructing spruce ( Picea abies ) and pine ( Pinus sylvestris ) seedlings, with the aim of establishing a workflow capable of capturing geometry and texture for applications in machine learning and virtual testing environments.
Reproduction assets foundThe paper's Data Availability Statement states that the raw seedling image data and finalized textured meshes (the paper's phenotyping/3D reconstruction inputs and outputs) are freely available on Zenodo under DOI 10.5281/zenodo.19823955, which appears in the allowed URL list.Dataset · publicand without adjusting the scanning parameters, while also re-
Data Availability Statement
taining texture and color. In contrast to prior approaches that
require manual intervention or do not preserve visual informa- Raw image data and finalized textured meshes are freely available at
Zenodo.org with https://doi.org/10.5281/zenodo.19823955.
tion, the proposed workflow enables a semi-automated recon-
struction process suitable for dataset generation. As shown, the
methodology is effective for the digital reconstruction of small References
and slender structured flexible objects and holds potential for
Abbood, S. A., H. A. Ajjah, A. H. H. Alboabidallah, M. U. MohaOpen asset ↗Zenodopdf-layout-page:14 lines:50-74Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Abstract This paper presents a deep learning model to detect cotton plant pests and classify diseases, which must overcome limited datasets, class imbalance, and feature redundancy. At the preprocessing phase, the Gaussian blur filtering and Contrast Limited Adaptive Histogram Equalization (CLAHE) are used to sharpen images by improving their clarity and contrast. To increase and diversify the data, Spa-GAN-based data augmentation is used to produce realistic synthetic samples. To obtain an accurate Region of Interest (RoI), an Attention-Guided Multi-Scale Residual U-Net (AGMS-UNet) is considered to segment local and global structural information. The proposed framework makes three major contributions: (i) a new attention-based feature extractor, TriAttnNet , that incorporates spatial, channel, and contextual attention to represent diseases on a fine-grained level; (ii) a new optimization strategy, Hybrid Mongoose Ray Chaotic Optimization (HMRCO), which includes chaotic strategies to better tune the parameters and explore the feature space; and (iii) classification layer with focal loss for final decision. Experimental analyses prove that the suggested method is much more effective than the current state-of-the-art models, providing a powerful and understandable solution to precision agriculture and sustainable cotton crop health monitoring. Experimental results show that TriAttnNet achieves 98.66% accuracy, 98.71% recall, and 98.81% F1-score, which is better than the state-of-the-art algorithms, such as EfficientNetB1-CBAM (96.38%) and BERT-ResNet-PSO (95.69%). The proposed system is computationally feasible and interpretable, and it is interpretable to provide a practical solution to precision agriculture and sustainable monitoring of the health of cotton crops.
Why it matches plant phenotyping methods綿植物の病害を画像から検出・分類する深層学習手法が研究の中心であり、植物の病害状態を直接推定して性能比較・検証しているため。
abstractThis paper presents a deep learning model to detect cotton plant pests and classify diseases
Reproduction assets foundThe paper's plant image input is the public Kaggle Cotton Plant Disease Dataset, explicitly cited with URL. Authors' code/models are only available upon request, so no public code asset qualifies.Dataset · publicThe dataset of this study is taken from the publicly available Kaggle repository, Cotton Plant Disease
Dataset [25].Open asset ↗Kagglepdf-page:6 lines:1-48Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Deep learning has improved automated plant disease detection by increasing recognition accuracy and robustness compared with traditional vision-based methods. Self-supervised learning (SSL) further reduces dependence on manual labels, but its transferability across heterogeneous agricultural datasets remains insufficiently characterized. Here, we evaluate a contrastive SSL pretraining and fine-tuning pipeline, termed PlantCLR, for plant disease classification under cross-dataset transfer with target-domain fine-tuning. PlantCLR combines SimCLR-style contrastive pretraining with a lightweight convolutional classifier to balance representation quality and deployment efficiency. Experiments on PlantVillage and Cassava Leaf Disease show strong performance, achieving 99.10% accuracy and 99.04% F1-score on PlantVillage, and 96.83% accuracy and 96.70% F1-score on Cassava. Feature embedding visualization using t-SNE and explanation maps using Grad-CAM indicate improved class separability and attention to disease-relevant regions. These results suggest that contrastive SSL can improve representation transfer while maintaining computational efficiency, supporting scalable plant disease diagnostics in practical agricultural settings. Code is available at GitHub .
Why it matches plant phenotyping methods植物病害を画像から分類するPlantCLR手法を開発し、異なるデータセット間で性能評価・検証しているため、植物の病害状態を推定するフェノタイピング手法が中心である。
abstractHere, we evaluate a contrastive SSL pretraining and fine-tuning pipeline, termed PlantCLR, for plant disease classification under cross-dataset transfer with target-domain fine-tuning.
Reproduction assets foundThe paper's plant disease detection experiments use two publicly available image datasets with explicit Kaggle URLs in the Data availability statement. The authors also state code is available at GitHub, but no concrete URL is provided, so no code asset is included.Dataset · publicThe Cassava Leaf Disease Classification dataset is available at https://www.kaggle.com/c/cassava-leaf-disease-classificationOpen asset ↗Kaggle · cassava-leaf-disease-classificationlines:232-268Dataset · publicthe PlantVillage dataset is available at https://www.kaggle.com/datasets/emmarex/plantdiseaseOpen asset ↗Kaggle · emmarex/plantdiseaselines:232-268Code / dataset availability confirmedEurope PMC · checked 15 Sept 2026
Crop diseases significantly threaten global food security by directly affecting the crop yield and quality. The traditional diagnostic methods are labour intensive and human error prone. However, the existing deep learning solutions suffer with poor generalization due to the sharp loss landscapes. The proposed work addresses this limitation and optimizes the Convolutional Neural Network (CNN) using the Sharpness-Aware Minimization (SAM). This method minimizes both the training loss and loss landscape sharpness and enables the model to converge to a flatter-minima with improved generalization. The proposed work is evaluated on 60,000 corn leaf image samples for four classes with 15,000 balanced samples per class after augmentation. The optimized CNN model has achieved 99.66% test accuracy at 0.33% classification error rate and outperforms the conventional optimizers like Adam (98.44% accuracy) and the Stochastic Gradient Descent (SGD). The state-of-the-art analysis presents a 99% average precision rate along with 99.66% F1-score and 0.0013% mean squared error (MSE). The quantized model achieves an inference latency of 22.7 ms/image (≈44 FPS) on a Raspberry Pi 4 and reduces model overfitting and enhances feature discriminability. These results underscore the potential of SAM-based optimization in precision agriculture by driving a scalable automation of disease management. This work bridges the gap between theoretical advances in deep learning optimization and practical deployment in resource-constrained farming environments.
Why it matches plant phenotyping methodsトウモロコシ葉画像から病害を分類するCNNの最適化と性能評価が中心であり、植物の病害状態を画像から推定するフェノタイピング手法に該当する。
abstractThe proposed work addresses this limitation and optimizes the Convolutional Neural Network (CNN) using the Sharpness-Aware Minimization (SAM).
Reproduction assets foundThe paper's Data availability statement lists the public corn leaf image datasets used for its disease-classification experiments (Kaggle corn/maize leaf disease dataset, New Bangladeshi crop disease dataset, New Plant Diseases Dataset, and the MahindiNet maize leaf disease dataset on Science Data Bank). No author codeDataset · publicg.; Gireesh Kumar: Formal Analysis, Visualization, Writing – Review & Editing, Resources.
Funding
Open access funding provided by Manipal University Jaipur. Open access funding provided by Manipal University Jaipur, Jaipur. No external funding was received for this research.
Data availability
Corn or Maize Leaf Disease Dataset, https://www.kaggle.com/datasets/smaranjitghose/corn-or-maize-leaf-disease-dataset [ 33 ] New Bangladeshi crop disease dataset. https://www.kaggle.com/datasets/nafishamoin/new-bangladeshi-crop-disease [ 38 ] New Plant Diseases Dataset, https://www.kaggle.com/datasets/vipoooool/new-plant-diseases-dataset [ 46 ] Mohammed Abo-Zahhad et al. (2023). MahindiNet: Maize Leaf DOpen asset ↗Kagglelines:2568-2620Dataset · publicby Manipal University Jaipur. Open access funding provided by Manipal University Jaipur, Jaipur. No external funding was received for this research.
Data availability
Corn or Maize Leaf Disease Dataset, https://www.kaggle.com/datasets/smaranjitghose/corn-or-maize-leaf-disease-dataset [ 33 ] New Bangladeshi crop disease dataset. https://www.kaggle.com/datasets/nafishamoin/new-bangladeshi-crop-disease [ 38 ] New Plant Diseases Dataset, https://www.kaggle.com/datasets/vipoooool/new-plant-diseases-dataset [ 46 ] Mohammed Abo-Zahhad et al. (2023). MahindiNet: Maize Leaf Disease Dataset[DS/OL]. V1. Science Data Bank. https://cstr.cn/31253.11.sciencedb.12556 . CSTR:31,253.11.sciencedb.12556 [ 55 ] Open asset ↗Kagglelines:2568-2620Code / dataset availability confirmedCrossref · checked 14 Sept 2026
Published31 Mar 2026Journal of Wireless Mobile Networks, Ubiquitous Computing, and Dependable ApplicationsCited by 0 · OpenAlex ↗
The aspect of crop monitoring takes into consideration the timely detection of crop stages, leaf disorders, and deficiencies to enhance crop yield and decrease losses in agriculture. However, most of the current methods are limited to either disease detection or nutrient evaluation and do not examine the conditions of crops at various stages of growth, even though several AI -IoT-based solutions have been suggested to be applied to crop health monitoring. In addition, the estimation of the severity of the diseases is neglected, and this restricts decision-making in favor of the farmers. To address these constraints, the paper presents a Parametrized Elliptical Cauchy Fuzzy Inference System (PECFIS) combined with a Deep Glorot Bessel Elliott Softplus Convolutional Neural Network (DGBESCNN), proposed as an AI-based solution for crop monitoring and IoT support. The IoT devices in the form of drones are used to get real-time field images, and they are preprocessed in terms of noise reduction, contrast enhancement by LHM-CLAHE, conversion to HSV color space, and feature discrimination by vegetation indexing, as well as C3MEK-Means. PECFIS is used to determine eight key stages of rice growth and the severity of leaf diseases, whereas DGBESCNN provides proper classification of leaf diseases and nutrient deficiencies at each growth stage. The evaluation of the proposed framework was conducted using publicly available datasets on rice leaf disease and nutrient deficiency. The results of the experiments show that the system achieves high classification performance, with an accuracy of 98.82, a precision of 98.65, a recall of 98.73, an F1-score of 98.59, and low error rates (MSE = 0.0135, RMSE = 0.116). The findings show that the developed AI-IoT system is superior to available approaches and can serve as a dependable, real-time, and scalable solution in precision agriculture and intelligent crop monitoring.
Why it matches plant phenotyping methodsドローン画像からイネの生育段階と葉病害の重症度を推定・分類するAI-IoT手法が研究の中心であり、植物状態の取得・抽出方法を技術的に評価している。
abstractThe IoT devices in the form of drones are used to get real-time field images
Reproduction assets foundThe paper evaluates its PECFIS-DGBESCNN crop monitoring framework on two publicly available Kaggle datasets (Nutrient Deficiency Symptoms in Rice, 1,156 images; Rice Leaf Diseases, 120 images), with explicit dataset links provided by the authors. No author code, models, or other paper-specific assets are shared.Dataset · publicn of the low-cost ground-based IoT and weather sensors and enhanced robustness in the
current unfavorable environmental conditions.
Future Enhancement
In the future, enhanced techniques will be developed to classify the numerous types of nutrient
deficiencies in rice crops for improved productivity in agriculture.
Dataset link: https://www.kaggle.com/datasets/guy007/nutrientdeficiencysymptomsinrice
https://www.kaggle.com/datasets/vbookshelf/rice-leaf-diseases/data
References
[1] Aggarwal, M., Khullar, V., Goyal, N., Alammari, A., Albahar, M. A., & Singh, A. (2023).
Lightweight federated learning for rice leaf disease classification using non independent and
identically distributed images. SuOpen asset ↗Kaggle · guy007/nutrientdeficiencysymptomsinricepdf-raw-page:21 lines:1-50Dataset · publicstness in the
current unfavorable environmental conditions.
Future Enhancement
In the future, enhanced techniques will be developed to classify the numerous types of nutrient
deficiencies in rice crops for improved productivity in agriculture.
Dataset link: https://www.kaggle.com/datasets/guy007/nutrientdeficiencysymptomsinrice
https://www.kaggle.com/datasets/vbookshelf/rice-leaf-diseases/data
References
[1] Aggarwal, M., Khullar, V., Goyal, N., Alammari, A., Albahar, M. A., & Singh, A. (2023).
Lightweight federated learning for rice leaf disease classification using non independent and
identically distributed images. Sustainability, 15(16), 12149.
https://doi.org/10.3390/su151612149
[2] AlfOpen asset ↗Kaggle · vbookshelf/rice-leaf-diseasespdf-raw-page:21 lines:1-50Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Abstract Abstract. Accurate and timely identi cation of plant diseases is essential for improving crop productivity and ensuring sustainable agricultural practices. This paper presents a comprehensive image dataset of fruit and leaf diseases covering six economically important horticultural crops: Apple, Banana, Citrus, Guava, Mango, and Papaya. The dataset comprises high-quality RGB images representing both healthy and diseased samples, with disease symptoms including spots, lesions, discoloration, blight, rot, and fungal and bacterial infections captured under diverse real-world conditions. Variations in illumination, background complexity, viewing angles, growth stages, and symptom severity are intentionally included to enhance the robustness and generalizability of learning models developed using this data. The dataset is structured in a class-wise manner and preprocessed to support direct integration with deep learning frameworks. It is extensively used to train, validate, and evaluate deep learning based plant disease classi cation models, enabling automatic feature learning from raw images without manual intervention. Experimental usage demonstrates that the dataset is well suited for convolutional neural networks and attentionbased architectures, facilitating e ective discrimination between multiple disease categories across di erent crops and plant organs. By providing a uni ed multi-crop, multi-disease benchmark, this dataset aims to accelerate research in automated crop disease diagnosis, precision agriculture, and intelligent decision-support systems for sustainable farming.
Why it matches plant phenotyping methods植物の葉・果実の病徴画像を収録したデータセット／ベンチマークであり、病害状態の画像ベース推定を中心的に扱うため。
abstractThis paper presents a comprehensive image dataset of fruit and leaf diseases covering six economically important horticultural crops
Reproduction assets foundThe paper's core asset is the ABCGMP fruit and leaf disease image dataset, publicly deposited on Mendeley Data, with author analysis code also stated to be available on GitHub. Both are paper-specific, public, and actionable.Dataset · publicData is available on Mendeley:1Open asset ↗pdf-page:33 lines:1-56Code · publicCode availability: Code is available on GitHub 2Open asset ↗GitHubpdf-page:33 lines:1-56Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
CoffeeField / plotFruitObject detectionGrowth / development / phenology
Introduction Coffee cherry ripeness assessment is critical for harvesting efficiency and product quality, yet traditional manual inspection methods suffer from subjectivity and low efficiency. Methods To address the challenges of detecting small, occluded, and densely distributed coffee cherries in complex field environments, this study proposes an Occlusion and Density Aware Network (ODANet). Built upon the YOLOv8 framework, ODANet integrates three innovative modules: (1) Condition-Guided Windowed Attention (CGWA), which incorporates occlusion and density maps as auxiliary guidance signals for efficient feature enhancement; (2) Attention-guided Space-Preserving Convolution (ASPC), which employs space-to-depth transformation with cascaded attention to preserve spatial information during downsampling; and (3) Dual-Adaptive Dynamic Upsampling (DADU), which achieves content-adaptive feature reconstruction through dual-branch offset prediction with learnable fusion weights. Results Comprehensive evaluation on a publicly available dataset demonstrates that ODANet achieves state-of-the-art performance among 17 diverse detection architectures, attaining 76.7% mAP@0.5 with a 6.3 percentage point improvement over baseline YOLOv8, while maintaining computational efficiency (8.1 GFLOPs, 30.4M parameters) suitable for real-time deployment. Ablation studies validate the contributions of each module: ASPC improves performance by 2.2%, DADU by 0.6%, and CGWA by 3.5%. Discussion The model demonstrates robust performance across varying lighting conditions, occlusion levels, and growth stages, making it particularly suitable for practical agricultural deployment. This research provides an efficient solution for small object detection in precision agriculture.
