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:1-78Plant phenotyping relevance match · UnverifiedOpenAlex · checked 15 Sept 2026
Published10 Sept 2026ISPRS Journal of Photogrammetry and Remote SensingCited by 0 · OpenAlex ↗
Accurate and dynamic monitoring of wheat phenotypes is essential for breeding decision-making and crop management. However, RGB image-based phenotyping still suffers from expensive pixel-level annotation, unstable organ-level segmentation across growth stages, and limited multi-trait extraction under complex field conditions. To address these issues, a high-throughput phenotyping framework (WheatScoper) was proposed, enabling organ-level segmentation and plot-level multi-trait extraction. To reduce annotation cost, a structure-aware geometry-assisted annotation (SAGA) algorithm was developed, yielding an approximately 7.6-fold improvement in annotation efficiency over fully manual annotation. To enable efficient organ-level segmentation, a lightweight semantic segmentation network (WheatScopeNet) was developed by integrating parallel hybrid spatial modeling with cross-scale feature fusion. On the held-out test set from the same site and growing season, WheatScopeNet achieved an mIoU of 0.869 and an mDice of 0.930. Leveraging the segmentation results, an automated system was established to extract 41 multi-view image-derived traits (I-traits) across four core phenotypic dimensions. The extracted I-traits supported the estimation of eight manually measured agronomic traits, with R 2 values ranging from 0.477 to 0.697. Notably, the correlations between stay-green-related-traits and yield varied distinctly with viewing-position. Only upper side-view indicators remained significantly correlated with yield, with Side-up final GPAR showing the strongest association, whereas top-view GPAR-derived indicators showed weak associations. Finally, a web-based platform integrating cascaded inference, segmentation visualization, and automatic I-trait extraction was developed. The platform provides an end-to-end solution for field wheat phenotyping and supports breeding decision-making and crop management.
Why it matches plant phenotyping methodsRGB画像から小器官を分割し、多数の植物形質を自動抽出・推定する手法とプラットフォームが研究の中心であるため、植物フェノタイピング手法として明確に採用。
abstracta high-throughput phenotyping framework (WheatScoper) was proposed, enabling organ-level segmentation and plot-level multi-trait extraction.
Abstract Purpose Agrivoltaic vineyards show strong spatio-temporal variability in canopy shading, but field methods to quantify panel-induced shading at canopy scale remain limited. Shading is a key factor because it affects plant physiological and morphological traits, with potential consequences for yield and production quality. This study developed a near-surface time-lapse RGB imaging approach to derive temporally explicit shading metrics in an agrivoltaic vineyard of Vitis vinifera cv. Falanghina in Southern Italy. Methods Two representative vine positions beneath the photovoltaic structure were monitored: Agrivoltaic Shade (AVS), with greater exposure to panel-induced shading, and Agrivoltaic Light (AVL), with lower exposure. Image-based canopy shading percentage was calculated through a dedicated processing workflow and integrated with radiometric and physiological measurements, including continuous photosynthetically active radiation (PAR), canopy-level spectral photon flux measurements, photosynthetic photon flux density (PPFD), band-specific photon flux densities, red:far-red ratio (R:FR), stomatal conductance (gₛ), and leaf temperature. PAR measurements beneath the panels were compared with a full-sun control area. Results AVS showed significantly higher shading than AVL (76.14% vs 39.45%, p Conclusion The proposed workflow offers a low-cost, non-destructive tool to quantify shading dynamics and support site-specific assessment of crop microenvironments in agrivoltaic systems. The approach provides crop-relevant information for precision monitoring and management of spatially heterogeneous light conditions across different crop species. Impact The data provided in this manuscript enable the quantification of in-season photovoltaic-induced canopy shading dynamics in an agrivoltaic vineyard using proximal RGB time-lapse imaging and crop-level radiometric measurements. These metrics reflect the spatial and temporal variability of light availability within the vineyard and support site-specific assessment of crop microenvironments and precision management of agrivoltaic systems.
Why it matches plant phenotyping methodsブドウ樹冠の遮光状態をRGBタイムラプス画像から定量化する手法を開発し、専用処理ワークフローと実測値で評価しており、植物フェノタイピング手法が中心である。
abstractThis study developed a near-surface time-lapse RGB imaging approach to derive temporally explicit shading metrics in an agrivoltaic vineyard of Vitis vinifera cv. Falanghina in Southern Italy.
Abstract Accurate estimation of maize leaf nitrogen content is important for improving nitrogen-use efficiency and supporting precision crop management. However, leaf-level hyperspectral modeling is challenged by high spectral redundancy and heterogeneous spectral responses among local leaf regions. This study proposes a Hyperspectral–Region Aggregation Network (HSRAN) for maize leaf nitrogen content estimation from region-level hyperspectral spectra. HSRAN consists of a Spectral Adaptive Recalibration Encoder (SARE) and a Context-Aware Gated Aggregation Module (CAGM). SARE performs band-wise residual recalibration and extracts regional spectral representations, whereas CAGM models contextual dependencies among regional features and performs gated attention-based aggregation for leaf-level prediction. Field experiments were conducted in 2024 and 2025 at the jointing, silking, and maturity stages. HSRAN was evaluated against PLSR, RF, XGBoost, SVR, 1D-CNN, MLP, and Transformer1D models. Across the stage-specific and pooled datasets, HSRAN achieved the highest R² and the lowest RMSE while maintaining competitive MAE values. On the pooled full-growth-period dataset, HSRAN achieved an R² of 0.84, an RMSE of 3.63 g kg⁻¹, and an MAE of 2.59 g kg⁻¹. At the jointing, silking, and maturity stages, the corresponding R² values were 0.56, 0.76, and 0.72, respectively. Ablation experiments indicated that integrating SARE and CAGM improved R² from 0.80 to 0.84. To interpret regional contributions, the learned attention weights were mapped back to the original leaf coordinates recorded during regional sampling. Regions near leaf veins, tips, and margins often received relatively higher attention weights, suggesting that their local spectra provided informative cues for model prediction. These findings indicate that spectral–regional joint modeling can improve leaf-level hyperspectral estimation of maize nitrogen content. HSRAN provides a practical framework for non-destructive nitrogen assessment in maize.
Why it matches plant phenotyping methodsトウモロコシ葉の窒素含量という植物形質を非破壊推定するためのハイパースペクトル深層学習手法を開発し、複数手法との比較・アブレーション検証を行っており、フェノタイピング手法が中心である。
abstractThis study proposes a Hyperspectral–Region Aggregation Network (HSRAN) for maize leaf nitrogen content estimation from region-level hyperspectral spectra.
Abstract Background and Aims Drought reduces wheat yields, yet field-scale quantification of root water uptake (RWU) remains challenging because below-ground processes are difficult to monitor. This study developed a non-invasive hydrogeophysical framework integrating Electrical Resistivity Tomography (ERT), TDR-based soil monitoring, and depth-aware Random Forest calibration to quantify depth-resolved RWU and evaluate genotype-specific water-use strategies under terminal drought. Methods Time-lapse ERT (44 surveys, ≥ 3 week⁻ 1 ) was combined with TDR sensor measurements of soil water content (n = 278 paired ρ–θ observations) to convert resistivity measurements into depth-resolved RWU estimates across 0.1–1.0 m depth. Five petrophysical models were evaluated using date-grouped fivefold cross-validation, with the depth-aware Random Forest performing best. Three wheat genotypes with contrasting root architectures were monitored under terminal drought (142 mm available water). ERT-derived RWU were analysed alongside stomatal conductance, chlorophyll fluorescence, and grain yield. Results ERT resolved RWU strategies among genotypes. WM-203 exhibited aggressive, coordinated multi-layer water extraction across the soil profile (r = 0.80–0.98), whereas WM-140 showed a delayed uptake strategy characterized by early deep-layer dominance followed by mid- and deep-profile engagement, and IPLR-760 displayed inconsistent uptake with mid-profile hydraulic decoupling. Genotypic RWU rankings were consistent with stomatal conductance and grain yield, spanning from 7.0 t ha⁻ 1 in WM-203 to 1.5 t ha⁻ 1 in IPLR-760 despite comparable total water extraction. Conclusion ERT-based quantification of RWU provides a robust, non-invasive approach for resolving genotype-specific water-use strategies under field conditions. The framework enables characterization of water-use coordination patterns and offers a tool for phenotyping drought-resilient wheat genotypes.
Why it matches plant phenotyping methodsERT・TDR・Random Forestを統合し、圃場コムギの根系水吸収を定量化する方法を開発・検証し、乾燥耐性遺伝子型の表現型評価に用いているため、フェノタイピング手法が中心である。
abstractThis study developed a non-invasive hydrogeophysical framework integrating Electrical Resistivity Tomography (ERT), TDR-based soil monitoring, and depth-aware Random Forest calibration to quantify depth-resolved RWU and evaluate genotype-specific water-use strategies under terminal drought.
Reproduction assets foundThe paper's Data availability statement explicitly states that the code and supporting data for this ERT-based root water uptake study are publicly available on the authors' GitHub repository, which is listed in allowed_urls. This qualifies as a paper-specific public code/data asset for the phenotyping analysis.Code · publicsity of Jerusalem. This research was supported by the Chief
Scientist of the Israeli Ministry of Agriculture and Food Secu-
rity (grant no. 12–01-0056) and the Israeli Council for Higher
Education (Project: Future Crops for Carbon Farming).
Data availability The code and supporting data for this study
are publicly available at:
https://github.com/emmaiyke/ERT_RWU_Wheat_Project
Additional datasets are available from the corresponding
author upon reasonable request.
Declarations
Competing interests 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.
Open Access This article isOpen asset ↗ERT_RWU_Wheat_Project · emmaiyke/ERT_RWU_Wheat_Projectpdf-raw-page:22 lines:1-95Plant phenotyping relevance match · UnverifiedEurope PMC · checked 15 Sept 2026
Field / plotFlowerClassificationObject detectionGrowth / development / phenology
Abstract Dioecious crops face significant pollination challenges due to the asynchrony in flowering between male and female plants. This asynchrony varies spatially across orchards, requiring targeted interventions in zones where synchrony is lacking. Assisted pollination addresses this deficiency, albeit at a substantial operational cost that could be optimised through spatial phenological mapping. Manual assessment proves economically infeasible at commercial scales, while existing computer vision systems are unable to classify phenological stages and integrate geospatial information. This study presents the Mobile Phenological Mapping (MPM) Framework, which integrates GNSS-synchronised smartphone video with automated phenological detection to generate plant-level phenological distribution maps validated in commercial kiwifruit (Actinidia chinensis) orchards. This modular framework comprises (i) training and validation data acquisition, (ii) model optimisation, (iii) operational pipeline, and (iv) performance evaluation. MPM employs hierarchical deep learning across three stages: structure detection, gender classification, and phenological stage classification. Video frames are georeferenced through timestamp matching with GNSS metadata, enabling spatial phenological mapping. Operational validation across four commercial orchard zones demonstrated mean absolute percentage errors of 17.2% for structure detection and 20.1% for gender classification. The framework reduces monitoring time from 113 to 1.6 hours per hectare, decreasing labour costs from €2 060 (113 hours × 18.20 € per hour) to €29 (1.6 hours × 18.20 € per hour) per hectare based on the Portuguese hourly labour cost for minimum wage workers. When integrated with routine orchard operations, video acquisition incurs negligible additional cost. MPM provides growers with precision phenological maps for targeted pollination interventions. While validated in a kiwifruit orchard, the modular architecture can be adapted to other crops by replacing the training data.
Why it matches plant phenotyping methodsスマートフォン動画とGNSSを用いて植物体レベルの性別・生育段階を自動検出し、フェノロジー分布を作成する手法と、その性能評価・商業園での検証が研究の中心である。
abstractThis study presents the Mobile Phenological Mapping (MPM) Framework, which integrates GNSS-synchronised smartphone video with automated phenological detection to generate plant-level phenological distribution maps validated in commercial kiwifruit (Actinidia chinensis) orchards.
Accurate litchi counting from whole-tree images is essential for yield estimation, orchard management, and plant phenotyping, but remains challenging in real orchards because fruits occur in dense, heavily occluded clusters and vary markedly in scale, illumination, and appearance across ripening stages, particularly when green fruits resemble surrounding foliage. Existing methods have shown promise, but their robustness in complex orchard environments remains limited. To address these challenges, we propose FG-LCNet, a two-stage foreground-guided litchi counting framework. In the first stage, an enhanced fruit-cluster detector improves the localization of small and ambiguous clusters under complex canopy backgrounds. In the second stage, the detected foreground regions are fed into a density-regression network with hybrid attention, while a consistency-based training strategy is introduced to improve robustness to appearance and illumination variations. To support this study, a large-scale litchi counting dataset was established, consisting of 1,126 whole-tree images collected from five orchards and spanning three ripening stages, with approximately 120,000 fruit-level dot annotations and more than 20,000 cluster-level bounding boxes. FG-LCNet achieved the best overall counting performance, with an MAE of 7.44 and an RMSE of 11.01. It showed clear advantages in high-density fruit-cluster scenarios and cross-orchard validation, while maintaining competitive results across orchard-region and maturity-stage subsets. The framework further retained inference efficiency suitable for practical deployment. These results indicate that FG-LCNet provides an effective solution for robust litchi counting and offers potential for other clustered fruit-counting tasks.
Why it matches plant phenotyping methods果実数という植物器官形質を whole-tree 画像から推定する二段階画像解析手法を開発し、データセット構築と交差果樹園検証まで行っており、表現型取得・抽出法が中心である。
abstractwe propose FG-LCNet, a two-stage foreground-guided litchi counting framework.
Reproduction assets foundThe paper's implementation code is explicitly stated as publicly available at the authors' GitHub repository (FG-LCNet). The litchi counting dataset (1,126 whole-tree images with ~120,000 dot annotations and 20,000+ bounding boxes) is not yet fully public: a ~100-image annotated subset is promised upon acceptance, and,Code · publicdustry Technology Research System (CARS-32-21), Hainan Modern Agricul-
655
tural Industry Technology System (HNARS-08-G02).
656
Conflicts of Interest
657
The authors declare that there is no conflict of interest regarding the publication of this article.
658
Data Availability
659
The implementation code is publicly available at https://github.com/johnhamtom/FG-LCNet .
660
Upon acceptance, a representative subset of approximately 100 annotated litchi images will be
661
released to support reproducibility and preliminary benchmarking. The full dataset is being further
662
organized for future release. Before full release, the complete dataset can be obtained from the
663
corresponding authorOpen asset ↗johnhamtom/FG-LCNetpdf-raw-page:28 lines:1-81Plant phenotyping relevance match · UnverifiedbioRxiv · checked 15 Sept 2026
Water scarcity and increasingly irregular rainfall threaten avocado production in Mediterranean regions, yet the long term physiological responses of mature trees to sustained deficit irrigation remain poorly understood. We conducted a two-year field study integrating continuous monitoring of the soil plant atmosphere continuum, drone-based multispectral imaging, canopy structural analysis, and fruit phenotyping in a mature avocado orchard subjected to three irrigation regimes. The two study years differed markedly in rainfall, providing a unique opportunity to evaluate how environmental conditions modulate tree responses to water limitation. Trees under severe deficit irrigation showed depletion of water in deeper soil layers and a flattened physiological profile, with near-zero diel variation in leaf thickness and trunk water potential, indicating minimal transpiration and decoupling of tree water status from environmental demand. Drone telemetry via NDVI detected stress during fruit growth and maturation, but not during flowering or the new summer leaf flush, revealing greater drought sensitivity at later maturation stages. Although canopy area did not differ among irrigation treatments, canopy surface roughness increased significantly under deficit irrigation, thereby identifying a novel structural indicator of drought stress. Despite large physiological differences among treatments, fruit number remained stable, while fruit weight decreased significantly under severe deficit irrigation, particularly in the wetter year, suggesting that annual rainfall modulates the trade-off between fruit retention and fruit growth. This study provides the first continuous, multi-scale characterization of avocado performance under sustained deficit irrigation in Mediterranean conditions. By integrating plant-based sensors, remote sensing, and artificial intelligence, we reveal previously undescribed stress dynamics and identify new indicators for precision irrigation management in fruit crops.
Why it matches plant phenotyping methods継続的な植物センサー、ドローン画像、樹冠構造解析、果実表現型計測を統合し、NDVIや樹冠表面粗さなどのストレス指標を抽出する方法が研究の主要部分であるため。
abstractWe conducted a two-year field study integrating continuous monitoring of the soil plant atmosphere continuum, drone-based multispectral imaging, canopy structural analysis, and fruit phenotyping
This study assessed the integration of Unmanned Aerial Vehicles (UAVs) and satellite images (Sentinel-1 and Sentinel-2) in advanced machine-learning techniques to monitor the ABV of quinoa crops (Jacha Grano variety) across the Bolivian Altiplano. The proposed method follows a two-step procedure. First, UAV RGB images were used in photogrammetric and deep-learning (Convolutional Neural Networks-CNN) models to estimate reference quinoa ABVs at a 10 m spatial resolution from the crop canopy 3D model and classification, respectively. Secondly, several spectral and polarization/texture indices derived from Sentinel-2 and -1 images were integrated into three decision-tree-based machine-learning models (Random Forest-RF, Gradient Boosting-GB, eXtreme Gradient Boosting-XGB), and one CNN-based machine-learning model to estimate ABV. Additionally, a Stacking Model (STM) build on top of the three decision-tree-based models was considered for comparison. Model evaluation was also performed in a two-step approach. First, a 10-fold cross-validation strategy was used to highlight ABV sensitivity to Sentinel-2 and Sentinel-1 alone and in combination. Secondly, a Leave-One-Plot-Out Cross-Validation (LOPOCV) strategy was used to avoid autocorrelation between the training and evaluation dataset and therefore provided more insight into ABV mapping potential. The results showed that the combination of Sentinel-1 and Sentinel-2 features in the CNN model achieved the best predictive performance with R2 and RMSE values of 0.64 and 0.39 m3 ∙ 100 m−2, respectively. These findings highlight the potential of integrating multi-source information in advanced artificial intelligence algorithms for quinoa ABV monitoring, offering new insights toward the identification of sustainable practices across remote regions with complex socio-economic contexts.
Why it matches plant phenotyping methodsUAV画像・衛星センサー・機械学習を統合し、キノアの地上部バイオマス体積という植物形質を推定する手法を開発・比較検証しており、フェノタイピング手法が中心である。
abstractUAV RGB images were used in photogrammetric and deep-learning (Convolutional Neural Networks-CNN) models to estimate reference quinoa ABVs
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:1-38Plant phenotyping relevance match · UnverifiedOpenAlex · checked 15 Sept 2026
Early detection of tree-seedling establishment is essential for monitoring regeneration success in coastal-dune plantations, where conventional field assessments remain labour-intensive and spatially limited. This study presents a deep-learning workflow for detecting early-stage Pinus pinaster seedlings using multispectral UAS-derived point clouds. Field surveys in the Quiaios National Forest, Portugal, mapped approximately 1500 seedlings using RTK GNSS positioning, biometric measurements, and field photographs. Multispectral imagery acquired with a DJI Mavic 3 Multispectral platform was processed through Structure-from-Motion to generate calibrated orthomosaics, terrain products, and dense point clouds. Training-data preparation combined pine-centred buffers, spectral conditioning, manual refinement and point-cloud class assignment. Point Transformer V3 models were trained in ArcGIS Pro and evaluated using field-mapped buffers withheld from model training within plantation-line areas. The Baseline high-recall model achieved 88% object-level recall at the operational threshold of at least three classified Pine-Seedling points per buffer. The refined hard-negative model retained 84% recall while reducing off-buffer detections from 243 to 41. False-negative analysis showed that omissions were associated with reduced crown diameter and limited branch development under the adopted buffer-based retrieval framework. These results support transformer-based multispectral point-cloud classification for scalable monitoring of early-stage pine regeneration in heterogeneous coastal environments.
Why it matches plant phenotyping methodsUASマルチスペクトル点群とPoint Transformer V3により、マツ幼苗の存在・定着状態を植物個体レベルで推定する手法を開発・評価しており、検出性能も検証しているため、植物フェノタイピング手法が中心である。
abstractThis study presents a deep-learning workflow for detecting early-stage Pinus pinaster seedlings using multispectral UAS-derived point clouds.
Near-infrared imagery is essential for vegetation monitoring, precision agriculture, and environmental remote sensing, but multispectral UAV systems remain significantly more expensive and less accessible than conventional RGB imaging platforms. This study presents a lightweight artificial intelligence framework for reconstructing the NIR spectral band exclusively from the red spectral band acquired by a UAV. The proposed methodology formulates the reconstruction task as a pixel-wise nonlinear regression problem and employs a compact multilayer perceptron (MLP) containing only 609 trainable parameters, without exploiting spatial neighborhood information. The framework was developed and evaluated using 280 synchronized multispectral UAV image sets acquired with a DJI Phantom 4 Multispectral platform over a heterogeneous agricultural landscape in the Republic of Moldova. Of these, 252 image sets were used for model development, and 28 were reserved as a held-out within-mission test subset. Quantitative evaluation on a held-out test dataset from the same acquisition mission yielded a mean squared error of 0.010329, a root mean squared error of 0.101632, a mean absolute error of 0.079883, a coefficient of determination of 0.253383, and a Pearson correlation coefficient of 0.683637 between measured and reconstructed normalized NIR digital intensities. The results indicate that the model captures part of the red–NIR relationship under the evaluated acquisition conditions; however, the moderate coefficient of determination suggests that the reconstructed values are an approximation rather than a replacement for measured NIR observations. An illustrative NDVI-based assessment showed that broad spatial vegetation patterns remained identifiable. Rather than introducing a new neural network architecture, this work establishes a compact empirical baseline to investigate the practical performance and limitations of pixel-wise NIR reconstruction from a single red-band value with minimal model complexity.
Why it matches plant phenotyping methodsUAV画像からNIRを再構成し、NDVIを含む植生状態の推定に用いる計算・センシング手法が研究の中心で、独立データによる技術評価も行っている。
abstractThis study presents a lightweight artificial intelligence framework for reconstructing the NIR spectral band exclusively from the red spectral band acquired by a UAV.
Field / plotLeafClassificationDisease symptoms / severity
Early and accurate detection of plant diseases is critical in precision agriculture to improve crop management and yield. Mungbean ( Vigna radiata L.) is highly susceptible to several foliar diseases, including yellow mosaic, powdery mildew, leaf crinkle, and cercospora leaf spot, which cause substantial productivity losses. Despite expanding applications of deep learning in plant disease diagnosis, systematic multi-architecture evaluation for mungbean disease classification under natural field conditions remains limited. This study addresses this gap by evaluating five state-of-the-art deep convolutional neural network (DCNN) architectures on a large-scale, field-acquired mungbean dataset that captures real-world variability across environmental conditions and disease severity levels, distinguishing it from controlled laboratory studies. A total of 5,617 original images across five classes were used. Data augmentation was applied exclusively to the training subset after stratified splitting to prevent data leakage. The dataset was partitioned into training (70%), validation (15%), and testing (15%) subsets. VGG16, VGG19, ResNet50V2, DenseNet121, and InceptionV3 were evaluated using identical transfer learning and fine-tuning protocols. Model performance was assessed using AUC-ROC, Cohen's kappa coefficient, McNemar's test for pairwise statistical comparisons, five-fold cross-validation, and Grad-CAM-based interpretability. On the independent test set, InceptionV3 achieved the highest accuracy (98.47%) and macro-F1 (98.49%), followed by VGG16 (98.36%) and VGG19 (97.89%). AUC-ROC values exceeded 0.997 for all models, confirming excellent class discrimination. Grad-CAM visualizations further confirmed that model predictions were based on biologically relevant disease symptoms. The findings demonstrate the effectiveness of deep learning for robust disease recognition under realistic field conditions and highlight the potential of AI-based diagnostic tools for crop health monitoring, precision agriculture, and decision-support systems in mungbean production.
Why it matches plant phenotyping methods圃場画像からマングビーン葉の病徴・病害状態を推定する深層学習手法を複数モデルで評価・検証しており、植物病害フェノタイピング手法が中心です。
abstractsystematic multi-architecture evaluation for mungbean disease classification under natural field conditions remains limited
Automated fruit counting and yield estimation systems are necessary for efficient orchard management. This study presents a computer vision system based on video multi-object-tracking for fruit load estimation in apple orchards and provides a comprehensive analysis of the system performance under diverse scanning conditions. The system integrates fruit detection, tracking, localization within orchard, and fruit load map generation. Experiments were carried out in an experimental apple orchard containing 420 apple trees. Data was collected with two different RGB-D sensors (Azure Kinect DK and ZED 2) at three different scanning distances (125 cm, 175 cm, and 225 cm) on two different dates prior to the harvest. Comparing the two evaluated sensors, Azure Kinect provided more consistent performance across different dates. Results also show that the longer scanning distance improves accuracy due to seeing the full tree view gives better fruit counts than close partial views. Between the two dates, best results were achieved near harvest due to fruit color at this stage, achieving a Mean Absolute Percentage Error (MAPE) of 6.91 % and a determination coefficient (R 2 ) of 0.733 (using ZED2 sensor at 225 cm distance). Finally, a test comparing scanning from one or both sides of the tree row showed that bilateral scanning improved fruit load estimation at the stretch level by incorporating information from both sides of the canopy. The results of this work demonstrate the effectiveness of the video fruit tracking systems as a useful tool for automating fruit load estimation.
Why it matches plant phenotyping methods動画ベースの果実検出・追跡手法を開発・評価し、リンゴ樹の果実負荷量を推定することが研究の中心であるため、植物フェノタイピング手法として含める。
abstractThis study presents a computer vision system based on video multi-object-tracking for fruit load estimation in apple orchards and provides a comprehensive analysis of the system performance under diverse scanning conditions.
Brown Rot (Monilinia spp.) and Leaf Curl (Taphrina deformans) are principal fungal diseases affecting peach (Prunus persica L. Batsch) production, lacking validated AI-based diagnostic tools in tropical highland orchards. This study presents a compact Convolutional Neural Network (3658 trainable parameters), applied identically to fruit and leaf classification, integrated with a background-removal preprocessing pipeline and evaluated through stratified 5-fold cross-validation on 800 in-situ images from four orchards in Cómbita and Choachí, Colombia. The proposed architecture achieved mean accuracies of 82.8% (fruit) and 95.3% (leaf), with AUC values of 0.87 and 0.98, and a trained model footprint of approximately 100 KB, supporting storage- and bandwidth-efficient deployment. Benchmarked against ImageNet-pretrained MobileNetV3-Small and MobileNetV2 under an identical protocol, the proposed architecture matched or exceeded MobileNetV3-Small on leaf classification despite a 257-fold smaller parameter count, and achieved comparable or lower inference latency than both larger backbones. To our knowledge, this is the first validated system for simultaneous detection of both pathogens in Prunus persica under real field conditions, combining a compact, deployment-ready architecture with an ablation-verified preprocessing pipeline. The proposed model was deployed in the DurAPP web platform, giving peach growers in tropical highland regions a practical, low-footprint diagnostic tool suited to smallholder farming conditions.
Why it matches plant phenotyping methodsモモ果実・葉の病徴を画像から分類するCNN、前処理、交差検証、他モデル比較、実地検証、プラットフォーム展開が中心であり、植物病害状態の画像ベースフェノタイピング手法に該当する。
abstractThis study presents a compact Convolutional Neural Network (3658 trainable parameters), applied identically to fruit and leaf classification, integrated with a background-removal preprocessing pipeline and evaluated through stratified 5-fold cross-validation on 800 in-situ images from four orchards
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).
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Open Research Europe 2026, 6:322 Last updated: 14 SEP 2026Open asset ↗GEN4OLIVE Olive Varieties Databasepdf-raw-page:8 lines:1-44Plant phenotyping relevance match · UnverifiedEurope PMC · checked 15 Sept 2026
Published2 Sept 2026The Science of the total environment
Urban air pollution may alter plant metabolism long before visible damage becomes apparent. Raman spectroscopy was evaluated as a rapid, non-destructive approach to resolve these biochemical adjustments. Mature Quercus ilex L. trees were sampled along a well-defined pollution gradient in Tuscany (Italy), spanning high, intermediate, and low levels of NO₂ and PM₁₀. Leaf Raman spectra revealed coordinated modulation of primary and secondary metabolism. Pigment-related bands (chlorophylls and carotenoids) increased toward the most polluted site, while inducible flavonoid signals showed site-dependent variation consistent with oxidative pressure in superficial tissues. These patterns were consistent with destructive biochemical analyses and chlorophyll fluorescence measurements, which indicated acclimation rather than photoinhibition damage. A composite Raman index showed a close site-level association with NO₂ exposure, suggesting that nitrogen-related urban pollution was the main exposure component linked to the observed metabolic response. Overall, Raman spectroscopy captures the chronic metabolic imprint of urban air pollution in Q. ilex, resolving coordinated pigment reinforcement and defensive activation without sample destruction. This approach provides a rapid and scalable framework for linking atmospheric chemistry to plant functional status in biomonitoring applications.
Why it matches plant phenotyping methods植物の代謝・機能状態を非破壊的に推定するRaman分光法を評価し、スペクトル指標と生化学・蛍光測定の整合性を検証しているため、手法が中心的です。
abstractRaman spectroscopy was evaluated as a rapid, non-destructive approach to resolve these biochemical adjustments.
Abstract Agricultural pest and disease monitoring plays a vital role in ensuring crop productivity, reducing pesticide consumption, and promoting sustainable agricultural development. Although deep learning techniques have achieved remarkable success in plant health diagnosis, many existing models remain computationally intensive and are difficult to deploy on resource-constrained edge devices used in practical agricultural environments. To address these challenges, this study proposes a practical lightweight deep learning framework based on an improved ShuffleNetV2 architecture for real-time maize pest and disease recognition under complex field conditions.The proposed model incorporates the Ghost module to reduce redundant feature generation, the Efficient Channel Attention (ECA) mechanism to enhance feature representation, and the HardSwish activation function to improve nonlinear learning capability while maintaining computational efficiency. Extensive experiments were conducted on a maize pest and disease dataset containing multiple disease and pest categories collected under natural field conditions. Experimental results demonstrate that the proposed model achieves superior recognition accuracy while significantly reducing model parameters and computational complexity compared with several mainstream lightweight convolutional neural networks.The results show that the proposed method achieves an accuracy of 93.00%, a recall of 92.76%, and an F1-score of 92.42%, while maintaining extremely low computational cost (0.03 GFLOPs) and model size (1.16 MB). Furthermore, the proposed model was successfully deployed on a Raspberry Pi platform, demonstrating excellent real-time inference capability and low computational resource consumption. The framework is suitable for practical agricultural applications, including intelligent crop monitoring, UAV-assisted field inspection, and mobile diagnostic systems. By enabling rapid and accurate in-field identification of maize pests and diseases, the proposed approach supports timely crop protection decisions, reduces unnecessary pesticide application, and contributes to sustainable agriculture through practical edge-AI deployment.
Why it matches plant phenotyping methodsトウモロコシの病害状態を画像から認識する軽量深層学習法の開発・評価が中心であり、植物病害フェノタイプの取得手法に該当する。
abstractthis study proposes a practical lightweight deep learning framework based on an improved ShuffleNetV2 architecture for real-time maize pest and disease recognition under complex field conditions.
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:639-658Plant phenotyping relevance match · UnverifiedCrossref · checked 15 Sept 2026
Accurate and efficient monitoring of tea plant growth parameters via remote sensing is essential for precision plantation management. However, spectral indices relying solely on reflectance often exhibit limited sensitivity in capturing complex tea canopy characteristics. This study developed a data-driven framework integrating spectral reflectance, frequency-domain harmonic components, and spatial texture features to construct tri-feature fusion indices (TFIs) and establish machine learning and deep learning models for tea growth monitoring. Ten-band multispectral imagery was acquired using a UAV alongside synchronous field measurements of leaf and plant biomass and nitrogen accumulation. TFIs were constructed through exhaustive feature combinations and optimized via a data-driven search strategy. Subsequently, random forest (RF), multilayer perceptron (MLP), convolutional neural network (CNN), and transformer models were evaluated using a leave-one-site-out cross-validation (LOSO-CV) strategy. The selected TFIs showed strong associations with tea growth parameters within the investigated dataset, with R2 values up to 0.63 and 0.62 for leaf dry matter and leaf nitrogen accumulation, respectively. Models incorporating selected TFIs achieved cross-validated R2 values of 0.56 for leaf dry matter (MLP), 0.59 for plant dry matter (MLP), 0.73 for leaf nitrogen accumulation (MLP), and 0.68 for plant nitrogen accumulation (CNN). These models exhibited competitive predictive performance comparable to RF, although no statistically significant differences in mean absolute error were observed under site-held-out evaluation. Furthermore, model-derived spatial maps provided insights into fine-scale spatial heterogeneity and potential interannual variations in tea growth parameters across representative plantations from 2024 to 2025. Overall, this study provides a UAV-based framework for tea growth parameter estimation by integrating multi-domain information without requiring additional environmental observations.
Why it matches plant phenotyping methodsUAVマルチスペクトル画像から茶植物の乾物量・窒素蓄積を推定する特徴量融合および機械学習・深層学習フレームワークを開発し、サイト外交差検証で評価しており、植物形質の取得・推定手法が中心である。
abstractThis study developed a data-driven framework integrating spectral reflectance, frequency-domain harmonic components, and spatial texture features to construct tri-feature fusion indices (TFIs) and establish machine learning and deep learning models for tea growth monitoring.
Fruit quality is a critical determinant of economic returns in pear production, and maintaining an appropriate fruit load (FL) is essential for achieving high yield and quality. As a direct indicator of canopy photosynthetic capacity and assimilate supply, leaf number constitutes the key biological basis of reasonable FL determination under the leaf-to-fruit ratio concept. However, accurate and efficient estimation of leaf number in mature pear trees remains technically challenging, limiting its practical use in precision FL regulation. Here, we propose a data-driven framework for leaf number and reasonable FL estimation by integrating 3D point cloud-derived canopy structure with machine learning. A pipeline for extracting 3D architectural traits was developed and implemented in the software tool FTPCT, enabling rapid and standardized trait acquisition. Through correlation analysis, multicollinearity diagnosis, and variance inflation factor screening, five key traits strongly associated with leaf number were identified and incorporated into five machine learning models optimized using Bayesian optimization. Among them, the optimized random forest regression model achieved the highest and most stable performance, with R 2 of 0.85, RMSE of 239.74, and MAE of 149.26 for test dataset. SHAP analysis identified tree crown volume as the dominant contributor to leaf number estimation. Field validation demonstrated that FL regulation guided by the proposed framework significantly improved fruit weight and size without reducing yield compared with conventional practices. Notably, the proposed approach avoids explicit leaf-level reconstruction and relies on less canopy-scale traits, substantially reducing data requirements and computational cost, and thereby offering strong potential for rapid, field-deployable FL regulation in large-scale orchards.
Why it matches plant phenotyping methods3D点群から樹冠構造形質を抽出し、葉数と適正着果量を推定する手法およびソフトウェアを開発・検証しており、植物表現型取得が中心である。
abstractA pipeline for extracting 3D architectural traits was developed and implemented in the software tool FTPCT, enabling rapid and standardized trait acquisition.
Reproduction assets foundThe paper's phenotyping analysis assets are the authors' publicly released LeafNumPred source code and trained models, and the FTPCT software for 3D trait extraction from pear tree point clouds. Phenotype/point-cloud datasets are only available on request.Code · public. Supplementary data
The following is the Supplementary data to this article:
Multimedia component 1
mmc1.docx (1.6MB, docx)
Data availability
Data will be made available on request. Anyone who wants to obtain other public data can contact us at taost@njau.edu.cn. The source codes and models have been made publicly available at https://github.com/Zhang-Fanhang/LeafNumPred, and the FTPCT software has been released at https://github.com/Zhang-Fanhang/FTPCT/tree/Installation-package.
References
1.Tao S., Khanizadeh S., Zhang H., Zhang S. Anatomy, ultrastructure and lignin distribution of stone cells in two Pyrus species. Plant Sci. 2009;176:413–419. [Google Scholar]
2.Zhang F., Wang Q., Yuan K.Open asset ↗Zhang-Fanhang/LeafNumPredhtml-lines:284-315Code · publical variations [34,35]. The method for calculating these traits are shown in the Supplementary information 1.
2.5. Software implementation for 3D trait extraction (FTPCT)
To facilitate efficient and standardized extraction of canopy structural traits from point cloud data, we used a standalone software tool, FTPCT (available at: https://github.com/Zhang-Fanhang/FTPCT/tree/Installation-package), which integrates the trait extraction procedures applied in this study. The software provides a graphical user interface, enabling users to process tree-level point cloud data and extract key 3D structural traits without requiring advanced programming skills.
FTPCT implements a series of predefined proOpen asset ↗Zhang-Fanhang/FTPCThtml-lines:138-149Plant phenotyping relevance match · UnverifiedOpenAlex · Europe PMC · checked 14 Sept 2026
Plant Phenomics studies the phenotypic dynamics that form plant phenotypes by systematically measuring traits using phenotyping methods from the quantum to the ecosystem levels. It has emerged as an interdisciplinary field advancing sensing, computation, and plant biology. However, Plant Phenomics has lacked a unifying framework that integrates its community's core concepts from the formal and life sciences. Central to this framework is the definition of the phenome as a set of phenes that govern phenotypic dynamics across all spatial and temporal scales of biological and ecological organization and in interaction with the environment. This paradigm moves beyond gene-centric views and recognizes the equal importance of all spatial and temporal scales in forming plant phenotypes, advancing Plant Phenomics as a data-driven discipline and its emerging profession, the plant phenomicist.
Why it matches plant phenotyping methods植物フェノミクスの概念・枠組みを扱うレビューであり、植物形質の系統的測定とフェノタイピング手法を主題としているため、方法論レビューとして適格。
abstractPlant Phenomics studies the phenotypic dynamics that form plant phenotypes by systematically measuring traits using phenotyping methods from the quantum to the ecosystem levels.
Aboveground biomass density (AGBD) is a key indicator in agricultural systems, directly reflecting crop carbon storage potential and yield levels. The World Food Studies (WOFOST) model is widely used for crop growth simulation due to its process-based interpretability. However, its application is limited by complex calibration demands and struggles with spatial heterogeneity. To address these limitations, this paper proposes an assimilation system that integrates Synthetic Aperture Radar (SAR) data into a modified WOFOST model, which requires simple calibration. WOFOST is run in potential production mode, which assumes ideal conditions to reduce input data requirements. Before assimilation, phenology-related temperature sums are aligned with phenology and meteorological data to match local growth stages. Two quantities are then estimated and updated in the model through data assimilation by minimizing the difference between SAR-derived and simulated AGBD. These quantities are the proposed yield reduction factor, which represents the proportional decrease in potential CO 2 assimilation under stresses, and the initial total dry weight at sowing. Validation experiments were conducted using multi-year cotton datasets from two farms in Georgia, USA, differing in whether irrigation was applied. Compared to WOFOST simulations and evaluated against in situ AGBD measurements, the assimilation results improve agreement and reduce error (approximately 43% RMSE reduction at the rainfed site and 15% at the irrigated site). It also delivers spatial maps of biomass, together with model-derived yield and harvest-index diagnostics, and remains operational under frequent cloud cover where optical observations are sparse. This SAR-based assimilation strategy reduces calibration demands, providing a novel and practical pathway to extend WOFOST applications to diverse agricultural scenarios.
Why it matches plant phenotyping methodsSARデータを作物成長モデルに同化して綿の地上部バイオマスを推定する手法を開発し、複数年・複数圃場データで検証しているため、植物形質取得が中心である。
abstractthis paper proposes an assimilation system that integrates Synthetic Aperture Radar (SAR) data into a modified WOFOST model
Global trait axes reveal overarching dimensions of plant functional variation. However, how these dimensions are spatially organized within and across forest types remains unclear. We combined drone-based full-range imaging spectroscopy with crown-level measurements of 16 physiological, morphological and biochemical traits across temperate, subtropical and tropical forests in China to enable spatially-explicit trait mapping. Through site-training scenario, leaf-to-canopy scaling and spectral-domain modelling tests, we find that reliable canopy trait retrieval depends not only on trait and spectral coverage, but also on preserving trait-spectral relationships across sites and scales. Spectral predictions recovered observed multivariate covariation, summarizing crown variation into a leaf-economics dimension and two additional biochemical dimensions related to hydro-thermal regulation and defence/metabolism. Mapping these dimensions revealed distinct community-level trait organization alongside substantial species- and crown-level variation within forests. These findings link remotely sensed trait retrieval to environmental filtering and plant functional differentiation, providing a scalable framework for monitoring forest functional diversity.
Why it matches plant phenotyping methodsドローン分光画像と冠レベル形質測定を用いた植物形質の空間マッピング手法が中心で、スケーリングおよびスペクトルモデルの検証も行っている。
abstractWe combined drone-based full-range imaging spectroscopy with crown-level measurements of 16 physiological, morphological and biochemical traits across temperate, subtropical and tropical forests in China to enable spatially-explicit trait mapping.
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 ).
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Roumet, P.
,
Bertrand, Y.Open asset ↗CIMMYT data repository · 10.71682/10549399lines:280-433Plant phenotyping relevance match · UnverifiedEurope PMC · checked 14 Sept 2026
Whitefly-transmitted begomoviruses cause tomato leaf curl disease (ToLCD). In India, at least 15 begomoviruses are known to cause ToLCD, posing a major challenge to resistance breeding. Although several Ty resistance loci have been introgressed from wild tomato relatives, variable resistance responses are frequently observed, likely due to mixed infections and the absence of a standardized disease scoring system. Moreover, limited knowledge of the infecting begomoviruses in resistant genotypes has hindered the effective use of donor lines in breeding programs. This study evaluated 17 homozygous Ty-gene donor tomato genotypes under natural epiphytotic conditions and identified the associated begomoviruses. To quantify disease severity, a robust disease scoring system was developed using coefficient of infection (CI) by integrating symptom parameters- leaf curling, leaf smalling, stunting, and fruiting, with population-level disease incidence. Field evaluations for two years revealed that genotypes carrying both Ty-2 and Ty-3 loci showed higher resistance, though variability existed among them. Genotypes with Ty-3 alone or Ty-5 + Ty-6 combinations also displayed substantial tolerance, and five genotypes were identified as highly resistant. Molecular indexing revealed frequent mixed infections and identified multiple begomoviruses, including a newly characterized species, tomato leaf curl Ty Pusa virus, alongside tomato leaf curl New Delhi virus, tomato leaf curl Palampur virus, tomato leaf curl Gujarat virus, and tomato leaf curl Joydebpur virus. These findings highlight a shift in begomovirus predominance and possible recombination-driven emergence of new variants. This study provides an integrated framework for evaluating ToLCD resistance and emphasizes the need for continuous reassessment of resistance sources to ensure durable tomato cultivar development.
Why it matches plant phenotyping methods植物の病徴と発病率を統合した病害重症度スコアリング法を開発し、抵抗性評価に適用しており、表現型取得法が研究の中心である。
abstractTo quantify disease severity, a robust disease scoring system was developed using coefficient of infection (CI) by integrating symptom parameters- leaf curling, leaf smalling, stunting, and fruiting, with population-level disease incidence.
Year-to-year climate variability poses a challenge for agriculture by increasing crop yield variability; therefore, there is a need to identify genotypes that can withstand these fluctuations. With the right selection criteria, genotypes with yield stability across variable environmental conditions can be selected. Methods such as Finlay-Wilkinson random regression (FWRR) may allow us to use sparse datasets-common in plant breeding pipelines-and incorporate genomic data to leverage phenotypic information from related genotypes to predict yield stability. Our objective was to examine how the number of environments and the variance among those environments affect stability predictions. We also integrate FWRR as a genomic prediction tool for characterizing yield stability, comparing it to the traditional genomic prediction models as a reference. We used three datasets: one highly unbalanced dataset for oats (Avena sativa L.) and two completely balanced datasets with different numbers of environments for barley (Hordeum vulgare L.) and wheat (Triticum aestivum L.). We fit standard Finlay-Wilkinson (FW) and FWRR models to estimate grain yield and stability under various scenarios. We found that the estimated stability values obtained were similar using balanced datasets for FW or FWRR. FWRR also achieved moderate predictive ability for stability using unbalanced datasets under 10-fold cross-validation (CV1) with new genotypes. In terms of environmental representation, selecting the right set of environments for inclusion in the model was more important than adding more environments. Our results suggest the possibility of using FWRR to select stable genotypes earlier in line development, as well as to design resource-efficient stability-testing schemes.
Why it matches plant phenotyping methodsFWRRを用いて穀類の収量安定性を推定・予測する統計的手法を検討し、環境数やデータ構成による予測性能を評価しているため、収量形質の計算的フェノタイピング手法が中心です。
abstractMethods such as Finlay-Wilkinson random regression (FWRR) may allow us to use sparse datasets-common in plant breeding pipelines-and incorporate genomic data to leverage phenotypic information from related genotypes to predict yield stability.
Abstract Tree crowns are complex, three‐dimensional structures whose morphology varies among species, individuals and environments. Although light detection and ranging (LiDAR) provides high‐resolution, single‐tree point clouds that advance species discrimination and the assessment of intraspecific variation in situ, crown shape is still commonly reduced to low‐dimensional metrics (e.g. crown diameter or crown base height), losing much of its three‐dimensional geometric complexity. We introduce a fully 3D geometric morphometric framework that captures crown shape directly from LiDAR point clouds at both species and individual levels. Pre‐segmented LiDAR single‐tree point clouds of eight temperate forest species were converted into three‐dimensional shape representations using radial bounding volumes (RBVs), which partitioned each crown into a standardized set of vertical layers and radial sectors. Surface points automatically digitized from each RBV formed geospatially aligned, 3D pseudolandmark configurations representing geometric morphometric crown shapes. These configurations served as the input data for multivariate analyses of crown shape variation within and between species. Twelve structural traits, including crown and stem dimensions, were extracted from the same RBVs and integrated into analyses of trait–shape associations. The morphospace of crown shape was structured along different axes of variation in broadleaf species than in conifers. Within these groups, species pairs—such as Fagus versus Quercus and Picea versus Pinus —exhibited contrasting intraspecific morphological gradients, with different structural traits driving shape variation in each. Crown base height and total crown height emerged as the strongest predictors of crown shape. Differences in crown shape among species were primarily captured by symmetric components, with asymmetry providing a negligible signal. Interspecific differentiation was largely driven by architectural variation rather than pure size differences. Morphological differences derived from pseudolandmarks and convolutional neural network features exhibited stronger correlations in conifers than in broadleaf species. We present a reproducible, LiDAR‐native framework for quantifying and comparing 3D crown morphology within and across species. Using the RBV approach, geospatially aligned pseudolandmarks can be derived from any pre‐segmented, single‐tree LiDAR point cloud, enabling scalable, multi‐regional analyses of intraspecific variability. This framework provides a robust foundation for integrating crown shape into ecological, evolutionary, silvicultural and modelling studies, including assessments of environmental effects and architectural constraints.
Why it matches plant phenotyping methodsLiDAR点群から樹冠形状を抽出・定量化する3D幾何形態計測フレームワークを開発し、再現可能な植物形態計測手法として検証・適用しているため。
abstractWe introduce a fully 3D geometric morphometric framework that captures crown shape directly from LiDAR point clouds at both species and individual levels.
Maize ear geometry (length, width, curvature, and volume) is closely tied to yield and grain-filling outcomes, but existing high-throughput phenotyping pipelines remain constrained by the cost, labor, and specialized hardware they require. We developed and validated a low-cost pipeline that reconstructs a watertight 3-D mesh of a maize ear from a single 20-second video captured with a consumer-grade DSLR on a motorized turntable under uniform LED illumination. Camera poses from a multi-seed COLMAP procedure initialize a Neural Radiance Field (NeRF), and a cylindrical holder of known diameter, visible in every frame, provides automatic metric scaling with downstream geometric quality control. Applied to 300 ears spanning a diverse maize inbred panel, 250 (83.3%) passed automated processing and quality control. Skeleton length agreed with manual caliper measurements across all 250 ears (R^2 = 0.964, RMSE = 4.68 mm), and convex-hull volume agreed with water-displacement volume on a 15-ear subset spanning the full size range (R^2 = 0.982, RMSE = 5.26 mL). Residual length error grew with ear curvature, whereas bounding-box height, which records the same straight-line chord as calipers, showed no such trend; the discrepancy therefore originates in the measurement definition, since calipers record the chord while skeleton length traces the geodesic arc. The capture hardware costs approximately 607 USD, and operator involvement fell from roughly five minutes to one minute per ear, with all downstream processing running unattended. The platform provides a foundation for breeding-scale 3-D ear phenotyping.
Why it matches plant phenotyping methodsトウモロコシ雌穂の3D形態形質を抽出する低コスト画像計測パイプラインを開発し、手動測定および体積測定で技術検証しているため、方法が研究の中心である。
abstractWe developed and validated a low-cost pipeline that reconstructs a watertight 3-D mesh of a maize ear
To overcome YOLOv11’s limitations in complex field environments, this paper proposed SDD-YOLOv11n, a lightweight real-time detector for soybean diseases. The model reconstructed the backbone using GhostConv to minimize redundancy and integrates a C3k2_Star module to enhance small lesion detection against background noise. Additionally, a Detect Efficient (DE) head further compressed the architecture. Experimental results verified the model's efficiency, achieving a parameter count of 1.88 M and a weight size of 3.9 MB—reductions of 27.3% and 25% compared to YOLOv11n, respectively. Furthermore, the model maintained high detection performance with a Mean Average Precision (mAP50) of 75.6% and an F1-score of 69.3%, demonstrating its effectiveness in balancing architectural efficiency and accuracy in complex field environments.
Why it matches plant phenotyping methods圃場のダイズ病害病斑を画像から検出する軽量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。
titleREAL-TIME AND PRECISE DETECTION OF FIELD SOYBEAN RUST AND BACTERIAL SPOT BASED ON IMPROVED YOLOV11N
Rice false smut is a major panicle disease that affects rice yield and grain quality and is an important target for resistance evaluation in breeding programs. Accurate field phenotyping is important for disease assessment and resistance screening, yet current assessment relies heavily on manual visual scoring and smut ball counting, which are laborious and subject to evaluator variation. In close-range single-panicle images, false smut balls are often small, dense, occluded, adhered, making automatic detection and severity grading difficult. To address these challenges, we developed a YOLOv12-RSLW detector by integrating RepGhost, SimAM, LSCD, and WIoU into YOLOv12. Detection boxes were then used to guide the Segment Anything Model for panicle and lesion mask extraction, allowing calculation of the lesion-to-panicle area ratio as a supplementary indicator for count-based severity grading. A total of 1911 original field images were collected. After augmentation, the dataset contained 5663 images, including 4531 training images, 566 validation images, and 566 test images. Detection performance was evaluated on the test set, while SAM segmentation was assessed using 80 manually annotated original images. YOLOv12-RSLW achieved 92.06% mAP@0.5, 91.46% precision, and 87.01% recall, with 3.45 M parameters and 6.0 GFLOPs. Compared with the baseline YOLOv12, mAP@0.5 and recall increased by 3.60 and 4.37 percentage points, respectively. Within the augmented dataset, 41.2% of samples initially assigned to Grade 1 and 28.1% of those assigned to Grade 2 met the area-ratio criteria for potential reassignment to higher grades. The framework provides a quantitative approach to rice false smut severity phenotyping and may support future resistance breeding after further validation.
Why it matches plant phenotyping methodsイネいもち病の病徴を画像から検出・分割し、病斑面積比に基づく重症度を定量化する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ある。
abstractTo address these challenges, we developed a YOLOv12-RSLW detector by integrating RepGhost, SimAM, LSCD, and WIoU into YOLOv12.
This paper presents an integrated system design for autonomous quadcopter flight path generation using the MAVLink protocol and a custom Ground Control Station (GCS) for precision agricultural crop monitoring. The system combines three coverage path algorithms (Boustrophedon, Spiral, and Energy-Optimized), a Pixhawk 4 / ArduPilot flight stack, a MicaSense RedEdge-P multispectral payload, and a ROS2-based GCS for mission planning, telemetry, and vegetation-index-based crop health assessment. The 2.8 kg quadcopter (450 mm frame, 4-cell LiPo) achieves 22–25 minutes of flight time. Across five field sizes (0.5–10 ha), the Energy-Optimized path achieved 96.5% coverage efficiency with 4.2% overlap and a 12.4% energy reduction over the Boustrophedon baseline. NDVI-based crop segmentation achieved pixel accuracy of 92.5% (maize), 94.1% (rice), and 90.8% (wheat), and four-class crop-health classification achieved a weighted F1-score of 90.0%. MAVLink 2.0 command latency averaged 15.8 ms with 99.3% packet delivery at ranges up to 800 m. An ablation study showed additional gains of 1.5–3.1% coverage from wind compensation and 2.1–2.8% from terrain-following.
Why it matches plant phenotyping methods自律ドローン、マルチスペクトル撮像、NDVIセグメンテーションによる作物健康状態推定を統合し、飛行・画像解析性能を定量評価しているため、植物状態の取得・抽出が技術的に実質的な構成要素である。
abstractThe system combines three coverage path algorithms (Boustrophedon, Spiral, and Energy-Optimized), a Pixhawk 4 / ArduPilot flight stack, a MicaSense RedEdge-P multispectral payload, and a ROS2-based GCS for mission planning, telemetry, and vegetation-index-based crop health assessment.
Cauliflower emergence rate and seedling growth are key indicators of field conditions and varietal potential. Traditional manual surveys are unsuitable for continuous monitoring across multiple varieties. This study integrates UAV RGB imagery with the DualSlim-YOLO model to estimate cauliflower emergence rates and monitor seedling growth. Built on YOLOv11, the model incorporates a lightweight feature extraction structure and an optimized detection-scale configuration. It reduces computational complexity while maintaining detection accuracy, thereby improving the efficiency of cauliflower seedling detection. DualSlim-YOLO achieved P, R, F1-score, mAP@0.5, and mAP@0.5:0.95 of 95.35%, 96.75%, 96.05%, 98.55%, and 86.65%, respectively. The number of parameters was reduced by 38.61%, while the inference speed increased by 22.16%, demonstrating good lightweight performance. Based on this model, UAV images of 171 cauliflower varieties acquired at 7, 21, and 28 d after transplanting were used for seedling detection and emergence rate estimation. In addition, 18 time-series seedling phenotypic traits were extracted, enabling a comprehensive quantitative evaluation of emergence dynamics and early-growth performance across multiple cauliflower varieties. This method effectively screens cauliflower varieties for high emergence rates, rapid emergence, and excellent seedling growth performance. It provides technical support for high-throughput, nondestructive seedling phenotyping and early germplasm screening under field conditions.
Why it matches plant phenotyping methodsUAV画像と軽量YOLOモデルを用いて、カリフラワー苗の検出、出芽率推定、18種類の時系列表現型形質抽出を行う手法が中心であり、モデル性能も検証している。
abstractThis study integrates UAV RGB imagery with the DualSlim-YOLO model to estimate cauliflower emergence rates and monitor seedling growth.
Plant phenotyping relevance match · UnverifiedOpenAlex · Europe PMC · bioRxiv · Crossref · checked 11 Sept 2026
Published30 Aug 2026bioRxiv (Cold Spring Harbor Laboratory)
Abstract The integration of digital technologies for high-throughput field phenotyping is critical for accelerating crop improvement in agriculture. However, extracting traits from remote sensing data remains constrained by fragmented workflows, manual intervention, and limited interoperability among existing tools, resulting in delays that hinder timely biological insight and decision-making. To address these challenges, we present PhenoStream (Phenotyping Streaming), a scalable, end-to-end cyberinfrastructure designed to automate the full lifecycle of aerial imagery–based phenotyping, from data acquisition to plot-and genotype-level inference. The framework integrates automated data ingestion from distributed field sites, geospatial processing, and AI-enabled trait extraction within a unified, user-accessible graphical interface. Its modular and extensible architecture supports adaptable trait modeling and seamless integration of new data sources, enabling deployment across diverse crops, environments, and experimental designs. We demonstrate the system across a large multi-location field trial network of bioenergy crops, where it enables high-throughput characterization of spatiotemporal growth dynamics, genotype-by-environment (G×E) interactions, and predictive modeling of key agronomic traits. By significantly reducing processing latency and manual effort, the platform facilitates near-real-time analysis and reproducible workflows. This work establishes a generalizable and scalable pathway for operationalizing very-high-spatial resolution aerial phenotyping in agricultural research. By bridging data acquisition and analytics, the end-to-end cyberinfrastructure provides a foundation for integrating heterogeneous and unstructured data streams—including remote sensing, environmental, and management data—toward data-driven decision making in agriculture.
Why it matches plant phenotyping methods航空画像から作物形質を自動抽出するエンドツーエンドのフェノタイピング基盤を開発・実証しており、形質取得と解析ワークフローが研究の中心です。
abstracta scalable, end-to-end cyberinfrastructure designed to automate the full lifecycle of aerial imagery–based phenotyping, from data acquisition to plot-and genotype-level inference.
Background: Faba bean is an important legume crop valued for its nutritional and soil-enriching benefits, yet its productivity is severely affected by foliar diseases. Automated image-based detection using deep learning provides a rapid and reliable approach for early disease identification and improved crop management. Methods: This study developed a machine learning-based automated framework for multi-class classification of Faba bean leaf diseases using transfer learning with the VGG16 convolutional neural network. A dataset of 8,021 RGB images collected under natural field conditions was used, comprising four classes: healthy, rust, gall and chocolate spot. Images were resized to 224 × 224 pixels and normalized prior to training. The pretrained convolutional layers of VGG16 were frozen and a custom classification head with global average pooling and dropout regularization was added. Model performance was evaluated using classification metrics. Result: The proposed model achieved an overall classification accuracy of 92.34% and a macro-averaged F1-score of 0.9227 on the test dataset. Strong classification performance was observed across all disease categories, with particularly high predictive accuracy for healthy and rust classes. The findings demonstrate the effectiveness of transfer learning for plant disease detection and highlight its potential for scalable, automated crop health monitoring in precision agriculture.
Why it matches plant phenotyping methods植物葉画像から病害状態を自動推定する深層学習手法の開発・性能評価が中心であり、植物フェノタイピング手法に該当する。
abstractThis study developed a machine learning-based automated framework for multi-class classification of Faba bean leaf diseases using transfer learning with the VGG16 convolutional neural network.
Xylella fastidiosa (Xf) is among the most devastating phytosanitary threats to Mediterranean agriculture, causing Olive Quick Decline Syndrome (OQDS). Since containment efficacy depends on timely intervention, scalable in-field screening tools are needed. This study evaluates a portable digital electronic nose, based on a carbon-nanotube sensor array combined with artificial intelligence algorithms, for the in-field screening of Xf through volatile organic compound (VOC) profiling. Three replicate acquisitions were performed on 130 olive trees (390 measurements) across four cultivars (Cellina di Nardò, Ogliarola Salentina, Ogliarola Barese, and Leccino) in four Italian regions (Apulia, Calabria, Lazio, and Tuscany). Plant status was assigned from the official status of the sampling area (demarcated OQDS focus versus Xf-free area) and supported by real-time quantitative PCR (qPCR) on every plant; within demarcated sites, plants with undetectable DNA in sampled twigs were retained as Xf+ following phytosanitary criteria, giving 216 infected and 174 healthy samples. The multidimensional sensor signals were processed with an optimized Shallow Neural Network. Under plant-grouped 80/20 validation, keeping each plant’s replicates in the same subset, the model achieved (93.3 ± 4.0)% accuracy, (97.7 ± 3.5)% sensitivity, and (88.2 ± 8.3)% specificity (mean ± SD). A feature-importance analysis revealed a reproducible, though not chemically resolved, VOC-related response pattern. This low-cost, portable Internet of Things (IoT) device offers a proof-of-concept screening approach for Xf surveillance, pending plant-level and external validation.
Why it matches plant phenotyping methods植物の感染状態をVOCセンサーとAIで直接推定する現地スクリーニング手法を開発・評価しており、植物病害状態の取得が研究の中心である。
abstractThis study evaluates a portable digital electronic nose, based on a carbon-nanotube sensor array combined with artificial intelligence algorithms, for the in-field screening of Xf through volatile organic compound (VOC) profiling.
Abstract Purpose Evaluate how soil and canopy sensing can map within-block variability in tart cherry orchards and identify indicators robust enough for repeatable management decisions. Methods Soil apparent electrical conductivity (ECa) was mapped in spring 2022 across four commercial tart cherry blocks (8.5–10.5 ha; approximately 3,500 trees per block), followed by canopy sensing in 2023–2024. Canopy structure was measured using unmanned aerial vehicle (UAV) photogrammetry and mobile terrestrial laser scanning (MTLS) using light detection and ranging (LiDAR), and canopy density using mobile ceptometry. Spatial layers were aligned to per-tree grid cells. An August 2025 campaign compared UAV- and LiDAR-derived tree height with ground-truthed height. Results Soil-to-canopy relationships were weak to moderate but consistent within blocks ( r = 0.10–0.40), with strength and direction varying by site conditions. Canopy density was more strongly associated with UAV-derived volume than height. UAV-derived 90th-percentile height best predicted ground-truthed height ( R ² = 0.89; RMSE = 0.34 m), whereas LiDAR showed a weaker relationship and greater error ( R ² = 0.70; RMSE = 0.52 m). Cross-sensor agreement was moderate to strong ( r = 0.41–0.65). Per-tree rankings were stable between years for UAV height and volume. Conclusion Whole-block sensing revealed persistent spatial patterns that could support management-zone delineation. UAV photogrammetry provided accurate canopy metrics, MTLS offered measurements suited to routine orchard operations, ceptometry added seasonal canopy-density information, and ECa provided soil context. Occasional ECa mapping combined with strategically timed UAV surveys and other sensors as needed could reduce redundant sensing while supporting fertilizer evaluation, pruning, and labor allocation.
