Plant phenotyping methods.

RQ-PointNeXt: An End-to-End 3D Point Cloud Instance Segmentation Method for Field Cotton Boll Phenotyping →

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.

FG-LCNet: A two-stage foreground-guided network for whole-tree litchi counting →

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.

A methodological framework for the standardised evaluation of olive genetic resources: GEN4OLIVE harmonized protocols →

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.

Assessing cotton boll-opening concentration for harvest decision-making via foundation model-enhanced cross-scale phenotyping. →

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.

Areca Nut Disease Classification Using Sailfish Optimization Algorithm with Dynamic Elastic Boundary Strategy and Convolution Neural Networks →

In recent years, areca nut plants have been vulnerable to different diseases that appear as distinct colors on leaves, caused by bacteria or fungi. These symptoms disrupt photosynthesis and reduce yield, affecting productivity and crop health. Therefore, accurate plant disease classification is essential for detecting distinct disease shapes and sizes. Existing Deep Learning (DL) models have several limitations that prevent them from distinguishing between various plant diseases due to similar characteristics. To overcome this limitation, a Dynamic elastic boundary strategy Sailfish Optimization Algorithm and Convolution Neural Network (DSFO-CNN) method is proposed to identify and accurately classify arecanut plant diseases. The Visual Geometry Graph-19 (VGG-19) model extracts features that have significant information about disease in arecanut plants. The proposed arecanut plant disease classification model employed feature selection and drop cyclic learning rate, which adjusts the CNN learning rate to efficiently learn the subtle information about various leaf and nut diseases to enhance classification. The experimental results of the DSFO-CNN demonstrate superior performance compared to existing approaches.

Why it matches plant phenotyping methodsアレカヤシの葉・果実に現れる病徴を画像から分類するCNNベース手法を提案・評価しており、植物病害状態の取得・推定が中心的な方法論的貢献である。

abstractTherefore, accurate plant disease classification is essential for detecting distinct disease shapes and sizes.

Application of the OliveID morphometric tool for the identification of archaeobotanical carbonized olive endocarps: evidence for morphological continuity with the modern Throumbolia cultivar. →

Introduction This study evaluates the applicability of digital morphometric analysis to images of archaeological carbonized olive endocarps as a proof-of-concept initial approach for archaeobotanical investigations. Conventional morphometric analyses of olive endocarps largely rely on manual measurements, limiting reproducibility and quantitative comparison. Methods Ten archaeological endocarps were selected from previously published archaeological assemblages based on the integrity of their outlines, apex-base morphology and overall preservation quality. Quantitative descriptors describing endocarp size, symmetry, curvature and contour geometry were extracted using the OliveID software and compared with a modern morphometric reference database comprising Greek and international olive cultivars. Results Reliable contour extraction and quantitative descriptor computation were successfully achieved for all archaeological specimens despite carbonization. Preliminary comparison of representative morphometric descriptors showed that the archaeological specimens were positioned within the morphometric variation observed among the modern reference collection. Hierarchical clustering consistently associated the archaeological endocarps with the modern Throumbolia morphotype, while distinguishing them from elongated, globular and mucro-bearing cultivars. Discussion These findings demonstrate the feasibility of applying digital image-based morphometric analysis to sufficiently preserved archaeological carbonized olive endocarps and indicate a similar morphometric affinity between the analyzed archaeological material and the modern Throumbolia cultivar. This proof-of-concept study highlights the potential of digital morphometric approaches for quantitative archaeobotanical investigations of archaeological olive remains, while emphasizing the need for larger archaeological datasets and standardized image acquisition to further validate the observed morphometric similarity.

Why it matches plant phenotyping methodsOliveIDを用いて炭化オリーブ内果皮の輪郭からサイズ、対称性、曲率、形状記述子を抽出し、デジタル画像形態計測の適用可能性と再現性を評価している。植物器官の形質抽出法が研究の中心である。

abstractThis study evaluates the applicability of digital morphometric analysis to images of archaeological carbonized olive endocarps as a proof-of-concept initial approach for archaeobotanical investigations.

Image dataset of manalagi apple fruits for multi-class disease classification using deep learning. →

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.

CocoaDeep: A preliminary study of the performance sensitivity to datasets of Faster RCNN, YOLO and transformer networks for cocoa pod detection. →

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.

A high-performance detection model ISA-YOLO for eggplant pests and diseases. →

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.

What you plant may not be what you bought: morphological and genetic discordance in specialty Coffea arabica L. cultivars from Ecuador. →

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

A Novel Multi Class Real World Fruit and Leaf Disease Image Dataset for Crop Health Analysis →

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.

A Deep Learning Model for Chili Pepper Fruit Shape Classification Using DenseNet-121 and CBAM. →

Traditional manual grading of fresh chili peppers suffers from inconsistent quality control and low efficiency. To meet the demand for accurate fruit shape recognition during the post-harvest stage, this study proposes an intelligent recognition method based on an improved DenseNet-121 network. This approach facilitates the application of machine vision in agricultural sorting equipment. DenseNet-121 serves as the backbone network. The Convolutional Block Attention Module (CBAM) is introduced to enhance feature focus on fruit shapes. A regularization strategy (Dropout = 0.3, weight decay = 1 × 10 -4 ) and a cross-entropy loss function with label smoothing (LS = 0.1) are integrated to optimize decision boundaries. These configurations prevent the model from overfitting to hard training labels and yield a robust classification architecture. Experimental results demonstrate that the proposed model achieves a precision of 90.09%, a recall of 89.60%, an F1-score (the harmonic mean of precision and recall) of 89.53%, and an overall accuracy of 89.74%. The model contains 7.09 M parameters and requires a single-frame inference time of 7.35 ms. Comprehensive evaluations indicate that the proposed model achieves an optimal balance among environmental noise robustness, prediction accuracy, and computational efficiency. Consequently, by maintaining high fine-grained classification accuracy alongside a low memory footprint and rapid inference speed, the model demonstrates strong potential for real-time deployment on resource-constrained edge devices within actual agricultural optical sorting equipment.

Why it matches plant phenotyping methodsチリペッパー果実の形状という植物器官形質を画像から分類する深層学習手法の開発・評価が中心であり、単なる品質測定ではない。

abstractExperimental results demonstrate that the proposed model achieves a precision of 90.09%, a recall of 89.60%, an F1-score (the harmonic mean of precision and recall) of 89.53%, and an overall accuracy of 89.74%.

CitrusGS: 3D Gaussian splatting for sparse-view CT reconstruction and precise morphological phenotyping of citrus fruit →

Computed tomography enables non-destructive phenotyping of fruit internal structure but traditionally requires hundreds of projections, limiting throughput. Under sparse-view conditions, conventional and learning-based methods both suffer from streaking artifacts and regional distortions that degrade trait quantification. This study present CitrusGS, an integrated framework that achieves high-fidelity 3D reconstruction and precise morphological phenotyping of citrus fruit from only 15 projections using radiative 3D Gaussian splatting. Our method employs sparse-point initialization, optimized loss composite, and dual-stage pruning to suppress artifacts while preserving anatomically critical details with significantly higer convergence efficiency. In the citrus fruit datasets, CitrusGS achieves 29.78 dB PSNR and 0.870 SSIM, outperforming corresponding baseline method by 1.58 dB and 0.067 in SSIM, and enables automated extraction of ten external and internal phenotypic traits with R 2 larger than 0.944. Moreover, the framework shows initial zero-shot transferability across pathological citrus samples and additional horticultural specimens without retraining. By reconciling acquisition efficiency with anatomical fidelity using low-cost X-ray hardware, CitrusGS provides a promising framework for high-throughput, non-destructive phenotyping in breeding and grading applications.

Why it matches plant phenotyping methods柑橘果実の疎視野CT再構成法を開発・検証し、内部・外部形質を自動抽出するフェノタイピングが中心である。

abstractThis study present CitrusGS, an integrated framework that achieves high-fidelity 3D reconstruction and precise morphological phenotyping of citrus fruit from only 15 projections using radiative 3D Gaussian splatting.

PD-ViCo: an explainable AI-based contrastive captioner vision transformer with patch dropout for multi-class brinjal disease classification. →

Brinjal (eggplant) is a critical crop in South Asia, especially in Bangladesh, but its production is drastically affected by numerous diseases that inhibit yield and quality. Manual diagnosis of disease is time-consuming, subjective, and prone to errors, necessitating automated, scalable technology. To address these issues, this paper proposes PD-ViCo, a lightweight, efficient transformer-based model for brinjal fruit disease classification using Simple Vision Transformer (ViT) with Patch Dropout and Contrastive Captioner (CoCa) methods. One new dataset of 1,823 field-harvested brinjal images encompassing five disease classes including Phomopsis Blight, Fruit and Shoot Borer, Fruit Cracking, Wet Rot, and Healthy samples were prepared through real-world agricultural data collection from Bangladesh. The approach includes extensive preprocessing, class balancing (under-sampling/oversampling), and resilient augmentation methods. The PD-ViCo model significantly improves classification performance under data imbalance with patch dropout regularization and CoCa-style aggregation, resulting in better generalization and robustness. On a range of imbalanced, under-sampled, and oversampled datasets, PD-ViCo achieved a classification accuracy of 99.12% and F1-score of 97.76%, outperforming both ViT and Swin Transformer across all key evaluation metrics. Explainability was also applied using Grad-CAM and Grad-CAM + + , generating visual explanations of model decisions and maintaining conformity to disease-affected regions in the images. These visualizations ensure the credibility of the model and its usability for real agricultural conditions. This study demonstrates that PD-ViCo is a highly accurate, interpretable, and lightweight model for multi-class brinjal disease diagnosis. Not only does it advance state-of-the-art in agricultural AI, but it also provides a valuable dataset and an understandable decision-making protocol that can be applied directly by farmers, agronomists, and agricultural technologists.

Why it matches plant phenotyping methods植物画像から病害状態を分類するモデル、データセット、説明可能性評価を中心に開発・検証しており、植物フェノタイピング手法として適格。

abstractthis paper proposes PD-ViCo, a lightweight, efficient transformer-based model for brinjal fruit disease classification

BerryBox: An affordable computer vision system for postharvest phenotyping of cranberry and other small fruits →

Abstract Fruit size, shape, color, and percent fruit rot are important quality traits for breeding cranberry ( Vaccinium macrocarpon Ait.). Image analysis can be used to measure these traits, but affordable hardware for standardized image capture and integrated user‐friendly software pipelines are lacking. Additionally, no image‐based method exists to estimate percent fruit rot, an otherwise tediously and subjectively measured trait. We created the BerryBox, a simple and inexpensive lightbox, camera mount, and accompanying software pipeline to standardize the capture and analysis of postharvest fruit images. Trained deep neural network models were highly accurate for segmenting sound fruit (F1 score: 99.4%) and detecting rotten fruit (F1 score: 98.5%). We applied the BerryBox to images of cranberries harvested across 3 years from a 156‐clone breeding population. Narrow‐sense heritability estimates of image‐based fruit color, shape, size, and percent fruit rot ranged from 0.37 to 0.95. Random subsampling showed that 25–30 berries per genotype were sufficient to describe the variation in the full dataset. We demonstrated the utility of BerryBox traits in a small‐scale genetic linkage mapping analysis, detecting significant marker–trait associations that coincided with those of traditionally measured traits. The BerryBox software was able to accurately segment fruit from images of blueberries without model retraining, showing its applicability to other similarly shaped fruits. The software pipeline and BerryBox materials and assembly instructions are publicly available for others to adopt for low‐cost image‐based phenotyping.

Why it matches plant phenotyping methodsクランベリー等の果実形質と腐敗率を画像から抽出する低コスト撮像装置・ソフトウェアパイプラインを開発し、精度検証と他果実への適用性評価を行った、中心的な植物フェノタイピング手法研究である。

abstractWe created the BerryBox, a simple and inexpensive lightbox, camera mount, and accompanying software pipeline to standardize the capture and analysis of postharvest fruit images.

A curated image dataset for sapodilla fruit (Manilkara zapota) disease and fruit quality analysis. →

Sapodilla (Manilkara zapota), or chickoo, is a key tropical fruit, very popular in India, Mexico, and Thailand, as it is nutritionally and economically valuable. Nonetheless, the production of sapodillas is often affected by several diseases, which reduce fruit quality and quantity. The dataset used in this paper is a sapodilla fruit image dataset, comprising 1,518 images, gathered in the field under the practicing conditions on 18 February 2025, 22 February 2025, in Rahu village, Pune district, Maharashtra, India, with the use of smartphone cameras. The data is sorted into four categories, namely: Anthracnose, Bacterial rot, Healthy, and Sap bleeding. The photographs were taken in different backgrounds and in different lighting conditions to represent real-life cultivation conditions. The data is expected to be useful in machine learning-based plant disease detection, classification, and analysis, and spur the creation of intelligent and sustainable agricultural systems.

Why it matches plant phenotyping methodsサポディラ果実の病害・健全状態を画像で記録したデータセット自体が中心で、植物病害の画像ベース表現型解析に利用できる。

titleA curated image dataset for sapodilla fruit (Manilkara zapota) disease and fruit quality analysis.

DiffPlantCT: a training-free, annotation-free approach to cross-species plant CT image segmentation. →

Traditional deep learning-based plant computed tomography (CT) image segmentation methods require a large amount of high-quality manually labeled data for model training specific to each species, leading to substantial labor costs and poor adaptability to new species. These limitations hinder the application of CT imaging in large-scale cross-species plant phenotyping analysis. Therefore, developing annotation-free and training-free plant CT image segmentation methods is of significant research and application value in reducing research costs and promoting the efficiency of cross-species analysis. To achieve this, we introduce an unsupervised zero-shot segmentation framework for cross-species plant CT images, DiffPlantCT. It is a 2D-to-3D framework that first segments all 2D slices and then assembles them in their original order to generate a 3D CT segmentation. For each slice, this framework directly constructs discriminative clustering features by combining the general semantic priors provided by the self-attention layers in a pre-trained stable diffusion model with the intrinsic grayscale distribution of original image, thereby completely avoiding the need for manual annotations. The method ultimately outputs segmentation results solely through unsupervised clustering, achieving zero-shot generalization without any model training or fine-tuning. To evaluate the feasibility of DiffPlantCT in cross-species segmentation, we benchmark the segmentation performance on two public datasets (walnut fruit and barley spike) and two self-collected datasets (wheat spike and rice panicle). The results show that DiffPlantCT achieved the best performance, with a 41.6% improvement in overall mIoU compared to the state-of-the-art unsupervised method. For the first time, we demonstrate annotation-free, training-free segmentation of cross-species plant CT images successfully.

Why it matches plant phenotyping methods植物CT画像から3D形状を抽出する、アノテーション不要・学習不要の分割手法を開発し、複数作物データセットで性能評価しており、表現型取得手法が研究の中心である。

abstractwe introduce an unsupervised zero-shot segmentation framework for cross-species plant CT images, DiffPlantCT.

Toward accurate prediction of apple firmness and brix across countries, seasons and cultivars with hyperspectral imaging. →

Traditional apple maturity assessment methods are destructive and time- and labour-intensive, yielding only population-level approximations. Hyperspectral imaging provides a non-destructive alternative to assess individual fruit, but progress has been constrained by the lack of large, diverse datasets that support robust model generalisation. This study presents a multi-cultivar, multi-season, multi-country hyperspectral apple dataset to enable generalisable prediction of soluble solids content (Brix) and firmness. Using this dataset, we adopt an iterative modelling framework to evaluate deep learning architectures, image resolutions, cultivar encoding, seasonal effects, and feature-specific models. Wavelength and spatial region importance were also analysed. The best predictive performance was achieved using Vision Transformer (ViT) models trained on edge-cropped 40 × 40 pixel images with explicit cultivar encoding, with Brix and firmness modelled independently. Although seasonal specificity was observed, models trained across all three seasons achieved the strongest overall performance. A 50% reduction in spectral wavebands did not compromise prediction accuracy. Key wavelength ranges contributing to Brix and firmness prediction were identified across the visible-near-infrared spectrum. Spatial regions were unimportant for Brix prediction but showed relevance for firmness. The optimised ViT model achieved firmness prediction performance comparable to previous studies (RMSE = 0.76 kgf, R[Formula: see text] = 0.63), while Brix prediction accuracy was lower (RMSE = 0.91 [Formula: see text]Brix, R[Formula: see text] = 0.75), likely reflecting increased biological and environmental variability captured in the dataset. Overall, this work demonstrates that hyperspectral imaging combined with deep learning and large, diverse datasets enables robust, non-destructive prediction of apple quality attributes across production conditions.

Why it matches plant phenotyping methodsリンゴ果実の硬度とBrixという植物器官形質を、ハイパースペクトル画像と深層学習で非破壊推定するデータセット・モデル・汎化性能評価が研究の中心である。

abstractThis study presents a multi-cultivar, multi-season, multi-country hyperspectral apple dataset to enable generalisable prediction of soluble solids content (Brix) and firmness.