Why it matches plant phenotyping methodsコーヒーチェリーの成熟度という植物器官の状態を画像から推定する検出手法を開発し、複数モデル比較・アブレーションで技術的に検証しているため、植物フェノタイピング手法が中心である。
abstractthis study proposes an Occlusion and Density Aware Network (ODANet)
Reproduction assets foundThe paper analyzes a publicly available coffee cherry dataset hosted on Kaggle, explicitly linked in the data availability statement. This is the paper-specific image dataset used for its coffee cherry ripeness detection experiments. No author code or model checkpoints are stated as available.Dataset · publicPublicly available datasets were analyzed in this study. This data can be found here: https://www.kaggle.com/datasets/harisyunanda/dataset-coffee-cherry/data .Open asset ↗Kaggle · harisyunanda/dataset-coffee-cherrylines:682-758Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Sugarcane diseases significantly reduce crop yield and quality, posing persistent challenges to the agricultural sector. This study presents a novel ensemble framework that integrates Vision Transformer and Swin Transformer architectures for accurate sugarcane leaf disease detection. By combining global self-attention with localized window-based attention mechanisms, the proposed model effectively captures multi-scale visual features associated with diverse disease symptoms. Experimental evaluation on a large, labeled sugarcane leaf dataset achieved a validation accuracy of 98.16% and a test accuracy of 97.06%, outperforming several convolutional neural network baselines. Additionally, a large language model (LLM) interface is employed as a post-prediction decision-support module, generating disease-specific descriptions and management suggestions based solely on the predicted disease class. This integrated framework indicates the potential effectiveness of transformer-based ensemble models combined with intelligent advisory support for practical decision-making in precision agriculture.
Why it matches plant phenotyping methodsサトウキビ葉の病徴を画像から分類するTransformerベースの手法開発と性能評価が中心であり、植物病害状態のフェノタイピングに該当する。
abstractThis study presents a novel ensemble framework that integrates Vision Transformer and Swin Transformer architectures for accurate sugarcane leaf disease detection.
Reproduction assets foundThe paper's sugarcane leaf disease image dataset (19,926 images, six classes) is explicitly stated to be publicly available on Kaggle; no author code or model checkpoints are shared.Dataset · publicThe Sugarcane Plant Diseases Dataset used in this study is publicly available on Kaggle at: https://www.kaggle.com/datasets/akilesh253/sugarcane-plant-diseases-dataset . The dataset is released for academic research and benchmarking purposes.Open asset ↗Kagglelines:112-131Code / dataset availability confirmedEurope PMC · checked 15 Sept 2026
Published28 Mar 2026Metabolomics : Official journal of the Metabolomic SocietyCited by 0 · OpenAlex ↗
Introduction Pearl millet is a high nutritional cereal recognised for its agro-climatic resilience, making it relevant for food security under climate change scenarios. Phenotypic traits are indicative of crop performance, stability and adaptability, yet the potential of metabolomics to predict these traits has not been explored. Objectives This study aimed to identify metabolite-trait associations in the Brazilian germplasm core collection, comprising 203 pearl millet genotypes, by combining untargeted metabolomics with machine-learning models. Methods Grains metabolic profiles were obtained using untargeted UHPLC-LTQ-Orbitrap-HRMS. Phenotypic data were sourced from standardised evaluations conducted by Embrapa across different years and field trials within the Sete Lagoas experimental station (Minas Gerais, Brazil). Generalised linear modelling with penalisation (GLM) and Random Forest was applied to explore the correlation between metabolism and 21 phenotypic traits. Results GLM successfully predicted eight qualitative and seven quantitative traits. Prediction accuracy was higher for qualitative traits, reflecting their comparatively simpler genetic architecture, whereas quantitative traits also achieved satisfactory performance (R² ≥ 0.6). Key predictors included phenolic compounds, amino acids, fatty acids, and carbohydrates. Notably, several associations corresponded to metabolites involved in nitrogen metabolism and vegetative growth, underscoring biologically meaningful links between metabolic profiles and trait variation. Conclusions This exploratory study presents the first metabolome characterisation of a pearl millet germplasm bank, coupled with predictive modelling of phenotypic traits. However, our findings are constrained by the single-environment design and the absence of population-structure assessment. To establish the stability and biological relevance of these results, future work should incorporate multi-environment trials and pathway-level analyses accounting for population structure.
Why it matches plant phenotyping methodsメタボロームを入力として機械学習で植物の表現型形質を予測し、複数形質で予測精度を評価しているため、単なる生物学的測定ではなく形質推定手法の検証が中心です。
abstractThis study aimed to identify metabolite-trait associations in the Brazilian germplasm core collection, comprising 203 pearl millet genotypes, by combining untargeted metabolomics with machine-learning models.
Reproduction assets foundThe paper deposits its metabolomics and phenotypic metadata in a public repository (Recherche Data Gouv, DOI 10.57745/GU6WDG). No author analysis code or trained model deposit is stated; supplementary materials are not linked to a qualifying URL.Dataset · public.623/2023; 26/210.152/2023; 26/201.317/2022), National Council for Scientific and Technological Development (CNPq) (407350/2023-3; 314100/2023-7), Coordination for Improvement of Personnel with Higher Education (CAPES) (financial code 001).
Data availability
The metabolomics and metadata reported in this paper are available via https://doi.org/10.57745/GU6WDG.
Declarations
Competing interests
The authors declare no competing interests.
References
Alonso-Blanco C Méndez-Vigo B
Genetic architecture of naturally occurring quantitative traits in plants: An updated synthesis
Current Opinion in Plant Biology 2014 18 37 43
10.1016/j.pbi.2014.01.002
24565952
Alonso-Blanco, C., & Méndez-VigoOpen asset ↗10.57745 · GU6WDGlines:121-160Code / dataset availability confirmedCrossref · Europe PMC · checked 15 Sept 2026
Accurate plant health monitoring relies on hyperspectral imagery to extract vegetation spectral signatures and compute vegetation indices (VIs), which are critical for phenotyping and crop condition assessment. However, the requirement for high spectral resolution significantly increases the cost and complexity of data acquisition. In this study, we proposed a novel machine learning-based framework for predicting VIs from down-sampled hyperspectral reflectance data. The aim was to reduce the dependency on high-resolution spectral imagery without compromising prediction accuracy. The framework integrated correlation-based feature selection with four regression models to identify and utilize the most informative spectral bands from coarsely sampled data. The system was trained and validated using a data set consisting of 555 spectral signatures collected from olive leaves at five stages of dehydration, with spectral resolutions ranging from 1 to 100 nm. A total of 25 vegetation indices, commonly used in the estimation of water stress, chlorophyll, and nitrogen, were predicted on various sampling scales. Experimental results show that even with 100 nm spectral resolution, the proposed framework achieves high prediction accuracy, with coefficients of determination reaching 0.99 for RVSI, VOPT, and SPADI indices. These findings demonstrate that accurate vegetation index estimation is achievable with significantly fewer spectral bands, offering a cost-effective solution for large-scale plant health monitoring. This framework lays the groundwork for the development of low-cost, data-efficient remote sensing systems for precision agriculture, especially in crops such as olives, where health dynamics are sensitive to water and nutrient status.
Why it matches plant phenotyping methodsオリーブ葉のハイパースペクトルデータから植物状態に関わる植生指数を推定する、低コストな機械学習・スペクトル測定フレームワークの開発と検証が中心である。
abstractwe proposed a novel machine learning-based framework for predicting VIs from down-sampled hyperspectral reflectance data
Reproduction assets foundThe paper's Data Availability statement points to a Figshare deposit (DOI 10.6084/m9.figshare.26950660.v2), which per the statement hosts the study's data — the 555 olive-leaf hyperspectral signatures and vegetation index measurements underlying the phenotyping analysis. This is a paper-specific, publicly accessible,直接Dataset · publicnm.
(PDF)
S2 File
Inclusivity in global research questionnaire.
(PDF)
Acknowledgments
The authors thank the Advanced Center of Electric and Electronic Engineering - AC3E ANID. The authors acknowledge the support provided by Universidad Técnica Federico Santa María and the Direction of Post-Grade programs DDP.
Data Availability
https://doi.org/10.6084/m9.figshare.26950660.v2 .
Funding Statement
This work was funded by the ANID FB240002 basal center AC3E, and ANID national doctorate scholarship, folio N°21231129. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
References
1. Ruiz-Carrasco B, Fernández-Lobato L, López-Open asset ↗figshare · 10.6084/m9.figshare.26950660.v2lines:266-293Code / dataset availability confirmedOpenAlex · Europe PMC · checked 15 Sept 2026
ABSTRACT Hyperspectral remote sensing is a powerful, high-throughput phenotyping tool that quantifies physiologically and structurally relevant wavelengths across diverse genotypes and over varying temporal scales. In this study, we combined tower-based continuous hyperspectral sensing with genome-wide association studies to analyze 1,423 wavebands (400-900 nm) and derivative vegetation indices across 505 genotypes and the genetic architecture of hyperspectral phenotypes over time in Populus trichocarpa Torr. & Gray grown under field conditions. Wavelengths related to chlorophyll and carotenoid absorption spectra exhibited the strongest genetic variation resulting in 98 significant SNP associations. Notably, we found substantial overlap in genetic association between the blue and red spectral regions, indicative of carotenoids and chlorophyll, respectively, and identified more than 10 candidate genes associated with chloroplast function, underpinning photosynthetic activity. Furthermore, fluctuations in associations for vegetative indices, such as the chlorophyll:carotenoid index (CCI), across the growing season reveal a temporally dynamic genetic architecture of physiological traits associated with fall senescence of this temperate tree species. Finally, we also observed correlations (⍴=0.3, p 0.5, p<1x10 -16 ), reinforcing the value of hyperspectral measurements for predicting traits linked to tree productivity. These findings highlight the potential of high-throughput, rapid, hyperspectral genome wide association studies GWAS to uncover physiologically meaningful genetic variation and offer promising insights for future acceleration for plant breeding.
Why it matches plant phenotyping methodsタワー型連続ハイパースペクトルセンシングを用いて多数の遺伝子型の生理・構造形質を時系列で取得し、表現型解析とGWASに substantively 適用しているため、フェノタイピング手法が中心的である。
abstractHyperspectral remote sensing is a powerful, high-throughput phenotyping tool that quantifies physiologically and structurally relevant wavelengths across diverse genotypes and over varying temporal scales.
Reproduction assets foundThe paper's hyperspectral phenotype dataset (tower-based hyperspectral traits for 505 Populus trichocarpa genotypes) is explicitly stated to be publicly available through the Oak Ridge National Laboratory LabKey data portal with DOI 10.25983/CBI/3012775. This is a paper-specific, public, actionable phenotype dataset. ADataset · publicHyperspectral phenotype data are publicly available through the Oak Ridge National Laboratory LabKey data portal (DOI: 10.25983/CBI/3012775).Oak Ridge National Laboratory LabKey data portal · 10.25983/CBI/3012775lines:163-201Code / dataset availability confirmedCrossref · Europe PMC · checked 5 Sept 2026
Abstract The precise classification of plant diseases is crucial for ensuring food security for all people and boosting agricultural productivity. Although there has been significant progress in this field using deep learning approaches, cross-dataset training hasn’t drawn as much attention from researchers as intra-dataset training has. Moreover, very few models have successfully blended intra-dataset and cross-dataset training approaches. This paper proposes a novel attention-based Convolutional Neural Network (CNN) to overcome these limitations. The model improves feature extraction and classification accuracy across multiple datasets by using attention mechanisms. It was tested on five datasets (Digipathos, Northern Leaf Blight (NLB), PlantVillage, PlantDoc, and the CD&S dataset) that covered leaf diseases of both corn and potatoes. During intra-dataset training, the model achieved the highest classification accuracy of 99.38% when trained on images of potato leaves from the PlantVillage dataset. During cross-dataset training, the model exhibited the highest average classification accuracy of 82.93% for corn leaf diseases when trained on images from the CD&S dataset with their backgrounds removed. When compared to the techniques taken into consideration in this study under comparable experimental conditions, the results demonstrate improved performance. This study shows how the model may be flexible for both intra- and cross-datasets, offering a flexible way to categorize diseases that affect plants. Because of its ability to generalize across different datasets, it may be helpful in real-world agricultural applications with a wide variety of image quality and situations. This encourages the advancement of precision farming techniques and disease control.
Why it matches plant phenotyping methods植物葉の画像から病害状態を分類するCNN手法の開発・データセット間検証が中心であり、植物病害の表現型推定に該当する。
abstractThis paper proposes a novel attention-based Convolutional Neural Network (CNN) to overcome these limitations.
Reproduction assets foundThe paper's plant disease classification experiments rely on five publicly available leaf-image datasets, each cited with an explicit public access URL in the reference list: PlantVillage (GitHub), PlantDoc (GitHub), Digipathos (Embrapa), NLB (SciDB), and CD&S (OSF). No author analysis code or trained model checkpoint,Dataset · publicHughes, D., & Salathé, M. (2015). An open access repository of images on plant health to enable the development of mobile disease diagnostics. arXiv preprint arXiv:1511.08060. Dataset accessed via GitHub: https://github.com/spMohanty/PlantVillage-DatasetOpen asset ↗GitHub · spMohanty/PlantVillage-Datasethtml-lines:1013-1082Dataset · publicDataset available at: https://github.com/pratikkayal/PlantDoc-DatasetOpen asset ↗GitHub · pratikkayal/PlantDoc-Datasethtml-lines:979-1012Dataset · publicCD&S dataset: Handheld imagery dataset acquired under field conditions for corn disease identification and severity estimation. arXiv preprint arXiv:2110.12084. Dataset available at: https://osf.io/s6ru5/files/osfstorageOpen asset ↗OSF · s6ru5html-lines:1013-1082Code / dataset availability confirmedEurope PMC · checked 14 Sept 2026
This study addresses the challenge of detecting white grape clusters (Vitis vinifera L) in high-density vineyard canopies, a critical task for precision viticulture and yield estimation. Traditional statistical and image-processing methods have struggled with occlusion issues. In this work, over 100 field RGB images were collected at La Bergonza (Toledo, Spain) and expanded through data augmentation, with various preprocessing strategies tested to enhance cluster visibility. Convolutional Neural Network (CNN) architectures were compared, highlighting YOLOv8 as superior to Mask R-CNN in both accuracy and efficiency. YOLOv8, trained for up to 100 epochs on equalized and augmented datasets, achieved outstanding performance: 84.9% precision, 72.6% recall, and mAP@0.5 of 83%, far surpassing Mask R-CNN (17% precision, 26% recall). The model successfully detected partially hidden clusters, including those invisible to human experts, better than previous studies that required controlled backgrounds or artificial lighting. Results confirm that combining RGB equalization with data augmentation optimizes detection. These findings underscore the potential of deep learning and low-cost RGB imaging systems to enable automated, scalable solutions for yield estimation and canopy analysis. In conclusion, YOLOv8 emerges as a promising tool for accurate grape bunch detection under field conditions, overcoming previous limitations.
Why it matches plant phenotyping methodsブドウ房を対象としたRGB画像とCNNによる検出手法を開発・比較し、精度を定量評価しているため、植物器官の表現型取得が中心である。
abstractIn this work, over 100 field RGB images were collected at La Bergonza (Toledo, Spain) and expanded through data augmentation, with various preprocessing strategies tested to enhance cluster visibility.
Reproduction assets foundThe paper's Data Availability Statement points to the authors' public GitHub repository containing the original grape-cluster image dataset and annotations used in this study. The ultralytics repository is a generic third-party library, not a paper-specific asset.Dataset · publicData Availability Statement: The original data presented in the study are openly available at
[https://github.com/upmValeriano/racimosUva.git.]Open asset ↗upmValeriano/racimosUvapdf-page:13 lines:1-66Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
The growing global demand for food production, coupled with the increasing threat of plant diseases, necessitates advanced and automated solutions for crop health monitoring. Among various crops, pome fruits such as apples and pears are widely cultivated yet highly susceptible to multiple diseases that can significantly reduce yield and quality. Existing approaches for disease detection and severity classification are often limited by their dependency on manual inspection and their inability to handle complex real-world imagery, especially when multiple diseases coexist on a single leaf. To address these limitations, this research introduces a novel dual-model deep learning framework for multi-disease severity detection and classification in pome fruit leaves. A fine-tuned MobileNetV2 backbone is employed to extract high-level discriminative features from a specialized pome leaf dataset annotated with multiple disease types and severity levels. The proposed system integrates a lightweight Lite-U-Net for semantic segmentation to isolate diseased regions and an enhanced Lite-YOLACT for instance segmentation using a linear combination of prototype masks and mask coefficients. Moreover, a new multi-disease severity scale is proposed to quantify the impact of multiple coexisting infections on a single leaf, an aspect not addressed in previous studies. To enhance interpretability, an improved Grad-CAM technique generates visual heatmaps highlighting the most influential regions in the model's decision-making process, providing transparency and validation for agricultural experts. Experimental evaluations demonstrate that the proposed framework achieves 95% accuracy in disease severity estimation, effectively identifying and grading multiple infections simultaneously. This study represents a significant step forward in precision agriculture, offering an efficient, interpretable, and scalable deep learning solution for real-world crop health monitoring and management. The source code and trained models are publicly available at: https://github.com/mqasim0787/Multi-Disease-Severity .