Why it matches plant phenotyping methodsUAVフォトグラメトリ、LiDAR、セプトメトリーによる樹冠の高さ・体積・密度の取得を中心に、地上実測との検証とセンサー間比較を行っているため、植物フェノタイピング手法の実質的な適用・検証に該当する。
abstractCanopy structure was measured using unmanned aerial vehicle (UAV) photogrammetry and mobile terrestrial laser scanning (MTLS) using light detection and ranging (LiDAR), and canopy density using mobile ceptometry.
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:1-55Plant phenotyping relevance match · UnverifiedCrossref · checked 5 Sept 2026
Faba bean yield reflects complex relationships among genotype, environment, and agronomic traits. This study evaluated an explainable Tabular Prior-data Fitted Network (TabPFN) framework for estimating plot-mean single-plant yield and prioritizing traits using 398 plot-level observations, 13 measured agronomic predictors, and six derived features. On the reference 80/20 split, TabPFN achieved the best values for all four test metrics (R2 = 0.8746, RMSE = 1.9132 g plant−1, MAE = 1.0819 g plant−1, and MAPE = 8.16%). The Friedman test detected differences among the six models (χ2(5) = 16.75, p = 0.005); Nemenyi comparisons distinguished TabPFN from HistGradientBoosting and SVR, whereas the Holm-corrected Wilcoxon analysis confirmed only the TabPFN–SVR difference. Across 10 repeated 80/20 splits, TabPFN obtained the highest mean test R2 (0.8614 ± 0.0691), ranked first in eight splits, and produced a higher R2 than every tuned baseline in at least eight splits. SHAP, permutation importance, and LOCO analyses emphasized pod-, seed-, and biomass-related predictors. Repeated-split ablation showed that derived features improved TabPFN consistently, whereas removing selected target-proximal yield variables reduced performance for every model. The framework is therefore a harvest-time trait-estimation and trait-prioritization tool rather than an early-season forecasting system. Notably, TabPFN achieved this performance without the 100-trial Optuna search used for each baseline; only n_estimators was screened over four prespecified values.
Why it matches plant phenotyping methods単一個体収量を推定し、形質優先順位付けを行う機械学習フレームワークを評価・比較しており、植物形質抽出手法が研究の中心である。
abstractThis study evaluated an explainable Tabular Prior-data Fitted Network (TabPFN) framework for estimating plot-mean single-plant yield and prioritizing traits
In the process of agricultural intelligence, precise detection of plant organs serves as the foundation for core tasks such as crop phenotyping analysis and yield prediction. However, in complex field environments, small targets such as citrus flowers and shoots face challenges including scale variation, background interference, and dense occlusion, which severely impact detection accuracy. This study improves the YOLOv10 model by introducing the BAM (Bottleneck Attention Module) attention mechanism and GIoU (Generalized Intersection over Union) loss function, constructing a YOLOv10s-BAM-GIoU model suitable for citrus flower, fruit, and shoot recognition. The BAM attention mechanism enhances the model's feature extraction capability for small target organs under complex backgrounds through parallel channel and spatial attention branches; the GIoU loss function improves the localization accuracy of densely occluded targets by optimizing the geometric alignment between predicted and ground-truth boxes. Validation experiments were conducted on a self-constructed dataset. The experimental results show that the improved YOLOv10s achieves significant advantages in comprehensive detection accuracy, with an mAP50 of 89.1%, representing an improvement of 2.9%~9.5% over the original YOLOv10s and other comparative models. In fine-grained category detection, the model achieves mAP50 of 91.2%, 83.6%, and 92.5% for shoots, flowers, and fruits, respectively. Furthermore, while maintaining high detection accuracy, the model achieves a detection speed of 23.6 ms per frame, meeting real-time detection requirements. The research results demonstrate that the improved YOLOv10s model integrating the BAM attention mechanism and GIoU loss function achieves an optimal balance between accuracy and speed in citrus organ detection tasks, providing a preferred solution for field real-time detection systems.
Why it matches plant phenotyping methods柑橘の花・果実・シュートという植物器官を画像から検出する改良モデルを開発し、データセットで精度と速度を検証しており、表現型取得手法が中心である。
abstractThis study improves the YOLOv10 model by introducing the BAM (Bottleneck Attention Module) attention mechanism and GIoU (Generalized Intersection over Union) loss function, constructing a YOLOv10s-BAM-GIoU model suitable for citrus flower, fruit, and shoot recognition.
Abstract The integration of digital technologies for high-throughput field phenotyping is critical for accelerating crop improvement in agriculture. However, extracting traits from remote sensing data remains constrained by fragmented workflows, manual intervention, and limited interoperability among existing tools, resulting in delays that hinder timely biological insight and decision-making. To address these challenges, we present PhenoStream (Phenotyping Streaming), a scalable, end-to-end cyberinfrastructure designed to automate the full lifecycle of aerial imagery-based phenotyping, from data acquisition to plot- and genotype-level inference. The framework integrates automated data ingestion from distributed field sites, geospatial processing, and AI-enabled trait extraction within a unified, user-accessible graphical interface. Its modular and extensible architecture supports adaptable trait modeling and seamless integration of new data sources, enabling deployment across diverse crops, environments, and experimental designs. We demonstrate the system across a large multi-location field trial network of bioenergy crops, where it enables high-throughput characterization of spatiotemporal growth dynamics, genotype-by-environment (G×E) interactions, and predictive modeling of key agronomic traits. By significantly reducing processing latency and manual effort, the platform facilitates near-real-time analysis and reproducible workflows. This work establishes a generalizable and scalable pathway for operationalizing very-high-spatial resolution aerial phenotyping in agricultural research. By bridging data acquisition and analytics, the end-to-end cyberinfrastructure provides a foundation for integrating heterogeneous and unstructured data streams-including remote sensing, environmental, and management data - toward data-driven decision making in agriculture.
Why it matches plant phenotyping methods植物の航空画像から形質を自動抽出するエンドツーエンドのフェノタイピング基盤を開発・実証しており、形質取得ワークフローとプラットフォームが研究の中心である。
abstracta scalable, end-to-end cyberinfrastructure designed to automate the full lifecycle of aerial imagery-based phenotyping, from data acquisition to plot- and genotype-level inference.
Agricultural operations such as pepper harvesting, fruit counting, and field phenotyping rely on accurate visual recognition and instance segmentation algorithms. However, pepper fruits in complex field environments often exhibit slender and curved shapes, partial occlusion, ambiguous boundaries, and adhesion between adjacent instances. Existing object detection and instance segmentation methods therefore struggle to obtain complete fruit masks, which adversely affects subsequent fruit counting, contour measurement, and picking-point localization. To improve the instance segmentation accuracy of occluded peppers in complex field scenes, this study proposes OccPepSeg-YOLO, an improved model based on YOLO11n-seg. First, a P2FreqFusion module is introduced to fuse shallow, high-resolution detail features with deep semantic features, thereby enhancing the representation of fruit edges and tip regions. Second, an ASC module is designed to model the directional and scale-related morphological characteristics of pepper fruits, while a BoundaryGate module strengthens responses at occlusion interfaces and boundaries between adjacent instances. Finally, an OccPepSegment multi-scale prototype segmentation head is constructed, and a BDoU loss function is introduced to improve the boundary consistency of instance masks. Experiments on a self-constructed field-pepper instance segmentation dataset showed that OccPepSeg-YOLO achieved M-P, M-R, M-mAP50, and M-mAP50–95 values of 93.87%, 92.09%, 97.17%, and 82.31%, respectively, representing improvements of 5.59, 3.18, 3.83, and 9.52 percentage points over YOLO11n-seg. Further comparisons with representative YOLO-based instance segmentation models, including YOLOv8n-seg, YOLOv9c-seg, YOLO12n-seg, and YOLOv26n-seg, demonstrated that OccPepSeg-YOLO achieved the best overall segmentation performance. In particular, its M-mAP50–95 exceeded the best competing result obtained by YOLOv9c-seg by 8.35 percentage points. Under a unified repeated-inference protocol on an RTX 3090 GPU using FP32 precision, a batch size of 1, and 640 × 640 inputs, OccPepSeg-YOLO achieved a mean inference latency of 15.801 ± 1.238 ms, a P95 latency of 17.323 ms, and a throughput of 63.29 FPS. These results demonstrate that the proposed model can produce more complete pepper instance masks under leaf occlusion, fruit overlap, and complex background conditions, providing technical support for field-pepper recognition, fruit counting, and visual perception by agricultural robots.
Why it matches plant phenotyping methods圃場画像からピーマン果実のインスタンスマスクを抽出する手法を開発・比較検証しており、果実カウントや輪郭計測に利用可能な植物形質取得が中心である。
abstractAgricultural operations such as pepper harvesting, fruit counting, and field phenotyping rely on accurate visual recognition and instance segmentation algorithms.
Plant phenotyping relevance match · UnverifiedOpenAlex · Europe PMC · checked 14 Sept 2026
Structural failure of cereal stems during late-season climate extremes is a critical determinant of yield stability. In barley, breakage of the stem below the spike, known as head loss, leads to major yield losses, particularly in hot and dry regions where the crop is widely grown. Despite a predicted increase in head loss risk due to global warming, current understanding of the genetic, physiological, anatomical, and environmental factors that control head loss remains limited. Overcoming these knowledge gaps is essential to providing a systems-level strategy for barley breeders to develop climate-ready cultivars that are resilient to stem breakage and suitable for industry adoption. Here, we review present knowledge and highlight opportunities for innovation to mitigate head loss through interdisciplinary approaches that combine precise phenotyping through mechanical testing of stem strength and flexibility, high-throughput phenotyping through drone-based spike counting, and genetic modification strategies informed by studies on hormonal regulation and cell wall composition. Coupled with genotypic data, these efforts will enable the development of a genomic selection platform to facilitate future breeding programs. The framework and tools discussed here are broadly applicable to improving stem resilience in other cereal crops.
Why it matches plant phenotyping methods茎の強度・柔軟性や穂数を対象とする表現型計測手法をレビューし、機械試験とドローンによる高スループット計測を育種基盤として論じているため、表現型手法が中心的です。
abstractHere, we review present knowledge and highlight opportunities for innovation to mitigate head loss through interdisciplinary approaches that combine precise phenotyping through mechanical testing of stem strength and flexibility, high-throughput phenotyping through drone-based spike counting
Maize diseases affecting leaves, stalks, and ears can substantially reduce yield and quality; therefore, rapid and accurate recognition in complex field environments is important for intelligent agricultural monitoring. To address the large-scale variation, weak fine-grained texture, and strong background interference associated with multi-part maize diseases, this study proposes YOLOv11-MPD (YOLOv11 for Maize Multi-Part Disease Detection), a maize disease detection algorithm based on YOLOv11n. The method jointly improves spatial position awareness, shallow detail preservation, local-context modeling, key semantic-region enhancement, and lightweight detection-head reconstruction. RFCAConv, C3k2_RFCAConv, and Detect_LSDECD are introduced into the baseline network to strengthen directional texture modeling, multi-scale feature aggregation, and detection-head feature representation. FG-RFCAConv, HGD-C3k2, LCA-C3k2, and GRN-BiAttn are further designed for high-frequency differential gated detail compensation, P3 high-resolution detail enhancement, local-context fusion, and global-response-normalized attention regulation, respectively. Experimental results show that YOLOv11-MPD achieves Precision, Recall, mAP50, and mAP50-95 of 72.3%, 72.8%, 79.5%, and 50.2%, improving YOLOv11n by 2.4, 2.5, 2.9, and 2.4 percentage points, respectively, while reducing parameters from 2.6 M to 2.4 M. These results indicate that, within the scope of the dataset used in this study, YOLOv11-MPD improves multi-part maize disease detection under complex field conditions. However, the current conclusions are limited to the constructed dataset, and further validation using larger multi-region, multi-season, and multi-device datasets is required to evaluate its broader generalization ability.
Why it matches plant phenotyping methodsトウモロコシの葉・茎・穂における病害状態を画像から検出するアルゴリズムを開発し、性能比較・検証しており、植物表現型取得が研究の中心です。
abstractthis study proposes YOLOv11-MPD (YOLOv11 for Maize Multi-Part Disease Detection), a maize disease detection algorithm based on YOLOv11n.
Plant phenotyping relevance match · UnverifiedbioRxiv · Europe PMC · OpenAlex · checked 13 Sept 2026
Lodging in sorghum presents a significant challenge for plant breeders due to the trade-off between lodging resistance and grain yield. Manually measuring lodging across thousands of plots is time-consuming, expensive, and error-prone, making selection for lodging resistance challenging in breeding programs. Unmanned aerial vehicle (UAV)-derived metrics provide a potential high-throughput alternative; however, it remains unclear whether photogrammetric heights derived from UAV imagery can estimate plot-level lodging severity in large sorghum breeding trials. This study developed a framework for predicting plot-level lodging from UAV imagery across 2,675 sorghum breeding plots. Multi-temporal canopy height data were collected at two critical time points: maximum crop height and at manual lodging assessment. Height percentiles were extracted from UAV-derived point clouds generated using photogrammetric algorithms. These data were used to develop parametric, non-parametric, and ensemble prediction models, which were evaluated using three statistical metrics. The ensemble model, averaging predictions from all models, achieved the highest accuracy with Pearson correlations of r = 0.80-0.84 and lowest root mean square error (RMSE=16-18%), explaining 64-70% of variation in manual lodging counts. Model diagnostics and iterative refinement, including inspection of UAV imagery and dataset curation, had minimal impact on model performance, demonstrating the robustness of the approach. Model performance was consistent across sites, with minimal effects of stratified sampling on accuracy, confirming the ensemble approach as optimal for plot-level lodging assessment. This study demonstrates that integrated multi-temporal UAV imagery offers a practical alternative to labor-intensive manual evaluation methods by enabling high-throughput lodging assessment suitable for implementation in sorghum breeding programs.
Why it matches plant phenotyping methodsUAV画像と写真測量点群からソルガム区画の倒伏程度を推定する取得・解析フレームワークを開発し、実データで精度評価しており、植物表現型測定法が研究の中心である。
abstractThis study developed a framework for predicting plot-level lodging from UAV imagery across 2,675 sorghum breeding plots.
Field / plotLiDAR / point cloudRootMorphology / geometry measurementRoot system architecture
Coarse root systems govern tree anchorage, yet remain among the least documented components of tree architecture: excavation is irreversible, and established 3D methods rely on specialist scanners and lengthy post-processing. We evaluated whether a consumer smartphone records exposed coarse root architecture metrically, and which traits agree most closely with manual measurement. Four fully exposed Scots pine (Pinus sylvestris L.) root systems in northwestern Poland were scanned with an iPhone 17 Pro running Scaniverse, at about 30 min of acquisition and 5 h of processing per tree. Clouds were registered, cleaned and oriented to magnetic north in CloudCompare; of eight architectural metrics, four were validated against manual references at 95 cross-sections on 44 roots, and four were exploratory. Visible root length (root-mean-square error, RMSE, 22.2 cm, 8.4%), azimuth (RMSE 3.58°, mean absolute error 2.47°) and depth (RMSE 3.18 cm, 14.9%) agreed most closely with the reference; 70 of 77 first-order roots were detected with no false positives. Diameter was the weakest metric and the only one dependent on the operator (RMSE 0.46 and 0.29 cm for two operators on the same clouds). Smartphone LiDAR thus turns an irreversible excavation into a permanent, measurable record of the traits relevant to anchorage, provided that centimetre-level diameters are not required.
Why it matches plant phenotyping methodsスマートフォンLiDARによる露出根系の3D形態計測ワークフローを開発・検証し、手動測定と複数の根系形質を比較しているため、植物フェノタイピング手法が中心である。
abstractWe evaluated whether a consumer smartphone records exposed coarse root architecture metrically, and which traits agree most closely with manual measurement.
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:314-336Plant phenotyping relevance match · UnverifiedCrossref · checked 5 Sept 2026
Introduction Accurate estimation of aboveground biomass (AGB) is essential for monitoring pasture productivity and supporting sustainable management of integrated crop–livestock (ICL) systems. We hypothesized that integrating multispectral, thermal, and canopy-structural information derived from unmanned aerial vehicles (UAVs) would improve AGB prediction relative to spectral information alone, and that Generalized Additive Models for Location, Scale and Shape (GAMLSS) would accommodate seasonal heteroscedasticity while maintaining predictive performance comparable to Random Forest (RF) and Support Vector Machine (SVM) models. Methods We collected 280 destructive biomass samples from two ICL paddocks and one continuously grazed pasture in the Brazilian Cerrado between 2022 and 2024. Twenty-four UAV-derived predictors, including spectral bands, vegetation indices, canopy surface temperature, and canopy height, were evaluated using repeated five-fold cross-validation. Model transferability was assessed by withholding one management paddock at a time. Results and discussion Under repeated five-fold cross-validation, GAMLSS achieved the lowest prediction error (R² = 0.69 ± 0.01; RMSE = 2.15 ± 0.04 Mg ha⁻¹), followed closely by SVM (R² = 0.68 ± 0.01; RMSE = 2.19 ± 0.03 Mg ha -1 ); RF showed lower accuracy (R 2 = 0.53 ± 0.01; RMSE = 2.63 ± 0.02 Mg ha -1 ). In the paddock-transferability assessment, GAMLSS also showed the lowest error (R 2 = 0.63 ± 0.04; RMSE = 2.34 ± 0.26 Mg ha -1 ). For GAMLSS, the complete multisensor configuration reduced RMSE by 6.2% compared with the spectral-only configuration. The selected model was used to generate spatially explicit maps of AGB and standing aboveground biomass carbon, estimated from the mean measured carbon concentration of forage biomass. Integrating multispectral, thermal, and structural UAV data with distributional regression improves AGB estimation and enables spatial monitoring of tropical pastures under contrasting management conditions.
Why it matches plant phenotyping methodsUAVのマルチセンサーデータと統計モデルを用いて牧草の地上部バイオマスを推定し、交差検証と圃場間移 transferability 評価を行っており、植物形質の取得・推定手法が研究の中心である。
titleUAV multisensor data and GAMLSS improve forage biomass estimation in Cerrado integrated crop–livestock pastures
Field / plotLiDAR / point cloudStem / branchWhole plant / canopy / plot / fieldClassification2D/3D reconstructionSegmentationArchitecture / morphology / geometry
The separation of a forest plot into individual trees and the automatic extraction of their stem structures from terrestrial laser scanning data are complicated by dense stands, occlusions, and the diversity of biomorphological forms. Existing algorithms usually solve scene partitioning, voxel classification, and tree growing as independent tasks, which leads to error accumulation at subsequent processing stages. This paper proposes a unified model for spatial fragmentation and biomorphological forest segmentation comprising three interrelated stages: scene partitioning by estimated stem coordinates using a Voronoi diagram, probabilistic voxel- or point-level classification, and bottom-up tree growing guided by spatial connectivity and stem membership criteria. For the semantic module, tabular, volumetric, and point-based approaches are compared: gradient boosting with layer-by-layer inference, TabNet, a three-dimensional convolutional neural network, PointNet2, and two-stage pipelines in which gradient boosting builds an initial stem mask for subsequent neural segmentation. The experiment was conducted on 567 mixed-species trees. Considering both quality and computational performance, the {CatBoost; CNN3D} pipeline was selected as the preferred solution, achieving AUC = 0.9966 and IoU = 0.9831. The obtained results show that combining interpretable layer-by-layer classification with subsequent spatial analysis improves the quality of stem structure reconstruction, which is important for automatic forest inventory tasks.
Why it matches plant phenotyping methods地上レーザースキャンから個体樹木と幹構造を自動抽出する統合セグメンテーション手法を開発・比較しており、植物形態の取得が研究の中心である。
abstractThe separation of a forest plot into individual trees and the automatic extraction of their stem structures from terrestrial laser scanning data are complicated by dense stands, occlusions, and the diversity of biomorphological forms.
To establish an accurate and interpretable prediction framework for soybean lodging grade and clarify the core regulatory traits and differentiated driving mechanisms of soybean lodging under high-density drip irrigation cultivation, 356 spring soybean germplasm accessions were used as experimental materials in this study. Morphological and mechanical traits including plant height (PH), stem pulling force (SPF), internode number (IN) and petiole length (PL) were measured over two consecutive years of field phenotyping. Two composite evaluation indices, plant height/stem pulling force ratio (PH/SPF) and plant height/internode number ratio (PH/IN), were further constructed. Four machine learning algorithms were adopted to develop multi-classification models for soybean lodging grade prediction. SHAP analysis combined with three global sensitivity approaches (perturbation analysis, Sobol’ method and Morris screening) was applied to decipher the regulatory patterns of key traits. The results showed that lodging grade significantly affected soybean grain yield and explained 25–28% of the phenotypic yield variation; yield reduction tended to plateau under severe lodging. Compared with single indicators such as SPF and PL, the two derived composite indices could stably distinguish soybean accessions with different lodging grades and exhibited stronger discriminatory power. Model comparison revealed that the XGBoost model achieved optimal prediction accuracy and generalization stability for lodging grade, with a weighted F1-score of 95.34% on the test set, significantly outperforming the conventional linear model. Interpretability analysis demonstrated that the PH/IN, PH, and PH/SPF acted as the primary positive traits promoting lodging, while SPF was the sole protective trait. Driving factors of lodging presented obvious gradient heterogeneity: mild lodging was dominated by the imbalance of plant architecture ratio, whereas severe lodging was governed by the cumulative effects of PH and IN. Strong interactions existed among all measured traits. The interpretable machine learning framework established in this study can provide theoretical support and technical references for lodging-resistant germplasm screening and targeted plant architecture regulation for densely planted soybean under drip irrigation systems.
Why it matches plant phenotyping methods大豆の倒伏状態を形態・力学形質から機械学習で推定し、モデル性能比較と解釈性解析を行う枠組み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。
abstractTo establish an accurate and interpretable prediction framework for soybean lodging grade and clarify the core regulatory traits and differentiated driving mechanisms of soybean lodging
Abstract Purpose : The system for diagnosing diseases in Solanaceae crops (SolanAPP), including tomatoes, potatoes, peppers, and eggplants, represents a promising tool for supporting decision-making in agricultural fields using AI. This system reconciles the computational intensity of multitasking models with the infrastructural limitations of rural environments, thereby increasing digital literacy. Its architecture is based on two fundamental pillars: (i) autonomous, offline operation for the detection and classification of diseases in Solanaceae crops; (ii) a georeferenced epidemiological surveillance network with agricultural recommendations for crop monitoring. Methods : The core diagnostic process combines crop-specific semantic segmentation and disease classification models exported to TensorFlow Lite, enabling on-device visual inference and pixel-level severity estimation. An optional online layer integrates Groq’s large language model (LLM)-based reasoning and Firebase services to generate structured agronomic explanations and facilitate the creation of georeferenced community reports when a connection is available. Preprocessing and management of the dataset were performed using the Roboflow platform. The mobile app was developed natively in Kotlin. Model performance was rigorously evaluated using accuracy, recall, F1 score, mean IoU, mPA, inference latency, model size, and decision matrix. The optimal model for the crop was selected using Simple Additive Weighting (SAW). Finally, the overall framework quality and usability were evaluated in Cuba through a user validation survey using a 5-point Likert scale and aligned with the ISO/IEC 25010 software quality model. Results : The model that yielded the best results for most crops was DeepLabV3+ with MobileNetV2, which achieved a classification accuracy of over 97\% while operating with lower inference latency. Beyond individual diagnoses, the system incorporates a collaborative georeferencing feature that allows users to share observations and precise geographic coordinates of detected pathologies to facilitate regional epidemiological monitoring. The user satisfaction survey yielded a satisfaction rating of 4.5/5, with users highlighting the importance of offline diagnosis. Conclusion : Plant disease diagnosis using computer vision can support earlier intervention in resource-constrained agricultural settings, but practical deployment requires models that are accurate, lightweight, interpretable, and usable under limited connectivity. SolanAPP, an offline-first Android framework for detecting foliar pathologies in Solanaceae crops, not only establishes a framework for disease identification in complex natural environments but also provides a theoretical and practical foundation for automated agronomic treatment recommendations and community-based crop surveillance. Impact SolanAPP is a free framework that supports the synergy between multitask deep learning for offline disease diagnosis and LLM-driven reasoning for decision-making in the field. Beyond the quantitative metrics obtained from the selected models, the deployment of SolanAPP in rural contexts serves a fundamental socio-technical purpose: it acts as a catalyst for open access, digital literacy, and agronomic decision-making under unfavorable development conditions. It also represents a strong effort to foster a collaborative epidemiological surveillance network in the agricultural sector. Although it faces challenges, such as the use of field images for model training, this framework marks a promising step in the deployment of edge AI, balancing technical accuracy with practical utility.
Why it matches plant phenotyping methods植物病害を画像からセグメンテーションし、病害のピクセル単位の重症度を推定する手法と、オフライン実装・性能評価を中心とした研究であり、植物状態の計測方法が中核です。
abstractThe core diagnostic process combines crop-specific semantic segmentation and disease classification models exported to TensorFlow Lite, enabling on-device visual inference and pixel-level severity estimation.
Abstract Plant diseases represent major constraints on agricultural productivity, often resulting in significant yield losses. This study presents FitoView, a cloud-based mobile decision support system that integrates deep learning with real-time weather forecasting for sustainable plant disease management. Demonstrated through a case study on Cercospora leaf spot in chili pepper, the system employs custom YOLOv8 models for automated disease detection, classification, and pixel-level severity quantification, combined with meteorological data from the OpenMeteo API. The core innovation lies in an integrated decision matrix that considers three dimensions: AI-assessed disease severity, 48-hour climatic risk forecasts, and optimal spraying conditions, generating four contextualized management scenarios with tailored re-evaluation periods (3-10 days). OpenMeteo API validation across four cities in Sergipe demonstrated very strong correlations, with Pearson coefficients (r) of 0.90-0.97 for temperature, 0.81-0.95 for humidity, and 0.92-0.95 for solar radiation, corresponding to R² values of 0.65-0.94. The YOLOv8 object detection model achieved perfect precision (100%) and macro-averaged recall of 89% across all disease classes, with Cercospora leaf spot detection reaching perfect metrics (100% precision, recall, and F1-score). Field validation in Lagarto, Sergipe, confirmed the system’s practical use: it accurately detected Cercospora leaf spot, estimated severity, and, combined with climatic risk, generated recommendations for alternative treatment and short-term re-evaluation. The Progressive Web Application architecture, deployed on a Cloud Platform, ensures accessibility without installation requirements, while the modular design enables scalability to additional crops and diseases, representing a significant advancement toward democratizing AI-powered precision agriculture tools for smallholder farmers in Brazil.
Why it matches plant phenotyping methods植物病害の検出・分類と病斑のピクセルレベル重症度推定をYOLOv8で実装・検証したシステムであり、植物状態の取得・定量化が中心的な技術貢献です。
abstractThe core innovation lies in an integrated decision matrix that considers three dimensions: AI-assessed disease severity, 48-hour climatic risk forecasts, and optimal spraying conditions
Maize ( Zea mays L.) is a highly adaptable crop grown worldwide across diverse climates and management practices, with uses across multiple sectors. Consequently, the traits prioritized in maize research and breeding programs vary depending on the specific objectives. Core traits, however, such as flowering time, plant and ear height, and stalk and root lodging, which are important for evaluating and improving the performance and stability of maize genotypes, are routinely evaluated across breeding programs, regardless of their goals. Standardized measurement of these core traits is essential to ensure data reliability and comparability, enabling the integration of phenotypic data across different experiments. Such efforts ultimately support better decision-making and accelerate the development of improved maize genotypes. This is particularly important in public sector programs, where large-scale evaluations, critical for assessing the value of specific genotypes, are often only feasible through collaboration across programs. Here, we provide a protocol for the standardized collection of phenotypic data, specifically focusing on how to measure core traits in maize field trials. These methods promote consistency and accuracy in the evaluation of these traits, and support communication and coordination among groups in the public sector and other research settings. Further, such standardization facilitates the integration and comparison of data across programs, enabling robust longitudinal and multienvironment analyses.
Why it matches plant phenotyping methodsトウモロコシの主要形質を対象に、圃場試験での表現型データ収集を標準化するプロトコル自体を提示しており、測定方法が研究の中心である。
abstractHere, we provide a protocol for the standardized collection of phenotypic data, specifically focusing on how to measure core traits in maize field trials.
Abstract Ascochyta blight is a widely occurring chickpea fungal disease that can cause severe yield loss. Breeding for crop resistance benefits from high‐throughput evaluation of plant–pathogen interactions in genotypes which can serve as sources of resistance. Current practice for the evaluation is human visual scoring of disease symptoms, which is limited in throughput and precision. Here, we developed open‐source sensor‐based phenotyping methods using red, green, blue (RGB) and multispectral imaging to measure resistance components and predict disease severity classes in chickpea and wild relatives grown outdoors over three seasons. Pots were imaged at multiple time points with a ground‐based platform, providing 86,792 RGB and 8199 multispectral images. Lesion count was estimated with YOLOv5 (You Only Look Once version 5) object detection (F1 score = 0.27–0.30), fractional green canopy cover was estimated from RGB images, and vegetation indices were extracted from multispectral images. A model trained on growth rates of fractional green canopy cover normalized to control genotypes could predict disease severity classes with an accuracy of 65% –81 % ( 0.43–0.59) on unseen data from three different seasons. The developed methods provide a pathway to predict visual disease severity scores and support the breeding of crops for disease resistance. They may also be used to characterize disease progression, to find underlying resistance mechanisms, and for early disease detection.
Why it matches plant phenotyping methodsRGB・マルチスペクトル画像と地上センサープラットフォームを開発し、病斑数、緑色キャノピー被覆率、病害重症度を推定・予測する手法が研究の中心であるため。
abstractHere, we developed open‐source sensor‐based phenotyping methods using red, green, blue (RGB) and multispectral imaging to measure resistance components and predict disease severity classes in chickpea and wild relatives grown outdoors over three seasons.
Abstract This study evaluated the potential of UAV-derived RGB spectral indices to predict fiber quality traits in cotton genotypes. Nineteen genotypes were assessed under a randomized complete block design, and RGB imagery acquired at full flowering was used to calculate GLI, NGRDI, SCId, and SI. Significant genetic variability and moderate-to-high heritability were observed for both fiber traits and spectral indices. GLI was positively associated with the Spinning Consistency Index, whereas NGRDI was associated with fiber length uniformity. Regression models showed moderate predictive ability (R² LOOCV between 32.4–35.4%; and accuracy between 0.57–0.60). GLI and NGRDI demonstrated potential as complementary tools for large-scale phenotyping and preliminary genotype selection, although they do not replace conventional fiber quality analyses. Further studies across additional developmental stages are needed to improve prediction accuracy.
Why it matches plant phenotyping methodsUAV由来RGB画像からスペクトル指標を算出し、ワタの繊維品質形質を予測する手法を評価しており、大規模フェノタイピングへの応用と予測性能の検証が中心である。
abstractThis study evaluated the potential of UAV-derived RGB spectral indices to predict fiber quality traits in cotton genotypes.
The rapid detection and continuous monitoring of crop health and disease outbreaks are critical components of modern precision agriculture, essential for maintaining global food security. Traditional field-based scouting methods, while accurate, are often labor-intensive, time-consuming, and limited by spatial coverage, making them inadequate for large-scale agricultural operations. Remote sensing (RS) technologies—spanning satellite imagery, drone-based aerial platforms, and proximal sensors—offer a powerful, non-destructive, and scalable alternative for capturing high-resolution spectral and temporal data. This paper provides a comprehensive evaluation of current remote sensing applications in crop health monitoring and disease surveillance. We analyze how vegetation indices derived from multispectral and hyperspectral data, such as NDVI and red-edge parameters, serve as sensitive indicators of physiological stress and pathogen infection, often manifesting before visible symptoms appear. Furthermore, we explore the integration of machine learning and artificial intelligence algorithms in automating disease identification and severity mapping. By synthesizing recent advancements in sensor technology and data analytics, this paper demonstrates that remote sensing is indispensable for proactive, site-specific management. The findings emphasize that a multi-scale RS approach—integrating broad-scale satellite monitoring with high-resolution drone sorties—enables farmers to optimize input efficiency, minimize yield losses, and enhance the overall resilience of agro-ecosystems against biotic and abiotic stressors.
Why it matches plant phenotyping methods作物の健康・病害を対象に、リモートセンシング、センサー、植生指数、機械学習による状態・重症度推定を包括的に評価するレビューであり、フェノタイピング手法が中心です。
abstractThis paper provides a comprehensive evaluation of current remote sensing applications in crop health monitoring and disease surveillance.
Plant disease and plant stress early warning systems have advanced through deep learning, remote sensing, digital phenotyping, disease forecasting, and sensor networks. Detection accuracy, precision, recall, F1-score, and area under the curve remain indispensable, but they are insufficient for judging whether a warning can support timely and proportionate phytoprotection under field variability. This Mini Review argues that intelligent plant health warning systems should be evaluated not only as prediction models, but also as safety-relevant decision-support systems embedded in biological, agronomic, and operational contexts. We first relate AI-based detection to established plant disease forecasting and decision-support traditions, including weather-based models, epidemiological forecasting, and integrated disease management. We then adapt selected safety-assurance concepts, including risk assessment, failure mode and effects analysis, Bow-tie reasoning, warning-threshold governance, reliability analysis, resilience thinking, and response closure, to host-pathogen-environment warning chains. The proposed framework links AI or sensor outputs with pathogen biology, host susceptibility, environmental conduciveness, inoculum pressure, uncertainty assessment, risk classification, threshold decisions, human or automated verification, intervention, and feedback learning. Illustrative crop-pathogen scenarios, including wheat rust, rice blast, potato late blight, grapevine downy mildew, and citrus greening, show how safety assurance can complement existing forecasting and decision-support systems rather than replace them. The framework remains conceptual, and whether these added assurance functions improve existing warning systems requires comparative evaluation under field conditions. Future systems should be evaluated through detection performance and response-oriented indicators such as lead time, calibration, false-alert burden, missed-warning rate, response completion, disease suppression, economic value, and learning after field action.
Why it matches plant phenotyping methods植物病害・ストレスの検出を含む知的警戒システムについて、AI・リモートセンシング・デジタルフェノタイピング・センサーネットワークの評価枠組みを体系的に論じる方法論レビューであり、方法論が中心です。
abstractPlant disease and plant stress early warning systems have advanced through deep learning, remote sensing, digital phenotyping, disease forecasting, and sensor networks.
Precision agriculture increasingly requires intelligent systems capable of integrating multimodal sensing with transparent decision support to enable timely and reliable crop management. This study proposes a hybrid intelligent IoT framework integrating environmental monitoring, wearable plant physiological sensing, AI-based pest-monitoring, machine-learning-based prediction of crop physiological stress, and explainable fuzzy rule-based decision support into a unified architecture for crop stress assessment. A novel Physiological Stress Index (PSI) was developed by combining vapor pressure deficit, relative humidity, Delta-T, leaf capacitance, and relative irradiance to provide an interpretable indicator of crop physiological stress. The proposed framework was experimentally validated under real field conditions using a commercial environmental monitoring station, wearable leaf sensors, AI-enabled pest-monitoring devices, and cloud-based analytics. Correlation analysis confirmed strong relationships between PSI and the principal environmental variables (VPD: r = 0.980, Delta-T: r = 0.990, RH: r = −0.961), demonstrating the internal consistency and sensitivity of the proposed index. At the 15 min forecasting horizon, Linear Regression and Gradient Boosting demonstrated virtually identical performance: Gradient Boosting achieved a marginally lower RMSE and higher R2 (RMSE = 0.0273; R2 = 0.9810), whereas Linear Regression achieved a slightly lower MAE (MAE = 0.0186). At the 1 h forecasting horizon, Gradient Boosting achieved the strongest performance (R2 = 0.9034), indicating increasing relevance of nonlinear modelling at longer prediction horizons. The proposed framework demonstrates the feasibility of combining multimodal sensing, machine learning, explainable artificial intelligence, and edge-enabled IoT technologies to support proactive, transparent, and intelligent precision agriculture.
Why it matches plant phenotyping methods植物の生理的ストレス状態を多モーダルセンサーと機械学習で推定する方法を開発し、圃場で検証しており、フェノタイピング手法が中心である。
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:158-191Plant phenotyping relevance match · UnverifiedCrossref · checked 5 Sept 2026
Plant diseases destroy 20–40% of global food production annually, posing a critical threat to food security for a projected population of 9.7 billion by 2050. Conventional diagnostic approaches relying on expert visual assessment are slow, costly, and unsuitable for modern agricultural scales. While deep convolutional neural networks demonstrated early promise, single-modality, image-centric systems consistently fail under real-world field conditions characterized by variable lighting, co-occurring infections, and cultivar diversity. This review synthesizes a decade of progress across four interconnected frontiers: the evolution of deep learning architectures for plant disease detection; the adaptation of foundation models including CLIP, SAM, and DINOv2 to agricultural contexts; the development of multimodal fusion frameworks integrating imagery, environmental, genomic, and hyperspectral data; and the transition from static disease diagnosis to descriptive comparison of reported metrics, which suggested that multimodal approaches frequently reported improved diagnostic performance relative to corresponding single-modality baselines, although direct cross-study comparison was limited by methodological heterogeneity. A systematic review following PRISMA guidelines identifies eligible comparative studies. Descriptive comparison of reported performance metrics across these studies indicated that multimodal approaches generally achieved higher accuracy and sensitivity than single-modality models, particularly for pre-symptomatic disease detection. Eight critical research gaps are identified, including the absence of a unified agricultural foundation model and limited climate-aware forecasting under non-stationary climate projections. A structured research agenda is proposed to accelerate translation from laboratory performance to globally equitable, field-deployable crop protection systems.
Why it matches plant phenotyping methods植物病害の画像ベース検出・予測手法を対象とする系統的レビューであり、植物の病徴・病害状態を観測から推定するフェノタイピング手法のレビューとして中心的です。
titleMultimodal Deep Learning and Foundation Models for Early Detection and Forecasting of Plant Diseases
Abstract In modern agriculture, it is essential to identify the early symptoms of plant diseases and to accurately maintain the productivity of the crop and reduce economic losses. Foliar diseases are a special concern in peach because they can cause yield as well as quality if not timely detected. Artificial intelligence, machine learning and deep learning are some of the advanced technologies that are gaining great importance in today's agriculture, especially with the image analysis applications. In this study, a deep learning method for automated detection and classification of three peach leaf diseases and healthy class was presented based on image data. The dataset were taken at different phenological and disease stages under temperate conditions in Kashmir with four classes Healthy, Leaf Curl, Shot hole and Rust. Three convolutional neural networks (CNNs) architectures were applied, VGG-16, ResNet 50 and Xception were trained using transfer learning and Inception-V4 was trained from scratch for a comparative study of the learning strategies. Data augmentation techniques were applied to improve generalization. Results show that all models were able to learn disease specific features well. The result of Inception-V4 was found to be highest with 97.50%, followed by ResNet-50 with 94.49%, VGG-16 with 92.04% and Xception with 75.95%. The results of transfer learning-based architectures were also good and competitive but the best results obtained from the Inception-V4 architecture reveal its capability in modelling complex visual patterns. The results highlight the potential of deep learning techniques for early detection of diseases in peach, supporting precision agriculture and better disease management.
Why it matches plant phenotyping methodsモモ葉の画像から病害症状を自動検出・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いるため。
abstracta deep learning method for automated detection and classification of three peach leaf diseases and healthy class was presented based on image data.
Abstract A systematic review based on 174 Scopus-records of studies using YOLO-type one-stage detectors for detecting citrus fruits, their count, and yield estimation followed PRISMA guidelines 2020. The title/abstract-screening process, done in duplicate (κ=0.920) yielded 90 included study-records, followed by two further post-hoc exclusions. Each study in the 80 reporting on fruit-level detection showed an average precision of 89.6%, recall of 85.9%, and mAP@0.5 of 91.0%. However, coverage for any individual metric rarely exceeded half of the studies, and only 13% were able to report the more stringent mAP@0.5:0.95. Both YOLOv8 and YOLOv5 were each utilized as the backbone architecture by approximately 22.2% of the studies. From 2025, YOLOv11 has also been emerging. Half of all studies modified architectural components including attention modules, lightweight architectures, and variants of IoU loss functions. Original contributions are generally concentrated in downstream tracking, sensor fusion, and yield modeling rather than the detector itself. A custom-made seven-domain risk of bias tool was developed and utilized by two reviewers who arbitrated discrepancies (91.5%). Results showed that all but one of the reviewed studies had a high level of risk due to almost universal lack of statistical validation and limited dataset diversity; a sensitivity analysis excluding the most risky studies left the performance profiles nearly identical. We conclude that the field has converged around a common technical toolkit but continues to lack standardized benchmarks, multispectral data, and rigorous field-deployment validation.
Why it matches plant phenotyping methods柑橘果実の検出・計数・収量推定に用いる画像解析手法を体系的にレビューし、性能評価、リスク・オブ・バイアス、標準化やベンチマーク不足を検討しており、植物フェノタイピング手法が中心である。
abstractA systematic review based on 174 Scopus-records of studies using YOLO-type one-stage detectors for detecting citrus fruits, their count, and yield estimation followed PRISMA guidelines 2020.
Abstract Purpose Timely, accurate, and field-scale crop yield mapping is essential for precision crop management, yet most existing studies rely on late- or full-season data, limiting in-season decision-making. This study aims to develop a stage-aware earliest possible corn yield mapping framework that balances early data availability, predictive accuracy, and spatial fidelity by integrating Sentinel-2 imagery, vegetation indices (VIs), and accumulated growing degree days (AGDD). Methods Corn yield data were collected from a commercial farm over three growing seasons (2018–2020). The final modeling dataset included 51,794 Sentinel-2 10 m aggregated yield samples across three seasons: 2018 ( n = 16400), 2019 ( n = 18534), and 2020 ( n = 16860). Sentinel-2 raw spectral bands and derived VIs were organized for V4, V6, R1, R5, and R6 growth stages based on AGDD- and DAP-defined corn growth-stage windows, also confirmed visually on-ground, allowing observations from different planting and harvest dates across the three growing seasons to be aligned by crop developmental stage rather than calendar date. A stage-wise Pearson correlation and frequency-based selection identified informative and non-redundant VI subsets across crop development. Four machine learning models: Random Forest (RF), XGBoost (XGB), k-Nearest Neighbors (kNN), and a Neural Network (NNET; multi-layer perceptron) were trained using 13 input configurations, including individual growth stages and multi-stage combinations capturing phenological progression. Models were tuned via randomized search, trained on 2018–2019 data, and independently validated on the 2020 season. Yield predictions were mapped directly at 10 m Sentinel-2-pixel resolution without spatial interpolation to preserve fine-scale variability. Results Model performance was strongly influenced by phenological stage selection. Among single-stage inputs, R1 was the earliest stage where reliable yield mapping could be availed (RF: R² = 0.56, RMSE = 29.50%). While combining V6 with R1 stage inputs substantially improved predictive performance (RF: R² = 0.70, RMSE = 24.13%) for the yield mapping at the R1 stage, where V6-stage signals provided complementary yield-related information. The full-season combination (V4 + V6 + R1 + R5 + R6) produced the highest accuracy (RF: R² = 0.72, RMSE = 23.28%) but would be less suitable for early in-season decision-making. Early- or late-stage-only inputs (V4, R5, R6) showed weaker and less stable cross-year performance. Among algorithms, RF consistently generalized best to the independent 2020 dataset and is recommended for operational use. XGB showed strong training performance but reduced cross-year stability, kNN yielded moderate accuracy, and NNET achieved accuracy comparable to RF while closely reproducing observed spatial patterns such as center-pivot effects and edge gradients. Direct 10 m mapping preserved yield heterogeneity and avoided smoothing artifacts common in interpolation-based approaches. Conclusion Stage-aware feature selection and phenology-informed input combinations are critical for balancing yield prediction timeliness and accuracy. For operational in-season yield mapping, the RF model using the V6 + R1 stage combination provides a practical and reliable solution, enabling early, accurate, and spatially detailed yield estimates with robust cross-year performance. This study presents a deployable framework for integrating satellite time series and weather data into conventional (non-sequential) machine learning models to support proactive, within-season decision-making in precision agriculture.
Why it matches plant phenotyping methods衛星画像・気象データと機械学習を統合し、作物の収量という明示的な植物形質を圃場内10 m解像度で推定する手法を開発・独立年で検証しており、フェノタイピング手法が中心である。
abstractThis study aims to develop a stage-aware earliest possible corn yield mapping framework that balances early data availability, predictive accuracy, and spatial fidelity by integrating Sentinel-2 imagery, vegetation indices (VIs), and accumulated growing degree days (AGDD).
Conventional breeding for ideotypes in target environments remains challenging due to genotype-by-environment interactions and the genetic complexity of key agronomic traits. Traditional multi-environment field trials are costly and time-consuming, limiting rapid genetic gain. These challenges highlight the need for digital tools to support rice breeding. However, two major approaches, genomic prediction (GP) and gene-based crop models (GBCMs), have distinct advantages. In this study, a dataset derived from a natural rice population comprising 210 genotypes, genotyped with about 650,000 markers, rice dry matter, and yield across three environments, was used to develop two genomic prediction models, genomic best linear unbiased prediction (GBLUP) and a convolutional neural network (CNN), together with a gene-based crop modeling framework. The effectiveness of these models in predicting rice traits and assisting in breeding selection was subsequently evaluated. Prediction results indicated that biomass and yield could be effectively predicted by all models, with Normalized Root Mean Square Error (NRMSE) values ranging from 10.60% to 18.59% and 9.93% to 18.19%, respectively. In terms of predictive accuracy, parameter-based crop models achieved the highest predictive accuracy, although it was confined to theoretical simulations. This was followed by the GBCM and CNN, whereas the GBLUP exhibited the lowest performance. Furthermore, GGE biplot analysis revealed the predictions of the GBCM aligned more closely with field observations than those of the CNN, emphasizing the potential of GBCM as a practical surrogate for digital breeding. These results provide valuable insights into modeling genotype-by-environment interactions and support the development of data-informed breeding strategies for future rice improvement.
Why it matches plant phenotyping methodsイネの乾物量・収量という植物形質を予測する複数の計算モデルを開発・比較評価しており、形質推定手法が研究の中心である。
abstractIn this study, a dataset derived from a natural rice population comprising 210 genotypes, genotyped with about 650,000 markers, rice dry matter, and yield across three environments, was used to develop two genomic prediction models, genomic best linear unbiased prediction (GBLUP) and a convolutional neural network (CNN), together with a gene-based crop modeling framework.
Lodging is a major yield-limiting factor in soybean, but efficient large-scale phenotyping and genetic dissection of this complex trait remain challenging for breeding programs. To bridge this gap, this study developed an integrated, breeding-oriented framework that links UAV-based high-throughput phenotyping with candidate gene identification. Field experiments involving 741 diverse soybean genotypes were conducted over two years, with UAV remote sensing performed at key reproductive stages (from R5 to R7). We identified UAV-derived structural (relative plant height), textural (homogeneity, dissimilarity, correlation), and spectral (NDVI, EVI, NDRE) features as the most sensitive indices for retrieving lodging severity. The fusion of these complementary features, coupled with the XGBoost algorithm, achieved high classification accuracy (0.81–0.92) across genotypes, growth stages, and years. This reliable phenotyping pipeline enabled the precise selection of contrasting genotypes (lodging-resistant vs. lodging-prone) for transcriptomic analysis. Transcriptome sequencing revealed 13,447 differentially expressed genes, with significant enrichment in phenylpropanoid and starch–sucrose metabolic pathways. Moreover, the haplotype analysis within a natural population identified superior allelic variants of two candidate genes ( Glyma.19G249100 and Glyma.05G142200 ) significantly associated with soybean lodging resistance. This work can effectively bridge the gap between scalable field phenotyping and the discovery of functionally validated breeding targets, providing an efficient and translational framework to accelerate the development of lodging-resistant soybean varieties.
Why it matches plant phenotyping methodsUAV画像・リモートセンシング特徴量とXGBoostを統合し、ダイズの倒伏重症度を大規模に推定・検証する育種向け表現型解析パイプラインが研究の中心である。
abstractthis study developed an integrated, breeding-oriented framework that links UAV-based high-throughput phenotyping with candidate gene identification
Canopy 3D architecture is a critical determinant of light interception, photosynthetic efficiency, and final yield in cotton, yet its rapid and accurate characterisation remains challenging in field conditions. To achieve efficient, non-destructive, and quantitative monitoring of the canopy structure of field-grown cotton, this study proposes a 3D structure-based technology stack for high-efficiency, low-cost, and high-precision phenotyping extraction. This stack directly addresses the technical bottlenecks of traditional 3D data acquisition, namely high cost, long processing time, and low operational efficiency, which have hindered large-scale application. We developed a pipeline that integrates a fast reconstruction algorithm with a scale-recovery mechanism using ground control points (GCPs), enabling the generation of true-scale 3D point clouds from UAV aerial images in a cost- and time-effective manner. Using only 141 UAV images and with a reconstruction time of approximately 20 min, we efficiently reconstructed high-quality, scale-accurate point clouds of two 5.5 m × 5.5 m cotton plots, significantly outperforming SfM-MVS and Instant-NGP in terms of both reconstruction efficiency and point cloud completeness. This method, whose current validation is confined to a single season, one growth stage, and two experimental plots, not only achieves a breakthrough by using fewer input images with high efficiency, but also ensures point cloud accuracy and completeness, showing strong potential for rapid field monitoring and real-time management. Based on the high-quality reconstructed point clouds, we further quantitatively evaluated canopy characteristics at harvest, analyzing the coefficient of variation of canopy height, porosity distribution, and canopy volume fraction. The core shortcomings and optimization strategies for the existing canopy structure were identified, providing scientific data support and practical technical references for precision cultivation management and mechanization-compatible planting in cotton.
Why it matches plant phenotyping methodsUAV画像からの3D点群再構成とスケール復元パイプラインを開発・比較検証し、綿花キャノピー形質を定量化することが研究の中心であるため含める。
abstractthis study proposes a 3D structure-based technology stack for high-efficiency, low-cost, and high-precision phenotyping extraction.
Accurate estimation of the cotton seedling Leaf Area Index (LAI) is essential for yield prediction and precision crop management. Traditional manual methods are limited by low throughput, while two-dimensional remote sensing techniques often struggle with sparse canopy cover and soil background interference. Although three-dimensional LiDAR presents a promising alternative, existing deep learning approaches typically depend on costly fully supervised point-wise annotations. To address this challenge, this study proposes an end-to-end framework that integrates UAV-based LiDAR, weakly supervised segmentation, and physical parameter inversion. A weakly supervised network, termed CogNet, was developed—incorporating self-distillation and structure-aware label propagation—to achieve precise segmentation of cotton plants using only 10% sparse annotations. Following instance segmentation via Density-Based Spatial Clustering of Applications with Noise (DBSCAN), individual plant phenotypic traits were extracted. A nonlinear Extreme Gradient Boosting (XGBoost) model was then constructed to invert LAI by leveraging allometric relationships between 3D structural parameters and leaf area. Experimental results showed that CogNet achieved an Intersection over Union (IoU) of 85.34%, effectively mitigating overfitting to label noise and achieving performance competitive with the fully supervised RandLA-Net (82.13%). Notably, under the specific conditions of this cotton seedling dataset characterized by strong geometric priors, the weakly supervised model demonstrated enhanced robustness against annotation inconsistencies. The framework attained a plant detection rate of 96.2%, and the XGBoost model delivered high estimation accuracy (R² = 0.879, RMSE = 0.138). This study demonstrates that weakly supervised learning can substantially reduce annotation costs while maintaining model performance, providing an efficient and cost-effective solution for field-scale crop phenotyping.
Why it matches plant phenotyping methodsUAV-LiDAR、弱教師ありセグメンテーション、個体形質抽出、LAI推定を統合した作物フェノタイピング手法の開発・評価が研究の中心である。
abstractthis study proposes an end-to-end framework that integrates UAV-based LiDAR, weakly supervised segmentation, and physical parameter inversion.
Sun-induced chlorophyll fluorescence (SIF) is an effective proxy for vegetation photosynthesis, but tower-based retrieval suffers from atmospheric path interference under humid and variable conditions. We present a DOAS-based SIF retrieval algorithm that operates in Fraunhofer lines (680–686 nm, 745–758 nm) and water vapour-sensitive bands (717–727 nm). It constructs an adaptive reference spectrum from SCOPE simulations and PCA and incorporates H2O absorption cross-sections into the fitting process for active atmospheric correction. The algorithm is implemented in a dedicated tower-based system integrating a 1° scanning gimbal with a high-resolution spectrometer. Validation with simulated and field data demonstrates the following: (1) the algorithm retrieves SIF with high fidelity (correlation coefficients >0.9 across all windows); (2) it exhibits lower water-vapour sensitivity and greater cloudy-sky stability than FLD, 3FLD, and SFM, achieving the lowest coefficient of variation (CV = 0.356); (3) over a complete wheat–rice rotation, the retrieved SIF tracks crop growth and phenological stages. This work provides a reliable solution for automated, high-precision tower-based SIF observation under complex atmospheric conditions.
Why it matches plant phenotyping methods植物の光合成状態を示すSIFを取得するタワー型分光観測システムとDOAS補正アルゴリズムを開発し、シミュレーションおよび圃場データ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 present a DOAS-based SIF retrieval algorithm
Field / plotLiDAR / point cloudMultispectral / hyperspectralLeafMorphology / geometry measurementLeaf traits
Canopy Leaf Area Index (CLAI) is a stand attribute containing information on the real-time health and growth potential of managed pine plantations. Current remote sensing techniques for quantifying CLAI rely on simple linear models applied to satellite multispectral imagery, or on techniques based on light detection and ranging (LiDAR) data that are costly and less frequently collected. This study demonstrates a convolutional neural network (CNN) approach to retrieving CLAI from 10 m Sentinel-2 multispectral imagery with a model trained on gridded LiDAR-based CLAI estimates. We demonstrate large gains in accuracy with the CNN compared to traditional linear models based on vegetation indices (e.g., Simple Ratio), but also clear shortfalls in model skill when predicting “blind” in some spatial domains that were completely excluded during model training. Pixel-scale root mean squared error ranged from 0.34 to 0.64 by domain when exposed to CLAI training data from all available spatial domains, but rose to 0.58–1.74 when predicting without prior domain-specific training. Prediction accuracy was consistently lower when applied to completely unobserved USGS LiDAR-based CLAI estimates. Traditional linear models, in contrast, had the advantage of usually lower prediction error across unobserved spatial domains (0.43–1.98), but with lower maximum accuracy. These results demonstrate a potential route for deploying more complex models for LiDAR “mimicry”, e.g., between data acquisitions widely separated in time, but advocate for the development and use of more stable generalized approaches for use in unobserved managed pine stands.
Why it matches plant phenotyping methodsLiDARで得た林分の葉面積指数をSentinel-2画像とCNNから推定する手法を開発・比較検証しており、植物キャノピー形質の取得が研究の中心です。
abstractThis study demonstrates a convolutional neural network (CNN) approach to retrieving CLAI from 10 m Sentinel-2 multispectral imagery with a model trained on gridded LiDAR-based CLAI estimates.
Field / plotPhotogrammetry / SfM / MVSLiDAR / point cloudMultispectral / hyperspectralWhole plant / canopy / plot / field2D/3D reconstruction
The Greater Cape Floristic Region (GCFR) in South Africa is a fire-prone biodiversity hotspot where high species richness, structural complexity, and small plant sizes (0.0001–4 m2) pose substantial challenges for remote sensing-based biodiversity assessment. Spectral similarity among species and the mismatch between plant size and sensor pixel dimensions limit the capacity of current and forthcoming spaceborne systems to resolve individual species and accurately detect plot-level diversity changes. We therefore developed a physics-based simulation framework that couples fynbos trait measurements with radiative transfer modeling in the DIRSIG (Digital Imaging and Remote Sensing Image Generation) environment towards quantifying information loss across spectral and spatial scales and to define theoretical limits for biodiversity monitoring. We constructed a three-dimensional virtual scene of post-fire fynbos communities in Grootbos Private Nature Reserve, integrating high-resolution imagery, terrestrial laser scanning (TLS), and structure-from-motion (SfM)-derived point clouds. Field measurements of mean diameter and percent cover were used to scale vegetation models and constrain species abundance. We distributed plant instances using a blue noise sampling algorithm, guided by density maps derived from unmanned aerial system (UAS) imagery. Species-specific optical properties were parameterized using field-measured reflectance data and the PROSPECT radiative transfer model, while terrain structure was derived from SfM-based digital terrain models. The integrated scene was used to simulate multispectral (DJI Mavic 3 MSI), hyperspectral (AVIRIS-NG), and light detection and ranging (LiDAR) observations. Agreement between simulated outputs were evaluated against corresponding field-acquired datasets using spectral signatures and vegetation indices. This framework enables systematic assessment of sensor specification effects on spectral biodiversity metrics and provides a pathway for evaluating theoretical limits of species discrimination across airborne and satellite platforms.
Why it matches plant phenotyping methods植物群落の種判別・多様性指標を対象に、物理ベースの仮想シーンとマルチモーダルセンシングを開発し、実測データで検証しているため、植物状態の取得・推定法が中心である。
abstractWe therefore developed a physics-based simulation framework that couples fynbos trait measurements with radiative transfer modeling in the DIRSIG (Digital Imaging and Remote Sensing Image Generation) environment towards quantifying information loss across spectral and spatial scales and to define theoretical limits for biodiversity monitoring.
Introduction In a complex orchard environment, canopy apples are obscured by various factors, making it hard for apple harvesting robots to accurately determine which apples can be directly harvested. Furthermore, the complex obstruction leads to difficulties in identifying keypoints on the apples and caculating the axis direction, directly affecting the robot's determination of grasping positions. Methods To solve these issues, a two-dimensional (2D) axis estimation method for pickable canopy apples based on a YOLO cascade network was proposed. Firstly, the study introduced SPDConv for lossless downsampling and adopts dynamic upsampling to improve segmentation boundary accuracy, constructing an instance segmentation network named the YOLO-SD model to select pickable apples according to different occlusion conditions and growth states. Secondly, the geometric center of the mask image was located using its minimum enclosing circle, and the region of interest was extracted through morphological dilation. Then, by integrating the RFAConv, SCSA attention, and MBConv modules, a keypoint detection network YOLO-RSM was constructed to extract keypoints of pickable apples. Finally, a 2D axis construction strategy was proposed, which adaptively constructs the growth axis based on the visibility of keypoints. Results Experimental results show that the overall average accuracy mAP50 of the YOLO-SD model for apple segmentation reached 95.2%, and the parameter quantity was reduced to 2.47 M. The average accuracy of the YOLO-RSM model for keypoint detection has reached 90.3%, which is 2.4%, 2.6%, and 4.7% higher than that of the YOLOv8n, YOLO11n, and YOLO12n models respectively. The 2D axis estimation algorithm has an average axis angular error of 7.23° ± 16.73°, and an axis estimation accuracy of 92.68%. Discussion The proposed method can achieve high-precision canopy apple segmentation, keypoint detection, and 2D axis estimation, thus offering technical support for the picking operations of apple harvesting robots.
Why it matches plant phenotyping methodsリンゴ果実のセグメンテーション、キーポイント抽出、成長軸（器官形態）の推定を中心に新規画像解析法を開発・検証しており、単なる収穫対象の検出を超える植物器官形質の推定に該当する。
abstracta two-dimensional (2D) axis estimation method for pickable canopy apples based on a YOLO cascade network was proposed.
Abstract In real field scenarios in agriculture, automatic segmentation of plant diseases is an important technique for precision farming. However, it remains exceptionally challenging due to blurred lesions, complex morphological structures, irregular backgrounds, and severe class imbalance. While traditional convo lutional networks struggle to capture long-range semantic context and standard vision transformers fail to preserve sharp localized boundaries, this paper proposes an efficient, attention-gated hybrid framework optimized for field deployment. Our architecture leverages a hierarchical Mix Transformer (MiT-B2) encoder stream integrated with an Atrous Spatial Pyramid Pooling (ASPP) scale-space context bridge and a custom Cross-Scale Multimodal Attention Gate (CMAG) to isolate discriminative disease markers selectively. Evaluated on the highly challenging and unbalanced PlantSeg dataset, our framework achieves competitive mean Intersection over Union (mIoU) of 66.57% and an F1-score of 79.93%, while maintaining a highly compact parameter footprint of only 30.37 M. Experimental evaluations demonstrate that the proposed system establishes a new performance milestone, outperforming current competitive architectures and proving highly viable for resource-constrained edge devices. To further enhance out-of-distribution stability, we outline future directions to extend our top-performing candidate variants into a Level 1 meta-stacking ensemble optimized via few-shot learning and partial backbone fine-tuning.