Horticultural temporal fruit monitoring via 3D instance segmentation and re-identification using colored point clouds →

Accurate and consistent fruit monitoring over time is a key step towards automated agricultural production systems. However, this task is inherently difficult due to variations in fruit size, shape, occlusion, orientation, and the dynamic nature of orchards where fruits may appear or disappear between observations. In this article, we propose a novel method for fruit instance segmentation and re-identification on 3D terrestrial point clouds collected over time. Our approach directly operates on dense colored point clouds, capturing fine-grained 3D spatial detail. We segment individual fruits using a learning-based instance segmentation method applied directly to the point cloud. For each segmented fruit, we extract a compact and discriminative descriptor using a 3D sparse convolutional neural network. To track fruits across different times, we introduce an attention-based matching network that associates fruits with their counterparts from previous sessions. Matching is performed using a probabilistic assignment scheme, selecting the most likely associations across time. We evaluate our approach on real-world datasets of strawberries and apples, demonstrating that it outperforms existing methods in both instance segmentation and temporal re-identification, enabling robust and precise fruit monitoring across complex and dynamic orchard environments. • We propose a new performant approach to autonomous fruit tracking in real greenhouses. • It segments fruits using learning-based instance segmentation and RGB 3D point clouds. • Segmented fruits are encoded by a 3D CNN and matched via attentive data association. • Experiments on real strawberry and apple datasets show our method outperforms others. • Our approach enables precise temporal fruit monitoring in real and complex scenarios.

Why it matches plant phenotyping methods果実を個体単位で3D点群からセグメンテーションし、時系列追跡する画像解析手法の開発・評価が研究の中心であり、植物器官の状態を抽出するため適格。

abstractwe propose a novel method for fruit instance segmentation and re-identification on 3D terrestrial point clouds collected over time

PhenoSnap: An AI-Powered Web Application for Automated Specialty Crop Trait Extraction →

Manual quantification of specialty crop traits, such as flowers and fruits, is often labor-intensive, time-consuming, and inconsistent, limiting scalability and precision. We present PhenoSnap, an artificial intelligence (AI)-powered web application that provides an intuitive and efficient interface for automated specialty crop trait extraction from images. PhenoSnap bridges the gap between advanced computer vision technologies and practical agricultural applications by eliminating the need for programming expertise. This ready-to-use solution can enable growers, breeders, and Extension faculty to accelerate field work and enhance decision-making related to strawberry and tomato yield estimation for breeding selections and strawberry runner management. Written by Santhi Daggubati, Xu Wang, Xue Zhou, Shubham Singh, and Jessica Chitwood-Brown, and published by the UF/IFAS Department of Agricultural and Biological Engineering, June 2026.

Why it matches plant phenotyping methods画像から花・果実などの植物形質を自動抽出するAIウェブアプリケーションの開発・提供が中心であり、植物フェノタイピング手法およびソフトウェアとして適格。

abstractWe present PhenoSnap, an artificial intelligence (AI)-powered web application that provides an intuitive and efficient interface for automated specialty crop trait extraction from images.

Contrastive multi-view representation learning for multi-camera plant phenotyping: A cotton field study →

Attempts to deploy computer vision in agricultural tasks often suffer from a shortage of annotated data. One strategy to alleviate the impact of limited data is Self-Supervised Learning (SSL), which involves pre-training a model on a pretext task that utilizes automatically generated annotations. The primary objective of this study is to leverage a multi-camera view dataset of cotton boll images for contrastive learning in order to enable phenotyping tasks with minimal data annotation. This dataset was collected in the field using six camera views. The efficacy of two contrastive learning frameworks (SimCLR and MoCo) in producing representations when positive examples originate from different cameras was investigated, and a comprehensive study of how the camera positions affect performance was conducted. After self-supervised pre-training, linear evaluation and semi-supervised learning experiments were performed on boll detection and plot status downstream tasks. In general, using multiple camera views with SimCLR and MoCo improves cotton boll detection mean average precision by 14% compared to vanilla SimCLR and MoCo. Through careful investigation using synthetic data, it was determined that relative camera poses with an intermediate amount of overlap seem more likely to perform well. Neither MoCo nor SimCLR was consistently superior to the other in this context. The representations embed meaningful features about the cotton plants, such as overall boll density, but also less meaningful ones, such as lighting variations. This technique could potentially accelerate the development of phenotyping algorithms based on data collected from field robots. • A contrastive learning method based on comparing multi-camera views was developed. • The method was tested with images of cotton bolls from a ground robot. • The method outperformed baseline contrastive learning approaches.

Why it matches plant phenotyping methodsマルチカメラ画像とコントラスト学習による植物表現学習・フェノタイピング手法の開発と評価が中心であり、綿花のボール検出性能を検証している。

abstractThe primary objective of this study is to leverage a multi-camera view dataset of cotton boll images for contrastive learning in order to enable phenotyping tasks with minimal data annotation.

Image-based high-throughput phenotyping enables genetic analyses of pod morphological traits in mungbean ( Vigna radiata (L.) R. Wilczek) →

Mungbean (Vigna radiata (L.) R. Wilczek) is a vital source of digestible proteins and is well-suited for the plant-based protein industry. In this study, we analyzed pod morphological traits in the Iowa Mungbean Diversity (IMD) panel of 372 genotypes (2022-2023) using image-analysis-based phenotyping on 2,418 pod images. Pod morphological traits were extracted using deep learning image analysis, achieving excellent agreement with manual measurements (r > 0.96 for pod length (PL) and seed-per-pod (SPP)). Four complementary genome-wide association studies models identified 65 significant SNPs (-log10(P) ≥ 5.56) associated with pod curvature, length, width, and SPP traits. A significant SNP (5_35265704) on chromosome 4 was linked to pod dimensional traits, length, width, and curvature. A candidate gene, Virad04G0076900, located 15.6 kb from this SNP, is part of the GH3 gene family and has an Arabidopsis ortholog (AT4G27260) known for influencing organ elongation, pod, and seed development. Another SNP, 5_210437 on chromosome 6, has been found to be significantly associated with both PL and SPP. A candidate gene, Virad06G0002400 (36.5 kb from this SNP), encodes a potassium transporter and shares homology with the Arabidopsis gene HAK5 (AT4G13420), known to influence pod growth. Image-based measurements achieved genomic prediction accuracies ranging from 0.61 to 0.85 across various traits, demonstrating comparable accuracy to manual methods for linear traits and up to 22% improvement for complex shape traits. These results highlight the potential of deep learning-assisted phenomics integrated with genomic tools to accelerate selection for improved pod architecture in mungbean breeding programs across the Midwestern United States and globally.

Why it matches plant phenotyping methods深層学習による画像解析でマメ pod の形態形質を抽出し、手動測定との一致度を検証しており、画像ベース表現型取得が研究の中心です。

abstractusing image-analysis-based phenotyping on 2,418 pod images

Multispectral imaging for zeaxanthin content in the exocarp of chili peppers. →

This study developed a model to predict zeaxanthin content in peppers using multispectral imaging and chemical data. A one-dimensional convolutional neural network (1D CNN) model was identified as the optimal single-modal model after comparing four machine learning algorithms. On the prediction dataset, the model achieved a determination coefficient ( Rp 2 ) of 0.7639. Building upon the 1D CNN framework, a multimodal feature fusion model (MCSF) was constructed by integrating the chemical measurements of capsanthin and total carotenoid contents using a multilayer perceptron. This enhanced model demonstrated excellent predictive accuracy and robustness, with Rp 2 values of 0.9318 and 0.9211 across different spectral ranges. For high-throughput detection purposes, a simplified model that replaced measured capsanthin with a comprehensive red index still performed well, with an Rp 2 of 0.8912 and an RPD of 3.11. This strategy provides a new solution for the efficient spectral detection of plant chemicals affected by multicollinearity in their absorption spectra.

Why it matches plant phenotyping methodsマルチスペクトル画像と機械学習を用いて、トウガラシ果皮のゼアキサンチン含量という植物器官の形質を非破壊・高スループット推定する手法を開発・評価しており、フェノタイピング手法が中心である。

abstractThis study developed a model to predict zeaxanthin content in peppers using multispectral imaging and chemical data.

A multi-stage, pixel-level annotated apple dataset for precision agriculture research. →

This article presents a comprehensive dataset of 1406 RGB images of apples ( Malus domestica ), covering three key growth stages-immature (green), semi-mature (color transition), and mature (red). The dataset serves as a resource for detecting and segmenting apples across different developmental phases. Each image includes pixel-level instance segmentation masks annotated in JSON format using the VGG Image Annotator (VIA), ensuring compatibility with deep learning frameworks. The dataset's real-world variability-spanning lighting conditions, occlusions, and clustered fruit arrangements-enhances its utility for training generalizable computer vision models in precision agriculture. It supports tasks such as fruit detection, segmentation and growth-stage classification, addressing the scarcity of annotated data for transitional maturity phases. With 2574 annotated apple instances, this dataset facilitates research on maturity grading and transfer learning for agricultural robotics. By standardizing annotations and incorporating diverse field conditions, this dataset reduces preprocessing overhead and accelerates the development of deployable AI solutions for orchard management. It is particularly valuable for improving model robustness in heterogeneous environments, thereby advancing data-driven horticultural practices.

Why it matches plant phenotyping methodsリンゴ果実の発育段階・成熟度という植物器官の状態を対象に、画素単位アノテーション付き画像データセットを構築しており、観測・抽出手法の再利用可能な基盤が中心である。

abstractThis article presents a comprehensive dataset of 1406 RGB images of apples ( Malus domestica ), covering three key growth stages-immature (green), semi-mature (color transition), and mature (red).

Morphometric Properties of Olive (Olea europaea) Pits: A Dataset for Cultivar Identification and Analysis. →

Image analysis of pits and grains provide alternative routes for overcoming the invasive approach of genomic tools in the investigation of archaeological or modern plant material, which is only seldom a viable option due to the complex and laborious methodologies required. Nevertheless, any investigation of pit morphology and cultivar interpretation requires a high quality, comprehensive dataset for comparison. Such a benchmark dataset for the morphology of olive (Olea europaea) pits is presented in this paper, designed to facilitate similar research and establish a base for future investigations. The dataset was established by image analysis of pits of 18 olive cultivars that were photographed in both lateral and dorsal positions. A dedicated MATLAB® code was developed to extract the silhouettes of each pit and to calculate 16 morphometric traits of each view of the pit. Altogether, a total of 1008 photos of 504 pits of the 18 cultivars, together with their detailed morphometric description and statistical analysis are available here. These were used to test the accuracy of the dataset and the new approach in representing the different cultivars.

Why it matches plant phenotyping methodsオリーブ核の画像から形態形質を抽出する専用コードと、検証用ベンチマークデータセットを開発・提示しており、植物形質取得法が中心である。

abstractSuch a benchmark dataset for the morphology of olive (Olea europaea) pits is presented in this paper, designed to facilitate similar research and establish a base for future investigations.

Research on Apple Surface Disease Detection Method Based on Improved YOLOv11s. →

Apple surface diseases are crucial factors affecting the quality and yield of apples. Traditional manual inspection methods suffer from low efficiency and poor real-time performance. To address these issues, this paper proposes an apple surface disease detection method based on an improved YOLOv11s. Firstly, three groups of GAM attention mechanisms are integrated into the neck structure of the YOLOv11s to enhance the efficiency of feature fusion and the capability of semantic information transmission. Secondly, the original convolutional downsampling in the backbone network is replaced with a Haar-based feature downsampling module, enabling the model to retain more high-frequency detail information during the downsampling process. In addition, the WFU module is introduced to realize the dynamic allocation of feature weights, enhancing the model's ability to recognize multi-scale defect features. Finally, the PIOUv2 loss function is adopted to optimize bounding box regression, improving the model's detection performance for tiny defect spots. In addition, various data augmentation methods for small datasets are employed to improve the model training performance and effectively avoid the problem of data overfitting. The experimental results demonstrate that the F1-score of the proposed model is increased by 4.2%, and the mAP@50:95 is boosted by 2.4%. The detection performance outperforms various comparative models, which verifies the effectiveness and superiority of the proposed method.

Why it matches plant phenotyping methodsリンゴ表面の病斑・欠陥を画像から検出する改良YOLO手法の開発と比較検証が研究の中心であり、植物の病害状態を直接推定するフェノタイピング手法に該当する。

abstractthis paper proposes an apple surface disease detection method based on an improved YOLOv11s.

Enhanced convolutional block attention module with Learnable Gated Fusion (LGF-CBAM) for cocoa pod disease identification. →

Accurate detection of cocoa pod diseases is vital to reducing yield losses and supporting sustainable agriculture. Although deep learning models have shown promise in plant disease classification, their performance often varies between datasets due to limitations in feature extraction and generalisation. This study introduces a Learnable Gated Fusion Convolutional Block Attention Module (LGF-CBAM) integrated with a ResNetV2-101 backbone to improve discriminative feature learning and improve robustness in cocoa disease classification. Unlike the standard CBAM, which processes attention modules sequentially, LGF-CBAM adaptively balances the importance of spatial and channel cues through trainable gating parameters normalized with a softmax function. Incorporating LGF-CBAM provided outstanding results on the Cocoa_Pod_Disease_Gh dataset, achieving 98.95% accuracy along with F1 and PPV scores of 99.11%. The cross-dataset evaluation confirmed robustness, with accuracies of 98.53% on Cocoa Diseases (YOLOv4), 97.96% on Black and Borer Pod Rot, and 96.19% on Cacao Diseases in Davao. Although greater variability in the Coffee and Cocoa dataset reduced accuracy to 94.00%, the model still maintained strong adaptability under diverse conditions. These findings establish LGF-CBAM as a state-of-the-art framework that outperforms all other referenced systems, offering high accuracy, stability, and generalization. In general, this research contributes to a novel attention-based deep learning framework that can support early and reliable identification of cocoa pod diseases, providing a scalable solution for precision agriculture.

Why it matches plant phenotyping methodsカカオ果実の病害状態を画像から分類する深層学習手法を開発し、複数データセットで性能・頑健性を評価しており、植物フェノタイピング手法が研究の中心である。

abstractThis study introduces a Learnable Gated Fusion Convolutional Block Attention Module (LGF-CBAM) integrated with a ResNetV2-101 backbone to improve discriminative feature learning and improve robustness in cocoa disease classification.

AgroDualNet: a dual deep learning-based crop disease forecasting and fruit ripening detection. →

Proper diagnosis of crop diseases and accurate measurement of fruit ripeness is essential in enhancing agricultural productivity, but conventional methods of diagnosis are time-consuming, error-prone, and inefficient. With the rapid development of AI, deep learning (DL), and IoT, there is increasing demand for combined solutions that jointly address plant health monitoring and harvest optimization in a reproducible and deployment-oriented manner. This study develops a new bi-phasic DL framework, AgroDualNet, that predicts crop diseases and identifies fruit ripeness stages to optimize yield quality and minimize agricultural losses. The work explicitly targets improved classification reliability, broader class evaluation, rigorous validation and generation of decision-ready outputs for precision agriculture. AgroDualNet comprises two modules. The crop-disease prediction module integrates ResNet50 with a Convolutional Block Attention Module (CBAM), and a Sequential Minimal Optimization (SMO)-based SVM classifier to enhance feature learning and classification performance Several different architectural designs are benchmarked and the resultant model is tested on both a dedicated 3-class subset and a large multi-class model of the PlantVillage dataset with leakage safe protocol(augmentation applied only on training data), cross-validation, statistical significance testing as well as ablation. The fruit-ripeness module employs YOLOv8 for real-time fruit localization and MobileNetV2 for lightweight ripeness classification suitable for edge deployment and a prototype decision-support layer maps predictions to actionable recommendations. That is able to run on the edge. Experiments show that the hybrid CBAM + ResNet50 + SMO model achieves 99.6% accuracy for crop disease classification on a three-class configuration of the PlantVillage dataset and maintains consistently higher accuracy than strong baseline in a 38-class setting, with statistically significant results confirmed by McNemar's test (p < 0.001) outperforming baseline and intermediate architectures in accuracy, precision, Recall and F1-Score The fruit ripeness pipeline achieves 98.88% classification accuracy across four ripeness stages (unripe, semi-ripe, ripe, over-ripe) on a combined Kaggle and real-field apple dataset with low inference time, confirming its suitability for near real-time deployment on edge devices. Cross-validation, Statistical significance tests and ablation studies collectively validate the robustness and significance of these gains and the decision-support layer demonstrates the feasibility of converting raw predictions into interpretable, recommendation-oriented outputs. AgroDualNet provides an efficient and unified system for monitoring plant diseases and evaluating fruit ripeness, with statically validated performance across both focused and full multi-class settings, addressing two critical challenges in precision agriculture with a single extensible framework. The dual-module design of AgroDualNet, which combines disease prediction with ripeness analysis and a preliminary decision-support prototype offers a more comprehensive and practically relevant AI-driven monitoring solution than conventional single-task models. By emphasizing multi-class validation on PlantVillage, leakage-aware experimentation, statistical verification, and system-level integration, this works supports real-time, precise and automated guidance to reduce crop losses, improve harvest timing, and enable smarter farm-level decision making.