Why it matches plant phenotyping methods果樹葉の病斑領域を画像から分割し、複数病害の重症度を定量推定する深層学習フレームワークが研究の中心であり、植物状態の画像ベース表現型計測に該当する。
abstractthis research introduces a novel dual-model deep learning framework for multi-disease severity detection and classification in pome fruit leaves.
Reproduction assets foundThe paper's authors publicly release source code and trained models on GitHub, and the study analyzes two public Kaggle plant-image datasets (DiaMOS Plant and PlantVillage) used directly for the multi-disease severity phenotyping experiments.Code · publicThe source code and trained models are publicly available at: https://github.com/mqasim0787/Multi-Disease-Severity .Open asset ↗https://github.com/mqasim0787/Multi-Disease-Severity · mqasim0787/Multi-Disease-Severitylines:1-23Dataset · publicThe datasets analyzed during the current study are available publicly in the Kaggle repository, DiaMOS dataset (1) and PlantVillage Dataset (2) 0.1. [https://www.kaggle.com/datasets/alexandraneagu101/diamos-plant-dataset]Open asset ↗https://www.kaggle.com/datasets/alexandraneagu101/diamos-plant-dataset · diamos-plant-datasetlines:964-977Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Precise detection of crop leaf damage is essential for real-time plant health monitoring and yield estimation. However, conventional deep learning models often exhibit poor generalization when deployed across varying species and complex, unstructured field environments. To address these limitations, we propose a new modeling paradigm that shifts from traditional task-specific training to foundation model adaptation. Specifically, we introduce a novel architecture integrating the DinoV3 foundation model with a Unet framework to achieve robust leaf lesion segmentation. By incorporating a Spatial Prior Module (SPM) and a Projection Module, our approach effectively bridges the gap between general-purpose pre-training and domain-specific requirements. Experimental results on coffee and black gram datasets demonstrate that this paradigm consistently outperforms standard networks, including Unet, Unet++, and SwinUnet. On the coffee leaf dataset, the proposed model achieves an Intersection over Union (IoU) of 78.31% and a Pixel Accuracy of 88.00%, surpassing the baseline Unet by over 10.5% in IoU. Remarkably, the architecture reduces inference time by approximately 93.6% (from 63.41s to 4.07s), proving that high-parameter foundation models can be adapted for extreme computational efficiency in agricultural scenarios. To further validate scalability, we conduct additional experiments on a larger dataset, AMG HS . The proposed paradigm achieves the best overall detection performance while maintaining superior computational efficiency, confirming its robustness under increased data scale. Interpretability analysis reveals that the foundation model backbone effectively captures high-level semantic features of lesions, providing a clear explanation for its superior performance and cross-domain reliability. This research establishes a scalable, high-performance paradigm for intelligent crop protection, demonstrating that coupling customized encoders with foundation models is a superior strategy for cross-domain agricultural tasks.
Why it matches plant phenotyping methods植物葉の病変を画像からセグメンテーションし、葉の損傷状態を定量化する手法の開発・検証が研究の中心であるため。
abstractwe introduce a novel architecture integrating the DinoV3 foundation model with a Unet framework to achieve robust leaf lesion segmentation.
Reproduction assets foundThe paper analyzes two publicly available plant image datasets hosted on Mendeley Data: a coffee leaf rust/leaf miner dataset and a black gram leaf disease dataset, both explicitly linked in the Data Availability Statement. No author analysis code or trained model checkpoints are disclosed.Dataset · publicPublicly available datasets were analyzed in this study. This data can be found here: https://data.mendeley.com/datasets/vfxf4trtcg/5; https://data.mendeley.com/datasets/45djgf3p96/1.Open asset ↗html-lines:473-493Dataset · publicPublicly available datasets were analyzed in this study. This data can be found here: https://data.mendeley.com/datasets/vfxf4trtcg/5; https://data.mendeley.com/datasets/45djgf3p96/1.Open asset ↗html-lines:473-493Code / dataset availability confirmedEurope PMC · checked 14 Sept 2026
Abstract Tomato leaf diseases significantly impact agricultural productivity, necessitating accurate and efficient diagnostic methods. Deep learning has emerged as a robust approach for plant disease detection, but challenges such as inefficient feature extraction, classification, model complexity and limited computational resources hinder its widespread adoption. This study introduces a PhytoNet (Mish-Optimized SqueezeNet) Framework to enhance tomato leaf disease prediction. The SqueezeNet architecture, known for its lightweight design, is optimized with the Mish activation function to improve feature extraction and classification capabilities while maintaining computational efficiency. The methodology involves training the SqueezeNet model on 10 classes of mendaley dataset of tomato leaf images, encompassing multiple disease classes and healthy samples. Data preprocessing techniques, including image augmentation and normalization, are employed to ensure model robustness. The integration of the Mish activation function in critical layers enhances non-linearity, aiding in better gradient flow and improved performance during training. Model evaluation is conducted using metrics such as accuracy, precision, recall and F1-score. Experimental results demonstrate that the PhytoNet outperforms traditional SqueezeNet and other lightweight architectures in terms of classification accuracy, achieving over 0.9957 accuracy on the dataset. Additionally, the model maintains low computational overhead, making it suitable for deployment on resource-constrained devices. Hence, the proposed framework effectively balances accuracy and efficiency, addressing critical limitations in existing plant disease detection models. This work underscores the potential of lightweight and activation-optimized deep learning frameworks for real-time agricultural applications, paving the way for scalable and sustainable solutions in precision farming.
Why it matches plant phenotyping methodsトマト葉画像から病害状態を推定する深層学習モデルを開発・評価しており、植物病害フェノタイピング手法が中心的な貢献である。
abstractThis study introduces a PhytoNet (Mish-Optimized SqueezeNet) Framework to enhance tomato leaf disease prediction.
Reproduction assets found保存済みの本文根拠を更新済みルールで再検証し、公開資産1件を確認しました。Dataset · publicThe dataset used in this study,Open asset ↗pdf-page:38 lines:1-41Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Early detection of maize leaf diseases is essential to prevent yield losses. Existing vision-based models face challenges in real-world environments due to data imbalance, lighting variations, and interpretability. This study presents MaizeFormerX, a lightweight Vision Transformer designed for cross-domain, explainable maize disease detection on resource-limited settings. MaizeFormerX employs multi-scale patch embeddings and a Cross-Scale Attention Fusion (CSAF) module to capture both detailed lesion textures and larger disease patterns. The CSAF output is processed through a transformer encoder stack using multi-head self-attention to model long-range dependencies. Robust preprocessing and dataset-specific augmentations were applied to improve feature extraction and address class imbalances in the Dataverse, Tanzania, and Plagues Maiz datasets. For interpretability, Grad-CAM was used for pixel-level saliency mapping in an efficient web application. When benchmarked against MobileViT, EfficientFormer, TinyViT, and Swin Transformer, MaizeFormerX achieved 97.8% accuracy on Dataverse, 97.5% on Tanzania, and 96.9% on Plagues Maiz, outperforming Swin Transformer V2 by 2–3%. Cross-domain testing yielded 88.9% accuracy when trained on Dataverse and tested on Tanzania, surpassing baseline performance by 3–6%. Class-wise analysis revealed F1 scores over 98% for Healthy and MLB classes with 6× augmentation, and over 97% for MSV. Ablation studies highlighted the significance of the cross-scale attention module for high MCC during domain shifts. This study introduces a precise, explainable, and efficient image-based method for classifying maize diseases, which could aid in more targeted crop management, reduce unnecessary agrochemical use, and promote sustainable maize production in future decision-support environments.
Why it matches plant phenotyping methodsトウモロコシ葉の病徴を画像から分類する手法の開発・ベンチマーク・交差ドメイン検証が中心であり、植物病害状態の画像ベース表現型計測に該当する。
abstractThis study presents MaizeFormerX, a lightweight Vision Transformer designed for cross-domain, explainable maize disease detection on resource-limited settings.
Reproduction assets foundThe paper's Data Availability statement explicitly lists three public maize leaf image datasets used for its phenotyping/disease-classification experiments (Dataverse, Tanzania/Mendeley, Plagues Maiz/figshare) and an authors' GitHub repository containing all code, preprocessing pipelines, and experimental configs. All四Dataset · publicThe datasets used in this study are publicly available and sourced from Dataverse (https://doi.org/10.7910/DVN/LPGHKK)Open asset ↗Dataverse · 10.7910/DVN/LPGHKKhtml-lines:2304-2339Code · publicAll code, preprocessing pipelines, and experimental configurations used in this work are available at: https://github.com/rezaul-h/MaizeFormerX/.Open asset ↗github · rezaul-h/MaizeFormerXhtml-lines:2304-2339Code / dataset availability confirmedEurope PMC · checked 15 Sept 2026
Many Artificial Intelligence and Machine Learning technologies have been applied to detect rice diseases. These approaches are either unable to identify the diseases or have a slow recognition speed. Therefore, an improved Faster-RCNN (Faster-RCNN-Pro) model is proposed to overcome these issues. First, SENet attention modules are embedded in the backbone of Faster-RCNN to enhance confidence of objects that are difficult to recognize by enhancing key image information and suppressing background information. Second, structure of the feature extraction network and RPN are improved by using multi-feature scale fusion to increase the utilization of micro-target features. Third, the quantization error introduced in the process of pooling the region of interest is then eliminated by ROI Align. Finally, a balanced L1 loss function is designed to effectively reduce the imbalance between samples with a large gradient that are difficult to learn, and samples with a small gradient that are easy to learn. The experiment results show that the improved model has a better detection accuracy and robustness in recognizing the fine features of rice leaf diseases. Therefore, the application of this model to the intelligent identification of rice leaf disease can significantly improve the accuracy and reduce the misjudgment rate.
Why it matches plant phenotyping methodsイネ葉の病害状態を画像から識別する改良Faster-RCNNを開発・評価しており、植物病害表現型の取得手法が研究の中心である。
abstractan improved Faster-RCNN (Faster-RCNN-Pro) model is proposed to overcome these issues.
Reproduction assets foundThe paper's rice leaf disease detection experiments were performed on a public Kaggle image dataset (rice blast, brown spot, hispa, healthy leaves), which the authors explicitly state is publicly available with a URL matching the allowed list. No author analysis code or trained model checkpoints are disclosed.Dataset · publical Internet of Things, aiming to recognize large-scale rice leaf diseases. Moreover, it is beneficial for the modernization of the agricultural industry.
Acknowledgments
The authors would like to thank the anonymous reviewers.
Data Availability
All relevant data for this study are publicly available from the Kaggle repository ( https://www.kaggle.com/minhhuy2810/rice-diseases-image-dataset ).
Funding Statement
This work is supported by the National Natural Science Foundation of China (62402308).
References
1. Mondal S, Ghosh S, Mukherjee A. Application of biochar and vermicompost against the rice root-knot nematode (Meloidogyne graminicola): an eco-friendly approach in nematode management. JOpen asset ↗Kaggle · minhhuy2810/rice-diseases-image-datasetlines:220-237Code / dataset availability confirmedEurope PMC · checked 15 Sept 2026
Oranges, mandarins, bitter oranges, and lemons are examples of citrus fruits that make delicious meals and are highly nutritious. Citrus fruits suffer from a variety of infections that affect their yield. The Department of Agriculture wants to increase the production of oranges and lemons. On the other hand, several plant diseases and their advanced stages have impacted production. The quality of fruit influences market value and its financial effect. Therefore, accurate detection of ailments and their severity is crucial for improving the output and market value of oranges and lemons. To automatically evaluate and predict diseases in citrus leaves and fruits, this paper has proposed a modified convolutional neural network (ICNN) model. Python is used to create the ICNN model, and testing is performed using benchmark datasets from various repositories. The research presented here shows that ICNN performs better than traditional deep learning and machine learning models, such as the Convolutional Neural Network (CNN) and K-Nearest Neighbours (KNN). This illustrates how machine learning models require supplementary approaches to extract parameters from data that arrives in non-automated ways. Additionally, to improve the accuracy of their classification or prediction, deep learning models require pre-trained models. As a result, ICNN, an enhanced deep learning model that can automatically predict disease with higher accuracy than other models, represents an advancement over standard CNNs. Compared with KNN and CNN, ICNN achieves 99.69% accuracy.
Why it matches plant phenotyping methods柑橘の葉・果実の病害と重症度を画像から自動推定するCNN手法を開発し、ベンチマークデータセットで比較評価しており、植物フェノタイピング手法が中心である。
abstractTo automatically evaluate and predict diseases in citrus leaves and fruits, this paper has proposed a modified convolutional neural network (ICNN) model.
Reproduction assets foundThe paper's Data Availability statement explicitly lists three public Kaggle URLs as the datasets used and analysed in the study (citrus/plant leaf disease image datasets). These are paper-specific, publicly accessible image assets directly supporting the phenotyping/disease-classification analysis. The Mendeley URL (3Dataset · publicg agricultural specialists to properly understand and accept the model’s predictions.
Author contributions
Arunapriya.R – Problem Statements, Implementation and Testing Dr.S.P.Valli – Results, Conclusion, and Summary.
Data availability
The datasets used and/or analysed during the current study available and mentioned in below [ https://www.kaggle.com/code/ghazanfarali96/leaf-disease-classification-using-cnn-lstm-rnn ]. (https:/ www.kaggle.com/code/ghazanfarali96/leaf-disease-classification-using-cnn-lstm-rnn ). [ https://www.kaggle.com/code/moazeldsokyx/plant-leaf-diseases-detection-using-cnn ]. (https:/ www.kaggle.com/code/moazeldsokyx/plant-leaf-diseases-detection-using-cnn ). [ https://wwOpen asset ↗kagglelines:372-388Dataset · publicts, Conclusion, and Summary.
Data availability
The datasets used and/or analysed during the current study available and mentioned in below [ https://www.kaggle.com/code/ghazanfarali96/leaf-disease-classification-using-cnn-lstm-rnn ]. (https:/ www.kaggle.com/code/ghazanfarali96/leaf-disease-classification-using-cnn-lstm-rnn ). [ https://www.kaggle.com/code/moazeldsokyx/plant-leaf-diseases-detection-using-cnn ]. (https:/ www.kaggle.com/code/moazeldsokyx/plant-leaf-diseases-detection-using-cnn ). [ https://www.kaggle.com/code/ritzing/plant-disease-detection-using-keras-cnn-model ]. (https:/ www.kaggle.com/code/ritzing/plant-disease-detection-using-keras-cnn-model ).
Declarations
Competing interOpen asset ↗kagglelines:372-388Code / dataset availability confirmedEurope PMC · checked 15 Sept 2026
To address the challenge of balancing model lightweight and detection accuracy in maize leaf disease detection, as well as the limitations of edge device deployment resources, we propose an enhanced target detection model, YOLOv11n-DualPC-Lite.Firstly, the C2fDualPConv module was designed, integrating PartialConv to replace some C3k2 modules in the backbone and neck networks. This approach enhances feature representation while reducing the number of parameters. Secondly, the Slim-Neck architecture is introduced in the neck network. To improve accuracy without increasing the number of parameters, the VoVGSCSPC_SimAm module enables the new Slim-Neck structure to reduce parameters while strengthening feature representation. Finally, an EfficientHead detection head is introduced that uses an inverted bottleneck MBConv module to improve performance. This significantly reduces computational load while efficiently extracting features. This study constructed a maize leaf disease dataset integrating a publicly available Kaggle dataset and a field-collected dataset from Anhui Science and Technology University's experimental plots. The dataset includes four categories: Blight, Common_Rust, Gray_Leaf_Spot, and Health. Through techniques such as rotation and gamma correction, the dataset was expanded from 3,876 to 5,165 images for model training and performance validation. Test results show this improved model performs better than other popular lightweight models overall, with a mAP50 score of 90.9%. Meanwhile, the model has only 2.13 million parameters; its computational complexity is reduced to 4.55 G, and the model size is 4.41 MB. Compared with the original YOLOv11n, its mAP50 is 1.9% higher, while the number of parameters is down by 17.8%, computational complexity is cut by 29.3%, and file size is reduced by 15.7%. When run on a Raspberry Pi 5, the model's detection speed reaches 2.3 FPS, an increase of 27.8%. This model achieves a good balance between detection accuracy and lightweight performance for maize leaf diseases, providing an efficient and practical method for real-time crop disease monitoring.