Why it matches plant phenotyping methods植物病害領域の画像セグメンテーション手法を開発・評価し、病変の分割性能を定量検証しているため、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す。
abstractautomatic segmentation of plant diseases is an important technique for precision farming.
Plant diseases remain a threat to global agricultural productivity, food security and livelihoods, especially in developing countries where the availability of experts in agriculture is still limited. The recent progress in AI, particularly deep learning and computer vision, has ushered in new possibilities for automated plant disease diagnosis, especially for plant image-based systems. This paper provides a systematic review of the deep learning methods employed for plant disease diagnosis, highlighting CNN-based methods, the application of transfer learning, explainable AI (XAI) methods and deployment issues. In the framework of PRISMA 2020, the relevant peer reviewed literature from 2016 to 2025 was systematically identified, screened and analysed on the most important academic databases. The review compared some of the most popular architectures such as GoogLeNet, DenseNet-121, MobileNetV2, EfficientNet, Attention-CNNs and Vision Transformers. Results showed very high classification accuracy in controlled lab conditions with DenseNet-121 achieving ~99.75% accuracy with good computational efficiency. But it also revealed a big gap between the lab and the field, mainly due to environmental variations, domain shifts, and dependence on datasets. Some innovative and emerging technologies like explainable AI, hyperspectral imaging, few-shot learning, and lightweight mobile architectures showed promise of enhancing the interpretability, early detection of disease, and the use of smart phones in low-resource agricultural settings. In conclusion, the study suggests that in order to be implementable in the field, future intelligent agricultural diagnosis systems must be able to balance predictive accuracy, explainability, computational efficiency and field adaptability. The results enrich the existing knowledge on precision agriculture and serve as useful information for researchers, agricultural technologists, and policymakers working on the creation of AI-based systems for crop protection.
Why it matches plant phenotyping methods植物病害を画像から診断する深層学習手法を体系的に比較・レビューしており、植物の病徴・病害状態の推定方法が中心である。
abstractThis paper provides a systematic review of the deep learning methods employed for plant disease diagnosis
Plant diseases lead to substantial yield losses and pose a persistent threat to global food security, creating an urgent demand for high-throughput, accurate, scalable, and non-destructive disease-monitoring approaches. Remote sensing has emerged as a powerful tool, yet progress in plant disease detection remains fragmented across various disciplines, tasks, sensing methods, and data modalities. This review introduces a hex-view perspective to synthesise remote-sensing-based plant disease detection within a cohesive conceptual framework. Instead of treating sensing technologies, algorithms, and datasets independently, the hex-view incorporates six interconnected dimensions that jointly capture how biological processes, the measurement scale, and data characteristics constrain disease detectability, including when detection is possible and how reliably it can be achieved. The hex-view framework comprises six interconnected dimensions and forms an integrated framework called BTSCAD: (1) Biology (B): plant–pathogen interactions constituting the biological foundation of disease development and expression. (2) Task (T): the diverse disease-detection tasks and their corresponding research objectives. (3) Sensor (S): the sensing modalities that define the data acquisition type and richness of captured information. (4) Condition (C): the environmental conditions, sensing platforms, and spatial scales that shape disease observations and bridge controlled experiments and real-world deployment across leaf, canopy, plot, and regional scales. (5) Algorithm (A): the classical and state-of-the-art data-analysis algorithms used to extract disease-related information from sensor data. (6) Dataset (D): the data sources that underpin model development, evaluation, and generalisability. The hex-view perspective provides a clear framework for interpreting previous research and identifying future research directions. This review lays a structured foundation for developing robust, interpretable, and transferable disease-detection systems, supporting advancements in precision agriculture, high-throughput phenotyping, and sustainable crop production.
Why it matches plant phenotyping methods植物病害を対象としたリモートセンシングによる病徴・病害状態の検出方法を、センサー、条件、アルゴリズム、データセットの観点から体系化する方法論レビューであり、植物フェノタイピング手法が中心です。
abstractThis review introduces a hex-view perspective to synthesise remote-sensing-based plant disease detection within a cohesive conceptual framework.
Localized soil-moisture deficits, that is, irregular sub-field patches where crops experience water stress well before visible wilting, are a leading cause of yield variability in row-crop agriculture. These zones are difficult to detect at the spatial resolution and revisit frequency required for timely irrigation response. This paper presents a reinforcement-learningguided autonomous quadrotor unmanned aerial vehicle (UAV) platform that fuses onboard Visual Simultaneous Localization and Mapping (Visual SLAM) with a pushbroom hyperspectral imaging payload to construct georeferenced, canopy-registered maps of a Crop Water-Stress Index (CWSI) in near real time. Rather than flying a fixed lawnmower survey, the platform is guided by an adaptive-sampling policy trained with Proximal Policy Optimization (PPO) that reallocates flight time and sensor dwell toward regions of emerging water stress as evidence accumulates mid-flight. We present the complete engineering pipeline: airframe and sensor design, a keyframe-based Visual SLAM front and back end that provides centimeter-scale geolocation without continuous reliance on Real-Time Kinematic (RTK) GNSS lock, a hyperspectral preprocessing and spectralindex chain (NDVI, NDRE, NDWI/NDMI) used to derive CWSI through a learned regression, the partially observable Markov Decision Process (POMDP) formulation and reward shaping used to train the sampling policy, and the fused system architecture tying these subsystems together. In simulated field trials over a 0.8-hectare test plot, the reinforcement-learning-guided policy achieved a 92% water-stress-zone detection rate versus 61% for a fixed-grid baseline, while reducing mission flight time by approximately 32%. We further report an ablation study isolating the contribution of SLAM-derived canopy structure to CWSI accuracy, a sensitivity analysis across field complexity, and a full error budget for the fused pipeline. We close with a discussion of validation limitations, broader scientific and agricultural impact, and a roadmap toward multi-UAV fleet deployment for whole-farm monitoring
Why it matches plant phenotyping methodsUAV、Visual SLAM、ハイパースペクトル画像、機械学習を統合し、作物の水ストレス状態を推定・地図化する技術パイプラインを開発・評価しており、植物表現型取得が中心である。
abstractThis paper presents a reinforcement-learningguided autonomous quadrotor unmanned aerial vehicle (UAV) platform that fuses onboard Visual Simultaneous Localization and Mapping (Visual SLAM) with a pushbroom hyperspectral imaging payload to construct georeferenced, canopy-registered maps of a Crop Water-Stress Index (CWSI) in near real time.
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:1-55Plant phenotyping relevance match · UnverifiedCrossref · checked 5 Sept 2026
Abstract Visual assessments of growing forest nursery plants are time-consuming and often result in a lack of information at a physiological level. There exists a need for health screening in nurseries, that is fast and efficient, to improve overall health monitoring and nursery productivity. Rapid handheld sensors such as rapid thermal devices, leaf porometers and moisture meters, can provide regular information at a physiological level, that can improve the understanding of the impact of stress on young plant cuttings and their decline in health over time. This paper evaluates the utility and reliability of contemporary sensor technologies, to operationally monitor stress phases in juvenile forest plant cuttings during progressive moisture (dry-down) conditions. Furthermore, to assess whether thermal sensors could be used as an indicator, in conjunction with other variables such as soil water content or stomatal conductance, is needed operationally for fast screening during limited planting windows. Near Infra-Red Analysis (NiRA) data was collected to understand detailed plant functions at a finer reflectance level. A relationship was found where the increase in thermal signals reflects a depletion of water content, resulting in an eventual decline in stomatal conductance and, ultimately, plant mortality. Several algorithms were used in a preliminary test, using RapidMiner software, to discriminate between the four phases of plant health decline using physiological variables and NiRA data. Both Gradient Boosting Trees (GBT) and Deep Learning (DL) showed the best performances, achieving favourable accuracies of 96.8% and 91.2% without NiRA data, 84.6% and 88.2% with NiRA data, with shorter training times. Using thermal technology weighted amongst the highest of the best performing variables using GBT, the utility and accuracy showed good discrimination between the stages of plant decline and is encouraged for future research in this field.
Why it matches plant phenotyping methods植物のストレス段階を熱センサー、ポロメータ、含水率計、NiRAおよび機械学習で測定・識別する方法の有用性と信頼性を評価しており、表現型取得・判定手法が中心である。
abstractThis paper evaluates the utility and reliability of contemporary sensor technologies, to operationally monitor stress phases in juvenile forest plant cuttings during progressive moisture (dry-down) conditions.
Field / plotLiDAR / point cloudWhole plant / canopy / plot / field2D/3D reconstructionYield / biomass estimationBiomass / plant weight
Reliable aboveground biomass (AGB) estimates for woody crops are essential for carbon accounting and for Measurement, Reporting and Verification (MRV) frameworks. However, it remains unclear how LiDAR modality and sampling geometry influence plot-scale and tree-scale AGB predictions in intensively managed Mediterranean orchards. In this study, we benchmarked four LiDAR modalities, namely open national airborne laser scanning from the Spanish National Aerial Orthophotography Plan (PNOA/ALS), a dedicated Riegl airborne laser scanner (ALS), unmanned laser scanning (ULS) and mobile laser scanning (MLS), across three woody-crop sites in Córdoba (southern Spain): IFAPA, Doña María, and Villaseca. Plot-level LiDAR metrics (mean height, 95th height percentile, maximum height, and canopy-cover proxies) were extracted from normalized point clouds and related to field AGB using Random Forest and XGBoost regression models, together with an ensemble predictor, under an 80/20 train–test split. In parallel, TreeQSM-based Quantitative Structure Models (QSMs) were evaluated as an independent tree-level three-dimensional reconstruction approach. XGBoost achieved the lowest errors at IFAPA (RMSE = 0.400 Mg ha−1; R2 = 0.994) and Villaseca (RMSE = 0.872 Mg ha−1; R2 = 0.995), whereas PNOA/ALS was competitive at Doña María (RMSE = 0.725 Mg ha−1; R2 = 0.994). TreeQSM closely matched the field inventory at the low-biomass IFAPA site but tended to overestimate biomass at Doña María and Villaseca, and only 28% of scanned trees yielded usable reconstructions. The results support the use of cross-platform LiDAR for orchard AGB and carbon mapping and identify the conditions under which open national LiDAR can enable scalable MRV of Mediterranean woody crops.
Why it matches plant phenotyping methodsLiDAR複数プラットフォームと3D再構成を比較・検証し、樹木・区画レベルの地上部バイオマスという植物形質を推定する手法が研究の中心である。
Abstract Understanding the allometric relationships between leaf area and other plant traits is essential for non-destructive growth monitoring and efficient crop management. However, no comprehensive study has yet modeled leaf area in quinoa ( Chenopodium quinoa Willd.) using simple morphological traits across different sowing dates. This study aimed to quantify allometric relationships between leaf area and plant height, leaf dry weight, stem dry weight, panicle dry weight, and total dry matter, and to evaluate whether these relationships are modified by sowing date. A two-year field experiment was conducted with 12 sowing dates under a randomized complete block design with three replications. Leaf area index (LAI) dynamics were described using a logistic model, and allometric relationships were fitted using power-law equations. The results showed that LAI followed a logistic trend across all sowing dates, with maximum values ranging from 2.7 to 7.9. Plant height provided the most reliable prediction of leaf area (R² = 0.83, b = 1.2), followed by leaf dry weight (R² = 0.72, b = 0.97). The allometric coefficients for stem dry weight (b = 1.54, R² = 0.74) and panicle dry weight (b = 1.95, R² = 0.71) showed greater variability. A striking finding was the exceptionally high allometric coefficient (b = 4.95) recorded on May 6 of the second year, indicating a pronounced shift in resource allocation toward leaf area expansion. Total dry matter was a weak predictor (R² = 0.54), likely due to leaf fall during the growing season. The hypothesis that sowing date modifies allometric relationships was confirmed, as evidenced by considerable variation in allometric coefficients across sowing dates. This study provides, for the first time, a comprehensive set of allometric models for quinoa across multiple sowing dates. Plant height and leaf dry weight are recommended as simple, rapid, and non-destructive indicators for leaf area estimation, facilitating improved crop monitoring and management under diverse environmental conditions.
Why it matches plant phenotyping methods草丈や乾物重から葉面積を非破壊推定するアロメトリックモデルを中心に開発・評価しており、植物形質の取得手法が実質的な主題である。
abstractThis study aimed to quantify allometric relationships between leaf area and plant height, leaf dry weight, stem dry weight, panicle dry weight, and total dry matter, and to evaluate whether these relationships are modified by sowing date.
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 · 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:63-74Plant phenotyping relevance match · UnverifiedCrossref · checked 14 Sept 2026
In Nigeria, maize is the most widely cultivated grain, largely supporting food security for about half of the population. Research has indicated that there is annual production is declaiming to approximately 50% in maize, this is due to crop diseases and pest damage. This research presents a deep learning surveillance system for crop disease prediction and pesticides recommendations based on a DenseNet-121 architecture for continuous video streams. The research was evaluated on a curated field dataset collected from three states in Nigeria; Adamawa, Borno, and Taraba State. The system achieved a mean accuracy of 98.2% and a mean F1-score of 0.982. The results reflect a strong discriminative capacity across the diverse textural maize diseases.
Why it matches plant phenotyping methodsトウモロコシの病害状態を映像から推定する深層学習手法の開発・評価が中心であり、植物病害表現型の画像ベース計測に該当する。農薬推薦も含むが、病害分類性能が明示的に評価されている。
abstractThis research presents a deep learning surveillance system for crop disease prediction and pesticides recommendations based on a DenseNet-121 architecture for continuous video streams.
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:205-225Plant phenotyping relevance match · UnverifiedCrossref · checked 14 Sept 2026
Published17 Aug 2026NOUN Interdisciplinary Journal of Computing, E-Learning & Application (NOUN-IJCEA)Cited by 0 · OpenAlex ↗
Manual inspection of grain plant leaves for defects is subjective and labor-intensive. Few studies have compared deep learning methods on a combined multi-crop dataset. The study collected locally 5,640 leaf images from rice, maize, and guinea corn farms in Nigeria and grouped them into six classes representing defective and healthy leaves for each crop. Three models were trained: YOLOv8 for end-to-end detection and classification, EfficientNetB0 for standalone image classification, and a hybrid that used YOLOv8 for leaf detection followed by EfficientNetB0 for patch classification. The hybrid achieved 99.85% accuracy on the test set, slightly above EfficientNetB0 (99.82%) and YOLOv8 (mAP 0.995). The hybrid also supplies bounding box locations, helping farmers identify exactly where damage appears. This system offers a reliable, field-deployable tool for monitoring grain crop health.
Why it matches plant phenotyping methods穀物葉の健全・欠損状態を画像から検出・分類する深層学習システムの開発とモデル比較が中心であり、植物の病害・損傷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する。
abstractManual inspection of grain plant leaves for defects is subjective and labor-intensive.
Plant phenotyping relevance match · UnverifiedbioRxiv · Europe PMC · checked 5 Sept 2026
Red crown rot of soybean (RCR), caused by Calonectria ilicicola, is an emerging soilborne disease whose quantification is challenging due to its complex symptom development across root and foliage levels. This study developed and evaluated a multi-scale framework to improve the assessment of RCR severity from controlled environments to field conditions using root imaging and standardized visual scales. Under controlled conditions, a standard area diagram (SAD) for root necrosis was developed and validated, and SAD-assisted evaluations significantly improved accuracy, precision, and inter-rater agreement compared with unaided assessments. In field conditions, a diagrammatic symptom scale (DSS) was developed using consensus-rated images from experts and showed high reliability, repeatability, and reproducibility across 18 raters, with strong intra- and inter-rater agreement. This study developed and evaluated complementary methods to improve the assessment of RCR severity from controlled environments to field conditions using root imaging and standardized visual scales.
Why it matches plant phenotyping methods根の壊死と地上部症状という植物病害状態の定量評価法を開発・検証しており、画像化と標準視覚尺度が研究の中心であるため。
abstractThis study developed and evaluated a multi-scale framework to improve the assessment of RCR severity from controlled environments to field conditions using root imaging and standardized visual scales.
Quantitative flowering phenotypes are needed to support breeding and harvest management in Hypericum perforatum L. (St. John’s wort), but manual flower assessment is slow and difficult to standardize under field conditions. UAV-Hyp is a multi-temporal UAV RGB dataset containing 12,653 high-resolution images acquired at 26 measurement dates across the complete flowering period of 15 H. perforatum accessions. The images represent variable illumination, soil moisture, weed pressure, and developmental stages. The dataset provides 59,163 plant bounding boxes and 107,054 flower bounding boxes. As an application example, cascaded YOLOv8 plant and flower detectors achieved mAP@0.50:0.95 values of 0.977 and 0.950, respectively. UAV-Hyp supports scalable flower quantification and the development of time-series phenotyping methods for genotype comparison and quality-oriented medicinal-plant breeding.
Why it matches plant phenotyping methods植物の開花形質を定量化するUAV画像データセットを提供し、検出性能も評価しているため、フェノタイピング用データセット・解析手法が中心です。
abstractUAV-Hyp is a multi-temporal UAV RGB dataset containing 12,653 high-resolution images acquired at 26 measurement dates across the complete flowering period of 15 H. perforatum accessions.
Field / plotLeafSegmentationDisease symptoms / severity
Camellia oleifera leaf disease segmentation under natural field conditions is important for precision plant protection but remains challenging because lesions often show small target areas, blurred boundaries, uneven illumination, complex backgrounds, and coexisting symptoms. To address these problems, this paper proposes BFMambaNet, a Boundary-Frequency-guided Global Semantic Mamba Network for fine-grained disease segmentation. The model adopts an encoder-decoder framework and introduces a Global Semantic Mamba-based spatial selective feature modeling block to capture long-range lesion context and reduce semantic confusion. A gated wavelet spatial enhancement block is further designed to strengthen high-frequency boundary details while suppressing noisy responses. During training, boundary-frequency auxiliary supervision guides contour localization and pathological texture recovery without additional manual boundary labels. A reinforcement-learning-guided adaptive loss controller adjusts class-wise reweighting factors and loss-component weights according to the training state, improving optimization stability. A pixel-level dataset containing 1400 images and seven disease categories was constructed for evaluation. Experimental results show that BFMambaNet achieves 92.39% Precision, 91.43% Recall, 91.26% Dice, and 85.46% mIoU, outperforming representative CNN-based, Transformer-based, and Mamba-based models. Evaluations on environmental subsets confirm superior robustness, outperforming VMamba by 3.70% mIoU under uneven illumination, 3.55% mIoU under complex backgrounds, and 5.10% mIoU under coexisting symptoms. Cross-dataset validation on Apple leaf diseases further proves its generalization with 3.39% mIoU and 3.84% Dice improvements over U-Mamba, while maintaining a competitive inference speed of 30 FPS. Qualitative results also show clearer boundaries, fewer missed small lesions, and more stable predictions in complex field scenarios.
Why it matches plant phenotyping methods植物葉の病斑・病害状態を画像から画素単位で推定するセグメンテーション手法を開発し、データセット構築、性能評価、環境別評価、クロスデータセット検証まで行っており、病害フェノタイピング手法が中心である。
abstractA pixel-level dataset containing 1400 images and seven disease categories was constructed for evaluation.
Drought stress severely limits foxtail millet yield and quality, yet current drought-resistance indices are exclusively yield-oriented and ignore grain-filling quality. Our two-year (2024–2025) experiments with 24–48 varieties revealed that yield and blighted grain rate (BGR) are partially decoupled (e.g., Zhangzagu 18: yield 2307 kg/ha, BGR 0.444; Zhonggu 19: yield 1622 kg/ha, BGR 0.280). We therefore constructed the Yield–Quality Synergy Index (YQSI = DYI − BGR), which penalizes varieties with poor grain filling. The YQSI tied for first place with DYI in comprehensive screening performance and achieved the highest inter-annual stability (Spearman ρ = 0.823, Jaccard = 0.438, composite score = 1.261). Sensitivity analysis confirmed robustness of the equal-weight formula across a 4-fold range of quality-penalty weights. Six strongly drought-resistant germplasms with balanced yield and quality were identified. Using UAV multimodal data (RGB, multispectral, and thermal infrared) acquired during grain filling, a Random Forest model predicted a YQSI with overall R2 = 0.819 and an F1 score of 0.933 for variety screening. Feature-importance analysis highlighted NDVI, WDRVI, and red-edge texture as key predictors. This study provides a quality-constrained drought-resistance evaluation framework and demonstrates the potential of UAV-based high-throughput phenotyping for foxtail millet breeding.
Why it matches plant phenotyping methodsUAVのRGB・マルチスペクトル・熱赤外データから干ばつ耐性指標を予測する高スループット表現型解析手法が研究の中心であり、モデル性能も評価している。
abstractUsing UAV multimodal data (RGB, multispectral, and thermal infrared) acquired during grain filling, a Random Forest model predicted a YQSI with overall R2 = 0.819 and an F1 score of 0.933 for variety screening.
Existing reviews on AI in tea production are either agriculture-generic or limited to isolated tasks. This review thoroughly compares vision technologies (RGB, hyperspectral, near-infrared, thermal, Light Detection and Ranging (LiDAR), Unmanned Aerial Vehicle (UAV)) and establishes a task-oriented algorithm selection framework for the tea industry. For small-sample or near-linear problems, traditional machine learning (ML) (support vector machine (SVM); partial least squares regression (PLSR)) remains effective. For unstructured field tasks, deep learning achieves superior performance: pest detection accuracy exceeds 97%, tea bud detection reaches 96.8% with RGB images, and hyperspectral imaging predicts nitrogen content with R 2 > 0.90 and tea polyphenols with R 2 up to 0.925. Algorithm choice further differentiates by task granularity: lightweight convolutional neural networks (CNNs) balance speed and accuracy for edge deployment at 16 fps; You Only Look Once (YOLO) series detectors enable real-time localization on mobile platforms at 93.1% accuracy, 24 ms per target. No single algorithm dominates all tea tasks; selection is a trade-off among accuracy, speed, data availability, and computational constraints. These findings outline a structured analysis of the challenges and pathways for transitioning computer vision (CV) from laboratory research toward field-deployable tools.
Why it matches plant phenotyping methods茶作物の画像センシング技術と解析アルゴリズムを体系的に比較し、害虫検出や窒素含量予測など植物状態・形質の推定方法を扱う方法論レビューである。
abstractThis review thoroughly compares vision technologies (RGB, hyperspectral, near-infrared, thermal, Light Detection and Ranging (LiDAR), Unmanned Aerial Vehicle (UAV)) and establishes a task-oriented algorithm selection framework for the tea industry.
This study investigates the automatic classification of crop phenological stages from low-altitude UAV RGB imagery. The dataset included 11,489 images of five crops: sunflower, rapeseed, soybean, wheat, and barley. The images were annotated using the Biologische Bundesanstalt, Bundessortenamt und Chemische Industrie (BBCH) scale, with labels corresponding to either single stages or stage ranges to reflect heterogeneous field conditions and transitional crop states. A pretrained ResNet18 model was adapted to the task using transfer learning. Training was conducted in two stages: first, the classification head was optimized while the backbone remained frozen; second, the entire network was fine-tuned. The model achieved strong internal test accuracy across all crops, with 100% test accuracy for rapeseed and barley, more than 99% for the remaining crops, and a mean accuracy of 99.73% under the studied survey conditions. The results also compare favorably with previously reported studies on UAV-based phenological classification. Overall, the findings support the potential of low-altitude UAV imagery and deep learning for localized phenological assessment of selected field zones in precision agriculture, while broader deployment requires validation across independent fields, seasons, regions, and survey conditions.
Why it matches plant phenotyping methodsUAV画像と深層学習により作物の生育（フェノロジー）段階を自動推定する手法が研究の中心であり、植物状態の取得・分類に直接関わる。
abstractThis study investigates the automatic classification of crop phenological stages from low-altitude UAV RGB imagery.
Accurate field detection of candidate tea shoots could support plantation monitoring, yield estimation, fresh-leaf assessment, and future selective-harvesting research. Wuyi rock-tea shoots are small and slender, have weak visual boundaries, and are easily confused with branches, petioles, and complex canopy backgrounds. Here, we developed YOLO11s-CSNG for candidate shoot detection in natural plantation scenes. The model combines a channel-spatial feature enhancement bottleneck, a normalized Wasserstein distance constraint for bounding-box regression, and ghost convolution layers in the detection head. We evaluated the model through detector comparisons, module ablations, and repeated training with five matched random seeds on a natural-scene dataset containing four Wuyi rock-tea cultivars. Across the five matched seeds, the mean mAP@0.5 increased from 67.37 ± 0.91% to 67.97 ± 0.90% on the validation set and from 61.29 ± 0.40% to 61.88 ± 0.66% on the internal test set. Neither paired difference was statistically significant: The 95% confidence intervals included zero, and the exact two-sided paired-permutation p values were 0.375 and 0.250, respectively. The mean mAP@0.5:0.95 did not improve. YOLO11s-CSNG retained a model size and model-only edge-inference time comparable to YOLO11s, providing a compact design for candidate shoot-region detection under the sampled field conditions.
Why it matches plant phenotyping methods茶芽という植物器官の画像検出手法を開発し、比較・アブレーション・反復検証を行っているため、植物フェノタイピング手法が中心である。
abstractHere, we developed YOLO11s-CSNG for candidate shoot detection in natural plantation scenes.
Photosynthesis is among the most consequential yet genetically complex traits in crop plants, and translating its natural variation into actionable genomic targets remains a central challenge for breeding climate-resilient varieties. To start addressing this, researchers are generating increasingly large, multi-environment field photosynthesis datasets. Yet, these data have been structurally under-analysed since their inception. Here we report the outcomes of the first dedicated hackathon focused on computational mining of such field data held in Accra, Ghana, in March 2026. Bringing together data scientists, plant physiologists, geneticists, and breeders from Europe and Africa, these interdisciplinary teams used photosynthetic data collected with hand-held fluorometers to genome-wide marker data across four crop species: cowpea (Vigna unguiculata), barley (Hordeum vulgare), common bean (Phaseolus vulgaris), and potato (Solanum tuberosum). Despite using different species and methods, independent teams identified the same three key findings. First, mechanism-informed feature engineering and dynamic modelling recover genetic signals that are not detected or discarded in standard analysis pipelines, resulting in traits with improved heritability and meaningful associations with yield. Secondly, machine learning methods proved effective at uncovering genetic associations, with temporally resolved features substantially outperforming single time-point measurements. Third, raw chlorophyll fluorescence and absorbance traces consistently contained more information and predictive power than the extracted parameters currently used. A defining feature of this event was having experimentalists and data scientists working together, enabling AI approaches to be grounded in domain knowledge and biological mechanisms rather than relying on data alone.
Why it matches plant phenotyping methods圃場光合成データから時間分解特徴量や遺伝的シグナルを抽出する計算手法を中心に扱っており、植物生理形質の実質的なフェノタイピング手法応用に該当する。
abstractmechanism-informed feature engineering and dynamic modelling recover genetic signals that are not detected or discarded in standard analysis pipelines, resulting in traits with improved heritability and meaningful associations with yield.
Field / plotMultispectral / hyperspectralClassificationGrowth / time-series analysisGrowth / development / phenology
Aquatic plants are vital for lake ecosystem functioning and water-quality stability, yet their community dynamics and phenology rhythms remain insufficiently understood, due to the lack of effective strategies for fine-scale species mapping and phenology extraction. In this study, based on Sentinel-2 MSI imagery, we developed an integrated framework combining machine learning and a priori ecological knowledge to quantify the spatiotemporal changes in aquatic plant distribution, species composition and phenological dynamics for eight dominant species in five regulating lakes along the Eastern Route of the South-to-North Water Diversion Project in China. Results showed that the proposed framework enabled accurate aquatic plant identification, achieving an overall classification accuracy of 96.16% and over 90% accuracy for each species. Since 2016, aquatic vegetation coverage has substantially declined in most lakes, mainly due to the retreat of submerged vegetation. Community structure has shifted from submerged-plant dominance to emergent and floating-leaved dominance in two of them. Phenologically, we found that most aquatic vegetation exhibited a longer growing season, characterized by earlier growth onset (-0.28 days/year) and peak timing (-0.67 days/year) and delayed senescence (0.54 days/year). Correlation analysis indicated that aquatic vegetation dynamics was associated with climate variation, nutrient enrichment, turbidity, and water diversion, with warming and solar radiation likely promoting the growth of some emergent species, while nutrient enrichment and turbidity could be linked with submerged vegetation decline and earlier phenological shifts. Overall, this study provides an effective framework for species-level mapping and phenological monitoring of aquatic vegetation, offering valuable support for the management and conservation of lake ecosystems.
Why it matches plant phenotyping methodsSentinel-2画像と機械学習等を統合した、植物種分布・構成・フェノロジーを抽出する手法を開発し、精度検証と大規模適用を行っているため、植物フェノタイピング手法が中心である。
abstractwe developed an integrated framework combining machine learning and a priori ecological knowledge to quantify the spatiotemporal changes in aquatic plant distribution, species composition and phenological dynamics for eight dominant species in five regulating lakes
The uniformity of maize plant spacing serves as a critical indicator for assessing sowing quality, seed vigor, and field seedling emergence stability. However, manual measurement is inefficient, and complex field conditions make automatic seedling detection and plant spacing measurement challenging. Aiming at the challenges of missed detection, insufficient accuracy for small targets, and large errors in plant spacing calculation under complex field conditions, this study constructs a high-quality dataset containing 693 maize seedling images and implements preprocessing enhancement for images degraded by haze or dust. An intelligent maize seedling detection and plant spacing measurement method based on improved YOLOv8 is proposed. The Global Attention Mechanism (GAM) is embedded into the backbone network to strengthen cross-dimension information interaction between channels and spaces, suppress background interference, and reduce the missed detection rate. The Bi-directional Feature Pyramid Network (BiFPN) is adopted to replace the original PAFPN for enhanced multi-scale feature fusion and deep semantic representation. A new 160 × 160 high-resolution small-object detection layer is added to significantly improve the detection performance of weak and small seedlings. Experimental results demonstrate that the improved model achieves a precision, recall, mAP50, and mAP50-95 of 89.4%, 90.3%, 94.4%, and 49.4%, respectively, which are 2.6, 0.5, 1.5, and 2.7 percentage points higher than those of the original YOLOv8 model. These results indicate that the proposed model improved maize seedling detection performance under complex field conditions. Automatic plant spacing calculation is realized based on detection outputs; the average plant spacing of the dataset is 30.42 cm, with a relative error of only 4.93% compared with the preset sowing spacing of 32 cm. The proposed method can efficiently accomplish field seedling identification, plant spacing quantification, and sowing quality evaluation, providing reliable technical support for precision maize sowing, seeder parameter optimization, and intelligent field management, which is of great significance for promoting the intelligent upgrading of grain crop production.
Why it matches plant phenotyping methodsトウモロコシ幼苗の検出画像から株間という植物形態・配置形質を自動抽出するYOLOv8手法を開発し、データセット構築と性能検証まで行っており、フェノタイピング手法が中心である。
abstractAutomatic plant spacing calculation is realized based on detection outputs
Abstract Purpose Long-term monitoring of crop biophysical and biochemical traits remains challenging in high-latitude regions due to short growing seasons, frequent cloud cover, and highly variable weather. In this context, unmanned aerial vehicles (UAVs) offer flexible, high-resolution observations, but their added value relative to low-cost proximal sensors and their effectiveness for radiative transfer model (RTM) inversion across diverse crop canopies remain insufficiently quantified. This study evaluated the potential of a two-band proximal spectral reflectance sensor (SRS) and a five-band multispectral UAV sensor for retrieving leaf area index (LAI), leaf chlorophyll content (LCC), and canopy chlorophyll content (CCC) using PROSAIL inversion across major crops in Northern Europe over two growing seasons (2023–2024). Methods and Results Two inversion approaches – look-up table (LUT) and artificial neural network (ANN) were applied to PROSAIL simulations. UAV–PROSAIL–ANN outperformed LUT-based inversion and SRS observations, achieving the highest accuracy for LAI (R 2 = 0.81–0.95; RMSE = 0.27–0.77 m 2 /m 2 ), followed by CCC (R 2 = 0.58–0.94; RMSE 2 ), while LCC remained less accurately estimated (R 2 = 0.26–0.78; RMSE 2 ). Across sensors and methods, retrieval accuracy decreased in the order of LAI, CCC, and LCC, reflecting the stronger spectral control of canopy structure compared to biochemical traits. Conclusions The UAV–PROSAIL–ANN framework effectively captured spatial and temporal variability in crop traits, producing canopy-scale maps consistent with field observations. These results demonstrate the robustness and scalability of hybrid PROSAIL–ANN inversion for high-latitude crop monitoring, while highlighting current limitations in biochemical trait retrieval using multispectral data.
Why it matches plant phenotyping methodsUAV・近接分光センサーとPROSAIL反転、ANNを用いてLAIや葉・群落クロロフィルを推定し、精度比較と圃場観測との整合性評価を行うことが研究の中心である。
abstractThis study evaluated the potential of a two-band proximal spectral reflectance sensor (SRS) and a five-band multispectral UAV sensor for retrieving leaf area index (LAI), leaf chlorophyll content (LCC), and canopy chlorophyll content (CCC) using PROSAIL inversion across major crops in Northern Europe over two growing seasons (2023–2024).
Reproduction assets foundThe paper's Data availability statement explicitly deposits the authors' UAV image processing code (irradiance normalization, vignetting, exposure compensation, radiometric calibration) in a public GitHub repository under GPL v3.0; other data are available only upon request.Code · publicData availability Code to perform irradiance normalization, vignetting, exposure compensation, and radio-
metric calibration is available at https://github.com/fieldSITES/scripts/tree/main/UAV under GNU General
Public License v3.0. Other data will be made available upon request.Open asset ↗UAVpdf-page:34 lines:1-40Plant phenotyping relevance match · UnverifiedCrossref · checked 14 Sept 2026
Published14 Aug 2026Journal of Intelligent Decision Making and Information ScienceCited by 0 · OpenAlex ↗
This paper explores how deep learning methods can be used to monitor the health of crops and identify diseases, particularly for the apple crop. As the need for food security and sustainable farming methods increases, there is a strong demand for early detection of crop diseases. We have used a Convolutional Neural Network (CNN), based on the model of VGG16 architecture, since the model is known to be effective in image classification. The dataset contained 7771 training images for to enhance machines deep learning regarding plant diseases. Following that, validation image collection of 1747 images divided into four health conditions of the apple crops. In addition, the model was evaluated using 196 new images as a final test. To enhance the model capacity for recognizing diseases of real leaves rather than just memorize exact training pictures, data augmentation was used with ImageDataGenerator of TensorFlow. This means the training images were zoomed, rotated, and shifted to enable the machine detects more variations. Ten epochs of training were performed to measure the model accuracy. The results indicated that the model obtained significant improvement in training and validation accuracy from 56.43% to 78.12% and 92.94 to 96.93%, respectively. Most impressively, the final test dataset, which contained completely new images, scored an accuracy rate of 98%. The results indicate that in the architecture field the application of deep learning methodologies is effective, suggesting that automated detection of diseases by using sophisticated image analysis manages crop diseases identification efficiently. Combination of these methods successfully creates avenues for novel research to built real-time systems of crop disease monitoring, which help farmers increase their productions and farm their lands sustainably.
Why it matches plant phenotyping methodsリンゴ葉の画像から病害・健全状態をCNNで推定する画像ベース植物フェノタイピング手法であり、学習・検証・未知画像で性能評価を行っているため含める。
abstractWe have used a Convolutional Neural Network (CNN), based on the model of VGG16 architecture, since the model is known to be effective in image classification.
Accurate estimation of aboveground biomass (AGB) in dryland savanna woodlands is constrained by sparse field data, which has motivated widespread fusion of field plots with spaceborne LiDAR reference data from the Global Ecosystem Dynamics Investigation (GEDI). Here, we show that such fusion can substantially inflate apparent model accuracy when the two reference sources sample different spatial domains. Using 44 field plots from the Abu-Gadaf Natural Reserved Forest (AGNRF), Sudan, and 56 GEDI L4A footprints drawn from a 50 km buffer surrounding the reserve, we trained Random Forest (RF), Gradient Boosting (GB) and Classification and Regression Tree (CART) models on Sentinel-1, Sentinel-2, SRTM and Dynamic World predictors and evaluated them under 10-fold, 2 km block spatial cross-validation. The merged dataset yielded apparently moderate performance (RF: RMSE = 9.40 Mg ha−1, R2 = 0.33). However, GEDI-derived AGB was 2.1 times higher than field-measured AGB (18.71 vs. 8.89 Mg ha−1; Kolmogorov–Smirnov D = 0.53, p
Why it matches plant phenotyping methods圃場・GEDI・衛星データを統合して植物群落の地上部バイオマス（AGB）を推定し、空間交差検証でモデル精度と空間ドメイン不一致によるバイアスを評価している。植物形質の推定手法の検証が中心で、単なる生物学的実験の routine measurement ではない。
abstractAccurate estimation of aboveground biomass (AGB) in dryland savanna woodlands is constrained by sparse field data, which has motivated widespread fusion of field plots with spaceborne LiDAR reference data from the Global Ecosystem Dynamics Investigation (GEDI).
High-throughput phenotyping is key in modern breeding for rapidly and cost-effectively evaluating salt-adaptive traits. However, few studies have combined spectral reflectance indices (SRIs) with deep learning to assess field-grown wheat under salt stress. In this study, we developed optimized 2D and 3D SRIs integrated with artificial neural network (ANN) to assess chlorophyll a (Chl a), chlorophyll b (Chl b), total chlorophyll (TChl), and grain yield (GY) in 32 recombinant inbred lines (RILs) and four cultivars under 150 mM NaCl field conditions. ANOVA revealed that genotype contributed the largest proportion of the treatment sum of squares across all traits (60–80%), followed by the genotype × year interaction (8–15%), whereas year contributed the smallest proportion (1–5%). Heatmap clustering of these traits clearly distinguished salt-tolerant from salt-sensitive genotypes. The study findings highlight using four key traits as screening criteria for salt tolerance in wheat. Our optimized 2D/3D spectral indices showed moderate to strong predictive power (R 2 = 0.25–0.75), outperforming earlier indices. Multi-season data improved accuracy by 15–25%, with best predictions for Chl a and TChl (R 2 = 0.34–0.75) versus Chl b and GY (R 2 = 0.25–0.64). Top models included ANN-3D-SRIs-8 for Chl a (R 2 = 0.735/0.644), ANN-3D-SRIs-3 for Chl b (R 2 = 0.611/0.549), ANN-2D-3D-SRIs-3 for TChl (R 2 = 0.713/0.619), and ANN-2D-SRIs-2 for GY (R 2 = 0.648/0.553). This framework combines optimized indices and machine learning for scalable, high-throughput phenotyping to advance precision breeding of salt-tolerant wheat.
Why it matches plant phenotyping methodsスペクトル指数とニューラルネットワークを開発・評価し、コムギのクロロフィルと収量を高スループット推定する方法が研究の中心である。
abstractwe developed optimized 2D and 3D SRIs integrated with artificial neural network (ANN) to assess chlorophyll a (Chl a), chlorophyll b (Chl b), total chlorophyll (TChl), and grain yield (GY)
Nitrogen is an important element present in vital substances such as plant proteins and chlorophyll, the content of which directly reflects the nutrient status of crops, and provides a theoretical basis for crop nutrient diagnosis, growth monitoring and yield potential prediction. Taking the chip-level visible/near-infrared spectral sensor AS7263 as the data acquisition module and the Arduino Uno single-chip microcomputer development board as the control module, a portable crop leaf spectral sensing system was designed in this study. The spectral reflectance and nitrogen content of wheat leaves were obtained through field experiments. Principal Component Analysis (PCA) was used to eliminate abnormal spectral data. Combined with pretreatment algorithms including Multiplicative Scatter Correction (MSC) and Standard Normal Variate (SNV), the prediction models for wheat leaf nitrogen content were established based on Partial Least Squares (PLS), Support Vector Machine (SVR), Random Forest (RF) and a Back Propagation (BP) neural network. The results showed that compared with SNV, the model performance based on the spectral data after MSC pretreatment was better. The test set R 2 values of PLS, SVR, RF and BP models were 0.61, 0.75, 0.83, and 0.89, and the root mean square errors (RMSEs) were 4.62 mg g -1 , 4.38 mg g -1 , 3.39 mg g -1 and 3.27 mg g -1 , respectively. The MSC-BP prediction performance was the best, and the non-destructive and accurate detection of nitrogen in wheat leaves was realized, which verified the feasibility of micro-spectral sensing technology in crop nutrition diagnosis.
Why it matches plant phenotyping methods小型可见/近红外光谱传感系统及预测模型是论文核心，用于无损估计小麦叶片氮含量这一植物生理性状，并报告了模型比较与验证性能。
abstracta portable crop leaf spectral sensing system was designed in this study
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:1110-1162Plant phenotyping relevance match · UnverifiedEurope PMC · checked 5 Sept 2026
Abstract China's rice production and environmental sustainability are largely dependent on the cold black soil region in Northeast China, where precise water and nitrogen management is challenged by water scarcity and high carbon emissions. To overcome the limitations of conventional empirical management and improve the accuracy of evapotranspiration (ET) estimation in controlled-irrigation paddy fields, this study proposes a novel framework integrating unmanned aerial vehicle (UAV) multispectral and thermal infrared observations, the FAO-56 dual crop coefficient approach, and the NSGA-II multi-objective optimization model. To parameterize and validate this methodology, field data comprising four lower limit thresholds for controlled irrigation and four nitrogen fertilizer application rates were acquired from the Rice Research Site of Farm 856, Heilongjiang Province, China. This integrated approach was used to systematically evaluate rice growth, water consumption, resource use efficiency, and greenhouse gas emissions under different water-nitrogen treatments. Based on these evaluations, an irrigation optimization scheme was developed using daily crop evapotranspiration (ETc). The results indicated that water, nitrogen, and their interaction significantly affected rice yield, irrigation water use efficiency (IWUE), partial factor productivity of nitrogen (PFPN), and global warming potential (GWP). Treatments W3N2 (80%+155 kg/ha N) and W3N3 (80%+200 kg/ha N) achieved the highest yields, 11,883.51 and 11,436.82 kg/ha, respectively, whereas W2N1 (70%+110 kg/ha N) exhibited the best comprehensive performance, with a TCQ value of 0.65. Among the tested vegetation indices, the normalized difference vegetation index (NDVI) showed the strongest correlation with the basal crop coefficient, with an R²of 0.85. The NDVI -crop water stress index ( CWSI ) coupled model achieved the highest ET c estimation accuracy (R 2 = 0.89, RMSE = 0.39 mm/day), reducing the RMSE by 10.3% compared to the traditional, Multi-objective optimization revealed obvious trade-offs among high yield, water saving, high nitrogen efficiency, and low emissions. Scenario S5 was identified as the optimal solution, with an irrigation amount of 669.94 mm, a nitrogen rate of 117.48 kg/ha, a yield of 11,473.43 kg/ha, and the highest coordination degree of 0.86. These results demonstrate that coupling UAV multispectral and thermal infrared imagery with the FAO-56 model can effectively improve ETc estimation and provide reliable data support for water-nitrogen multi-objective optimization in cold-region rice production.
Why it matches plant phenotyping methodsUAVマルチスペクトル・熱赤外画像とFAO-56を結合し、イネの蒸発散量を推定する手法を開発・検証しており、ETc推定精度も定量評価しているため、単なる灌漑試験ではなく植物状態の計測手法が中心です。
abstractthis study proposes a novel framework integrating unmanned aerial vehicle (UAV) multispectral and thermal infrared observations, the FAO-56 dual crop coefficient approach, and the NSGA-II multi-objective optimization model.
This study presents a multi-scale framework for reconstructing snow avalanche (SA) frequency and assessing vegetation structural responses in data-scarce mountain environments. The approach integrates dendrogeomorphological reconstructions, satellite-based spectral disturbance detection, and UAV-based Structure-from-Motion (SfM) photogrammetry, complemented by field data, and was applied to two avalanche paths in the Piatra Craiului Mountains (Southern Carpathians, Romania). Tree ring analyses allowed reconstruction of spatially explicit minimum avalanche chronologies for the 1980–2025 period. These reconstructions were combined with a DEM-based upslope algorithm to derive spatially variable avalanche return periods, revealing the highest frequencies in release and upper-track sectors and progressively longer return periods toward lower-track zones. Sentinel-2 imagery was used to assess the surface footprint of a reconstructed avalanche event in 2018. Among the tested spectral indices, the Moisture Stress Index (MSI) showed the most spatially coherent response, while the combined MSI-NDMI-NBR approach reduced index-specific noise. UAV-SfM photogrammetry supports high-resolution mapping of vegetation structure and surface states. Vegetation was classified using a machine-learning-based object-oriented approach (Random Forest) integrating spectral, geometric, structural, and textural parameters. The multi-parameter feature set yielded very high classification accuracy (Cohen’s Kappa ≈ 0.95). Across avalanche return-period gradients, both UAV-derived and field-based metrics showed a systematic associations between tree height and avalanche frequency, whereas tree age and stem diameter exhibited more variable, path-dependent responses. The proposed framework provides a transferable basis for linking avalanche disturbance regimes with vegetation structure and surface stability in mountain landscapes lacking long-term observational records.
Why it matches plant phenotyping methodsUAV-SfMと機械学習による植生構造・樹高の高解像度推定が研究枠組みの主要部分であり、分類精度も評価しているため、植物状態の画像ベース表現型計測として含める。
abstractUAV-SfM photogrammetry supports high-resolution mapping of vegetation structure and surface states.
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:220-232Plant phenotyping relevance match · UnverifiedOpenAlex · checked 15 Sept 2026
Accurate estimation of pasture biomass is essential for determining cattle stocking rates and grazing durations. The objective of this study was to comparatively evaluate five sensor-based systems for estimating aboveground Bermudagrass (Cynodon dactylon) biomass and identify the leading sensing approach for continued development and broader validation. The five systems included Structure-from-Motion (SfM), Ultrasound Sensor and Ski (US-Ski), Inertial Measurement Unit and Ski (IMU-Ski), Inertial Measurement Unit and Roller (IMU-Roller), and Depth Camera (DC). These systems were deployed on unmanned aerial and ground vehicles to measure crop height under identical field conditions. Regression models relating measured crop height to wet biomass yield (WBY) were developed as a common calibration framework for statistically comparing sensor performance. These empirical allometric equations were intended to support comparative benchmarking of the sensing systems and were not developed as final operational biomass prediction models for immediate field deployment. The influence of vegetation coverage on yield predictions generated by the crop height-based equations was also examined. The results indicated that the IMU-Ski system demonstrated the strongest overall comparative performance (R2 = 0.97; SeY = 1112 kg-wet/ha), followed by the DC system (R2 = 0.97; SeY = 1132 kg-wet/ha). Based on its overall benchmarking performance, including calibration accuracy, residual error and simplicity, the IMU-Ski system was identified as the leading sensing approach for continued development and broader validation among the five evaluated methods. The results also indicated that addition of vegetation coverage into the crop height-based regression models did not significantly improve prediction accuracy under the experimental conditions evaluated.
Why it matches plant phenotyping methods複数のセンサーシステムによる牧草バイオマス推定を比較・校正・ベンチマークしており、植物形質の取得法と技術性能の評価が研究の中心です。
abstractcomparatively evaluate five sensor-based systems for estimating aboveground Bermudagrass (Cynodon dactylon) biomass
Accurate tree volume estimation is central to forest management and carbon accounting. Allometric equations are widely used but limited in transferability across species, regions, and environmental conditions. Mobile Laser Scanning (MLS) offers a promising alternative through direct measurement of tree geometry; however, the influence of tree shape on MLS accuracy remains poorly understood. This study evaluated MLS-derived estimates of stem diameters, total tree height, and merchantable stem volume against destructive reference measurements from 176 trees spanning eight species (four hardwood, four softwood) in Wallonia, Belgium. A Zeb Horizon RT scanner was used; tree architectural descriptors extracted from the point cloud were tested for associations with measurement error. Across 7,824 stem diameter measurements, MLS achieved a mean error of 0.46 cm, with precision declining above 15 m. MLS-derived height outperformed Vertex IV clinometer measurements for hardwood species (RMSE% = 6.88 vs. 8.78) but performed slightly less well for softwoods (RMSE% = 7.36 vs. 6.14). QSM-based volume estimates systematically underestimated reference values, while taper-based reconstruction produced nearly unbiased estimates with an RMSE of 15.72%. Correlation analyses and PCA showed that tree architectural variables explained only a small fraction of MLS error variability. Diameter and height errors were largely independent of structural attributes, while volume errors showed moderate associations with tree size and crown density. These findings indicate that tree architecture is not a primary source of MLS measurement uncertainty. Future MLS-based forest inventory efforts should prioritize acquisition and processing optimization, as scanning conditions and forest structure appear more influential than tree shape.
Why it matches plant phenotyping methodsMLSによる樹木形状・直径・樹高・幹材積の非破壊推定を、破壊測定と比較検証し、測定誤差の要因を評価した方法検証研究である。
titleNon-destructive tree volume estimation using mobile laser scanning: Impact of the tree shape on measurement error.
India’s economy is heavily reliant on agriculture, with a diverse array of crops grown on vast tracts of land. Fruit cultivation, especially papaya, has become more popular in recent years because of its high nutritional and financial value. To increase yield, maximize resource use and lessen reliance on chemical pesticides, modern techniques like protected cultivation and hydroponics are being used more and more. Fruit crops grown in controlled or semi-controlled environments are still susceptible to nutrient imbalances despite these developments, which can have a substantial impact on plant health, fruit quality and overall productivity. Papaya leaf nutrient deficiencies frequently show up in the early stages of growth and can result in poor fruit development and decreased yield if they are not detected in time. To support early diagnosis and better crop management, the current study focuses on creating an effective method for identifying nutrient deficiencies in papaya leaves using a deep learning (DL) framework based on transfer learning (TL). In this nutrient and micronutrient deficiency study and field work observation during year 2024 to 2026 with different climate and weather conditions done in order to tackle a new but related classification task, in the context of plant health assessment, several well-established architectures including InceptionV3, VGG19, DenseNet and Xception have been widely explored for leaf image analysis. Studies commonly utilize publicly available datasets, such as papaya leaf image repositories hosted on platforms like IEEE DataPort, to fine-tune these models for efficient feature extraction and accurate identification of nutrient and micronutrient deficiency patterns. This body of work demonstrates the growing role of transferring convolutional neural network (CNN) models in advancing automated crop monitoring and decision support systems.
Why it matches plant phenotyping methodsパパイヤ葉画像から栄養・微量栄養素欠乏という植物状態を深層学習で識別する手法の開発が研究の中心であり、植物フェノタイピングに該当する。
abstractthe current study focuses on creating an effective method for identifying nutrient deficiencies in papaya leaves using a deep learning (DL) framework based on transfer learning (TL).
Improving nitrogen use efficiency (NUE) is essential for sustainable agriculture, yet conventionally measured plant characteristics have limited value as NUE proxies. Here we show that artificial intelligence (AI) can uncover previously unrecognized phenotypic variation associated with NUE, revealing genetic variation that is largely missed by conventional phenotypes. We trained a convolutional neural network (CNN) on 25,080 maize images to learn features that distinguish how plants respond to low- and high-N conditions, achieving 96.7% accuracy. The learned features were defined as deep phenotypes. Compared with conventional phenotypes, deep phenotypes showed greater phenotypic variation and higher heritability, enabling the identification of 523 significant loci compared with 21 for conventional phenotypes. We next investigated candidate genes underlying these loci and used these findings to interpret the learned features. Lower CNN layers primarily reflected visual patterns overlapping with conventional phenotypes, whereas deeper layers encoded additional features associated with N-responsive genetic variation. To validate candidate genes identified by the AI framework, we functionally characterized Liguleless2 (LG2), a basic-leucine zipper (bZIP) transcription factor, and demonstrated that lg2 mutants exhibit enhanced root architecture and increased N uptake efficiency. Field trials of 200 hybrids across diverse N environments further supported the AI findings, with each beneficial allele increasing ear weight by an average of 18 g per plot under low-N conditions. These results show how integrating AI and biology can uncover biologically relevant variation underlying complex traits such as NUE and enhance the interpretability of AI models.
Why it matches plant phenotyping methodsCNNで植物画像からN応答に関連する「deep phenotypes」を抽出する手法が研究の中心であり、従来形質との比較や遺伝的妥当性検証も行っている。
abstractWe trained a convolutional neural network (CNN) on 25,080 maize images to learn features that distinguish how plants respond to low- and high-N conditions, achieving 96.7% accuracy.
Conventional methods of plant distance and volume measurements are limited by low efficiency, limited spatial coverage, and high measurement error. LiDAR and RGB-D imaging offer cost-effective, precise, and non-destructive techniques for plant distance and volume measurements. This study aimed to measure cabbage height, volume, and distance using LiDAR and RGB-D imaging. The sensors were mounted on a 1.6 kW electric field scouting platform (EFSP) for data collection. Point cloud (PCD) data were collected using LiDAR, whereas data processing, visualization, and measurements were done using commercial software and open-source programming scripts. A total of 20 cabbage plants were analyzed. LiDAR data processing included data frame screening, outlier removal, denoising, voxelization, and generation of 3D PCD density maps. Depth image processing included importing raw data and metadata shaping using intrinsic camera parameters, visualization, extraction of depth points, and pixel-level measurements of distances and volume. RGB image processing involved image conversion, segmentation, normalization, binary masking, mask cleaning, region extraction of cabbages, separation of ROI and preparation of contours, Delaunay triangulation and convex hull preparation, ROI overlay, bounding box preparation, sharing boundary between two boxes, conversion to pixel distances, and for visualization, plant height, volume measurements, and center to center distance measurement for measuring the plant distance. LiDAR demonstrated higher measurement accuracy for cabbage plant height, circumferential volume (geometric canopy volume), and plant distance, followed by RGB-D imaging, while RGB imagery showed comparatively lower performance under the study field conditions. Overall, LiDAR and RGB-D imaging provided reliable and non-destructive approaches for cabbage geometric characterization under field conditions, although accurately capturing complex plant geometry remains challenging. Positive and negative values of bias represent the over- and under-estimated results, respectively. Future studies should include larger and more diverse plant datasets exhibiting diversified size, shape, and geometric structure to further improve the robustness and general applicability of the proposed sensing approaches.
Why it matches plant phenotyping methodsLiDAR、RGB、RGB-Dを用いてキャベツの高さ・体積・株間距離を取得し、処理手順と測定精度を比較評価する手法研究であり、植物表現型取得が中心である。
abstractThis study aimed to measure cabbage height, volume, and distance using LiDAR and RGB-D imaging.
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 confirmedEurope PMC · checked 5 Sept 2026
Field / plotLeafClassificationStress / disease detectionDisease symptoms / severity
Automated plant disease recognition from field photographs remains challenging: models trained on laboratory datasets collapse on in-the-wild images, and the current state of the art on PlantWild-the largest open in-the-wild benchmark (18,542 images, 89 classes)-relies on text prototypes derived from a language model to reach 76.18% top 1 accuracy. We ask whether text supervision is truly necessary or whether the bottleneck is the diversity of the visual representation. Our central methodological finding is that backbone selection and fusion matter far more than classifier-head engineering : across 118 experiments, a simple fixed-weight linear-prototype combination on top of three complementary frozen backbones yields larger and more reproducible gains than any head-level adaptive routing mechanism we test. Specifically, through a systematic study of six frozen vision backbones (three CLIP, two DINOv3, and one DINOv2), three classifier heads, and four fusion configurations, completed in a single day on one consumer GPU, we establish three findings. (i) A single self-supervised backbone (DINOv2 ViT-L/14) already surpasses text-augmented MVPDR (77.56% vs. 76.18%). (ii) Concatenating three complementary backbones (DINOv2 + DINOv3 + CLIP) reaches 80.23% ± 0.41% (five seeds), exceeding the published MVPDR accuracy by +4.05 points and our own reproduction of MVPDR under an identical evaluation protocol by +7.96 points, without any language supervision. (The difference between the two deltas reflects evaluation-protocol differences-our split, model-selection criterion, and training schedule-rather than any discrepancy in the reported numbers; see Section 4.6.6 for a full reconciliation.) (iii) Every form of learned routing we test-per-class gating, backbone gating, sample-wise gating-is inessential; the gain is entirely attributable to backbone diversity and a simple linear-prototype scoring combination. On the smaller PlantDoc benchmark, the same principle transfers but with substantially higher seed variance: the best configuration reaches 80.09% at a favourable seed but 76.97% ± 1.48% over five seeds-a suggestive rather than robust gain. Beyond the accuracy headline, we provide a pathology-aware per-class analysis showing that DINOv2/v3 dominate on fine-texture lesion classes (rusts, mildews, and leaf spots) whilst CLIP's narrow advantage concentrates on organ/species-level identification (rice leaf and potato late blight). All primary claims are validated over five seeds, and all code, feature caches, and result files are released for full reproducibility.
Why it matches plant phenotyping methods植物病害の画像認識を対象に、複数の視覚基盤モデル融合と分類器を体系比較・検証しており、病害状態の推定手法が研究の中心である。
abstractOur central methodological finding is that backbone selection and fusion matter far more than classifier-head engineering
Reproduction assets foundThe paper states that its code, cached features, and result files will be released, but no authors' public URL or repository is provided in the supplied blocks (future-tense availability language only). The DINOv3 GitHub link and OpenReview link are third-party backbone resources, not paper-specific assets.Code · publicAll primary claims are validated over five seeds, and all code, feature caches, and result files are released for full reproducibility.Open asset ↗lines:332-335Plant phenotyping relevance match · UnverifiedOpenAlex · Crossref · Europe PMC · checked 5 Sept 2026
Within the context of climate change, quinoa ( Chenopodium quinoa Willd.) is a climate-resilient crop with high nutritional value. The effects of deficit irrigation on quinoa growth and physiological performance under arid conditions remain insufficiently understood. This study evaluated ten quinoa genotypes (two commercial varieties and eight accessions) under two irrigation regimes to identify traits and spectral indices associated with water-stress tolerance. We combined manual phenotyping of agromorphological and physiological traits with multispectral and spectroradiometer measurements to calculate 35 vegetation indices across 13 and 5 dates, respectively. Deficit irrigation reduced plant height (18%), specific leaf area (8%), yield (43%), harvest index (26%), relative water content (7%), and dry matter accumulation (36%), while relative chlorophyll content (SPAD, Soil Plant Analysis Development) and stomatal density increased by 16% and 13%, respectively; accession ACC_23 exhibited the highest water-use efficiency (5.9 g kg -1 ). A univariate analysis of 35 vegetation indices across 13 dates showed that: Health Index(HIV), Normalized Green-Red Difference Index (NGRD), Red-Green Ratio (RG) and Plant Senescence Reflectance Index (PSRI), were the most sensitive, detecting significant differences between irrigation treatments in up to 32 of the 130 possible genotype-by-date comparisons. Integrating remote sensing into crop phenotyping represented a significant methodological improvement by enhancing phenotyping efficiency, improving detection of deficit irrigation effects, and facilitating identification of tolerant quinoa genotypes for arid production systems.
Why it matches plant phenotyping methodsリモートセンシングと多時点の植 phenotyping を統合し、35の植生指数の感度比較によって水ストレス関連形質を抽出する方法適用が、研究の主要な技術的要素として明示されています。
abstractWe combined manual phenotyping of agromorphological and physiological traits with multispectral and spectroradiometer measurements to calculate 35 vegetation indices across 13 and 5 dates, respectively.
MaizeField / plotClassificationGrowth / development / phenology
Integrating precision agriculture (PA, a data-driven agricultural management system) with deep learning (DL) models can effectively support various activities, including yield prediction, crop health monitoring, field task automation, and decision-making. Taking advantage of such data-driven methodologies typically requires desktops, high-performance computing systems, and cloud clusters for data analysis, but their portability limits in-field applications. However, a single board computer, such as Raspberry Pi, offers a compact, lightweight, cost-efficient, easy-to-use, and feature-rich portable computing device which is ideal for in-field decision-making in PA applications. One such in-field application is crop growth stage classification for better crop management. Therefore, in this study, eight corn growth stages were classified using PhenoCam (near-surface [proximal] remote sensing network camera)imagery collected from ten PhenoCam sites. Four lightweight DL models were developed, ELiteCrop0, ELiteCrop1, ELiteCrop4, and MobNetCropV2, and evaluated across five image vertical clipping levels(0 %–40 %) using a supercomputer. The optimized model was subsequently deployed on a Raspberry Pi5 for edge inference. Model training accounted for the majority of the total CPU time, exceeding 97 %, while the testing times ranged from 0.01 min to 0.12 min, enabling real-time applications. Among the models, ELiteCrop0 achieved the most balanced performance with a confusion-matrix diagonal ratio(CMDR) of 0.93, followed by ELiteCrop1 (CMDR = 0.92). Overall, model performance decreased with increasing vertical clipping; therefore, a moderate image clipping (0 %–10 %) was recommended for improved computational efficiency. Analysis with a supercomputer produced an intrasite (same train sites)accuracy of 0.90–0.93 (Raspberry Pi: 0.78–0.81) and an intersite (new test sites) accuracy of 0.48–0.50(Raspberry Pi: 0.41–0.43), indicating challenges with model generalization. Raspberry Pi successfully processed ≈ 1000 images/min under safe operating conditions (68◦C). Future work should focus on extending the multi-site dataset to improve cross-site performance. Hence, this study presents a scalable and cost-effective solution for real-time corn growth stage monitoring in PA.