Why it matches plant phenotyping methods植物病害状態と果実成熟度を画像から推定する深層学習パイプラインの開発・比較検証が中心であり、PlantVillageおよび実圃場データで交差検証、アブレーション、統計検定を実施しているため、植物フェノタイピング手法として含める。

abstractThis study develops a new bi-phasic DL framework, AgroDualNet, that predicts crop diseases and identifies fruit ripeness stages

Explainable deep learning-based comparative study for guava fruit and leaf disease classification: advancing agricultural diagnostics through AI. →

Introduction Early detection of plant diseases is essential for maintaining crop health and ensuring sustainable agricultural productivity. Guava fruit and leaf diseases, if not identified at an early stage, can lead to significant yield losses. Recent advances in deep learning offer promising solutions; however, challenges remain in achieving both high accuracy and model interpretability for practical agricultural deployment. Methods This study proposes an explainable deep learning-based framework for the classification of guava fruit and leaf diseases. A real-world dataset consisting of 527 annotated images across five classes-Disease Free, Phytophthora, Red Rust, Scab, and Styler and Root Rot-was utilized. Six hybrid model architectures were developed by integrating transfer learning backbones (VGG16, MobileNetV2, InceptionV3, and ResNet50) with custom convolutional neural network (CNN) classifiers. Model performance was evaluated using accuracy, precision, recall, F1-score, and class-wise metrics. To enhance transparency, Gradient-weighted Class Activation Mapping (Grad-CAM) was employed to visualize disease-relevant regions. Results Among all evaluated models, the proposed VGG16 + MobileNetV2 hybrid architecture achieved the best performance, attaining an accuracy of 96%, an F1-score of 0.96, and strong generalization across all disease classes. Comparative analyses using confusion matrices, ROC-AUC curves, precision-recall curves, and radar plots confirmed the superior and consistent performance of the proposed model over other hybrid configurations. Discussion The results demonstrate that combining deep feature extractors with lightweight architectures enhances both classification accuracy and computational efficiency. The integration of Grad-CAM provides meaningful visual explanations, increasing trust and interpretability in AI-assisted disease diagnosis. This framework shows strong potential for deployment in real-time smart farming systems and mobile-based diagnostic applications, particularly in resource-constrained agricultural environments.

Why it matches plant phenotyping methodsグアバの葉・果実画像から病害状態を推定する深層学習手法が研究の中心であり、複数モデルの比較評価とGrad-CAMによる説明可能性検証も行っているため、植物フェノタイピング方法論として採用する。

abstractThis study proposes an explainable deep learning-based framework for the classification of guava fruit and leaf diseases.

Distilled vision transformers with CNN fusion for robust cashew apple maturity prediction. →

Introduction Cashew apple is a nutrient-rich fruit containing abundant minerals, vitamins, and energy. However, its fleshy texture and delicate skin significantly limit its storage life and market value. Accurate maturity grading is therefore essential for improving post-harvest management and transportation efficiency. Methods This study proposes a lightweight vision transformer (ViT) student model trained using multi-granular knowledge distillation (KD) from a stronger data-efficient image transformer (DeiT)-Base teacher. The distillation framework integrates response-based soft-label supervision, attention transfer, and token-level feature regression to enhance representation learning under limited data conditions. Auxiliary lightweight architectures, including MobileNet, ConvNeXt, and EdgeNeXt, were trained independently to provide complementary predictions, and a weighted fusion strategy was employed for ensemble evaluation. Results The proposed ensemble ViT-KD with EdgeNeXt achieved 90% accuracy under the evaluated test split. To ensure statistical reliability and address potential partition bias, a stratified fivefold cross-validation was conducted on the dataset, yielding a mean accuracy of 86.89% ± 2.89% with consistent F1 scores and recall. The relatively low variance across the folds indicates stable internal generalization. Comparative experiments with conventional convolutional neural network (CNN) baselines and lightweight CNN baselines such as MobileViT-S and ShuffleNetV2 were performed, with the proposed ensemble framework achieving improved accuracy while maintaining computational efficiency. Computational analysis indicates that the stand-alone distilled ViT maintains a real-time inference capability of 8.79 ms per image, which supports suitability for edge-oriented agricultural applications. Discussion These results highlight the effectiveness of knowledge-distilled lightweight transformers for data-efficient maturity grading of cashew apples.

Why it matches plant phenotyping methodsカシューナッツ果実の成熟度という植物器官の状態を画像から推定する手法を開発し、交差検証・比較実験・推論速度評価まで行っており、フェノタイピング手法が中心である。

abstractThis study proposes a lightweight vision transformer (ViT) student model trained using multi-granular knowledge distillation (KD) from a stronger data-efficient image transformer (DeiT)-Base teacher.

Mixed-scale multivariate analysis reveals phenotypic structure in wood apple (Feronia limonia L.). →

Wood apple (Feronia limonia L.) is an underutilized perennial fruit tree with substantial ecological, nutritional, and economic potential, yet its phenotypic diversity and trait organization remain poorly characterized. Here, we applied a mixed-scale multivariate framework to resolve phenotypic structure in 62 wood apple genotypes using 31 ordinal and categorical vegetative, leaf, floral, fruit, and seed descriptors. Trait interrelationships were examined through the complementary use of Spearman’s rank correlation and Cramér’s V association analyses, capturing both directional rank-based dependencies and scale-independent categorical linkages. Hierarchical clustering based on Gower distance separated the genotypes into three distinct phenotypic clusters, with inter-cluster dissimilarities (0.92–1.18) consistently exceeding intra-cluster variation (0.42–0.55), indicating well-supported phenotypic stratification based on cluster validation. Multiple Correspondence Analysis (MCA) explained 23.30% of total inertia across the first two dimensions, with tree growth habit, branch angle, tree shape, and fruit color emerging as the principal drivers of phenotypic differentiation. Vegetative and leaf traits formed a tightly integrated module, whereas fruit-related traits displayed weaker monotonic but persistent categorical associations, reflecting partial phenotypic independence. The strong concordance among association analyses, clustering, and MCA indicates structured patterns of coordinated and partially independent trait associations in wood apple. Overall, this study demonstrates the effectiveness of mixed-scale multivariate approaches for resolving complex trait architecture in underutilized perennial fruit crops and provides a quantitative phenotypic framework to support germplasm conservation, parent selection, and ideotype-oriented improvement of wood apple.

Why it matches plant phenotyping methods混合尺度の多変量解析を用いて植物遺伝資源の表現型構造を定量化する手法が研究の中心であり、単なる生物学的実験の routine 測定ではない。

abstractHere, we applied a mixed-scale multivariate framework to resolve phenotypic structure in 62 wood apple genotypes using 31 ordinal and categorical vegetative, leaf, floral, fruit, and seed descriptors.

Frost damage segmentation in grapevine organs using YOLOv11s with ASPP and dynamic confidence thresholding. →

Climate change, particularly increasing frequency and intensity of spring frost events, poses a serious threat to viticulture by reducing yield and product quality. This study proposes an image processing and machine learning-based framework for early, rapid, and accurate segmentation of frost damage in vineyards using YOLOv11s enhanced with Atrous Spatial Pyramid Pooling (ASPP). A unique dataset called FGVL dataset from Sultana seedless grape vineyards in Manisa, Türkiye, following a severe frost event in April 2025. FGVL includes 418 frost-damaged grapes, 510 frost-damaged leaves, 395 healthy grapes, and 698 healthy leaves, all manually annotated by experts under natural field conditions. By integrating ASPP into YOLOv11s, proposed model improved multi-scale contextual feature extraction and achieved mAP@50 of 0.7686, demonstrating stronger performance in instance segmentation of small, overlapping, and visually similar grapevine organs. In addition, Dynamic Confidence Thresholding (DCT) strategy was introduced to improve prediction reliability in dense and visually complex vineyard scenes. Despite challenges such as background clutter, object overlap, and small target structures, model maintained stable performance with low computational demand, requiring only 6.45 GB of GPU memory. Proposed framework offers an accurate, efficient, and practically deployable early recognition system for frost damage assessment in viticulture.

Why it matches plant phenotyping methodsブドウの器官における霜害状態を画像からセグメンテーションする手法を開発・評価しており、植物の病害・障害状態の取得が研究の中心である。

abstractThis study proposes an image processing and machine learning-based framework for early, rapid, and accurate segmentation of frost damage in vineyards using YOLOv11s enhanced with Atrous Spatial Pyramid Pooling (ASPP).

Herbarium-based measurements are reliable predictors of fresh plant traits in Neotropical Myrtaceae →

Premise: Herbarium specimens are increasingly used to extract morphological traits for ecological and evolutionary studies, yet the effects of tissue desiccation on trait measurements remain poorly understood. Here, we tested whether higher tissue water content leads to greater measurement changes after herborization (H1) and whether fresh trait values can be reliably predicted from herbarium measurements (H2). Methods: We evaluated the reliability of herbarium-based measurements by comparing fresh and dried traits of leaves, flowers, fleshy fruits, and seeds across 262 individuals representing 133 Neotropical Myrtaceae species. Phylogenetic least square models and machine-learning regressions were used to test H1 and H2. Results: Leaves and flowers generally shrank after herborization, fruits size metrics tended to increase, and seeds were largely unaffected. Water content was significantly associated with the magnitude of herborization effects in flowers and some leaf and seed traits. Fresh trait values were accurately predicted from herbarium measurements. Prediction errors were lowest for leaf traits, followed by fruits, flowers, and seeds. Discussion: These results partially support H1 and support H2, indicating that herbarium specimens can be reliably used for trait analyses when organ-specific responses are considered, providing a practical framework to account for potential desiccation bias in functional trait research.

Why it matches plant phenotyping methodsハーバリウム標本による植物形態形質測定の信頼性評価と、生鮮形質の予測手法が研究の中心であり、植物フェノタイピング手法の検証に該当する。

abstractWe evaluated the reliability of herbarium-based measurements by comparing fresh and dried traits of leaves, flowers, fleshy fruits, and seeds across 262 individuals representing 133 Neotropical Myrtaceae species.

A Comprehensive Image Dataset of Fruit and Leaf Diseases Across Six Horticultural Crops for Deep Learning Applications →

Abstract Abstract. Accurate and timely identi cation of plant diseases is essential for improving crop productivity and ensuring sustainable agricultural practices. This paper presents a comprehensive image dataset of fruit and leaf diseases covering six economically important horticultural crops: Apple, Banana, Citrus, Guava, Mango, and Papaya. The dataset comprises high-quality RGB images representing both healthy and diseased samples, with disease symptoms including spots, lesions, discoloration, blight, rot, and fungal and bacterial infections captured under diverse real-world conditions. Variations in illumination, background complexity, viewing angles, growth stages, and symptom severity are intentionally included to enhance the robustness and generalizability of learning models developed using this data. The dataset is structured in a class-wise manner and preprocessed to support direct integration with deep learning frameworks. It is extensively used to train, validate, and evaluate deep learning based plant disease classi cation models, enabling automatic feature learning from raw images without manual intervention. Experimental usage demonstrates that the dataset is well suited for convolutional neural networks and attentionbased architectures, facilitating e ective discrimination between multiple disease categories across di erent crops and plant organs. By providing a uni ed multi-crop, multi-disease benchmark, this dataset aims to accelerate research in automated crop disease diagnosis, precision agriculture, and intelligent decision-support systems for sustainable farming.

Why it matches plant phenotyping methods植物の葉・果実の病徴画像を収録したデータセット／ベンチマークであり、病害状態の画像ベース推定を中心的に扱うため。

abstractThis paper presents a comprehensive image dataset of fruit and leaf diseases covering six economically important horticultural crops

ODANet: an occlusion and density aware network for small object detection of coffee cherry ripeness in complex field environments. →

Introduction Coffee cherry ripeness assessment is critical for harvesting efficiency and product quality, yet traditional manual inspection methods suffer from subjectivity and low efficiency. Methods To address the challenges of detecting small, occluded, and densely distributed coffee cherries in complex field environments, this study proposes an Occlusion and Density Aware Network (ODANet). Built upon the YOLOv8 framework, ODANet integrates three innovative modules: (1) Condition-Guided Windowed Attention (CGWA), which incorporates occlusion and density maps as auxiliary guidance signals for efficient feature enhancement; (2) Attention-guided Space-Preserving Convolution (ASPC), which employs space-to-depth transformation with cascaded attention to preserve spatial information during downsampling; and (3) Dual-Adaptive Dynamic Upsampling (DADU), which achieves content-adaptive feature reconstruction through dual-branch offset prediction with learnable fusion weights. Results Comprehensive evaluation on a publicly available dataset demonstrates that ODANet achieves state-of-the-art performance among 17 diverse detection architectures, attaining 76.7% mAP@0.5 with a 6.3 percentage point improvement over baseline YOLOv8, while maintaining computational efficiency (8.1 GFLOPs, 30.4M parameters) suitable for real-time deployment. Ablation studies validate the contributions of each module: ASPC improves performance by 2.2%, DADU by 0.6%, and CGWA by 3.5%. Discussion The model demonstrates robust performance across varying lighting conditions, occlusion levels, and growth stages, making it particularly suitable for practical agricultural deployment. This research provides an efficient solution for small object detection in precision agriculture.

Why it matches plant phenotyping methodsコーヒーチェリーの成熟度という植物器官の状態を画像から推定する検出手法を開発し、複数モデル比較・アブレーションで技術的に検証しているため、植物フェノタイピング手法が中心である。

abstractthis study proposes an Occlusion and Density Aware Network (ODANet)

Convolutional Neural Networks for Detecting White Grape Clusters in High-Density Vineyards →

This study addresses the challenge of detecting white grape clusters (Vitis vinifera L) in high-density vineyard canopies, a critical task for precision viticulture and yield estimation. Traditional statistical and image-processing methods have struggled with occlusion issues. In this work, over 100 field RGB images were collected at La Bergonza (Toledo, Spain) and expanded through data augmentation, with various preprocessing strategies tested to enhance cluster visibility. Convolutional Neural Network (CNN) architectures were compared, highlighting YOLOv8 as superior to Mask R-CNN in both accuracy and efficiency. YOLOv8, trained for up to 100 epochs on equalized and augmented datasets, achieved outstanding performance: 84.9% precision, 72.6% recall, and mAP@0.5 of 83%, far surpassing Mask R-CNN (17% precision, 26% recall). The model successfully detected partially hidden clusters, including those invisible to human experts, better than previous studies that required controlled backgrounds or artificial lighting. Results confirm that combining RGB equalization with data augmentation optimizes detection. These findings underscore the potential of deep learning and low-cost RGB imaging systems to enable automated, scalable solutions for yield estimation and canopy analysis. In conclusion, YOLOv8 emerges as a promising tool for accurate grape bunch detection under field conditions, overcoming previous limitations.

Why it matches plant phenotyping methodsブドウ房を対象としたRGB画像とCNNによる検出手法を開発・比較し、精度を定量評価しているため、植物器官の表現型取得が中心である。

abstractIn this work, over 100 field RGB images were collected at La Bergonza (Toledo, Spain) and expanded through data augmentation, with various preprocessing strategies tested to enhance cluster visibility.

Development of a spontaneous disease diagnosis tool by executing an enhanced convolutional neural network model for citrus fruits and leaves. →

Oranges, mandarins, bitter oranges, and lemons are examples of citrus fruits that make delicious meals and are highly nutritious. Citrus fruits suffer from a variety of infections that affect their yield. The Department of Agriculture wants to increase the production of oranges and lemons. On the other hand, several plant diseases and their advanced stages have impacted production. The quality of fruit influences market value and its financial effect. Therefore, accurate detection of ailments and their severity is crucial for improving the output and market value of oranges and lemons. To automatically evaluate and predict diseases in citrus leaves and fruits, this paper has proposed a modified convolutional neural network (ICNN) model. Python is used to create the ICNN model, and testing is performed using benchmark datasets from various repositories. The research presented here shows that ICNN performs better than traditional deep learning and machine learning models, such as the Convolutional Neural Network (CNN) and K-Nearest Neighbours (KNN). This illustrates how machine learning models require supplementary approaches to extract parameters from data that arrives in non-automated ways. Additionally, to improve the accuracy of their classification or prediction, deep learning models require pre-trained models. As a result, ICNN, an enhanced deep learning model that can automatically predict disease with higher accuracy than other models, represents an advancement over standard CNNs. Compared with KNN and CNN, ICNN achieves 99.69% accuracy.

Why it matches plant phenotyping methods柑橘の葉・果実の病害と重症度を画像から自動推定するCNN手法を開発し、ベンチマークデータセットで比較評価しており、植物フェノタイピング手法が中心である。

abstractTo automatically evaluate and predict diseases in citrus leaves and fruits, this paper has proposed a modified convolutional neural network (ICNN) model.

Manifold-based learning for high-throughput single-peanut phenotyping. →

Peanut (Arachis hypogaea L.), a major legume crop valued for its high oil content, displays complex genotypic-phenotypic interactions shaped by environmental influences, yet these relationships remain poorly understood. We present a high-throughput phenotyping framework that captures the geometry of peanut pods using digital microscopy or smartphone imaging integrated with manifold-learning for large-scale analysis and visualization. Using over 6500 pods collected across China, we identify a geographically distinct morphological signature and demonstrate accurate cultivar discrimination. This scalable approach establishes the foundation for a Large Geometric Model capable of predicting phenotypic traits and accelerating precision agriculture. Our pipeline offers a transformative tool for peanut breeding and sustainable crop improvement.

Why it matches plant phenotyping methodsデジタル顕微鏡・スマートフォン画像と多様体学習を統合し、ピーナッツ莢の形態を大規模に取得・解析する高スループット表現型解析フレームワークが中心である。

abstractWe present a high-throughput phenotyping framework that captures the geometry of peanut pods using digital microscopy or smartphone imaging integrated with manifold-learning for large-scale analysis and visualization.