Why it matches plant phenotyping methodsトウモロコシ葉の病徴を画像から検出・分類する軽量モデルを開発し、データセット構築、性能比較、エッジデバイス検証まで行っており、植物病害状態の画像ベース表現型取得が中心である。
abstractwe propose an enhanced target detection model, YOLOv11n-DualPC-Lite
Reproduction assets foundThe paper's maize leaf disease detection study uses a public Kaggle maize leaf disease image dataset (Dataset 1) combined with a field-collected dataset. The Kaggle dataset is a public, paper-specific image asset directly used for the model's training and validation. No author analysis code, trained model checkpoints,或Dataset · publicre, the model was successfully run on a Raspberry Pi 5 edge device, realizing stable, real-time detection and providing a workable technical method for field disease monitoring.
2
Materials and methods
2.1
Dataset introduction
The dataset constructed in this study comprises two datasets: Dataset 1 from the Kaggle data website ( https://www.kaggle.com/datasets/hendriyunuswijaya/maize-leaf-disease ) and Dataset 2 collected from the experimental field at Anhui Science and Technology University in Chuzhou City, Anhui Province. Dataset 1 contains a total of 4,188 images, including 1,162 images in the Health category. All images depict only specific regions of healthy maize leaves without complex Open asset ↗Kaggle · hendriyunuswijaya/maize-leaf-diseaselines:46-63Code / dataset availability confirmedCrossref · Europe PMC · checked 5 Sept 2026
Introduction Crop diseases have to be diagnosed early to save crop yields and food safety. Commonly used conventional practices are time-consuming and likely to involve human error. Automatic plant disease detection is a highly efficient technology that has been brought into existence by the development of deep learning and computer vision technology and can effectively detect the signs of diseases in plant species. Sustainable agriculture and early intervention depend on accurate and interpretable detection of plant diseases. Methods This study introduces a hybrid model based on deep learning techniques that effectively identifies and categorizes leaf diseases. The proposed model, LeafFusionNet, incorporates Convolutional Neural Network (CNN) and Vision Transformer (ViT) with an efficient attention module, LeafTAM (Leaf Texture Attention Module), to effectively capture both global and local information. This architecture is enhanced by the addition of a Gabor filter layer before the CNN-ViT fusion, hence augmenting the model’s ability to extract physiologically relevant texture features. Results and discussion The model was trained and validated on the Plant Village dataset. This model attained an accuracy of 99.33%, 99% precision, recall, and F1 score, demonstrating strong generalization on new data when compared with the state-of-the-art models. This proposed hybrid model can be utilized to develop a strong agricultural diagnostics system. These results point to the possibility of designing a powerful, interpretable system by utilizing transformer-based vision modules, Gabor filters, and explainability systems such as Grad-CAM.
Why it matches plant phenotyping methods植物葉の病徴を画像から検出・分類する深層学習手法を開発し、PlantVillageデータセットで訓練・検証しており、植物病害状態の表現型取得が研究の中心です。
abstractThis study introduces a hybrid model based on deep learning techniques that effectively identifies and categorizes leaf diseases.
Reproduction assets foundThe paper's only analysis input is the public PlantVillage dataset, explicitly linked in the data availability statement; no author code or models are shared. The CABI Global Burden of Crop Loss reference is only a background statistic, not a phenotyping asset.Dataset · publicPublicly available datasets were analysed in this study. This data can be found here: https://www.kaggle.com/datasets/mohitsingh1804/plantvillage.Open asset ↗Kaggle · mohitsingh1804/plantvillagehtml-lines:554-590Code / dataset availability confirmedEurope PMC · checked 15 Sept 2026
Premise Plants are frequently exposed to combinations of abiotic and biotic stresses that pose a greater threat to yield and productivity than individual stresses. However, knowledge of the impact of many stress combinations in numerous plants is limited due to the lack of experimental data, which could take decades to generate. To overcome this limitation, we utilized existing literature data from various plant species and stress combinations to derive biological inferences, thereby gaining a comprehensive understanding of plant responses through a computational tool. Methods Public databases were used to gather literature on the impact of various abiotic and biotic stress combinations. Then, a composite artificial neural network (ANN)-based multi-target classification and regression deep learning model was developed using machine learning algorithms. Results The model predicted the impact of stress interactions in plants, including the morphological parameters affected and percentage changes in those parameters, with an overall accuracy of 76.33%. Predicted reductions in yield were validated in rice under combined drought and heat stress. Discussion The ANN-based model developed in this study is a valuable resource for plant researchers seeking to understand the impact of stress combinations. The tool can make use of multivariate and complex combined stress datasets.
Why it matches plant phenotyping methods植物のストレス応答として形態形質や収量変化を予測するANNベースの計算ツールを開発し、イネで予測を検証しており、表現型推定が中心である。
abstracta composite artificial neural network (ANN)-based multi-target classification and regression deep learning model was developed using machine learning algorithms
Reproduction assets foundThe paper's ANN model code (scripts, Jupyter Notebooks, example datasets) is publicly available on GitHub, and the underlying morphological combined-stress phenotype dataset is publicly downloadable from SCIPDb. Supporting Information appendices contain raw/processed training data and validation data but no explicit作者-Code · publicnteraction in plants. Applications in Plant Sciences
14(2): e70047. 10.1002/aps3.70047
Piyush Priya, Prachi Pandey, Rubi Jain, and Manu Kandpal contributed equally to this work.
DATA AVAILABILITY STATEMENT
The scripts, Jupyter Notebooks, quick start guide, and example datasets used in this study are freely available at GitHub ( https://github.com/scipdatabase/Prediction_model ). The literature sources used for data extraction and for training the ANN model are provided in the Supporting Information. For details on various stress combinations and input data features, readers may refer to the Stress Combinations and their Interactions in Plants Database (SCIPDb) (Priya et al., 2023 ), availablOpen asset ↗scipdatabase/Prediction_modellines:392-432Dataset · public), Python package scikit‐learn v1.4.2 ( https://scikit-learn.org/stable/ ), and Google Tensorflow version 2.17.0 ( https://www.tensorflow.org/ ) were used to implement the deep learning model in this study.
Data mining
The SCIPDb FTP server was utilized to download the morphological dataset for 41 distinct stress combinations ( https://db.nipgr.ac.in/plant_complete/downloads.php ; accessed on December 2021) (Priya et al., 2023 ). The dataset integrated into SCIPDb has been obtained through literature mining performed by employing relevant and carefully designed keywords (Appendix S1 ). The major search engines (Appendix S2 ) and the inclusion of various keyword variants ensured comprehensiveOpen asset ↗lines:41-51Dataset · publicdel ). The literature sources used for data extraction and for training the ANN model are provided in the Supporting Information. For details on various stress combinations and input data features, readers may refer to the Stress Combinations and their Interactions in Plants Database (SCIPDb) (Priya et al., 2023 ), available at https://db.nipgr.ac.in/plant_complete/index_orangesunset.php .
REFERENCES
Ahuja, I.
, De Vos R. C. H., Bones A. M., and Hall R. D.. 2010. Plant molecular stress responses face climate change. Trends in Plant Science
15: 664–674.
Atkinson, N. J.
, Lilley C. J., and Urwin P. E.. 2013. Identification of genes involved in the response of Arabidopsis to simultaneous bioticOpen asset ↗lines:392-432Code / dataset availability confirmedOpenAlex · Crossref · Europe PMC · checked 5 Sept 2026
Precision greenhouse agriculture enhances plant health and crop yields by continuously monitoring key plant parameters. Stem diameter is such a parameter and is monitored to support decisions on plant care. However, traditional contact-based methods induce thigmomorphogenic effects that impact plant growth. Here, we introduce the Optical Caliper (OC), a novel contactless device for precise, non-invasive stem diameter measurement. The OC operates by projecting a collimated light beam to cast a shadow of the stem onto a high-resolution image sensor. The shadow size is a measure for the stem diameter. Controlled laboratory tests show the OC offers an accuracy comparable to that of a Digital Caliper (DC). Field trials on irregular tomato and cucumber stems demonstrate a repeatability of 0.1-0.2 mm. The OC's non-invasive design and high repeatability exceed the performance of a DC, making it particularly suited for accurately monitoring soft, variable plant structures. Bringing the advantage of avoiding thigmomophogenic effects and thus optimizing crop yield, the OC is a promising tool for high-throughput plant phenotyping and precision agriculture applications.
Why it matches plant phenotyping methods植物の茎径を非接触・高精度に測定する光学デバイスを開発し、実験室および圃場で精度・再現性を検証しており、植物表現型取得法が研究の中心です。
abstractHere, we introduce the Optical Caliper (OC), a novel contactless device for precise, non-invasive stem diameter measurement.
Reproduction assets foundThe paper's measurement data (optical caliper, digital caliper, and micrometer readings on reference cylinders and tomato/cucumber stems) is openly deposited on the SURF data repository of The Hague University of Applied Sciences. No author analysis code or trained models are explicitly deposited; other allowed URLs (DDataset · publicThe data gathered during this study is openly available via https://hhs.data.surf.nl/s/nqnFYBf42KPA75P (accessed on 10 February 2026).Open asset ↗hhs.data.surf.nlhtml-lines:282-314Code / dataset availability confirmedEurope PMC · bioRxiv · checked 5 Sept 2026
Grapevine Trunk diseases (GTDs) represent a major threat for the wine industry. Despite several break-through, their etiology remains unclear and no curative treatment is currently available. Wood anatomy and water transport contribute to the symptoms of young plant decline. This study investigates wood anatomical alterations in two Alsatian grapevine cultivars presenting different susceptibility to GTDs, focusing on wood structure over six months of vegetative growth and in response to infection. Using a validated FasGa staining protocol, wood sections from transverse, tangential, and radial directions were stained to differentiate lignified and cellulosic tissues. Microscopic analysis was performed at x4, x10, and x40 magnifications, yielding a dataset of 4771 images. To support this high-throughput quantitative analysis of microscopy images, a computational model was developed, enabling reliable and efficient assessment of anatomical traits. Pre-established woody tissues presented higher xylem vessels diameter in Gewurztraminer than Riesling, with a dorsoventral arrangement whereas the number of vessels remained the same all over the cross section. No significant anatomical changes were observed in established woody tissues, whereas newly formed xylem anatomy showed a possible rearrangement during infection, especially in Gewurztraminer cultivar. Furthermore, colorimetric analysis quantified the lignification of woody tissues in response to wounding damage compared to un-treated plants. While definitive conclusions remain limited due to the experimental timeframe and sample variability, the findings highlight the need for longer-term studies and broader cultivar evaluation. Code and microscopy images have been made publicly available, providing a scalable digital tool for future research in plant vascular systems.
Why it matches plant phenotyping methods植物組織画像から木部解剖形質と木化を定量する計算モデルを開発・検証し、大規模画像データセットと公開コードを提供しており、表現型取得手法が研究の中心である。
abstractTo support this high-throughput quantitative analysis of microscopy images, a computational model was developed, enabling reliable and efficient assessment of anatomical traits.
Reproduction assets foundThe paper's microscopy image dataset (4771 grapevine wood images) is publicly deposited on Zenodo with an explicit DOI matching an allowed URL. The authors also state their Python analysis pipeline is available at github.com/courbot/vineside, but that URL is not among the allowed URLs, so only the Zenodo image dataset,Dataset · publicThis database can benefit the research community, and is publicly available
online at https://doi.org/10.5281/zenodo.18850060 [35].Open asset ↗Zenodo · 10.5281/zenodo.18850060pdf-page:4 lines:1-56Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Reliable identification of maize leaf diseases is critical for mitigating crop losses, particularly in regions where farmers have limited access to experts. Although vision transformers (ViTs) have recently demonstrated strong performance in image recognition, their weak inductive bias and limited modeling of local texture patterns make them non-ideal for fine-grained maize leaf disease classification. To address these limitations, we propose ConvDeiT-Tiny, a lightweight hybrid ViT that improves DeiT-Ti by placing depthwise convolutions in parallel with multi-head self-attention modules in the first three transformer blocks. The local and global features captured by the convolution and attention modules are concatenated along the embedding dimension and fused using a multilayer perceptron. This results in richer token representations without significantly increasing model size. Across three datasets, ConvDeiT-Tiny (6.9 M parameters) consistently outperformed DeiT-Ti, DeiT-Ti-Distilled, and DeiT-S (21.7 M parameters) when trained from scratch. With transfer learning, ConvDeiT-Tiny achieved an accuracy of 99.15%, 99.35%, and 98.60% on the CD&S, primary, and Kaggle datasets, respectively, surpassing many previous studies with far fewer parameters. For explainability, we present gradient-weighted transformer attribution visualizations showing the disease lesions driving model predictions. These results indicate that injecting local inductive bias in early transformer blocks is beneficial for accurate maize leaf disease classification.
Why it matches plant phenotyping methodsトウモロコシ葉の病徴画像を対象に、病害分類のための新規Vision Transformerモデルを開発・比較しており、植物病害状態の画像ベース表現型推定が中心である。
abstractwe propose ConvDeiT-Tiny, a lightweight hybrid ViT that improves DeiT-Ti by placing depthwise convolutions in parallel with multi-head self-attention modules in the first three transformer blocks.
Reproduction assets foundThe authors publicly release their analysis code and dataset splits (including their field-collected primary maize leaf image dataset) via a GitHub repository, and the paper's classification experiments use the public Kaggle Corn or Maize Leaf Disease Dataset (COMLDD). Both are paper-specific, public, and actionable.Code · publicThe program code and dataset splits for the three datasets used in this study, including our primary data, can be found at https://github.com/DamarisWaema/ConvDeiT-Tiny (accessed on 18 March 2026).Open asset ↗DamarisWaema/ConvDeiT-Tinylines:121-289Dataset · publicGhose S.
Corn or Maize Leaf Disease Dataset
Available online: https://www.kaggle.com/datasets/smaranjitghose/corn-or-maize-leaf-disease-dataset (accessed on 10 July 2025)Open asset ↗lines:474-623Code / dataset availability confirmedEurope PMC · checked 15 Sept 2026
Deploying rice disease detectors in the field remains challenging because models that are accurate in the lab are often poorly calibrated and provide limited uncertainty estimates, raising the risk of costly misclassification. This paper proposes a multi-objective Big-Bang Big-Crunch (MO-BBBC) framework that jointly performs disease detection and variety classification while optimizing six deployment-oriented criteria: classification error, calibration quality, uncertainty estimation, model size, inference latency, and energy consumption. The proposed framework presents conditional temperature scaling, an adaptive scheme that mitigates over-calibration and preserves reliability. The framework is implemented in Python on a lightweight two-headed classifier and evaluated on the Paddy Doctor dataset, MO-BBBC base framework achieves 90.6% disease accuracy and 97.9% variety accuracy; improves calibration to [Formula: see text] ([Formula: see text]% better than strong post-hoc baselines); achieves micro-AUC of 0.994/0.999 and micro-AP of 0.961/0.994 (disease/variety); delivers robust OOD detection (AUROC = 0.887/0.886); and supports real-time inference at [Formula: see text] ms and [Formula: see text] ms per 64-sample batch on CPU/GPU with Monte Carlo Dropout uncertainty. The resulting Pareto set enables practitioners to trade accuracy for efficiency and reliability, narrowing the gap between prototype validation and field deployment in precision agriculture.
Why it matches plant phenotyping methods植物病害状態を画像から検出する分類・校正・不確実性推定フレームワークが研究の中心であり、植物の病害表現型を対象とした手法開発と評価に該当する。
abstractThis paper proposes a multi-objective Big-Bang Big-Crunch (MO-BBBC) framework that jointly performs disease detection and variety classification while optimizing six deployment-oriented criteria
Reproduction assets foundThe paper publicly releases its authors' analysis code (MO-BBBC framework, calibration, leakage audits, evaluation scripts) on GitHub, and a Zenodo deposit containing the paper-specific split indices, metadata, and reproducibility notebook. The underlying PaddyDoctor plant image dataset used for all phenotyping/class- Code · publicaddyDoctor images and to reproduce the results reported in the manuscript.
All code used to implement the MO–BBBC framework, multitask classifier, uncertainty-aware curricula, calibration routines, and evaluation scripts (including leakage audits, OOD evaluation, and generation of all tables and figures) is freely available at: https://github.com/manhas82/MO-BBBC-Rice.git .
Declaration of competing interest
The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
Ethics statement
This study uses only publicly available plant imagery and does not involve human participants, animalOpen asset ↗https://github.com/manhas82/MO-BBBC-Rice.gitlines:361-386Dataset · publicAll data underlying the findings in this study are available without restriction. The minimal dataset underlying the reported analyses (including the exact group-aware train/validation/test split indices, supporting metadata, and a complete reproducibility notebook) is publicly available on Zenodo at: https://doi.org/10.5281/zenodo.18471419 .