Why it matches plant phenotyping methodsトウモロコシの生育段階という植物状態をPhenoCam画像から推定する深層学習モデルを開発・評価し、Raspberry Piへ展開して性能検証しているため、フェノタイピング手法が中心である。
abstractTherefore, in this study, eight corn growth stages were classified using PhenoCam (near-surface [proximal] remote sensing network camera)imagery collected from ten PhenoCam sites.
Field / plotLeafStem / branchPhysiological trait estimationGrowth / time-series analysisStress response / toleranceWater status / transpiration
Live fuel moisture content is a key determinant of live fuel flammability, yet its destructive and discontinuous measurement limits high-temporal-resolution monitoring. This study evaluated whether leaf electrical potential can serve as a non-invasive proxy for LFMC and flammability-related traits under natural drought conditions. From February to July 2025, leaf and trunk electrical potentials were monitored weekly in Salvia rosmarinus individuals from a Mediterranean shrubland, while LFMC, essential oil yield, fatty-acid fraction, and laboratory-based flammability metrics-ignition time, combustion duration, and flame height-were assessed bi-weekly. Leaf electrical potential was strongly associated with LFMC (R 2 = 0.64, p < 0.001), decreasing as plants underwent seasonal drought-induced dehydration. Periods of high temperature and low rainfall reduced both LFMC and electrical potential, coinciding with shorter ignition times, which declined to approximately 20-30 s during the driest period. Based on the observed shifts in ignition time, combustion duration, and flame height, three empirical LFMC response zones were identified, with leaf electrical potential closely tracking transitions in plant hydration and flammability. These results suggest that plant electrophysiology may provide a promising non-invasive indicator of live fuel water status and seasonal flammability dynamics, with potential applications in wildfire risk monitoring when combined with conventional LFMC, meteorological, and remote-sensing approaches.
Why it matches plant phenotyping methods葉の電気的電位をLFMC（水分状態）および可燃性関連形質の非破壊・連続的な指標として評価しており、植物状態の取得方法の検証が研究の中心である。
abstractThis study evaluated whether leaf electrical potential can serve as a non-invasive proxy for LFMC and flammability-related traits under natural drought conditions.
Field / plotMultimodalNeRF / 3D Gaussian SplattingLiDAR / point cloudRGB / grayscaleStereoFruitWhole plant / canopy / plot / fieldMorphology / geometry measurementObject detection
Binocular stereo vision is a low-cost and scalable 3D perception technology that shows strong potential in agricultural phenotyping and smart agriculture. By estimating depth from multi-view RGB images, it enables non-contact, high-precision sensing of crop structure, canopy morphology, growth dynamics, and livestock traits, providing essential support for digital and intelligent agricultural production. With recent advances in deep learning-based stereo matching, multimodal sensor fusion, and 3D reconstruction, its robustness and accuracy in complex field environments have been significantly improved. This paper systematically reviews recent progress in agricultural applications of binocular stereo vision, covering system architectures, traditional and deep learning-based stereo matching methods, point cloud reconstruction techniques, and emerging supervision strategies such as 3D Gaussian splatting. It further summarizes key applications, including high-throughput phenotyping, fruit localization and robotic harvesting, weed detection and precision spraying, autonomous navigation, and livestock body condition assessment, highlighting its role in multi-task agricultural perception systems. Finally, the paper discusses major challenges, including low-texture matching difficulty, occlusions in complex environments, cross-domain generalization, real-time lightweight deployment, and limited dataset availability. Future directions are outlined in foundation model-based visual perception, self- and weakly supervised learning, multimodal fusion, and edge-efficient model design, aiming to support large-scale deployment in smart agriculture.
Why it matches plant phenotyping methods農業における双眼ステレオビジョンのシステム、ステレオマッチング、3D再構成を体系的にレビューし、作物構造・群落形態・生育動態の非接触計測とハイスループット表現型解析を主要対象としているため。
abstractThis paper systematically reviews recent progress in agricultural applications of binocular stereo vision, covering system architectures, traditional and deep learning-based stereo matching methods, point cloud reconstruction techniques
LiDAR (Light Detection and Ranging) and RGB-D camera imaging have emerged as essential tools in agricultural applications, particularly for plant size and distance measurements, enabling non-destructive, cost-effective, and precise estimation. The objective of this study was to measure the plant canopy dimensions and distance between apples using commercial LiDAR, and an RGB-D camera with a speed sprayer platform was used to determine whether LiDAR provides a higher measurement accuracy under field conditions. Data were collected in an apple orchard in Muju, Republic of Korea. Commercial 3D LiDAR, a terminal box, an RGB-D camera, a microcontroller, a power supply, and individual display monitors were integrated into a customized data acquisition (DAQ) box for LiDAR point cloud (PCD), RGB, and depth imagery data collection. Commercial software was used for data acquisition, data conversion (pcap to PCD), segmentation of regions of interest (ROI), and pre-processing of data. PCD processing and measurement consisted of data frame selection, data conversion, outlier removal, downsampling, denoising, ground point removal by filtering, voxelization, and density map generation using an open access programming language script. Depth image processing included importing raw data, shaping metadata using intrinsic camera parameters, visualizing depth images, extracting depth points, and measuring the plant canopy at the pixel level. RGB image analysis involved grayscale conversion, thresholding, segmentation of ROI, contour preparation, noise removal, and binary masking for eliminating the background. Estimated results were compared to measured results. LiDAR measurements showed the closest agreement with the measured results for plant height, canopy volume, plant spacing, and row distance, outperforming both RGB and depth imaging. Under field conditions, plant spacing and row distance were estimated with accuracies of 97.5% and 94.7%, respectively, exhibiting higher measurement accuracies than RGB and depth imagery data results. Despite some discrepancies due to complex plant geometry and dynamic data collection, the results support data collection strategies critical for precision horticulture.
Why it matches plant phenotyping methodsLiDARとRGB-D画像を用いたリンゴ樹の樹冠寸法・体積・樹間距離・列間距離の取得と精度比較が研究の中心であり、植物表現型計測手法の開発・検証に該当する。
abstractThe objective of this study was to measure the plant canopy dimensions and distance between apples using commercial LiDAR, and an RGB-D camera with a speed sprayer platform was used to determine whether LiDAR provides a higher measurement accuracy under field conditions.
Field / plotLiDAR / point cloudStem / branchYield / biomass estimationBiomass / plant weight
Integrating ground-based and aerial remote sensing for individual tree-level stem volume modeling remains underexplored in Mediterranean mixed forests, despite the growing need for cost-effective, automated forest inventory approaches. This study evaluated the combined use of Handheld Laser Scanning (HLS) and Unmanned Aerial Vehicle (UAV)-based Structure from Motion (SfM) photogrammetry for individual-tree stem volume modeling in a mixed stand in Castilla y León, Spain, dominated by Pinus halepensis, Pinus pinea, Quercus faginea, and Cupressus sempervirens. Two open-source HLS processing tools; the Forest Structural Complexity Tool (FSCT) and 3D Forest Inventory (3DFin), were compared for individual tree attribute extraction, with FSCT outperforming 3DFin across all species. Reference stem volumes were derived by applying species-specific Spanish National Forest Inventory (SNFI) allometric equations to FSCT-extracted diameter and height values. Random Forest models were then built using UAV-SfM crown metrics as predictors, testing two image overlap configurations: 80 × 80 F (80% front and side overlap) and 80 × 60 CF (80% front, 60% side, cross-flight). The 80 × 80 F configuration produced the best-performing model (R2 = 0.730), with 80 × 60 CF achieving comparable accuracy (R2 = 0.688), results confirmed by spatially independent leave-one-plot-out cross-validation (LOPO-CV R2 = 0.627 and 0.613, respectively). These results show that combining HLS and UAV-SfM through a predominantly open-source workflow offers a viable, reproducible approach to stem volume modeling in structurally complex Mediterranean mixed forests.
Why it matches plant phenotyping methodsHLSとUAV-SfMを用いて個体樹の直径・樹高から幹材積を推定する再現可能な計測・解析ワークフローを構築し、複数ツールと飛行条件を比較検証しているため、植物表現型取得が中心である。
abstractIntegrating ground-based and aerial remote sensing for individual tree-level stem volume modeling remains underexplored
Crop straw-to-grain ratio (SGR) estimation underpins regional straw resource assessment, yet national inventories rely on fixed coefficients that ignore structured variation across variety, environment, and phenotype. We introduce a Structured Multi-Kernel Heteroscedastic Gaussian Process (GP) framework that models SGR variation through three additive kernels heuristically motivated by the genotype–environment–phenotype (G+E+P) framework—capturing variety-associated variation, spatially structured variation, and environmental and management covariates—and employs an input-dependent noise model for prediction-specific uncertainty quantification. To prevent information leakage, target encoding and feature scaling are recomputed within each cross-validation fold. Evaluated via internal leave-one-out cross-validation on 80 rice samples (42 varieties, six Chinese provinces), the model achieves R2=0.541 with a prediction interval coverage probability of 0.95. Ablation identifies variety-associated variation as the largest contributor among the modeled factors (ΔR2=−0.024) and the multi-kernel design, by incorporating variety-specific information, substantially improves upon a covariate-only RBF GP (ΔR2=0.103). On point-prediction accuracy, Gradient Boosting achieves R2=0.58, slightly ahead of the Heteroscedastic GP (R2=0.54), underscoring that the primary advantage of the GP lies in its input-dependent uncertainty quantification. However, leave-one-county-out validation yields R2≈0 (with σ escalating to 24.4), confirming that the model does not yet generalize to unsampled counties; all reported performance is therefore internal to the nine sampled counties. The framework couples an agronomically motivated additive kernel structure with input-dependent uncertainty quantification, offering a path toward uncertainty-aware prediction from small field datasets.
Why it matches plant phenotyping methods作物のわら・穀粒比という植物関連形質を対象に、不確実性定量化を備えた予測手法を開発・検証しており、単なるルーチン測定ではなく計算的な形質推定が中心である。
abstractWe introduce a Structured Multi-Kernel Heteroscedastic Gaussian Process (GP) framework that models SGR variation
Accurate assessment of crop water status is critical for precision irrigation and sustainable water management in agriculture. This study develops a UAV-based thermal infrared inversion framework for high-resolution canopy temperature retrieval and irrigation decision support in tea plantations. The proposed approach integrates multi-frame image mosaicking, threshold-based canopy extraction, and a gray-temperature calibration model to generate spatially continuous canopy temperature maps. Crop water stress was quantified using the Crop Water Stress Index (CWSI), and its reliability was further evaluated by analyzing its relationship with stomatal conductance. The framework further estimates soil moisture status and irrigation requirements based on a threshold-based irrigation strategy. The results show that the linear gray-temperature calibration model achieved a maximum absolute error of less than 0.3 °C and that the calculated CWSI and estimated irrigation requirement were strongly correlated with measured stomatal conductance, with R 2 up to 0.91. The proposed method provides a practical technical workflow from UAV thermal imagery acquisition to canopy temperature retrieval and quantitative irrigation decision-making, demonstrating its potential for precision irrigation management in tea plantations.
Why it matches plant phenotyping methodsUAV熱画像から茶園の樹冠温度と水ストレスを推定する取得・抽出・較正手法を開発し、気孔コンダクタンスとの関係で検証しており、植物状態の計測が中心である。
abstractThis study develops a UAV-based thermal infrared inversion framework for high-resolution canopy temperature retrieval and irrigation decision support in tea plantations.
This study investigates the automatic classification of crop phenological stages from low-altitude UAV RGB imagery. The dataset included 11,489 images of five crops: sunflower, rapeseed, soybean, wheat, and barley. The images were annotated using the Biologische Bundesanstalt, Bundessortenamt und Chemische Industrie (BBCH) scale, with labels corresponding to either single stages or stage ranges to reflect heterogeneous field conditions and transitional crop states. A pretrained ResNet18 model was adapted to the task using transfer learning. Training was conducted in two stages: first, the classification head was optimized while the backbone remained frozen; second, the entire network was fine-tuned. The model achieved strong internal test accuracy across all crops, with 100% test accuracy for rapeseed and barley, more than 99% for the remaining crops, and a mean accuracy of 99.73% under the studied survey conditions. The results also compare favorably with previously reported studies on UAV-based phenological classification. Overall, the findings support the potential of low-altitude UAV imagery and deep learning for localized phenological assessment of selected field zones in precision agriculture, while broader deployment requires validation across independent fields, seasons, regions, and survey conditions.
Why it matches plant phenotyping methodsUAV画像と深層学習により作物の生育・フェノロジー段階を自動推定する方法が研究の中心であり、植物状態の抽出性能も評価している。
abstractThis study investigates the automatic classification of crop phenological stages from low-altitude UAV RGB imagery.
Unmanned aerial vehicle (UAV) imagery can support plot-scale crop phenotyping, but spectral, RGB and structural predictors may contribute differently to different traits. We compared six predefined feature groups for predicting soybean SPAD and plant height (PH) in a 1.3 ha field experiment in Sanya, China. The field contained 6197 soybean planting plots, of which 234 had paired SPAD and PH measurements. Multispectral bands, vegetation indices (VIs), RGB descriptors and digital surface model (DSM) metrics were extracted from DJI Mavic 3 Multispectral imagery. Six regression algorithms were evaluated using random fivefold cross-validation, spatial block cross-validation and nested spatial cross-validation. Under random cross-validation, ExtraTrees with multispectral bands, VIs and RGB descriptors produced the numerically highest SPAD performance (R2 = 0.589; RMSE = 6.66), while BayesianRidge with multispectral bands, VIs and DSM metrics produced the highest PH performance (R2 = 0.760; RMSE = 7.14 cm). Nested spatial cross-validation yielded R2 = 0.473 and RMSE = 7.56 for SPAD and R2 = 0.690 and RMSE = 8.13 cm for PH. G4 was selected in four of the five outer folds for SPAD, although the selected algorithm varied, and G5 was selected in all five outer folds for PH. VIs improved prediction of both traits relative to the original bands. Adding RGB descriptors produced only a small and model-dependent improvement for SPAD, whereas adding DSM metrics produced a larger and more consistent improvement for PH. The complete feature set did not outperform G4 for SPAD or G5 for PH. The retained models were applied to all 6197 plots to map SPAD, PH and their field relative combinations. Because all of the validations used one field and one UAV acquisition date, the results describe performance within this experiment and do not establish transferability to other sites, years or growth stages.
Why it matches plant phenotyping methodsUAVマルチスペクトル・RGB・構造特徴からSPADと草丈を推定する特徴抽出および回帰手法を、複数の空間交差検証で比較・評価しており、植物表現型取得が研究の中心である。
titleTrait-Specific Contributions of UAV Multispectral, RGB and Structural Features to Soybean SPAD and Plant Height Phenotyping
Semi-arid rangelands support livelihoods and key ecosystem services, yet sustainable management depends on accurate and scalable monitoring of herbaceous aboveground biomass (AGB). Field-based measurements are spatially limited, while satellite-derived vegetation indices often perform poorly in complex savanna systems such as the Kalahari. Using unoccupied aerial vehicle (UAV) structure-from-motion (SfM) photogrammetry, we evaluate the ability of fine-scale canopy height and spectral reflectance metrics to predict herbaceous biomass across a grazing intensity gradient. Canopy height consistently predicted AGB across all grazing levels, whereas normalised difference vegetation index (NDVI) effects were weak and grazing-dependent. The UAV-derived canopy height showed strong relationships with total herbaceous AGB, explaining up to 72% of observed variation, whereas vegetation greenness measured using NDVI showed limited predictive power. In contrast, predicting biomass of foraging importance proved challenging, with UAV-derived structural and spectral metrics explaining only a small proportion of variation. Together, these findings highlight the value of UAV-derived structural measurements over traditional spectral indices for fine-scale rangeland monitoring in semi-arid systems, while underscoring the limitations of current UAV-based spectral and structural metrics for assessing forage value across species and sites.
Why it matches plant phenotyping methodsUAV SfMフォトグラメトリから植物群落の canopy height を抽出し、地上部バイオマス予測性能を評価しており、植物形質取得法の技術的適用・検証が中心である。
abstractUsing unoccupied aerial vehicle (UAV) structure-from-motion (SfM) photogrammetry, we evaluate the ability of fine-scale canopy height and spectral reflectance metrics to predict herbaceous biomass across a grazing intensity gradient.
Semi-arid rangelands support livelihoods and key ecosystem services, yet sustainable management depends on accurate and scalable monitoring of herbaceous aboveground biomass (AGB). Field-based measurements are spatially limited, while satellite-derived vegetation indices often perform poorly in complex savanna systems such as the Kalahari. Using unoccupied aerial vehicle (UAV) structure-from-motion (SfM) photogrammetry, we evaluate the ability of fine-scale canopy height and spectral reflectance metrics to predict herbaceous biomass across a grazing intensity gradient. Canopy height consistently predicted AGB across all grazing levels, whereas normalised difference vegetation index (NDVI) effects were weak and grazing-dependent. The UAV-derived canopy height showed strong relationships with total herbaceous AGB, explaining up to 72% of observed variation, whereas vegetation greenness measured using NDVI showed limited predictive power. In contrast, predicting biomass of foraging importance proved challenging, with UAV-derived structural and spectral metrics explaining only a small proportion of variation. Together, these findings highlight the value of UAV-derived structural measurements over traditional spectral indices for fine-scale rangeland monitoring in semi-arid systems, while underscoring the limitations of current UAV-based spectral and structural metrics for assessing forage value across species and sites.
Why it matches plant phenotyping methodsUAV-SfMによるキャノピー高とスペクトル指標から植物群落のバイオマスを推定し、手法の予測性能を比較評価しており、植物形質取得が研究の中心です。
abstractUsing unoccupied aerial vehicle (UAV) structure-from-motion (SfM) photogrammetry, we evaluate the ability of fine-scale canopy height and spectral reflectance metrics to predict herbaceous biomass across a grazing intensity gradient.
Semi-arid rangelands support livelihoods and key ecosystem services, yet sustainable management depends on accurate and scalable monitoring of herbaceous aboveground biomass (AGB). Field-based measurements are spatially limited, while satellite-derived vegetation indices often perform poorly in complex savanna systems such as the Kalahari. Using unoccupied aerial vehicle (UAV) structure-from-motion (SfM) photogrammetry, we evaluate the ability of fine-scale canopy height and spectral reflectance metrics to predict herbaceous biomass across a grazing intensity gradient. Canopy height consistently predicted AGB across all grazing levels, whereas normalised difference vegetation index (NDVI) effects were weak and grazing-dependent. The UAV-derived canopy height showed strong relationships with total herbaceous AGB, explaining up to 72% of observed variation, whereas vegetation greenness measured using NDVI showed limited predictive power. In contrast, predicting biomass of foraging importance proved challenging, with UAV-derived structural and spectral metrics explaining only a small proportion of variation. Together, these findings highlight the value of UAV-derived structural measurements over traditional spectral indices for fine-scale rangeland monitoring in semi-arid systems, while underscoring the limitations of current UAV-based spectral and structural metrics for assessing forage value across species and sites.
Why it matches plant phenotyping methodsUAV-SfMによるキャノピー高とスペクトル指標を用いた植物バイオマス推定を比較・評価しており、植物形質の取得・推定手法が研究の中心である。
abstractUsing unoccupied aerial vehicle (UAV) structure-from-motion (SfM) photogrammetry, we evaluate the ability of fine-scale canopy height and spectral reflectance metrics to predict herbaceous biomass across a grazing intensity gradient.
Magnetic field (MF) technologies have been explored in agriculture since the 1930s, with research activity increasing markedly since 2016. However, they have not achieved mainstream adoption, partly because no MF-specific validated methodology exists for evaluating their effects under realistic field conditions. Unmanned Aerial Vehicle (UAV)-based multispectral sensing represents a potential pathway to address this limitation by providing spatially explicit, non-destructive estimates of key canopy physiological variables at field scale, thereby enabling, for the first time, the systematic evaluation and validation of MF treatment responses under open-field conditions. To realise this potential, however, a common evidential basis must first be established by identifying crop physiological variables that are both consistently modulated by MF treatments and reliably detectable by UAV remote sensing. This study addressed this challenge through a dual-stream evidence synthesis of 216 peer-reviewed publications, comprising 102 studies on MF treatments in agricultural crops and 114 studies on UAV-based multispectral monitoring. Evidence from both research domains was synthesised to identify physiological variables that are simultaneously responsive to MF treatments and detectable through UAV remote sensing. Five direct bridge variables were identified: chlorophyll content, nitrogen use efficiency (NUE)/nitrogen assimilation, above-ground biomass (AGB), leaf area index (LAI), and yield. Chlorophyll content emerged as the strongest bridge variable, combining consistent MF responsiveness with UAV estimation accuracies of up to R2 = 0.90. Based on these findings, a conceptual framework was developed linking MF treatments, UAV-derived vegetation indices, ground-truth measurements, and machine-learning approaches for field-scale validation. The review revealed a complete absence of integration between the two research domains within the reviewed corpus, despite their strong biological and methodological compatibility. The proposed framework is conceptual and remains to be experimentally validated; it provides the first operational pathway for evaluating MF technologies under realistic farming conditions and may support future research on sustainable and digitally enabled crop production systems.
Why it matches plant phenotyping methodsUAVマルチスペクトルセンシングによる作物生理形質の推定をレビューし、地上真値・植生指数・機械学習を統合した検証フレームワークを提案しており、植物表現型の取得・推定方法が中心です。
abstractUnmanned Aerial Vehicle (UAV)-based multispectral sensing represents a potential pathway to address this limitation by providing spatially explicit, non-destructive estimates of key canopy physiological variables at field scale
Leaf chlorophyll content (LCC) is a key indicator for assessing the photosynthetic capacity and nutritional status of winter wheat. Among traditional LCC estimation methods, empirical models lack a physical basis and have poor generalisability, while physical models are widely applicable but suffer from ill-posed inversion problems. Hybrid inversion methods, which integrate radiation transfer models such as PROSAIL with machine learning, offer both the interpretability of physical models and the efficiency of machine learning; however, they are still affected by the domain shift between simulated and measured data, which limits their generalisation performance. Transfer Component Analysis (TCA), a domain adaption method, can effectively alleviate this problem. In this study, hyperspectral and LCC data were collected in the field, and simulated data were generated using the PROSAIL model; a sensitivity analysis was conducted to identify LCC-sensitive bands. A genetic algorithm was applied to the measured data for band selection and, together with the results of the sensitivity analysis, yielded an optimal set of 30 characteristic bands for subsequent modelling. Three datasets were constructed: measured data only, a direct mixture of measured and simulated data, and a TCA-fused mixture of measured and simulated data. Four models-gradient boosting regression (GBR), random forest (RF), support vector regression (SVR) and deep neural network (DNN)-were developed for each dataset. The results show that: (1) the LCC-sensitive bands are concentrated in the 450-660 nm and 680-720 nm ranges; (2) the model built on the TCA-fused data (R² = 0.722, RMSE = 6.792) outperformed those built on the measured-only data (R² = 0.682, RMSE = 7.259) and the directly mixed data (R² = 0.616, RMSE = 7.976); (3) for the TCA-fused data, the four models differed considerably in accuracy, with SVR performing best (R² = 0.723, RMSE = 5.363), followed by RF (R² = 0.630, RMSE = 6.201) and GBR (R² = 0.575, RMSE = 6.650), whereas the DNN performed worst (R² = 0.388, RMSE = 7.947), probably owing to the limited sample size.
Why it matches plant phenotyping methods冬小麦の葉緑素含量という植物形質を、ハイパースペクトルデータとPROSAIL・機械学習・転移学習で推定する手法を開発・比較しており、形質取得とモデル性能評価が研究の中心である。
abstractHybrid inversion methods, which integrate radiation transfer models such as PROSAIL with machine learning, offer both the interpretability of physical models and the efficiency of machine learning
Field / plotRGB / grayscaleLeafSegmentationGrowth / development / phenology
Bud flushing timing is a crucial attribute for forest geneticists and physiologists studying adaptive variation in tree species. In clonal populations such as Norway spruce seed orchards, accurate assessment of bud flushing is essential, as this attribute strongly influences survival and fitness. However, traditional bud-flushing assessment relies on visual scoring scales that are inherently subjective and susceptible to observer bias, leading to inconsistencies when multiple technicians collect data. To address these limitations, we introduce a novel quantitative phenotype derived from segmented RGB images for quantifying bud flushing that objectively measures the ratio of light-green current-year needles to the total visible needle area of each grafted ramet. By extracting and summarizing digital image data for each ramet, this approach provides a standardized and reproducible assessment of bud flushing phenology. We evaluated clonally replicated ramets in two sites across two seasons and compared this image-derived flushing ratio with conventional visual scoring and color indices. Using mixed models, we quantified genetic control and cross-orchard stability of clonal performance. The image-derived flushing ratio tracked visual-score progression but showed higher broad-sense heritability (0.54–0.70) than visual scoring (0.45–0.65) and canopy color indices (0.20–0.51). Although site means differed strongly, clonal ranking remained stable between orchards for the image-derived flushing ratio and for visual scoring, whereas color indices showed lower stability and greater uncertainty. Overall, these results support the image-derived flushing ratio as a structure-based phenotype that improves the precision and cross-site transferability of genetic evaluation of bud flushing in Norway spruce seed orchards.
Why it matches plant phenotyping methodsRGB画像のセグメンテーションから bud flushing の定量形質を開発し、従来の視覚評価や色指数と比較検証しており、植物表現型取得法が研究の中心である。
abstractwe introduce a novel quantitative phenotype derived from segmented RGB images for quantifying bud flushing
Accurate retrieval of crop structural and physiological traits from remote sensing data remains challenging due to limited field observations and poor cross-platform generalization of data-driven models. This study develops a physics-informed transfer learning framework to quantify the contributions of improving simulated data fidelity and increasing model complexity to retrieving winter wheat leaf area index (LAI) and canopy chlorophyll content (CCC) from hyperspectral observations. Two PROSAIL-D datasets with default and physically optimized leaf angle distributions were generated to represent different levels of simulation fidelity. Four dual-branch deep learning architectures (CNN, CNN–SE, CNN–Transformer, and CNN–SE–Transformer) integrating spectral bands and vegetation indices were pretrained on simulated datasets and transferred to real observations using progressive fine-tuning. Model performance was assessed using ground-based and unmanned aerial vehicle (UAV) hyperspectral datasets, and SHapley Additive exPlanations (SHAP) analysis was applied to interpret feature contributions. Results demonstrated that transfer learning substantially improved cross-domain generalization, while enhancing simulation fidelity provided greater performance gains than increasing network complexity. The CNN–Transformer model pretrained on physically optimized simulations achieved the highest accuracy and robustness for both LAI and CCC retrieval. At ground and UAV scales, it achieved LAI estimation accuracies of R2 = 0.55 (RMSE = 0.63) and R2 = 0.53 (RMSE = 0.62), respectively. For CCC estimation, the model obtained R2 = 0.59 at both scales, with RMSE values of 36.12 μg cm⁻2 and 37.56 μg cm⁻2 for ground and UAV observations, respectively. SHAP analysis indicated that physically optimized simulations shifted model attention toward physiologically relevant vegetation indices, whereas default simulations induced stronger dependence on unstable visible wavelengths. Physically informed simulation design combined with transfer learning effectively reduces simulation to reality discrepancies, whereas increasing deep model complexity alone provides limited improvement. The proposed framework offers an accurate, interpretable, and scalable solution for cross-platform crop trait retrieval from hyperspectral observations.
Why it matches plant phenotyping methodsハイパースペクトル観測から冬コムギのLAIと群落クロロフィル含量を推定する物理情報付き転移学習フレームワークを開発し、地上およびUAVデータで性能評価しており、植物形質取得・推定手法が中心である。
abstractThis study develops a physics-informed transfer learning framework to quantify the contributions of improving simulated data fidelity and increasing model complexity to retrieving winter wheat leaf area index (LAI) and canopy chlorophyll content (CCC) from hyperspectral observations.
Understanding the spatial structure of tree communities is fundamental for evaluating ecological interactions and management dynamics in agroforestry systems. However, the structural complexity and small spatial scale of traditional agroecosystems often limit the use of conventional remote sensing approaches. Recent advances in drone-based photogrammetry offer new opportunities to reconstruct the three-dimensional structure of vegetation at high spatial resolution and to quantify tree-level structural attributes. In this study, we applied aerial photogrammetry from unmanned aerial vehicles (UAVs) to characterize the spatial structure of agroforestry systems in traditional home gardens (THGs) in the Yucatan Peninsula, Mexico. The immediate neighborhood structure of the tree community of 20 THGs distributed along a south–north precipitation gradient was analyzed using two focal species as anchor references: Spondias purpurea and Annona muricata. High-resolution orthomosaics and three-dimensional point cloud models were generated to estimate structural attributes, including tree height, crown area, crown surface area, and canopy volume, which were combined with field measurements of diameter at breast height. Spatial indices describing aggregation, dominance, and neighborhood diversity were calculated to evaluate tree spatial organization and potential interaction patterns. The UAV-derived structural metrics revealed significant differences in canopy architecture across regions and between focal species. Regardless of the focal species, trees in the southern region exhibited greater height, crown diameter, and canopy volume than those in the northern region. Moreover, the spatial arrangement of tree communities also differed depending on which focal species was considered as the anchor, suggesting contrasting strategies of canopy dominance and spatial coexistence. Finally, our results validate the use of drone-based photogrammetry as an effective approach for capturing fine-scale spatial structure in complex agroforestry systems. By enabling detailed three-dimensional reconstruction of tree canopies, UAV remote sensing offers an affordable, simple approach to investigate neighborhood interactions, management effects, and structural dynamics in traditional agroecosystems that are difficult to assess using conventional field- or satellite-based methods.
Why it matches plant phenotyping methodsUAV空撮フォトグラメトリと3D点群から樹高・樹冠面積・樹冠表面積・林冠体積を推定し、その有効性も検証しており、植物形質取得法が研究の中心である。
abstractHigh-resolution orthomosaics and three-dimensional point cloud models were generated to estimate structural attributes, including tree height, crown area, crown surface area, and canopy volume
Efficient nitrogen (N) management is essential for sustaining crop productivity while minimizing environmental impacts associated with nitrogen losses. However, the high spatial and temporal variability of soil nitrogen dynamics and crop nitrogen status makes field-scale monitoring challenging, while conventional soil and plant sampling methods are labor-intensive, destructive, and provide limited spatial coverage. Recent advances in remote sensing technologies and machine learning (ML) offer promising alternatives for high-throughput, non-destructive monitoring of crop nitrogen status and related nitrogen dynamics in agroecosystems. This review synthesizes current progress in the use of proximal and remote sensing platforms, including unmanned aerial vehicles (UAVs), satellites, and ground-based sensors for assessing crop nitrogen status and inferring soil nitrogen availability. We examine spectral, thermal, and structural indicators, together with emerging sensor-fusion and time-series approaches. We also evaluate ML algorithms, including emerging foundation model approaches, for estimating crop nitrogen status and inferring soil nitrogen indicators, highlighting their performance, limitations, and transferability across environments. Particular emphasis is placed on field-scale applications in heterogeneous and water-limited systems, where nitrogen-water interactions critically influence crop responses. Finally, we discuss current challenges, including data scarcity, model generalization, and operational constraints, and outline future directions toward integrated, real-time decision support systems for precision nitrogen management. Overall, this review provides a comprehensive framework for leveraging remote sensing and data-driven approaches to improve nitrogen monitoring and enhance nitrogen use efficiency in diverse cropping systems.
Why it matches plant phenotyping methods作物の窒素状態という植物形質を対象に、リモートセンシングと機械学習による推定手法を体系的にレビューしており、フェノタイピング手法が中心である。
abstractThis review synthesizes current progress in the use of proximal and remote sensing platforms, including unmanned aerial vehicles (UAVs), satellites, and ground-based sensors for assessing crop nitrogen status and inferring soil nitrogen availability.
Ground-level ozone (O 3 ) adversely affects rice physiology and is associated with yield reductions. This study developed a high-resolution assessment framework integrating multi-source satellite remote sensing with econometric methods to quantify the impacts of O 3 on rice production in China's primary rice-growing region-the Middle and Lower Reaches of the Yangtze River (MLYR)-from 2019 to 2023. We fused Sentinel-5P TROPOMI total ozone column (TOC) data, a harmonized multi-satellite solar-induced chlorophyll fluorescence (SIF) product (LHSIF), high-precision rice distribution maps, and ERA5 meteorological reanalysis data. In addition to SIF, we examined multiple vegetation indicators (chlorophyll content, leaf area index, and vegetation indices) to capture broad physiological responses. A bidirectional fixed-effects panel model was employed to control for spatiotemporal confounders, revealing a significant inhibitory effect of O 3 on photosynthesis (β = -1.334 × 10 -5 , p 3 concentrations would increase regional SIF by 36.36%, while a commensurate 10% reduction in annual exposure could elevate rice yields by approximately 8.4%. This spaceborne remote sensing approach provides a robust and transferable methodology for the precise regional monitoring of ozone stress and for informing targeted mitigation strategies to safeguard crop productivity.
Why it matches plant phenotyping methods衛星リモートセンシングによるSIF等の植物生理指標を用いてイネのオゾンストレスを地域スケールで推定する評価フレームワーク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。
abstractThis study developed a high-resolution assessment framework integrating multi-source satellite remote sensing with econometric methods to quantify the impacts of O 3 on rice production
Accurate, field-deployable diagnostic tools are needed to close the diagnostic gap that limits fungicide targeting among smallholder tomato farmers in Northern Nigeria. This study developed and validated a lightweight convolutional neural network (CNN) for automated diagnosis of five major tomato fungal diseases plus three additional common conditions, trained on field-collected leaf images from Kano and Kaduna States. A MobileNetV2 architecture pre-trained on ImageNet was fine-tuned via transfer learning on more than 10,000 images across ten disease and health classes, using farm-level dataset splitting to prevent data leakage and five-fold cross-validation for model selection.
Why it matches plant phenotyping methodsトマト葉画像から病害・健全状態を直接推定するCNNを開発し、データ分割と交差検証で技術検証しており、植物状態の取得・推定手法が中心である。
abstractThis study developed and validated a lightweight convolutional neural network (CNN) for automated diagnosis of five major tomato fungal diseases plus three additional common conditions
Purpose Conventional plant disease detection is time-consuming and prone to human error. The purpose of this study is to propose an edge artificial intelligence (AI)-based deep learning framework for plant disease detection under real-field conditions. The model integrates convolutional neural networks (CNNs) with a Sliding Window Mean Absolute Deviation (SWMAD) preprocessing technique to address illumination variability and complex background conditions. Design/methodology/approach A dual-layer CNN model is developed for plant disease classification using HSV segmentation, flood-fill segmentation and SWMAD preprocessing to handle real-field variations. The model is trained on PlantVillage and real farm images and deployed via TensorFlow Lite for real-time offline detection. TensorFlow Lite is used to enable efficient on-device inference for deployment in resource-constrained environments. Findings Benchmark experiments conducted on the PlantVillage dataset achieved a classification accuracy of 99.91% under controlled conditions. On the hybrid dataset comprising PlantVillage and real-field images, the optimized CNN framework achieved a validation accuracy of 95.01% following extensive evaluation of optimizers, layer architectures and worker configurations. The integration of the proposed SWMAD preprocessing technique into the finalized architecture further improved the validation accuracy to 97.38%, demonstrating enhanced robustness and classification performance under practical agricultural conditions in the final deployed model. Originality/value The originality of this study lies in several novel contributions. First, we introduce an SWMAD-based preprocessing technique, which enhances local statistical variations in leaf images by capturing pixel-level deviations from neighborhood intensity means. Unlike, conventional preprocessing methods, SWMAD is specifically designed to handle real-field challenges such as illumination variation, noise and complex backgrounds. The improvement in validation accuracy demonstrates the effectiveness of the proposed approach in capturing more discriminative features compared to existing techniques, thereby improving overall model robustness and reliability in practical agricultural environments.
Why it matches plant phenotyping methods植物病害という植物状態を画像から推定する深層学習・前処理・エッジ展開手法が研究の中心であり、実環境での検証も行っているため。
abstractThe purpose of this study is to propose an edge artificial intelligence (AI)-based deep learning framework for plant disease detection under real-field conditions.
This paper explores how deep learning methods can be used to monitor the health of crops and identify diseases, particularly for the apple crop. As the need for food security and sustainable farming methods increases, there is a strong demand for early detection of crop diseases. We have used a Convolutional Neural Network (CNN), based on the model of VGG16 architecture, since the model is known to be effective in image classification. The dataset contained 7771 training images for to enhance machines deep learning regarding plant diseases. Following that, validation image collection of 1747 images divided into four health conditions of the apple crops. In addition, the model was evaluated using 196 new images as a final test. To enhance the model capacity for recognizing diseases of real leaves rather than just memorize exact training pictures, data augmentation was used with ImageDataGenerator of TensorFlow. This means the training images were zoomed, rotated, and shifted to enable the machine detects more variations. Ten epochs of training were performed to measure the model accuracy. The results indicated that the model obtained significant improvement in training and validation accuracy from 56.43% to 78.12% and 92.94 to 96.93%, respectively. Most impressively, the final test dataset, which contained completely new images, scored an accuracy rate of 98%. The results indicate that in the architecture field the application of deep learning methodologies is effective, suggesting that automated detection of diseases by using sophisticated image analysis manages crop diseases identification efficiently. Combination of these methods successfully creates avenues for novel research to built real-time systems of crop disease monitoring, which help farmers increase their productions and farm their lands sustainably.
Why it matches plant phenotyping methodsリンゴ葉画像から健康状態・病害を推定するCNN画像解析手法が研究の中心であり、学習・検証・新規画像での評価も実施しているため、植物病害表現型の手法研究として含める。
abstractThis paper explores how deep learning methods can be used to monitor the health of crops and identify diseases, particularly for the apple crop.
Crop stress develops through a sequence that begins with molecular and biophysical perturbation, progresses through physiological dysfunction, and only later becomes visually apparent. Precision agriculture therefore requires sensors that can shorten the interval between stress onset and actionable diagnosis while preserving spatial context. This critical narrative review examines the complementary roles of nanosensors, plant-wearable and implantable electronics, proximal sensing, unmanned aerial vehicles, satellite remote sensing, and geographic information systems in early crop-stress detection. Literature published from 2000 to 1 June 2026 was selected through live searches of accessible scholarly indexes, DOI registries, publisher records, institutional repositories, and citation networks, with foundational studies retained where necessary. The evidence shows that nano-enabled interfaces can measure early biochemical, ionic, volatile, electrical, and microclimatic signals at high temporal resolution, whereas geospatial technologies reveal the distribution, persistence, and management relevance of stress across canopies and fields. Optical nanotube sensors, surface-enhanced Raman probes, electrochemical microneedles, ion-selective wearables, and flexible leaf sensors have demonstrated biologically meaningful signals before visible symptoms in controlled or pilot field settings. Yet most remain constrained by sparse sampling, crop-specific calibration, bio-interface effects, power and communication burdens, uncertain durability, and limited agronomic validation. Geospatial methods are operationally more mature, particularly thermal and multispectral imaging for water stress and hyperspectral imaging for disease and nutrient-related changes, but they often infer stress through non-specific proxies that are confounded by canopy structure, atmosphere, soil background, phenology, and co-occurring stresses. The strongest future architecture is therefore not a contest between nanoscale and landscape-scale sensing. It is a multiscale system in which physiologically specific plant sensors anchor and interpret spatial imagery, while remote sensing directs where high-specificity measurements and interventions are most valuable. Progress depends on prospective field trials, reference measurements, uncertainty-aware data fusion, interoperability, lifecycle safety assessment, and decision thresholds linked to economic and agronomic outcomes.
Why it matches plant phenotyping methods植物ストレス状態の検出に用いるナノセンサー、ウェアラブルセンサー、熱・マルチスペクトル・ハイパースペクトル画像などを中心に批判的に統合した方法レビューであり、単なる農業応用紹介ではなく、センサー性能、校正、検証、データ融合を論じている。
abstractThis critical narrative review examines the complementary roles of nanosensors, plant-wearable and implantable electronics, proximal sensing, unmanned aerial vehicles, satellite remote sensing, and geographic information systems in early crop-stress detection.
Smallholder tomato farmers in Northern Nigeria correctly identify major fungal diseases only about 41% of the time using unaided visual inspection, contributing to fungicide misapplication and avoidable yield loss. This study evaluated the field impact of SmartfarmerApp, a smartphone-based diagnostic application built on a validated convolutional neural network, on farmer disease identification accuracy. A pre-test/post-test controlled design allocated 240 tomato farmers across eight Local Government Areas in Kano and Kaduna States to an intervention group (n = 120, received the application) or a control group (n = 120, continued with conventional information sources), using computer-generated random allocation stratified by location and gender.
Why it matches plant phenotyping methodsトマトの病害状態を画像・視覚観察から判定するスマートフォン診断アプリを対象に、現場での識別精度を対照評価しており、植物病害フェノタイピング手法の応用・検証が中心である。
abstractThis study evaluated the field impact of SmartfarmerApp, a smartphone-based diagnostic application built on a validated convolutional neural network, on farmer disease identification accuracy.
Accurate, non-destructive assessment of watermelon ripeness remains a significant challenge in horticultural production, particularly under field conditions where traditional visual and tactile evaluation methods are subjective and often inconsistent. Although mechanical, acoustic, and spectroscopic techniques have demonstrated promising performance, their reliance on controlled laboratory environments limits their practical applicability in real-world agricultural settings. This study presents a field-deployable, AI-assisted computer vision system designed for objective, real-time classification of watermelon ripeness. The proposed prototype combines controlled illumination with RGB imaging and convolutional neural networks trained on thousands of annotated outdoor images collected over multiple growing seasons. A phased development strategy—encompassing proof-of-concept modelling, field integration, and multi-season validation—supports robustness against variable lighting conditions and environmental influences. The anticipated outcome is a reliable, non-destructive decision-support tool for growers, capable of identifying ripe fruit for manual harvesting while providing a technological foundation for future autonomous harvesting and precision agriculture applications.
Why it matches plant phenotyping methodsスイカ果実の成熟度という植物器官の状態を、RGB画像とCNNで非破壊推定する手法を開発し、圃場統合と複数季節の検証まで行うため、フェノタイピング手法が中心です。
abstractThis study presents a field-deployable, AI-assisted computer vision system designed for objective, real-time classification of watermelon ripeness.
Background Accurate and efficient detection of citrus leaf diseases is important for orchard monitoring, early intervention, and intelligent disease management. However, practical application in natural orchard environments remains challenging because of complex backgrounds, large variation in symptom scale, strong interclass similarity, and limited edge computing resources. Methods In this study, a lightweight object detection model, SKM-YOLOv11, was developed based on YOLOv11n for citrus leaf disease recognition in natural scenes. A self-built dataset was constructed from public images and field images, containing 6414 images across six classes. StarNet-S050 was introduced as the backbone, C3k2-Star was designed to enhance feature fusion across scales, and a lightweight shared detection head, MNS-Head, was constructed to reduce prediction redundancy. Results Compared with YOLOv11n, SKM-YOLOv11 increased Precision, Recall, and mAP @0.5 by 2.92, 1.47, and 0.95 percentage points, respectively. Meanwhile, FLOPs, parameter count, and model size were reduced by 31.7%, 32.7%, and 34.55%, respectively. Edge deployment on Jetson Orin NX Super achieved an inference speed of 72.45 frames per second. Conclusion The proposed model has strong potential for real-time citrus disease screening on resource-constrained devices and provides a feasible solution for edge-based intelligent disease management in natural orchards.
Why it matches plant phenotyping methods柑橘葉の病害状態を画像から認識する軽量物体検出モデルを開発し、データセット、精度比較、エッジ実装性能まで評価しており、植物表現型（病害状態）の取得・推定手法が中心である。
abstracta lightweight object detection model, SKM-YOLOv11, was developed based on YOLOv11n for citrus leaf disease recognition in natural scenes.
Plant phenotyping relevance match · UnverifiedOpenAlex · Crossref · Europe PMC · checked 5 Sept 2026
Accurate identification and effective prediction of the maize tasseling stage are of great significance for guiding precision field management and ensuring stable crop yields. Conventional manual observation methods suffer from high labor intensity, poor timeliness, and strong subjectivity. In this study, based on an unmanned aerial vehicle (UAV) remote sensing platform, LiDAR point cloud data and RGB imagery were simultaneously acquired to construct digital surface models (DSMs) and digital terrain models (DTMs). Multi-dimensional statistical features were extracted to establish a high-precision plant height estimation method applicable to the entire growth cycle of maize. On this basis, the Logistic growth curve function was introduced to fit the dynamic changes in plant height, enabling the identification and early prediction of the maize tasseling stage based on the plant height growth curve. The research results indicate the following: (1) For maize plant height estimation, the LiDAR sensor outperforms RGB. The optimal accuracy is achieved by combining the 99th percentile of DSM with the minimum DTM, yielding a root mean square error (RMSE) of 0.17 m. (2) Based on the high-accuracy plant height time series, the point of inflection (POI) achieves the highest accuracy in tasseling stage identification, with an RMSE of 2.586 d under the reconstructed time series. (3) Prediction accuracy of the tasseling stage improves with increasing plant height threshold, and optimal performance is observed when the threshold is ≥1.6 m with a growth rate between 0.11 and 0.13. This study establishes a technical framework of "time-series perception-dynamic simulation-feature identification-early prediction", providing a scientific basis for automated monitoring and precision management of the maize tasseling stage. It holds significant theoretical and practical value for the advancement of smart agriculture and crop phenotyping research.
Why it matches plant phenotyping methodsUAV LiDAR/RGBによる草丈推定と時系列成長曲線から、トウモロコシの抽だい期を識別・予測する技術フレームワークが研究の中心であり、植物形質取得と検証を伴うため採用。
abstractMulti-dimensional statistical features were extracted to establish a high-precision plant height estimation method applicable to the entire growth cycle of maize.
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:201-219Plant phenotyping relevance match · UnverifiedOpenAlex · checked 15 Sept 2026
To improve the instance segmentation accuracy of mango fruits and peduncles in complex mountainous orchard scenes and provide visual decision support for robotic harvesting, this study proposes a model-driven perception and picking-point localization method. Specifically, an RGB-D mango dataset was constructed under natural orchard conditions, covering strong illumination, shadows, backlighting, fruit overlap, branch and leaf occlusion, and peduncle crossing. An improved lightweight instance segmentation model named SHS-YOLOv8n-seg was then developed based on YOLOv8n-seg. StarNet_s1 was introduced as the backbone to enhance feature extraction under complex backgrounds. Furthermore, a high-frequency and spatial perception feature pyramid network was adopted to strengthen multi-scale feature fusion and improve the representation of slender peduncles. The SPPF module was used to expand the receptive field, and the parameter-free SimAM attention mechanism was introduced to enhance target responses while suppressing background interference. In the single-run comparison, the proposed model achieved Precision, Recall, mAP@50, and mAP@50:95 values of 89.62%, 88.17%, 90.19%, and 67.94%, respectively. Compared with the baseline YOLOv8n-seg model, these values increased by 2.42, 2.90, 2.75, and 2.57 percentage points, respectively. Moreover, fruit–peduncle matching, geometric constraints, RGB-D depth information, and PCA-based local direction estimation were combined to infer the picking point and recover its 3D coordinates from the segmentation masks. In the evaluation of 57 RGB-D images, the picking point position accuracy reached 98.2%, while the local peduncle direction accuracy reached 91.2%. Overall, the proposed method can accurately segment mango fruits and peduncles in complex natural environments and convert the segmentation results into picking point positions, 3D coordinates, and local direction information, thereby providing theoretical and technical support for intelligent mango harvesting robots.
Why it matches plant phenotyping methodsマンゴー果実・果梗の画像セグメンテーションと3D形状情報の抽出手法を開発・評価しており、単なる収穫対象の位置検出を超えて、再利用可能な植物器官の形態情報を取得する方法が中心である。
abstractfruit–peduncle matching, geometric constraints, RGB-D depth information, and PCA-based local direction estimation were combined to infer the picking point and recover its 3D coordinates from the segmentation masks
Plant height is a key 3D phenotypic trait for assessing crop growth, biomass accumulation, and lodging resistance. To overcome the practical limitations of conventional plant height measurement methods, this study proposes a novel vision foundation model-based framework named Depth for Plant Height (Depth4PH) for plant height estimation in agricultural scenes using low-cost monocular RGB imaging. As part of our contributions, a synthetic–real coupled multimodal dataset was constructed by integrating Blender virtual agricultural scenes (Blender VAS) with real field images. Building upon the existing Depth Anything V2 foundation model, we developed a novel module called Transfer-based Agricultural Metric Depth Anything V2 (TAM-Depth V2) for absolute metric depth estimation through parameter-efficient fine-tuning, depth decoder reconstruction, and joint loss optimization. Furthermore, we designed a novel multi-source prompt-based segmentation framework, MSP-SAM2, to generate positive and negative prompts for zero-shot crop instance segmentation. Finally, a new inverse physical plant height estimation algorithm, RANSAC-Per, was introduced to estimate plant height by combining truncated percentile statistics with local RANSAC micro-plane fitting, thereby reducing the effects of depth noise and field microtopographic variation. The result showed that TAM-Depth V2 achieved stable absolute depth estimation, with an RMSE of 0.1162 m and an AbsRel of 4.25%. Compared to the original box-prompted SAM 2, MSP-SAM2 achieved a 4.4% improvement in mIoU, reaching 91.6% and a recall of 93.2%. On a 350-plant multi-crop test set, Depth4PH achieved R 2 = 0.948, RMSE = 12.23 cm, and MAE = 8.82 cm, and MAPE =10.15%, with crop-specific RMSEs ranging from 3.99 cm (cucumber) to 20.73 cm (maize), significantly outperforming the traditional Global-MinMax baseline (which had an RMSE of 22.62 cm). These results indicate that Depth4PH provides a promising foundational pathway for high-throughput crop phenotyping. With future optimization for edge deployment, it holds significant potential to support high-throughput monitoring in precision agriculture.
Why it matches plant phenotyping methods植物高の画像取得・深度推定・セグメンテーション・高さ抽出アルゴリズムを一体化した植物表現型計測フレームワークの開発と検証が中心であり、データセット構築と性能評価も含む。
abstractthis study proposes a novel vision foundation model-based framework named Depth for Plant Height (Depth4PH) for plant height estimation in agricultural scenes using low-cost monocular RGB imaging.
Spike count and spatial arrangement are among the strongest determinants of grain yield in wheat, yet reliable spike-level phenotyping under field conditions remains challenging. Field-acquired images are often affected by occlusion, heterogeneous illumination, and dense canopy overlap. In addition to these visual complexities, the effort required to generate large-scale instance-level annotations makes it difficult to build the extensive labeled datasets typically needed for robust segmentation models. This paper addresses both problems. The core methodological contribution is a semi-automated iterative annotation workflow: a YOLOv11x-seg model trained on a small manually annotated set is applied to unlabeled field images, and its predictions, after post-processing to remove duplicated, fragmented, and merged detections, are incorporated back into training. To prevent augmentation from distorting the training distribution, we introduce a distribution-aware augmentation strategy guided by Fréchet Inception Distance (FID), which retains only those augmented samples that remain within an acceptable distance from the original data distribution. Together, these components allowed us to build an effective training set from 3,899 high-resolution RGB images (4000 × 3000 pixels) of durum wheat collected at the CREA Research Centre for Cereal and Industrial Crops, with substantially reduced manual annotation effort. On the independent test set(242 images), the final YOLOv11x-seg model (M5 model) achieved a mask-level precision of 86.73%, recall of 83.02%, F1-score of 84.83%, mAP@50 of 89.42%, and mAP@50:95 of 60.51%. Spike masks were used to derive image-based traits including spike count, spike density, canopy coverage, spike area, spatial distribution, and vegetation indices. Their relationships with measured grain yield were explored through statistical analysis and machine-learning-based yield estimation.Both statistical and machine-learning analyses demonstrated that image-derived spike traits provided meaningful information for grain yield estimation, with canopy coverage showing the strongest positive association with yield. Using repeated nested cross-validation with out-of-fold (OOF) predictions, XGBoost achieved the highest yield estimation performance ( R OOF 2 = 0.312 , RMSE = 106.61 g/plot), supporting the potential of near-image phenotyping for late-stage yield estimation in wheat. These results show that semi-automated iterative annotation can enable practical wheat spike segmentation and image-based phenotyping under realistic open-field conditions. While grain yield estimation should be interpreted within the context of the experimental setting, the proposed framework highlights the value of image-derived spike traits for late-stage phenotyping and yield assessment in breeding experiments rather than for early-season yield forecasting.
Why it matches plant phenotyping methods半自動アノテーション、YOLOv11x-segによる小麦穂の画像セグメンテーション、分布認識型データ拡張、形質抽出と検証が中心的な方法論的貢献である。
abstractThe core methodological contribution is a semi-automated iterative annotation workflow
Advancements in stay-green phenotyping are increasingly utilizing hyperspectral sensing technology to assess crop response under extreme environmental conditions. Yet, the effectiveness of different spectral features in explaining stay green remains to be fully elucidated. This includes identifying which bands and spectral indices are more effective in capturing the genotypic differences in stay-green traits. The main objective of this study was to evaluate hyperspectral leaf reflectance as a means to estimate stay-green visual scores (SGVS) as an indicator of drought tolerance and to further understand whether chlorophyll absorption-band spectral indices can differentiate SGVS classifications during post-flowering stages of maize. The experiment was conducted over two growing seasons in Germany, comprising 18 maize genotypes under two contrasting water availability conditions. We measured leaf hyperspectral reflectance using a spectroradiometer in the second, fourth, and sixth week after flowering, along with stay-green traits measurements. We employed raw spectral reflectance, hyperspectral vegetation indices (VIs) in combination with random forest (RF) and ANN models to predict SGVS. Results showed that drought stress significantly affected stay-green-related traits and led to a 43.5% decrease in grain yield in the inbred lines. The grain dry yield (GDY) was positively correlated with stay-green visual scores (SGVS), with higher SGVS associated with higher GDY. Stay-green traits were correlated with various VIs, with the best correlation observed for the Chl_NDI (r = 0.91). Stay-green groups were successfully classified using the selected VIs, with the water-absorption band VIs performing better than the chlorophyll-absorption band VIs and other VIs. Similarly, for predicting the SGVS, the water absorption band indices (R² = 0.79 ± 0.04 and RMSE = 0.12 ± 0.01) outperformed the chlorophyll absorption band indices when using RF. Leave-one-out-location/year cross-validation revealed pronounced variation in model transferability driven by environmental and temporal domain shifts. RF consistently outperformed ANN, showing greater robustness to inter-site heterogeneity and interannual variability, whereas performance degraded most in spectrally distinct environments or atypical seasons. Interestingly, RDIS_3b (1280, 1250, 1180 nm), NDIS_2b (2190, 1510 nm), and NDWI2 (860, 1241 nm) were identified as the most critical predictors in the RF models, across merged and separated datasets. These findings demonstrate the potential of spectral signatures, particularly water-absorption band spectral indices, for quantitative phenotyping of stay-green as a proxy for drought tolerance in maize breeding programs; however, multisite, multiyear calibration is needed to enhance generalizability.
Why it matches plant phenotyping methodsトウモロコシのstay-green形質を対象に、葉のハイパースペクトル反射を用いた形質推定・分類モデルを評価し、交差検証で転移性と頑健性も検証しているため、センサー型表現型計測手法が中心である。
abstractThe main objective of this study was to evaluate hyperspectral leaf reflectance as a means to estimate stay-green visual scores (SGVS)
Accurate and efficient acquisition of seedling density and growth information is of great significance for guiding modern agricultural field management. Although drone imagery has been widely used in seedling monitoring, the inherent trade-off between operational efficiency and image resolution limits the effectiveness of remote sensing-based seedling detection. To address this challenge, this study proposes an integrated analytical method combining super-resolution reconstruction and object detection. The approach first employs the Real-ESRGAN model to enhance low-resolution image quality, then utilizes the YOLOv12 model to accurately localize cotton seedlings, and finally generates visualizations of seedling density and growth uniformity. Experimental results demonstrate that super-resolution reconstruction enhances the detection algorithm's capability for small targets, increasing the object detection precision by 3.3%. With the incorporation of super-resolution reconstruction, the seedling counting accuracy reaches 92.08%, representing a 46.15% improvement over the method without super-resolution, thereby effectively enhancing the algorithm's counting capability. Furthermore, this method achieves image detail equivalent to that obtained at 7.5 meters flight altitude while operating at 30 meters, reducing data acquisition time to 1/16 of the original requirement. In practical applications, the visualized results of seedling density and growth uniformity provide precise decision-making support for thinning, replanting, and differentiated field management. The proposed method is not only applicable to cotton but can also be extended to staple crops such as corn, wheat, and rice, with additional potential applications in forestry and ecological monitoring.
Why it matches plant phenotyping methodsUAV画像の超解像化と物体検出により、ワタ苗の密度・生育均一性を定量化する手法が研究の中心であり、性能評価も行っているため。
abstractThe approach first employs the Real-ESRGAN model to enhance low-resolution image quality, then utilizes the YOLOv12 model to accurately localize cotton seedlings, and finally generates visualizations of seedling density and growth uniformity.
To address the challenges of insufficient sensor stability and poor consistency among multi-source data during crop phenotyping in unstructured field environments, this study develops a hardware-software co-optimization framework for wheat canopy sensing based on a four-wheel-drive, high-clearance phenotyping platform. A multi-sensor stabilization device integrated with an ESO-LQR control strategy suppresses pitch disturbances during motion. A ROS-based hierarchical framework coordinates LiDAR, cameras, and inertial sensors, while spatial calibration and timestamp-based software synchronization ensure spatiotemporal consistency. A tightly coupled LiDAR-IMU SLAM algorithm enables centimeter-level 3D reconstruction of farmland. To mitigate terrain effects, a two-stage ground point extraction method integrating verticality and spatial distribution features improves canopy height estimation. Field experiments demonstrate stable platform operation at 1.5 m s⁻¹ while maintain high efficiency and data quality, with a coverage efficiency of 95.2%, retained-point ratio of 85.3%, and an MTF of 0.35 for image clarity. Phenotypic evaluation shows strong agreement between predicted wheat plant height and manual measurements, with R² values of 0.898 and 0.729 and RMSE values of 1.30 cm and 1.64 cm at the jointing and grain-filling stages, respectively. Moreover, at the jointing stage, both the 2D green area index (GAI) and the 3D point-cloud-based canopy coverage exhibit strong consistency with ImageJ-derived results (R² = 0.873 and 0.910). These findings demonstrate that the proposed approach enables stable and efficient acquisition of crop phenotypic information in complex field environments, providing a solid technical foundation for digital field monitoring, data-driven crop management, and intelligent agricultural systems.
Why it matches plant phenotyping methods小麦キャノピーの表現型取得を目的としたマルチセンサープラットフォーム、データ同期・3D再構成・キャノピー高さ推定を開発し、手動測定やImageJとの一致性を検証しているため、方法が研究の中心である。
abstractthis study develops a hardware-software co-optimization framework for wheat canopy sensing based on a four-wheel-drive, high-clearance phenotyping platform.
• Development of yellow color index (YCI) for yield estimation at flowering stage • Development of web-based interface (YCPM-UAV) for canola yield prediction using UAVs • Global application capability for UAVs datasets to predict canola yield using YCPM-UAV • Multi-sensor and multi-spectrum data fusion to find most suited indices for canola • Multiple and stepwise regression analysis for selection of most influencing VIs Canola ( Brassica napus L.) is a globally significant oilseed crop, yet accurate yield estimation remains challenging due to the complex and unique nature of the crop, especially at the flowering stage. Traditional field-based yield estimation methods are labor-intensive, time-consuming, and destructive, necessitating innovative approaches for early and non-destructive yield prediction. The main objective of the study is to develop a novel web-based platform, YCPM-UAV (Yellow Color Prediction Model using Unmanned Aerial Vehicles), for early and accurate canola yield estimation using high-resolution multi-sensor datasets acquired through low-altitude UAVs (LA-UAVs). To achieve this objective, a comprehensive two-year field study (2022-2024) was conducted across ten farmers’ fields in different geographical locations. Multisensor data (RGB, multispectral, and thermal) were acquired using UAVs at seven growth stages. Several vegetation indices (VIs), yellow color-based indices, and a thermal index were calculated. Linear, multiple, and stepwise regression analyses were performed to evaluate relationships of remote sensing indices with ground-truth yield data collected from 1200 sampling points. Multiple and stepwise regression analyses indicated that the newly developed Yellow Color Index (YCI) exhibited the strongest correlation with actual canola yield at the flowering stage across both years (Year 1: R 2 = 0.84, RMSE = 39.30 g m⁻²; Year 2: R² = 0.88, RMSE = 31.57 g m⁻²). Based on proposed predictive modeling, the YCPM-UAV web interface was developed, featuring automated data processing and spatial analysis with a testing accuracy of 88%. The YCPM-UAV platform provides farmers, researchers, and policymakers with a timely, user-friendly, and actionable decision-support tool for canola yield estimation at the field scale, contributing to improved crop management and food security. Future studies should incorporate additional canola varieties, irrigated and non-irrigated fields, and deep learning algorithms to further improve model robustness.