AutoSiQ: a curated haploid Arabidopsis thaliana inflorescence dataset with a fine-grained silique ontology and a deep learning application for haploid fertility quantification. →

Doubled haploid (DH) technology can fast-track crop breeding. Haploid induction yields haploids with only one set of genomes, which are usually sterile. Haploid fertility (HF) is the ability of haploid plants to set seed, and it is a critical bottleneck in DH pipelines. Genetic mechanisms to restore HF hold immense potential in DH crop breeding, yet its phenotyping remains manual, destructive, and inconsistent. While recent advances in imaging and machine learning have improved throughput for general plant traits, no curated image dataset exists for Arabidopsis thaliana that explicitly represents HF. Here, we present AutoSiQ, a dataset and baseline deep learning pipeline for automated HF quantification. AutoSiQ includes high-resolution scanned inflorescences annotated with a seven-class ontology encompassing green siliques, green fertile siliques, mature siliques, fertile siliques, cracked fertile siliques, cracked siliques, and flowers. This multi-class annotation scheme preserves biologically meaningful information beyond binary fertile/non-fertile distinctions, enabling reliable fertility estimation and future phenotyping applications. We release baseline object detection models (YOLOv5), trained using the AutoSiQ dataset, and evaluate their performance across confidence thresholds. Model predictions strongly correlate with manual counts, achieving R² up to 0.94 for total silique number estimation. We further demonstrate AutoSiQ's utility for automated haploid fertility rate (HFR) estimation and genotype discrimination between two contrasting genotypes (WT and bmf2 mutant). A longitudinal analysis identifies ~60 days after sowing (DAS) as the optimal harvest time for maximizing mature silique counts by balancing between the number of immature buds and silique shattering. By releasing both the dataset and baseline code, AutoSiQ provides a reproducible and extensible foundation for high-throughput fertility phenotyping in haploid Arabidopsis .

Why it matches plant phenotyping methodsハプロイド稔性を画像から定量するデータセットと深層学習パイプラインを開発・評価しており、植物フェノタイピング手法が中心である。

abstractHere, we present AutoSiQ, a dataset and baseline deep learning pipeline for automated HF quantification.

Tomato Multi-Angle Multi-Pose Dataset for Fine-Grained Phenotyping. →

Abstract Observer bias and inconsistencies in traditional plant phenotyping methods limit the accuracy and reproducibility of fine-grained plant analysis. To address these limitations, TomatoMAP is introduced as a comprehensive dataset for Solanum lycopersicum . The dataset contains 68,080 RGB images: 3,616 high-resolution macrophotographs (3648 × 5472) with semantic annotations, and 64,464 moderate-resolution images (1080 × 1440) captured from 12 plant poses at four camera elevations. Each image is accompanied by manually annotated bounding boxes for seven regions of interest (leaves, panicle, flower clusters, fruit clusters, axillary shoot, shoot, and whole-plant area) and by labels spanning 50 BBCH classes representing phenologically growth stages. A general cascading structure is proposed. For real-time applicability, models emphasizing the accuracy-efficiency trade-off (MobileNetv3, YOLOv11, and Mask R-CNN) are prioritized and benchmarked against multiple state-of-the-art models. Performance is assessed using accuracy, mAP, inference FPS, and normalized confusion matrices. In a study involving five domain experts, AI models trained on TomatoMAP achieves comparable accuracy levels. Reliability of automated fine-grained phenotyping is supported by Cohen’s Kappa statistics and inter-rater agreement heatmaps.

Why it matches plant phenotyping methodsトマトの多視点画像、器官領域・生育ステージ注釈を備えたデータセットを構築し、画像モデルの精度・効率・専門家一致度をベンチマークしており、植物フェノタイピング手法が中心である。

titleTomato Multi-Angle Multi-Pose Dataset for Fine-Grained Phenotyping.

Enhancing strawberry maturity assessment using mid-infrared spectral analysis with advanced variable selection and supervised classification. →

Accurate and non-destructive assessment of fruit maturity is critical for sustainable agricultural practices. This study proposes a novel framework for evaluating strawberry ripeness using Mid-Infrared (MIR) spectroscopy combined with metaheuristic feature selection and supervised classification. A dataset of 443 strawberries spanning eight maturity stages was analyzed using six metaheuristic algorithms—Binary Grey Wolf Optimizer, Binary Particle Swarm Optimizer, Bee Colony Optimizer, Genetic Algorithm, Ant Colony Optimizer, and Gravitational Search Optimizer—integrated with four classifiers: Naïve Bayes, Decision Tree, Linear Discriminant Analysis, and Support Vector Machine. A new fitness function was designed to optimize classifier performance, and results were validated through Self-Organizing Map Neural Networks, cross-validation, and statistical significance testing. The Genetic Algorithm–Linear Discriminant Analysis combination achieved the highest and most stable accuracy (94.6–99%), outperforming existing image-based, deep learning, and conventional spectroscopic approaches while retaining interpretability. These findings demonstrate that metaheuristic-driven MIR analysis provides a robust, explainable, and efficient method for precise strawberry maturity assessment, offering significant potential for advancing eco-friendly and intelligent agricultural practices.

Why it matches plant phenotyping methodsイチゴ果実の成熟度という植物器官の状態を、MIR分光と特徴選択・分類器で非破壊推定する方法を開発し、交差検証や統計検定で性能評価しており、フェノタイピング手法が中心である。

abstractThis study proposes a novel framework for evaluating strawberry ripeness using Mid-Infrared (MIR) spectroscopy combined with metaheuristic feature selection and supervised classification.

BrinjalFruitX: A field-collected image dataset for machine learning and deep learning-based disease identification in brinjal fruits. →

Brinjal (Solanum melongena) or eggplant is one of the four most essential vegetable crops that are grown in Bangladesh and contribute significantly to the agricultural industry of the country. Brinjal supports the livelihood of numerous small farmers; however, brinjal is severely susceptible to various fruit diseases, which have serious impacts on yield quality and may cause considerable economic losses. While most existing plant disease datasets primarily focus on leaf-related disorders, only a limited number include fruit-related diseases and even those contain very few classes. This gap is significant because fruit diseases directly affect crop quality, market value, and overall yield. This is why we present here a new and comprehensive dataset that is unparalleled, exclusively for brinjal fruit diseases. This data set consists of 1823 high-quality, labelled images, across five distinct classes: Phomopsis Blight, Shoot and Fruit Borer, Fruit Cracking, Wet Rot, and Healthy Fruit. The images were collected from real farm conditions in numerous areas of Bangladesh to ensure a robust sample of varied environmental and farming practices impacting the growth of diseases. This dataset is designed with the unique aim to support plant disease research and enhance training of deep learning models for autonomous disease detection. Lastly, the dataset will allow early disease detection, enhancing crop management practice, reduction of losses, and increasing farmers' economic returns. The release of this dataset will encourage agricultural research as well as practical use in precision agriculture.

Why it matches plant phenotyping methodsナス果実の病徴を対象とした画像データセットの構築・公開が中心であり、植物の病害状態を画像から識別する再利用可能な表現型データ資源に該当する。

abstractwe present here a new and comprehensive dataset that is unparalleled, exclusively for brinjal fruit diseases.

OctoSplat: Hybrid OctoMap-Gaussian Splatting for Active Semantic Mapping and Phenotyping with Horticultural Robots →

Semantic reconstruction of agricultural scenes plays a vital role in tasks such as phenotyping and yield estimation. However, traditional approaches based on manual scanning or fixed camera setups remain a major bottleneck, while active-mapping methods based solely on occupancy grids are too coarse for accurate trait estimation. To address this gap, we propose an active 3D reconstruction framework for horticultural environments using a mobile manipulator. The system integrates OctoMap with 3D Gaussian Splatting to enable accurate and efficient target-aware mapping. A low-resolution OctoMap provides probabilistic occupancy information for informative viewpoint selection and collision-free planning, while 3D Gaussian Splatting leverages geometric, photometric, and semantic information to optimize 3D Gaussians for high-fidelity scene reconstruction. We further introduce a robust mapping strategy that mitigates semantic segmentation and depth noise, together with a background pruning method that reduces memory and computational cost. We validate our framework across simulated, laboratory, and real greenhouse scenes, showing consistent improvements across three state-of-the-art Gaussian Splatting backbones. In simulation, where ground-truth geometry is available, our approach outperforms occupancy-based mapping in both reconstruction accuracy and runtime efficiency: compared with a 0.01m-resolution OctoMap, it doubles the fruit-level F1 score under noisy conditions while achieving up to a threefold reduction in runtime. Beyond simulation, novel-view synthesis quality also improves consistently in laboratory and real greenhouse environments, with PSNR and mIoU improving by up to 1.5 dB and 18%, respectively. Finally, the reconstructed semantic maps enable fruit counting and volume estimation with accuracies approaching 80%.

Why it matches plant phenotyping methods園芸ロボット向けの3D再構成・能動マッピング手法を開発し、果実の計数・体積推定という植物形質の取得に適用・検証しているため、フェノタイピング手法が中心的です。

titleOctoSplat: Hybrid OctoMap-Gaussian Splatting for Active Semantic Mapping and Phenotyping with Horticultural Robots

A Biomass-Driven 3D Structural Model for Banana (Musa spp.) Fruit Fingers Across Genotypes →

Banana (Musa spp.) fruit morphology is a key determinant of yield and quality, yet modeling its 3D structural dynamics across genotypes remains difficult. To address this challenge, we developed a generic, biomass-driven 3D structural model for banana fruit fingers that quantitatively links growth and morphology. Field experiments were conducted over two growing seasons in Hainan, China, using three representative genotypes. Morphological traits, including outer and inner arc length, circumference, and pedicel length, along with dry (Wd) and fresh weight (Wf), were measured every 10 days after flowering until 110 days. Quantitative relationships between morphological traits and Wf, as well as between Wd and Wf, were fitted using linear or Gompertz functions with genotype-specific parameters. Based on these functions, a parameterized 3D reconstruction method was implemented in Python, combining biomass-driven growth equations, curvature geometry, and cross-sectional interpolation to simulate the fruit’s bending, tapering, and volumetric development. The resulting dynamic 3D models accurately reproduced genotype-specific differences in curvature, length, and shape with average fitting R2 > 0.95. The proposed biomass-driven 3D structural model provides a methodological framework for integrating banana fruit morphology into functional–structural plant models.

Why it matches plant phenotyping methodsバナナ果実の形態形質を推定・再現するバイオマス駆動型3D構造モデルを開発し、遺伝子型間の形状を検証しており、フェノタイピング手法が中心である。

abstractwe developed a generic, biomass-driven 3D structural model for banana fruit fingers that quantitatively links growth and morphology.

Spatially resolved analysis of growth dynamics in pome and drupe fruits of Rosaceae using 3D Gaussian Splatting. →

Fruit growth has long been described using single- or double-sigmoid curves; however, these temporal models cannot fully capture the spatial heterogeneity that ultimately shapes a fruit. Here, we present a three-dimensional analysis pipeline that non-destructively tracks spatial fruit growth dynamics from field-collected imagery. Surface landmarks were drawn, and video recordings were taken throughout development for three pome fruits, apple ( Malus × domestica ), Japanese pear ( Pyrus pyrifolia ) and European pear ( Pyrus communis ), and two drupe fruits, peach ( Prunus persica ) and Japanese apricot ( Prunus mume ), to track their motion. Using 3D Gaussian splatting, we successfully reconstructed 3D models of the fruits, and the landmark displacement could be measured with high accuracy, with R 2 ≥ 0.98 when compared to manual recordings. We found a common spatial growth gradient in the longitudinal growth shared in the pomes and drupes of the Rosaceae; proximal (stem-end) regions exhibited more pronounced growth than the distal (stylar) end. An exception was found in European pear 'Bartlett,' which showed relatively vigorous growth in the distal region, explaining its distinct shape with expanded distal end. Transverse expansion varied far less than longitudinal expansion, with a possible association with initial fruit morphology. Inter-fruit growth variability peaked in the fastest-growing regions, particularly in the distal area of the European pear, highlighting the link between growth vigor and phenotypic variance. These results provide foundational insights into the developmental dynamics of both pome and drupe fruits of the Rosaceae family, contributing to the optimization of fruit size, shape, and uniformity.

Why it matches plant phenotyping methods3D画像解析パイプラインと3D Gaussian Splattingを用いて果実の空間的成長を非破壊計測し、手動記録との精度比較で検証しているため、植物表現型取得法が中心である。

abstractHere, we present a three-dimensional analysis pipeline that non-destructively tracks spatial fruit growth dynamics from field-collected imagery.

Lightweight MSW-YOLOv8n-Seg: the instance segmentation of maturity on cherry tomato with improved YOLOv8n-Seg. →

Introduction Automatic and accurate segmentation of cherry tomato maturity in natural environment is the foundation for automatic picking. Lacking of significant differences in adjacent maturity and the problem of mutual occlusion between fruits usually affect the picking process. According to the changes in phenotypic characteristics of cherry tomato during its mature period and the Chinese national standard GH/T 1193-2021, a lightweight maturity instance segmentation method of cherry tomato with 5 levels, including green, turning, pink, light red and red was proposed based on improved YOLOv8n-Seg model, named as MobileViTv3-SK-WIoU-YOLOv8n-Seg (MSW-YOLOv8n-Seg). Methods In this model, MobileViTv3 was introduced into the original YOLOv8 model as backbone for feature extraction to reduce the parameters of the original model; selective kernel (SK) attention module was added to the neck part to improve the feature expression ability of the model; the complete intersection over union (CIoU) loss function in the original head part was replaced with wise intersection over union (WIoU), which can effectively filter low-quality samples and improve the stability and reliability of the model in complex scenes. The proposed model can better balance the relationship between segmentation speed, accuracy, and model computational complexity. Results The experimental results show that the bounding box precision, recall and mean average precision (mAP)@0.5 of the improved model on the test sets were 90.8%, 86.3% and 83.9% respectively, and the model size was 6.0 MB. Compared with YOLOv7-Mask, YOLOv8n-Seg, YOLOv9s-Seg, YOLO11n-Seg, Mask R-CNN (Mask region-based convolutional neural network) and Mask2Former, the bounding box precision increased by 9.6%, 5.2%, 5.7%, 12.3%, 13.3% and 5.0%, the recall increased by 7.8%, 7.4%, 8.8%, 13.1%, 13.9% and 0.1%, and the mAP@0.5 increased by 10.5%, 3.0%, 0.9%, 15.0%, 13.8% and 1.4% respectively. In terms of inference speed, the MSW-YOLOv8n-Seg has the highest inference speed, with FPS of up to 52.9 f·s -1 and latency of only 18.2ms, which demonstrates its real-time processing capability. Discussion The results show that the improved MSW-YOLOv8n-Seg model is optimal, and it suitable for instance segmentation scenarios with high real-time performance and can provide effective exploration for automated cherry tomato fruit picking.

Why it matches plant phenotyping methodsチェリートマト果実の成熟度という植物状態を画像から推定するインスタンスセグメンテーション手法を開発し、精度・速度・モデルサイズを比較検証しており、表現型取得法が中心である。

abstracta lightweight maturity instance segmentation method of cherry tomato with 5 levels, including green, turning, pink, light red and red was proposed based on improved YOLOv8n-Seg model

CropNeRF: A Neural Radiance Field-Based Framework for Crop Counting →

Rigorous crop counting is crucial for effective agricultural management and informed intervention strategies. However, in outdoor field environments, partial occlusions combined with inherent ambiguity in distinguishing clustered crops from individual viewpoints poses an immense challenge for image-based segmentation methods. To address these problems, we introduce a novel crop counting framework designed for exact enumeration via 3D instance segmentation. Our approach utilizes 2D images captured from multiple viewpoints and associates independent instance masks for neural radiance field (NeRF) view synthesis. We introduce crop visibility and mask consistency scores, which are incorporated alongside 3D information from a NeRF model. This results in an effective segmentation of crop instances in 3D and highly-accurate crop counts. Furthermore, our method eliminates the dependence on crop-specific parameter tuning. We validate our framework on three agricultural datasets consisting of cotton bolls, apples, and pears, and demonstrate consistent counting performance despite major variations in crop color, shape, and size. A comparative analysis against the state of the art highlights superior performance on crop counting tasks. Lastly, we contribute a cotton plant dataset to advance further research on this topic.

Why it matches plant phenotyping methodsNeRFと3Dインスタンスセグメンテーションを用いて作物個体・器官数を推定する画像ベース表現型計測手法を開発・検証しており、方法が研究の中心である。

abstractwe introduce a novel crop counting framework designed for exact enumeration via 3D instance segmentation.

Open RGB imaging workflow for morphological and morphometric analysis of fruits using deep learning: a case study on almonds. →

Background High-throughput phenotyping is addressing the current bottleneck in phenotyping within breeding programs. Imaging tools are becoming the primary resource for improving the efficiency of phenotyping processes and providing large datasets for genomic selection approaches. The advent of artificial intelligence (AI) brings new advantages by enhancing phenotyping methods using imaging, making them more accessible to breeding programs. In this context, we have developed an open Python workflow for analyzing morphology, color, and morphometric traits using AI, which can be applied to fruits and other plant organs. Results The workflow was implemented in almond (Prunus dulcis (Mill.) D. A. Webb), a species where breeding efficiency is critical due to its long breeding cycle. Over 25,000 kernels, more than 20,000 nuts, and over 600 individuals were phenotyped, making this the largest morphological study conducted in almond so far. The best segmentation and reconstruction approaches achieved error rates below 1%. Weight and area variables enabled accurate estimation of kernel thickness, with a root mean squared error of 0.47. Fifty-five heritable morphological, morphometric, and color traits were identified, highlighting their potential as target traits in breeding programs. Conclusion The proposed workflow demonstrated robust performance across diverse datasets and was effective with limited training data for fine-tuning. Its compatibility with the output of AI-based labeling tools allows users to fully leverage the advantages of these technologies-reducing manual effort, accelerating dataset preparation, and streamlining the fine-tuning process of segmentation models. This flexibility enhances the scalability and practical applicability of the workflow in real-world phenotyping scenarios, especially in the context of breeding programs.