The underlying images and labels used in this work come from the public PaddyDoctor image dataset [ 18 ], which can be accessed from the official project page https://paddydoc.github.io/dataset/ and via its IEEE DataPort record https://ieee-dataport.org/documents/paddy-doctor-visual-image-dataset-automated-paddy-disease-classOpen asset ↗Zenodo · 10.5281/zenodo.18471419lines:361-386Dataset · publicvalidation/test split indices, supporting metadata, and a complete reproducibility notebook) is publicly available on Zenodo at: https://doi.org/10.5281/zenodo.18471419 .
The underlying images and labels used in this work come from the public PaddyDoctor image dataset [ 18 ], which can be accessed from the official project page https://paddydoc.github.io/dataset/ and via its IEEE DataPort record https://ieee-dataport.org/documents/paddy-doctor-visual-image-dataset-automated-paddy-disease-classification-and-benchmarking . The Zenodo record contains the files needed to reconstruct our exact experimental partitions from the original PaddyDoctor images and to reproduce the results reportedOpen asset ↗lines:361-386Dataset · publicproducibility notebook) is publicly available on Zenodo at: https://doi.org/10.5281/zenodo.18471419 .
The underlying images and labels used in this work come from the public PaddyDoctor image dataset [ 18 ], which can be accessed from the official project page https://paddydoc.github.io/dataset/ and via its IEEE DataPort record https://ieee-dataport.org/documents/paddy-doctor-visual-image-dataset-automated-paddy-disease-classification-and-benchmarking . The Zenodo record contains the files needed to reconstruct our exact experimental partitions from the original PaddyDoctor images and to reproduce the results reported in the manuscript.
All code used to implement the MO–BBBC framework, multiOpen asset ↗IEEE DataPortlines:411-413Code / dataset availability confirmedEurope PMC · checked 14 Sept 2026
Recognizing lineages is a central challenge in plant systematics, making it essential to explore multiple analytical tools. In this context, this study investigates how frond shape can assist in discriminating against lineages within the Scaly clade of Microgramma (Polypodiaceae), and tests whether the integration of multiple lines of evidence enables a more consistent recognition of lineages than exclusively macromorphological approaches. We analyzed 271 specimens representing eight species, using Elliptical Fourier Analysis (EFA) to quantify frond shape, followed by multivariate statistical tests (PCA, MANOVA, LDA). Evolutionary relationships between spectral and morphometric data were assessed through phylogenetic generalized least squares (PGLS) regressions and phylogenetic partial least squares (Phylo-PLS) analyses. Dimorphic species exhibited higher discrimination capacity (average accuracy of 80–83%). Fertile and combined fronds yielded the highest accuracy values. Morphologically similar species, such as M. reptans and M. tobagensis, showed significant overlap, whereas M. percussa achieved the best performance (average accuracy of 80%). Morphometric-spectral integration showed a strong correlation (R² = 0.72; P = 0.003), and both the combined datasets (spectra and outline) and the individual datasets of spectral and shape features revealed a high phylogenetic signal (λ = 1–0.84), indicating partial coevolution between frond shape, chemical composition, and the evolutionary history of the group. Outline morphometry combined with infrared spectroscopy within a phylogenetic framework improves lineage discrimination, although overlap zones persist, reflecting complex evolutionary processes. Our study highlights the potential of integrative systematics to elucidate species boundaries in groups with high morphological disparity, as well as the need for broad sampling and multi-evidence approaches in future systematic reviews.
Why it matches plant phenotyping methodsフロンド形状をElliptical Fourier Analysisで定量化し、赤外分光との統合を用いて系統識別性能を評価しており、植物器官形質の取得・解析手法が研究の中心です。
abstractusing Elliptical Fourier Analysis (EFA) to quantify frond shape, followed by multivariate statistical tests (PCA, MANOVA, LDA).
Reproduction assets foundThe authors state that raw data, processed data, and R analysis code for the frond outline morphometrics are publicly available on GitHub (Microgramma-Outline), and the FT-NIR spectral data repository (Microgramma-FTNIR) is referenced in the methods. Both are paper-specific, public, and actionable.Code · publicSciELO Preprints - Este documento é um preprint e sua situação atual está disponível em: https://doi.org/10.1590/SciELOPreprints.15500
573 The raw data, processed data, and R analysis code are publicly available on GitHub:
574 https://github.com/labevofern/Microgramma-Outline.git.
575
576 REFERENCES
577 Ackerly D.D. (2004) Adaptation, Niche Conservatism, and Convergence: Comparative
578 Studies of Leaf Evolution in the California Chaparral. The American Naturalist, 163, 654–
579 671.
580 Adams D.C., Collyer M.L. (2018) Multivariate Phylogenetic Comparative Methods:
581 Evaluations, Comparisons, and RecoOpen asset ↗labevofern/Microgramma-Outline · Microgramma-Outlinepdf-layout-page:25 lines:1-48Dataset · publicbiting the highest
157 perpendicular distance from the line connecting the first and last bands in the R² × ranking
158 plot (Fig. S2). Following the methods described in Mendonça et al. (2026), spectral data were
159 acquired using a PerkinElmer Frontier™ near-infrared Fourier transform spectrometer (FT-
160 NIR) available at (https://github.com/labevofern/Microgramma-FTNIR).
161 Phylogenetic comparative analyses
162 To provide a phylogenetic framework for comparative morphometric and spectral analyses,
163 we used the pruned version of the Microgramma chloroplast phylogenetic inference from
164 Mendonça et al. (2026). This tree was based on the Bayesian phylogenetic tree published by
165 AOpen asset ↗labevofern/Microgramma-FTNIR · Microgramma-FTNIRpdf-layout-page:8 lines:1-55Code / dataset availability confirmedOpenAlex · Europe PMC · checked 5 Sept 2026
Peanut (Arachis hypogaea L.), a major legume crop valued for its high oil content, displays complex genotypic-phenotypic interactions shaped by environmental influences, yet these relationships remain poorly understood. We present a high-throughput phenotyping framework that captures the geometry of peanut pods using digital microscopy or smartphone imaging integrated with manifold-learning for large-scale analysis and visualization. Using over 6500 pods collected across China, we identify a geographically distinct morphological signature and demonstrate accurate cultivar discrimination. This scalable approach establishes the foundation for a Large Geometric Model capable of predicting phenotypic traits and accelerating precision agriculture. Our pipeline offers a transformative tool for peanut breeding and sustainable crop improvement.
Why it matches plant phenotyping methodsデジタル顕微鏡・スマートフォン画像と多様体学習を統合し、ピーナッツ莢の形態を大規模に取得・解析する高スループット表現型解析フレームワークが中心である。
abstractWe present a high-throughput phenotyping framework that captures the geometry of peanut pods using digital microscopy or smartphone imaging integrated with manifold-learning for large-scale analysis and visualization.
Reproduction assets foundThe authors state that the peanut pod image dataset, extracted phenotypic trait data, and the Orange Data Mining workflow (.ows) used for analysis are publicly available in their GitHub repository.Dataset · publicThe image dataset of peanut pods analyzed in this study and the extracted phenotypic trait data are publicly available in the GitHub repository: https://github.com/pengwengkung/Complex-geometry-peanut .Open asset ↗pengwengkung/Complex-geometry-peanutlines:169-192Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Accurate delineation of crop growth stages under real-world field conditions remains a long-standing challenge in computational phenotyping, particularly for wheat whose developmental phases are characterized by subtle, continuous morphological transitions and environmental noise. In this study, we propose AMFR-Net, an Adaptive Multi-Scale Feature Refinement Network tailored for fine-grained wheat stage identification using ground-level RGB imagery. Unlike conventional architectures that struggle with ambiguous inter-stage boundaries and rigid receptive structures, AMFR-Net leverages a ResNet-101 backbone augmented by a novel Adaptive Multi-Scale Attention Fusion (AMSAF) module-comprising cross-scale interaction blocks and confidence-weighted feature aggregation-to hierarchically recalibrate spatial-semantic representations. This design enables the network to adaptively amplify phenologically salient cues while suppressing irrelevant context, ensuring robust generalization under constrained annotation and deployment conditions. Evaluated on the expert-labeled CGIAR benchmark, AMFR-Net achieves state-of-the-art performance across all major metrics (Top-1 Accuracy: 89.10%; Macro-F1: 89.10%; AUC: 97.88%) and demonstrates superior discriminability in phenologically adjacent stages compared to lightweight and deep CNN baselines. Ablation studies validate the synergistic effect of multi-level attention and scale-aware refinement. The proposed framework offers a scalable, interpretable, and field-deployable solution for in-situ phenology monitoring, and sets a foundation for future integration of multimodal sensing, weak supervision, and cross-seasonal adaptation.
Why it matches plant phenotyping methods小麦の生育ステージを地上RGB画像から推定する新規深層学習手法を開発し、ベンチマーク、比較、アブレーションで検証しており、植物フェノタイピング手法が研究の中心です。
abstractwe propose AMFR-Net, an Adaptive Multi-Scale Feature Refinement Network tailored for fine-grained wheat stage identification using ground-level RGB imagery.
Reproduction assets foundThe paper's phenotyping analysis is built on the public CGIAR Wheat Growth Stage Challenge dataset (ground-level RGB wheat images with growth-stage labels), which the authors explicitly state is publicly available on Zindi with a direct link. No author analysis code, trained model checkpoints, or supplementary code/deeDataset · publicPublicly available datasets were analyzed in this study. This data can be found here: Dataset name: CGIAR Wheat Growth Stage Challenge Primary repository: Zindi (official competition page) Direct link: https://zindi.africa/competitions/cgiar-wheat-growth-stage-challengeAccession/Open asset ↗Zindilines:808-824Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Doubled haploid (DH) technology can fast-track crop breeding. Haploid induction yields haploids with only one set of genomes, which are usually sterile. Haploid fertility (HF) is the ability of haploid plants to set seed, and it is a critical bottleneck in DH pipelines. Genetic mechanisms to restore HF hold immense potential in DH crop breeding, yet its phenotyping remains manual, destructive, and inconsistent. While recent advances in imaging and machine learning have improved throughput for general plant traits, no curated image dataset exists for Arabidopsis thaliana that explicitly represents HF. Here, we present AutoSiQ, a dataset and baseline deep learning pipeline for automated HF quantification. AutoSiQ includes high-resolution scanned inflorescences annotated with a seven-class ontology encompassing green siliques, green fertile siliques, mature siliques, fertile siliques, cracked fertile siliques, cracked siliques, and flowers. This multi-class annotation scheme preserves biologically meaningful information beyond binary fertile/non-fertile distinctions, enabling reliable fertility estimation and future phenotyping applications. We release baseline object detection models (YOLOv5), trained using the AutoSiQ dataset, and evaluate their performance across confidence thresholds. Model predictions strongly correlate with manual counts, achieving R² up to 0.94 for total silique number estimation. We further demonstrate AutoSiQ's utility for automated haploid fertility rate (HFR) estimation and genotype discrimination between two contrasting genotypes (WT and bmf2 mutant). A longitudinal analysis identifies ~60 days after sowing (DAS) as the optimal harvest time for maximizing mature silique counts by balancing between the number of immature buds and silique shattering. By releasing both the dataset and baseline code, AutoSiQ provides a reproducible and extensible foundation for high-throughput fertility phenotyping in haploid Arabidopsis .
Why it matches plant phenotyping methodsハプロイド稔性を画像から定量するデータセットと深層学習パイプラインを開発・評価しており、植物フェノタイピング手法が中心である。
abstractHere, we present AutoSiQ, a dataset and baseline deep learning pipeline for automated HF quantification.
Reproduction assets foundThe paper's AutoSiQ dataset (annotated scanned Arabidopsis inflorescence images with seven-class silique ontology and manual fertility counts) is publicly deposited on Zenodo per the data availability statement. The YOLOv5 GitHub repository is a generic third-party library, not an authors' code asset.Dataset · publicThe datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: https://zenodo.org/records/17905566 .Open asset ↗zenodo · 17905566lines:367-402Code / dataset availability confirmedOpenAlex · Crossref · checked 13 Sept 2026
Abstract Background: Next-generation models of fire behavior and smoke production rely on gridded, 3D inputs of wildland fuel complexes. We used a hierarchically scaled sampling design to characterize canopy and surface fuels that are common to prescribed burning programs in the southeastern and western US. Sampling included airborne laser scanning, terrestrial laser scanning, close-range photogrammetry, and destructive field sampling. The objective of this study was to use a combination of airborne laser scanning (ALS), terrestrial laser scanning (TLS), structure-from-motion photogrammetry (SfM), and field observations to create co-located 3D datasets of live and dead understory fuels for use in wildland fuel mapping and prescribed burn decision support Results: Using our integrated, co-located methods, we produced hierarchically-scaled datasets detailing the structure and composition of canopy and surface fuels across 9 southeastern pine sites, 5 western pine sites, and 4 western grassland sites. These are now publicly available at within the Wildland Fire Science Initiative data repository (https://doi.org/10.60594/W4859C). In this paper, we detail methods and the repository structure. Conclusions: The study was designed to evaluate and advance methods for 3D fuel characterization and to provide consistently scaled and labelled datasets for model training and evaluation. More specifically, machine learning models can be used to parse 3D point clouds collected from ALS, TLS, and structure-from-motion photogrammetry into fuel objects and metrics. Calibration with field plots will allow our hierarchically-scaled datasets to be used as the foundation for synthetic fuelbed mapping, starting with fine-scale objects such as individual shrubs or downed wood and scaling to vegetation patches and operational burn units.
Why it matches plant phenotyping methodsALS、TLS、SfMと現地観測を統合して植物群落の3D構造・燃料特性を取得し、手法の評価・改良と公開データセット構築を主目的としているため、植物形質計測法が中心である。
abstractThe objective of this study was to use a combination of airborne laser scanning (ALS), terrestrial laser scanning (TLS), structure-from-motion photogrammetry (SfM), and field observations to create co-located 3D datasets of live and dead understory fuels for use in wildland fuel mapping and prescribed burn decision support
Reproduction assets foundThe paper's hierarchically scaled ALS/TLS/SfM point clouds, field fuel measurements, and analysis scripts are explicitly stated to be open source and archived in the Wildland Fire Science Initiative data repository (DOI 10.60594/W4859C), a paper-specific public asset directly reproducing this study's phenotyping/fuel-3Dataset · publicThe datasets and analysis scripts for this study are open source and are being archived with the Wildland Fire Science Initiative data repository (doi.org/10.60594/W4859C), including project metadata, methods documentation and data libraries (Prichard and Rowell 2025).Open asset ↗Wildland Fire Science Initiative data repository · 10.60594/W4859Clines:384-403Code / dataset availability confirmedEurope PMC · OpenAlex · checked 14 Sept 2026
Sun-induced fluorescence (SIF) has emerged as a promising tool for tracking photosynthetic dynamics, yet its application in monitoring biotic stress remains underexplored in field conditions. In this study, we investigated the effects of Cercospora leaf spot (CLS), a destructive foliar disease of sugar beet (Beta vulgaris L.), for which traditional monitoring methods often fail to capture subtle disease effects or distinguish between structural and physiological stress responses. CLS infection was induced through artificial inoculation and manually scored. Canopy-level reflectance indices were acquired along with red and far-red passive SIF signals and active PSII efficiency traits using FloX and LIFT sensors mounted on an automated high-throughput phenotyping platform. The results demonstrate that SIF effectively detects CLS in sugar beet, with responses comparable with structural and disease- specific indices. Despite visible symptoms, PSII efficiency (Fq'/Fm') remained stable across treatments, indicating limited impairment of leaf photosynthetic efficiency at early stages. However, the canopy-level electron transport rate varied significantly and showed a strong relationship with red and far-red SIF, suggesting that CLS primarily affects canopy light absorption and utilization. After structural normalization, SIF yield remained largely unchanged, confirming that observed SIF reductions were mainly driven by canopy structural alterations. Overall the study demonstrates the effectiveness of SIF for large-scale disease monitoring and integration into high-throughput phenotyping, while also revealing structural and physiological factors influencing the SIF signal under disease stress.
Why it matches plant phenotyping methodsSIFおよびPSIIセンサーを搭載したハイスループット表現型解析プラットフォームで、サトウダイコンの病害状態と構造・生理応答を評価する手法の実質的な適用・検証が中心である。
abstractCanopy-level reflectance indices were acquired along with red and far-red passive SIF signals and active PSII efficiency traits using FloX and LIFT sensors mounted on an automated high-throughput phenotyping platform.
Reproduction assets foundThe paper's phenotyping dataset (SIF, reflectance indices, LIFT PSII traits, disease scores from the CLS sugar beet field trial) is deposited in the open access Jülich DATA repository under DOI 10.26165/JUELICH-DATA/FOQOFI. No separate author analysis code repository with explicit availability language is stated; R/lmeDataset · publicThe dataset has been deposited in the open access Jülich DATA reposi ease using UAV-supported image data and deep learning. Sugar Industry
tory: https://doi.org/10.26165/JUELICH-DATA/FOQOFI. 147, 79–86.