Why it matches plant phenotyping methodsUAVマルチセンサー画像からカノーラ収量を推定する指標・回帰モデル・Webプラットフォームを開発し、複数年データで検証しており、植物形質取得・推定が中心である。
titleDevelopment of web-based YCPM-UAV interface for early yield prediction of canola crop using UAV multi-sensor data
• First PRISMA-ScR mapping of 79 HSI-ML asymptomatic detection studies (42 species, 74 pathogens) • Controlled-to-field accuracy gap quantified: 91.4% vs. 86.3% (5.1 pp, p = 0.0163 ) • 56.8% of studies omit temporal sampling documentation (CV = 139%) • SWIR underutilization (11.8%) reflects economic, not scientific, barriers • DBVS proposed as standardized temporal metric for cross-study comparability Plant disease management requires non-invasive detection methods capable of identifying infections before visible symptom manifestation, thereby enabling timely intervention. Hyperspectral imaging combined with machine learning and deep learning (HSI-ML) achieves 90.2% classification accuracy in controlled environments for asymptomatic plant detection; however, systematic characterization of methodological practices across this rapidly expanding field remains absent. This PRISMA-ScR compliant scoping review mapped 79 peer-reviewed studies (2010–2025) encompassing 42 plant species and 74 pathogenic agents using a Population-Concept-Context framework. Visible-near-infrared (VNIR) systems dominated deployment (61.8%, n = 49 ), while short-wave infrared (SWIR) systems remained substantially underutilized (11.8%, n = 9 ) due primarily to economic rather than scientific constraints. Among 67 unique algorithms identified, machine learning methods accounted for 30.7% (SVM, random forests, and PLS-DA predominant), whereas deep learning represented 28.4% (2D-CNN, 3D-CNN, and hybrid architectures). Critical methodological gaps emerged: 56.8% of studies omitted temporal sampling documentation (detection latency range: 1–56 days post-inoculation; coefficient of variation = 139%). Platform-stratified analysis revealed controlled environments achieved 91.4% ± 6.6% classification accuracy ( n = 48 ) versus 86.3% ± 9.1% for field/UAV deployments ( n = 26 ), representing a significant 5.1 percentage-point performance decrease ( p = 0.0163 ). Detection accuracy exhibited a weak negative correlation with detection timing ( ρ = − 0.33 , p = 0.067 ), though this association did not reach conventional statistical significance. Methodological heterogeneity—rather than algorithmic limitations—constitutes the primary barrier to field operationalization. Adoption of Days Before Visible Symptoms (DBVS) as a standardized temporal metric could resolve an estimated 40–50% of cross-study variance currently attributed to inconsistent asymptomatic-phase definitions.
Why it matches plant phenotyping methods植物病害の無症状感染をHSIと機械学習で検出する手法群を対象に、79研究の方法、精度、時間指標、標準化課題を体系的に評価したレビューであり、フェノタイピング手法が中心です。
titleEarly detection of plant pathogens in the asymptomatic phase: A scoping review of hyperspectral imaging combined with machine learning
Accurate plant population estimation is critical for crop monitoring, yield prediction, and field management in precision agriculture. However, challenges such as complex backgrounds, overlapping plants, and the need for large-scale coverage make seedling counting from UAV imagery difficult. In this study, we propose a novel automated pipeline for maize seedling counting based on high-resolution UAV orthomosaic images. The pipeline begins with an automatic field-based plot extraction method that isolates individual planting regions without the need for manual intervention. A lightweight object detection model, YOLOv8n-CA, is then employed, incorporating Coordinate Attention to enhance feature localization while maintaining fast inference. To further accelerate the process, we introduce the ‘In-Range Sliding’ strategy, which limits inference to only planting regions, reducing computational overhead. Extensive experiments demonstrate the effectiveness of our approach, achieving a mean absolute error (MAE) of 0.587 and a coefficient of determination ( R 2 ) of 94.19 % at the plot level. Additionally, our system enables spatial feature extraction such as seedling spacing, supporting more refined agronomic analysis. This work provides an efficient and scalable solution for plant counting, offering valuable insights for large-scale, rapid post-processing agricultural monitoring.
Why it matches plant phenotyping methodsUAV画像と深層学習によるトウモロコシ幼苗の計数・圃場区画抽出パイプラインを開発し、計数精度を検証しているため、植物表現型取得法が中心である。
abstractwe propose a novel automated pipeline for maize seedling counting based on high-resolution UAV orthomosaic images.
Rice panicle number per unit area is a key determinant of yield, but manual counting remains time-consuming and labor-intensive. This study proposes CEG-YOLO, a lightweight deep learning model for in-field rice panicle detection and counting using consumer-grade RGB imaging devices. The model introduces three improvements to YOLOv11s to address specific challenges in field scenarios: C2f-Fast replaces standard convolutions with depthwise convolutions to reduce computational cost for edge deployment; SPPF-ECA integrates an attention mechanism to suppress complex background interference; and GhostConv reduces feature redundancy to improve detection of dense panicles. A dataset of 5,175 images was collected from four rice cultivars planted at three densities using an iPhone 12. The proposed model achieved 93.9% average precision (AP) on the test set, outperforming YOLOv11s which achieved 89.1%, while reducing parameters to 7.8 million and floating-point operations (FLOPs) to 16.5 billion. Robustness evaluation yielded coefficients of determination (R²) values of 0.91 to 0.94 for lighting, 0.89 to 0.94 for planting density, and 0.90 to 0.94 for cultivar. A cross-year field test using an NVIDIA Jetson Orin NX edge device on 120 quadrats in 2025 achieved R² of 0.91, root mean square error (RMSE) of 4.0, and mean absolute error (MAE) of 3.3 at 20 frames per second, confirming practical deployability. This study demonstrates that smartphone-based proximal phenotyping with an optimized deep learning model can provide accurate, low-cost rice panicle counting for breeding and production applications.
Why it matches plant phenotyping methodsイネ穂数という植物形質をRGB画像から推定する深層学習モデルを開発し、精度・頑健性・実地展開性能を検証しており、フェノタイピング手法が研究の中心である。
abstractThis study proposes CEG-YOLO, a lightweight deep learning model for in-field rice panicle detection and counting using consumer-grade RGB imaging devices.
Plant height (PH) and aboveground biomass (AGB) are critical agronomic traits that determine the yield potential of maize ( Zea mays L . ). However, the application of genomic selection (GS) and genome-wide association studies (GWAS) in maize breeding is often hindered by the limitations of phenotypic data collection, which is typically characterized by low throughput and inadequate accuracy. To address this challenge, we employed an unmanned aerial vehicle (UAV) equipped with LiDAR and RGB cameras for high-throughput assessment of pH and AGB in a panel of 817 maize hybrids derived from 364 inbred lines over two growing seasons. Our results demonstrated that the integration of UAV-derived LiDAR point clouds with crop surface models (CSMs) enabled robust estimation of pH across multiple years ( R 2 > 0.90). Furthermore, a three-dimensional AGB estimation model was developed using UAV-derived PH and canopy coverage (CC), achieving high estimation accuracy ( R 2 > 0.83). Subsequently, the UAV-derived PH and AGB were utilized for GS and GWAS analyses. Replicated 10-fold cross-validation showed that the mean predictability was 0.504 for PH and 0.402 for AGB across eight commonly used GS models. Moreover, of the 66,066 potential crosses derived from the 364 inbred lines, the top 200 crosses selected for AGB showed up to twice the AGB of the bottom 200 crosses. Field validation demonstrated that the mean ear weight (EW) in the AGB top group was 39.0% higher than that in the bottom group. A total of 16 and 11 significant SNPs were identified by at least two GWAS methods for PH and AGB, respectively. Based on these SNPs, 81 candidate genes were functionally annotated, six of which were simultaneously associated with both traits. The candidate gene association analysis suggested that variations in the promoter region of ZmFLA9 may affect both traits. Overall, our study highlights the potential of UAV-based high-throughput phenotyping to accelerate maize genomic breeding by enabling rapid, precise, and large-scale trait assessment.
Why it matches plant phenotyping methodsUAVのLiDAR・RGBデータから草丈と地上部バイオマスを推定する高スループット表現型測定モデルを開発・検証しており、フェノタイピング手法が研究の中心です。
abstractwe employed an unmanned aerial vehicle (UAV) equipped with LiDAR and RGB cameras for high-throughput assessment of pH and AGB
Accurate and non-destructive counting of rice seedlings is crucial for yield estimation and precision agriculture, yet remains challenging in UAV videos due to dense distribution and strong temporal appearance similarity. This study proposes an efficient tracking-based rice seedling counting framework that integrates an improved Yolov11n detector with a robust multi-object tracking strategy to achieve reliable video level counting. The proposed detector, termed DMNP-YOLO, enhances feature representation, localization robustness, and computational efficiency through Dynamic Snake Convolution, a multi-scale feature attention module, Shape-IoU combined with Normalized Wasserstein Distance, and BatchNorm scaling factor based structured channel pruning, resulting in reductions of 40.5% in Params and 15.2% in GFLOPs while achieving a precision of 0.901 and an mAP@0.5 of 0.921. Building upon accurate frame-level detections, a trajectory based counting mechanism is realized by embedding an Anchor–Angle–Distance association strategy into ByteTrack, which explicitly enforces geometric and temporal consistency across frames, significantly improving tracking stability in dense seedling scenes. As a result, Multi-Object Tracking Accuracy is increased by 5.3 percentage points, identity switches are reduced by 33.3%, and counting accuracy is improved by 3.7 percentage points. Extensive experiments demonstrate that the proposed tracking-based counting framework achieves a mean absolute error of 16.47, a mean absolute percentage error of 6.48%, and an R² of 0.95969. Field scale validation further confirms its practical applicability, achieving an overall rice seedling counting accuracy of 93.4% and demonstrating strong robustness in real world agricultural environments.
Why it matches plant phenotyping methodsUAV画像と検出・追跡アルゴリズムにより圃場のイネ幼苗数を推定する手法を開発し、精度検証と実圃場検証を行っており、植物表現型の取得方法が研究の中心である。
titlePrecisely tracking and counting of field rice seedlings based on UAV platform with DMNP-YOLO and Improved-Bytetrack
The extent of canopy coverage (CC) prior to the booting stage is a useful indicator of environmental adaptation and may help anticipate key developmental events such as heading and flowering. We used UAV-based high-throughput phenotyping to monitor CC in a 262-line F 8 recombinant inbred line population grown under four irrigation-year environments across two seasons. To quantify CC dynamics, we fitted regression models using either days after sowing (DAS) or accumulated active temperature (AT). These models showed a high goodness-of-fit (overall coefficient of determination ( R 2 ) > 0.90 across environments; per-timepoint prediction R 2 = 0.60‒0.99 with root mean squared error (RMSE) = 0.00‒0.02) and were used to derive 31 CC-related traits. Principal component analysis (PCA) showed that the first two components explained 80.00% of total variance in CC traits, with PCA1 accounting for 48.88%‒62.51% of the variance for DAS-based traits and 50.26%‒54.93% for AT-based traits. PCA1 reflected early canopy vigor and rapid coverage increase, while PCA2 reflected canopy maintenance after jointing. Genotypes in the top 15% for PCA1 differed significantly in flowering time, heading time, and plant height from those in the bottom 15%. Cross-environment comparisons showed moderate to high consistency of CC traits (average correlation ( r ) = 0.41‒0.65 for DAS-standardized CC of 20‒160 DAS and 0.48‒0.67 for AT-standardized CC of 100‒1000 AT). Using CC features derived from both DAS and AT, we trained a random forest model to predict flowering time, highlighting the contribution of both temporal and thermal information to predictive accuracy. This model achieved an independent test set R 2 of 0.81 with an RMSE of 1.25 days within the current dataset. All 31 CC-derived traits were also used for QTL mapping. Inclusive composite interval mapping identified 156 QTL detection events across 15 chromosomes (0.80%‒27.70% phenotypic variance explained), which were consolidated into 26 QTL regions, including loci such as QCC.caas.7A (671.47‒680.09 Mb on 7A) and QCC.caas.5D2 (426.67‒459.42 Mb on 5D). Several of these regions co-localized with previously reported genes associated with tillering, flowering time, winter hardiness and plant height. These findings indicate that CC, characterized by DAS- and AT-based traits, is genetically tractable and predictive of flowering within the current dataset, supporting its potential as a phenology-related trait for wheat improvement. Further validation across broader environments, years, and genetic backgrounds will be needed before broader application.
Why it matches plant phenotyping methodsUAV高スループット表現型解析を用いて小麦のキャノピー被覆動態を定量化し、31形質を抽出・検証しているため、表現型取得と解析が研究の中心である。
abstractWe used UAV-based high-throughput phenotyping to monitor CC in a 262-line F 8 recombinant inbred line population grown under four irrigation-year environments across two seasons.
Accurate, field-scale mapping of crop growth stages is critical for supply-sensitive vegetable production, where timely harvests require detailed phenological information. Consecutive growth stages often involve rapid and subtle morphological changes and are influenced by challenging open-field conditions, which frequently result in misclassification when stages are treated as independent, discrete categories. To address this issue, CropMap is proposed as a growth-stage mapping framework that integrates Hierarchical Semantic Segmentation Networks (HSSN) with multispectral unmanned aerial vehicles (UAVs) imagery. CropMap incorporates the structured biological progression of crop development into the learning objective through tree-based label constraints, allowing the model to recognize phenological continuity and reduce confusion between adjacent stages. The framework is evaluated on the publicly available National Information Society Agency of Korea (NIA) field crop growth-stage dataset, a large-scale, multi-institutional UAV dataset containing 337,665 multispectral patches across six hierarchically related growth stages of Chinese cabbage and radish, curated by the NIA. CropMap achieves a test-set mean Intersection over Union (mIoU) of 0.5382, representing a 5% relative improvement over the best-performing transformer baseline (SegFormer; mIoU = 0.5124). Performance varies across classes: background separation is strong (IoU = 0.9128) and the rosette stage is well distinguished (IoU = 0.6354), while the leaf expansion stage remains the primary challenge (IoU = 0.3541), reflecting the inherent difficulty of mapping this spectrally and morphologically transitional class. These findings indicate that hierarchy-aware learning reduces inter-stage confusion for most phenological classes, but transitional growth stages remain a significant limitation for field-scale deployment. The framework provides a foundation for stage-resolved crop monitoring to support harvest timing and supply forecasting in high-value vegetable systems.
Why it matches plant phenotyping methods作物の生育段階という植物状態を、マルチスペクトルUAV画像と階層型セマンティックセグメンテーションで推定する手法が研究の中心であり、公開データセット上で性能評価も行っている。
abstractCropMap is proposed as a growth-stage mapping framework that integrates Hierarchical Semantic Segmentation Networks (HSSN) with multispectral unmanned aerial vehicles (UAVs) imagery.
Wild rice (Oryza spp.) harbors abundant genetic variation and represents an important germplasm resource for improving yield-related traits in cultivated rice. Panicle number is a key phenotypic trait for evaluating tillering capacity and yield potential in wild rice. However, existing approaches for acquiring panicle-number phenotypes remain limited by low efficiency, high dependence on manual operation, and cumbersome matching between plant targets and accession identifiers. In this study, we proposed an AI-driven UAV phenotyping framework for high-throughput panicle counting of wild rice accessions for germplasm evaluation. The framework integrates field plant localization, accession identifier binding, flight route planning, plant-by-plant video acquisition, spatiotemporal registration, video slicing, and panicle detection and tracking, enabling structured panicle-number outputs indexed by accession identifier. To address the small scale, loose structure, morphological variation, and wind-induced swaying of wild rice panicles in UAV imagery, a wild rice panicle detection model was constructed, and WRPD-Tracker was developed for cross-frame identity association and non-redundant counting. The wild rice panicle detection model achieved an AP@50 of 91.56%, representing a 6.16-percentage-point improvement over the DEIM baseline, with 3.70 M parameters and 6.55 G FLOPs, while WRPD-Tracker achieved a HOTA of 65.1% and a MOTA of 79.0%, representing a 5.8-percentage-point improvement in HOTA over the baseline tracker. At the final counting level, UAV-based counts were highly consistent with manual ground counts, with an R² of 0.992 and an MAE of 0.37 panicles. This framework enables batch acquisition of panicle-number phenotypes in wild rice and provides quantitative support for germplasm evaluation, panicle-number trait comparison, and subsequent yield-related phenotypic studies.
Why it matches plant phenotyping methodsUAV画像とAIによるイネ穂数の取得・追跡・計数手法を開発し、手動計数と技術検証しており、植物フェノタイピング手法が研究の中心です。
abstractwe proposed an AI-driven UAV phenotyping framework for high-throughput panicle counting of wild rice accessions for germplasm evaluation.
Cover crops offer essential agroecosystem benefits, including reduced soil erosion, weed suppression, and improved soil health. Aboveground biomass (AGB) is a key indicator of these benefits; however, field-based quantification is often limited, which hinders effective cover crop management decisions. This study integrated unmanned aerial vehicle (UAV)-based multispectral imagery with machine learning (ML) models to estimate AGB in cover crops across two water-limited regions of Texas. Ground-truth and imagery data were collected over three years (2023–2025) for winter rye ( Secale cereale L.) in Lamesa and two years (2023–2024) for winter wheat ( Triticum aestivum L.) in Chillicothe under varying irrigation regimes. Five ML algorithms, random forest, support vector regression, extreme gradient boosting, partial least squares regression (PLSR), and artificial neural network (ANN), were evaluated across four individual and eleven feature fusion datasets. The ANN model consistently achieved the highest predictive accuracy, particularly when vegetation indices were combined with structural features (R² = 0.87, RMSE = 9.08 g m - ²), while PLSR showed the weakest performance. Grouped validation (leave-one-year-out, leave-one-species-out, and leave-one-treatment-out) revealed reduced model performance compared to random (70/30) splitting of pooled data, yet the ANN maintained moderate predictive ability, indicating reasonable generalizability across years, species, and management conditions. Shapley additive explanations (SHAP) revealed key predictors in the ANN model, including plant height, chlorophyll vegetation index, chlorophyll sensitive index, blue band reflectance, modified chlorophyll absorption in reflectance index, dissimilarity, correlation, and enhanced green vegetation index. These findings demonstrate the effectiveness of UAV-ML integration for accurate AGB estimation and highlight the potential for scalable, data-driven cover crop monitoring in water-limited environments and beyond.
Why it matches plant phenotyping methodsUAVマルチスペクトル画像と機械学習を統合し、植物の地上部バイオマスを推定する手法を開発・比較検証しており、表現型取得が研究の中心である。
abstractThis study integrated unmanned aerial vehicle (UAV)-based multispectral imagery with machine learning (ML) models to estimate AGB in cover crops across two water-limited regions of Texas.
Low-cost uncooled snapshot hyperspectral sensors mounted on UAV platforms offer new opportunities for field-scale remote sensing high-throughput phenotyping, but their reliability is constrained by sensor-intrinsic artefacts, particularly dark current. In this study, we present the first spatio-spectro-temporal characterisation and correction of dark current in the Senop HSC-2 dual-CMOS Fabry-Perot snapshot hyperspectral camera. Six controlled dark experiments (∼6,100 image cubes) revealed that dark current in the sensor is highly structured and reproducible, exhibiting CMOS-specific baseline offsets, monotonic temporal drift, pixel-wise dark signal non-uniformity (DSNU) with wavelength-dependent structure, and persistent hot pixels, and exposure-dependent baseline shifts that do not scale linearly with integration time. These results confirm that conventional single-frame dark subtraction is insufficient for quantitative analysis in uncooled snapshot hyperspectral sensors. Building on this characterisation, a modular correction framework was developed to stabilise the dark signal across spatial, spectral, and temporal domains. Across laboratory datasets, the framework reduced temporal drift by 70-85%, DSNU variance by approximately 37.5%, and suppressed >99.9% of persistent hot pixels, substantially improving radiometric stability. Corrected data exhibited simultaneous spatial uniformity, temporal stability, and spectral integrity, enabling downstream radiometric processing without introducing spectral distortion. Application of Senop HSC-2 to UAV-acquired wheat canopy imagery demonstrated effective transfer to field conditions, improving spectral continuity and robustness of vegetation indices after dark current correction. These results establish a transferable calibration approach for affordable snapshot hyperspectral sensors and demonstrate that rigorous dark current correction is essential for achieving quantitative radiometric performance in UAV-based phenotyping and precision agriculture applications without active thermal control, extending calibration principles traditionally applied in satellite hyperspectral systems to low-cost UAV snapshot sensors.
Why it matches plant phenotyping methodsUAVハイパースペクトルセンサの暗電流を空間・スペクトル・時間的に補正する手法の開発と検証が中心であり、圃場のコムギ群落画像への適用も行っているため、植物フェノタイピング手法として採用する。
abstractIn this study, we present the first spatio-spectro-temporal characterisation and correction of dark current in the Senop HSC-2 dual-CMOS Fabry-Perot snapshot hyperspectral camera.
Biomass is a key trait in pasture plant breeding and agronomy, but measuring Dry Matter Yield or Fresh Weight across large numbers of samples is labour intensive and costly. Efficient biomass assessment systems must balance accuracy, speed, and cost, while ideally enabling non-destructive measurements. We developed a rapid, real-time, non-destructive, and remotely controlled LiDAR-based platform to estimate biomass in grass monocultures by measuring sward height at high spatial resolution. The system operates under ambient light conditions at a ground speed of 2.7 km per hour. It was evaluated in small-plot perennial ryegrass trials at two field sites in New Zealand, across two seasons at site A and one season at site B. At site A, correlations between LiDAR-derived height and fresh weight ranged from 0.33 to 0.74 across individual measurement cycles, with an overall multilevel R² of 0.72. At site B, the multilevel correlation increased to R² = 0.88. Weekly LiDAR scans at site B were used to estimate plot-level growth rates for 60 plots, demonstrating improved temporal resolution. Statistically significant differences in growth rate within regrowth cycles were detected among plots. The platform reliably differentiates perennial ryegrass plots based on biomass and offers higher temporal resolution than traditional methods.
Why it matches plant phenotyping methodsLiDARプラットフォームを開発し、草高から牧草バイオマスと成長率を非破壊推定・検証しており、植物形質取得手法が研究の中心です。
abstractWe developed a rapid, real-time, non-destructive, and remotely controlled LiDAR-based platform to estimate biomass in grass monocultures by measuring sward height at high spatial resolution.
Multi-temporal data from unoccupied aerial systems (UAS) offer insights into growth parameters for winter wheat breeding decisions. Weekly UAS data were collected during the 2019 and 2020 growing seasons from dryland and irrigated nurseries at Bushland, Texas, within the Texas A&M Uniform Variety Trials. Canopy cover (CC) was extracted from orthomosaic images and modeled using a double-sigmoid function with a second-order derivative that captured genotypic variation in canopy growth and senescence with high coefficients of determination (R² > 0.99) and low root mean square error (RMSE) values ranging from 1.73 to 4.06. Analysis of variance (ANOVA) revealed highly significant genotypic effects (p<0.001) for yield, heading, and Green Leaf Area Duration (LAD) in all environments except 2020 dryland, where no significant differences among genotypes were detected. Extracted parameters showed positive correlations with agronomic traits, particularly under rainfed and stress-prone conditions. The end decrease stage (EDS) was correlated with grain yield (r=0.56 in 2019 dryland, and r=0.53 in 2020 irrigated, p<0.001), and the start decrease stage (SDS) was highly correlated with yield (r=0.53 in 2020 irrigated, p<0.001). The maximum decrease rate date (MDRD) was positively correlated with yield in 2019 dryland (r=0.55, p<0.001), while LAD had a correlation of r=0.56 in 2019 dryland and r=0.58 in 2020 irrigated (p<0.001). These findings demonstrate that double-sigmoid model provides a powerful, non-invasive framework for quantifying canopy development, senescence timing, and stress responses. By distinguishing genetics from environmental influences on canopy dynamics, this approach enhances selection accuracy and accelerates the development of stress-resilient winter wheat cultivars.
Why it matches plant phenotyping methodsUAS画像からキャノピー被覆を抽出し、二重シグモイドモデルで生育・老化動態を定量化する手法が研究の中心であり、精度評価と遺伝型・農業形質との検証も行っている。
titleA double-sigmoid approach for high-throughput phenotyping of winter wheat growth dynamics
Accurate monitoring of cotton plant moisture content (PMC) is crucial for guiding irrigation practices. To address the limited capacity of single-source remote sensing data to characterize the water status of cotton plants, as well as the lack of quantitative reference values for suitable PMC levels at different growth stages, this study constructed a cotton PMC estimation model based on multimodal UAV remote sensing data. Furthermore, the suitable reference levels of PMC at different growth stages were investigated according to the response relationship between PMC and yield at each growth stage. Five soil moisture gradients were established, and at each growth stage, fresh and dry weights of cotton shoots were measured to calculate the PMC. A UAV platform equipped with multiple sensors was used to collect visible-light (RGB), multispectral (MS), and thermal infrared (TIR) images of the cotton canopy. Three feature selection methods were employed to identify moisture-sensitive parameters: Pearson correlation analysis, principal component analysis (PCA) for dimensionality reduction, and recursive feature elimination (RFE). Using the selected parameters, four machine learning algorithms, AdaBoost, random forest (RF), CatBoost, and k-nearest neighbors (KNN), were applied to construct and validate PMC estimation models. The suitable PMC levels at different growth stages were identified based on the response relationship between measured PMC and yield under different water gradients. The results showed that the RFE feature selection method identified eight water-sensitive parameters, and the CatBoost model integrating multimodal data performed best, with R² and RMSE reaching 0.807 and 0.033%, respectively, on the test set, providing a reliable method for high-resolution spatial mapping of field-scale PMC. On this basis, the response of yield to PMC was analyzed, revealing that when PMC was maintained at 83.8%, 85.9%, 79.3%, 78.0%, and 67.7% at the bud, initial flowering, peak flowering, peak boll-setting, and boll opening stages, respectively, the theoretical maximum yield of 6579–6667 kg/hm² could be achieved. This study realized high-precision remote sensing monitoring of PMC and further explored the appropriate moisture content thresholds for different growth stages, providing a quantitative reference for precision water regulation in cotton fields.
Why it matches plant phenotyping methodsUAVのマルチモーダル画像と機械学習により、綿植物の水分含量を推定・検証する手法が研究の中心であり、植物状態の高解像度マッピングにも応用している。
abstractthis study constructed a cotton PMC estimation model based on multimodal UAV remote sensing data
Quantifying the canopy growth dynamics and light interception capacity under different management practices laid the physiological foundation for potato yield formation. However, the traditional manual measurement methods are labour-intensive, time-consuming, and incapable of capturing time-series dynamics. To address this, we proposed a novel high-throughput strategy that integrates UAV-based RGB imaging with a piecewise physiological model. Furthermore, how Nitrogen(N)-Potassium(K) interaction affects the temporal canopy growth dynamics, light interception, and tuber yield was determined. The results indicated that: (1) Among the 11 secondary indices extracted from the canopy growth dynamic curves, the interaction of N and K had the greatest effect on the maximum canopy duration and the total canopy growth curve integral. The direct path coefficients of N and K inputs on these two parameters were 0.847 and 0.805, and 0.234 and 0.148, respectively. (2) There was a strong linear relationship between the integral area under the curve (S∫) and the total plant dry weight, with R² at 0.90 in 2023-2024. A simplified net photosynthetically active radiation utilisation assessment framework that achieved high accuracy with minimal parameter was built. (3) Prolonging the maximum canopy continuous coverage time is the main way to improve potato yield. The overall effect of N input on yield was significantly higher than that of K fertiliser, with a total effect value of 1.428. Optimising the N-K interaction improves nutrient precision and light interception. The integration of UAV remote sensing and the crop physiological-ecological model enables the tracking of potato canopy dynamics, which is helpful for optimising management practices to improve potato yield.
Why it matches plant phenotyping methodsUAV RGB画像と生理モデルを統合した高スループット手法を開発し、ジャガイモのキャノピー成長動態と光 interception を時系列で推定することが中心である。
abstractTo address this, we proposed a novel high-throughput strategy that integrates UAV-based RGB imaging with a piecewise physiological model.
Accurate prediction of foxtail millet yield is essential for effective field management and high-throughput breeding. Despite advances in UAV-based yield prediction for major crops, existing studies predominantly rely on single-temporal features (SFs) extracted at noon, overlooking significant diurnal dynamic signals that characterize crop responses to water stress. To address this research gap, we propose a novel approach utilizing diurnal cross-temporal features (CFs) derived from UAV-based multispectral and thermal imagery to enhance yield prediction accuracy under different irrigation regimes. During the flowering and grain-filling stages, UAV images were acquired across eight time slots (T1–T8) within a single day to capture the complete diurnal trajectory of canopy physiological responses. SFs were extracted at each time slot, and CFs were derived through summation, averaging, and range operations across multiple slots. A systematic four-step workflow was developed to determine the optimal UAV flight frequency and timing by balancing prediction accuracy with operational costs. Three ensemble learning algorithms (Random Forest (RF), Adaptive Boosting (AdaBoost), and Extreme Gradient Boosting (XGBoost)) were evaluated using multiple feature sets incorporating SFs, CFs, and their integration. Results demonstrated that CFs more comprehensively captured dynamic crop responses to water stress than SFs. Canopy features from afternoon combinations generally exhibited stronger yield correlations than morning combinations. The [T5, T8] combination was identified as optimal, providing a practical balance between prediction accuracy and operational cost. Model comparison revealed that RF exhibited greater robustness across different water treatments, whereas AdaBoost achieved higher accuracy on the test set. Feature importance analysis confirmed the dominance of CFs, with ∑VSWI ranking first across both models and growth stages. This study provides a systematic framework for utilizing diurnal dynamic signals in crop yield prediction, offering new methodological insights for precision agriculture and high-throughput phenotyping of foxtail millet and other dryland crops.
Why it matches plant phenotyping methodsUAVマルチスペクトル・熱画像から作物特徴量を抽出し、収量という植物形質を推定する手法と、撮影頻度・時刻を最適化するワークフローが研究の中心であるため。
abstractwe propose a novel approach utilizing diurnal cross-temporal features (CFs) derived from UAV-based multispectral and thermal imagery to enhance yield prediction accuracy
Citrus fruit cracking causes substantial yield and economic losses, yet its relationship with plant water status (PWS) and irrigation management remains insufficiently characterized. Unlike previous UAV-based irrigation studies that focused on water-stress detection or yield estimation, this study introduces a dynamic, physiology-based framework that links temporal PWS trajectories during key phenological stages to fruit-cracking risk at the individual-tree scale. UAV-based multispectral, thermal, and LiDAR data, combined with field physiological measurements and machine-learning models, were evaluated in an irrigation management experiment in an ‘Ori’ mandarin orchard (Israel) across three contrasting growing seasons (2023–2025). Several irrigation treatments with different irrigation timings and water inputs were applied during the growing season to evaluate their effects on temporal PWS dynamics and fruit cracking. Trunk growth (TG), stem water potential (SWP), stomatal conductance (SC), and plant area index (PAI) were measured throughout the two seasons and estimated using Random Forest models (R 2 > 0.783). These indicators were subsequently used to predict yield and fruit cracking with high accuracy (yield: R² = 0.896; cracking: R² = 0.845). Cracking was lowest in 2023 (∼3%), with ∼25% lower irrigation, suggesting reduced irrigation may reduce cracking risk. Higher cracking in 2024 (∼14%, vs ∼8% in 2025) coincided with intense heat events. Mid-season SWP and SC were strongly associated with yield formation and cracking patterns. These findings demonstrate that monitoring temporal PWS dynamics can support precision irrigation management by identifying high-risk zones and enabling irrigation strategies that stabilize PWS, reduce the incidence of cracking, and improve yield under variable climatic conditions.
Why it matches plant phenotyping methodsUAVマルチセンサーと機械学習により、樹体水分状態などの植物形質を推定し、収量・果実裂果を予測する技術的枠組みが研究の中心である。
abstractthis study introduces a dynamic, physiology-based framework that links temporal PWS trajectories during key phenological stages to fruit-cracking risk at the individual-tree scale.
The precise identification of unsound soybean seeds is a critical step in deep soybean processing and seed selection. The accuracy of this identification directly influences the quality of subsequent processed products, as well as the germination rate and yield of soybean crops. This study proposes a nondestructive identification method for unsound soybean seeds based on hyperspectral imaging (HSI), Gramian Angular Field (GAF), and a Dual-Channel Residual-Squeeze-and-Excitation Network with GAF Fusion (DC-RSEN-GF). According to common damage types, soybeans were categorized into six classes: sound seeds, thermal-damaged seeds, insect-damaged seeds, broken seeds, spotted seeds, and moldy seeds. Spectral data from these six soybean categories were acquired using a hyperspectral camera and transformed into two-dimensional GAF images. The DC-RSEN-GF network integrates one-dimensional spectral data with two-dimensional GAF images. After preprocessing with Savitzky-Golay (SG) smoothing, high-precision classification was achieved through residual blocks, an attention mechanism (using SENet), and feature fusion. Compared to five benchmark models-Extremely Randomized Trees (ERT), Linear Discriminant Analysis (LDA), Support Vector Machine (SVM), VGG19, and ResNet18-the DC-RSEN-GF model achieved superior performance, with accuracy, precision, specificity, and F1-scores of 96.36%, 96.43%, 97.92%, and 96.36%, respectively. The accuracy, precision, and F1-scores are all superior to traditional machine learning and existing deep learning models, demonstrating better classification capabilities. In addition, t-distributed Stochastic Neighbor Embedding (t-SNE) was employed for visual analysis of soybean spectra, further validating the reliability of the DC-RSEN-GF model. The proposed detection method, based on HSI and DC-RSEN-GF, enables accurate and nondestructive identification of unsound soybean seeds and holds significant potential for practical application.
Why it matches plant phenotyping methodsハイパースペクトル画像と深層学習を用いて、種子の損傷・病変状態を非破壊的に分類する取得・解析手法が研究の中心であり、植物状態の表現型測定に該当する。
abstractThis study proposes a nondestructive identification method for unsound soybean seeds based on hyperspectral imaging (HSI), Gramian Angular Field (GAF), and a Dual-Channel Residual-Squeeze-and-Excitation Network with GAF Fusion (DC-RSEN-GF).
Field / plotMRI / PETMultispectral / hyperspectralX-ray / CTRoot2D/3D reconstruction
Mycorrhizal fungi form essential symbiotic relationships with plant roots, facilitating nutrient exchange and promoting plant health. Understanding their interactions can benefit from advanced imaging techniques capable of visualizing nutrient exchange and structural colonization at subcellular resolution across large sample sizes. This review explores novel imaging approaches that are revolutionizing our understanding of root-mycorrhizal fungal symbioses. Several techniques can now visualize and characterize mycorrhizal fungi and associated root structures non-destructively and in three dimensions, for example X-ray computed tomography (micro-CT), X-ray fluorescence (XRF), and X-ray absorption near edge structure (XANES) spectroscopy. Metabolic processes and nutrient exchange can be tracked through positron emission tomography (PET), fluorescent nanoparticles (FNPs), and the monitoring of electrical signalling. Artificial intelligence (AI)-powered image processing software is enabling high-throughput analysis of complex images generated from a range of sources. Mycorrhiza systems are also able to be tracked in-field at multiple scales: hyperspectral imaging can detect mycorrhizal associations at the kilometre scale, while portable MRI imagers can detect changes at the tissue scale. These converging technologies enable the direct, continuous measurement of structural and metabolic root-mycorrhizal fungi interactions, paving the way for a mechanistic understanding of these vital symbiotic partnerships and their impact on plant health and ecosystem functioning.
Why it matches plant phenotyping methods植物根と菌根の構造・代謝・栄養交換を画像およびセンサーで直接測定する手法を扱うレビューであり、植物状態の取得技術が中心である。
abstractThis review explores novel imaging approaches that are revolutionizing our understanding of root-mycorrhizal fungal symbioses.
Japanese agriculture faces pressing challenges, including a declining and aging farming population and the need to adapt to climate change. To address these issues, Smart Agriculture is being introduced to improve production efficiency. Among these, unmanned aerial vehicles (UAVs) have gained attention for their ability to rapidly monitor entire fields. We proposed a machine learning-based crop growth diagnosis system that generates spatiotemporal data for multiple vegetation indices (VIs) using the quartile method and diagnoses crop growth based on patterns of change in these values. The experimental site consisted of five paddy fields within an 80 m × 50 m plot in Iwate Prefecture, Japan, equipped with weather and water sensors. Ground-truth data (overall length, culm length, panicle number, and stem number) were collected approximately one week before harvest. UAV monitoring was conducted four times using a multispectral camera, and growth analysis was performed with six VIs. Correlation analysis revealed a positive relationship between crop growth and the daily average water level during the drainage period, and a negative relationship with the daily temperature range in mid-June. A combined cluster-label representation, constructed from clustering results of all VIs for each mesh, enabled integrated analysis and visualization of multi-index patterns. Grid size optimization showed no significant differences in correlation trends between 1 m × 1 m and 5 m × 5 m resolutions. For non-crop area removal, a comparison of three image segmentation methods demonstrated that the Otsu Method achieved the highest performance. Finally, to facilitate practical use in the field, we prototyped a report interface for the diagnosis system. Future work will focus on developing a comprehensive field diagnosis system to clarify field environments, with the aim of addressing fragmentation and enclaves in Japanese farms.
Why it matches plant phenotyping methodsUAVマルチスペクトル画像と植生指数、画像分割、クラスタリングを統合した作物生育診断システムの開発・評価が中心であり、作物形質との相関検証や実用インターフェースも扱っている。
abstractWe proposed a machine learning-based crop growth diagnosis system that generates spatiotemporal data for multiple vegetation indices (VIs) using the quartile method and diagnoses crop growth based on patterns of change in these values.
Accurate and timely crop yield prediction and forecasting are important for improving agricultural productivity and supporting informed management decisions. In this study, we developed and evaluated a framework for estimating in-season potato yield at the field scale using Sentinel-2 satellite time series. A Grouped TreeSHAP Stability Selection (GTSS) was first applied to identify a compact, phenology-aware subset of spectral bands and vegetation indices, thereby reducing redundancy and mitigating overfitting in small-data settings. Two deep learning architectures tailored for limited training data were then introduced: LiteTemporalConv, a lightweight temporal convolutional network, and MS-ConvBiGRU-Attn, a hybrid encoder combining multi-scale convolutions, bidirectional GRUs, and an attention mechanism. Both models were benchmarked against widely used machine learning methods, including Random Forest, Support Vector Machine, Extreme Gradient Boost, Partial Least Squares, as well as standard deep learning baselines (CNN and GRU). Results showed that the proposed models outperformed both machine learning and conventional deep learning baselines, with LiteTemporalConv achieving the highest accuracy under 10-fold cross-validation (R² = 0.84; RMSE = 3.18 t ha⁻¹; rRMSE = 6.36%) and MS-ConvBiGRU-Attn yielding similarly strong performance (R² = 0.82; RMSE = 3.53 t ha⁻¹; rRMSE = 7.03%). By comparison, the best baseline, XGB, achieved an R² of 0.79 with an rRMSE of 9.8%. The two best-performing models were further evaluated on an independent spatial dataset to assess their generalization beyond the training region. In an additional experiment, both deep learning models trained on mid-season observations showed predictive stability for late-season yield estimation. Overall, the results highlight the importance of targeted feature selection and lightweight encoders for yield modeling in data-scarce conditions.
Why it matches plant phenotyping methodsSentinel-2時系列からジャガイモ収量を推定する特徴選択・深層学習手法を開発し、複数モデルとのベンチマークと独立データでの検証を行っており、植物形質取得が中心である。
abstractwe developed and evaluated a framework for estimating in-season potato yield at the field scale using Sentinel-2 satellite time series
In-season fine-scale (i.e., within-field experiment plot scale) crop grain yield (GY) prediction is critical for optimizing inputs, minimizing environmental impacts, and supporting sustainable food production. Traditional approaches, such as field surveys, are often costly and inefficient over large areas. As an alternative, remote sensing combined with crop simulation models (CSMs) has been increasingly applied for in-season GY prediction. This study investigates the potential of integrating Uncrewed Aircraft Systems (UAS)-based remote sensing data, deep learning, and CSMs to predict maize and soybean GY using a data assimilation approach. UAS multispectral imagery was collected, along with field-measured maize above-ground biomass (AGB) and soybean leaf area index (LAI) during the 2022 and 2023 growing seasons at experimental fields in Brookings, South Dakota. Maize AGB was measured at two growth stages, while soybean LAI was collected across four stages. One-dimensional convolutional neural networks (1D-CNNs) were used to estimate maize AGB and soybean LAI from canopy spectral, textural, and structural features derived from UAS imagery. These UAS and deep learning–derived crop traits were assimilated into DSSAT-Maize and DSSAT-Soybean models to optimize parameters, and the optimized models were subsequently used to predict GY. For maize, the DSSAT-Maize model achieved an R² of 0.62, an RMSE of 717.8 kg ha⁻¹, and an rRMSE of 6.7% for GY prediction. For soybean, the DSSAT-Soybean model achieved an R² of 0.81, an RMSE of 207.3 kg ha⁻¹, and an rRMSE of 4.9%. Overall, these results highlight the potential of combining high-resolution UAS data and deep learning–derived crop traits within a CSM framework through data assimilation, enabling fine-scale, in-season yield predictions and supporting precise agricultural management.
Why it matches plant phenotyping methodsUAS画像と深層学習により、作物のAGBおよびLAIという植物形質を推定する取得・解析手法が研究の中心であり、作物モデルへの同化と性能評価も行っている。
abstractOne-dimensional convolutional neural networks (1D-CNNs) were used to estimate maize AGB and soybean LAI from canopy spectral, textural, and structural features derived from UAS imagery.
• DL model trained on MS data achieved the highest accuracy with an R 2 of 75.29% • Linear Regression Coefficient-Based feature selection with SVM and PCA with Linear Regression significantly improved model performance. • NIR and red-edge bands in the MS dataset consistently outperformed the RGB dataset • More represented rice variety (Sona) achieved a strong R 2 of 80.21% on MS data Accurate crop yield prediction is critical for agricultural planning, food security assessment, and farm-level decision-making. In Nepal, however, rice yield estimation is still predominantly based on traditional approaches, where local agricultural extension offices collect field-level observations that are subsequently aggregated at district, provincial, and national scales, often limiting spatial detail and timeliness. This study aims to develop a field-scale rice yield estimation framework by integrating Unmanned Aerial Vehicle (UAV)-derived remote sensing data with machine learning (ML) and deep learning (DL) techniques. High-resolution multispectral (MS) and RGB UAV imagery were used to evaluate the influence of Vegetation Indices (VIs), including HUE and VNDVI from RGB data and RGBVI and Simple Ratio (SR) from MS data, along with plant characteristics and farm management practices (e.g., application of Zyme and Zinc Potash) on rice yield. The predictive performance of Support Vector Machines (SVM), Linear Regression (LR), Decision Trees (DT), Random Forests (RF), and deep neural network models were systematically assessed. Data preprocessing included feature selection based on importance ranking, Yeo–Johnson power transformation, and Principal Component Analysis (PCA) to improve model stability and performance. Among conventional ML models, LR combined with PCA achieved a coefficient of determination (R²) of 69.09% using MS data, while SVM yielded the best performance using RGB data (R² = 68.27%). Overall, deep neural networks outperformed other models, achieving R² values of 75.29% and 64.60% for MS and RGB data, respectively. Model performance varied notably across rice varieties; the Sona variety (n = 127) achieved the highest coefficient of determination (R² = 80.21% for MS and 76.34% for RGB), whereas varieties with fewer samples exhibited lower predictive performance. Results further indicate that ranking features by importance, rather than eliminating them, enhances predictive accuracy, particularly when using LR-derived feature importance, which proved critical for improving the performance of both LR and SVM models.
Why it matches plant phenotyping methodsUAV画像からイネ収量を推定する手法・フレームワークの開発と、複数の機械学習モデルの系統的評価が研究の中心であり、単なる収量のルーチン測定ではない。
abstractThis study aims to develop a field-scale rice yield estimation framework by integrating Unmanned Aerial Vehicle (UAV)-derived remote sensing data with machine learning (ML) and deep learning (DL) techniques.
Abstract has not been obtained from indexed metadata or an accessible article page.
Why it matches plant phenotyping methodsマルチスペクトル・ハイパースペクトル画像を比較し、作物の圃場区画レベル収量を推定する方法論が題名上の中心であるため、植物表現型計測の方法比較・検証として含める。
titleA comprehensive comparison of multispectral and hyperspectral imagery for plot-level crop yield prediction of kidney beans, snap beans, and potatoes
Accurate and timely crop yield estimation is fundamental for global food security, agricultural policy, and farm management. The Copernicus Sentinel-2 constellation has catalyzed a paradigm shift in Earth observation for agriculture, enabling field and sub-field scale monitoring. This review synthesizes recent advances in crop yield estimation that leverage Sentinel-2 data. A dominant theme is the transition from regional-scale to high-resolution field-level assessments, driven by three approaches: (i) empirical models using vegetation indices coupled with machine and deep learning (e.g., Random Forest, Convolutional Neural Networks); (ii) integration of process-based crop growth models (e.g., WOFOST, SAFY) through data assimilation of Sentinel-2 derived biophysical variables such as Leaf Area Index; and (iii) data fusion of Sentinel-2 with Sentinel-1 Synthetic Aperture Radar to overcome cloud cover. The synthesis shows that Sentinel-2-based frameworks can explain a large fraction of within-field yield variability, while performance remains constrained by limited ground-truth data, cloud gaps, and model transferability. Looking ahead, knowledge-guided models, self-supervised foundation-model pre-training, lightweight edge workflows, improved ground observations, and multi-sensor fusion are key pathways toward robust, operational decision-support tools for precision agriculture.
Why it matches plant phenotyping methods圃場・圃場内スケールの作物収量という植物形質を対象に、Sentinel-2等による推定手法、モデル統合、データ融合、性能制約を体系的にレビューしており、方法論が中心である。
abstractThis review synthesizes recent advances in crop yield estimation that leverage Sentinel-2 data.
Crop residues support soil health by reducing erosion, improving water retention, and contributing to carbon sequestration. Accurate estimation of crop residue biomass is essential for understanding residue distribution patterns and improving sustainable land management practices. Remote sensing, especially high-resolution UAV-based imaging, is a powerful tool for monitoring residue over agricultural fields, and many studies use remote sensing datasets for mapping residue cover (a 2D metric). However, few studies have evaluated residue biomass using remote sensing, despite biomass being more ecologically informative. This study uses high-resolution UAV multispectral imagery to predict crop residue biomass using feature selection and machine learning. Candidate predictors included raw bands, spectral indices, texture metrics, and digital-surface-model-derived topographic variables. Three feature selection methods—recursive feature elimination with cross-validation, Pearson correlation screening, and least absolute shrinkage and selection operator regression, were applied on the training set to identify informative predictors. Four machine learning models (Random Forest Regression, Support Vector Regression, CatBoost, and k-Nearest Neighbors [kNN]) were evaluated individually and in combination using simple averaging, weighted averaging, and stacked ensemble strategies. Results show that Pearson-selected features paired with kNN achieved the best performance (R 2 = 0.61, RMSE = 188.71 g m -2 ). Ensemble approaches did not outperform the best individual model, suggesting limited benefit from meta-learning under small-sample conditions. Across selection methods, red- and blue-band-related predictors were consistently retained, while textural and topographic variables were selected more selectively, indicating context-dependent contributions. Overall, simpler models with targeted feature selection can outperform more complex ensembles for UAV-based crop residue biomass estimation.
Why it matches plant phenotyping methodsUAVマルチスペクトル画像から作物残渣バイオマスを推定し、特徴選択法と複数の機械学習モデルを比較・評価することが中心で、植物由来バイオマスという明示的な状態量を技術的に推定している。
abstractThis study uses high-resolution UAV multispectral imagery to predict crop residue biomass using feature selection and machine learning.
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:97-113Plant phenotyping relevance match · UnverifiedCrossref · checked 5 Sept 2026
Field / plotLiDAR / point cloudRGB / grayscaleRootStem / branchWhole plant / canopy / plot / fieldMorphology / geometry measurement2D/3D reconstructionVisualization / data managementArchitecture / morphology / geometry
Diameter at breast height (DBH) is a crucial indicator for obtaining tree phenotypes in orchard management, plantation monitoring, and agroforestry systems. LiDAR technology has high measurement accuracy, but it is costly and difficult to deploy flexibly in outdoor scenarios, while smartphones have emerged as a viable alternative due to their portability and low cost. In this paper, we propose a DBH estimation method based on monocular depth estimation, supported by a mobile application for algorithm deployment and result visualization. To address the limited computing resources on mobile devices, we design HR-DiffusionDepth, a lightweight diffusion-based monocular depth estimation network for smartphones, which generates pixel-wise 3D coordinates from a single image using camera intrinsics, thereby replacing LiDAR for DBH calculation. Experiments on the KITTI and SPREAD datasets show that HR-DiffusionDepth achieves the best depth estimation accuracy among similar lightweight models, reducing Abs Rel by up to 25.3% relative to the state-of-the-art (SoTA) lightweight baseline, with only 6.26 M parameters. The validation results show that the root mean square error (RMSE) of DBH estimation is 3.10 cm and the mean absolute error (MAE) is 2.25 cm, demonstrating the potential of this approach for agricultural scenarios such as orchards and plantations.
Why it matches plant phenotyping methodsスマートフォン画像と軽量深度推定ネットワークにより樹木DBHを推定する手法を開発・検証しており、植物形質取得が研究の中心である。
abstractwe propose a DBH estimation method based on monocular depth estimation, supported by a mobile application for algorithm deployment and result visualization.
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:54-60Plant phenotyping relevance match · UnverifiedCrossref · checked 5 Sept 2026
With the rapid development of artificial intelligence, UAV remote sensing, and agricultural Internet of Things technologies, crop growth monitoring is evolving from manual inspection and single-source analysis toward intelligent decision-making based on multisource perception. However, existing methods still suffer from limited robustness under environmental variations, insufficient integration between UAV imagery and sparse ground sensor observations, and weak capability for transforming predictions into practical agricultural management recommendations. This study proposes a UAV–ground sensor collaborative lightweight framework for crop growth assessment and agricultural decision support. The proposed framework integrates UAV RGB and multispectral imagery with ground sensor observations through a region-level aerial–ground alignment mechanism and a sensor-guided attention fusion module, enabling environmental conditions to enhance visual feature interpretation. Furthermore, a fact-constrained decision module is developed to generate management recommendations based on crop status, environmental risks, and field information. Experimental results demonstrate that the proposed method achieves superior performance in crop growth classification and yield-trend prediction, reaching Accuracy, Precision, Recall, and F1-score values of 92.47%, 91.86%, 91.39%, and 91.62%, respectively, with an RMSE of 0.381 and an R2 of 0.902. The lightweight framework requires only 6.18M parameters and 0.91G FLOPs, achieving 39.56 ms inference latency and 25.28 FPS on edge devices. The proposed framework also improves decision reliability, achieving an expert agreement rate of 89.34% and a risk identification accuracy of 90.18%. Economic analysis indicates that the proposed framework reduces labor cost, water consumption, and fertilizer input by 49.7%, 26.7%, and 23.0%, respectively, while increasing net benefit by 46.1% compared with conventional field management practices. These results demonstrate that the proposed method provides an accurate, interpretable, and deployable AI-driven solution for intelligent crop management in smallholder and medium-sized farming systems.
Why it matches plant phenotyping methodsUAV画像と地上センサーを融合し、作物生育状態を評価する取得・推定フレームワーク自体を開発しており、植物状態の推定方法が中心的です。
abstractThis study proposes a UAV–ground sensor collaborative lightweight framework for crop growth assessment and agricultural decision support.
High-throughput phenotyping requires AI-enabled computer vision models that generalize across genotypes, locations, and growing seasons, yet such models often lose accuracy under new conditions. Annotating real imagery for every genotype-by-environment (G x E) combination a breeding program encounters is prohibitively expensive. We quantify how G x E shifts affect AI-based detection of cowpea flowers and pods across two California locations and two growing seasons. Flower detection mAP@50 fell from 76.3% to as low as 50.6% under unseen shifts, and pod detection was more sensitive. Feature-space and image-quality diagnostics confirmed these losses track measurable distributional shifts. Because closing this gap with real data alone is not practical, we test whether synthetic imagery, rendered from a procedural 3D cowpea model, can substitute for that annotation burden. Synthetic supervision alone improved over pretraining but remained limited by a domain gap driven by camera image formation, not scene content. A domain-gap-aware camera-realism augmentation strategy, optimized against measured real-image statistics via Wasserstein distance, narrowed this gap, and a linear HDR representation converted a smaller measured gap into a larger detection gain than an 8-bit representation. Optimized HDR synthetic data combined with as few as five real images matched or exceeded the real-data baseline for spatial generalization, and pod detection benefited most at the lowest shot counts, with more modest gains under temporal shift. These results show that synthetic data can overcome the generalization limits of AI-based flower and pod detection, but only when the domain gap is measured and optimized rather than assumed away.
Why it matches plant phenotyping methods花・莢という植物器官の画像検出を対象に、異なる遺伝型・環境への一般化、合成画像、カメラリアリズム拡張、HDR表現を技術的に評価しており、植物表現型取得手法が研究の中心である。
abstractHigh-throughput phenotyping requires AI-enabled computer vision models that generalize across genotypes, locations, and growing seasons
Accurate monitoring of agronomic phenology is essential for yield estimation and food security assessment. However, currently available maize phenology datasets usually represent only a limited number of growth stages, restricting their application in process-based crop modeling and stage-specific agricultural management. Here, we present a high-resolution maize phenology dataset for Northeast China spanning 2001-2024 at 500-m spatial resolution and daily temporal resolution. By coupling MODIS spectral information with meteorological drivers in an energy-driven XGBoost framework, we retrieved eight key agronomic stages: Emergence, Three-leaf, Seven-leaf, Jointing, Flowering, Silking, Milking, and Maturity. Validation against observations from 91 agrometeorological stations during 2009-2024 demonstrates robust performance, with an overall RMSE of less than 5 days and R² values greater than 0.63 across all stages. Beyond overall accuracy, the dataset shows strong spatial consistency and temporal stability, preserves coherent regional phenological gradients, and captures interannual variations over the 24-year period. This long-term, multi-stage dataset provides a valuable benchmark for crop model calibration, climate change impact assessment, and the development of adaptive agricultural strategies in one of the world's major maize-producing regions.
Why it matches plant phenotyping methodsMODISスペクトル情報と気象データ、XGBoostを組み合わせてトウモロコシの8つの生育段階を推定し、観測データで検証した高解像度フェノロジーデータセットであり、植物形質の取得・抽出手法とベンチマークが中心です。
abstractHere, we present a high-resolution maize phenology dataset for Northeast China spanning 2001-2024 at 500-m spatial resolution and daily temporal resolution.
Published30 Jul 2026The international archives of the photogrammetry, remote sensing and spatial information sciences/International archives of the photogrammetry, remote sensing and spatial information sciencesCited by 0 · OpenAlex ↗
Abstract. The harvest mouse, Micromys minutus (Pallas, 1771) is the smallest rodent in Japan and now listed in the Red Data Books of Tokyo, 2 prefectural capitals, and 28 prefectures in Japan due to drastic decline of grasslands. For the harvest mouse, the height and density of the tall grass species where nesting occurs are considered particularly important. However, it has been difficult to continuously and extensively acquire information on the three-dimensional structure of herbaceous vegetation. With recent development of UAV technology, UAV data are beginning to be applied to the analysis of herbaceous vegetation. For acquiring three-dimensional information via UAV, methods include using LiDAR sensors or generating 3D point cloud data from aerial photographs using SfM. This study evaluates whether UAV LiDAR or UAV SfM is more suitable for estimating the height of tall grass species such as Japanese silver grass (Miscanthus sinensis), which serve as important nesting sites for the harvest mouse. As a result of analysis, the proposed method was found to be effective to estimate grass height regardless of whether UAV LiDAR or UAV SfM is used. However, when comparing the accuracy of canopy height estimation using UAV LiDAR data alone, UAV SfM data alone, and combined UAV LiDAR and SfM data, combined UAV LiDAR and SfM data found to perform best. Maximum canopy height was found to be best estimated using the combination of median of hand-measured five maximum canopy height values and maximum height calculated using the combined UAV LiDAR and SfM data.
Why it matches plant phenotyping methodsUAV LiDARとSfMを用いて植物群落の草丈・キャノピー高を推定し、センサー間の精度を比較評価することが研究の中心であるため、植物フェノタイピング手法として適格。
abstractThis study evaluates whether UAV LiDAR or UAV SfM is more suitable for estimating the height of tall grass species such as Japanese silver grass (Miscanthus sinensis)
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:895-974Plant phenotyping relevance match · UnverifiedCrossref · OpenAlex · checked 5 Sept 2026
Accurate estimation of crop plant height using unmanned aerial vehicles (UAVs) is essential for field-scale crop monitoring and phenotyping. Most previous studies using UAV-based structure-from-motion (SfM) photogrammetry have relied on raster-based crop surface models (CSMs) and have evaluated their performance using accuracy metrics such as the coefficient of determination ( R 2 ) and root mean square error (RMSE). However, such evaluations provide limited insight into how estimation behavior varies across space and time, particularly during dynamic crop growth stages. To address this gap, this study conducted a time-series comparison of rice plant height estimates derived from UAV-SfM-generated dense point clouds (DPCs) and raster-based CSMs in farmer-managed paddy fields in Cambodia, which are characterized by heterogeneous micro-environmental conditions. Rice plant height was measured throughout the growing season and UAV-derived estimates were evaluated using regression analysis, analysis of covariance, and canopy cover dynamics. In the pooled analysis, both approaches achieved high overall accuracy, with R 2 = 0.92 and RMSE = 7.2 cm for the CSM-based approach and R 2 = 0.90 and RMSE = 8.8 cm for the DPC-based approach. However, time-series analyses revealed that CSM-derived plant height estimates exhibited strong location-dependent variability and sensitivity to early-stage canopy development, whereas DPC-based estimates showed more consistent performance across locations and growth stages. Regression coefficients derived from CSM-based estimates varied significantly among locations, whereas those from DPC-based estimates did not, suggesting that point-based representations may provide more spatially consistent estimation behavior under heterogeneous field conditions. By explicitly considering temporal dynamics, canopy development, and data representation, this study highlights the limitations of current raster-based UAV-SfM workflows for structurally complex crop canopies and suggests that DPC-based approaches may offer a useful complementary representation for crop monitoring and phenotyping, particularly when spatial consistency across heterogeneous field conditions is important.
Why it matches plant phenotyping methodsUAV-SfMによるイネの草丈推定手法を、3D点群と作物表面モデルで時系列比較・検証しており、表現形式と技術性能の評価が研究の中心です。
titleA comparative analysis of 3D point clouds and crop surface models for rice plant height estimation using UAV-SfM
Introduction Wheat leaf biomass is a key indicator of crop growth, nitrogen status, and yield potential, and its accurate estimation is essential for precision agriculture. Unmanned aerial vehicle (UAV) remote sensing provides multi-stage phenological observations for non-destructive biomass monitoring. However, existing approaches often fail to capture the superimposed temporal patterns inherent to crop phenology, including short-term physiological fluctuations driven by management events and long-term seasonal growth trends, as well as the cumulative causal effects of early-stage conditions on final biomass accumulation. Methods This study proposed a dual-branch perception and hybrid attention integrated framework (DBAFN) for temporal estimation of wheat leaf biomass from UAV multi-temporal observations across key growth stages. Results and discussion Experimental results demonstrated that the DBAFN achieved the best performance, with the coefficient of determination (R²) of 0.87, root mean square error (RMSE) of 38.41 g/m², mean absolute error (MAE) of 27.77 g/m², and relative RMSE (RRMSE) of 17.29%. Overall, the proposed framework provided an effective solution for temporal biomass estimation and demonstrated strong generalization capability, as further validated by independent experiments across different ecological regions and wheat genotypes (R² = 0.816-0.820). Compared with conventional machine learning models, the DBAFN showed consistently higher accuracy and lower prediction error. Multi-source feature analysis indicated that the combination of reflectance, vegetation indices, and canopy height provides the most accurate estimation. Ablation experiments further confirmed the effectiveness of each module in improving model performance. The SHapley Additive exPlanations (SHAP) analysis revealed that the canopy height and key spectral features contribute most to biomass prediction, highlighting the importance of integrating structural and physiological information. This study demonstrates that integrating multi-scale temporal dynamics, hybrid attention mechanisms, and transformer-based dependency modeling significantly improves the reliability of UAV-based biomass estimation. It offers a practical, data-driven pathway for intelligent crop monitoring and precision nitrogen management.