Why it matches plant phenotyping methods植物器官の形態・色・形状特性を抽出するオープンなRGB画像解析ワークフローを開発し、分割・再構成精度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す。

abstractwe have developed an open Python workflow for analyzing morphology, color, and morphometric traits using AI, which can be applied to fruits and other plant organs.

PlantSpecLab: A comprehensive open-source platform for high-throughput plant spectral data processing and phenotypic modeling. →

High-throughput plant phenotyping with hyperspectral imaging (HSI) is pivotal for accelerating crop improvement to address global food security. Adoption is limited by a data-processing bottleneck, forcing a trade-off between costly, inflexible commercial software and programming-intensive open-source libraries. To overcome this barrier, we developed PlantSpecLab, an open-source, no-code platform that unifies the HSI workflow from image processing to modeling within a single interactive interface. The platform introduces spectrally guided segmentation strategies (Range Averaging, Difference Enhancement) and a spectral Fractional-Order Differencing (FOD) preprocessor to enhance extraction of subtle, physiologically relevant features. Across diverse in-house and public datasets, FOD-preprocessed spectra improved model performance over conventional pipelines, yielding 87.35% accuracy for tomato maturity and R 2 = 0.878 for fruit firmness. In cross-software benchmarks, PlantSpecLab matched the accuracy of ENVI and code-based Python pipelines while reducing end-to-end workflow time by >90% (>80 min to ∼8 min). PlantSpecLab provides a transparent, efficient analytical environment that lowers the technical barrier to HSI analysis. This enables researchers to prioritize biological interpretation while minimizing computational overhead.

Why it matches plant phenotyping methods植物のハイパースペクトル画像から表現型特徴を抽出・モデル化するオープンソース基盤を開発し、既存ソフトウェアとの性能・処理時間を比較検証しているため、フェノタイピング手法が中心である。

abstractwe developed PlantSpecLab, an open-source, no-code platform that unifies the HSI workflow from image processing to modeling within a single interactive interface.

Enhancing annotations for 5D apple pose estimation through 3D Gaussian Splatting (3DGS) →

Automating tasks in orchards is challenging because of the large amount of variation in the environment and occlusions. One of the challenges is apple pose estimation, where key points, such as the calyx, are often occluded. Recently developed pose estimation methods no longer rely on these key points, but still require them for annotations, making annotating challenging and time-consuming. Due to the abovementioned occlusions, there can be conflicting and missing annotations of the same fruit between different images. Novel 3D reconstruction methods can be used to simplify annotating and enlarge datasets. We propose a novel pipeline consisting of 3D Gaussian Splatting to reconstruct an orchard scene, simplified annotations, automated projection of the annotations to images, and the training and evaluation of a pose estimation method. Using our pipeline, 105 manual annotations were required to obtain 28,191 training labels, a reduction of 99.6%. Experimental results indicated that training with labels of fruits that are $\leq95\%$ occluded resulted in the best performance, with a neutral F1 score of 0.927 on the original images and 0.970 on the rendered images. Adjusting the size of the training dataset had small effects on the model performance in terms of F1 score and pose estimation accuracy. It was found that the least occluded fruits had the best position estimation, which worsened as the fruits became more occluded. It was also found that the tested pose estimation method was unable to correctly learn the orientation estimation of apples.

Why it matches plant phenotyping methodsリンゴの姿勢推定アノテーションを大幅に効率化する3D再構成・自動ラベル投影パイプラインを開発し、姿勢推定性能も評価しているため、植物フェノタイピング手法が中心である。

abstractWe propose a novel pipeline consisting of 3D Gaussian Splatting to reconstruct an orchard scene, simplified annotations, automated projection of the annotations to images, and the training and evaluation of a pose estimation method.

TomatoRipen-MMT: transformer-based RGB and NIR spectral fusion for tomato maturity grading. →

Computer vision and multispectral imaging have increasingly become essential tools in modern precision agriculture. Accurate ripeness assessment is critical for yield optimization, reducing post-harvest losses, and enabling automated harvesting systems. However, traditional RGB-based approaches struggle to differentiate subtle maturity changes, and existing solutions often fail under varying lighting, occlusion, or cultivar-specific conditions. To address these challenges, this study focuses on the integration of complementary spectral cues for reliable tomato ripeness evaluation. The work utilizes a curated RGB-NIR tomato dataset comprising 224 hyperspectral samples, processed into aligned multimodal image pairs with balanced ripeness categories.The proposed TomatoRipen-MMT model employs a multimodal Transformer framework with dual encoders, cross-spectral attention, and a joint decoder to fuse spatial and biochemical cues. The novelty of the methodology lies in the dynamic cross-attention mechanism, which learns inter-modal dependencies between RGB and NIR signals for enhanced ripeness interpretation. Performance metrics including accuracy, precision, recall, F1-score, mIoU, and AUC were used to comprehensively evaluate the system. Experimental results demonstrate that TomatoRipen-MMT significantly outperforms all baseline RGB-only, NIR-only, and fusion methods, achieving 94.8% classification accuracy and 82.6% mIoU. These findings establish the effectiveness of multimodal Transformers for robust, high-precision fruit maturity assessment in controlled and greenhouse environments.

Why it matches plant phenotyping methodsトマト果実の成熟度という植物器官の状態を、RGB・NIR画像融合とTransformerで推定する手法を開発・評価しており、フェノタイピング手法が中心です。

abstractThe proposed TomatoRipen-MMT model employs a multimodal Transformer framework with dual encoders, cross-spectral attention, and a joint decoder to fuse spatial and biochemical cues.

YOLO-SAM AgriScan: A Unified Framework for Ripe Strawberry Detection and Segmentation with Few-Shot and Zero-Shot Learning. →

Traditional segmentation methods are slow and rely on manual annotations, which are labor-intensive. To address these limitations, we propose YOLO-SAM AgriScan, a unified framework that combines the fast object detection capabilities of YOLOv11 with the zero-shot segmentation power of the Segment Anything Model 2 (SAM2). Our approach adopts a hybrid paradigm for on-plant ripe strawberry segmentation, wherein YOLOv11 is fine-tuned using a few-shot learning strategy with minimal annotated samples, and SAM2 performs mask generation without additional supervision. This architecture eliminates the bottleneck of pixel-wise manual annotation and enables the scalable and efficient segmentation of strawberries in both controlled and natural farm environments. Experimental evaluations on two datasets, a custom-collected dataset and a publicly available benchmark, demonstrate strong detection and segmentation performance in both full-data and data-constrained scenarios. The proposed framework achieved a mean Dice score of 0.95 and an IoU of 0.93 on our collected dataset and maintained competitive performance on public data (Dice: 0.95, IoU: 0.92), demonstrating its robustness, generalizability, and practical relevance in real-world agricultural settings. Our results highlight the potential of combining few-shot detection and zero-shot segmentation to accelerate the development of annotation-light, intelligent phenotyping systems.

Why it matches plant phenotyping methodsイチゴ果実の検出・セグメンテーションを行う画像ベース手法を開発し、複数データセットで性能評価している。単なる収穫対象の位置特定ではなく、果実マスク抽出を行うため、植物表現型取得手法が中心である。

abstractOur approach adopts a hybrid paradigm for on-plant ripe strawberry segmentation

CitriBEiTNet: A Hybrid CNN-Transformer Architecture Combining MobileNetV2 with BEiT's Global Attention for Automated Citrus Leaf Disease Diagnosis →

Citrus farming plays an essential role in agriculture; however, diseases like canker, greening, black spot, and melanose significantly reduce yield and fruit quality. Efficient classification of citrus leaf diseases is important for crop health maintenance and optimal crop yield. Traditional methods for leaf disease detection are slow, labor-intensive, and often inaccurate, which highlights the need for automated solutions. This research presents a novel hybrid approach for identifying citrus diseases by combining a vision transformer with deep learning architectures. Using Bidirectional Encoder Representation from Image Transformers (BEIT) and MobileNetV2 as feature extractors, the proposed model captures distinctive features from images, which are then classified using Support Vector Machine (SVM). The dataset includes four different disease categories and a healthy class. Data augmentation techniques are applied to improve model robustness. The experimental findings demonstrate that CitriBEiTNet achieves a remarkable training accuracy of 99.82% and a testing accuracy of 99.57%, outperforming current leading techniques. This model provides an efficient, scalable, and economical approach for early disease identification, enabling farmers to take preventive measures and improve agricultural yields.

Why it matches plant phenotyping methods柑橘葉画像から病害状態を自動分類する深層学習手法の開発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。

abstractThis research presents a novel hybrid approach for identifying citrus diseases by combining a vision transformer with deep learning architectures.

ORANGE PLANT LEAF DISEASE DETECTION AND CLASSIFICATION WITH IMAGE PROCESSING USING A DEEP CONVOLUTIONAL NEURAL NETWORK →

The farming of citrus is a crucial component of Pakistan’s fruit-based agricultural economy. But, the foliar diseases citrus canker, black spot, and greening have been posing a constant threat on citrus’s productivity. An optimal solution is an early and accurate detection of these diseases to improve the productivity. Therefore, this paper proposes an automated citrus leaf disease detection and classification framework based on deep convolutional neural networks (DCNNs). The proposed solution has five stages: image acquisition (dataset), preprocessing, data augmentation, deep feature extraction and optimization, and disease classification. Firstly, the images are obtained from a public dataset downloaded from Kaggle. Secondly, preprocessing techniques are used to improve the image quality and shape, thirdly the data augmentation techniques are used to enhance the model generalization, fourthly pre-trained models DenseNet-121, MobileNet, and InceptionV3 with transfer learning technique to extract deep features, and finally Adam optimizer and categorical cross-entropy loss function are used to fine tune the pre-trained models for classifications. The proposed model is evaluated on accuracy, precision, recall, and F1-score metrics. All the models demonstrated robust performance while DenseNet-121 achieved the best performance. The evaluation results assured the robustness of the use of transfer learning-based DCNN in citrus leaf disease detection.

Why it matches plant phenotyping methods柑橘葉の病害状態を画像から直接検出・分類する深層学習ワークフローが研究の中心であり、植物病害フェノタイピング手法に該当する。

abstractTherefore, this paper proposes an automated citrus leaf disease detection and classification framework based on deep convolutional neural networks (DCNNs).

LBS-YOLO: a lightweight model for strawberry ripeness detection. →

Introduction The traditional strawberry picking operation has long relied on manual work. With the aging trend of the population becoming more and more obvious, the application of intelligent picking technology has become an irreversible trend. However, existing recognition methods still face bottlenecks such as suboptimal recognition accuracy and low computational efficiency. To address these issues, this study constructs a lightweight detection model, LBS-YOLO, based on an improved YOLOv11n architecture, significantly the model's accuracy and interference robustness while greatly compressing the parameter quantity. Methods The LBS-YOLO model is built upon YOLOv11n as the baseline network. In order to enhance the ability of backbone network feature representation, the model designs a lightweight LAWDS module. This design combines channel attention with spatial reconstruction operation to optimize the information retention efficiency in the down-sampling process, thus effectively enhancing the multi-scale feature representation ability and gradient flow propagation performance. Then in the feature fusion stage, the model introduces a Bidirectional Feature Pyramid Network (BiFPN), which not only enables cross-scale feature fusion but also achieves adaptive weighting through a learnable weight allocation mechanism. At last, adopts the C3k2_Star module to replace the conventional C3K2 for improved feature representation. Results On the used strawberry dataset, the LBS-YOLO model reached 88.6% mAP@0.5 and 75.8% mAP@0.5:0.95, which were 2.2 and 1.3 percentage points higher than YOLOv11n, respectively. The LBS-YOLO model improves the recall rate from 83.2% of YOLOv11n to 86.4%, and the F1-score from 81.2% to 82.9%. Its computational complexity is 6.6 GFLOPs and its reasoning speed is 260.7 FPS. Even better, LBS-YOLO only needs 3.4MB of storage space and 1.6 million parameters, which are 34.6% and 38% less than YOLOv11n respectively. Discussion The experiment demonstrates that, the LBS-YOLO model can significantly reduce the number of parameters and effectively improve the detection accuracy and operation efficiency. It successfully alleviated the problems of false detection and missed detection, thereby providing reliable technical support for strawberry growth monitoring, maturity identification and automatic picking.

Why it matches plant phenotyping methodsイチゴの成熟度という植物状態を画像から推定する軽量検出モデルを開発・評価しており、フェノタイピング手法が中心である。

abstractthis study constructs a lightweight detection model, LBS-YOLO, based on an improved YOLOv11n architecture

Simultaneous Identification on Tomato Variety and Maturity Based on Local and Global Feature Fusion. →

Varieties show their unique characteristics in morphology, growth, and fruits. Tomato maturity is related to multiple dimensional characteristics including color, texture, smell, etc. An effective classification method of tomato variety and maturity is crucial for evaluating its growth and yield. However, due to the complex growth environment, some problems such as leaf occlusion and fruit shaded by each other make it difficult to accurately and efficiently identify them. To solve these problems, this study innovatively proposes a simultaneous detection model on tomato variety and maturity based on improved YOLOv8n, with the combination of frequency-adaptive dilated convolution (FADC) feature extraction module and the high-level screening-feature path aggregation network (HSPAN) with the aim of local and global feature fusion by the channel attention module and feature selection fusion mechanism. In addition, we use the Powerful-IoU (PIoU) loss function to replace the original Complete IoU (CIoU) to enhance the accuracy of bounding boxes. We also introduce a dynamic detection head as the final output of the model, which can adaptively adjust the focus of feature extraction according to the color and size of tomato fruits, thereby improving the recognition accuracy. Experimental results show that our model with better global perception capability achieves the highest detection accuracy and lower computation complexity among the comparative models.

Why it matches plant phenotyping methodsトマト果実の成熟度という観察可能な植物状態を画像から推定する検出モデルを開発しており、特徴抽出・検出ヘッド・損失関数の改良と比較評価が研究の中心である。

abstractthis study innovatively proposes a simultaneous detection model on tomato variety and maturity based on improved YOLOv8n

Pomegranate disease detection and classification dataset for deep learning applications: A case study from Halabja city. →

Timely and accurate detection of pomegranate fruit diseases is critical for minimizing crop losses, preserving fruit quality, and supporting sustainable agricultural practices. This study introduces the Halabja Pomegranate Fruit Disease Image Dataset, a systematically compiled collection of images from orchards in one of Iraq's major pomegranate-producing regions. The dataset comprises 2178 original images and 28,314 augmented images, categorized into four specific classes: ectomyelois ceratoniae, colletotrichum spp., sunburn, and healthy fruit samples. To create an ecological setting and ensure significant class variation, images were captured in natural outdoor environments. A standard preprocessing step was applied, which involved resizing all images to 512×512 pixels and using several image augmentation techniques to improve the flexibility and robustness of machine learning models. The unique characteristics of this dataset make it highly suitable for developing machine learning and deep learning models aimed at plant disease detection and other computer vision tasks in precision agriculture. Its contextual relevance and content diversity make it valuable for building an effective diagnostic tool capable of functioning in real field conditions.

Why it matches plant phenotyping methods植物病害状態を画像で分類するデータセットの構築が中心で、再利用可能な植物表現型データとして適格です。

abstractThis study introduces the Halabja Pomegranate Fruit Disease Image Dataset

UAV-based monocular 3D panoptic mapping for fruit shape completion in orchard →

Accurate fruit shape reconstruction under real-world field conditions is essential for high-throughput phenotyping, sensor-based yield estimation, and orchard management. Existing approaches based on 2D imaging or explicit 3D reconstruction often suffer from occlusions, sparse views, and complex scene dynamics as a result of the plant geometries. This paper presents a novel UAV-based monocular 3D panoptic mapping framework for robust and scalable fruit shape completion in orchards. The proposed method integrates (1) Grounded-SAM2 for multi-object tracking and segmentation (MOTS), (2) photogrammetric structure-from-motion for 3D scene reconstruction, and (3) DeepSDF, an implicit neural representation, for completing occluded fruit geometries with a neural network. We furthermore propose a new MOTS evaluation protocol to assess tracking performance without requiring ground truth annotations. Experiments conducted in both controlled laboratory conditions and an operational apple orchard demonstrate the accuracy of our 3D fruit reconstruction at the centimeter level. The Chamfer distance error of the proposed shape completion method using the DeepSDF shape prior reduces this to the millimeter level, and outperforms the traditional method, while Grounded-SAM2 enables robust fruit tracking across challenging viewpoints. The approach is highly scalable and applicable to real-world agricultural scenarios, offering a promising solution to reconstruct complete fruits with visibility higher than 10% for precise 3D fruit phenotyping at a large scale under occluded conditions.