Ispizua Yamati FR, Bömer J, Noack N, Linkugel T, Paulus S, Mahlein
A-K. 2025. Configuration of a multisensor platform for advanced plant phe
References notyping and disease detection: case study on cercospora leaf spot in sugar
Ač A, Malenovský Z, Olejníč ková J, Gallé A, Rascher U, Mohammed beet. Smart AgricultOpen asset ↗Jülich DATA · 10.26165/JUELICH-DATA/FOQOFIpdf-layout-page:14 lines:52-72Code / dataset availability confirmedEurope PMC · bioRxiv · checked 15 Sept 2026
1 Summary Zinc (Zn) deficiency limits rice productivity and poses a risk to human health, particularly in populations reliant on rice-based diets. Although rice germplasm exhibits wide variation in Zn-deficiency tolerance, the underlying physiological mechanisms remain poorly resolved. Evidence across the literature for Zn-deficiency–induced secretion of 2′-deoxymugineic acid (DMA) is inconsistent. This study clarifies the role of DMA secretion as a Zn-deficiency stress response. We developed and validated a sensitive LC–ESI–Q–TOF–MS method for selective detection of DMA in rice root exudates. Five rice genotypes with contrasting Zn-deficiency tolerance were grown hydroponically and DMA secretion measured. Zn-deficiency increased DMA exudation across all genotypes, with sensitive genotypes also showing higher secretion compared with control, supporting DMA’s role as a general response to Zn stress rather than being restricted to efficient genotypes. Fold-change responses exceeded previous studies, likely due to more severe stress exposure. Our results confirm that DMA secretion is induced under Zn-deficiency in rice as part of the micronutrient stress response. However, the lack of increased Zn uptake indicates that additional tolerance mechanisms are involved. These findings reconcile inconsistencies in the literature and position DMA secretion as an important, but not exclusive, component of Zn-deficiency adaptation in rice.
Why it matches plant phenotyping methodsイネ根滲出液中のDMAを選択的に検出するLC–MS法を開発・検証し、亜鉛欠乏応答という植物生理状態を測定しているため、化学分析が単なる付随測定ではなく中心的な方法貢献である。
abstractWe developed and validated a sensitive LC–ESI–Q–TOF–MS method for selective detection of DMA in rice root exudates.
Reproduction assets foundThe paper's Data availability statement points to a public Zenodo deposit containing the datasets generated and analysed in this study (DMA exudation and Zn uptake measurements in rice).Dataset · publicthe experiments, developed the
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methods and analysed the results. The experimental data were collected by C.R. assisted by
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G.L.M., C.T. and D.J.W. Data analysis and writing of paper by all authors.
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The data sets generated and/or analysed during the current study are available on Zenodo,
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CC-BY 4.0 International license
perpetuity. It is made available under a
preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in
The copyright holder for this
this version posted March 18, 2026.
;
https://doi.org/10.64898/2026.03.16.71158Open asset ↗Zenodo · 18184803pdf-raw-page:21 lines:1-47Code / dataset availability confirmedOpenAlex · Europe PMC · checked 14 Sept 2026
A detailed characterization of root system architecture (RSA) and growth dynamics is key to develop stress-resilient maize varieties. We evaluated sixty-five Mediterranean maize inbred lines using automated high-throughput phenotyping under controlled conditions. Shoot and root traits were extracted from imaging data during early vegetative development, revealing significant genotype-specific variation in root biomass-related traits (total root length, total root volume), root architecture (root angle, root system depth, root system width), and relative growth rates. Notably, lines previously classified as heat and drought stress-resilient or stress-sensitive based on above-ground development did not group according to particular root traits, indicating that multiple strategies may underlie tolerance to combined stress. We identified lines with contrasting RSA, including deeper roots, shallower roots, or overall larger root systems, that offer new opportunities for resilience breeding. Our results underscore root traits as critical yet underexploited targets for improving stress resilience and resource efficiency.
Why it matches plant phenotyping methods自動化ハイスループット画像解析により根系形態・成長形質を抽出する表現型取得が研究の主要手段であり、根系構造の実質的な応用解析に該当する。
abstractWe evaluated sixty-five Mediterranean maize inbred lines using automated high-throughput phenotyping under controlled conditions.
Reproduction assets found保存済みの本文根拠を更新済みルールで再検証し、公開資産1件を確認しました。Supplement · publicSupplementary Materials
The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/plants15060935/s1 , Figure S1: Repeatability of image-derived shoot (a) and root traits (b) of the tested 65 maize inbred lines over time.Open asset ↗lines:68-215Code / dataset availability confirmedEurope PMC · checked 15 Sept 2026
Abstract Disease detection and categorization in rice leaf play a crucial role in mitigating crop damage and supporting sustainable agriculture. Traditional approaches, which often rely on manual inspection, are limited by labor intensity, variability and error susceptibility. This paper introduces a Hybrid Convolutional Vision Transformer (CVT) model with Spatial Attention (SA) to enhance the detection accuracy and classification reliability in rice leaves. The proposed CVT framework integrates a Convolutional Neural Network (CNN), which is the backbone for initial feature extraction with a Vision Transformer (ViT) in advanced feature representation. Convolutional Neural Network captures the essential textures and shapes, while the Vision Transformer applies attention across image patches, effectively learning the complex spatial dependencies necessary for identifying disease-specific characteristics within diverse field environments. Further, SA module refines the model by assigning greater weight to diseased regions, reducing interference from non-leafbackground areas. Experimental results on rice leafdataset demonstrate that the hybrid CVT with SA model achieves over 98.12% feature extraction accuracy, 98.56% classification accuracy in dataset 1 and 98.26% feature extraction accuracy, 98.67% classification accuracy in dataset 2 across multiple rice leaf categories, outperforming baseline CNN and ViT models. Spatial Attention heat maps highlight the most important locations during decision-making process, making the model more interpretable. This hybrid CVT model offers a scalable solution for rice leaf disease detection and categorization, with potential applications in precise agriculture systems, including drone-based or mobile implementations for field monitoring. The presented model exhibits maximum performancethan the othertraditional methods.
Why it matches plant phenotyping methodsイネ葉の病害状態を画像から推定する深層学習モデルの開発と比較評価が論文の中心であり、植物病害フェノタイピング手法に該当する。
abstractThis paper introduces a Hybrid Convolutional Vision Transformer (CVT) model with Spatial Attention (SA) to enhance the detection accuracy and classification reliability in rice leaves.
Reproduction assets foundThe paper uses two public Kaggle rice leaf disease image datasets as its phenotyping inputs, with explicit URLs. The authors' code and generated data are only available on request, so no code/model asset qualifies.Dataset · publicconducted interviews with Department
of Agriculture—particularly those from the Regional Crop Protection Center. Images of several
rice plant diseases are collected using the means available, which included digital cameras and
smart phones. After gathering, all the imagesare pre-processed and included in the dataset.
Dataset 1: https://www.kaggle.com/datasets/nashehannafii/datasetleafblast
Dataset 2: https://www.kaggle.com/datasets/vbookshelf/rice-leaf-diseases
4.2 Data preprocessingOpen asset ↗kaggle · nashehannafii/datasetleafblastpdf-raw-page:13 lines:1-17Dataset · publicm the Regional Crop Protection Center. Images of several
rice plant diseases are collected using the means available, which included digital cameras and
smart phones. After gathering, all the imagesare pre-processed and included in the dataset.
Dataset 1: https://www.kaggle.com/datasets/nashehannafii/datasetleafblast
Dataset 2: https://www.kaggle.com/datasets/vbookshelf/rice-leaf-diseases
4.2 Data preprocessingOpen asset ↗kaggle · vbookshelf/rice-leaf-diseasespdf-raw-page:13 lines:1-17Code / dataset availability confirmedCrossref · checked 14 Sept 2026
Background: A major challenge to agricultural productivity in the tea industry is disease. that affects the quantity and quality of tea leaves produced. The extensive development of computational methods for treating diseases has been widely used due to fast and accurate detection. Methods: The proposed method uses sequential Convolutional Neural Network (CNN) computations with many hidden layers to classify diseased and healthy tea leaves into multiple groups. By enhancing feature identification, this structure increases the criteria for accurate disease detection. The data having 5 diseased and one healthy category is obtained from the Kaggle database. After preprocessing the data, it is split into 80:20 ratios for training and testing steps. CNN is constructed using the Keras Sequential API in Jupiter notebook using Anaconda environment. Result: The total accuracy of the ML neural network training for classification was 98.52%. After 50 epochs of training, the model performed well, achieving high accuracy on training and validation datasets. The examination of the confusion matrix showed that several tea leaf diseases may be identified with high accuracy and few misclassifications. In general, the model demonstrated remarkable precision in differentiating between unhealthy and undamaged tea leaves.
Why it matches plant phenotyping methods茶葉画像から病害状態をCNNで分類する手法が研究の中心であり、植物の病徴・健全性という状態を直接推定しているため、植物フェノタイピング手法として含める。
abstractThe proposed method uses sequential Convolutional Neural Network (CNN) computations with many hidden layers to classify diseased and healthy tea leaves into multiple groups.
Reproduction assets foundThe paper's tea leaf disease image dataset is publicly available on Kaggle, with an explicit dataset link in the references. No author code or trained model is publicly deposited; other data are available only upon request.Dataset · publical tealeaf disease recognition
using a convolutional neural network model. Symmetry.
11(3): 343. https://doi.org/10.3390/sym11030343.Cho, O.H., Na, I.S. and Koh, J.G. (2024). Exploring advanced machine
learning techniques for swift legume disease detection.
Legume Research. 47(7): 1221-1227. doi: 10.18805/LRF-789.
Dataset Link: https://www.kaggle.com/datasets/shashwatwork/identifying-disease-in-tea-leafs?select=tea+sickness+
dataset. (Accessed on 06/05/2024).
Datta, S. and Gupta, N. (2023). A novel approach for the detection
of tea leaf disease using deep neural network. Procedia
Computer Science. 218: 2273-2286. https://doi.org/10.1016/j.procs.2023.01.203.Deka, N. and Goswami, K. (2020). EcOpen asset ↗Kaggle · shashwatwork/identifying-disease-in-tea-leafspdf-raw-page:8 lines:1-75Code / dataset availability confirmedEurope PMC · bioRxiv · Crossref · checked 15 Sept 2026
Quantitative studies of plant growth and environmental responses increasingly rely on time-series imaging, yet automated segmentation remains challenging due to continuous growth, large non-rigid morphological change, and frequent self-occlusion. Traditional image-processing pipelines and task-specific deep learning models often require extensive annotated datasets and retraining, limiting portability across species, developmental stages, and imaging conditions. Here we present SAP (Segment Any Plant), a plant-focused framework that leverages the pretrained Segment Anything Model 2 (SAM2) to enable few-shot, training-free segmentation of plant time-series imagery. SAP integrates interactive prompting, automated temporal mask propagation, and centerline extraction within a web-based interface, allowing users to move from raw images to quantitative descriptors of organ shape and dynamics without programming expertise. Across multiple systems, including Arabidopsis thaliana rosette development, root growth, sunflower gravitropism, and confocal root microscopy, SAP achieves high segmentation accuracy (mean IoU 0.89–0.93) and sub-pixel centerline precision from single-frame prompting. By reducing the need for task-specific retraining, SAP provides a transferable framework for reproducible time-series phenotyping across diverse experimental contexts.
Why it matches plant phenotyping methods植物の時系列画像から器官形状・動態を抽出するセグメンテーション手法とWeb基盤を開発し、複数系で精度検証しているため、植物フェノタイピング手法が中心である。
abstractHere we present SAP (Segment Any Plant), a plant-focused framework that leverages the pretrained Segment Anything Model 2 (SAM2) to enable few-shot, training-free segmentation of plant time-series imagery.
Reproduction assets foundThe paper's authors publicly release both the SAP analysis code (GitHub repository) and the datasets generated/analyzed in the study (Zenodo), including raw images, ground-truth and SAP-generated segmentation masks, centerline validation data, and supplementary videos. Both are paper-specific, public, and directly cit.Dataset · publicCode Availability. The code is available at
https://github.com/merozlab/plant-segmentation-app.Data Availability. The datasets generated and an-
alyzed during this study are available on Zenodo at
https://doi.org/10.5281/zenodo.18732705. This includes
raw images and segmentation masks for the sunflower
gravitropism and Arabidopsis root growth experiments,
SAP-generated masks for the Lee et al. (9) and Strauss
et al. (13) datasets, centerline validation data, and supple-
mentary videos.
Funding. Y.M. acknowledges support from the Israel Sci-
ence Foundation ResOpen asset ↗zenodo · 10.5281/zenodo.18732705pdf-raw-page:9 lines:1-74Code / dataset availability confirmedCrossref · checked 14 Sept 2026
Published13 Mar 2026DMPedia Lecture Notes in Computer Science & EngineeringCited by 0 · OpenAlex ↗
This paper presents a practical pipeline for image-based plant disease detection that operates without pre-trained weights or internet access. A compact Efficient Net-like convolutional network is trained from random initialisation on the Plant Village dataset (∼ 41,000 snapshots, 15 classes) at 224 × 224 resolution. Adam, Intensive Augmentation, Reduce LROn Plateau, Early Stopping, and the sampling of the optimal checkpoint to stabilise convergence and avoid overfitting are used to optimise the geometry. Despite early validation oscillations typical of de novo training, the model converges reliably and attains 98.4%–98.9% accuracy on held-out data, with a highly diagonal confusion matrix and uniformly strong per-class precision/recall. These results show that carefully tuned schedules and lightweight regularization can substitute for transfer learning when bandwidth or policy constraints prevent downloading external backbones, enabling classroom, extension, and field deployments. The paper details dataset preparation, architecture and training choices, learning curve behavior, and common failure modes, and concludes with limitations and a roadmap for higher-resolution, field-domain generalization and efficient on-device inference.
Why it matches plant phenotyping methods植物病害状態を画像から推定する深層学習パイプラインが研究の中心であり、モデル、データ準備、学習、検証性能が具体的に記述されているため。
abstractThis paper presents a practical pipeline for image-based plant disease detection
Reproduction assets foundThe paper's phenotyping input is the public PlantVillage Kaggle dataset (15-class pepper/potato/tomato subset), explicitly cited with the allowed Kaggle URL. No author code or model checkpoints are released.Dataset · public[3] PlantVillage, “PlantVillage Dataset,” Kaggle, 2018. [Online]. Available:
https://www.kaggle.com/datasets/emmarex/plantdiseaseOpen asset ↗Kaggle · emmarex/plantdiseasepdf-page:10 lines:1-61Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Field / plotMultimodalWhole plant / canopy / plot / fieldClassificationGrowth / development / phenology
Abstract Phenological monitoring of Actinidia chinensis is critical for optimising operational costs and yield prediction. However, current manual assessment methods are time-consuming, making them impractical for large-scale precision agriculture applications. Most existing phenological datasets focus exclusively on image data without spatial validation. The Multi-Modal Actinidia chinensis Phenology Dataset is composed of (i) 1 665 annotated images of phenological stages from bud to fruit set and (ii) georeferenced videos with systematic manual ground truth of spatial stage distributions. The dataset employs an adapted 17-class BBCH system that consolidates visually similar stages, excludes problematic categories, and introduces generic structural classes to address practical annotation difficulties. Additionally, the data is organised hierarchically across various plant structures, genders, and phenological stages. The annotated images offer versatility for a range of applications, including training data for computer vision models to detect phenological stages. Furthermore, the georeferenced videos facilitate the validation of automated counting algorithms. This combined approach enables plant-level detection accuracy and provides an illustrative methodology for spatial validation that users can extend to additional orchards, promoting the development and benchmarking of automated phenological monitoring systems for precision agriculture applications in kiwifruit production.