Why it matches plant phenotyping methodsUAVマルチ時期リモートセンシングから小麦葉バイオマスという植物形質を推定する手法を提案し、独立地域・遺伝子型で検証しているため、フェノタイピング手法が中心である。
abstractThis study proposed a dual-branch perception and hybrid attention integrated framework (DBAFN) for temporal estimation of wheat leaf biomass from UAV multi-temporal observations across key growth stages.
Abstract Deep learning has achieved remarkable success in rice disease diagnosis; however, existing methods often suffer from limited interpretability and poor robustness against open-world environmental noise. To address these challenges, this study proposes the Knowledge-Guided Multi-Task Rice Network (MTRNet) built upon a ResNet-50 backbone. Unlike conventional "black-box" models, MTRNet employs expert knowledge injection via a phytopathological matrix to explicitly disentangle disease features into Shape, Color, and Location attributes within a multi-head architecture. Furthermore, to mitigate false positives in complex field scenarios, a non-parametric Cascade Inference System (CIS)—comprising a biological grayscale filter and a visual consistency check—is introduced for robust Out-of-Distribution (OOD) detection and anomaly rejection. Experiments on a benchmark dataset of 5,932 field images, which primarily comprises four main rice diseases (Rice Leaf Blast, Brown Spot, Bacterial Leaf Blight, and Tungro), demonstrate that MTRNet achieves a diagnostic accuracy of 99.83%. Crucially, in an open-world robustness evaluation involving 1,000 non-agricultural noise samples, the proposed system achieved an 81.80% OOD rejection rate. By balancing diagnostic accuracy with structural transparency, this framework effectively narrows the gap between laboratory benchmarks and real-world agricultural applications.
Why it matches plant phenotyping methodsイネ病害の画像から病徴を診断する深層学習・OOD検出手法を提案し、実画像データで性能評価しており、植物の病害状態の取得・推定が研究の中心である。
abstractthis study proposes the Knowledge-Guided Multi-Task Rice Network (MTRNet) built upon a ResNet-50 backbone.
Long-duration flood inundation can substantially suppress crop growth and cause yield loss, particularly in semi-arid agricultural regions increasingly affected by extreme rainfall. Timely crop damage assessment is critical for disaster response and insurance-related decision-making, but direct yield-loss observations are often unavailable during or shortly after flooding. This study proposes a phenology-guided regression framework for early crop damage assessment using multi-source SAR–optical observations. The study was conducted on the Tumochuan Plateau, Inner Mongolia, China, where severe rainfall beginning on 23 July 2025 caused widespread cropland inundation. Sentinel-2 EVI time series from 2022 to 2025 were fitted using a Savitzky–Golay (SG) filter, and annual area under the EVI curve (AUC) loss in 2025 relative to the 2022–2024 historical mean was used as a proxy for flood-induced crop damage. Optical features from Landsat-8/9 and Sentinel-2, together with SAR backscatter features from Sentinel-1, Lutan-1, and Gaofen-3, were incorporated into machine learning regression models. SAR features improved pixel-wise prediction, with the Random Forest model achieving the highest R2 of 0.62 using early-period features and 0.77 using later-period features. Village-scale aggregation further improved performance, yielding an early-period R2 of 0.84 across 123 and 0.78 across 122 villages. These results demonstrate the feasibility of SAR–optical and phenology-guided regression for early crop damage assessment under long-duration inundation.
Why it matches plant phenotyping methodsSAR・光学画像とフェノロジー指標を用いて作物被害を推定する回帰手法が研究の中心であり、作物状態（洪水被害）を定量化・検証しているため。
abstractThis study proposes a phenology-guided regression framework for early crop damage assessment using multi-source SAR–optical observations.
Corn stunt is one of the most important diseases affecting maize (Zea mays L.) production in tropical regions of the Americas. The disease is caused by a complex of pathogens transmitted by the corn leafhopper (Dalbulus maidis), and its predominantly quantitative inheritance complicates the identification of tolerant genotypes under field conditions. In this context, we aimed to perform a comprehensive phenotypic stratification of corn stunt tolerance in a tropical public maize diversity panel and to identify contrasting inbred lines for breeding and genetic studies. A total of 360 inbred lines were evaluated under natural infection using three complementary disease-response traits: survivor plant health score (SPHS), proportion of survivor plants (PSP), and whole-plant health score (WPHS). Multi-trait mixed-model analyses revealed significant genotypic variation, moderate to high broad-sense heritability, and significant genotype × environment interactions for all evaluated traits. A multi-trait index (MSI), calculated from standardized best linear unbiased predictions (BLUPs), successfully integrated the three phenotypic components and enabled robust stratification of the diversity panel, identifying 60 highly tolerant and 60 highly susceptible inbred lines. Further, a genomic principal component analysis demonstrated that these phenotypic extremes were distributed across both tropical and subtropical germplasm, indicating that tolerance is not restricted to a single genetic background. The proposed phenotypic framework provides a robust and reproducible strategy for characterizing quantitative disease tolerance, identifying valuable parental germplasm, and establishing well-defined phenotypic extremes for future investigations of the genetic architecture of corn stunt tolerance.
Why it matches plant phenotyping methods複数の植物病害応答形質を統合する統計的フェノタイピング枠組みと指標を中核として、耐性の再現可能な層別化手法を提示しているため。
abstracta comprehensive phenotypic stratification of corn stunt tolerance
Accurate and quick detection of plant leaf diseases is essential for precision agriculture to intervene promptly and boost crop yields. A new deep learning model called ResVNet has been introduced in this study. It combines the powerful local feature detection of ResNet152 with the global attention capabilities of Vision Transformer (ViT) and utilises Low-Rank Adaptation (LoRA) to accelerate fine-tuning. The PlantVillage dataset, which contains both healthy and diseased tomato samples, was used to train and test ResVNet. Experimental evaluation on the PlantVillage tomato dataset using stratified 5-fold cross-validation demonstrates that the proposed ResVNet model achieves a mean classification accuracy of 97.45%, along with superior macro-precision, macro-recall, and macro-F1 scores compared to existing deep learning architectures. The results of the confusion matrix and the ROC analysis validate its discriminatory power. The results highlight the potential of architectures strengthened with transformers in agricultural diagnostics. For real-time disease detection in the field, ResVNet is perfect for edge device deployment on drones and smartphones thanks to its high accuracy and adaptability. The application of Explainable AI (XAI) technologies for interpretability, integration with the Internet of Things (IoT), and multi-crop classification will all be explored in future studies. We will also look into model compression approaches so we can deploy efficiently in low-resource settings without sacrificing performance.
Why it matches plant phenotyping methods植物葉の病害状態を画像から分類する深層学習手法を開発し、PlantVillageで交差検証して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。
abstractA new deep learning model called ResVNet has been introduced in this study.
Abstract Pests and diseases are major constraints to cereal production, reducing crop yield, farm profitability, and food security worldwide. Timely detection of crop health threats and accurate assessment of infection severity are essential for effective crop protection, yet conventional field scouting remains labor-intensive, subjective, and unsuitable for real-time decision-making. Although recent advances in the Internet of Things (IoT) and deep learning have enhanced automated crop monitoring, most existing approaches focus on single-task disease classification and provide limited support for severity-aware management. This study proposes ResMDCL-PDM (Residual Network with Multi-Dimensional Compensation Layer for Pest and Disease Management), an IoT-enabled multi-task deep learning framework for precision pest and disease management in maize and rice production. The framework combines field-based environmental sensing with a modified ResNet-50 architecture enhanced by a Multi-Dimensional Compensation Layer (MDCL) to jointly identify crop species, classify pest and disease categories, and estimate infection severity. Field images collected from maize and rice farms at the Federal University of Agriculture, Abeokuta, Nigeria, were integrated with publicly available benchmark datasets. Following preprocessing and data augmentation, 8,556 annotated images were used for model development and evaluation. The proposed framework achieved an overall classification accuracy of 97.8% , outperforming AlexNet, VGG16, MobileNetV3, DenseNet121, EfficientNet-B0, and the baseline ResNet-50. High precision, recall, and F1-score, together with ablation analysis, confirmed the effectiveness of the proposed MDCL. The results demonstrate that integrating IoT-enabled monitoring with multi-task deep learning provides reliable, severity-aware decision support for targeted crop protection and offers a practical, scalable solution for sustainable precision agriculture.
Why it matches plant phenotyping methods植物画像から病害・害虫カテゴリーと感染重症度を推定するIoT・深層学習フレームワークの開発と評価が中心であり、感染植物の状態を直接測定する方法論的研究である。
abstractThis study proposes ResMDCL-PDM (Residual Network with Multi-Dimensional Compensation Layer for Pest and Disease Management), an IoT-enabled multi-task deep learning framework for precision pest and disease management in maize and rice production.
Plant diseases have long been considered a major threat to global food production systems. Therefore, early diagnosis is vital to mitigate the risk of these diseases. This task can be challenging, as the number of harmful diseases is substantial. One technology that has gained widespread interest is artificial intelligence, specifically deep learning, which is used to identify plant diseases using leaf patterns. This paper presents two deep learning models, a custom CNN model and a transfer learning model based on the DenseNet-121 architecture. Experiments were carried out using the PlantCity dataset, which consists of twelve subsets of diverse crop species representing fruits, vegetables, and grains with variations among the subsets, including the number of classes, the subset sizes, class distribution, and visual complexity of disease symptoms. The two models were evaluated using multiple metrics, including accuracy, loss, precision, recall, and F1-score. Explainable AI using the LIME technique was deployed to better interpret the acquired results. Results showed that the developed transfer learning model based on DenseNet-121 had superior performance over the CNN model, with accuracies ranging from 86% to 99% across eleven experimented crops. In order to perform an independent experimental validation for the developed model, future work will focus on constructing a local crop dataset captured from Iraqi fields to evaluate the developed models based on the local environment.
Why it matches plant phenotyping methods葉画像から植物病害状態を推定する深層学習手法を開発し、複数作物・指標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 paper presents two deep learning models, a custom CNN model and a transfer learning model based on the DenseNet-121 architecture.
Timely forecasting of maize productivity is essential to support precision agriculture and optimize management practices. In this study, we analyzed the potential of integrating ground-based measurements and UAV-derived spectral data for predicting maize grain yield (GY) under different fertilization conditions. Field data were collected at two key phenological stages: early vegetative stage (V7) and pre-harvest (R4). Ground-based measurements included SPAD, above-ground biomass (AGB), and leaf area index (LAI), while multispectral and hyperspectral imagery was acquired by drone. A series of Ordinary Least Squares (OLS) models was developed to evaluate the predictive performance of individual variables and their combinations. Model robustness was assessed using two validation strategies: Leave-One-Treatment-Out (LOTO) to assess model performance across the treatments included in the experimental design and random sampling to assess performance within the dataset. The results showed that yield prediction was less accurate during the early growth stages, where data fusion significantly improved the model’s accuracy (R2 = 0.82; MAE = 6.36 q ha−1; MAPE≈7 %). The predictive performance of VIs alone increased substantially in the pre-harvest stage, with the combination of red-edge indices and LAI proving to be the best model for late yield prediction (R2 = 0.86; MAE = 6.56 q ha−1; MAPE≈7%). Comparison of multispectral and hyperspectral data revealed comparable predictive performance, suggesting that multispectral sensors may already capture the key spectral information needed for yield forecasting. Furthermore, random validation consistently produced more optimistic results than the LOTO method, highlighting the importance of using validation strategies that explicitly account for the experimental design when evaluating model performance across the treatments included in the study. Overall, the present study demonstrates that yield prediction is highly dependent on the phenological stage and validation approach, and that integrating complementary data sources can improve model performance, particularly during the early growth stages. These findings should be interpreted as a proof-of-concept based on a single-site, single-season experiment with a limited sample size (n = 12), and therefore require further validation across multiple environments and growing seasons.
Why it matches plant phenotyping methodsUAVマルチ／ハイパースペクトル画像と地上測定を統合し、トウモロコシ収量を予測する方法を開発・比較・検証しており、植物形質の取得・推定が研究の中心である。
abstractA series of Ordinary Least Squares (OLS) models was developed to evaluate the predictive performance of individual variables and their combinations.
Field / plotLeafWhole plant / canopy / plot / fieldObject detectionPhysiological trait estimationGrowth / time-series analysisLeaf traitsWater status / transpiration
Abstract Understanding the vulnerability of plants to more severe and frequent drought events and developing adaptive management strategies requires robust methods for quantifying long‐term changes in plant water stress (PWS). Most data‐driven explorations of long‐term trends in PWS have focused on alterations in canopy structure (e.g., leaf area index) or canopy structure‐dependent variables (e.g., gross primary productivity and evapotranspiration). This is largely because long‐term trends in canopy structure are relatively easy to detect from satellite observations. However, a focus on structural responses limits our ability to detect physiological stress due to challenges in isolating it from the effects of structural greening. Consequently, this difficulty hampers a comprehensive examination of long‐term PWS in the context of global greening trends. To address this gap, we developed a new process‐based metric for PWS to isolate physiological responses from structural greening, which we then used to detect global PWS trends over the past four decades. Combining site‐level and satellite observations at the half‐degree resolution across the globe, we found that accounting for greening‐related changes substantially alters the sign of long‐term PWS trends inferred from traditional approaches. Specifically, our study reveals a significant increase in PWS that is only detectable when accounting for structural greening trends. When greening trends are not accounted for, global PWS appears to have decreased over time. Overall, our results highlight the need to integrate structural dynamics and greening into PWS detection. Such an integration of observations and land models will improve our understanding of plant‐water‐energy interactions.
Why it matches plant phenotyping methods植物の生理的な水ストレスを定量化する新しいプロセスベース指標を開発し、衛星・地上観測で検証・適用しており、表現型測定法が研究の中心である。
abstractTo address this gap, we developed a new process‐based metric for PWS to isolate physiological responses from structural greening, which we then used to detect global PWS trends over the past four decades.
Abstract Detecting crop diseases early and responding promptly is vital for protecting agricultural productivity. It also helps maintain the quality and quantity of yields and reduces the risk of disease transmission to humans and livestock. Effective disease management is therefore critical to ensuring both global and local food security. However, traditional methods often based on visual inspection and delayed human judgment, are typically insufficient for identifying diseases at an early stage. Recent developments in Artificial Intelligence (AI) and the Internet of Things (IoT) offer new opportunities to address these challenges. By integrating IoT sensor networks with AI techniques such as machine learning and deep learning, it becomes possible to monitor plant health in real time and detect diseases with greater accuracy. This review explores the strengths and limitations of current AI-enabled IoT solutions in agriculture. It highlights how these systems leverage large-scale data and advanced image processing to outperform conventional methods in terms of speed, precision, and efficiency. Such improvements can significantly reduce crop losses and support more sustainable agricultural practices. Finally, the paper reviews key research trends, identifies current challenges, and outlines future directions in the field. It emphasizes the transformative potential of smart agriculture in advancing plant disease management and promoting environmentally responsible food production. This systematic review was conducted in strict accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) 2020 guidelines, synthesizing a final selection of 152 peer-reviewed papers. The overarching aim is to critically evaluate and map literature published between 2015 and 2026 using a systematic approach that addresses the integration of the IoT, AI, Machine Learning (ML), Deep Learning (DL), Convolutional Neural Networks (CNN), sensor technologies, and sustainable agricultural practices in the context of plant disease detection.
Why it matches plant phenotyping methods植物病害の症状・健康状態をAI、画像処理、IoTセンサーで検出する手法を主題とした系統的レビューであり、植物フェノタイピング手法のレビューに該当する。
titleA comprehensive review of artificial intelligence and Internet of Things integration based plant disease detection for sustainable agriculture
Field / plotLeafObject detectionStress / disease detectionDisease symptoms / severity
Plant diseases are generally caused by pest, insects, pathogens and decrease the productivity to large scale if not controlled within time. Agriculturists are facing lose due to various crop diseases. It becomes tedious to the cultivators to monitor the crops regularly when the cultivated area is huge that is in acres. The proposed system provides the solution for regularly monitoring the cultivated area and provides the automated disease detection using remote sensing images. The proposed system intimates the agriculturist about the crop diseases to take further actions. The objective of the proposed system is to early detection of diseases as soon as it starts spreading on the outer layer of the leaves. The proposed system works in two phases: the first phase deals with training data sets. This includes, training both healthy and as well as diseased data sets. The second phase deals with monitoring the crop and identifying the disease using Canny?s edge detection algorithm.
Why it matches plant phenotyping methods植物葉の画像から病害状態を自動検出するコンピュータビジョン手法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。
abstractThe proposed system provides the solution for regularly monitoring the cultivated area and provides the automated disease detection using remote sensing images.
Alternanthera philoxeroides, an invasive alien species, spreads rapidly in river systems via vegetative propagation from stem fragments, requiring river-system-scale monitoring to understand its expansion dynamics and habitat preferences. This study used multi-temporal Sentinel-2 data to analyze spatio-temporal variations in fractional vegetation cover (FVC) within a 3.5 km river reach. FVC estimates derived from vegetation indices were validated against high-resolution aerial images, with an EVI-based model achieving the highest accuracy (RMSE = 9.2%), enabling reliable monitoring even in narrow (~24 m) channels. Time-series analysis from 2019 to 2024 revealed downstream expansion beginning in 2022. Annual maximum FVC (Cmax) was used to assess relationships with removal records and bank structures, showing that removal effects were temporary and more pronounced in the first year, while steel sheet-pile banks limited vegetation growth compared to concrete revetments. These results demonstrate that Sentinel-2 data can provide an effective and accessible tool for evaluating invasive plant dynamics and management effectiveness in low-flow river systems where A. philoxeroides dominates the floating vegetation community.
Why it matches plant phenotyping methodsSentinel-2時系列から侵入植物の植生被覆率を推定し、航空画像で精度検証しており、植物状態の取得・評価手法が中心です。
abstractFVC estimates derived from vegetation indices were validated against high-resolution aerial images, with an EVI-based model achieving the highest accuracy (RMSE = 9.2%)
Field / plotWhole plant / canopy / plot / fieldStress / disease detectionPlant / canopy temperatureWater status / transpiration
Efficient irrigation management requires complementary information on atmospheric demand, soil conditions, and crop water stress. This study presents a low-power Internet of Things (IoT)-based irrigation system that integrates these components within a unified monitoring and control framework. The system combines LoRa communication, ESP32-based sensor nodes, soil and meteorological sensing, FAO-56 reference evapotranspiration (ET0), and canopy-temperature-based Crop Water Stress Index (CWSI). Irrigation decisions rely on the complementary use of ET0, in situ soil measurements, and CWSI rather than on a single indicator. A hybrid time-, event-, and query-driven acquisition strategy was implemented to adapt node activity and limit communication overhead. The system was deployed under outdoor conditions in Oujda, Morocco, demonstrating integrated sensing, wireless data transmission, crop-stress monitoring, and automated irrigation control. Energy characterization further showed distinct consumption profiles across sensing, communication, actuation, and low-power operating states, supporting the use of duty cycling to limit active node operation. The results demonstrate the feasibility of integrating environmental, soil, and crop-level information within a low-power IoT framework for adaptive irrigation management.
Why it matches plant phenotyping methods低消費電力IoT基盤の開発・実証が中心で、作物の水ストレスをCWSIで取得・監視する植物フェノタイピング要素が技術的に組み込まれている。
abstractThis study presents a low-power Internet of Things (IoT)-based irrigation system that integrates these components within a unified monitoring and control framework.
Plant phenotyping relevance match · UnverifiedCrossref · Europe PMC · checked 5 Sept 2026
Introduction Climate extremes increasingly threaten agricultural production, yet many artificial intelligence systems in agriculture remain local, reactive and narrowly trained for one crop, region or sensing modality. Methods We present AgriFM, a multimodal geospatial foundation model that combines satellite image time series, radar, thermal observations, weather trajectories, soil properties, topography and sparse management variables to estimate crop-stress and yield-failure risk across crops and regions. AgriFM was pretrained using self-supervised objectives on 2.4 million field-season sequences and evaluated on a curated benchmark spanning maize, wheat, soybean, rice and sorghum across five agroclimatic regions. Results In held-out geography and time-split evaluations, AgriFM improved early stress detection and yield-failure prediction over statistical, crop-model and deep-learning baselines. The largest gains occurred during compound drought and heat events, for which AgriFM produced alerts 18 to 24 days earlier than the satellite-only baseline while maintaining improved calibration. Phenology-conditioned fusion improved transfer across planting calendars, and uncertainty calibration reduced false alerts at fixed recall. Discussion Because the study is based on retrospective datasets, these findings establish cross-region retrospective performance rather than prospective field efficacy. The results support further field-based evaluation of multimodal foundation models for climate-resilient crop monitoring.
Why it matches plant phenotyping methods作物ストレス状態と収量失敗リスクを衛星・レーダー・熱画像等から推定する基盤モデルを開発し、複数作物・地域のベンチマークで評価しており、植物状態の取得・推定手法が中心である。
abstractWe present AgriFM, a multimodal geospatial foundation model that combines satellite image time series, radar, thermal observations, weather trajectories, soil properties, topography and sparse management variables to estimate crop-stress and yield-failure risk across crops and regions.
The use of a combined assessment of the informational significance of vegetation indices for predicting the yield of spring wheat, taking into account varietal specificity and agrotechnical factors, has been studied. The test site was the field experience in the forest-steppe zone of the Novosibirsk Priobye. In the experiment, spring wheat of the Suenga and Novosibirsk 41 varieties was cultivated using intensive agricultural technology. For the analysis, data obtained using the DJI Phantom 4 Multispectral Phantom unmanned aerial vehicle during the crop growing period in 2023–2025 were used. Vegetation index values were calculated using five spectral channels: blue (B, 450 ± 16 nm), green (G, 560 ± 16), red (R, 650 ± 16), red edge (RE, 730 ± 16) and near-infrared (NIR, 840 ± 26 nm). For the analysis of informational importance, the following indices were used as predictors of crop yield: NDVI, NDWI, GNDVI, LAI, CVI, GCI, and ChlRE. For assessing the informativeness of the indices, independent methods were used: the F-statistic of one-way regression (ANOVA F-test), evaluation of mutual information (Mutual Information, MI), and feature importance of the random forest algorithm (Random Forest, RF). Each of the scores was normalized in the range [0; 1] using the min-max normalization method, after which a combined score was calculated as a weighted sum. For the Suenga variety, the stable predictors regardless of the experimental variants were CVI (tillering) and ChlRE (stem elongation and heading), while for Novosibirsk 41, the set of informative predictors significant ly depended on the combination of plant protection and fertilizer systems. It was found that chlorophyll content indices (GCI, ChlRE) increased the predictive relationship with yield under fertilization, while the water status index (NDWI) lost informativeness when fertilizers were applied.
Why it matches plant phenotyping methodsUAVマルチスペクトル画像から植生指数を抽出し、複数の統計・機械学習手法を統合して小麦収量予測における指標の有用性を評価しており、植物形質推定ワークフローが中心です。
abstractThe use of a combined assessment of the informational significance of vegetation indices for predicting the yield of spring wheat
Pod shattering is a major domestication-related trait and one of the principal causes of pre-harvest yield losses in cowpea (Vigna unguiculata (L.) Walp.), particularly under hot and dry conditions. Rapid and reliable identification of shattering-resistant genotypes is essential for improving breeding efficiency. The present study evaluated a national core collection of 245 diverse cowpea genotypes over three consecutive years (2023–2025) to identify a simple phenotypic marker associated with pod-shattering resistance. Genotypes were screened using a modified Random Impact Method (RIM), and pod physical traits, including pod length, pod breadth, pod thickness, pod wall weight, seed-to-pod ratio, and dorsal suture morphology, were examined for their association with shattering response. A distinct and consistent morphological marker was identified in the dorsal suture of mature pods. Shattering-resistant genotypes exhibited a single, prominent dorsal ridge positioned above the dehiscence zone, whereas susceptible genotypes consistently displayed a two-ridged dorsal suture separated by a central depression that appeared to reduce tissue integrity and facilitate pod rupture under mechanical impact. The observed marker remained stable across years and environmental conditions, indicating its reliability as a rapid visual indicator of shattering resistance. The modified RIM provided a standardised, reproducible, and cost-effective approach for evaluating pod shattering while minimising environmental variation associated with field phenotyping. The identified dorsal ridge morphology offers a simple, non-destructive, and efficient phenotypic marker for large-scale germplasm screening and the selection of resistant genotypes. This marker can accelerate breeding for pod-shattering resistance, improve yield stability, and facilitate the development of climate-resilient cowpea cultivars adapted to drought-prone environments.
Why it matches plant phenotyping methods鞘の裂莢抵抗性を評価する標準化手法と、再現性のある形態マーカーを開発・検証しており、植物フェノタイピングが研究の中心である。
abstractGenotypes were screened using a modified Random Impact Method (RIM)
Abstract Chili is an important economic and nutritional crop with a relatively limited availability of different disease-resistant varieties. Leaf diseases, including those caused by fungi, bacteria, viruses, pests, or nutritional deficiencies, significantly compromise production and crop quality. Early detection of these diseases is key to reducing yield loss; however, traditional visual examinations are limited by time constraints, human subjectivity, and low detection sensitivity at early stages of infection. To overcome these challenges, this study proposes a deep learning–based framework for early multi-class detection of chili leaf diseases using convolutional neural networks (CNNs). A real-field dataset comprising 16,392 high-resolution images of chili leaves across six disease and healthy classes was collected from multiple regions of Bangladesh. The dataset was preprocessed, augmented, and split into training and validation sets using an 80:20 ratio. Five pre-trained CNN architectures—DenseNet121, EfficientNetB3, MobileNetV2, ResNet50, and InceptionV3 were evaluated using a transfer learning strategy. Experimental results demonstrate that MobileNetV2 achieved the best performance, attaining an overall classification accuracy of 96%. The results indicate that the proposed system demonstrates strong generalization capability and effectively discriminates visually similar chili leaf diseases. This work can be considered a valuable application in precision agriculture, providing an efficient, automated, and practical approach for in situ early diagnosis of chili leaf diseases through smart farm management.
Why it matches plant phenotyping methods唐辛子葉の病害状態を画像から分類するCNN手法の開発・比較評価とデータセット構築が研究の中心であり、植物病害フェノタイピングに該当する。
abstractA real-field dataset comprising 16,392 high-resolution images of chili leaves across six disease and healthy classes was collected from multiple regions of Bangladesh.
Precise characterization of alfalfa growth dynamics is essential for breeding accessions with superior regrowth capacity, persistence, and yield stability. However, traditional plot level and coarse scale observations suffer from low signal to noise ratios particularly before canopy closure when phenotypic data are strongly affected by weeds and soil background. Moreover, existing studies rarely capture the dynamic mechanisms of crop development across the entire growth cycle. To address this, the DINO-Pheno-Cluster framework is introduced as a foundation model driven and mechanism decomposed phenotyping approach. This decoupled framework first utilizes DINO-XMem, a few-shot individual plant segmentation network based on DINOv3 and a dual memory mechanism. It subsequently applies parameterized dynamic modeling guided by growth process knowledge. Validation utilized high frequency Unmanned Aerial Vehicle (UAV) imagery from 12 time points across three growing seasons covering 127 alfalfa accessions. DINO-XMem achieved an 89.54% mean Intersection over Union (mIoU) under a 10-shot setting and maintained 86.77% under extreme 1-shot conditions. It successfully resolved dense canopy oversegmentation outperforming fully supervised baselines by 4.08% to 11.97% in mIoU. Crucially, the extracted high purity time series trajectories were parameterized into specific biological indicators including maximum growth rate, comprehensive regeneration index, and seasonal stability index. Gaussian Mixture Model (GMM) clustering based on these mechanistic traits identified four distinct functional ideotypes comprising High yield/High regrowth, Upright/Sparse, High stability/Persistent, and Short/Dense, all validated by ground measured biomass. This workflow establishes a precision screening tool for multi harvest crops advancing crop phenomics toward process level analysis.
Why it matches plant phenotyping methods植物の時系列UAV画像から個体を分割し、成長・再生・安定性などの形質を抽出するフェノタイピング手法の開発と検証が中心である。
abstractthe DINO-Pheno-Cluster framework is introduced as a foundation model driven and mechanism decomposed phenotyping approach
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:97-124Plant phenotyping relevance match · UnverifiedOpenAlex · Europe PMC · checked 5 Sept 2026
Field / plotLiDAR / point cloudStem / branchMorphology / geometry measurementBiomass / plant weightPlant / canopy height
Abstract Context : Radiata pine breeding programmes rely on stem volume as a key objective, but phenotyping constraints limit selection intensity. UAV-LiDAR offers a scalable alternative to labour-intensive field measurements. Aims : We evaluated UAV-LiDAR-derived metrics as genetic selection proxies for stem volume in radiata pine genetic trials and quantified their utility relative to field-measured diameter at breast height (DBH). Methods: LiDAR metrics describing tree height and size were assessed against allometric stem volume (ASV) across 11 genetic trials (~27,000 trees, two trial series) using single-step genomic best linear unbiased prediction (ssGBLUP) with ~9,500 SNPs. Results : The 3D surface area of the individual tree convex hull (convexhull3D_area) had the highest correlation with ASV (up to r = 0.87) and similar heritability to DBH (mean h 2 = 0.26). LiDAR tree height had the highest heritability (mean h 2 = 0.37) and moderate to high genetic correlation with DBH. Selecting the top 100 genotypes by convexhull3D_area recovered 67-86% of potential ASV genetic gain, versus 88-96% for DBH. Including malformed trees in the genetic analyses of LiDAR traits marginally reduced their performance as stem volume proxies. Conclusion UAV-LiDAR-derived tree height and 3D convex hull surface present desirable properties to complement field phenotyping for stem volume selection in radiata pine. Their scalability, repeatability and high heritability support lower phenotyping costs, better early selection and accelerated genetic gain in radiata pine breeding.
Why it matches plant phenotyping methodsUAV-LiDARを用いて樹高・樹体サイズなどの形質を抽出し、茎体積の遺伝選抜プロキシとして相関・遺伝率・選抜効果を検証しており、植物フェノタイピング手法が中心である。
abstractWe evaluated UAV-LiDAR-derived metrics as genetic selection proxies for stem volume in radiata pine genetic trials
Proper nitrogen (N) management is essential for increasing the productivity of sugarcane (Saccharum spp.) and reducing the economic and environmental impacts associated with excessive fertilizer use. This study compared the performance of two portable spectroradiometers, FieldSpec 3 and HandHeld 2, in estimating foliar nitrogen content based on hyperspectral data in the visible and near-infrared regions, obtained throughout the crop cycle. The experiment was conducted in Piracicaba, São Paulo, Brazil, under four N rates: 0, 60, 120, and 180 kg ha−1. Spectral measurements were taken at the foliar and canopy levels at eight evaluation times, accompanied by laboratory determination of N content. Partial Least Squares Regression (PLSR) and Random Forest (RF) models were fitted using the spectral data and days after cutting (DAC), included as a categorical factor and evaluated using 10-fold internal cross-validation, based on the metrics R2, RMSE, MAE, and Willmott’s refined agreement index (dr). The foliar data performed better with PLSR (R2 = 0.727; RMSE = 1.381 g kg−1; MAE = 1.109; dr = 0.917) than canopy data (R2 = 0.591; RMSE = 1.489 g kg−1; MAE = 1.157; dr = 0.866). PLSR also outperformed RF at both acquisition levels. The green (~550 nm) and red edge (~740 nm) regions were the most relevant for N estimation. Under the evaluated conditions, model performance was associated with the spectral acquisition level and conditions, the instrumental configuration, and the modeling strategy employed.
Why it matches plant phenotyping methodsサトウキビ葉の窒素含量を分光計とPLSR/RFで推定し、取得レベル・機器・モデル性能を比較検証しており、形質取得手法が中心である。
abstractThis study compared the performance of two portable spectroradiometers, FieldSpec 3 and HandHeld 2, in estimating foliar nitrogen content based on hyperspectral data in the visible and near-infrared regions
Plant phenotyping relevance match · UnverifiedOpenAlex · Crossref · Europe PMC · checked 15 Sept 2026
Plant phenomics has undergone rapid development over the past two decades, driven by advances in imaging, robotics, artificial intelligence and data analysis. Whilst field phenotyping is increasingly operational and scalable, the relevance of controlled-environment (CE) phenotyping is questioned because of concerns regarding the limited transferability of results to agricultural conditions. This Expert View first addresses the limitations and risks of using CE as surrogate of outdoor conditions. However, we argue that CE enables the disentangling of interacting environmental drivers allowing causal analysis of plant responses to multiple abiotic and biotic stresses. CE platforms also provide access to complex traits that are difficult or impossible to measure in the field whilst providing a robust framework in combination of field approaches to interpret and predict field performance. We further discuss contexts where CE remains indispensable, including quarantine and biosafety regulations together with emerging opportunities for agricultural innovation. Whilst limitations of CE systems are acknowledged, including issues of extrapolation, pot effects, environmental realism, and the indispensable need for rigorous envirotyping, we conclude that CE phenotyping should be regarded as an enabling analytical framework that complements and strengthens field phenomics for crop adaptation research under climate change.
Why it matches plant phenotyping methods管理環境フェノタイピングとフィールドフェノミクスの役割・限界・分析枠組みを論じる専門的レビューであり、植物表現型計測の方法論が中心です。
titleWhy bother with controlled-environment phenotyping when field phenomics is already up and running?
In India, to increase the wheat yield production and support sustainable agricultural practices, timely and correct identification of wheat crop diseases such as yellow rust, brown rust, etc., is very much essential. Further, the majority of deep learning algorithms show high efficiency in plant disease detection and recognition, but these studies rely on handcrafted datasets captured under controlled laboratory conditions and accordingly will not perform well in the real world domain. Furthermore, there is a lack of real field wheat crop disease datasets collected in India, particularly from Haryana state, being the largest producer of wheat crops. Therefore, to address the issue of lack of region specific crop diseases dataset, which are region-specific, the wheat crop disease data set is curated, consisting of 2672 images of healthy and diseased leaves of wheat crops collected from the real field of CCS Haryana Agricultural University, Hisar. The dataset includes typically three classes of leaves of wheat crop, i.e., Yellow Rust (910), Brown Rust (922) and Healthy leaves (840) collected using both a DSLR camera and different smartphone cameras under natural lighting and field conditions. All images were validated and labeled by taking the expertise of wheat pathologists to ensure reliability on the dataset. The study also provides a comprehensive, systematic workflow for transforming raw data into a high-quality benchmark dataset for training using image preprocessing and augmentation techniques. Besides this, a comparative benchmarking analysis is performed under identical experimental conditions using three widely adopted deep learning architectures, which includes ResNet50, MobileNetV2 and EfficientNet-B0. The experimental results show that ResNet50 and EfficientNet-B0 achieve similar performance i.e. approximately 91% classification accuracy on real-field data. However, MobileNetV2 offers a lightweight alternative suitable for mobile and edge deployment. Furthermore, Grad-CAM based explainability analysis was performed to validate model predictions and highlight disease specific regions in wheat leaves. Therefore, this study contributes a practical region specific WheatDisease-HRY dataset and baseline benchmarking framework for developing robust AI based wheat disease diagnosis tools for real world agricultural applications in India.
Why it matches plant phenotyping methodsコムギ葉の病徴を画像から判定するデータセットを構築し、前処理・拡張、深層学習ベンチマーク、説明可能性解析までを中心的に扱うため、植物病害状態の画像ベース表現型手法として採用。
abstractThe study also provides a comprehensive, systematic workflow for transforming raw data into a high-quality benchmark dataset for training using image preprocessing and augmentation techniques.
Accurate estimation of crop water requirements is essential to improve irrigation efficiency for forage maize production. This study compared satellite- and UAV-derived normalized difference vegetation index (NDVI) models for estimating crop coefficients (K c ) and evaluated their operational performance for irrigation scheduling. K c -NDVI models were developed during the 2023 growing season and subsequently validated under field conditions during the 2024 season in two forage maize hybrids (N83N5 and Matador) under three irrigation strategies: conventional producer irrigation (ID1), satellite-based irrigation scheduling (ID2), and UAV-based irrigation scheduling (ID3). Both NDVI sources exhibited strong relationships with K c , with higher calibration accuracy for the UAV model (R 2 = 0.9414) than for the satellite model (R 2 = 0.8278). The UAV-based model applied 23-30% less irrigation water, maintaining high water productivity but also reducing crop growth, forage yield, and nutritional quality. In contrast, satellite-based irrigation scheduling promoted greater crop growth and produced the highest forage yield, reaching 59.8 t ha -1 in hybrid N83N5 while maintaining efficient water use. This treatment also improved forage quality by increasing dry matter and starch concentrations while reducing fiber fractions. The findings highlight the complementary potential of satellite and UAV imagery in precision irrigation and underscore the trade-offs between spatial detail, temporal resolution, and operational scalability. Furthermore, the results demonstrate that a stronger K c -NDVI relationship does not necessarily translate into improved irrigation scheduling performance. Under the conditions evaluated, the satellite-based model provided the best balance between water use, forage yield, and nutritional quality.
Why it matches plant phenotyping methods衛星・UAV画像からNDVIを用いて作物係数を推定する手法を開発し、別年・圃場条件で検証しており、植物群落状態の取得・推定が研究の中心である。
abstractK c -NDVI models were developed during the 2023 growing season and subsequently validated under field conditions during the 2024 season
Abstract Architectural analysis provides a powerful analytical framework for understanding the ontogenetic trajectories of tree species and their adaptive responses to environmental constraints. Despite their ecological, economic, and cultural importance in West African agroforestry systems, the architectural development of Khaya senegalensis (Desr.) A. Juss. (Meliaceae) and Pterocarpus erinaceus Poir. (Fabaceae), two overexploited taxa classified as Vulnerable on the IUCN Red List, had never been formally described. This study presents the first complete characterization of their architectural development, from the seedling stage to senescence, based on architectural and retrospective analyses conducted on 360 individuals per species across seven localities along a south-north bioclimatic gradient in Côte d'Ivoire, covering contrasting vegetation zones ranging from dense humid forest to dry Sudanian savanna. Both species display well-defined ontogenetic trajectories comprising four phases: juvenile establishment, architectural construction, reproductive transition, and crown restructuring associated with ageing. Distinct architectural models were identified: K. senegalensis conforms to Rauh's model, characterized by a monopodial orthotropic trunk with indefinite growth and rhythmic acrotonic branching; P. erinaceus follows Troll's model, in which the orthotropic trunk progressively gives rise to a sympodial plagiotropic system with mixed terminal and lateral flowering. Architectural units, defined as the minimal structural organization enabling a species to reach reproductive maturity, were established at the adult stage: that of K. senegalensis comprises four axis categories and five branching orders, while that of P. erinaceus comprises three axis categories and up to six branching orders in old trees. Significant variation in growth-unit morphology among habitats and localities ( P ) revealed the architectural plasticity of both species in response to ecological gradients. The calculated Favourable Development indices ( FDi ) identified Bouaké and Katiola as optimal zones for K. senegalensis , and Bouaké and Toumodi for P. erinaceus , providing objective spatial criteria for reforestation planning. These findings demonstrate that architectural traits are robust indicators of development, adaptive strategies, and crown functioning. By linking structural organization to productivity, resilience, and regeneration potential, this study provides a scientific basis for integrating architectural analysis into reforestation programmes, sustainable forest management, and the design of agroforestry systems for threatened African tree species facing growing climatic and anthropogenic pressures. Complementary regression analyses further showed that phytomer number, rather than internode elongation, primarily governs growth-unit length in both species, and that growth unit diameter scales positively with growth unit length; a multivariate analysis of variance (MANOVA) confirmed that ontogenetic stage and locality, but not habitat alone, robustly structure growth-unit morphology.
Why it matches plant phenotyping methods樹木の成長段階・分枝構造・成長単位形態を対象に、建築学的および回顧的解析を中心的手法として適用し、植物構造形質と発達状態を定量・比較しているため。
abstractThis study presents the first complete characterization of their architectural development, from the seedling stage to senescence, based on architectural and retrospective analyses conducted on 360 individuals per species across seven localities
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:307-347Plant phenotyping relevance match · UnverifiedOpenAlex · Crossref · checked 11 Sept 2026
Published23 Jul 2026The international archives of the photogrammetry, remote sensing and spatial information sciences/International archives of the photogrammetry, remote sensing and spatial information sciencesCited by 0 · OpenAlex ↗
Field / plotNeRF / 3D Gaussian SplattingThermalWhole plant / canopy / plot / field2D/3D reconstructionVisualization / data managementPlant / canopy temperature
Abstract. Urban trees provide critical ecosystem services in dense city environments, yet current workflows for monitoring their thermal behaviour remain confined to 2D desktop-based analysis with no three-dimensional spatial context or field-deployable visualization capability. This paper presents a complete pipeline for in-situ 3D thermal mesh visualization of urban trees in Augmented Reality (AR), combining Thermal InfraRed (TIR) image acquisition, Gaussian Splatting-based mesh reconstruction, quantitative validation, and mobile AR deployment. TIR images of a Tilia tomentosa acquired with a FLIR T560 camera are preprocessed with a standardized false-colour palette and fed into the MILo (Mesh-In-the-Loop Gaussian Splatting) framework to reconstruct a thermally attributed 3D mesh. Geometric evaluation against a Z+F IMAGER 5016 TLS reference using the M3C2 algorithm demonstrates that MILo recovers 13.5 times more canopy geometry than traditional multi-view stereo under thermal imagery, with a standard deviation of 4.0 cm. A colourmap inversion procedure recovers per-vertex temperature estimates from the GS-derived mesh colours, yielding a mean absolute difference of 0.7°C against direct T-Cam measurements (thermal camera mounted on the laser scanner), within the combined instrument accuracy of both sensors. The resulting thermal Gaussian Splat was deployed in a custom Android AR application supporting hybrid marker-based and GPS-based spatial anchoring for in-situ visualization. These results demonstrate the technical feasibility of GS-based thermal reconstruction and mobile AR as a medium for communicating three-dimensional canopy thermal information to educators and urban forestry practitioners.
Why it matches plant phenotyping methods都市樹木の葉冠温度と3D形状を取得・可視化する熱画像ベースの再構成パイプラインを開発し、TLSおよび熱カメラとの定量検証まで行っており、植物フェノタイピング手法が研究の中心である。
abstractThis paper presents a complete pipeline for in-situ 3D thermal mesh visualization of urban trees in Augmented Reality (AR), combining Thermal InfraRed (TIR) image acquisition, Gaussian Splatting-based mesh reconstruction, quantitative validation, and mobile AR deployment.
Abstract Uneven occurrence of potato leaf diseases necessitates site-specific treatment rather than conventional uniform spraying. This study presents a vision-guided autonomous variable-rate spraying system integrating real-time deep learning-based disease detection, temporal disease severity estimation, and PWM-controlled precision spray actuation for targeted crop protection. A composite dataset comprising 1,561 field images containing 14,166 annotated leaf instances was developed under dense canopy conditions. Comparative evaluation of object detection architectures showed that YOLOv26 achieved the highest detection performance with a peak mAP@0.5 of 0.961, outperforming YOLOv8 (0.924) by 3.7% and YOLOv12 (0.938) by 2.3%. The lightweight YOLOv26n variant was selected for embedded deployment. When deployed on a Raspberry Pi 5, the optimized ONNX model achieved an inference speed of approximately 10 FPS, corresponding to a spatial sampling interval of 0.018 m at an operating speed of 0.18 m/s. A 2 s temporal sliding window generated a stable canopy-level disease severity index, which was mapped to PWM duty cycles for variable-rate pesticide application. Field experiments involving 598 spatial spray decision instances validated the proposed perception-driven spray control framework. Compared with conventional constant-rate spraying, the system reduced agrochemical consumption by 32.75% (from 458 to 308 L/ha). These results demonstrate the feasibility of integrating embedded deep learning and adaptive spray control into a field-deployable autonomous spraying platform for precision potato disease management.
Why it matches plant phenotyping methodsジャガイモ葉の病徴検出とキャノピー病害重症度推定を中核とする視覚センシング・深層学習・噴霧制御プラットフォームの開発および実地検証であり、植物状態の定量的推定方法が中心である。
abstractThis study presents a vision-guided autonomous variable-rate spraying system integrating real-time deep learning-based disease detection, temporal disease severity estimation, and PWM-controlled precision spray actuation for targeted crop protection.
Plant disease phenotyping underpins resistance breeding, epidemiology and crop-loss management, yet it remains a recognised bottleneck. This review asked whether the two metrics that dominate the discipline, the disease severity index (DSI) and the area under the disease progress curve (AUDPC), adequately represent disease as a temporally unfolding process, and what the evidence says about dynamic alternatives. Reporting followed PRISMA 2020 and the Synthesis Without Meta-analysis (SWiM) guideline. Web of Science Core Collection, Scopus, PubMed and a Google Scholar grey-literature sweep were searched for records published between January 2020 and December 2025, retrieving 1,192 records; 874 remained after de-duplication, 128 full texts were assessed and 31 studies met the eligibility criteria. Citation chasing added 24 foundational works, giving 55 included studies. Records were dual-screened (Cohen's kappa = 0.86), appraised with an adapted Mixed Methods Appraisal Tool, and synthesised using vote counting by direction of effect, an evidence map and structured cross-study comparison; meta-analysis was inappropriate because outcomes were not commensurable. Thirty studies (54.5%) represented disease at a single assessment and eight (14.5%) collapsed the epidemic into one integrated area, whereas only twelve (21.8%) retained the full trajectory. Across six outcome domains, all 29 study-level comparisons favoured the temporally richer method and none reported a null or negative result, an asymmetry indicating probable reporting bias. Certainty was high for visual-assessment findings, moderate for sensing and dynamic modelling, and low for field-realised genetic gain. The phenotyping bottleneck has migrated from data acquisition to data representation.
Why it matches plant phenotyping methods植物病害フェノタイピング手法の動的評価を中心に、既存指標と代替手法を体系的に比較した方法論レビューである。
titleA Systematic Review of Dynamic Disease Phenotyping in Plant Pathology
Published23 Jul 2026The international archives of the photogrammetry, remote sensing and spatial information sciences/International archives of the photogrammetry, remote sensing and spatial information sciencesCited by 0 · OpenAlex ↗
Abstract. Tree growth determines how much CO2 is sequestered from the atmosphere and temporarily stored in woody biomass. At the same time tree growth is affected by increasing temperatures, more frequent drought periods, late frosts and other extreme events associated with climate change. While continuous measurements of radial (secondary) tree growth using dendrometers are well established, monitoring of shoot elongation (primary growth) has largely been neglected because suitable measurement techniques are lacking. As a result, the effects of climate change on primary tree growth remain insufficiently understood. This work aims at reconstructing native deciduous trees in 3D as a basis for measuring and monitoring shoot elongation over entire tree canopies. Here we explored the use of low-cost UAV photogrammetry and of a multi-camera CraneCam system under real-world conditions. Data were collected in two study areas over an entire growing season. We present sensor evaluations, photogrammetric data acquisition and processing strategies. A special focus is placed on the analysis of the resulting photogrammetric 3D point clouds in terms of accuracy, resolution and completeness. Results demonstrate 3D point accuracies of 5-6 mm for entire trees using consumer-grade UAVs weighing less than 250 g and a 3D reconstruction completeness between 92% and 98% depending on the UAV type. The paper introduces a novel 3Dßprinted ground-truth branch to evaluate the capability to reconstructing fine-detail structures such as thin tree shoots. Finally, we discuss operational challenges and initial experiments towards a skeletonization of entire trees based on photogrammetric point clouds.
Why it matches plant phenotyping methods樹冠全体のシュート伸長という植物形質を取得するための3D再構成手法を開発・評価しており、精度・解像度・完全性の検証も中心的に扱っている。
abstractThis work aims at reconstructing native deciduous trees in 3D as a basis for measuring and monitoring shoot elongation over entire tree canopies.
Published23 Jul 2026The international archives of the photogrammetry, remote sensing and spatial information sciences/International archives of the photogrammetry, remote sensing and spatial information sciencesCited by 0 · OpenAlex ↗
Abstract. Monitoring individual trees from unmanned aerial vehicle (UAV)-derived orthomosaics and digital surface models (DSMs) is important for forest management, but instance segmentation remains difficult in dense planted forests in Japan, where Structure from Motion (SfM)-derived DSMs often exhibit blurred crown boundaries, noise, and substantial variation in quality. Existing approaches can benefit from treetop information, but they are sensitive to threshold selection and may introduce false positives when incorrect treetop candidates are provided. To address this problem, we propose a method based on the polar coordinate transform and the fast Fourier transform (PFFT) that represents the local DSM shape around treetop candidates as compact descriptors and integrates them into Mask2Former. The descriptors are used both to suppress low-reliability candidates and to provide spatially meaningful treetop queries to the decoder, thereby improving the separation of adjacent crowns. We evaluated the method on Abies sachalinensis (Todo fir) plantation data acquired at two sites in Hokkaido, Japan, using Mask R-CNN and Mask2Former as baselines. Compared with standard Mask2Former, the proposed method improved mAP50 from 90.14% to 90.87%, mAP75 from 52.18% to 55.47%, and the F1 score at a confidence threshold of 0.5 from 89.86% to 92.08%. It also reduced the number of false positives by 41% without increasing false negatives. Qualitative results showed fewer over-merged crowns and better crown-boundary delineation. These results indicate that treetop-centered local shape cues are effective for instance segmentation in densely planted forests, although further validation across additional species and regions is needed.
Why it matches plant phenotyping methodsUAV由来データから個体樹冠を分離・ delineate する画像解析手法を開発し、複数ベースラインと定量比較しているため、植物形態計測法が中心である。
abstractwe propose a method based on the polar coordinate transform and the fast Fourier transform (PFFT) that represents the local DSM shape around treetop candidates as compact descriptors and integrates them into Mask2Former.
Field / plotLeafClassificationStress / disease detectionDisease symptoms / severity
This study aims to develop a classification system for papaya leaf diseases based on digital image processing using the Convolutional Neural Network (CNN) method with the MobileNetV3 architecture. The background of this research is the manual process of identifying papaya leaf diseases by farmers, which is often inefficient and prone to misdiagnosis. The research method adopts a software engineering approach using the Agile development model, allowing iterative and flexible system development. The dataset consists of papaya leaf images categorized into three classes: curl, ringspot, and healthy, obtained from field observations and secondary datasets. The data were processed through preprocessing stages before being used to train the CNN model. The results indicate that the best model was achieved using a learning rate of 0.001 and 30 epochs, with a validation accuracy of 95.56% and a testing accuracy of 88.89%. The model demonstrates high confidence in classifying images, particularly for the curl and healthy classes. However, the confusion matrix reveals that the model's performance on the ringspot class remains relatively low due to a high misclassification rate. Overall, the developed system is capable of automatically identifying papaya leaf diseases and has strong potential for implementation as an Android-based application to support early detection and decision-making in plant care.
Why it matches plant phenotyping methodsパパイヤ葉の画像から病害状態を推定するCNN分類手法の開発・評価が研究の中心であり、植物表現型計測に該当する。
abstractThis study aims to develop a classification system for papaya leaf diseases based on digital image processing using the Convolutional Neural Network (CNN) method with the MobileNetV3 architecture.
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:1-61Plant phenotyping relevance match · UnverifiedEurope PMC · Crossref · checked 5 Sept 2026
Abstract The diseases on sesame leaves have a huge implication on the production and earnings of farmers particularly in the developing areas. It is important to ensure that the disease is properly managed by identifying it early and correctly. The purpose of this study is to create a deep learning-based framework that could be used to categorize four of the most common scenarios involving sesame leaves, i.e. Healthy Leaf, Leaf Spot Disease, Yellowing Leaf Syndrome, and Leaf Damage by Insects using high-resolution images acquired in Pabna, Bangladesh. The preprocessing, augmentation and split of a set of 3,540 images were performed into training and validation sets. The pre-trained convolutional neural networks models were trained and tested on five models inceptionV3, EfficientNetB3, ResNet50, MobileNet, and DenseNet121 by measuring the metrics such as accuracy, precision, recall, and F1-score. MobileNet achieved the highest accuracy of 96.33%, precision of 96%, recall of 96%, and the F1-score of 96%, which is the best amongst them. The findings indicate that deep learning architectures are capable of classifying the sesame leaf diseases in a reliable and precision-oriented way that is not affected by different environmental circumstances. The study facilitates the creation of the automated, efficient methods of detecting the disease at an early stage, cutting down the number of pesticides used and enhancing crop control. Future direction will be to enlarge the dataset, add temporal data and to implement lightweight models so that it can be deployed to real-time field projects
Why it matches plant phenotyping methodsセサマ葉画像から病害状態をCNNで分類する手法の開発・比較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。
abstractThe purpose of this study is to create a deep learning-based framework that could be used to categorize four of the most common scenarios involving sesame leaves
Published23 Jul 2026The international archives of the photogrammetry, remote sensing and spatial information sciences/International archives of the photogrammetry, remote sensing and spatial information sciencesCited by 0 · OpenAlex ↗
Abstract. Accurate estimation of tree volume is essential for precision forestry and sustainable forest management. Traditional forest inventory methods rely on manual measurements of tree height and diameter, which are time-consuming and costly to conduct over large areas, and difficult to perform efficiently in dense forest stands. This study presents a data-driven approach for estimating tree volume from partial tree stem profiles derived from high-resolution datasets. While the study relies on harvester production data (Sweden) and field-measured tree stem profiles (Brazil), the framework is designed to support the estimation of tree volume from close-range remote sensing techniques, such as terrestrial photogrammetry using handheld cameras. Three modelling approaches were evaluated, including two machine learning models (XGBoost and Random Forest) using partial tree stem profile measurements as predictors, and one baseline model (XGBoost) using diameter at breast height and tree height as predictors. The models were developed using two independent datasets: harvester production data of Norway spruce (Picea abies (L.) H. Karst.) from Sweden and field-measured tree stem profiles of Slash pine (Pinus elliottii Engelm.) and Loblolly pine (Pinus taeda L.) plantations from Brazil. The results show that tree volume can be predicted with reasonable accuracy using partial tree stem profiles, although models incorporating tree height achieved the lowest prediction errors. The findings demonstrate that partial tree stem profiles provide valuable structural information for machine learning-based tree volume estimation. This framework supports the future integration of close-range remote sensing techniques into modern forest inventory systems.
Why it matches plant phenotyping methods樹幹プロファイルから樹木体積という植物形質を推定する機械学習・近距離リモートセンシング手法が研究の中心であり、複数モデルと独立データセットで評価している。
abstractThis study presents a data-driven approach for estimating tree volume from partial tree stem profiles derived from high-resolution datasets.
Seedling establishment represents a critical phase in early crop growth and development, directly influencing biomass accumulation and yield potential. To characterise early growth dynamics under field conditions, both growth rate and uniformity of emergence need to be assessed continuously; however, manual quantification of these dynamic traits in large-scale trials remains impractical. Here, we present LeafTip-RN, an open-source and deep learning (DL)-powered pipeline for dynamically measuring wheat (Triticum aestivum L.) early establishment in the field. To enable flexible and scalable data collection, ultralow-altitude drone phenotyping was employed, followed by the development of an optimised DL model to automate leaf-tip-related feature extraction from complex backgrounds. Notably, to address data sparsity arising from eight phenotyping timepoints, we integrated an image-to-video generative AI (GenAI) module into the pipeline to interpolate keyframes between early and late seedling stages (i.e. 18-40 days after sowing), resulting in a training library comprising 353,019 labelled leaf tips. Using the pipeline, we successfully quantified multiple agronomically important establishment-related traits (e.g. plot-level leaf tips and seedling spatial uniformity), followed by deriving their growth curves for 51 wheat varieties across two growing seasons (2024-2026). After validating these LeafTip-RN-derived traits, we further computed varietal relative growth rates and uniformity indices, based on which the 51 varieties were classified into high-, medium-, and low-performance groups, revealing discrepancies between LeafTip-RN-derived classification (18-40 DAS) and manual assessment at 40 DAS when dynamic early performance was considered. Finally, to facilitate broad adoption by the plant research community, we developed an openly accessible graphical user interface (GUI) for non-expert users to visualise and analyse rapid seedling developmental changes. Taken together, our study provides a scalable GenAI-powered solution for evaluating seedling establishment in wheat, offering valuable tools for breeders and researchers to identify varieties with enhanced early growth vigour and emergence dynamics that are extensible to other cereal crops.
Why it matches plant phenotyping methodsLeafTip-RNは、ドローン画像と深層学習・生成AIによって小麦の葉先や出芽均一性などの形質を自動抽出・連続推定する手法およびGUIを開発し、導出形質を検証しているため、植物フェノタイピング手法が研究の中心である。
abstractHere, we present LeafTip-RN, an open-source and deep learning (DL)-powered pipeline for dynamically measuring wheat (Triticum aestivum L.) early establishment in the field.
Precision agriculture increasingly relies on detailed structural information, such as canopy height and canopy volume, to enhance crop health monitoring and operational safety. However, existing methods based on costly LiDAR or RGB-D sensors are often impractical for large-scale deployment in dynamic and unstructured horticultural environments. Furthermore, conventional 2D segmentation and SLAM-based pipelines typically generate sparse, geometrically inconsistent semantic maps which are insufficient for actionable structural analysis in agricultural applications. To overcome these limitations, we propose a monocular 3D structural mapping framework tailored for horticultural plants via semantic scene completion. At inference, the proposed model takes a single RGB image as input and predicts voxel-wise geometry and semantics, from which task-oriented structural maps, including canopy height, canopy volume, and obstacle-aware traversability layers, are derived. Specifically, we first introduce a Depth-Aware Decoder Module that explicitly recovers depth in the spatial domain and fuses 2D-to-3D features, thereby mitigating depth ambiguity and reducing reliance on accurate pose. Second, an NCS-Guided Geometry Encoder is designed to inject normalized depth into voxel positional embeddings, enabling self-attention to perform global relational modeling within a depth-aware geometric coordinate system. In addition, a Global Encoder is utilized to refine local structural details, while an occupancy head produces the final 3D semantic completion outputs. We construct a horticultural 3D semantic scene dataset using an RGB-D sensor, which serves as a benchmark for evaluating our method, while the deployed model remains RGB-only. Extensive quantitative and qualitative experiments are conducted on both the Semantic-KITTI dataset and our dataset. On our dataset, the method achieves 82.31% occupancy IoU, 84.26% mIoU, and 86.25% precision. Beyond voxel-level evaluation, manual field measurements further show canopy height MAE values of 0.019-0.026 m and canopy volume proxy relative errors of 8.4%-11.4%. These results demonstrate the effectiveness of our approach in real-world agricultural scenarios, providing actionable structural insights for crop monitoring and autonomous robotic operations.
Why it matches plant phenotyping methods単眼RGB画像から植物の樹冠高・樹冠体積などの構造形質を推定する3Dフェノタイピング手法を開発し、データセット構築と実測検証も行っているため、方法が研究の中心である。
abstractwe propose a monocular 3D structural mapping framework tailored for horticultural plants via semantic scene completion.
Introduction Safeguarding the yield and quality of field crops against abiotic stresses is critical for large-scale agricultural production and precision agronomy. This study addresses the challenges of detecting concealed fruit stress and overcoming label scarcity in unmanned aerial vehicle (UAV) multispectral monitoring, using blossom-end rot (BER) in processing tomatoes as a case study. Methods We developed a leaf-fruit synergistic Roll and Color Disease Index (RCDI), integrating fruit incidence with visible canopy phenotypic features to characterize the combined canopy-fruit stress status associated with BER. A three-level screening strategy was used to identify the optimal spectral feature set. A Multi-model Collaborative Cyclic Self-Training (MCC-ST) framework was subsequently developed to address the limited availability of severity-labeled samples. Results The combination of GRVI, NDVI, and SAVI was identified as the optimal spectral feature set, achieving stable within-dataset binary classification performance of approximately 97% in repeated cross-validation. Under 30 random-seed repeated stratified three-fold cross-validations, MCC-ST + DT and MCC-ST + RF achieved RCDI-based BER severity-grading accuracies of 85.00% ± 0.31% and 85.07% ± 0.42%, respectively. Compared with the corresponding original DT and RF models, MCC-ST improved repeated-validation accuracy by 16.19-4.09 percentage points. Discussion The RCDI helps bridge the observational gap between canopy signals and concealed fruit stress, while MCC-ST alleviates the bottleneck associated with label scarcity. The proposed approach provides a promising framework for crop abiotic-stress monitoring under limited-label conditions.