Why it matches plant phenotyping methods果実形状を対象とするUAV画像・3D再構成・形状補完法を開発し、実験で精度評価しており、植物表現型取得が研究の中心である。

abstractThis paper presents a novel UAV-based monocular 3D panoptic mapping framework for robust and scalable fruit shape completion in orchards.

GAE-YOLO: a lightweight multimodal detection framework for tomato smart agriculture with edge computing →

Introduction The advancement of smart agriculture has witnessed increasing applications of computer vision in crop monitoring and management. However, existing approaches remain challenged by high computational complexity, limited real-time capability, and poor multi-task coordination in tomato cultivation scenarios. Methods To address these limitations, an intelligent tomato management system is proposed based on the Ghost-based Adaptive Efficient You Only Look Once (GAE-YOLO) algorithm. The lightweight architecture of the GAE-YOLO framework is achieved through the replacement of standard convolutional layers with Ghost Convolution (GhostConv) modules, while detection accuracy is significantly improved by the integration of both AReLU activation functions and Effective Intersection over Union (E-IoU) loss optimization. The system, implemented on a Jetson TX2 embedded platform, also incorporates ZED stereo vision for 3D localization and a PyQt6-based visualization platform. Results When implemented on Jetson TX2, the system achieving 93.5% mean Average Precision at 50% intersection over union (mAP@50) at 10.2 frames per second (FPS), which can be optimized to 27 FPS by employing TensorRT acceleration and 720p resolution for scenarios demanding higher throughput. Furthermore, it establishes standardized assessment systems for tomato maturity and yield prediction, and offers integrated modules for disease diagnosis and agricultural large language model consultation. Discussion This work establishes a new paradigm for edge computing in agriculture while providing critical technical support for smart farming development.

Why it matches plant phenotyping methodsトマトの成熟度・収量予測および病害診断を含む画像・3Dビジョン基盤を開発し、エッジ環境で性能評価しているため、植物表現型取得が中心的な研究である。

abstractan intelligent tomato management system is proposed based on the Ghost-based Adaptive Efficient You Only Look Once (GAE-YOLO) algorithm

KAN-GLNet: An enhanced PointNet++ model for canola silique segmentation and counting →

Accurate analysis of plant phenotypic traits is crucial for crop breeding and precision agriculture. This study proposes a lightweight semantic segmentation model named KAN-GLNet (Kolmogorov-Arnold Network with Global-Local Feature Modulation), based on an enhanced PointNet++ architecture and integrated with an optimized Density-Based Spatial Clustering of Applications with Noise (DBSCAN) algorithm, to achieve high-precision segmentation and automatic counting of canola siliques. A multi-view point cloud acquisition platform was built, and high-fidelity canola point clouds were reconstructed using Neural Radiance Fields (NeRF) technology. The proposed model includes three key modules: Reverse Bottleneck Kolmogorov-Arnold Network Convolution, a Global-Local Feature Modulation (GLFN) block, and a contrastive learning-based normalization module called ContraNorm. KAN-GLNet contains only 5.72M parameters and achieves 94.50% mIoU, 96.72% mAcc, and 97.77% OAcc in semantic segmentation tasks, outperforming all baseline models. In addition, the DBSCAN workflow was optimized, achieving a counting accuracy of 97.45% in the instance segmentation task. This method achieves an excellent balance between segmentation accuracy and model complexity, providing an efficient solution for high-throughput plant phenotyping. The code and dataset have been made publicly available at: https://anonymous.4open.science/r/KAN-GLNet-6432/.

Why it matches plant phenotyping methodsカノーラ莢のセグメンテーションと自動計数という植物形質抽出手法を、3D点群取得基盤・NeRF再構成・新規モデル・DBSCANワークフローとして開発・評価しており、植物フェノタイピング手法が中心である。

abstractThis study proposes a lightweight semantic segmentation model named KAN-GLNet (Kolmogorov-Arnold Network with Global-Local Feature Modulation), based on an enhanced PointNet++ architecture and integrated with an optimized Density-Based Spatial Clustering of Applications with Noise (DBSCAN) algorithm, to achieve high-precision segmentation and automatic counting of canola siliques.

Depth Imaging-Based Framework for Efficient Phenotypic Recognition in Tomato Fruit. →

Tomato is a globally significant horticultural crop with substantial economic and nutritional value. High-precision phenotypic analysis of tomato fruit characteristics, enabled by computer vision and image-based phenotyping technologies, is essential for varietal selection and automated quality evaluation. An intelligent detection framework for phenomics analysis of tomato fruits was developed in this study, which combines image processing techniques with deep learning algorithms to automate the extraction and quantitative analysis of 12 phenotypic traits, including fruit morphology, structure, color and so on. First, a dataset of tomato fruit section images was developed using a depth camera. Second, the SegFormer model was improved by incorporating the MLLA linear attention mechanism, and a lightweight SegFormer-MLLA model for tomato fruit phenotype segmentation was proposed. Accurate segmentation of tomato fruit stem scars and locular structures was achieved, with significantly reduced computational cost by the proposed model. Finally, a Hybrid Depth Regression Model was designed to optimize the estimation of optimal depth. By fusing RGB and depth information, the framework enabled efficient detection of key phenotypic traits, including fruit longitudinal diameter, transverse diameter, mesocarp thickness, and depth and width of stem scar. Experimental results demonstrated a high correlation between the phenotypic parameters detected by the proposed model and the manually measured values, effectively validating the accuracy and feasibility of the model. Hence, we developed an equipment automatically phenotyping tomato fruits and the corresponding software system, providing reliable data support for precision tomato breeding and intelligent cultivation, as well as a reference methodology for phenotyping other fruit crops.

Why it matches plant phenotyping methods深度カメラ、画像処理、深層学習を統合し、トマト果実の12形質を自動抽出・定量する装置とソフトウェアを開発しており、表現型取得法が研究の中心である。

abstractAn intelligent detection framework for phenomics analysis of tomato fruits was developed in this study, which combines image processing techniques with deep learning algorithms to automate the extraction and quantitative analysis of 12 phenotypic traits

Early Detection of Jujube Shrinkage Disease by Multi-Source Data on Multi-Task Deep Network. →

In the arid cultivation region of Xinjiang, China, shrinkage disease severely compromises the quality, yield, and market value of jujube. Published research has achieved high accuracy in detecting larger lesions using RGB imaging and hyperspectral imaging (HSI). However, these methods lack sensitivity in detecting early and subtle symptoms of disease. In this study, a multi-source data fusion strategy combining RGB imaging and HSI was proposed for non-destructive and high-precision detection of early-stage jujube shrinkage disease. Firstly, a total of 317 fruits of the 'Junzao' cultivar were collected during multiple stages of natural infection, covering early-stage shrinkage disease detection across different growth stages, including both green and mature red fruits. Secondly, morphological features were extracted from RGB images in multiple dimensions, while a three-stage feature selection strategy combining Principal Component Analysis (PCA), the Successive Projections Algorithm (SPA), and the Genetic Algorithm (GA) was implemented to identify four key wavelengths from HSI. Thirdly, a hybrid convolutional neural network-multilayer perceptron (CNN-MLP) architecture was constructed, with dynamic feature weighting employed to achieve effective multimodal fusion and optimize detection performance. Experimental results demonstrated that compared to the MLP and CNN models, the proposed method achieved approximately 8.0% and 5.4% improvements in accuracy and 38.6% and 32.4% improvements in F1 scores, respectively. It offers a robust and scalable solution for early disease detection and postharvest quality assessment in jujube production.

Why it matches plant phenotyping methodsRGB画像・HSIから果実の病斑形態と分光特徴を抽出し、マルチモーダル深層学習で植物病害状態を検出する手法の開発・性能評価が中心であるため。

abstracta multi-source data fusion strategy combining RGB imaging and HSI was proposed for non-destructive and high-precision detection of early-stage jujube shrinkage disease.

APTES: a high-throughput deep learning-based Arabidopsis phenotypic trait estimation system for individual leaves and siliques. →

High-throughput phenotyping of growth kinetics and organ size in the model plant Arabidopsis thaliana requires rapid and precise methods for trait estimation. To address this need, we developed the Arabidopsis Phenotypic Trait Estimation System, APTES, an open-access, high-throughput program that uses computer vision and deep learning to extract 64 leaf traits and 64 silique traits from photographs. The enhanced segmentation model Cascade Mask Region-based Convolutional Neural Network (Mask R-CNN) achieved precision (measure of positive prediction accuracy), recall (sensitivity in detection), and F1 score values (harmonic mean of precision and recall) of 0.965, 0.958, and 0.961, respectively, for individual leaf segmentation. These metrics demonstrated a consistent improvement of approximately 1 percentage point over the baseline model. For silique segmentation, our enhanced DetectoRS model for silique segmentation attained precision, recall, and F1 scores of 0.954, 0.930, and 0.942, respectively. Notably, precision increased by 1%, while the F1 score improved by 2 percentage points. Trait parameters were automatically calculated with coefficient of determination values for leaf and silique traits ranging from 0.776 to 0.976 and mean absolute percentage error values from 1.89% to 7.90%. We phenotyped 166 Arabidopsis accessions, using APTES, and subjected the resulting values to a genome-wide association study (GWAS), revealing 1,042 single-nucleotide polymorphisms (SNPs) as being significantly associated with 18 leaf and silique traits, and one significant SNP on chromosome 3 linked to silique number. Furthermore, we validated APTES across other public Arabidopsis databases and other plant species, with segmentation results demonstrating its applicability across diverse datasets. In conclusion, APTES is a valuable automated tool for leaf and silique segmentation and trait estimation, which should offer benefits to the broader plant science community. Supplementary information The online version contains supplementary material available at 10.1007/s42994-025-00239-y.

Why it matches plant phenotyping methods植物の葉・莢の形質を画像から抽出する深層学習システムを開発し、性能検証・他データセットでの妥当性確認まで行っており、フェノタイピング手法が研究の中心である。

abstractwe developed the Arabidopsis Phenotypic Trait Estimation System, APTES, an open-access, high-throughput program that uses computer vision and deep learning to extract 64 leaf traits and 64 silique traits from photographs.

An RGB-D Image Dataset for Lychee Detection and Maturity Classification for Robotic Harvesting →

Lychee is a high-value subtropical fruit. The adoption of vision-based harvesting robots can significantly improve productivity while reduce reliance on labor. High-quality data are essential for developing such harvesting robots. However, there are currently no consistently and comprehensively annotated open-source lychee datasets featuring fruits in natural growing environments. To address this, we constructed a dataset to facilitate lychee detection and maturity classification. Color (RGB) images were acquired under diverse weather conditions, and at different times of the day, across multiple lychee varieties, such as Nuomici, Feizixiao, Heiye, and Huaizhi. The dataset encompasses three different ripeness stages and contains 11,414 images, consisting of 878 raw RGB images, 8,780 augmented RGB images, and 1,756 depth images. The images are annotated with 9,658 pairs of lables for lychee detection and maturity classification. To improve annotation consistency, three individuals independently labeled the data, and their results were then aggregated and verified by a fourth reviewer. Detailed statistical analyses were done to examine the dataset. Finally, we performed experiments using three representative deep learning models to evaluate the dataset. It is publicly available for academic

Why it matches plant phenotyping methodsライチ果実の成熟段階という植物器官の状態をRGB-D画像から分類するデータセットを構築し、アノテーション検証と深層学習モデル評価を行っており、表現型取得・評価手法が中心である。

abstractwe constructed a dataset to facilitate lychee detection and maturity classification.

Deep learning driven, image-based phenotyping of seed processing efficiency in sainfoin ( Onobrychis viciifolia ). →

Introduction: spp.) is a perennial legume traditionally cultivated as a forage crop and is now emerging as a promising candidate for development as a perennial grain legume. Despite its potential, no research has addressed the breeding of sainfoin varieties with superior grain processing properties. Methods: We conducted a multifactorial experiment to evaluate the depodding and dehulling efficiency of five commercially available sainfoin varieties. Seeds were processed using two different methods (belt thresher and impact dehuller) across five sample sizes. A pre-trained Faster R-CNN (Region-based Convolutional Neural Network) object detection model was fine-tuned to identify intact pods, whole seeds, and split seeds from images of the processed mixtures. These predictions were used to calculate processing efficiency (PE) for each variety. A comprehensive power analysis was performed to determine the minimum sample size of sainfoin pods required to detect differences in PE with high statistical power. Results: We observed strong varietal differences in PE, as well as clear effects of the processing method. Belt threshing produced mixtures with more intact pods, while the impact dehuller generated a higher proportion of split seeds. Increasing sample size led to more intact pods across all varieties and methods, and notably decreased seed proportion in belt-threshed samples. Statistical modeling combined with object detection outputs revealed that a minimum of 2 g of pods is required to reliably detect an absolute proportional difference of 0.25 in PE between two breeding lines with 80% power. Discussion: Our findings demonstrate that sainfoin varieties differ significantly in processing efficiency and that processing outcomes depend strongly on both method and sample size. Integrating deep learning-based phenotyping with robust statistical design enables efficient evaluation of processing traits and provides actionable guidelines for breeding programs. While deep learning models offer powerful, cost-effective tools for plant phenotyping, their outputs must be paired with rigorous statistical design to yield reliable and actionable insights for crop improvement.

Why it matches plant phenotyping methods画像からポッド・種子を検出し、処理効率という植物由来形質を算出する深層学習ベースの表現型解析が研究の中心であるため。

titleDeep learning driven, image-based phenotyping of seed processing efficiency in sainfoin

Cott-ADNet: Lightweight Real-Time Cotton Boll and Flower Detection Under Field Conditions →

Cotton is one of the most important natural fiber crops worldwide, yet harvesting remains limited by labor-intensive manual picking, low efficiency, and yield losses from missing the optimal harvest window. Accurate recognition of cotton bolls and their maturity is therefore essential for automation, yield estimation, and breeding research. We propose Cott-ADNet, a lightweight real-time detector tailored to cotton boll and flower recognition under complex field conditions. Building on YOLOv11n, Cott-ADNet enhances spatial representation and robustness through improved convolutional designs, while introducing two new modules: a NeLU-enhanced Global Attention Mechanism to better capture weak and low-contrast features, and a Dilated Receptive Field SPPF to expand receptive fields for more effective multi-scale context modeling at low computational cost. We curate a labeled dataset of 4,966 images, and release an external validation set of 1,216 field images to support future research. Experiments show that Cott-ADNet achieves 91.5% Precision, 89.8% Recall, 93.3% mAP50, 71.3% mAP, and 90.6% F1-Score with only 7.5 GFLOPs, maintaining stable performance under multi-scale and rotational variations. These results demonstrate Cott-ADNet as an accurate and efficient solution for in-field deployment, and thus provide a reliable basis for automated cotton harvesting and high-throughput phenotypic analysis. Code and dataset is available at https://github.com/SweefongWong/Cott-ADNet.

Why it matches plant phenotyping methods綿花の花・ボール認識を対象とする画像解析手法を開発し、データセット作成、外部検証、性能評価まで行っており、植物器官の表現型取得が中心である。

abstractWe propose Cott-ADNet, a lightweight real-time detector tailored to cotton boll and flower recognition under complex field conditions.

A labeled image dataset of common tomato diseases for classification and object detection. →

Computer vision has emerged as a critical enabler of sustainable production in protected agriculture by offering efficient and non-invasive crop disease diagnosis. The development of accurate disease recognition models relies heavily on the availability of high-quality image datasets. This study introduces a tomato disease image dataset collected in 2024 from greenhouse facilities within a modern agricultural park in Sichuan Province, China. The dataset comprises 1026 high-resolution images, including 417 images of viral disease, 82 images of gray mold, and 527 images of bacterial wilt, totaling approximately 2.78 GB. Captured under real-world greenhouse conditions and from multiple angles and distances, the images effectively capture multi-scale phenotypic disease features. Manual annotation was conducted using the LabelImg tool under the guidance of plant pathology experts, with labeled regions covering leaves, fruits, and stems. Annotation files are stored in XML format, each corresponding to a specific image. This dataset is well-suited for research in disease classification, object detection, and phenotyping, and supports deep learning model training and cross-crop transfer learning applications.

Why it matches plant phenotyping methodsトマト病害の症状を画像で捉え、分類・検出モデル用に専門家アノテーションした再利用可能なデータセットであり、植物病害状態の表現型取得が中心である。

abstractThe development of accurate disease recognition models relies heavily on the availability of high-quality image datasets.

Spatially resolved analysis of growth dynamics in pome and drupe fruits of Rosaceae using 3D Gaussian Splatting →

Fruit growth has long been described using single- or double-sigmoid curves; however, these temporal models cannot fully capture the spatial heterogeneity that ultimately shapes a fruit. Here, we present a three-dimensional analysis pipeline that non-destructively tracks spatial fruit growth dynamics from field-collected imaginary. Surface landmarks were drawn, and video recordings were taken throughout development for three pome fruits, apple ( Malus × domestica ), Japanese pear ( Pyrus pyrifolia ) and European pear ( Pyrus communis ), and two drupe fruits, peach ( Prunus persica ) and Japanese apricot ( Prunus mume ), to track their motion. Using 3D Gaussian Splatting, we successfully reconstructed 3D models of the fruits, and the landmark displacement could be measured with high accuracy, with R 2 ≥ 0.98 when compared to manual recordings. We found a common spatial growth gradient in the longitudinal growth shared in the pomes and drupes of the Rosaceae; proximal (stem-end) regions exhibited more pronounced growth than the distal (stylar) end. An exception was found in European pear ‘Bartlett,’ which showed relatively vigorous growth in the distal region, explaining its distinct shape with expanded distal end. Transverse expansion varied far less than longitudinal expansion, with a possible association with initial fruit morphology. Inter-fruit growth variability peaked in the fastest-growing regions, particularly in the distal area of the European pear, highlighting the link between growth vigor and phenotypic variance. These results provide foundational insights into the developmental dynamics of both pome and drupe fruits of the Rosaceae family, contributing to the optimization of fruit size, shape, and uniformity.