Why it matches plant phenotyping methodsキウイフルーツの生育段階を対象とした注釈画像・地理参照動画のデータセットで、植物フェノロジー自動検出の訓練、検証、ベンチマークを目的とする方法論的成果である。
titleA Multi-Modal Dataset for Automated Phenological Stage Mapping in Actinidia chinensis
Reproduction assets foundThe paper is a Data Note describing the Multi-Modal Actinidia chinensis Phenology Dataset, which is explicitly stated to be publicly available on Zenodo with a DOI matching an allowed URL. The dataset contains the paper's own phenotyping assets: 1,665 annotated images with bounding-box phenological labels, georeferenedDataset · publicThe Multi-Modal Actinidia chinensis Phenology Dataset described in this Data Descriptor is publicly available
at Zenodo: https://doi.org/10.5281/zenodo.17371025. This dataset comprises two components: (1) 1 665
JPEG images (1 024 × 1 024 pixels) with corresponding Pascal VOC XML annotation files containing bounding
box coordinates and phenological class labels, and (2) 24 MP4 video files (3 840 × 2 160 pixels) with corresponding
GPX coordinate files and Excel validation files containing manual ground truth counts.Open asset ↗Zenodo · 10.5281/zenodo.17371025pdf-page:13 lines:1-62Code / dataset availability confirmedEurope PMC · checked 15 Sept 2026
Rice production is integral to the agricultural sector of India; over 65% of the populations are dependent on rice as their major staple. The cultivation of rice sustains this important agricultural sector; yet, there are many challenges encountered by rice producers, one of which is several types of disease that negatively impact yield and quality. Due to the fact that rice leaf smut, brown spot and bacterial leaf blights are among the most important types of diseases that can significantly reduce the yield and quality of rice, it is important to be diligent when identifying these diseases using accurate and speedy methods on an annual basis for successful and sustainable production of rice crops. As technology advances there continue to be emerging technologies such as Deep Learning (DL) as applied in agriculture to identify diseases and therefore reshape the agricultural paradigm so as to address agricultural disease challenges more readily. This research proposes a previously undemonstrated approach for identifying Rice Leaf Disease using EfficientNetV2; a Diffusion Bounded Attention method for disease detection. The quality of the input imagery has been greatly increased using a Preceding Noise Reduction (PNR) using the Guided Filopic Diffusion (GFD) technique, retaining important characteristics of Rice Leaves (Leaf Texture) which are critical for disease classification within agricultural imaging. To evaluate the performance of our model we utilized the Dice Similarity Coefficient (DSC). This coefficient measures how much the predicted image areas representing disease overlap with the actual affected areas of the image. Therefore, DSC is a reliable way to evaluate model segmentation capability. The Rice Leaf Diseases Dataset we used to identify and classify Rice Leaf Diseases was very comprehensive. Our model achieved an accuracy rate of 98.92% and also attained the best recall, precision and F1 score.
Why it matches plant phenotyping methodsイネ葉の病害症状を画像から検出・分類・セグメンテーションする手法が研究の中心であり、植物の病害状態を直接推定している。
abstractThis research proposes a previously undemonstrated approach for identifying Rice Leaf Disease using EfficientNetV2; a Diffusion Bounded Attention method for disease detection.
Reproduction assets foundThe paper's sole data asset is the public Kaggle Rice Leaf Diseases Dataset used for all experiments; no author code or models are deposited.Dataset · publicl analysis and data collection. N.K has done the initial drafting and statistical analysis. P.R. did the investigation. All the authors of the article have read and approved the final article.
Funding
Open access funding provided by Vellore Institute of Technology.
Data availability
The rice leaf disease data are assessed using https://www.kaggle.com/datasets/vbookshelf/rice-leaf-diseases
Declarations
Competing interests
The authors declare no competing interests.
References
1.
Upadhyay N Gupta N
Detecting fungi-affected multi-crop disease on heterogeneous region dataset using modified ResNeXt approach
Environ. Monit. Assess. 2024 196 7 610
10.1007/s10661-024-12790-0
38862723
Upadhyay, N. & Open asset ↗Kaggle · vbookshelf/rice-leaf-diseaseslines:553-627Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Accurate classification of maize yield potential is essential for food security and effective agricultural planning, particularly in regions characterized by environmental variability and socio-economic constraints. This study explores the binary classification of maize kernel weight into low ( n = 160). A Hybrid Cascade - Deep Belief Network (HCA-DBN) is proposed, utilizing the feature extraction capabilities of Deep Belief Networks (DBN) coupled with Hill Climbing Algorithm (HCA) as a lightweight hyperparameter tuning strategy. The model's performance was benchmarked against standard classifiers including Logistic Regression, Random Forest, XGBoost, Decision Tree, Multi-Layer Perceptron (MLP), and Support Vector Classifier (SVC). The proposed HCA-DBN achieved a peak classification accuracy of 94%, demonstrating its potential to outperform conventional baselines even under small sample conditions. Rigorous validation, including bootstrapping and stratified 10-fold cross-validation, confirmed the statistical stability of the results. While these findings serve as a proof-of-concept given the dataset constraints, this study contributes a methodological benchmark for field-based maize yield classification and provides a scalable framework for future validation on larger, multi-season datasets.
Why it matches plant phenotyping methodsトウモロコシの収量ポテンシャル（kernel weight）を分類する計算手法を提案し、複数モデルとのベンチマークおよび交差検証で技術的に評価しているため、植物形質推定法が中心である。
abstractA Hybrid Cascade - Deep Belief Network (HCA-DBN) is proposed, utilizing the feature extraction capabilities of Deep Belief Networks (DBN) coupled with Hill Climbing Algorithm (HCA) as a lightweight hyperparameter tuning strategy.
Reproduction assets foundThe paper's maize field phenotyping dataset (plant/ear traits, canopy temperature, chlorophyll from 160 tagged plants at VIT Sevur farm) is explicitly stated as publicly available via a Data in Brief DOI deposit, and the same dataset is cited in the references as a Mendeley Data deposit authored by the paper's authors.Dataset · publicPublicly available datasets were analysed in this study. This data can be found here: https://doi.org/10.1016/j.dib.2024.110367.Open asset ↗html-lines:851-875Dataset · publicRadhakrishnan S., Sandhya P., Venkatramana B., Pradeep Kumar T.
Analyzing various maize varieties grown organically: VIT Vellore’s phenotypic, yield, and canopy data. (2024) 1. Available online at: https://data.mendeley.com/datasets/6py9v57sf2/1Open asset ↗6py9v57sf2/1html-lines:900-924Code / dataset availability confirmedCrossref · checked 5 Sept 2026
Abstract Background Apoplastic pH is a central regulator of plant growth, development, and environmental adaptation, influencing cell expansion, nutrient uptake, and extracellular signaling. Many studies have successfully used HPTS to monitor relative changes in apoplastic pH in plants. At the same time, research increasingly targets pH-dependent biochemical and biophysical processes. Many enzymatic activities, ion binding events, and receptor–ligand interactions depend on defined proton concentrations. Accordingly, the development of reliable approaches to measure absolute pH in living tissues is gaining importance. Methods A calibration-based workflow was developed to enable quantitative assessment of absolute apoplastic pH using ratiometric HPTS imaging. The approach integrates a simplified two-point normalization strategy with an in-vitro derived sigmoidal calibration model, thereby minimizing the need for extensive in-vivo calibration curves. Confocal imaging was performed using HPTS excited at two wavelengths followed by ratiometric image processing. Data analysis is supported by a custom Fiji plugin, Ratio2pH, which converts ratiometric images into pixel-resolved maps of absolute pH. Results In vitro characterization revealed a robust, non-linear relationship between normalized HPTS ratios and pH, enabling accurate pH estimation within the physiologically relevant range of pH 5.0–7.0. When applied in-vivo to Arabidopsis thaliana roots, the workflow yielded extracellular pH estimates consistent with the pH of the incubation medium and detected reproducible pH shifts in response to pharmacological treatments. Conclusions This workflow enables reproducible, spatially resolved measurement of absolute apoplastic pH in living plant tissues. By combining a simplified calibration strategy with accessible image analysis tools, it facilitates quantitative extracellular pH measurements and their integration into biochemical and biophysical analyses.
Why it matches plant phenotyping methods生きた植物組織の絶対アポプラストpHを画像から定量する校正ワークフローを開発・検証し、Fijiプラグインも提供しているため、植物状態の取得法が中心である。
abstractA calibration-based workflow was developed to enable quantitative assessment of absolute apoplastic pH using ratiometric HPTS imaging.
Reproduction assets foundThe paper deposits its authors' analysis code and data publicly: the Ratio2pH Fiji plugin (Zenodo 10.5281/zenodo.15599805), a Python script for sigmoidal calibration curve fitting (Zenodo 10.5281/zenodo.17303477), and source data files and raw confocal images (Freidata 10.60493/t29wb-7my86). The Zenodo 15658668 ratiom�Code · publicThe Python Script for generating a user-defined sigmoidal calibration curve is available at Zenodo: https://doi.org/10.5281/zenodo.17303477Open asset ↗Zenodo · 10.5281/zenodo.17303477lines:175-235Dataset · publicSource data files and raw images are uploaded at Freidata, the data server of the University of Freiburg, available under https://doi.org/10.60493/t29wb-7my86Open asset ↗Freidata · 10.60493/t29wb-7my86lines:175-235Code / dataset availability confirmedOpenAlex · Europe PMC · checked 5 Sept 2026
BACKGROUND: Root biomass serves as a critical indicator of plant eco-physiological status and crop productivity, yet its non-destructive monitoring remains challenging because of its underground location. The use of transparent nutrient film technique (NFT) systems enables direct observation of entire root systems, rendering image-based phenotyping feasible. In this study, we investigated and compared the performance of RGB and hyperspectral imaging for predicting root dry weight in hydroponically grown spinach (Spinacia oleracea L.). RESULTS: Using 430 root segments divided from 60 plants, three models were developed: (1) an area-based regression based on root coverage, (2) a convolutional neural network (CNN) using RGB images, and (3) a partial least squares regression (PLSR) model using hyperspectral data (450-950 nm). The area-based regression exhibited limited accuracy (R² = 0.446) because of saturation at high root coverage. The CNN model improved predictive performance (R² = 0.739) but tended to overestimate sparse roots as a result of resolution constraints. The PLSR model achieved the highest accuracy (R² = 0.822, RMSE = 0.019 g/segment), with significantly lower error than RGB-based approaches (P < 0.01). Variable importance in projection analysis indicated that PLSR effectively exploited spectral signatures at 450 nm (background contrast) and 750 nm (tissue scattering), thereby maintaining stable accuracy across the full biomass range. When validated using 104 independent plants, the PLSR model achieved high predictive accuracy. Furthermore, as a proof of concept, this model successfully visualized the spatiotemporal dynamics of root biomass accumulation over 50 days, with only a 7.70% relative error at harvest. CONCLUSIONS: To our knowledge, this study is among the first to demonstrate the non-destructive monitoring of biomass distribution within entire root systems under production conditions. Hyperspectral imaging combined with PLSR outperforms RGB-based approaches by capturing spectral signatures that reflect internal tissue properties of roots, thereby overcoming limitations caused by morphological occlusion. This approach provides a robust tool for precision agriculture and high-throughput phenotyping, enabling continuous assessment of root growth through simple modifications to the existing hydroponic systems.
Why it matches plant phenotyping methodsRGB・ハイパースペクトル画像と機械学習／PLSRを用いて根乾物重を非破壊推定・検証する方法研究であり、植物表現型の取得と定量化が中心である。
abstractThe use of transparent nutrient film technique (NFT) systems enables direct observation of entire root systems, rendering image-based phenotyping feasible.
Reproduction assets foundThe paper's Data availability statement deposits the paper-specific phenotyping assets (raw hyperspectral images, RGB images, and root dry weight measurements) in a Zenodo record. The provided URL includes a token and 'preview=1', suggesting the record may not yet be fully open, but it is the authors' stated public URLDataset · publicThe datasets generated and analyzed during the model construction of the current study are available in the Zenodo repository: [https://zenodo.org/records/18072801?preview=1&token=eyJhbGciOiJIUzUxMiJ9.eyJpZCI6ImFiYTkzMzY2LTIzZjktNDlkMy1iZTBjLTk3M2E5YTUyOTFmZCIsImRhdGEiOnt9LCJyYW5kb20iOiIzNGE1ZjMxNDZhYjhiYjlhZWRiOWFjNzBkNzcwY2I3NyJ9.uR4HfosoSaVWhtSblMOS1v9bJFA5MvHwXvcW9uoNbcTWRDU4RNxZpVHjXTC3ulBM1JTlBbeHp_4T5EcILawxdg].The dataset includes:
- Raw hyperspectral images and data- RGB images
- Root dry weight measurementsOpen asset ↗Zenodo · 18072801lines:176-248Code / dataset availability confirmedEurope PMC · checked 15 Sept 2026
Service crops are grown to provide ecosystem services in viticulture, but their adoption remains limited due to their competition with grapevine for soil resources. To identify trade-offs between services, the effect of service crops management strategies on grapevine performances still need further research. This dataset presents data from two experiments conducted to study the effect of service crops management on soil resources and grapevine performances. The inter-row vegetation was sampled in two Mediterranean vineyards using quadrats for biomass estimation. In addition, an unmanned aerial vehicle (UAV) was regularly flown over the vineyards for a period spanning more than four years in total over the two vineyards. The dataset presented here includes both raw data acquired during fieldwork and processed data derived from this raw inputs. The raw data consists of image series captured by two UAVs during each flight campaign, including RGB and multispectral imagery. Images were acquired between 2021-06-10 and 2022-07-29 for the first vineyard, and between 2023-06-08 and 2025-03-12 for the second vineyard. Based on these raw data, the processed data comprises spatial vectors, raster layers, and dense point clouds generated from UAV images using a Structure from Motion (SfM) photogrammetry workflow, at a 5 cm spatial resolution. The raster layers and dense point clouds provide specific information on vineyard characteristics for each UAV flight date, including elevation, vegetation indices, visible and near-infrared reflectance, and canopy height. In addition, the processed data include measurements of vegetation dry biomass, as well as separate measurements of dry biomass and leaf area measured for selected service crops species. This dataset can be reused for the calibration and/or evaluation of classification algorithms aimed at discriminating vines from the inter-row vegetation, or as part of a larger dataset to explore relationships between remotely-sensed vegetation indices and field-measured vegetation biomass or surface.
Why it matches plant phenotyping methodsUAV画像とSfM処理により、植生指数・樹冠高・バイオマス等の植物形質を取得した再利用可能なデータセットで、分類アルゴリズムの校正・評価用途も明示されており、植物フェノタイピング手法・データ基盤が中心です。
abstractThe dataset presented here includes both raw data acquired during fieldwork and processed data derived from this raw inputs.
Reproduction assets foundThe paper is a Data in Brief article describing a public dataset on Research Data Gouv (doi: 10.57745/MXM55R) containing UAV RGB/multispectral imagery, SfM-derived rasters and point clouds, and field-measured vegetation biomass/leaf-area data from two Mediterranean vineyards — directly the paper's phenotyping inputs. ADataset · publicollected in vineyards located in southern France near Montpellier (43°32.5243′N, 3°50.8240′E). Data are stored on Research Data Gouv, a remote storage solution curated by the French Department of Research.
Data accessibility
Repository name: Research Data Gouv
Data identification number: doi: 10.57745/MXM55R
Direct URL to data: https://doi.org/10.57745/MXM55R
Related research article
None
1.
Value of the Data
•
The fine scale imaging of vineyards (i.e., 5 cm resolution) allows for classification of the vegetation in the vineyard inter-rows, and subsequent exploration of its respective dynamics.
•Open asset ↗Research Data Gouv · 10.57745/MXM55Rlines:1-47Code / dataset availability confirmedEurope PMC · checked 15 Sept 2026
Abstract Accurate tracking and measurement of pollen dispersal in the atmosphere are essential for assessing cross-pollination risks, particularly in the case of genetically engineered (GE) crops. We conducted a series of unique release-recapture field studies with GE switchgrass in Oliver Springs, Tennessee, USA. Two hundred transgenic switchgrass plants ({\it Panicum virgatum L.} `Performer') were planted at the center of a clear-cut field, with one block of 100 plants expressing orange fluorescent protein (OFP) under a maize ubiquitin promoter (PvUBI1) and another block of 100 plants expressing OFP driven by a maize pollen-specific promoter (Zm13). Pollen was sampled from the atmosphere using fixed (ground-based) and mobile (drone-based) sampling devices at different distances from the source field, with Lagrangian Stochastic dispersal simulations run for sampling periods using high-resolution wind measurements. The pollen emission rate was estimated by combining simulated and measured pollen concentrations, and strong diurnal trends were observed. Diurnal emission rate trends were positively correlated with wind speed, temperature, and vapor pressure deficit, while negatively correlated with relative humidity. In low-wind meandering conditions, incorporating changing wind direction into the dispersal modeling improved pollen emission rate estimation and model-measurement comparisons. This study assesses the effectiveness of high and low volume pollen samplers in relation to source strength up to 1 km from the source, enhancing understanding of pollen measurement techniques. Additionally, it is a proof-of-concept for drone-based pollen sampling and GMO pollen tracking using fluorescence measurements. Results from our experiments have significant implications for cross-pollination risk assessment, prediction, and management of airborne allergens.