Why it matches plant phenotyping methodsUAVマルチスペクトル画像からトマトの果実ストレス状態・BER重症度を推定する指標と、ラベル不足に対応する機械学習フレームワークを開発・検証しており、植物表現型取得・推定手法が研究の中心である。
abstractThis study addresses the challenges of detecting concealed fruit stress and overcoming label scarcity in unmanned aerial vehicle (UAV) multispectral monitoring, using blossom-end rot (BER) in processing tomatoes as a case study.
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:129-140Plant phenotyping relevance match · UnverifiedEurope PMC · Crossref · checked 5 Sept 2026
Abstract Outbreaks of plant diseases are major threats to world food security particularly in areas where real-time monitoring and quick decision support are constrained by low-power edge gadgets and untrustworthy connectivity. In order to overcome these issues, this paper presents a FPGA-Accelerated IoT implementation of a Causal-Attention Multi-Modal Deep Learning Network, named EpiFusionNet-Edge, that can be applied to monitor crop diseases with real-world farming scenarios with high precision and scalability. The framework incorporates five data modalities that are complementary in nature and they include RGB leaf pictures, microscopic foldscope images, UAV hyperspectral signatures, microclimate IoT sensor measurements and region-specific pathogen/pest pressure indexes giving a complete picture of the health of the plant. Dual causal-attention mechanism is proposed to simulate both spatial and temporal environmental factor activation, which helps to detect and make predictions at the early stage and provides an explanatory logic behind the decisions. Multi-task learning enables classification of diseases, quantification of their intensity at the level of a micro-prediction and prediction of outbreaks in the short term (1–30 days). In order to achieve deployability in resource-constrained settings, the proposed deep learning architecture is ensemble-distilled, structurally pruned, and INT8-quantized, and hardened on a Xilinx Zynq-7000 FPGA platform. The FPGA accelerator is 43.2x faster inference, 88 percent less power usage, and less than 10 ms latency, which allows real-time execution of continuous field monitoring with IoT sensors. Cross-condition assessment on multi-domain datasets shows that there are great improvements on cross-environment generalization rates with 98.6% classification accuracy, 92.7% severity estimation accuracy and less than 3.5% degradation with domain shift. Grad-CAM + + and causal feature traceability further add interpretability with the focus of the model and the pathological indicators proven by experts. The findings show the promise of using a combination of IoT sensing, multi-modal AI fusion, and FPGA hardware acceleration to develop a deployable and scalable and transparent system with regard to precision agriculture. This paper creates a roadmap to a new generation of smart farming systems that are able to conduct disease surveillance and actively protect crops at the periphery in an autonomous manner.
Why it matches plant phenotyping methods植物病害の画像・センサー観測から病害強度を定量化するマルチモーダル・エッジ推論基盤を開発し、精度・速度・消費電力・ドメインシフト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ある。
abstractthis paper presents a FPGA-Accelerated IoT implementation of a Causal-Attention Multi-Modal Deep Learning Network, named EpiFusionNet-Edge
Plant phenotyping relevance match · UnverifiedOpenAlex · Europe PMC · Crossref · checked 5 Sept 2026
Abstract Quantifying blueberry fruit yield and maturity is important for evaluating yield potential in breeding trials, but manual measurement remains slow, labor-intensive, and costly. Object detection and classification networks offer a high-throughput solution, yet few studies validate image-based counts against hand-harvested ground truth while explicitly accounting for canopy occlusion. Hence, this study developed a multi-class berry detection pipeline for immature and mature berries and validated image-based estimates against hand-harvest counts across 32 diverse southern highbush blueberry genotypes. Among the models evaluated, YOLOv8x achieved the highest detection performance, with an mAP50 of 0.82 and an mAP50–95 of 0.66. External validation produced F1 scores ranging from 0.74 to 0.91 for berry maturity classes. However, image-based detections systematically underestimated hand-harvested fruit counts, with R² values ranging from 0.40 to 0.61. Fruit occlusion varied widely among genotypes, from 42% to 90%, indicating that canopy structure strongly affects berry visibility. Incorporating image-derived canopy architecture, color, and texture features improved predictions of berry counts and maturity. Partial Least Squares regression provided the best performance, increasing R² values of hand-harvested fruit counts, ranging from 0.52 to 0.74. These results show that accounting for canopy occlusion improves image-based estimation of blueberry yield and supports more accurate high-throughput phenotyping.
Why it matches plant phenotyping methodsブルーベリーの収量・成熟度を画像から推定する検出パイプラインを開発し、手収穫値との外部検証および樹冠遮蔽・構造を考慮した改良を行っており、植物表現型取得法が中心である。
abstractthis study developed a multi-class berry detection pipeline for immature and mature berries and validated image-based estimates against hand-harvest counts
ABSTRACT Banana diseases impose severe production losses in tropical smallholder farming systems, yet accurate in-field visual diagnosis remains difficult: symptom expression varies across cultivars and growth stages, and several diseases produce morphologically overlapping foliar signs. We developed a probabilistic image-recognition framework for detecting five economically important banana diseases — Xanthomonas Wilt, Banana Bunchy Top Disease, Fusarium Wilt (Panama disease), Yellow Sigatoka, and Black Sigatoka — from in-field photographs, without any disease-specific fine-tuning of the vision backbone. The approach extracts frozen 1,152-dimensional embeddings from the DINOv3 vision foundation model and couples them with a conditional normalizing flow, trained on four publicly available datasets spanning diseased banana plants, healthy tissue, non-banana vegetation, and general natural imagery. On an independent test set the model achieved F1 scores exceeding 0.98, average precision values of 0.968–0.999, and AUROC values of 0.997–1.000 across all five diseases evaluated as binary detection problems. Multi-class accuracy was near-perfect, with limited confusion between Yellow Sigatoka and Black Sigatoka — a biologically plausible ambiguity attributable to overlapping early-infection foliar symptoms. Because the normalizing flow estimates explicit conditional probability densities rather than decision boundaries, two complementary log-likelihood ratios can be derived: a disease ratio comparing each disease class against healthy banana, and a plant ratio comparing banana against non-banana imagery. Together these define an interpretable two-dimensional diagnostic space that simultaneously quantifies evidence for disease presence and image relevance, cleanly separating diseased plants, healthy plants, and out-of-distribution images while flagging uncertain predictions for confirmatory testing. Inference on frozen embeddings is lightweight and compatible with smartphone deployment, providing a scalable, uncertainty-aware diagnostic tool for smallholder farming systems and disease surveillance programmes.
Why it matches plant phenotyping methodsバナナ葉の病徴を圃場画像から直接推定する確率的画像認識手法を開発し、独立テストセットで性能検証しているため、植物病害状態のフェノタイピング手法が中心である。
abstractWe developed a probabilistic image-recognition framework for detecting five economically important banana diseases
ABSTRACT Phenomic selection (PS) offers a cost‐effective , breeder‐friendly approach for public breeding programmes with limited access to genotyping or restricted financial resources for laboratory infrastructure. Since PS relies on high‐throughput phenotyping data, which is often derived from near‐infrared spectroscopy (NIRS) of harvested seeds, prediction is challenged by the high dimensionality and strong intercorrelation of NIRS data, which means that only a subset of wavelengths is informative. This study evaluates spectral variable selection models for predicting key morpho‐agronomic and quality traits in malt barley ( Hordeum vulgare L.) and assesses their performance under realistic breeding scenarios. Four NIRS‐based regularized regression models (Lasso, Enet, Ridge and a heritability‐filtered Ridge model) were tested to predict 10 morphological, agronomic and quality traits measured in two malt barley trials conducted during the 2022 and 2024 cropping seasons at three locations in Ethiopia using 100 genotypes in each trial. Model performance was evaluated across four practical breeding scenarios: within‐location unseen genotype prediction (WL‐uG), leave‐one‐location‐out prediction (LOLO), target environment unseen genotype prediction (TargetEnv) and across‐location wide adaptability (RuG). Accordingly, Cross‐validation identified stable, informative spectral predictors for each trait, scenario and trial. Among the models tested, Lasso and Enet consistently outperformed Ridge regression, with Enet showing the best predictive performance across scenarios. Prediction ability (r) ranged from 0.15 to 0.85 for quality traits, 0.16 to 0.79 for agronomic traits and 0.07 to 0.89 for morphological traits across scenarios. Thus, these findings underscore the importance of spectral predictor selection in improving predictive ability and demonstrate the transferability of PS in barley breeding.
Why it matches plant phenotyping methodsNIRSを用いた植物形質予測とスペクトル変数選択モデルの比較・検証が研究の中心であり、複数の形態・農業・品質形質に対する予測性能を交差検証している。
abstractThis study evaluates spectral variable selection models for predicting key morpho‐agronomic and quality traits in malt barley ( Hordeum vulgare L.) and assesses their performance under realistic breeding scenarios.
Agrophotovoltaic (APV) systems provide a unique opportunity for improving agricultural land-use efficiency by combining crop production with solar energy capture via photovoltaic panels. In-depth information on plant growth patterns within the spatially heterogenous microclimate created by APVs would enable better planning and management within such unconventional systems. Thus, the present study demonstrates the implementation of a customized robot-mounted 3D-multispectral imaging system for monitoring the growth and spectral reflectance patterns of a conventional soybean cultivar "Eiko" (EK) and a chlorophyll-deficient mutant variety MinnGold (MG) under an APV system. Weekly trends in canopy morphometric features revealed significant variations in canopy height, surface area, light penetration, and volume across the APV field depending on the proximity with the overhead solar panels for both EK and MG, with plants receiving adequate rainfall and intermittent shade performing the best. Furthermore, although spectral indices exhibited variations between EK and MG due to intrinsic differences in pigmentation, symptoms of stress could be detected for both genotypes within rain-shaded areas of the APV plot. Hence, the present investigation depicts the potential for complementary usage of robotics and machine vision for high-precision high-throughput crop monitoring under APVs, which would help improve crop management within such non-homogenous cultivation systems.
Why it matches plant phenotyping methodsカスタマイズしたロボット搭載3Dマルチスペクトル画像システムを実装し、植物形態・スペクトル・ストレス状態を高精度に取得することが研究の中心である。
abstractthe present study demonstrates the implementation of a customized robot-mounted 3D-multispectral imaging system for monitoring the growth and spectral reflectance patterns
Abstract Blanket-rate agrochemical scheduling — a practice wherein the same quantity of fertilizer or pesticide is spread uniformly across an entire field irrespective of spatial or temporal crop need — persists as the dominant farm management paradigm across rural India and large parts of South Asia. This approach generates cascading inefficiencies: excess nitrogen drains into waterways, off-target pesticide deposits devastate pollinators, input costs erode thin profit margins, and wide-scale greenhouse gas release from soil microbial activity accelerates climate change. The study documented here addresses this challenge through a purpose-built, four-layer intelligent field management platform. The platform ingests continuous data from drone-mounted multispectral cameras, in-field IoT soil probes, a wireless weather station, and cloud-sourced Sentinel-2 satellite imagery, then passes these inputs through a cascaded AI inference stack. A fine-tuned YOLOv8-L network performs real-time pest and foliar disease localisation; a ResNet-50 backbone quantifies canopy health across five stress gradients; a two-layer stacked LSTM projects short-horizon yield trajectories; and a Deep Q-Network autonomously plans drone spray routes weighted by field-specific prescription maps. Field validation spanned two consecutive growing seasons (Rabi 2022–23 and Kharif 2023–24) across six georeferenced plots covering 4.8 ha at Baramati, Maharashtra. Outcome metrics recorded during head-to-head comparison with conventional practice included a disease detection score of 95.6% mAP, a 47.3% reduction in total nitrogen applied, a 38.1% decrease in pesticide volume, and a 22.4% uplift in harvested grain weight. Together, these field-verified numbers substantiate the operational readiness of integrated AI precision agriculture for smallholder deployment.
Why it matches plant phenotyping methodsマルチスペクトル画像・深層学習による病害局在化とキャノピー健康状態の定量化を中核機能とする統合プラットフォームであり、植物の病害状態・生育状態を直接推定して現地検証している。
abstractThe platform ingests continuous data from drone-mounted multispectral cameras, in-field IoT soil probes, a wireless weather station, and cloud-sourced Sentinel-2 satellite imagery, then passes these inputs through a cascaded AI inference stack.
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。Code · publicData Availability The annotated image dataset (14,300 images, 23 classes), trained YOLOv8-L and ResNet-50 weights, LSTM model files, DQN policy checkpoint, and all analysis scripts are archived at https://github.com/precision-agri-ai (Zenodo DOI: 10.5281/zenodo.XXXXXXX).Open asset ↗precision-agri-ailines:161-182Plant phenotyping relevance match · UnverifiedCrossref · checked 5 Sept 2026
Remote sensing has become an important tool for crop monitoring and precision agriculture, yet its applications in sugar beet production remain fragmented across sensing platforms, target traits and modelling strategies. This review synthesises the development, current applications and future directions of remote sensing in sugar beet production, with particular attention to the transition from crop monitoring to precision management. A structured search was conducted in Scopus and the Web of Science Core Collection for publications from 2003 to 2025, and 181 relevant peer-reviewed articles were retained for thematic analysis. The literature shows a clear increase in sugar beet remote sensing studies, particularly after 2015, coinciding with the availability of Sentinel-2 imagery and, from 2016 onwards, the growing use of unmanned aerial vehicle-based sensing. It also indicates a gradual shift from crop mapping and canopy monitoring towards disease detection, weed mapping, yield prediction and management-oriented applications. Current studies demonstrate the value of satellite, unmanned aerial vehicle and proximal sensing for retrieving canopy traits, assessing biotic stresses, estimating root yield and supporting field-scale management. However, sugar beet presents specific challenges because its economic value depends not only on canopy development or root biomass, but also on sucrose concentration, recoverable sugar yield, and processing quality. These quality-related traits remain less studied and are difficult to infer directly from canopy observations. Modelling approaches have evolved from vegetation-index-based empirical models towards machine learning, deep learning, multi-temporal analysis, data fusion and crop model assimilation, but issues of model transferability, ground-truth availability and operational decision support remain unresolved. Future research should strengthen multi-source observations, external validation, quality-oriented prediction and decision-support workflows to promote robust, scalable and economically meaningful remote sensing applications in sugar beet production.
Why it matches plant phenotyping methodsサトウダイコンのリモートセンシングによるキャノピー形質、ストレス、根収量などの推定手法を体系的にレビューしており、センシング基盤とモデル化・検証課題が中心的に扱われている。
abstractThis review synthesises the development, current applications and future directions of remote sensing in sugar beet production, with particular attention to the transition from crop monitoring to precision management.
Smartphone-based precision spraying aims to restrict chemical application to target organs, but it also requires an organ-level perception model that operates on RGB alone at deployment, without dedicated depth sensors. Combining with monocular depth foundation models such as Depth Anything V2, RGB images can be enriched with dense pseudo-depth during training, turning close-range crop segmentation into a privileged-depth-guided learning problem where depth is available at training but absent at inference. Based on such close-range handheld capture, intra-foreground depth separability collapses while only the foreground–background depth gap remains partially preserved, exposing an imaging regime that we refer to as Close-Range Depth Degeneracy (CRDD) and that undermines the discriminative value of monocular depth for organ segmentation. Even with the available privileged-depth signal, existing RGB-D fusion and depth-branch hallucination routes still either introduce inference-time depth dependence or fail to retain the depth-conditioned effect inside RGB-side parameters under CRDD. How monocular pseudo-depth can serve as training-only privileged information for RGB-only close-range crop spraying under CRDD remains insufficiently studied. To this end, this paper proposes a privileged-depth modulation framework, MDM-Seg, by converting monocular depth from an inference-time modality into a CRDD-conditioned training signal to remove the inference-time depth dependence. Specifically, we characterize CRDD and propose a four-indicator depth-usability diagnostic that delivers a pre-training verdict on the target dataset, with verdicts validated against post-training segmentation outcomes. Then, we formalize the CRDD-conditioned training intervention as a depth-conditioned affine network (DepAN) that injects depth-gradient cues into decoder features, and define a depth hard-pixel mining loss (DHPM) to reweight per-pixel cross-entropy with depth-value evidence, both operating inside the main segmentation stream. Finally, we deploy MDM-Seg on RGB input alone and derive a lightweight consistency trace between the RGB-only and depth-conditioned heads, producing an image-level reliability cue for targeted-versus-fallback spraying without depth at inference. Extensive experiments on Pepper-Field-3940 demonstrate that our MDM-Seg achieves effective depth-conditioned RGB-only segmentation under CRDD, i.e., depth-conditioned modulation retained inside RGB-side parameters with no inference-time depth dependence, such as mIoU 0.8995 with the ResNet-101 configuration ( + 3.73 pp over the RGB-only DeepLabV3+ baseline), a lightweight training-side DepAN module, and an image-level reliability cue rank-correlated with segmentation quality (Spearman ρ = 0.74 ). On a Jetson Orin NX 16 GB with TensorRT FP16, the complete deployment-oriented MobileNetV2 dual-head prescription pipeline runs at 23.87 ms per image, corresponding to 41.89 FPS, 0.62 GB peak memory, and 0.56 J per image.
Why it matches plant phenotyping methods植物器官の画像セグメンテーション手法を開発・評価し、散布対象器官の状態をRGB画像から推定することが中心であるため。
abstractthis paper proposes a privileged-depth modulation framework, MDM-Seg
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:70-82Plant phenotyping relevance match · UnverifiedOpenAlex · checked 15 Sept 2026
Strawberry production in hydroponic systems requires precise and spatially explicit information on fruit load, maturity, and size to support harvest planning and quality control. This study presents an integrated computer vision and GNSS RTK framework that detects individual strawberries, estimates their maturity and physical dimensions, assigns fruits to operational size–maturity categories, and generates high-resolution yield maps in an open-field hydroponic system. RGB-D images are processed with YOLOv8-seg and a BoT-SORT-based tracking module to obtain instance-level masks, from which a color-based ripeness index and 3D point clouds are derived. After DBSCAN-based filtering, fruit length and width are computed in metric space and combined with ripeness percentage to assign each strawberry to one of nine operational size–maturity categories using predefined threshold rules. The system was evaluated in a commercial hydroponic crop in Arcabuco, Boyacá, Colombia, achieving accurate segmentation, with median IoU values up to 0.83 for bounding boxes and 0.71 for masks, and mean absolute errors of 2.51 mm in length and 1.85 mm in width with respect to Vernier caliper measurements. Yield maps aggregated in 1 m2 cells and by crop row revealed marked spatial variability in fruit density, maturity state, and size–maturity composition, allowing the identification of zones with a high concentration of fruits ready for harvest versus areas dominated by immature fruits. The proposed framework provides a practical and low-cost decision support tool for hydroponic strawberry management and may be adapted to other high-value horticultural crops after recalibration under different crop architectures, cultivars, and environmental conditions.
Why it matches plant phenotyping methodsRGB-D画像と追跡・3D解析により、イチゴ果実の成熟度、寸法、果実密度および収穫状態を個体レベルで推定し、精度検証も行う中心的なフェノタイピング手法研究である。
abstractThis study presents an integrated computer vision and GNSS RTK framework that detects individual strawberries, estimates their maturity and physical dimensions, assigns fruits to operational size–maturity categories, and generates high-resolution yield maps in an open-field hydroponic system.
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:1-68Plant phenotyping relevance match · UnverifiedEurope PMC · checked 14 Sept 2026
PotatoField / plotGrowth / time-series analysisGrowth / development / phenologyWater status / transpiration
Real-time measurement of belowground tuber growth has not been conducted in field crops. Here, a strain-gauge sensor was used to monitor potato tuber growth and estimate mean daily tuber water loss. Over the 13 days preceding harvest, tuber thickness increased by 0.90 mm, corresponding to a daily gain of 1.33 g, or a 4.8% increase. The greatest diurnal fluctuation was 0.453 mm, corresponding to a transpirational water loss of 9.4 ml, or 3% of the tuber’s water content. Daily transpiration showed a positive correlation with air temperature and vapor pressure deficit. This sensor will enable more precise input control and higher temporal resolution than current methods for below-ground crops, supporting improved crop management, yield prediction, and harvest decisions.
Why it matches plant phenotyping methods埋没ジャガイモ塊茎の成長・厚さ変動・水分損失をひずみゲージでリアルタイム測定する手法が研究の中心であり、植物器官形質の取得法として適格。
abstractHere, a strain-gauge sensor was used to monitor potato tuber growth and estimate mean daily tuber water loss.
High-throughput phenotyping (HTP) has advanced rapidly in recent decades, driven by technological developments across research and agricultural frameworks. Despite its success in measuring traits, it remains underutilized in field crop breeding programs. While the most critical and labor-intensive selection is conducted on heterozygous single plants or small plots at early stages, most phenotyping research focuses on stable genotypes grown in large plots. Here, we reconsider how HTP can be effectively integrated into breeding by accounting for methodologies, scale-related constraints, and technological limitations. Our focus remains on self-pollinated field crops, the predominant global food source. In light of climate change and food security needs, improving the integration of breeding and phenomics can accelerate genetic and technological advances in developing elite varieties.
Why it matches plant phenotyping methods圃場作物育種における高スループット表現型解析の方法論、規模制約、技術的限界を中心に論じるレビューであり、植物フェノタイピング手法の統合が主題である。
abstractHere, we reconsider how HTP can be effectively integrated into breeding by accounting for methodologies, scale-related constraints, and technological limitations.
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:1-81Plant phenotyping relevance match · UnverifiedCrossref · Europe PMC · checked 13 Sept 2026
Cassava brown streak disease (CBSD) threatens food security for millions in East Africa, yet its control remains limited by the absence of field-deployable molecular diagnostics. Here, we introduce ELLA (Electrochemical Lateral flow assay with Linked Analytics), a battery-free, smartphone-powered electrochemical lateral flow assay that delivers enzyme-linked immunosorbent assay (ELISA)-grade protein detection directly in the field. ELLA integrates near-field communication, a single-chip potentiostat, metal-pin electrodes, and ferrocene-labeled nanoparticles into a fully disposable cassette, enabling quantitative immunoassays without optical instrumentation or centralized laboratory infrastructure. Validated across laboratory studies and extensive field trials in Tanzania, ELLA achieved 95% agreement with ELISA and 89% agreement with RT-qPCR, outperforming ELISA’s limit of detection while maintaining a material cost below US$1. By coupling molecular test results with cloud-linked analytics, we further trained DeepELLA, a smartphone-based image classification model that enables scalable surveillance from field-acquired leaf images. Together, these advances unify electrochemical sensing, digital connectivity, and AI-assisted interpretation, enabling portable, ELISA-level diagnostics for plant, environmental, and health monitoring in resource-limited regions.
Why it matches plant phenotyping methods主軸は分子診断ですが、植物葉画像から病害状態を分類するDeepELLAも開発され、植物病害表現型の直接推定を含むため対象に含める。
abstractwe further trained DeepELLA, a smartphone-based image classification model that enables scalable surveillance from field-acquired leaf images
Unmanned aerial vehicle (UAV) photogrammetry offers a cost-effective approach to tree-level detection, however, Structure-from-Motion (SfM) outputs are sensitive to processing choices and site conditions, which can alter canopy representation and reduce individual-tree detection accuracy. Here, we systematically evaluate how SfM reconstruction quality and depth-map filtering influence RGB-only individual-tree detection under controlled acquisition conditions. Objectives were to (i) identify an optimal SfM-derived point-cloud configuration for delineating individual trees, and (ii) implement and test a segmentation workflow (local-maxima treetop detection plus Dalponte2016 in lidR) for detecting and counting trees. We assessed RGB-only SfM for individual-tree detection (ITD) across thirteen 1.21-ha loblolly pine ( Pinus taeda ) plots located in two counties in the state of Alabama in the southeastern United States; eight even-aged plantations and five mixed pine-hardwood stands, while holding image acquisition parameters constant. Using Agisoft Metashape Professional (Agisoft LLC, St. Petersburg, Russia), dense-cloud quality (Lowest, Low, Medium, High, Ultra High) and depth-map filtering (Disabled, Mild, Moderate, Aggressive) were varied in a 5 × 4 full-factorial design; assessment metrics included point-cloud density, canopy-surface completeness, canopy-height-model (CHM) agreement with field heights, and ITD precision/recall/F1. We identified a single high-resolution configuration (Ultra High + Disabled) by screening parameter sets for structural accuracy and suppression of false peaks. Using this configuration, CHMs matched field heights in Washington County, Alabama (R 2 = 0.96; RMSE = 0.44 m; bias = − 0.01 m) and in Cullman County, Alabama (R 2 = 0.44; RMSE = 1.14 m; bias = − 0.09 m); pooled performance was R 2 = 0.98; RMSE = 0.54 m; bias = − 0.01 m. ITD accuracy at the primary 3 m match radius yielded a precision of 0.03; recall = 0.29; F1 = 0.05 in the even-aged plantations (Washington) and a precision of 0.03; recall = 0.12; F1 = 0.05 in mixed pine–hardwood stands (Cullman); pooled F1 = 0.05. The selected parameters and workflow are reproducible and transferable, provide insight into RGB-SfM ITD performance, and indicate when lidar remains preferable for crown delineation.
Why it matches plant phenotyping methodsRGB-SfMによる個体樹の検出・樹高推定と、SfM設定およびセグメンテーションワークフローの系統的評価が研究の中心であり、植物の樹冠構造・樹高という形態形質を抽出する方法を検証している。
abstractwe systematically evaluate how SfM reconstruction quality and depth-map filtering influence RGB-only individual-tree detection
Reproduction assets foundThe paper's Code availability statement deposits the authors' SfM/ITD processing scripts publicly on OSF (DOI 10.17605/OSF.IO/UXBCZ). Phenotype/field datasets are only available on request, so they are not public assets.Code · publicThe workflow and processing scripts used in this study are publicly available through the Open Science Framework
(OSF) repository: Singh and Narine, [32]. Code Repository for Optimizing SfM Parameters for RGB-Only Individual-Tree
Detection in Loblolly Pine and Mixed Pine-Hardwood Stands. https://doi.org/10.17605/OSF.IO/UXBCZ.Open asset ↗10.17605/OSF.IO/UXBCZpdf-page:12 lines:1-70Plant phenotyping relevance match · UnverifiedCrossref · checked 5 Sept 2026
Accurate field crop counting supports phenotyping, crop monitoring, and yield-related analysis, but real field images often contain scale variation, target overlap, cluttered vegetation, shadows, and visually similar backgrounds. These factors make density-map regression difficult because weak target responses and accumulated false responses in non-target regions can both bias the final count. This study proposes Light-FCCNet, a compact multi-scale framework for accurate field crop counting under a limited parameter budget. The framework integrates three coordinated components: a lightweight feature pyramid aggregation module for compact scale-aware representation, a multi-attention fusion module for refining fused features and suppressing background-induced responses, and an FCC loss that combines pixel-level density regression, count consistency, and structural similarity. Light-FCCNet is evaluated on three public field crop counting datasets, namely GWHD, MTC, and URC. In the canonical ablation trajectory consisting of baseline, baseline_p1, baseline_p1_p2, and full configurations, the full model achieves the lowest errors, with MAE values of 13.28 on GWHD, 18.10 on MTC, and 61.23 on URC, corresponding to reductions of 18.0%, 25.3%, and 35.2% relative to the baseline. Compared with representative general counting baselines and our implementation of TasselNetV2++ under the same experimental protocol, Light-FCCNet obtains the lowest MAE on all three datasets while using only 0.92 M parameters. These results indicate that its advantage comes from the coordinated design of compact pyramid aggregation, attention-guided feature refinement, and counting-oriented supervision, rather than from any isolated module alone.
Why it matches plant phenotyping methods作物個体数を圃場画像から推定する新規CNN手法を開発し、複数データセットとアブレーションで性能検証しており、表現型取得・推定が研究の中心である。
abstractThis study proposes Light-FCCNet, a compact multi-scale framework for accurate field crop counting under a limited parameter budget.
Abstract Biotic stress is a major, yet under-quantified, driver of global soybean yield losses, and field-based phenotyping under pest pressure remains a critical bottleneck for crop improvement. Using multi-temporal data from soybean genotypes grown under insecticide-protected and unprotected conditions in Brazil, we present a UAV-based, large-scale and non-invasive framework for evaluating genotype performance under natural pest pressure. We introduce a three-dimensional metric that jointly captures productivity, feature-level similarity as a proxy for tolerance, and phenological response through days to maturity. This unified formulation enables field-based quantification of pest resilience and replaces labor-intensive and often unreliable direct pest collection and counting. To operationalize this framework, we integrate vegetation indices and self-supervised visual embeddings into a common representation space linking feature stability, performance response and phenological development. This approach enables robust identification of genotypes that maintain feature integrity, minimize developmental delay and sustain yield under pest pressure, with genotypic differences peaking during the pod-fill (R3–R4) and grain-fill (R5.1–R5.5) stages. Overall, this work establishes a scalable, field-ready paradigm for quantifying crop resilience to biotic stress and provides a practical pathway to accelerate breeding for stable yields under real-world agricultural conditions.
Why it matches plant phenotyping methodsUAVによる大規模な圃場フェノタイピング基盤と、植生指数・視覚埋め込みを統合した新しい耐虫性表現型の定量手法が研究の中心である。
abstractwe present a UAV-based, large-scale and non-invasive framework for evaluating genotype performance under natural pest pressure
Reproduction assets foundThe paper explicitly states that the analysis code is publicly available in the authors' GitHub repository (jianglong26/soybean-insect-resistance), which directly reproduces this paper's phenotyping pipeline (orthomosaic processing, VI/DINOv3 feature extraction, similarity analysis, genotype ranking). The paper also声明sCode · public540 The code used for analysis is available at https://github.com/jianglong26/Open asset ↗pdf-page:16 lines:1-45Plant phenotyping relevance match · UnverifiedCrossref · checked 5 Sept 2026
Accurate, high-throughput quantification of rice panicles is important for yield estimation and breeding-oriented rice phenotyping. However, unmanned aerial vehicle (UAV)-based panicle detection remains challenging because flight-altitude variation produces large target-scale changes. Flooded paddy backgrounds, leaf occlusion, and illumination fluctuations further obscure small panicle targets. To address these challenges, we constructed a composite multi-altitude dataset covering UAV imagery acquired from 3 to 20 m under varying field conditions. We then propose Panicle-DETR, a lightweight detection and counting framework based on a frequency-aware Cross Stage Partial (CSP) backbone. Rather than treating the Fast Fourier Transform (FFT) as a filter by itself, the proposed FasterFD module uses frequency-domain representations with learnable frequency-response reweighting to enhance panicle-related texture cues and reduce redundant background responses. A Lossless Feature Encoder is designed to preserve fine spatial information for small targets across altitude-induced scale changes, while a composite metric loss based on Normalized Gaussian Wasserstein Distance (NWD) and Inner-IoU improves localization for adherent and overlapping panicle clusters. On the composite dataset, Panicle-DETR achieved a Precision of 90.97%, a Mean Absolute Error of 4.28, and an R2 of 0.957 for single-frame panicle counting. With 13.78 M parameters and 53.0 GFLOPs, the framework achieved 16.9 FPS with 1.96 GB peak GPU memory in a battery-powered notebook benchmark, supporting its potential for resource-constrained field-side UAV image analysis.
Why it matches plant phenotyping methodsUAV画像からイネ穂の検出・計数という植物形質推定を中心に、マルチ高度データセットと専用解析フレームワークを開発・評価しているため。
abstractAccurate, high-throughput quantification of rice panicles is important for yield estimation and breeding-oriented rice phenotyping.
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:1-57Plant phenotyping relevance match · UnverifiedOpenAlex · checked 15 Sept 2026
Grapevine yellows diseases, including Flavescence Dorée (FD) and Bois Noir (BN), severely affect vineyards, making reliable detection methods essential. Detecting symptoms, particularly in Chardonnay variety, remains challenging due to year-to-year vine variability and the presence of symptoms that can be misleading. We present a dataset of multispectral images of grapevine leaves collected over four years (2021–2024). The dataset includes healthy leaves, grapevine yellows - overwhelmingly BN, and three other diseases (Esca, Discoloration, and Leafroll) with visually similar symptoms particularly for Leafroll, providing a diverse benchmark for disease recognition. Ground-truth labels were assigned based on field inspections conducted by Comité Champagne expert viticulturists who selected the vines before acquisitions and analyzed the images after acquisition. Images were acquired under laboratory conditions using a DJI Phantom 4 Multispectral camera from leaves collected in the Plumecoq Comité Champagne experimental vineyards. Leaves were collected on designated vines and placed on polystyrene boards on a 2x2 grid. One RGB image and five multispectral images corresponding to the Blue (B - 450 nm ± 16 nm), Green (G - 560 nm ± 16 nm), Red (R - 650 nm ± 16 nm), Red-Edge (RE - 730 nm ± 16 nm), and Near-Infrared (NIR - 840 nm ± 26 nm) bands were captured using the same acquisition system (camera-to-board distance of approximately 90 cm) over the four years.. For the vast majority, ambient light was used; for some acquisitions, indirect halogen spotlights were used. The 512x512 leaf images were manually cropped from the acquired original images with the same offsets between the bands; offsets were already present due to the parallax phenomenon. The dataset is organized into six folders (B, G, R, RE, NIR, and RGB). Each leaf is represented by one RGB image and five corresponding multispectral band images, enabling multimodal analysis and machine learning for grapevine disease detection. Each image filename encodes acquisition and annotation information as follows: Characters 1–2: acquisition year (21 = 2021, 22 = 2022, 23 = 2023, 24 = 2024). Character 3: image type/band (0 = RGB, 1 = B, 2 = G, 3 = R, 4 = RE, 5 = NIR). Character 4: class (J = Grapevine Yellows, T = Healthy, S = Esca, E = Leafroll, D = Discoloration). Character 5: illumination condition (0 = ambient light, G = additional left halogen spotlight, D = additional right halogen spotlight, 2 = additional both left and right halogen spotlightsl). Characters 6–9: image identifier, numbered sequentially from 0000. Character 10: relabelling status. After image acquisition, all leaves were independently reviewed by expert viticulturists on the recorded RGB images. A value of 1 indicates that the expert confirmed the original field label, 0 indicates that the original label was considered incorrect based on the information visible in the RGB image, and D indicates that the sample was reclassified as Discoloration. This dataset complements the "Multi-annual spectral data of Chardonnay grapevine leaves" dataset published on Recherche Data Gouv. While the previous dataset contains spectral measurements, the present dataset provides multispectral images acquired from the same grapevine leaves, enabling multimodal analyses that combine spectral signatures with image-based information. Note, however, that there is no bijection between the respective files.
Why it matches plant phenotyping methodsブドウ葉の病徴をマルチスペクトル画像で取得し、専門家ラベル付きの疾病認識用データセット／ベンチマークとして提供しており、植物状態の画像ベース表現型計測が中心である。
abstractWe present a dataset of multispectral images of grapevine leaves collected over four years (2021–2024).
Plant phenotyping relevance match · UnverifiedOpenAlex · Europe PMC · bioRxiv · Crossref · checked 5 Sept 2026
Abstract Understanding the link between genetic variation and observable traits is key to crop breeding. Hyperspectral imaging captures physiological and biochemical profiles, but current supervised methods require costly trait annotations and treat each observation as a static snapshot, ignoring the temporal dynamics of plant development. We introduce SST-MAE, a self-supervised framework that learns genotype-discriminative representations from plant hyperspectral developmental trajectories, without requiring phenotypic labels. The model learns to reconstruct masked information, capturing multiple growth trajectories. Validated on 194 field-grown lettuce genotypes across eight time points, the frozen encoder serves as a feature extractor for downstream genotype classification. SST-MAE outperforms raw spectral and linear baselines, achieving AUROC > 0.89 for anthocyanin pigmentation SNPs and 0.77 for leaf serration. The learned features are highly label-efficient, attaining near-full performance with only 30–50% of labeled data, offering a scalable pathway toward high-throughput genetic screening from image-based phenotypes.
Why it matches plant phenotyping methods植物のハイパースペクトル時系列から表現型関連表現を抽出する自己教師あり手法を開発し、複数遺伝子型・時点で検証しているため、表現型取得・解析手法が中心です。
abstractWe introduce SST-MAE, a self-supervised framework that learns genotype-discriminative representations from plant hyperspectral developmental trajectories, without requiring phenotypic labels.
Field / plotClassificationObject detectionTracking
1. 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. 2. 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. 3. 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 ± 0.045). 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 ± 0.062) identified solar radiation as the dominant driver of foraging activity, followed by temperature. 4. 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映像からハチの巣穴への入退出や採餌行動を自動抽出するハードウェア・コンピュータビジョン基盤を開発し、精度検証も行っているため、動物対象ではあるが植物フェノタイピングの範囲外です。
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
Plant phenotyping relevance match · UnverifiedOpenAlex · Europe PMC · checked 5 Sept 2026
Fall dormancy (FD) and forage yield (FY) are two key traits in alfalfa ( Medicago sativa L.) breeding programs. However, genetic progress has remained limited over the past decades, largely due to the complexity of alfalfa breeding and the reliance on labor-intensive phenotyping methods. High-throughput phenotyping (HTP) using unmanned aerial vehicles (UAVs) represents a promising alternative for rapid and non-destructive crop evaluation. The objectives of this study were to i) estimate FD using UAV-derived canopy height and RGB vegetation indices and ii) evaluate the predictive performance of machine learning (ML) models for FY estimation. A total of 210 alfalfa populations with diverse genetic backgrounds were evaluated over two growing seasons (2023 to 2025) across seven harvests under Mediterranean conditions in central Chile. FY was measured manually, while FD was estimated using both manual and UAV-based approaches. A total of 19 RGB-derived indices (VIs) including plant height (PH) were extracted and used as predictor variables. Five complex predictive ML models were evaluated: PLS, PCR, SVM, ANN, and MLR. The results showed that UAV-derived FD was significantly correlated with FD obtained through conventional methods ( R 2 = 0.88). The automated UAV-based FD phenotyping framework demonstrated slightly higher precision ( R 2 = 0.92) and broad-sense heritability ( H 2 = 0.69) compared to manual measurements ( R 2 = 0.87–0.89; H 2 = 0.64), providing a more reliable selection tool for breeders. Among the tested ML models, SVM and ANN achieved the highest accuracy ( R 2 ≈ 0.73) for FY prediction. These findings demonstrate that integrating low-cost RGB imagery with complex modeling offers a promising avenue that could assist in refining future selection strategies for this genetically complex species.
Why it matches plant phenotyping methodsUAV画像からアルファルファの休眠性と収量関連形質を推定する高スループット表現型解析手法を開発・検証し、手動測定との比較と機械学習モデル評価を行っているため、方法が研究の中心である。
abstractHigh-throughput phenotyping (HTP) using unmanned aerial vehicles (UAVs) represents a promising alternative for rapid and non-destructive crop evaluation.
Sustainable forest management requires inventory workflows that provide spatially explicit structural information while retaining field-based calibration and uncertainty control. This case study evaluated a field-calibrated UAV LiDAR workflow for individual-tree inventory in middle-aged and near-mature larch plantations in Chuanying District, Jilin City, China. UAV laser scanning point-clouds were integrated with six 30 m × 30 m field plots to assess three individual-tree extraction algorithms: point-cloud segmentation (PCS), marker-controlled region growing (MCRG), and region-based hierarchical cross-section analysis (RHCSA). Algorithm performance was evaluated using plot-level recall, precision, F-score, localization RMSE, tree-height and crown-width accuracy, bootstrap confidence intervals, exploratory Wilcoxon signed-rank comparisons, and leave-one-plot-out stability checks. MCRG provided the most balanced numerical performance under the tested configuration, with a mean F-score of 0.845, compared with 0.808 for PCS and 0.827 for RHCSA. However, the MCRG-RHCSA paired difference was not robust across the six plots, and the analysis should be interpreted as a dataset-specific workflow comparison rather than a universal algorithm ranking. Tree height was estimated with comparatively high accuracy, whereas crown-width estimation remained weak, indicating that vertical canopy structure was more reliable than lateral crown delineation. After calibration assessment, the workflow was applied to 157.47 ha of UAV LiDAR survey areas and generated 219,996 algorithm-based detections. These outputs are best interpreted as a spatial decision-support layer for compartment updating, density screening, and field-inspection prioritization, not as an independently verified wall-to-wall stem census.
Why it matches plant phenotyping methodsUAV LiDARによる個体樹の抽出・樹高・樹冠幅推定を中心に、複数アルゴリズムの精度比較、校正、安定性検証を行うワークフロー研究であり、植物形質取得手法が中核である。
abstractThis case study evaluated a field-calibrated UAV LiDAR workflow for individual-tree inventory
The assessment of water stress levels in plants should be essential part of precise irrigation management, and a good and quick method is useful in plant phenotyping. There are many options for this task, but the effectiveness varies between crop species and environments. Apparently open field applications face the most difficulties. This study aimed to test a large number of vegetation indices (VIs) and multivariate models based on hyperspectral reflectance data (325-1075 nm) regarding their correlation and prediction abilities to leaf stomatal conductance, relative water content (RWC), and detailed chlorophyll, and carotenoid components. Data of the abovementioned variables was collected during three consecutive growing seasons in processing tomato cultivated under different water supply regimes to provide data with varying water stress levels. Then the relation of the measured variables to 226 VIs was tested created according to the formulas collected in the Index DataBase (IDB Project, indexdatabas.de ). New VIs were also developed derived from the most important variables of the ML algorithms, customised to tomato water stress assessment. Standard normal variate and its combination with Savitzky-Golay first derivative were used for pre-processing the spectra and principal component regression (PCR), partial least squares regression (PLSR), elastic net (ENET), support vector regression (SVR), random forest (RF) and extreme gradient boosting (XGB) algorithms were tested. The newly developed indices outperformed the existing formulas, except in the case of β-carotene. The most reliable index was developed for RWC estimation; that was the difference of the reflectance on the 986 and 701 nm wavelengths. The ENET and SVR algorithms produced the best models depending on the pre-processing method. The blue, near-infrared (NIR) and green regions, respectively, were the most important regarding all models according to the variable importance analysis. The model with the best metrics was developed for chlorophyll-a (R 2 =0.82, nRMSE=11%, RPIQ=2.41), followed by RWC (R 2 =0.72, nRMSE=14%, RPIQ=2.53).
Why it matches plant phenotyping methodsハイパースペクトル反射データと多変量・機械学習モデルを用いて、トマトの水ストレス関連生理形質を推定し、新規指標も開発・評価しているため、表現型取得・推定手法が中心である。
abstractThis study aimed to test a large number of vegetation indices (VIs) and multivariate models based on hyperspectral reflectance data (325-1075 nm) regarding their correlation and prediction abilities to leaf stomatal conductance, relative water content (RWC), and detailed chlorophyll, and carotenoid components.
Apple orchard health monitoring is important for supporting timely crop management under the temperate conditions of Kashmir Valley. The present study evaluated the seasonal behaviour of four Sentinel-2-derived vegetation indices, namely the Normalized Difference Vegetation Index, Soil Adjusted Vegetation Index, Modified Soil Adjusted Vegetation Index and Enhanced Vegetation Index, in a 2 ha apple orchard at SKUAST-K, Shalimar, Kashmir, during the 2020 growing season. Sentinel-2 imagery acquired from April to September was processed using SNAP and QGIS, and mean vegetation index values were extracted for the orchard area. Monthly weather data, including average temperature and rainfall, were obtained from the on-campus meteorological observatory. Ground observations at 20 georeferenced points were used to support the interpretation of canopy development, phenological stage and visible plant health condition. All four vegetation indices showed a seasonal increase from April to July-August, followed by a decline during September-October, corresponding to canopy development, fruit maturation, harvest and senescence. Based on the monthly values presented in the study, temperature showed positive associations with the vegetation indices, with the strongest relationship observed for MSAVI, followed by NDVI and SAVI. Rainfall showed weak and non-significant associations with the indices during the study period. The results indicate that Sentinel-2-derived vegetation indices can reflect seasonal canopy dynamics in apple orchards under the studied conditions. MSAVI appeared particularly useful for representing canopy development, while field observations remained necessary for interpreting pest, disease and phenological effects.
Why it matches plant phenotyping methodsSentinel-2画像から植生指数を算出し、リンゴ樹冠の季節動態・健康状態を評価する測定ワークフローが研究の中心であり、植物状態の推定に直接用いられている。
abstractThe present study evaluated the seasonal behaviour of four Sentinel-2-derived vegetation indices
Accurate and reliable diagnosis of grape leaf diseases is essential for sustainable viticulture, enabling timely intervention, reducing economic losses, and supporting precision crop management. Although deep learning (DL) models have demonstrated remarkable classification performance, their reliability under real-world field conditions remains insufficiently explored. In particular, confidence estimates often fail to reflect true predictive correctness when models are exposed to distributional shifts, limiting their practical applicability. To address this challenge, this study proposes a confidence- and uncertainty-aware DL framework for grape leaf disease diagnosis that extends evaluation beyond conventional accuracy-based metrics. Two publicly available grape leaf datasets were employed for stratified five-fold cross-validation in binary and multiclass classification tasks, while a third independently collected dataset was reserved exclusively for leakage-free external validation. EfficientNet-B0 and MobileNetV3-Large were evaluated under four inference configurations: raw inference, temperature scaling (TempScaling), Monte Carlo dropout, and an ensemble strategy combining uncertainty estimation with calibration. External validation demonstrated that both architectures maintained discriminative capability under domain shift. Under ensemble inference, EfficientNet-B0 achieved an accuracy of 73.8%, a macro-F1 score of 73.3%, a Matthews correlation coefficient (MCC) of 0.468, and a receiver operating characteristic area under the curve (ROC-AUC) of 0.804, while MobileNetV3-Large achieved 71.8% accuracy, 71.2% macro-F1, an MCC of 0.429, and a ROC-AUC of 0.787. Despite these promising results, raw predictions exhibited substantial overconfidence, with Expected Calibration Error (ECE) values of 0.287 and 0.312 for EfficientNet-B0 and MobileNetV3-Large, respectively. TempScaling markedly improved calibration quality, reducing ECE to 0.038 and 0.042 without affecting classification performance. Ensemble inference further enhanced the balance between predictive discrimination and reliability. The results demonstrate that strong classification performance alone is insufficient for trustworthy deployment in agricultural environments. Confidence calibration and uncertainty quantification provide complementary information for identifying overconfident predictions and improving decision reliability under field variability. The proposed framework offers a reliability-oriented approach for developing trustworthy artificial intelligence systems for grape leaf disease diagnosis in precision agriculture.
Why it matches plant phenotyping methodsブドウ葉の病徴を画像から診断する深層学習手法を開発し、信頼度校正・不確実性推定と外部検証を中心に評価しているため、植物フェノタイピング手法として適格。
abstractthis study proposes a confidence- and uncertainty-aware DL framework for grape leaf disease diagnosis
Abstract Purpose of Review Ground-based 3D point cloud technologies, including static terrestrial laser scanning (TLS), mobile laser scanning (MLS), and close-range photogrammetry, are increasingly used for estimation of aboveground vegetation biomass as they provide detailed structural representations across vegetation types; however, a comprehensive synthesis of how point-cloud data are translated into biomass estimates remains lacking. This review evaluates current approaches, performance patterns, and methodological gaps in biomass estimation using 3D ground-based point clouds. Recent Findings We systematically reviewed and analyzed 160 research articles (comprising 171 device-specific studies) published until the end of 2025 (first appearing in 2010). Research was dominated by tree-based applications (74%), with limited attention to shrubs, grasslands or crops. TLS was the prevailing acquisition technology (78%), although MLS adoption is growing. Biomass estimation primarily relied on allometric equations, volume-based reconstructions (e.g., quantitative structure models, voxelizations, convex hull), and parametric regression models. Reported model performance was generally high in tree- and shrub-based studies (median R 2 > 0.8), but more variable in non-woody vegetation types. Despite rapid advances in 3D sensing, point-cloud-native deep-learning approaches remain rarely implemented in biomass estimation workflows. Summary Ground-based 3D sensing is maturing technically, yet methodological heterogeneity persists. Many workflows still depend on destructive calibration data, semi-manual preprocessing, and non-standardized modelling strategies, limiting reproducibility and cross-study comparability. Multi-sensor integration is emerging but lacks consistent upscaling frameworks. Future research should expand coverage of underrepresented vegetation types, promote standardized and automated processing pipelines, and systematically evaluate point-cloud-native deep learning architectures, both for extracting structural proxies and for assessing their capacity to estimate biomass directly.
Why it matches plant phenotyping methods3Dセンシングによる植物バイオマス推定手法を体系的にレビューし、取得技術、推定ワークフロー、性能、再現性、標準化を評価しており、表現型測定法が中心である。
abstractThis review evaluates current approaches, performance patterns, and methodological gaps in biomass estimation using 3D ground-based point clouds.
Plant phenotyping relevance match · UnverifiedCrossref · Europe PMC · checked 15 Sept 2026
Rising temperatures and changing weather conditions are accelerating the spread of plant diseases and increasing the threat to global food security. Reliable detection of leaf diseases is therefore essential to protect crop yields and ensure food quality. Deep learning has proven to be a powerful tool for classifying leaf diseases across various crops. Due to the natural variability of plants, plant diseases often appear in irregular structures. Surface unevenness, folds, or dirt particles are common in field images and can be mistakenly identified as important features by convolutional neural networks (CNNs). This is a challenge that has not been sufficiently addressed in previous studies. This study proposes a novel deep learning approach that takes into account both the specific visual characteristics of plant diseases and potential disturbances in the microstructure, such as surface irregularities or prominent leaf veins, which may mislead the model. Using stratified five-fold cross-validation on a peer-reviewed dataset, which comprises 2,801 images of radish leaves across five classes (healthy, three disease classes: mosaic virus, black leaf spot, and downy mildew, and one pest-affected class: flea beetle), the proposed method achieved an average and balanced accuracy of 99.86%, establishing a new dataset-level benchmark in the field and demonstrating its effectiveness. The results indicate that the proposed approach may provide a promising basis for future applications in agricultural field monitoring, automated sorting and post-harvest quality control, offering potential to reduce both food waste and associated costs.
Why it matches plant phenotyping methods植物の葉画像から病害状態を分類する深層学習手法の開発・交差検証が研究の中心であり、植物表現型（病害状態）の取得・推定に該当する。
abstractThis study proposes a novel deep learning approach that takes into account both the specific visual characteristics of plant diseases and potential disturbances in the microstructure
Orthoimagery derived from unmanned aerial vehicles (UAVs) has become a valuable data source for crop-growth monitoring. Individual plant-level (IPL) information enables high-throughput analyses by capturing plant-to-plant variability within fields. However, reliable IPL-based analysis requires accurate extraction of plant-specific regions, which remains challenging in soybean cultivation due to weed interference and canopy overlap. This study proposed an automatic preprocessing framework for IPL soybean growth monitoring that integrates deep-learning-based semantic segmentation with a furrow-guided region of interest (ROI) generation strategy using UAV imagery. A segmentation model was developed using combinations of RGB and multispectral orthoimagery, and a furrow line detection algorithm was designed to generate IPL ROIs aligned with crop rows. The ensemble model combining U-Net, DeepLabV3+, and SegFormer achieved the most stable performance (F1-score up to 0.94 and IoU up to 0.89). The furrow-guided ROI generation algorithm also accurately estimated crop counts, showing strong agreement with manual observations (R² = 0.90 and RMSE = 6.35). The generated IPL ROIs enabled accurate quantification of growth-related features, with strong agreement between automatically generated and manually delineated ROIs (R² > 0.90). Overall, the proposed preprocessing framework provides a practical and scalable solution for UAV-based high-throughput phenotyping in soybean and other ridge-based cropping systems.
Why it matches plant phenotyping methodsUAV画像から個体単位の植物領域を抽出し、成長形質を定量化する前処理・セグメンテーション手法が研究の中心であるため。
abstractThis study proposed an automatic preprocessing framework for IPL soybean growth monitoring that integrates deep-learning-based semantic segmentation with a furrow-guided region of interest (ROI) generation strategy using UAV imagery.
Reproduction assets foundThe authors state that the complete implementation of their IPL soybean preprocessing pipeline (semantic segmentation + furrow line detection) is publicly available on Zenodo. The annotated sample dataset, however, is only available upon request from the corresponding author, so it is not a public asset.Code · publicThe complete implementation of
this pipeline is publicly available at https://doi.org/10.5281/zenodo.21095307.Open asset ↗zenodo · 10.5281/zenodo.21095307pdf-page:7 lines:1-62Plant phenotyping relevance match · UnverifiedCrossref · checked 15 Sept 2026
Reliable ecological indicators of mangrove structure and carbon storage are essential for monitoring coastal ecosystem conditions, yet their accuracy remains uncertain in tall, structurally heterogeneous forests, where Earth observation products differ in sensor physics, spatial resolution, and acquisition dates. Here, we present a multi-scale framework to evaluate, calibrate, and improve two widely used ecological indicators of mangrove condition—canopy height and aboveground biomass (AGB)—across approximately 7000 ha of mangroves in the Marapanim estuary, northern Brazil. The framework integrates UAV photogrammetry, radar-derived digital elevation models (TanDEM-X and SRTM), and field measurements to quantify cross-scale discrepancies and identify the main sources of uncertainty affecting indicator retrieval. High-resolution UAV canopy-height models revealed exceptionally tall Avicennia forests reaching up to 53 m, among the tallest mangroves reported globally. At the local scale, mean AGB reached approximately 648 Mg ha −1 in the southern Avicennia -dominated sector and 430 Mg ha −1 in the northern mixed Rhizophora–Avicennia sector, with local maxima of ∼800 Mg ha −1 . In contrast, radar-derived products yielded substantially lower estimates of canopy height and biomass, with height differences of 8–10 m in tall and structurally heterogeneous stands. These discrepancies reflect the combined effects of sensor-dependent canopy representation, spatial averaging, and temporal mismatch between historical radar acquisitions and recent UAV observations. To improve the ecological interpretation of these products, we implemented a calibration strategy linking field and UAV measurements to satellite observations and complemented it with UAV-based three-dimensional volumetric reconstruction of individual trees as an independent structural check on allometric biomass estimates. Our results show that canopy height and AGB derived from coarse-resolution radar products can systematically underestimate mangrove structural condition and carbon storage in tall forests unless locally calibrated. Beyond documenting exceptionally tall and carbon-dense Amazonian mangroves, this study provides a transferable framework for evaluating and improving ecological indicators of forest structure and biomass in complex coastal ecosystems.
Why it matches plant phenotyping methodsUAV photogrammetry・レーダー・現地測定を統合し、マングローブの樹冠高と地上部バイオマスという植物形質の推定を評価・較正・改善する方法論が研究の中心である。
abstractHere, we present a multi-scale framework to evaluate, calibrate, and improve two widely used ecological indicators of mangrove condition—canopy height and aboveground biomass (AGB)—across approximately 7000 ha of mangroves in the Marapanim estuary, northern Brazil.
Whole plant leaf expansion (shoot expansion) under drought drives the trade-off between water saving for later grain production and canopy photosynthesis. Fine-tuning shoot expansion could therefore become a target of genetic progress for drought-prone environments. However, its components (axis production, i.e. tillering, leaf production on each axis, and individual leaf elongation) may have their own genotypic variability and plasticity under drought, making hard to calibrate crop simulation models and specify breeding targets. In this study, we focused on the genetic diversity of bread wheat and durum wheat to determine the links and trade-offs between the underlying processes of shoot expansion under drought and how it translates at the whole plant and canopy level. For that, we used non-destructive imaging both in the field and controlled condition platforms to determine their dynamics and analyze their relative contribution to the genotypic variability of whole-plant shoot expansion under drought. Results show that shoot expansion measured at plant level in controlled environment was associated with that measured at canopy level in the field, indicating that controlled phenotyping platforms can capture the genotypic variability of growth in the field. Both whole-plant and canopy expansion were associated with tillering rate. In addition, the sensitivity of shoot growth and tillering to soil water deficit were correlated, indicating that both tillering ability and sensitivity to water deficit drive the genotypic variability of shoot expansion. Overall, dissecting shoot- expansion dynamics allowed determining the links between shoot expansion traits under drought, and provides key targets in phenotyping, modelling and breeding for drought environments.
Why it matches plant phenotyping methods非破壊画像と管理環境・圃場のフェノタイピングプラットフォームを用いて、シュート伸長・分げつの動態を測定し、環境間での性能を比較しているため、表現型取得法の応用が研究の中心的要素です。
abstractFor that, we used non-destructive imaging both in the field and controlled condition platforms to determine their dynamics and analyze their relative contribution to the genotypic variability of whole-plant shoot expansion under drought.
Aims Climate change is altering northern peatland plant communities, shifting from Sphagnum mosses to vascular plants. This transition impacts ecological functions like carbon sequestration, making long-term vegetation monitoring at the site scale more critical than ever. However, current monitoring methods tend to focus on specific species or functional groups with limited spatial coverage. This study uses remote sensing to infer the spatial structure and temporal variations of peatland plant communities. Location Temperate peatland in Pyrenees Mountains, France (Bernadouze, Vicdessos). Methods Nine plots were selected across diverse microhabitats and sampled three times over the growing season of 2023 (May, June, and July). Plant species abundances were recorded, and 45 vegetation indices were derived from drone and Sentinel-2 multispectral imagery. Five vegetation indices were selected to fit a joint Species Distribution Model (JSDM) and a Random Forests (RF) model, and map species spatial distribution. Principal Coordinates Analysis (PCoA) identified plant community composition, and spatiotemporal variations were quantified in relation to environmental variables. Results Plant species occurrences could be predicted from multispectral imagery using the JSDM, with drone-based inferences (mean R 2 = 0.36) outperforming Sentinel-2 (mean R 2 = 0.29). Model performance was high for abundant species ( R 2 > 0.5), whereas predictions for rare species were less accurate ( R 2 R 2 > 0.65, P R 2 = 0.40; P R 2 = 0.04; P Conclusion This study demonstrates that drone multispectral imagery can be used to predict peatland vegetation richness and community composition and capture fine-scale heterogeneity in a small and fragmented peatland site, outperforming satellite data in spatial precision. Although our model was less accurate using satellite imagery, the use of Sentinel-2 imagery enabled long-term community tracking. By combining both, our predictive modelling framework provides a promising preliminary tool to monitor climate-induced shifts in species distributions, supporting targeted conservation.
Why it matches plant phenotyping methodsドローンおよび衛星マルチスペクトル画像から植物種の空間分布、植生多様性、群集組成を推定する画像・モデリング手法が研究の中心であり、植物状態の測定に直接結びつく。
abstractThis study uses remote sensing to infer the spatial structure and temporal variations of peatland plant communities.
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。Code · publicCodes to replicate main analyses are available at https://github.com/vjassey/peatland_vegetation_mapping .Open asset ↗vjassey/peatland_vegetation_mappinglines:369-375Plant phenotyping relevance match · UnverifiedEurope PMC · checked 5 Sept 2026
Early detection of heavy metal stress in plants is essential for effective environmental monitoring, particularly in contaminated urban areas. This study evaluated whether remote sensing combined with simplified anatomical diagnostics can provide a rapid and reliable method for detecting chromium (Cr) and nickel (Ni) stress in common urban weed species. Five species were selected: Trifolium pratense, Rumex acetosa, Alcea rosea, Amaranthus retroflexus, and Plantago lanceolata. Visible plant injuries were assessed using Evans Blue staining and image-based anatomical analysis, which enabled distinguishing between living, partially damaged, and dead cells. Multispectral observations using a MicaSense RedEdge-M camera allowed calculation of the Normalized Difference Vegetation Index (NDVI) to detect stress-related changes in photosynthetic apparatus. The studied species differed in their capacity to accumulate and translocate Cr and Ni. Metal bioaccumulation was low in all species (bioconcentration factor < 1), with the highest Ni accumulation observed in Plantago lanceolata. Translocation of both metals was the greatest in Trifolium pratense and Amaranthus retroflexus. Hydrogen peroxide levels increased in roots and leaves of all species, particularly in Alcea rosea. Despite the absence of visible injuries, microscopic anatomical changes were detected in T. pratense and R. acetosa, while NDVI values differed between sites. In summary, this study indicates that no simple relationship was found between physiological stress parameter values and NDVI. It is important to emphasize the need for continued research under controlled conditions with specific doses of PTEs salts. This should clearly demonstrate the relationship between plant physiological responses to stress and the results of multispectral observations.
Why it matches plant phenotyping methodsリモートセンシング、画像ベースの解剖診断、NDVIを用いた植物ストレス検出法の評価が研究目的として明示されており、植物状態の取得・推定が中心的です。
abstractThis study evaluated whether remote sensing combined with simplified anatomical diagnostics can provide a rapid and reliable method for detecting chromium (Cr) and nickel (Ni) stress in common urban weed species.