Why it matches plant phenotyping methods3D Gaussian Splattingを用いて果実の3D再構成と空間的成長形質の非破壊計測パイプラインを開発し、手動記録との精度比較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。

abstractHere, we present a three-dimensional analysis pipeline that non-destructively tracks spatial fruit growth dynamics

De-occlusion models and diffusion-based data augmentation for size estimation of on-plant oriental melons. →

Accurate fruit size estimation is crucial for plant phenotyping, as it enables precise crop management and enhances agricultural productivity by providing essential data for growth and resource efficiency analysis. In this study, we estimated the size of on-plant oriental melons grown in a vertical cultivation system to address the challenges posed by leaf occlusion. Data augmentation was achieved using a diffusion model to generate synthetic leaves to cover existing fruits and create an enriched dataset. Three instance segmentation models-mask region-based convolutional neural network (CNN), Mask2Former, and detection transformer (DETR)-and six de-occlusion models derived from these architectures were implemented. These models successfully inferred both visible and occluded areas of the fruit. Notably, Amodal Mask2Former and occlusion-aware RCNN (ORCNN) achieved average precision scores of 85.92 ​% and 85.35 ​%, respectively. The inferred masks were used to estimate the height and diameter of the fruit, with Amodal Mask2Former yielding a mean absolute error of 5.46 ​mm and 4.20 ​mm and a mean absolute percentage error of 4.86 ​% and 5.33 ​%, respectively. The results indicate enhanced performance of the transformer-based Amodal Mask2Former over CNN architectures in de-occlusion tasks and size estimation. Finally, the enhancement in de-occlusion models compared to conventional models was assessed and demonstrated across occlusion ratios ranging from 0 to 70 ​%. However, generating synthetic datasets with occlusion ratios over 70 ​% remains a limitation.

Why it matches plant phenotyping methods果実の遮蔽領域を復元し、画像から果実サイズを推定する手法の開発・評価が研究の中心であり、植物表現型計測に該当する。

abstractAccurate fruit size estimation is crucial for plant phenotyping

RGB image dataset for okra maturity classification to enhance agricultural quality and market readiness. →

Okra is a highly nutritious farming product that combats malnutrition issues while supporting sustainable agricultural methods. In order to keep its quality and versatility in preparation applications, it is important to classify its maturity stages into under-mature, mature, and over-mature categories. Classification is vital to identify the best time to harvest, satisfy market demands, minimize post-harvest losses, and optimize cooking uses. This data in brief uses a non-destructive approach to okra maturity classification based on a dataset of images taken under controlled illumination using a standard RGB camera. The dataset contains okra samples that were sourced from various farms and vegetable markets, ensuring that it encapsulates the natural variability found in real-world farm and market environments. The availability of such a large dataset enables the creation of precise classification models that can assist farmers in optimizing the time of harvest, fulfilling consumers' requirements, and improving market results. The research has great relevance to promoting agricultural quality evaluation and boosting market readiness using non-invasive techniques.

Why it matches plant phenotyping methodsRGB画像データセットによるオクラ果実の成熟段階分類が研究の中心であり、植物器官の状態を画像から推定する再利用可能なフェノタイピング資源に該当する。

titleRGB image dataset for okra maturity classification to enhance agricultural quality and market readiness.

DBA-ViNet: an effective deep learning framework for fruit disease detection and classification using explainable AI. →

Objective The primary aim of this research is to develop an effective and robust model for identifying and classifying diseases in general fruits, particularly apples, guavas, mangoes, pomegranates, and oranges, utilizing computer vision techniques. Material An open-source collection of fruit disease images, comprising both diseased and healthy samples from the first five fruit types, was used in this study. The data was split into 70% training, 15% validation, and 15% testing. A 5-fold cross-validation was used to maintain the generalizability and stability of the model's performance. Models For performance comparisons of these models on the dataset, we benchmarked state-of-the-art pre-trained convolutional neural network (ConvNet) models, including Swin Transformer (ST), EfficientNetV2, ConvNeXt, YOLOv8, and MobileNetV3. A new model, the Dual-Branch Attention-Guided Vision Network (DBA-ViNet), was introduced. A hybrid with two branches of DBA-ViNet can efficiently integrate global and local features for improved disease identification accuracy. Grad-CAM was used to visualize the regions that contributed to each prediction, helping to interpret the model. These heatmaps verified that DBA-ViNet can correctly direct its attention to disease-specific symptoms, thereby increasing trust and transparency in the classification results. Results The proposed DBA-ViNet achieved a high testing classification accuracy of 99.51%, specificity of 99.42%, recall of 99.61%, precision of 99.30% and F1 score of 99.45% outperforming baseline models in all evaluation metrics. While the improvements were consistent, statistical significance testing was not performed and will be explored in future work. Conclusion These results confirm the effectiveness of the proposed DBA-ViNet architecture in fruit disease detection, suggesting that incorporating both global and local feature extraction into the design of the double-branch attention mechanism for classification can achieve high accuracy and reliability. It is potentially practical in smart agriculture and the automated crop health monitoring system.

Why it matches plant phenotyping methods果実画像から植物の病害状態を推定する深層学習モデルを開発し、複数モデルとの性能比較・検証を行っており、植物フェノタイピング手法が中心である。

abstractThe primary aim of this research is to develop an effective and robust model for identifying and classifying diseases in general fruits

Tomato Multi-Angle Multi-Pose Dataset for Fine-Grained Phenotyping →

Observer bias and inconsistencies in traditional plant phenotyping methods limit the accuracy and reproducibility of fine-grained plant analysis. To overcome these challenges, we developed TomatoMAP, a comprehensive dataset for Solanum lycopersicum using an Internet of Things (IoT) based imaging system with standardized data acquisition protocols. Our dataset contains 64,464 RGB images that capture 12 different plant poses from four camera elevation angles. Each image includes manually annotated bounding boxes for seven regions of interest (ROIs), including leaves, panicle, batch of flowers, batch of fruits, axillary shoot, shoot and whole plant area, along with 50 fine-grained growth stage classifications based on the BBCH scale. Additionally, we provide 3,616 high-resolution image subset with pixel-wise semantic and instance segmentation annotations for fine-grained phenotyping. We validated our dataset using a cascading model deep learning framework combining MobileNetv3 for classification, YOLOv11 for object detection, and MaskRCNN for segmentation. Through AI vs. Human analysis involving five domain experts, we demonstrate that the models trained on our dataset achieve accuracy and speed comparable to the experts. Cohen's Kappa and inter-rater agreement heatmap confirm the reliability of automated fine-grained phenotyping using our approach.

Why it matches plant phenotyping methods植物の多視点画像取得、アノテーション付きデータセット、深層学習による分類・検出・セグメンテーションを中心に開発・検証した、明確な植物フェノタイピング手法研究です。

abstractwe developed TomatoMAP, a comprehensive dataset for Solanum lycopersicum using an Internet of Things (IoT) based imaging system with standardized data acquisition protocols.

Dataset of apples for grading by sweetness, ripeness and variety. →

The study created a detailed database for apple quality inspection using a cost-effective, self-designed multi-spectral imaging system. The system was optimized to allow spectral information to be obtained in 8 discrete wavebands, which enabled non-destructive determination of such key fruit components as ripeness, sugar type and cultivar. Stringent environmental conditions were maintained during image acquisition for optimal measurement consistency and experimental repeatability. The detailed dataset encompasses 32,463 multi-spectral images across three distinct classification categories. For sweetness evaluation, 1620 images spanning Brix values from 10 % to 15 % were collected from five apple varieties. Ripeness evaluation includes 29,160 images documenting the complete maturation cycle over 18 days, while variety classification contains 1683 images from three distinct cultivars. Each image was captured under controlled lighting conditions using eight specific wavelengths, ensuring spectral consistency crucial for machine learning applications. These multi-spectral images were concatenated for grading by sweetness, ripeness, and variety, creating a processed dataset of concatenated images optimized for AppleNet processing. The concatenation process combines the eight wavelength channels into unified image representations suitable for deep learning applications. Sample collection included the picking of different apple cultivars at different physiological development phases of fruit from local orchards. Single specimens were imaged sequentially using a multi-spectral technique. Information on sugar content concentration ( % Brix), maturation phase classification and varietal identification was recorded according to standard laboratory procedure. The resulting annotated database includes such quantitative reference points, which can be used to train supervised learning classifiers in computational classification systems. The reuse value of the dataset covers a wide range of applications such as machine learning-based fruit quality evaluation, agricultural automation and food industry examination. This dataset of ours can be used by researchers to develop and test algorithms to classify apples and estimate their ripeness and the presence of diseases. Furthermore, the proposed multi-spectral imaging can be generalized to cover other fruits and agricultural products, extending the application of the method in smart agriculture. This dataset serves as a valuable resource for researchers in computer vision, machine learning, and agricultural technology, fostering advancements in non-destructive fruit quality evaluation methodologies.

Why it matches plant phenotyping methodsリンゴの甘度・成熟度・品種を推定するマルチスペクトル撮像システムと、注釈付き大規模画像データセットを中心に構築しており、植物器官の品質・状態を定量化する再利用可能なフェノタイピング手法に該当する。

abstractThe study created a detailed database for apple quality inspection using a cost-effective, self-designed multi-spectral imaging system.

Adaptive Symmetry Self-Matching for 3D Point Cloud Completion of Occluded Tomato Fruits in Complex Canopy Environments. →

As a globally important cash crop, the optimization of tomato yield and quality is strategically significant for food security and sustainable agricultural development. In order to address the problem of missing point cloud data on fruits in a facility agriculture environment due to complex canopy structure, leaf shading and limited collection viewpoints, the traditional geometric fitting method makes it difficult to restore the real morphology of fruits due to the dependence on data integrity. This study proposes an adaptive symmetry self-matching (ASSM) algorithm. It dynamically adjusts symmetry planes by detecting defect region characteristics in real time, implements point cloud completion under multi-symmetry constraints and constructs a triple-orthogonal symmetry plane system to adapt to multi-directional heterogeneous structures under complex occlusion. Experiments conducted on 150 tomato fruits with 5-70% occlusion rates demonstrate that ASSM achieved coefficient of determination (R 2 ) values of 0.9914 (length), 0.9880 (width) and 0.9349 (height) under high occlusion, reducing the root mean square error (RMSE) by 23.51-56.10% compared with traditional ellipsoid fitting. Further validation on eggplant fruits confirmed the cross-crop adaptability of the method. The proposed ASSM method overcomes conventional techniques' data integrity dependency, providing high-precision three-dimensional (3D) data for monitoring plant growth and enabling accurate phenotyping in smart agricultural systems.

Why it matches plant phenotyping methodsトマト果実の遮蔽点群を補完し、果実の長さ・幅・高さを推定する新規アルゴリズムを開発・検証しており、植物形質取得が研究の中心である。

abstractThis study proposes an adaptive symmetry self-matching (ASSM) algorithm.

CitrusGAN: sparse-view X-ray CT reconstruction for citrus based on generative adversarial networks. →

3D phenotyping of the external and internal structures is important to breed new fruit species. As manual phenotyping is error-prone and time-consuming, developing high-throughput solutions with enhanced precision and low costs is necessary. This study presents CitrusGAN, a generative adversarial network-based method to reconstruct 3D citrus CT models from sparse-view X-ray images. The input X-rays are arranged in orthogonal pairs to provide additional information, and customized loss functions enable more effective learning of the mapping from 2D X-ray features to 3D CT volumes. Experimental results show that 6 views can generate high-quality citrus CT volumes, with a structural similarity index of 92.1 ​% and a peak signal-to-noise ratio of 26.374 ​dB compared with the real CT models. Moreover, the morphology of the generated model can be conveniently measured in the 3D space, facilitating the extraction of phenotypic traits including fruit length, width, height, volume, surface area, peel thickness, number of segments, and edible rate with high precision. As X-rays can be obtained using low-cost X-ray machines with high efficiency, the proposed method can be potentially developed into high-throughput equipment for fruit production lines or portable devices to realize in-field phenotyping.

Why it matches plant phenotyping methods柑橘の疎視野X線から3D CTモデルを再構成し、形態形質を抽出する手法を開発・検証しており、植物フェノタイピング手法が研究の中心である。

abstractThis study presents CitrusGAN, a generative adversarial network-based method to reconstruct 3D citrus CT models from sparse-view X-ray images.

A deep learning based approach for classifying the maturity of cashew apples. →

Over 95% of cashew apples are left to waste and rot on the ground. However, both cashew nuts and the often overlooked cashew apples possess significant nutritional and economic value. The cashew apple constitutes the major part (90%) of the cashew fruit, with the nut forming a modest portion (10%). Cashew nuts can be harvested and processed even after lying on the ground, but cashew apples are more delicate. Assessing the maturity status of these apples still requires human visual observation due to the challenges posed by their moisture content. Timely harvesting is crucial, as the pseudofruit is prone to microbial infections upon hitting the ground, making the process time- and labor-intensive. In this study, a Deep Learning based image classification model is presented, which can be used to automatically identify mature cashew apples. The model achieved an accuracy of 95.58% in classifying the cashew apples (immature vs. mature). Overall, the results highlight the potential of Deep Learning models for the classification of cashew apples and other fruits for precision agriculture purposes. This approach could enhance the harvesting process by enabling the utilization of the entire fruit and reducing the need for manual labor, thereby unlocking the full economic potential of the cashew tree.

Why it matches plant phenotyping methodsカシューナッツ果実の成熟状態という植物器官の状態を画像から自動推定する深層学習手法が研究の中心であり、単なる収穫位置検出ではないため。

abstractIn this study, a Deep Learning based image classification model is presented, which can be used to automatically identify mature cashew apples.

OpenPheno: an open-access, user-friendly, and smartphone-based software platform for instant plant phenotyping. →

BACKGROUND: Plant phenotyping has become increasingly important for advancing plant science, agriculture, and biotechnology. Classic manual methods are labor-intensive and time-consuming, while existing computational tools often require advanced coding skills, high-performance hardware, or PC-based environments, making them inaccessible to non-experts, to resource-constrained users, and to field technicians. RESULTS: To respond to these challenges, we introduce OpenPheno, an open-access, user-friendly, and smartphone-based platform encapsulated within a WeChat Mini-Program for instant plant phenotyping. The platform is designed for ease of use, enabling users to phenotype plant traits quickly and efficiently with only a smartphone at hand. We currently instantiate the use of the platform with tools such as SeedPheno, WheatHeadPheno, LeafAnglePheno, SpikeletPheno, CanopyPheno, TomatoPheno, and CornPheno; each offering specific functionalities such as seed size and count analysis, wheat head detection, leaf angle measurement, spikelet counting, canopy structure analysis, and tomato fruit measurement. In particular, OpenPheno allows developers to contribute new algorithmic tools, further expanding its capabilities to continuously facilitate the plant phenotyping community. CONCLUSIONS: By leveraging cloud computing and a widely accessible interface, OpenPheno democratizes plant phenotyping, making advanced tools available to a broader audience, including plant scientists, breeders, and even amateurs. It can function as a role in AI-driven breeding by providing the necessary data for genotype-phenotype analysis, thereby accelerating breeding programs. Its integration with smartphones also positions OpenPheno as a powerful tool in the growing field of mobile-based agricultural technologies, paving the way for more efficient, scalable, and accessible agricultural research and breeding.

Why it matches plant phenotyping methodsスマートフォンで植物形質を取得・解析するソフトウェアプラットフォームの開発が中心であり、複数の具体的な表現型解析ツールを提供している。

abstractwe introduce OpenPheno, an open-access, user-friendly, and smartphone-based platform encapsulated within a WeChat Mini-Program for instant plant phenotyping.

XFruitSeg-A general plant fruit segmentation model based on CT imaging. →

Identification of the phenotypes of fruits is critical for understanding complex genetic traits. Computed tomography (CT) imaging technology enables the noninvasive acquisition of three-dimensional images of fruit interiors, thus providing a robust data foundation for phenotypic analysis. Accurate segmentation of internal fruit tissues is essential, as it directly influences the accuracy and reliability of the results. Current methods are not optimized for the unique features of plant fruit images. This study introduces XFruitSeg, which is a general deep learning model for segmenting plant fruit CT images. The model uses a U-shaped encoder-decoder architecture and integrates multitask learning. A large convolutional kernel network, RepLKNet, expands the receptive field for feature extraction. Multiscale skip connections and a deep supervision mechanism improve the model's capacity to learn features of various sizes, and a contour feature learning branch specifically targets the interorganizational boundaries. An optimized composite loss function enhances the model's robustness when applied to imbalanced categories. Additionally, a dataset named XrayFruitData was established, which contains high-resolution images of twelve plant fruit varieties, with accurate annotations for orange, mangosteen, and durian fruits for model evaluation. Compared with four mainstream advanced models, XFruitSeg achieved superior segmentation performance on the orange, mangosteen, and durian datasets, with mean Dice coefficients of 95.21 ​%, 93.24 ​%, and 94.70 ​% and mean intersection over union (mIoU) scores of 91.09 ​%, 87.91 ​%, and 90.35 ​%, respectively. The results of extensive ablation experiments demonstrate the effectiveness of each component. Therefore, the proposed XFruitSeg model has been proven to be beneficial for high-precision analysis of internal fruit phenotyping traits.