Why it matches plant phenotyping methods固定・ドローン型サンプラーと蛍光測定、分散モデルを用いて植物由来花粉の放出量を推定し、サンプリング技術を評価することが中心であるため。
abstractPollen was sampled from the atmosphere using fixed (ground-based) and mobile (drone-based) sampling devices
Reproduction assets foundThe authors state that all sampling data, modeling code, and simulation results from this switchgrass pollen dispersal study are publicly available in a Virginia Tech figshare repository. The GitHub 3D-printing files are cited prior work (Powers et al. 2018), not a paper-specific asset.Dataset · public737 Statements and Declarations
738 Data and code availability
739 All sampling data, modeling code, and simulation results are made available in the
740 Virginia Tech Data repository:
741 https://figshare.com/s/54a308163b60865d55bf.
742 Competing interests
743 The authors have no competing interests to declare.
744 Funding
745 This work is supported in part by the Biotechnology Risk Assessment Program, project
746 award no. 2019-33522-29989, from the U.S. Department of Agriculture’s National
747 Institute of Food and Agriculture.
748 References
749 AdamovOpen asset ↗figsharepdf-layout-page:28 lines:1-46Code / dataset availability confirmedCrossref · checked 5 Sept 2026
Abstract Photosynthetic organisms have evolved multiple non-photochemical quenching (NPQ) processes, providing photoprotection by safely dissipating excess excitation energy. These processes involve various molecular players functioning on overlapping timescales from seconds to days, making it challenging to isolate and quantify their individual kinetics. In this study, we perform whole-leaf chlorophyll fluorescence lifetime and xanthophyll concentration measurements on wild-type and various newly characterized NPQ mutants of Nicotiana benthamiana , a vascular land plant. Based on these measurements, we construct a fluorescence lifetime-based quantitative kinetic model that disentangles individual photoprotection components and, when integrated additively, accurately predicts wild-type and mutant NPQ behaviors under various light-dark regimes. Additionally, the model quantifies the per-molecule quenching effectiveness of various xanthophylls and the contributions of six quenching components (qE V , qE A, qE Z, qE L, qZ, and qI) across different genotypes. It also suggests improved overall quenching efficiency at specific VDE:ZEP:PsbS overexpression stoichiometries, aligning with previous studies and supporting translational efforts to optimize photoprotection and enhance crop yields under dynamic light environments.
Why it matches plant phenotyping methods葉の蛍光寿命測定を基盤に、NPQ成分を分離・定量するモデルを構築しており、植物の光防護状態を取得・抽出する方法が研究の中心です。
abstractBased on these measurements, we construct a fluorescence lifetime-based quantitative kinetic model that disentangles individual photoprotection components and, when integrated additively, accurately predicts wild-type and mutant NPQ behaviors under various light-dark regimes.
Reproduction assets foundThe paper's fluorescence lifetime/pigment phenotyping data and the NPQ model code are both publicly deposited on Zenodo (DOI 10.5281/zenodo.16755870), per explicit Data availability and Code availability statements.Dataset · publicThe data supporting the findings of this study are available within the article and at https://doi.org/10.5281/zenodo.16755870 .Open asset ↗Zenodo · 10.5281/zenodo.16755870lines:171-237Code · publicThe codes for NPQ models used in this study are available at https://doi.org/10.5281/zenodo.16755870 .Open asset ↗Zenodo · 10.5281/zenodo.16755870lines:171-237Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
To achieve agricultural automation, deep learning applications for early and accurate disease detection in tomato plants have been extensively developed. However, there is a fundamental trade-off between computational efficiency and diagnostic accuracy in resource-constrained agricultural edge environments. This paper proposes an evaluation framework for seven architectures that represent standard, efficient, and hybrid CNN structures to assess their implementation potential. Through evaluations of explainability, computational efficiency, and diagnostic performance, seven lightweight architectures (ShuffleNetV2, MobileNetV3-Small, SqueezeNet, MobilePlantViT, DenseNet121, ResNet50, and VGG16) are thoroughly examined. Three significant findings are derived from experiments conducted on a subset of tomato diseases in the PlantVillage dataset. First, the MobilePlantViT architecture accurately strikes the ideal balance between efficiency and performance. Second, in order to quantitatively assess the explainability of XAI models (Grad-CAM, SHAP, and LIME) and identify the best option for edge devices, we propose the perturbation stability score (PSS) metric. Third, we test CPU inference measurements to better reflect the actual scenario and find that the hybrid design effectively leverages parallel computing. According to these findings, MobilePlantViT is the ideal architecture for applications that require operation on edge devices with limited resources and achieve high diagnosis accuracy (above 99.5%).
Why it matches plant phenotyping methodsトマト病害という植物状態を画像から分類する深層学習手法について、複数モデルの精度・計算効率・説明可能性を体系的に比較評価しており、病害フェノタイピング手法の技術評価が中心である。
abstractThis paper proposes an evaluation framework for seven architectures that represent standard, efficient, and hybrid CNN structures to assess their implementation potential.
Reproduction assets foundThe authors publicly deposited their paper-specific tomato phenotype image subsets (derived from PlantVillage and expert-curated PlantDoc) on Kaggle via explicit Data Availability links. No author analysis code or trained model checkpoints are shared; ONNX Runtime is a generic library, not a paper-specific asset.Dataset · publicThe datasets are available at the following links: https://www.kaggle.com/datasets/cthngon/tomato-plantvillage-datasets, https://www.kaggle.com/datasets/cthngon/tomato-only.Open asset ↗Kaggle · cthngon/tomato-plantvillage-datasetshtml-lines:710-734Dataset · publicWe enhanced the quality of the PlantDoc dataset by collaborating with experts to identify and crop regions containing disease-specific symptoms, while eliminating irrelevant image content. For long-term preservation and ease of access, we have stored copies of the datasets in the published repository. The datasets are available at the following links: https://www.kaggle.com/datasets/cthngon/tomato-plantvillage-datasets, https://www.kaggle.com/datasets/cthngon/tomato-only.Open asset ↗Kaggle · cthngon/tomato-onlyhtml-lines:710-734Code / dataset availability confirmedCrossref · checked 15 Sept 2026
Although the chasmophytic vegetation of Sicily has been examined previously, it remains insufficiently explored due to the formidable challenges associated with accessing vertical cliff habitats. This study employed drone-based surveys combined with Braun-Blanquet methodology to investigate cliff vegetation in the Peloritani and Madonie Mountains. High-resolution aerial imagery enabled species identification and cover estimation on inaccessible rock faces. Twenty-three new relevés were combined with 33 literature records for multivariate analysis. Cluster analysis and DCA revealed floristic differentiation between Peloritani and Madonie phytocoenoses, contrasting with communities from Apennines that we used as an outgroup. We describe Athamanto siculae-Saxifragetum australis for the calcareous cliffs of Rocca Salvatesta (Peloritani), characterized by Athamanta sicula , Hypochaeris laevigata , and Saxifraga callosa subsp. australis . Additionally, we propose to change the name Asperuletum gussonei to Cynanchicetum gussonei for the high-elevation vegetation of the Madonie dominated by Cynanchica gussonei . Drone methodology proved effective for documenting cliff vegetation, offering a safe and replicable approach for advancing phytosociological knowledge in extreme habitats. This research contributes to the syntaxonomic revision of Mediterranean chasmophytic vegetation within the alliance Saxifragion australis .
Why it matches plant phenotyping methodsドローン画像を用いてアクセス困難な崖面の植物種同定と被覆率推定を行う手法が、植生調査・分類の中心的手段として明示されているため。
abstractHigh-resolution aerial imagery enabled species identification and cover estimation on inaccessible rock faces.
Reproduction assets foundThe paper's drone-based phytosociological relevé dataset (the plant cover/trait measurements underlying the classification and DCA analysis) is published as Supplementary table S1 under an open license. Supplementary figure S1 is only an ordination diagram, and no author analysis code or raw drone imagery is stated to Dataset · publiclable under the Open
Database License (http://opendatacommons.org/licenses/odbl/1.0). The Open Database License (ODbL) is a license
agreement intended to allow users to freely share, modify, and
use this Dataset while maintaining this same freedom for oth-
ers, provided that the original source and author(s) are credited.
Link: https://doi.org/10.3897/ved.182223.suppl1
Supplementary material 2
Supplementary figure S1
Authors: Gianmarco Tavilla, Pietro Minissale, Salvatore Cambria
Data type: docx
Explanation note: The supplementary file includes the DCA or-
dination diagram of species scores.
Copyright notice: This dataset is made available under the Open
Database License (http://opendatacommOpen asset ↗10.3897/ved.182223.suppl1pdf-raw-page:13 lines:1-46Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Accurate flower-load assessment is critical for informed thinning strategies in orchard management. UAV-based deep learning automated counting offers efficiency advantages, yet precise counting is heavily dependent on abundant annotated data, which is scarce and costly to obtain in agricultural settings. While semi-supervised learning alleviates dependency on manual annotation, its application to UAV-based orchard imagery faces challenges: complex backgrounds and small target sizes, which undermine pseudo-label reliability. To address these challenges, this study proposes a two-stage framework to achieve separate counting of apple flowers at different phenological stages. First, a color-SAM flower extractor (CSAM-FE) is proposed to preprocess images using a strategy combining color thresholding with the Segment Anything Model (SAM), suppressing background noise and extracting high-quality flower clusters, thereby providing purified inputs for the subsequent counting network. Second, an uncertainty-guided semi-supervised flower counting network (USCount-Net) is proposed for accurate stage-specific flower counting with limited labeled data. The USCount-Net incorporates two key components: an adaptive pseudo-label filtering (PLF) mechanism based on frequent forward uncertainty estimation (FFUE) is designed to dynamically suppress noisy gradient backpropagation, mitigating error propagation from unreliable pseudo-labels; and a noise-sensitive adaptive gated fusion (AGF) module is introduced to fuse cross-scale features without redundancy, addressing significant scale variations across phenological stages and observation angles. Comparative experiments on a self-built apple flower counting dataset demonstrate that USCount-Net achieves lower MAE and RMSE than state-of-the-art methods at 10%, 30%, and 50% labeling ratios. The results demonstrate that the proposed methodology serves as methodological support for rapid and precise apple flower counting in low-annotation agricultural scenarios.
Why it matches plant phenotyping methodsリンゴ花の画像抽出・計数手法と半教師あり解析ネットワークを開発し、データセット上で比較評価しているため、植物表現型取得が中心である。
abstractthis study proposes a two-stage framework to achieve separate counting of apple flowers at different phenological stages.
Reproduction assets foundThe paper's Data availability statement explicitly provides public access to the authors' USCount-Net source code on GitHub and the self-built apple flower counting dataset (UAV images, annotations, flower cluster images) on Google Drive.Code · publicThe source code is publicly available at https://github.com/haohuihui5019/USCount-Net . And the source dataset can be accessed at https://drive.google.com/drive/folders/1KP8H0qIuct56hWre5GV6ZJnzwOpen asset ↗USCount-Netlines:681-780Dataset · publicThe source code is publicly available at https://github.com/haohuihui5019/USCount-Net . And the source dataset can be accessed at https://drive.google.com/drive/folders/1KP8H0qIuct56hWre5GV6ZJnzwOpen asset ↗lines:681-780Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
In agricultural automation, precise cotton segmentation is a key step for tasks such as intelligent harvesting and yield estimation. However, in complex field environments, factors such as background interference and irregular target shapes severely affect segmentation accuracy. Existing deep learning methods offer certain advantages but still generally suffer from limitations including insufficient accuracy, over-segmentation, and misidentification. To address these challenges, this study proposes a novel dual-branch cotton segmentation network, Cotton-aware Mamba-enhanced UNet (CMNet), which optimizes the ParaTransCNN architecture by incorporating the 2D Selective Scan (SS2D) module to replace the original Transformer branch, effectively balancing the extraction of local details and global semantic information while reducing computational burden. To enhance the model's perception of irregularly shaped cotton, a Deformable Convolutional Networks v1 (DCNv1) module is integrated into the Vision Mamba (VMamba) branch, further improving the delineation of target boundaries. Additionally, an Atrous Spatial Pyramid Pooling (ASPP) module is introduced at the end of the Convolutional Neural Network (CNN) branch to strengthen multi-scale feature representation. To optimize the fusion of channel and spatial information, the Spatial and Channel Squeeze-and-Excitation (scSE) attention mechanism replaces the original module, enhancing feature modeling capability. Experimental results on an in-field cotton image dataset demonstrate that CMNet outperforms existing mainstream methods, achieving Dice, mIoU, and Accuracy of 91.06%, 84.18%, and 98.10%, respectively, while reducing parameter count and computational complexity, thus exhibiting excellent performance. Furthermore, generalization experiments on multiple other plant datasets also achieved outstanding results, validating the model's adaptability and potential for broader applications in multi-crop segmentation tasks, providing valuable insights for smart agriculture segmentation research. The source code and dataset of this work are publicly available at https://github.com/halidanmu/CMNet.git.
Why it matches plant phenotyping methods綿花画像から植物領域を抽出する新規セグメンテーション手法を中心に開発・検証しており、植物表現型の画像取得・抽出ワークフローに該当する。
abstractthis study proposes a novel dual-branch cotton segmentation network, Cotton-aware Mamba-enhanced UNet (CMNet)
Reproduction assets foundThe authors explicitly state that the source code and dataset for CMNet are publicly available on GitHub. The paper also uses several public Roboflow plant image datasets in its generalization experiments, cited with public URLs in the references.Code · publicThe source code and dataset of this work are publicly available at https://github.com/halidanmu/CMNet.git.Open asset ↗halidanmu/CMNethtml-lines:106-109Dataset · publicELTE (2023). Assignment 2 dataset. Available online at: https://universe.roboflow.com/elte-msgqy/assignment_2-mjhau (Accessed November 5, 2025).Open asset ↗html-lines:754-834Dataset · publicLaola (2024). Defect banana dataset. Available online at: https://universe.roboflow.com/laola/defect-banana-qf4f6 (Accessed November 5, 2025).Open asset ↗html-lines:754-834Dataset · publicLuffy24312 (2023). Cnn dataset. Available online at: https://universe.roboflow.com/luffy24312/cnn-myqtl.Open asset ↗html-lines:835-919Dataset · publicVyuha T. (2025). Rose dataset. Available online at: https://universe.roboflow.com/tech-vyuha/rose-kfpuf (Accessed November 4, 2025).Open asset ↗html-lines:835-919Code / dataset availability confirmedEurope PMC · checked 14 Sept 2026
Reliable identification of maize leaf diseases is critical for mitigating crop losses, particularly in regions where farmers have limited access to experts. Although vision transformers (ViTs) have recently demonstrated strong performance in image recognition, their weak inductive bias and limited modelling of local texture patterns make them non-ideal for fine-grained maize leaf disease classification. To address these limitations, we propose ConvDeiT-Tiny, a lightweight hybrid ViT that improves DeiT-Ti by placing depthwise convolutions in parallel with multi-head self-attention modules in the first three transformer blocks. The local and global features captured by the convolution and attention modules are concatenated along the embedding dimension and fused using a multilayer perceptron. This results in richer token representations without significantly increasing model size. Across three datasets, ConvDeiT-Tiny (6.9M parameters) consistently outperformed DeiT-Ti, DeiT-Ti-Distilled, and DeiT-S (21.7M parameters) when trained from scratch. With transfer learning, ConvDeiT-Tiny achieved an accuracy of 99.15%, 99.35%, and 98.60% on the CD&S, primary, and Kaggle datasets, respectively, surpassing many previous studies with far fewer parameters. For explainability, we present gradient-weighted transformer attribution visualizations showing the disease lesions driving model predictions. These results indicate that injecting local inductive bias in early transformer blocks is beneficial for accurate maize leaf disease classification.
Why it matches plant phenotyping methodsトウモロコシ葉の病害状態を画像から分類する手法を新規に開発し、複数データセットで性能比較・検証しており、病害フェノタイピング手法が中心である。
abstractwe propose ConvDeiT-Tiny, a lightweight hybrid ViT that improves DeiT-Ti by placing depthwise convolutions in parallel with multi-head self-attention modules
Reproduction assets foundThe paper's Data Availability Statement points to a public GitHub repository containing the authors' program code and dataset splits (including their field-collected primary dataset). The paper also evaluates on the public Kaggle Corn or Maize Leaf Disease Dataset, a public plant-image dataset directly used for the论文'sCode · publicData Availability Statement: The program code and dataset splits for the three datasets used in this study,
including our primary data, can be found at https://github.com/DamarisWaema/ConvDeiT-Tiny.Open asset ↗DamarisWaema/ConvDeiT-Tinypdf-page:18 lines:1-60Dataset · public43. Ghose, S. Corn or Maize Leaf Disease Dataset. Available online:
https://www.kaggle.com/datasets/smaranjitghose/corn-or-maize-leaf-disease-dataset (Accessed on 10 July
2025).Open asset ↗pdf-page:21 lines:1-59