Plant phenotyping relevance match · UnverifiedCrossref · Europe PMC · checked 5 Sept 2026
CottonField / plotMultimodalFruitClassificationPhysiological trait estimationGrowth / development / phenology
Cotton fiber quality is shaped during boll development, boll opening, fluffing, and harvesting, but current assessment still relies largely on manual field inspection and postharvest laboratory testing. This limits timely harvest scheduling and plot-level quality management. To address this problem, we propose a self-supervised multimodal sensing framework for linking preharvest cotton boll status, environmental conditions, and postharvest fiber quality. First, the Cotton Boll Visual Phenotype Self-Supervised Encoding Module learns maturity-related visual representations by reconstructing masked image patches, so that boll cracking, lint exposure, and surface texture can be captured from unlabeled field images. Second, the Agricultural Sensor Temporal Masked Modeling Module reconstructs masked sensor observations to model temporal patterns in temperature, humidity, light, soil moisture, rainfall, and other environmental variables. Third, the Vision–Environment Cross-Modal Contrastive Fusion Module aligns image features with environmental features and produces a joint representation for downstream prediction. Field experiments were conducted using cotton boll images from different maturity and abnormal states, environmental sensor records, management information, and postharvest fiber quality measurements. The framework was evaluated for maturity classification, harvest-window recognition, and fiber quality prediction. The results showed that the proposed method performed consistently better than representative machine learning, single-modal deep learning, and multimodal fusion baselines, while few-shot and ablation experiments supported the value of self-supervised pretraining and multimodal fusion. These findings indicate that the proposed approach can provide useful information for preharvest cotton maturity assessment and harvest-quality management.
Why it matches plant phenotyping methods綿花の成熟状態を画像・環境センサーから抽出し、成熟度分類や収穫時期認識を行うマルチモーダル手法の開発・評価が中心であり、植物状態の表現型推定に該当する。
abstractwe propose a self-supervised multimodal sensing framework for linking preharvest cotton boll status, environmental conditions, and postharvest fiber quality.
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:1278-1317Plant phenotyping relevance match · UnverifiedEurope PMC · checked 5 Sept 2026
Abstract Purpose Symptom-triggered crop protection acts only after damage is committed, and the intervention window has narrowed. This review reframes pre-symptomatic sensing from a detection problem into a closed decision loop, establishing the physiological lead time of a signal, set against its detection confidence and the latency of the response it can trigger, as the organizing principle for anticipatory, site-specific decision-making. Methods A systematic-narrative synthesis was conducted across major bibliographic databases through June 2026. Studies reporting pre-symptomatic capability under field or realistic conditions were retained and coded onto a coupled lead-time × confidence × actionability framework spanning sensing, inference, and actuation. Results Optical modalities were found to dominate the evidence base, while electrophysiological and volatile signals extended achievable lead time. Single modalities were insufficient to separate biotic from abiotic stress, motivating heterogeneous fusion. Edge inference and temporal onset forecasting remained immature, detection confidence was rarely quantified, and the sensing-to-actuation loop was seldom closed. Reported performance degraded sharply from laboratory to field, particularly in perennial and smallholder systems. Conclusions A unifying Pre-Symptomatic Crop Intelligence framework is proposed, governed by the principle that system value is bounded by the weakest of lead time, detection confidence, and response latency; priorities identified include lead-time-labeled benchmarks, uncertainty-aware inference, field-robust fusion, and economic evaluation for perennial crops.
Why it matches plant phenotyping methods植物の病害・ストレス状態を早期に推定するセンシング手法を体系的に整理し、検出リードタイム、信頼度、融合推論、ベンチマークを評価するレビューであり、植物状態の取得・推定方法が中心である。
abstractThis review reframes pre-symptomatic sensing from a detection problem into a closed decision loop
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:1509-1560Plant phenotyping relevance match · UnverifiedEurope PMC · checked 5 Sept 2026
Abstract Accurate plot-level sugarcane yield forecasting is essential for optimizing agricultural management, resource allocation, and operational planning. Existing forecasting approaches are often limited by their inability to capture temporal crop dynamics and local biophysical variability, reducing their usefulness for real-time decision-making. To develop and evaluate a Machine Learning (ML)-based framework for short-term sugarcane yield forecasting at plot level using age-segmented Normalized Difference Vegetation Index (NDVI) derived from Sentinel-2 imagery, and to determine the earliest crop stage at which reliable yield predictions can be obtained. An integrated dataset was constructed by combining productivity records from 2,132 sugarcane plots across six harvest seasons (2016–17 to 2021–22) with NDVI time series derived from Sentinel-2 satellite imagery. NDVI observations were aggregated into phenology-based temporal intervals, from which statistical features were extracted. Ten ML regression algorithms were evaluated under two forecasting schemes: a global model trained with all observations and a sector-specific approach that developed localized models for individual production sectors. Model performance was assessed using RMSE and R² on an independent test set. The sector-specific approach outperformed the global model, achieving an RMSE of 12.48 TCH and an R² of 0.7840 on the independent test set, compared with an RMSE of 16.75 TCH and an R² of 0.5724 for the global model. Sparse Partial Least Squares (spls) and Support Vector Machines with Polynomial Kernel (svmPoly) were the most frequently selected algorithms. SHAP analysis revealed that Median NDVI was the dominant predictive feature, while the Elongation I stage was the most influential phenological period. Reliable forecasts were obtained from the fifth month of crop growth (RMSE = 14.13 TCH), and prediction accuracy improved progressively as the crop matured. The proposed framework also surpassed traditional expert estimations (RMSE = 15.47), providing earlier and more accurate yield forecasts. This study demonstrates that localized, sector-specific ML models combined with temporal NDVI dynamics can provide accurate and operationally useful plot-level sugarcane yield forecasts. The framework supports proactive agronomic management, improves planning and budgeting processes, and offers a scalable methodology for precision agriculture and sustainable sugarcane production systems.
Why it matches plant phenotyping methods圃場・区画レベルのサトウキビ収量という植物形質を、Sentinel-2 NDVI時系列と機械学習から推定する枠組みを開発・評価しており、予測手法が中心である。
abstractTo develop and evaluate a Machine Learning (ML)-based framework for short-term sugarcane yield forecasting at plot level using age-segmented Normalized Difference Vegetation Index (NDVI) derived from Sentinel-2 imagery
Plant diseases lead to substantial yield losses and pose a persistent threat to global food security, creating an urgent demand for high-throughput, accurate, scalable, and non-destructive disease monitoring approaches. Remote sensing has emerged as a powerful tool, yet progress in plant disease detection remains fragmented across various disciplines, tasks, sensing methods, and data modalities. This review introduces a hex- view perspective to synthesise remote sensing–based plant disease detection within a cohesive conceptual framework. Instead of treating sensing technologies, algorithms, and datasets independently, the hex-view incorporates six interconnected dimensions that jointly capture how biological processes, measurement scale, and data characteristics constrain disease detectability, including when detection is possible and how reliably it can be achieved. The hex-view framework comprises six interconnected dimensions and forms an integrated framework called BTSCAD: (1) Biology (B): Plant-pathogen interactions constituting the biological foundation of disease development and expression. (2) Task (T): The diverse disease detection tasks and their corresponding research objectives. (3) Sensor (S): The sensing modalities that define the data acquisition type and richness of captured information. (4) Condition (C): The environmental conditions, sensing platforms, and spatial scales that shape disease observations and bridge controlled experiments and real-world deployment across leaf, canopy, plot and regional scales. (5) Algorithm (A): The classical and state-of-the-art data analysis algorithms used to extract disease-related information from sensor data. (6) Dataset (D): The data sources that underpin model development, evaluation, and generalisability. The hex-view perspective provides a clear framework for interpreting previous research and identifying future research directions. This review lays a structured foundation for developing robust, interpretable, and transferable disease detection systems, supporting advancements in precision agriculture, high-throughput phenotyping, and sustainable crop production.
Why it matches plant phenotyping methods植物病害を対象としたリモートセンシングによる観察・検出法を、センサー、条件、アルゴリズム、データセットの観点から体系化する方法論レビューであり、植物状態の推定手法が中心である。
abstractThis review introduces a hex- view perspective to synthesise remote sensing–based plant disease detection within a cohesive conceptual framework.
Assessment of chlorophyll content is important to understand plant nitrogen status in precision agriculture. Traditional destructive methods for chlorophyll quantification are time-consuming, labor-intensive, and unsuitable for high-throughput phenotyping applications. The SPAD meter (Soil Plant Analysis Development) provides a rapid and non-destructive alternative by measuring leaf greenness as a proxy for chlorophyll content. Recent technological advances in imaging sensors and computational methods have enabled the development of low-cost approaches for predicting SPAD values. In this study, we propose an ensemble deep learning model-based Android application ( SPAD Predictor ) that was developed for predicting the SPAD value from RGB contact imaging. A total of 34 features, including color space features, RGB-derived features, and vegetation indices, were used to develop the model. The model consists of a lightweight Multi-Layer Perceptron (MLP) and Random Forest (RF) Regressor layer with stacking ensemble architecture. A linear regression was used as a meta-model to ensemble the MLP and RF layers. A permutation-based feature importance analysis showed that the a* channel, ExGR, RG, NRI and VARI indices played the most important roles in predicting SPAD value. The proposed ensemble deep learning model yielded R 2 t r a i n i n g of 0.987 and R 2 t e s t i n g of 0.89, RMSE of 3.25. The developed application was successfully deployed and was able to perform image submission, backend communication, prediction generation, result display, and history management. Field-level validation of the developed application yielded R 2 of 0.848, RMSE of 3.068, and MAE of 2.544. These findings indicate that the developed system has practical potential as a low-cost, field-applicable tool for estimating paddy leaf SPAD.
Why it matches plant phenotyping methodsRGB画像からイネ葉のSPAD値を推定するアプリと深層学習モデルを開発し、フィールド検証も実施しており、植物表現型取得手法が研究の中心である。
abstractwe propose an ensemble deep learning model-based Android application ( SPAD Predictor ) that was developed for predicting the SPAD value from RGB contact imaging.
Plant phenotyping relevance match · UnverifiedOpenAlex · Crossref · Europe PMC · checked 5 Sept 2026
In recent decades, global weather patterns have shifted dramatically, introducing greater unpredictability into agriculture. A major challenge in plant breeding is developing selection strategies that remain accurate under such uncertainty. Sparse testing is a well-established approach to increase the number of genotypes evaluated in field trials while keeping costs manageable. However, incorporating image-based data into sparse testing remains challenging. We developed a strategy to integrate high-throughput phenotyping data into sparse testing in potato breeding to improve predictive performance in multi-environment trials. Our approach involved constructing an environmental kernel derived from the covariance matrix of image-based data. We assessed the predictive performance of several regression models under sparse testing, including those based on genomic or phenomic data alone and in combination. Models using only the proposed environmental kernel achieved predictive accuracies comparable to, or exceeding, those of genomic prediction models in various sparse testing scenarios. The best results were observed for tuber yield, a key trait in potato breeding. These findings highlight the potential of image-based environmental kernels to improve the efficiency and accuracy of sparse testing. This approach is cost-effective and scalable, particularly useful for breeding programs with limited resources.
Why it matches plant phenotyping methods画像ベースの高スループット表現型データを環境カーネルとして構築し、ジャガイモ育種の疎試験に統合する方法が研究の中心であるため、表現型予測手法として収載する。
abstractWe developed a strategy to integrate high-throughput phenotyping data into sparse testing in potato breeding to improve predictive performance in multi-environment trials.
Accurate yield prediction for major grain and oilseed crops, including soybean, corn, wheat, and rice, is essential for food-security assessment and precision field management. This study presents a structured integrative review of UAV-based crop yield prediction and follows PRISMA-guided procedures for literature search, screening, and evidence synthesis. Seventy peer-reviewed studies published between 2018 and 2025 were synthesized within a "Data-Ground Truth-Model-Decision" framework. Beyond summarizing UAV platforms, sensor configurations, feature-engineering strategies, and model architectures, the review explicitly distinguishes among microplot, field, and regional prediction scales, and evaluates the characteristics and limitations of yield-label acquisition methods, including manual harvest, plot-combine harvest, and combine yield-monitor data. Existing evidence indicates that the reliability of UAV-based yield prediction depends not only on optimal image acquisition windows, multi-source feature fusion, and model architecture, but also on scale-consistent yield labels, spatially aware validation strategies, and clearly defined model outputs, such as plot-level scalar yield, field-scale yield maps, and regional yield estimates. Major bottlenecks include scale mismatch between UAV imagery and yield labels, error propagation during yield-map generation, limited cross-year and cross-region transferability, weak causal interpretability, and difficulties in deploying models under complex operational field conditions. Future research should emphasize scale-explicit benchmark datasets, quality-controlled ground-truth yield acquisition, UAV-satellite-ground data fusion, spatiotemporal deep learning, and edge-cloud collaborative systems that can translate prediction outputs into agronomic decisions. This review provides a practical pathway for developing robust, interpretable, and deployable UAV-based yield prediction systems for major grain and oilseed crops.
Why it matches plant phenotyping methodsUAV画像から作物の収量という植物形質を推定する手法を中心に、プラットフォーム、特徴量、モデル、検証尺度、グラウンドトゥルースを体系的にレビューしているため、方法レビューとして収載。
abstractThis study presents a structured integrative review of UAV-based crop yield prediction and follows PRISMA-guided procedures for literature search, screening, and evidence synthesis.
India’s economy is primarily based on agriculture. Agriculture has significant contribution in nation’s GDP. Food security and employment significantly influenced by agriculture. However factors like uncertain weather conditions, poor quality of seeds and plant diseases impact on agriculture productivity. Computer vision and DL algorithms are most crucial components of precision agriculture. Early detection can improve decision making, maximize pesticide use, and preserve harvests. Using CNN architectures, segmentation-based approaches, handcrafted feature-based methods, and hybrid approaches incorporating Machine Learning and Deep Learning this study seek to provide review of recent publications from 2020 to 2026. The review was carried out using a variety of publications with different datasets, methodologies, and outcomes. The findings show that DL, especially CNN and transfer learning models, performed better than machine learning techniques. It points out several significant problems, such as dataset imbalance, insufficient generalization, computing inefficiency, and a dearth of real-world data. Future research topics are also suggested which includes IoT-driven real-time solutions, lightweight architecture, domain adaption, and multimodal imaging. This review aims to develop plant disease detection technologies that are more dependable, scalable, and field deployable.
Why it matches plant phenotyping methods植物葉の病徴を画像から検出する機械学習・深層学習手法をレビューおよび実験的に扱っており、植物フェノタイピング手法が中心である。
titlePlant Leaf Disease Detection Using Machine Learning and Deep Learning: A Review and Experimental Study
Tomato (Solanum lycopersicum L.) quality grading based on visual inspection often yields inconsistent results and reduces market value. The 'Perfect Gold 111' variety presents distinct morphological traits, including a characteristic green-to-red color transition, specific calyx structure, and defect patterns such as greenback distribution and suberization. These characteristics differ substantially from internationally studied cultivars, rendering generic pre-trained models insufficient for accurate grading under the Thai TACFS 1503–2007 standard. This study developed an automated grading model for 'Perfect Gold 111' tomatoes using a deep learning model based on a flow-based (node-based) architecture integrated with the Robot Operating System (ROS) framework and implemented on the CiRA CORE platform. A total of 220 samples were collected and graded according to the TACFS 1503–2007 standard. Top and side-view images were used to create a dataset comprising 165 tomatoes for training and 55 for testing. Model performance was evaluated using Precision, Recall, F1-Score, and Accuracy, and was compared with manual grading performed by farmers. The AI model achieved 80.00% of accuracy, outperforming farmer grading, which achieved 52.72% accuracy. In addition, the model reduced misclassification among visually similar grades and provided consistent, quantitative assessments of color, shape, and defects. These findings highlight the potential of AI-based grading systems to improve quality consistency, reduce labor, and support automated postharvest sorting for both smallholder and industrial tomato production.
Why it matches plant phenotyping methodsトマトの色・形状・欠陥という観察可能な器官形質を画像から抽出し、深層学習による自動等級判定法を開発・検証しているため、植物フェノタイピング手法が中心です。
abstractThis study developed an automated grading model for 'Perfect Gold 111' tomatoes using a deep learning model based on a flow-based (node-based) architecture integrated with the Robot Operating System (ROS) framework and implemented on the CiRA CORE platform.
Artificial intelligence (AI) has emerged as a transformative tool for plant health monitoring, offering new opportunities for scalable, timely, and data-driven pest and disease management in agriculture. This review provides a comprehensive synthesis of AI-based methods for pest and plant disease detection, systematically organizing existing literature across sensing modalities, learning paradigms, and deployment scales. We distinguish between population-level pest monitoring, plant-centric visual inspection, and field-scale surveillance, as well as between post-symptomatic disease recognition and pre-symptomatic detection enabled by spectral imaging technologies. Beyond summarizing recent advances, this work places strong emphasis on critical analysis, discussing fundamental limitations related to data scarcity, domain shift, generalization under field conditions, and the challenge of disentangling biotic from abiotic stress factors. The review further examines the distinction between correlation-driven AI predictions and causal disease understanding, positioning AI as a complementary decision-support tool alongside established diagnostic methods. Building on these insights, we outline key future research directions, including multimodal sensor fusion, explainable and trustworthy AI, edge-based deployment for real-time monitoring, and the development of foundation models for unified agricultural intelligence. This review aims to serve as both an accessible entry point and a critical reference for advancing AI-driven plant health management.
Why it matches plant phenotyping methods植物の病害・害虫状態を画像・スペクトルなどで検出するAI手法を対象としたレビューであり、植物状態の取得・推定手法が中心である。
titleA Review on Artificial Intelligence Methods for Plant Disease and Pest Detection
Film mulching can promote maize canopy development by altering soil thermal conditions. However, commonly used air-temperature-based growing degree days (GDDs air ) may not adequately reflect mulch-induced soil warming or the effects of biodegradable film degradation on leaf area index (LAI) dynamics. To improve unified simulation of maize LAI under different film mulching conditions, field experiments were conducted in 2023 and 2024. Five treatments were established: 0.006, 0.008 and 0.010 mm biodegradable films (DM1, DM2 and DM3, respectively), a 0.010 mm conventional plastic film (PM), and a no-mulching control (CK). The compensation of increased soil temperature for air-temperature-based thermal accumulation during early maize growth was quantified. Modified Logistic LAI models were then developed using days after emergence (DAEs), GDDs air , soil-temperature-compensated growing degree days (GDDs stc ), and normalized GDDs stc (NGDDs stc ) as driving variables. The models were calibrated with observations from 2023 and independently validated with observations from 2024. The compensation effect acted through mulch-induced increases in 0-10 cm soil temperature during early maize growth and was stronger at the seedling stage than at the jointing stage. Compared with DM1 and DM2, daily compensation values were higher by 0.25-0.78 °C under DM3 and by 0.26-0.76 °C under PM. Independent validation showed that the GDDs stc -driven model had lower prediction error than the DAEs- and GDDs air -driven models. The NGDDs stc -driven model performed best; its RMSE values were 17.61%, 15.17% and 10.91% lower than those of the DAEs-, GDDs air - and GDDs stc -driven models, respectively. These results indicate that incorporating mulch-induced soil temperature compensation into the thermal time scale can more accurately represent maize canopy development under film mulching conditions.
Why it matches plant phenotyping methodsマルチ処理下のトウモロコシLAIという植物形質を推定するモデルを開発し、別年データで独立検証しており、形質推定手法が中心である。
abstractModified Logistic LAI models were then developed using days after emergence (DAEs), GDDs air , soil-temperature-compensated growing degree days (GDDs stc ), and normalized GDDs stc (NGDDs stc ) as driving variables.
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:526-568Plant phenotyping relevance match · UnverifiedCrossref · Europe PMC · checked 5 Sept 2026
Abstract This paper presents a novel medium-adaptive wideband near-field antenna for early detection of internal cavities in plant stems, including branches and small trunks. Unlike conventional antennas designed for free-space operation, the proposed antenna is explicitly engineered to operate in close proximity to a lossy, anisotropic, and dispersive cylindrical medium representing wood tissues. A physics-based electromagnetic model of the stem is incorporated into the design process, enabling accurate optimization under realistic dielectric loading conditions. The antenna consists of a compact quasi-planar dipole with blended arms integrated with a medium-adaptive dual-ring balun that ensures balanced current excitation and stable impedance matching under strong near-field loading. Both simulation and experimental measurements demonstrate wideband impedance matching to a 50 Ω source over the 2.0–3.0 GHz frequency range. Surface current distribution and specific absorption rate (SAR) analyses confirm efficient electromagnetic coupling into the stem tissues with minimal radiation leakage. To evaluate the sensing capability of the proposed design, a conceptual two-element antenna system is introduced as a feasibility study for cavity detection. The detection performance is assessed through a sensitivity-driven framework based on variations in both self- and mutual-scattering parameters. A comprehensive sensitivity analysis is conducted to quantify the response of the system to changes in cavity diameter, radial position, and angular location. The results demonstrate that while the reflection coefficient is primarily sensitive to near-surface inhomogeneities, the mutual coupling between antenna elements provides strong and reliable sensitivity to internal cavity characteristics. Based on the sensitivity analysis, an optimal operating frequency band centered at 2.76 GHz and an appropriate antenna clearance are identified to maximize detection performance. The proposed antenna and sensing methodology are further validated through experimental measurements, confirming the consistency with numerical results. Simulation results demonstrate cavity-detection sensitivity, while experimental measurements validate the antenna impedance matching and mutual-coupling characteristics. The compact geometry of the antenna enables scalable multi-element configurations, establishing a practical framework for non-destructive, microwave-based monitoring of internal tree degradation in agricultural and forestry applications.
Why it matches plant phenotyping methods植物茎内の空洞という状態をマイクロ波で非破壊検出するアンテナとセンシング手法を開発し、シミュレーションおよび実験で検証しており、植物フェノタイピング手法が中心である。
abstractThis paper presents a novel medium-adaptive wideband near-field antenna for early detection of internal cavities in plant stems, including branches and small trunks.
Plant phenotyping relevance match · UnverifiedOpenAlex · Crossref · Europe PMC · checked 5 Sept 2026
Here, we present a single-operator push-cart platform equipped with a 16-beam LiDAR. A push-button interface controls data acquisition, and the data processing pipeline removes ground points, filters noise, performs 5-cm voxelization, and produces plot-level canopy metrics. We validated biomass estimation in hairy vetch (Vicia villosa) and corn (Zea mays) leaf- and whole-plant thinning experiments. In vetch, voxelized estimation of plant volume correlated strongly with destructively measured biomass (r2 = 0.88), showing that the multi-beam LiDAR can produce biomass estimates comparable to previously reported methods. In corn, comparisons of perpendicular (0°) and multi-angle LiDAR beams showed significantly greater voxel counts in the upper canopy when angled beams were used (beam angle × height interaction, p < 0.001), demonstrating that multi-beam scanning provides greater penetration into the upper canopy than a single perpendicular scan plane. We also extended the suite of LiDAR-derived traits to include apparent leaf area index (LAI), mean tilt angle (MTA), persistent homology-based stand density, and plot-bounded foliage area density (FAD). The persistent homology algorithm distinguished between leaf-removal and plant-removal treatments (removal type × removal amount, p = 0.0039). LiDAR-derived LAI has been used to estimate canopy leaf area, but gap-fraction approaches do not fully exploit the ability of LiDAR to resolve distance. Plot-bounded FAD used ray length and interception distance within defined plot volumes and was more sensitive to plot-level treatments than apparent LAI or MTA, detecting differences associated with both the removal amount and removal type. These results show that a robust, portable, multi-beam LiDAR cart can reproduce plot-level canopy measurements and improve trait especially in research-sized plots.
Why it matches plant phenotyping methods携帯型マルチビームLiDARプラットフォームと処理パイプラインを開発・検証し、バイオマス、LAI、葉面積密度などの作物形質を推定しているため、フェノタイピング手法が研究の中心である。
titleA Single-Operator Push-Cart Multi-Beam LiDAR Platform for Multi-Trait Field Phenotyping
Phenotyping stomatal traits and their developmental plasticity is time-consuming but holds potential to improve water use efficiency and photosynthesis for designing stress-tolerant crops under climate change. Here, we develop a robust, high-throughput pipeline for phenotyping 14 stomatal traits in winter wheat related to size, variation, maximum conductance, and spatial patterning. We (1) analyze over 25,000 images from 60 wheat cultivars grown in growth chamber, greenhouse, and field conditions; (2) investigate the impact of light, temperature, and reduced water and nitrogen supply on stomatal traits and their developmental plasticity across adaxial and abaxial surfaces; and (3) evaluate genetic diversity and breeding progress of stomatal traits. Stomatal traits were highly broad-sense heritable, were largely plastic in response to environmental conditions, and showed genotype-specific responses. Stomatal traits of third leaves under controlled environments with stable light and temperature conditions reliably captured the genetic variance of flag leaves under field conditions. Our data suggests that the upper leaf surface contributed more to transpiration and cooling through consistently higher stomatal density, area, and maximum conductance, while the lower surface facilitated CO₂ diffusion via systematic proper patterning and spacing. Breeding maintains the genetic diversity of stomatal traits, and our pipeline facilitates breeders to target them to enhance water use efficiency in high-yielding modern cultivars.
Why it matches plant phenotyping methods高スループットで14種類の気孔形質を抽出するパイプラインを開発しており、植物フェノタイピング手法が研究の中心である。
abstractwe develop a robust, high-throughput pipeline for phenotyping 14 stomatal traits in winter wheat related to size, variation, maximum conductance, and spatial patterning.
Reproduction assets foundThe paper's Data and code availability section states that all data are publicly available in a Zenodo repository and that the stomatal identification and trait quantification code is in the authors' public GitLab repository. Both URLs appear verbatim in the supplied blocks and match allowed_urls. The Zenodo DOI in theCode · publicThe code for all the programs in this paper, including the stomatal identification and trait quantification, can be found in our GitLab repository, https://scm.cms.hu-berlin.de/intensive-plant-food-systems-public/2026-mabrouk-stomatal-phenotyping .Open asset ↗intensive-plant-food-systems-public/2026-mabrouk-stomatal-phenotypinglines:197-215Plant phenotyping relevance match · UnverifiedOpenAlex · Crossref · checked 15 Sept 2026
The selection of genotypes adapted to water stress requires experimental facilities that allow environmental control without compromising physiological and yield relevance. The objective of this study was to design and validate an outdoor phenotyping semi-controlled platform, PlaFe, which comprised sixty-two high-volume prismatic lysimeters arranged in rows 1.2 m long and spaced 0.6 m apart. Soil water dynamics were monitored weekly using a weighting system. To validate PlaFe, two soybean genotypes were exposed to two water scenarios for forty days from R2 + 7d, during two growing seasons. Two irrigation treatments were applied: irrigation to keep soil water content over 60–70 % of field capacity (EH0), and irrigation equivalent to 35 % of that applied in EH0 (EH1). Water consumption, crop biomass, and pod number were determined at maturity. On average, water stress reduced both biomass and pod numbers by 40 %. However, reproductive efficiency varied among genotypes. Canopy temperature increased by 0.56 °C as daily water consumption decreased, demonstrating its potential to assess drought. These results demonstrate PlaFe’s potential for the accurate evaluation of crop response and adaptation to diverse water scenarios without compromising the complex plant-environment interactions inherent to field conditions.
Why it matches plant phenotyping methodsPlaFeという屋外半制御型フェノタイピングプラットフォームを設計・検証しており、植物の水消費、バイオマス、莢数、群落温度などの表現型評価が研究の中心である。
abstractThe objective of this study was to design and validate an outdoor phenotyping semi-controlled platform, PlaFe
Context Precision agriculture can benefit from within-field boundary line analysis (BLA) to identify the most limiting factors impacting crop yield. In this study, the BLA was applied at the within-field scale using yield monitor data and key environmental factors, including evapotranspiration (ET), elevation, and the apparent soil electrical conductivity (ECa). Aims We aimed to develop and evaluate a novel BLA method to estimate Yp and quantify Yg at the within-field scale, and to assess the diagnostic potential of freely available proxy variables for identifying spatially variable yield-limiting factors in dryland wheat production. Methods We combined Mahalanobis distance-based filtering for data denoising with 2Dl kernel density estimation (KDE) and percentile thresholding to select high-density, high-yield points that define the upper yield envelope. A generalised additive model (GAM) was then used to produce the boundary line through these selected points to represent the Yp. Key results Results from the two case studies showed that this approach was robust and less sensitive to noise and outliers in fine-scale datasets. Freely available ET and elevation could be proxies to highlight the impact of some limiting factors, such as frost events or waterlogging. The ECa could identify areas where some potential soil-related factors (e.g. lower clay content reducing plant available water capacity) could be the limiting factors. Conclusions While the proxy variables effectively indicated potential limiting factors, ground-truth validation is required to confirm the underlying causal mechanisms. Implications Growers could benefit from the BLA approach to identify local yield constraints, estimate site-specific Yp and Yg, and fine-tune their inputs, leading to more efficient resource use and improved profitability.
Why it matches plant phenotyping methods作物収量という植物形質を推定する境界線分析法を開発・評価し、ノイズ除去、KDE、GAMによるワークフローを中心的に提示しているため。
abstractWe aimed to develop and evaluate a novel BLA method to estimate Yp and quantify Yg at the within-field scale
This research introduces a multimodal deep learning framework for early detection of plant pathogens to capture pre-symptomatic biochemical changes in plants while simultaneously modeling the environmental drivers of disease development. A hybrid fusion architecture combines 3D convolutional neural networks for spatial-spectral feature extraction from HSI cubes with transformer-primarily based temporal modeling of climate sequences. Cross-modal attention mechanisms dynamically weight discriminative features, which includes chlorophyll degradation bands and humidity thresholds, to permit joint representation learning. The framework achieved 94.5% accuracy in pathogen detection, outperforming unimodal HSI (84.1%) and climate- only (76.5%) baselines by 10-18 percentage points. Moreover, it detected fungal infections 5-7 days before visual symptom onset and had a 12.3% higher F1-rating compared to the current methods. Field simulations showed that precision application resulted in 41% reduction in fungicide use. By connecting proximal sensing with climatic analytics, this research contributes to precision agriculture by providing timely and eco-friendly pest control of diseases. The multimodal fusion framework is introduced to overcome the limitations of unimodal approaches. It integrates the most appropriate data sources, thus allowing the earliest and most accurate detection of plant pathogens.
Why it matches plant phenotyping methods植物の病害状態をハイパースペクトル画像から抽出するマルチモーダル手法の開発・評価が中心であり、単なる病原体診断や農薬施用試験ではない。
abstractThis research introduces a multimodal deep learning framework for early detection of plant pathogens to capture pre-symptomatic biochemical changes in plants
Plant phenotyping relevance match · UnverifiedOpenAlex · Europe PMC · bioRxiv · checked 15 Sept 2026
Abstract Flower-visiting insect populations are declining since the 1990s, especially because of the decrease of floral resources in agricultural settings. Mass flowering crops can help increase resource availability, and plant breeding can be directed towards selecting varieties attracting more flower-visiting insects. This requires the implementation of an automated high-throughput phenotyping tool for assessing the attractiveness of plant genotypes to flower-visiting insects. In this study, ( i ) we present a procedure to take standardized images of sunflower heads with camera traps continuously at day and night in the field; ( ii ) we trained two versions of a deep learning model, named PolliCrop, to automatically detect and identify the three insect classes visiting the most sunflower (non- Bombus bees, bumble bees, lepidopterans); ( iii ) we assessed and validated the ability of PolliCrop to correctly predict the true visitation frequencies of the insect classes on three sunflower genotypes; ( iv ) we presented two statistical approaches to compare the insect visitation frequencies between plant genotypes, one including weather variables, and the other one without. One PolliCrop version yielded satisfying performance to correctly detect the three insect classes. In particular, it correctly predicted the insect visitation frequencies on two sunflower genotypes in a range of ±10%. The other PolliCrop version can be useful in certain contexts of images and objectives. PolliCrop can be extended in the future to other crop species by training PolliCrop on new images captured in these crops. The field experimental design to set up for comparing the attractiveness between genotypes is also discussed.
Why it matches plant phenotyping methods植物遺伝型の花への訪花昆虫誘引性を推定する画像取得・深層学習パイプラインを開発し、訪花頻度の予測性能も検証しており、表現型取得法が中心である。
abstractwe present a procedure to take standardized images of sunflower heads with camera traps continuously at day and night in the field
0. Morphological traits such as floral area and body size are fundamental to ecological research, serving as inputs for studies of pollinator–plant interactions, habitat quality, and biodiversity monitoring. However, accurately measuring these traits from images remains challenging, particularly in complex field conditions where existing tools exhibit reduced accuracy and limited generalizability across taxa. We present EcoMorph, a modular morphological measurement system that leverages the Segment Anything Model 3 (SAM3) to quantify traits across diverse ecological contexts. Unlike task-specific segmentation models requiring domain-specific training data, SAM3’s prompt-based architecture enables segmentation of arbitrary biological structures from natural-language prompts, using the same underlying model across flowers, insects, and other targets without retraining. From the resulting segmentations, EcoMorph extracts three classes of measurement: area, linear dimensions, and object counts. We validated EcoMorph across two ecological scales. At the intermediate scale, EcoMorph-derived floral area agreed closely with manual ImageJ measurements (R 2 = 0.935, n = 74) under simple-background conditions and (R 2 = 0.928, n = 58) under complex-background conditions, with valid predictions for 95% of images. At the fine scale, EcoMorph-derived insect body area was strongly correlated with hand-measured intertegular distance (r = 0.810, n = 349), capturing body-size variation across species from the small Bombus impatiens to the large Xylocopa virginica . Object counts matched manual counts almost exactly for well-separated insects in an insect box (R 2 = 0.9997, n = 12). By combining prompt-based segmentation with modular measurement, EcoMorph enables high-throughput quantification of area, size, and abundance from heterogeneous image sources without taxon-specific training. This generality supports a broad range of ecological applications, including pollinator and plant trait research, biodiversity and abundance monitoring, and allometric biomass estimation.
Why it matches plant phenotyping methods画像から花の面積など植物形態形質を抽出する汎用システムを開発し、手動測定との一致で検証しており、植物フェノタイピング手法が中心である。
abstractWe present EcoMorph, a modular morphological measurement system that leverages the Segment Anything Model 3 (SAM3) to quantify traits across diverse ecological contexts.
Reproduction assets foundThe paper's Data and code availability statement provides a public Zenodo deposit containing the validation datasets and code used for the EcoMorph phenotyping measurements (floral area, insect morphometrics, counts), plus a public web deployment of the EcoMorph software itself.Code · publicValidation datasets and code are available here on Zenodo
https://zenodo.org/records/20980236.Open asset ↗Zenodo · 20980236pdf-page:2 lines:1-54Plant phenotyping relevance match · UnverifiedOpenAlex · checked 15 Sept 2026
Urban forest health may be monitored and supported with the implementation and maintenance of an accurate community tree inventory. The longitudinal recording of a tree’s attributes (i.e. diameter and height) may inform potential inputs and activities related to maintenance, health, and the establishment of a tree protection zone. Urban tree inventories feature barriers to implementation including resources (i.e. labour, time, and finances), competing priorities, and gaps in knowledge. The objectives of this case study were to investigate the feasibility of structure-from-motion (SfM) approaches to measure tree height and trunk diameter (1) with oblique RGB imagery, (2) with and without GCP, and (3) during leaf-off and leaf-on conditions. Structure-from-Motion datasets were obtained using Unoccupied Aerial Systems (UAS) – “drones” and related components – to collect oblique aerial imagery, which was processed with photogrammetry software Agisoft Metashape. Tree height measurements using leaf-on imagery (R2 = 0.58, RMSE = 1.34 m) were more accurate when compared to leaf-off imagery with Ground Control Points (GCP) (R2 = 0.47, RMSE = 3.41 m) and leaf-off imagery without GCPs (R2 = 0.43, RMSE = 3.49 m). Tree height measurements during the leaf-off period had no significant difference when comparing imagery with and without GCPs. Trunk diameter measurements using leaf-off imagery were not significantly different with the use of GCPs (R2 = 0.68, RMSE = 6.39 cm) compared to those without (R2 = 0.68, RMSE = 7.85 cm). This case study highlights the applicability and accuracy of Unoccupied Aerial Systems and Structure-from-Motion methods when collecting important urban tree inventory parameters, and presents an accessible, reliable, and replicable workflow for urban forestry practitioners with limited photogrammetry-related experience.
Why it matches plant phenotyping methodsUAS-SfMフォトグラメトリによる樹高・幹径という植物形態形質の推定法を開発・比較検証し、精度と再現可能なワークフローを評価しているため、方法が中心的です。
abstractThe objectives of this case study were to investigate the feasibility of structure-from-motion (SfM) approaches to measure tree height and trunk diameter
Plant phenotyping relevance match · UnverifiedOpenAlex · Europe PMC · Crossref · checked 5 Sept 2026
Abstract Precision field management and high-throughput plant phenotyping increasingly rely on remote sensing to capture spatial and temporal variability in crop performance. Unmanned aerial vehicle (UAV) – based sensing offers unique advantages for field-scale data collection, including high spatial resolution, flexible deployment, and scalable throughput. However, the full potential of UAV platforms remains constrained by labor-intensive operations across flight execution, data transfer, and processing workflows. This study presents a systematic evaluation of an automatic UAV-based crop sensing platform through a season-long, multi-crop field experiment. Data acquisition was conducted over a maize irrigation trial and a soybean breeding experiment, resulting in 176 completed flights over 28 days during the growing season. High-frequency flights on selected days captured diurnal dynamics in key canopy traits, including maize leaf rolling under drought stress and genotype-dependent plot temperature variation in soybean. In the maize irrigation experiment, significant differences in diurnal canopy cover ratio (CCR) were observed among irrigation treatments. The predictive relationship between CCR and final grain yield strengthened throughout the day, with the coefficient of determination (R 2 ) increasing from 0.05 in the early morning (RMSE = 3.05 Mg ha − 1 ) to 0.65 at midday (RMSE = 1.87 Mg ha − 1 ), highlighting the importance of temporal optimization in UAV-based sensing. Temperature measurements from the onboard thermal infrared camera showed a strong overall linear correlation with ground truth measurements (R 2 = 0.85). In the soybean trial, the highest plot temperature was observed on the fast-wilting genotype. Additionally, regression models were developed to estimate key crop traits, including canopy height (CH) and leaf area index (LAI), demonstrating the platform’s quantitative sensing capability. Overall, this study demonstrates that automatic UAV systems enable high-temporal-resolution crop monitoring while substantially reducing operational cost. The results highlight their potential for precise crop management and scalable field phenotyping. Future work will focus on integrating automated data processing pipelines to support near-real-time analytics and decision-making.
Why it matches plant phenotyping methods自動UAVのRGB・熱画像センシング platform を圃場で系統的に評価し、温度・キャノピー被覆率・高さ・LAIなどの植物形質を定量化しているため、フェノタイピング手法が研究の中心である。
abstractThis study presents a systematic evaluation of an automatic UAV-based crop sensing platform through a season-long, multi-crop field experiment.
ABSTRACT While whole-genome sequencing captures millions of single nucleotide polymorphisms (SNPs) and hyperspectral imaging (HSI) enables non-destructive plant phenotyping, integrating these modalities to link genotype to phenotype remains challenging due to their high dimensionality and non-linearity. This study presents DeepPheno a deep learning framework that predicts SNP genotypes from HSI data, using model predictability as a proxy for genotype-phenotype association. HSI data were acquired from 194 lettuce genotypes under field conditions. HSI data patches (20×20 pixels × 224 spectral bands) were used to train a hybrid CNN to predict the variant of a specific SNP. The framework was validated on SNPs with known phenotypic effects (anthocyanin, leaf serration, pale pigmentation), achieving high predictive performance (AUC ranging from 0.806 to 0.935), whereas models trained on randomly shuffled labels performed at chance (mean AUC ≈ 0.51). Extending the workflow to 50 randomly selected putatively neutral SNPs, most yielded low predictability, but two showed high performance (AUC > 0.76), suggesting uncharacterized genotype-phenotype links. Explainable AI, including SHAP and Grad-CAM, identified relevant spectral and spatial features driving these predictions, particularly the green and red-edge wavelengths associated with pigment dynamics and leaf structure. These results establish a framework for understanding complex genotype-phenotype interactions in plants and extracting these links from HSI data without predefining the exact trait values. It provides an avenue for high-throughput trait discovery and description and extends the integration of image-based phenomics with plant genetics.
Why it matches plant phenotyping methodsHSIと深層学習を統合し、遺伝子型関連の植物表現型情報を抽出する枠組みを開発・検証しており、フェノタイピング手法が研究の中心です。
abstractThis study presents DeepPheno a deep learning framework that predicts SNP genotypes from HSI data, using model predictability as a proxy for genotype-phenotype association.
Reproduction assets foundThe paper's Data Availability statement deposits authors' code, scripts, and supplementary material in a public GitHub repository, including a downscaled de-identified sample dataset demonstrating the pipeline. The raw HSI/genotype datasets are proprietary under NDA and not public.Code · publicThe code, scripts, and supplementary material supporting the findings of this study have been deposited in the GitHub repository at https://github.com/frankgyan/Utrecht-University--HSI .Open asset ↗frankgyan/Utrecht-University--HSIlines:195-223Code / 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 · checked 14 Sept 2026
Sweet potato is a nutritionally valuable crop that contributes to food security, owing to its storage roots rich in starch, sugars, and antioxidants, while requiring minimal cultivation inputs. Estimating its yield based on visible above-ground traits remains challenging due to weak and inconsistent correlations between shoot biomass and storage root development. Therefore, direct assessment of underground biomass is essential. In this study, we demonstrate the field application of ground penetrating radar (GPR) for non-destructive detection and yield estimation of sweet potato. GPR is a geophysical technique that typically transmits ultra high frequency radio waves into the soil and records reflections from subsurface objects. Electromagnetic wave simulations within the soil-root system revealed GPR signals that strongly correlate with root length, forming the basis for yield quantification. We developed an image-processing pipeline comprising static correction, gain adjustment, noise filtering, and hyperbola segmentation via the Hough transform to enable semi-automated storage root detection from GPR data. By integrating detection and quantification approaches, a linear regression model predicting sweet potato yield from GPR signals achieved moderate accuracy ( R 2 = 0.567, normalized RMSE 0.190). We established a non-destructive and low-labor approach for monitoring root systems, providing a foundation for rapid, scalable, and field-ready yield estimation in sweet potato and other root and tuber crops.
Why it matches plant phenotyping methodsGPRによる地下貯蔵根の検出・定量化と収量推定を中心に、信号処理および画像処理パイプラインを開発・評価しているため、植物フェノタイピング手法として収載する。
abstractWe developed an image-processing pipeline comprising static correction, gain adjustment, noise filtering, and hyperbola segmentation via the Hough transform to enable semi-automated storage root detection from GPR data.
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。Code · publicThe datasets analyzed during the current study consist of GPR line scans of the field at ALRC and list of sweet potato storage root weights. These data are available together with the analysis scripts on GitHub under open access. All data and scripts are the property of NARO and are distributed under the Creative Commons Attribution-NonCommercial 4.0 International License (CC BY-NC 4.0). The repository can be accessed at: https://github.com/mtei1/GPRScript.Open asset ↗mtei1/GPRScripthtml-lines:240-264Plant phenotyping relevance match · UnverifiedEurope PMC · checked 5 Sept 2026
Introduction Maize is one of the most important food crops in the world, and foliar diseases can lead to significant yield losses if identification is not performed on time. Experts conducting manual inspections find it less effective and more subjective. Deep learning-based approaches utilizing Convolutional Neural Networks (CNNs) and Vision Transformers (ViTs) have been demonstrated as a viable approach to automate disease diagnosis. Thus, while CNNs fail to capture wider context due to their local feature focus and ViTs need larger datasets and tend to miss finer-grained details. To overcome these limitations, we present EDISP a hybrid framework that connects Convolutional Neural Networks (CNNs) and Vision Transformers (ViTs) for local feature extraction, as well as global contextual learning. Methods The EDISP framework brings together the strengths of CNNs and ViTs to overcome their individual weaknesses. It is trained on a dataset that includes both controlled-environment and real-field maize leaf images, which helps it handle different environmental conditions. The data undergoes thorough preprocessing, including normalization, augmentation, and stratified splitting into training, validation, and test sets to support generalization. The CNN focuses on detailed local disease features, while the ViT captures broader contextual information across the maize leaf surfaces. Results The proposed EDISP model significantly outperforms standalone CNN and ViT Models in multiple performance metrics, achieving an overall classification accuracy of 99.40%, precision of 99.43%, recall of 99.38%, and an F1-score of 99.40%. Experimental results demonstrate that EDISP excels in identifying maize leaf diseases, including Common Rust, Gray Leaf Spot, Northern Leaf Blight, and Healthy leaves, with minimal false positives and negatives. External validation with an independent dataset further highlights the model's robustness and ability to generalize to real-world conditions. Discussion The EDISP hybrid architecture, integrating CNNs and ViTs, provides a stronger method for accurate, automated maize leaf disease detection. Its robust performance, consistent results on controlled and field datasets shows robustness in diverse environments. However, EDISP's effectiveness may be limited by image quality, lighting, or disease types not seen in training. These results highlight the promise of hybrid deep learning in precision agriculture and offer a scalable solution for disease detection, supporting farmers without expert diagnostic resources.
Why it matches plant phenotyping methodsトウモロコシ葉の病害状態を画像から検出・分類するCNN-ViT手法の開発と独立データセットによる検証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。
abstractwe present EDISP a hybrid framework that connects Convolutional Neural Networks (CNNs) and Vision Transformers (ViTs) for local feature extraction, as well as global contextual learning.
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:251-268Plant phenotyping relevance match · UnverifiedEurope PMC · checked 5 Sept 2026
This paper presents a method to estimate apple tree flower cluster count using image analysis techniques. The main research question is how accurately flower clusters on apple trees can be counted using a camera-based approach and weakly-supervised learning, compared to traditional visual estimation. A camera is used to capture images of blooming apple trees from two sides. These images are processed by a weakly-supervised model based on a ResNet feature extractor and a feature pyramid network serving as the feature aggregator. The model is trained and validated using reference data obtained through manual flower cluster counts in the orchard and from estimations based on camera images. The model was trained using field-validated data and visually-estimated data, enabling a comparative evaluation. The proposed model surpassed conventional image segmentation methods in estimating both manually counted and visually estimated flower clusters. The proposed method achieves a relative error of 10.26% in estimating flower cluster quantities, demonstrating its effectiveness and improved accuracy over traditional approaches. Its reliance on field-validated reference data adds to its robustness and practical relevance.
Why it matches plant phenotyping methodsリンゴ樹の花房数という植物形質を、カメラ画像と弱教師あり学習で推定する手法の開発・検証が研究の中心であるため。
abstractThis paper presents a method to estimate apple tree flower cluster count using image analysis techniques.
Purpose In recent years, there has been a growing use of unmanned aerial vehicle (UAV) based light detection and ranging (LiDAR) data for mapping plant area index (PAI) in orchards. However, using LiDAR time-series collected throughout the growing season to assess PAI variations in response to phenology, represents an understudied area of investigation. Furthermore, establishing the optimal spatial resolution for mapping biophysical variables of tree crops from LiDAR point cloud data remains poorly defined. Here, we assess the capability of a UAV-based LiDAR system to characterize cherry trees throughout the growing season, with a focus on monitoring PAI and the vertical structure of individual trees. Methods A time-series of 14 point cloud acquisitions with a density of 3300 points/m2 was collected between February and December 2022, covering all phenological stages of a cherry orchard in southern France. A voxel-based method was applied to create a three-dimensional grid within which PAI was estimated for each voxel. PAI was mapped by accumulating the individual voxel-based PAI values within each vertical voxel column. Results The results demonstrate that a voxel size of at least 0.7 m is required to retrieve reliable PAI estimates (RMSE = 0.58 m2.m−2, MAE = 0.48 m2.m−2, bias = 0.19 m2.m−2, rRMSE = 23%, and R2 = 0.51), while a voxel size of 1 m produced the most accurate PAI estimates (RMSE = 0.5 m2.m−2, MAE = 0.41 m2.m−2, bias = 0.07 m2.m−2, R2 = 0.59), when assessed against field-based PAI measurements obtained with a LAI-2200 Plant Canopy Analyzer. The temporal variation of canopy PAI illustrated the progression of key phenological stages, including flowering, leaf development, ripening and senescence, as well as the response of the canopy to drought stress (reduction in PAI due to leaf rolling) during the summer. The maps of PAI successfully described the variations in leaf canopy density for different cherry varieties and allowed assessment of the vertical PAI profile at the individual tree level, which provides valuable insight into tree condition. Conclusion This study confirms that seasonal UAV-LiDAR monitoring is a viable, informative approach for capturing orchard canopy dynamics at the individual tree and sub-canopy level, linking canopy structure to phenology, varietal differences, and stress responses across the growing season.
Why it matches plant phenotyping methodsUAV-LiDARとボクセル法による樹冠PAI・垂直構造の推定手法を開発・検証し、時系列および個体レベルで評価しているため、植物フェノタイピング手法が中心である。
abstractHere, we assess the capability of a UAV-based LiDAR system to characterize cherry trees throughout the growing season, with a focus on monitoring PAI and the vertical structure of individual trees.
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:1-51Plant phenotyping relevance match · UnverifiedOpenAlex · Crossref · Europe PMC · checked 15 Sept 2026
Field / plotCell / cellular structureWhole plant / canopy / plot / fieldGrowth / development / phenologyStress response / tolerance
Abiotic stress tolerance has been significantly weakened in modern crops during the domestication process. Regaining tolerance has become a critical task in light of current climate trends and their impact on global food security. Abiotic stress tolerance is an extremely complex trait and is conferred at various levels of plant functional organization and developmental stages, with regulatory mechanisms operating across multiple scales, from individual cells to tissues and the entire plant. The emergence of advanced molecular tools such as single-cell RNA sequencing and spatial omics technologies has revolutionized the field, advancing our understanding of plant responses to hostile environments. However, the implementation of this knowledge in crop breeding programmes is handicapped by the lack of appropriate phenotyping platforms. Here, we argue that current phenotyping methods may be excellent tools for functional validation of previously discovered traits but have limited predictive value in stress biology. We also propose that bridging the mismatch between omics technologies and phenotyping is the only way to account for cell-specific operation of key genes conferring stress tolerance and implementing them in breeding programmes. Some practical examples using cell-based phenotyping tools such as fluorescence dyes or electrophysiological methods are given, and current limitations and prospects of cell-based phenotyping are discussed.
Why it matches plant phenotyping methods細胞ベースの植物フェノタイピング手法を扱い、蛍光色素や電気生理学的方法の例、限界、展望を論じる方法論レビューである。
abstractSome practical examples using cell-based phenotyping tools such as fluorescence dyes or electrophysiological methods are given, and current limitations and prospects of cell-based phenotyping are discussed.
Introduction Canopy water content (CWC) is an important indicator of crop water status **and** supports precision irrigation decision-making. Plot-level CWC estimation using UAV imagery often relies on canopy mean features, whereas the role of within-plot canopy-signal distributional information remains insufficiently examined. Methods In this study, spring maize at the Shiyanghe site was monitored using UAV-based multispectral and thermal infrared imagery. Mean, percentile, and dispersion features were extracted from effective canopy pixels within each plot. RFECV feature selection, 50 repeated random train-test splits, paired statistical tests, simulated spatial aggregation, and four regression models were used to evaluate the stage- and scale-dependent contribution of these features. Results and discussion Water stress affected both overall spectral-thermal responses and within-plot signal distributions. Before tasseling, percentile and dispersion features were frequently selected and provided complementary information, especially for tree-based models and finer aggregation scales. After tasseling, mean features generally showed more stable performance, although some distributional features still contained CWC-related information. The supplementary Xinxiang site-internal analysis suggested that, under weak water-gradient and small-sample conditions, distributional features may be frequently selected but may not consistently improve prediction accuracy. Overall, the contribution of distributional features was growth-stage-, scale-, and model-dependent.
Why it matches plant phenotyping methodsUAVマルチスペクトル・熱赤外画像からトウモロコシ群落の水分含量を推定する特徴抽出・選択・回帰手法を中心に、反復分割や統計検定で技術的に評価しているため。
abstractPlot-level CWC estimation using UAV imagery often relies on canopy mean features, whereas the role of within-plot canopy-signal distributional information remains insufficiently examined.
Coffee is a major export earner for Uganda, raking in over USD 2 billion in 2025. The global price of coffee is tagged to the perceived quality in the cup which in turn is affected by the chemical composition of the green bean. Breeding for market-preferred Arabica coffee varieties is a major objective of coffee breeding programs. Determination of coffee bean chemical constituents is routinely done through expensive, slow and tedious laboratory procedures, making it unsustainable of resource-limited public sector coffee breeding programs. Here, we demonstrate the use of near-infrared spectroscopy (NIRS) and the machine learning algorithms partial least squares (PLS), random forest (RF) and support vector machine (SVM) for the prediction of caffeine, protein and trigonelline in Arabica coffee. NIRS provides a fast, accurate and reliable method of simultaneously predicting multiple sample constituents. Ripe coffee cherries were picked from 172 farmers' fields, air dried in the laboratory at room temperature and processed to green beans. NIRS spectra were taken on the milled green bean at 400-2500 nm, with a 0.5 nanometer (nm) step. Reference data for caffeine, protein and trigonelline were collected on the same sample scanned with NIRS. A set of 12 spectral pretreatments were applied prior to making calibrations with the PLS, RF and SVM algorithms and 70% of the data as a training set and 30% as a test set. Caffeine content of reference samples ranged from 1.94-3.0 g/100 g, protein content ranged from 11.16-15.94% while trigonelline ranged from 0.94-1.23 g/100 g. The best calibrations for all algorithms and analytes were obtained using raw (untreated) spectra, which gave the same results as the Savitzky-Golay (SG) pretreatment. For caffeine, the best model (R 2 p = 0.89, RMSEP = 0.007, RPD = 3.34) was obtained with the SVM algorithm, while for protein, the best model (R 2 p = 0.98, RMSEP = 0.14, RPD = 6.92) was obtained using the PLS algorithm. Finally, for trigonelline, all three models had very high prediction accuracies (R 2 p = 0.98-0.99, RMSEP = 0.007-0.009, RPD = 8.53-10.52). Collectively, these results demonstrate the potential of using NIRS for rapid and simultaneous prediction of coffee green bean constituents to aid selection decisions.
Why it matches plant phenotyping methodsコーヒー生豆の化学的形質を対象に、NIRSと機械学習による予測モデルを開発・検証しており、形質取得・推定法が研究の中心である。育種選抜への利用も明示されている。
abstractwe demonstrate the use of near-infrared spectroscopy (NIRS) and the machine learning algorithms partial least squares (PLS), random forest (RF) and support vector machine (SVM) for the prediction of caffeine, protein and trigonelline in Arabica coffee.
Tree growth determines how much CO2 is sequestered from the atmosphere and temporarily stored in woody biomass. At the same time tree growth is affected by increasing temperatures, more frequent drought periods, late frosts and other extreme events associated with climate change. While continuous measurements of radial (secondary) tree growth using dendrometers are well established, monitoring of shoot elongation (primary growth) has largely been neglected because suitable measurement techniques are lacking. As a result, the effects of climate change on primary tree growth remain insufficiently understood. This work aims at reconstructing native deciduous trees in 3D as a basis for measuring and monitoring shoot elongation over entire tree canopies. Here we explored the use of low-cost UAV photogrammetry and of a multi-camera CraneCam system under real-world conditions. Data were collected in two study areas over an entire growing season. We present sensor evaluations, photogrammetric data acquisition and processing strategies. A special focus is placed on the analysis of the resulting photogrammetric 3D point clouds in terms of accuracy, resolution and completeness. Results demonstrate 3D point accuracies of 5-6 mm for entire trees using consumer-grade UAVs weighing less than 250 g and a 3D reconstruction completeness between 92% and 98% depending on the UAV type. The paper introduces a novel 3Dprinted ground-truth branch to evaluate the capability to reconstructing fine-detail structures such as thin tree shoots. Finally, we discuss operational challenges and initial experiments towards a skeletonization of entire trees based on photogrammetric point clouds.
Why it matches plant phenotyping methods樹冠全体のシュート伸長を測定するための3D再構成手法を開発・評価し、センサー評価、取得・処理戦略、精度・完全性の検証を中心に扱っているため。
abstractThis work aims at reconstructing native deciduous trees in 3D as a basis for measuring and monitoring shoot elongation over entire tree canopies.
A bstract Quantifying root traits such as root length (RL) and root surface area (RSA) from minirhizotron imagery is a valuable approach for overcoming the phenotyping bottleneck that limits understanding and improvement of crop productivity, resource use efficiency and resilience in field experiments. However, current approaches remain labor-intensive, and deep learning (DL) methods suffer from limited generalization ability. We present RootQuant, an end-to-end DL model that simultaneously predicts RL and RSA directly from minirhizotron images using only whole-image trait values as supervision, thereby eliminating the need for pixel-level annotations. The model’s generalization ability was evaluated across species and fine-tuning configurations. The practical applicability of the model was further assessed under field conditions by converting image-derived RL estimates into volumetric root length density (vRLD). Using 118,191 maize and soybean images collected between 2009 and 2020, RootQuant trained on both species achieved an R 2 of 0.90 and an RMSE of 2.9 mm for RL, and an R 2 of 0.88 and an RMSE of 4.2 mm 2 for RSA. The same mixed-species model generalized strongly across species, yielding an 8% relative improvement in R 2 and a 30% lower RMSE on maize compared with the same architecture trained on a single species and applied zero-shot. Image-derived RL predictions converted to vRLD showed the expected depth-dependent decline in vRLD, as was also found by coincident destructive quantification of roots washed out of soil cores. By providing a generalist backbone model trained on a large dataset from two major crop species, RootQuant enables high-throughput simultaneous estimation of two relevant root traits directly from raw imagery without task-specific fine-tuning, thereby accelerating in situ root system analysis and phenotyping applications.
Why it matches plant phenotyping methodsミニライゾトロン画像から根長・根表面積を推定する深層学習手法を開発し、種間一般化と圃場適用性を評価しており、植物フェノタイピング手法が研究の中心である。
abstractWe present RootQuant, an end-to-end DL model that simultaneously predicts RL and RSA directly from minirhizotron images using only whole-image trait values as supervision
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:48-115Plant phenotyping relevance match · UnverifiedOpenAlex · Crossref · checked 5 Sept 2026
ABSTRACT Conventional field phenotyping methods are typically manual, time‐consuming, and destructive, creating a bottleneck for breeding progress. To address this challenge, robotics and automation technologies offer efficient sensing tools to monitor field evolution and crop development throughout the season. This study presents an end‐to‐end automated pipeline for terrestrial laser scanning (TLS) in plant breeding trials, built around a Husky ground robot equipped with a high‐resolution survey‐grade FARO 3D LiDAR scanner. Unlike prior TLS phenotyping approaches relying on manual scan placement or heuristic site selection, our system integrates a novel analytical 3D ray‐casting method for optimized TLS site planning with an offline route optimization algorithm that accounts for crop growth stages and field accessibility constraints. This enables efficient planning in complex breeding environments, reduces manual labor, and improves data collection efficiency, addressing scalability challenges in large breeding trials. Leveraging Real Time Kinematic‐Global Navigation Satellite System (RTK‐GNSS) and sensor fusion, the system achieved average errors below 0.6 cm for position and for heading, enabling point cloud registration with mean errors around 2 cm, comparable to traditional manual methods that require artificial targets. The platform was successfully deployed and evaluated in two distinct cotton breeding field layouts, demonstrating the platform's capability to autonomously collect accurate TLS data for quantitative plant phenotyping across varying plot configurations. The proposed autonomous phenotyping system advances scalable, efficient phenotyping workflows to support breeding programs for crop improvement, highlighting the potential for broader deployment in field phenomics.
Why it matches plant phenotyping methods植物育種試験向けの自律走行TLS・LiDAR計測プラットフォームと、3D計画・経路最適化・データ収集の技術的評価が中心であり、定量的植物表現型取得を目的とする。
abstractThis study presents an end‐to‐end automated pipeline for terrestrial laser scanning (TLS) in plant breeding trials
Plant phenotyping relevance match · UnverifiedOpenAlex · Europe PMC · Crossref · checked 5 Sept 2026
(L.) Merrill) is a highly important crop widely used for food, edible oil, animal feed, and microbial fermentation products. Traditional phenotypic measurement methods are often time-consuming, labor-intensive, destructive to plants, and prone to human error. High-Throughput Phenotyping (HTP) enables precise assessment of multiple soybean phenotypic features, including morphology, physiology, diseases, pests, and agronomic traits. Artificial Intelligence (AI) is a research field dedicated to developing algorithms for multiple tasks. This review highlights the application of HTP and AI in soybean breeding programs. We discuss the challenges of implementing HTP in soybean breeding and focus on the potential and limitations of Deep Learning (DL) to support soybean breeding goals. We demonstrate the application of HTP to key soybean traits, several HTP platforms, as well as DL applications across different datasets and strategies for developing large foundation models. While integrating AI into soybean breeding programs remains a challenge, leveraging HTP data and Large Language Models (LLMs) could reshape soybean breeding.
Why it matches plant phenotyping methods大豆育種におけるHTPとAIの応用、形質評価、プラットフォーム、データセットおよび深層学習を中心に扱うフェノタイピング手法レビューであり、方法論が中心的です。
abstractThis review highlights the application of HTP and AI in soybean breeding programs.
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:193-228