Why it matches plant phenotyping methods果実CT画像から内部組織を分割し、表現型解析を可能にする深層学習モデルと評価用データセットを開発・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 introduces XFruitSeg, which is a general deep learning model for segmenting plant fruit CT images.

Automated dynamic phenotyping of whole oilseed rape ( Brassica napus ) plants from images collected under controlled conditions. →

Introduction Recent advancements in sensor technologies have enabled collection of many large, high-resolution plant images datasets that could be used to non-destructively explore the relationships between genetics, environment and management factors on phenotype or the physical traits exhibited by plants. The phenotype data captured in these datasets could then be integrated into models of plant development and crop yield to more accurately predict how plants may grow as a result of changing management practices and climate conditions, better ensuring future food security. However, automated methods capable of reliably and efficiently extracting meaningful measurements of individual plant components (e.g. leaves, flowers, pods) from imagery of whole plants are currently lacking. In this study, we explore interdisciplinary application of MapReader, a computer vision pipeline for annotating and classifying patches of larger images that was originally developed for semantic exploration of historical maps, to time-series images of whole oilseed rape (Brassica napus) plants. Methods Models were trained to classify five plant structures in patches derived from whole plant images (branches, leaves, pods, flower buds and flowers), as well as background patches. Three modelling methods are compared: (i) 6-label multi-class classification, (ii) a chain of binary classifiers approach, and (iii) an approach combining binary classification of plant and background patches, followed by 5-label multi-class classification of plant structures. Results A combined plant/background binarization and 5-label multi-class modelling approach using a ‘resnext50d_4s2x40d’ model architecture for both the binary classification and multi-class classification components was found to produce the most accurate patch classification for whole B. napus plant images (macro-averaged F1-score = 88.50, weighted average F1-score = 97.71). This combined binary and 5-label multi-class classification approach demonstrate similar performance to the top-performing MapReader ‘railspace’ classification model. Discussion This highlights the potential applicability of the MapReader model framework to images data from across scientific and humanities domains, and the flexibility it provides in creating pipelines with different modelling approaches. The pipeline for dynamic plant phenotyping from whole plant images developed in this study could potentially be applied to imagery from varied laboratory conditions, and to images datasets of other plants of both agricultural and conservation concern.

Why it matches plant phenotyping methods植物全体画像から葉・花・莢などの構造を自動抽出・分類する動的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。

abstractautomated methods capable of reliably and efficiently extracting meaningful measurements of individual plant components (e.g. leaves, flowers, pods) from imagery of whole plants are currently lacking.

Mapping of cotton bolls and branches with high-granularity through point cloud segmentation. →

High resolution three-dimensional (3D) point clouds enable the mapping of cotton boll spatial distribution, aiding breeders in better understanding the correlation between boll positions on branches and overall yield and fiber quality. This study developed a segmentation workflow for point clouds of 18 cotton genotypes to map the spatial distribution of bolls on the plants. The data processing workflow includes two independent approaches to map the vertical and horizontal distribution of cotton bolls. The vertical distribution was mapped by segmenting bolls using PointNet++ and identifying individual instances through Euclidean clustering. For horizontal distribution, TreeQSM segmented the plant into the main stem and individual branches. PointNet++ and Euclidean clustering were then used to achieve cotton boll instance segmentation. The horizontal distribution was determined by calculating the Euclidean distance of each cotton boll relative to the main stem. Additionally, branch types were classified using point cloud meshing completion and the Dijkstra shortest path algorithm. The results highlight that the accuracy and mean intersection over union (mIoU) of the 2-class segmentation based on PointNet++ reached 0.954 and 0.896 on the whole plant dataset, and 0.968 and 0.897 on the branch dataset, respectively. The coefficient of determination (R 2 ) for the boll counting was 0.99 with a root mean squared error (RMSE) of 5.4. For the first time, this study accomplished high-granularity spatial mapping of cotton bolls and branches, but directly predicting fiber quality from 3D point clouds remains a challenge. This method provides a promising tool for 3D cotton plant mapping of different genotypes, which potentially could accelerate plant physiological studies and breeding programs.

Why it matches plant phenotyping methods3D点群の分割・個体抽出ワークフローを開発し、綿花の果実数と枝・果実の空間分布という植物形質を定量化・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 developed a segmentation workflow for point clouds of 18 cotton genotypes to map the spatial distribution of bolls on the plants.

PodNet: Pod real-time instance segmentation in pre-harvest soybean fields. →

Noninvasive analysis of pod phenotypic traits under field conditions is crucial for soybean breeding research. However, previous pod phenotyping studies focused on postharvest materials or were limited to indoor scenarios, failing to generalize to real-field environments. To address these issues, this paper employs an instance segmentation approach for the precise extraction of the pod area from multiplant RGB images in preharvest soybean fields. We first introduce a cost-effective workflow for constructing datasets of densely planted crop images with a uniform backdrop. Starting with video recording, high-quality static frames are collected by automatic selection. Then, a large vision model is explored to facilitate dense annotation and build a large-scale soybean dataset comprising 20k pod masks. Second, the pod instance segmentation model PodNet is developed based on the YOLOv8 architecture. We propose a novel hierarchical prototype aggregation strategy to fuse multiscale semantic features and a U-EMA prototype generation network to improve the model's perception performance for small objects. Comprehensive experiments suggest that lightweight PodNet achieves a superior mean average accuracy of 0.786 in the custom pod segmentation dataset. PodNet also performs competitively on in-field images without a backdrop and enables real-time inference on the edge computing platform. To the best of our knowledge, PodNet is the first pod instance segmentation model for preharvest fields. The low-cost and high-precision extraction of pods is not only a prerequisite for phenotypic analysis of the pod organs but also constitutes an important foundation in conducting cross-scale phenotyping from whole-plant to seed levels.

Why it matches plant phenotyping methods大豆莢の表現型抽出を目的に、データセット構築、インスタンスセグメンテーションモデル、実環境での性能評価を中心的に開発しているため。

abstractNoninvasive analysis of pod phenotypic traits under field conditions is crucial for soybean breeding research.

A comprehensive image dataset for carambola leaf and fruit disease classification and quality assessment. →

The Carambola ( Averrhoa carambola ), also known as starfruit, is a tropical fruit with significant economic and nutritional value. The creation of a comprehensive Carambola Leaf and Fruit Dataset is highly essential for the advancement of automated disease classification and quality assessment using machine learning algorithms. The dataset is developed to support machine learning application and bridging the gap between computer vision and agricultural research to help farmers in minimizing financial losses and promote sustainable agricultural practices. The images are collected through direct field survey under diverse environmental conditions from various locations in Bangladesh between October 2024 and January 2025. The dataset comprises 2,618 original images, an equal number of processed images, and 15,000 augmented images generated from the original images. It is categorized into five distinct classes representing unique health conditions of carambola leaf and fruits including Healthy Leaves, Yellow Leaves, Insect Hole Leaves, Healthy Fruits, and Unhealthy Fruits. This dataset supports sustainable agriculture by enabling early disease identification, reduced chemical usage, and improved crop management while minimizing economic losses for farmers. It serves as a valuable resource for the future research in machine learning based plant health monitoring and quality assessment.

Why it matches plant phenotyping methodsカランボラ葉・果実の健康状態や病害を画像から分類する包括的データセットの開発であり、植物状態の画像ベース表現型評価が中心です。

abstractThe creation of a comprehensive Carambola Leaf and Fruit Dataset is highly essential for the advancement of automated disease classification and quality assessment using machine learning algorithms.

Apple varieties, diseases, and distinguishing between fresh and rotten through deep learning approaches. →

Apples are one of the most productive fruits in the world, in addition to their nutritional and health advantages for humans. Even with the continuous development of AI in agriculture in general and apples in particular, automated systems continue to encounter challenges identifying rotten fruit and variations within the same apple category, as well as similarity in type, color, and shape of different fruit varieties. These issues, in addition to apple diseases, substantially impact the economy, productivity, and marketing quality. In this paper, we first provide a novel comprehensive collection named Apple Fruit Varieties Collection (AFVC) with 29,750 images through 85 classes. Second, we distinguish fresh and rotten apples with Apple Fruit Quality Categorization (AFQC), which has 2,320 photos. Third, an Apple Diseases Extensive Collection (ADEC), comprised of 2,976 images with seven classes, was offered. Fourth, following the state of the art, we develop an Optimized Apple Orchard Model (OAOM) with a new loss function named measured focal cross-entropy (MFCE), which assists in improving the proposed model's efficiency. The proposed OAOM gives the highest performance for apple varieties identification with AFVC; accuracy was 93.85%. For the apples rotten recognition with AFQC, accuracy was 98.28%. For the identification of the diseases via ADEC, it was 99.66%. OAOM works with high efficiency and outperforms the baselines. The suggested technique boosts apple system automation with numerous duties and outstanding effectiveness. This research benefits the growth of apple's robotic vision, development policies, automatic sorting systems, and decision-making enhancement.

Why it matches plant phenotyping methodsリンゴ画像から腐敗状態や病害を推定するデータセットと深層学習モデルを開発・評価しており、植物状態の画像ベース推定が中心である。

abstractwe first provide a novel comprehensive collection named Apple Fruit Varieties Collection (AFVC) with 29,750 images through 85 classes.

Comprehensive dataset on ripening stages of strawberries and avocados: From unripe to rotten. →

This paper presents a novel and innovative 14,630 fruit images dataset, consisting of 1333 original images and the remaining augmented images for strawberry and avocado fruits. The dataset records the growth of strawberries and avocados in four different stages: unripe, partially ripe, ripe, and rotten. Though the fruit ripening process is commonly known, a lack of systematic datasets to show the fruit changing from an unripe state to a rotting state was prevalent for the two fruits in question. Over two months, the dataset was collected through rigorous tracking to effectively provide a measure of each of the fruits' conditions. The fruits were obtained from Mahabaleshwar farms in Maharashtra, India, as well as from local markets in Maharashtra and Pune. The fruits were monitored continuously from the time of harvesting, and all observed changes were carefully recorded. The uniqueness of this dataset is that it covers both strawberries and avocados, which have different patterns of ripening and are highly commercially valuable. The images were annotated using the online annotation tool - makesense.ai, with a total of 1499 bounding boxes for each fruit. By encompassing these two diverse fruit types, the dataset provides a valuable resource for researchers, agriculturalists, and food scientists to investigate and compare the ripening behaviours of different fruit species.

Why it matches plant phenotyping methodsイチゴとアボカドの果実画像を用いて、未熟から腐敗までの可視的な成熟・状態を体系的に記録し、注釈付きデータセットとして提供しているため、植物器官の状態を対象とする画像ベースのフェノタイピングデータセットに該当する。

abstractThis paper presents a novel and innovative 14,630 fruit images dataset, consisting of 1333 original images and the remaining augmented images for strawberry and avocado fruits.

A comprehensive image dataset of plum leaf and fruit for disease classification. →

Plums, commonly known as Indian jujube, are economically important, valued for nutritional benefits and consumed by people from all over the world. The development of a comprehensive Plum leaf and fruit dataset is highly essential for advancing agricultural research and enabling effective disease management systems using machine learning techniques. This dataset serves as a foundational resource for machine learning based classification and bridges the gap between agricultural research and computer vision to support automated disease detection and fruit quality assessment. Researchers will be able to utilize this dataset to implement early disease detection which leads to improve crop management and supply quality and reduce the usage of chemicals. Proper utilization of this dataset can help farmers to reduce financial losses and encourage sustainable farming practices. The dataset was collected between December 2024 and February 2025 under various environmental conditions. It consists of 3,554 original images, an equal number of processed images and 18,000 augmented images generated from the original dataset. The dataset is categorized into six distinct classes: Shot Hole, Bacterial Spot, Wilted Leaf, Healthy Leaf, Unhealthy Plum, and Healthy Plum. This dataset contributes significantly to advance deep learning in agriculture enabling early disease detection and fruit quality monitoring.

Why it matches plant phenotyping methods植物の葉・果実画像から病害状態を分類するための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用の再利用可能な資源に該当する。

abstractThis dataset contributes significantly to advance deep learning in agriculture enabling early disease detection and fruit quality monitoring.

Open RGB Imaging Workflow for Morphological and Morphometric Analysis of Fruits using AI: A Case Study on Almonds. →

Abstract High-throughput phenotyping is addressing the current bottleneck in phenotyping within breeding programs. Imaging tools are becoming the primary resource for improving the efficiency of phenotyping processes and providing large datasets for genomic selection approaches. The advent of AI brings new advantages by enhancing phenotyping methods using imaging, making them more accessible to breeding programs. In this context, we have developed an open Python workflow for analyzing morphology and heritable morphometric traits using AI, which can be applied to fruits and other plant organs. This workflow has been implemented in almond (Prunus dulcis ), a species where efficiency is critical due to its long breeding cycle. Over 25,000 kernels, more than 20,000 nuts, and over 600 individuals have been phenotyped, making this the largest morphological study conducted in almond. As result, new heritable morphometric traits of interest have been identified. These findings pave the way for more efficient breeding strategies, ultimately facilitating the development of improved cultivars with desirable traits.

Why it matches plant phenotyping methodsAIを用いたRGB画像から果実の形態・形状形質を抽出するオープンPythonワークフローを開発・適用しており、植物表現型取得法が研究の中心である。

abstractwe have developed an open Python workflow for analyzing morphology and heritable morphometric traits using AI, which can be applied to fruits and other plant organs.

Phenotypic dynamics and temporal heritability of tomato architectural traits using an unmanned ground vehicle-based plant phenotyping system →

Large-scale manual measurements of plant architectural traits in tomato growth are laborious and subjective, hindering deeper understanding of temporal variations in gene expression heterogeneity. This study develops a high-throughput approach for characterizing tomato architectural traits at different growth stages and mapping temporal broad-sense heritability using an unmanned ground vehicle-based plant phenotyping system. The SegFormer with fusion of multispectral and depth imaging modalities was employed to semantically segment plant organs from the registered RGB-D and multispectral images. Organ point clouds were then generated and clustered into instances. Finally, six key architectural traits, including fruit spacing (FS), inflorescence height (IH), stem thickness (ST), leaf spacing (LS), total leaf area (TLA), and leaf inclination angle (LIA) were extracted and the temporal broad-sense heritability folds were plotted. The root mean square errors (RMSEs) of the estimated FS, IH, ST, and LS were 0.014, 0.043, 0.003, and 0.015 m, respectively. The visualizations of the estimated TLA and LIA matched the actual growth trends. The broad-sense heritability of the extracted traits exhibited different trends across the growth stages: (i) ST, IH, and FS had a gradually increased broad-sense heritability over time, (ii) LS and LIA had a decreasing trend, and (iii) TLA showed fluctuations (i.e. an M-shaped pattern) of the broad-sense heritability throughout the growth period. The developed system and analytical approach are promising tools for accurate and rapid characterization of spatiotemporal changes of tomato plant architecture in controlled environments, laying the foundation for efficient crop breeding and precision production management in the future.

Why it matches plant phenotyping methods植物形態形質を取得するUGV型マルチモーダル画像フェノタイピングシステムと解析手法の開発・定量評価が研究の中心であり、誤差検証も行っているため。

abstractThis study develops a high-throughput approach for characterizing tomato architectural traits at different growth stages and mapping temporal broad-sense heritability using an unmanned ground vehicle-based plant phenotyping system.

From blender to farm: Transforming controlled environment agriculture with synthetic data and SwinUNet for precision crop monitoring →

The aim of this study was to train a Vision Transformer (ViT) model for semantic segmentation to differentiate between ripe and unripe strawberries using synthetic data to avoid challenges with conventional data collection methods. The solution used Blender to generate synthetic strawberry images along with their corresponding masks for precise segmentation. Subsequently, the synthetic images were used to train and evaluate the SwinUNet as a segmentation method, and Deep Domain Confusion was utilized for domain adaptation. The trained model was then tested on real images from the Strawberry Digital Images dataset. The performance on the real data achieved a Dice Similarity Coefficient of 94.8% for ripe strawberries and 94% for unripe strawberries, highlighting its effectiveness for applications such as fruit ripeness detection. Additionally, the results show that increasing the volume and diversity of the training data can significantly enhance the segmentation accuracy of each class. This approach demonstrates how synthetic datasets can be employed as a cost-effective and efficient solution for overcoming data scarcity in agricultural applications.

Why it matches plant phenotyping methods合成画像、セグメンテーション、ドメイン適応を用いてイチゴの成熟状態を推定する画像解析手法を開発・実データで評価しており、植物器官の状態取得が中心である。

abstracttrain a Vision Transformer (ViT) model for semantic segmentation to differentiate between ripe and unripe strawberries using synthetic data

3D Hierarchical Panoptic Segmentation in Real Orchard Environments Across Different Sensors →

Crop yield estimation is a relevant problem in agriculture, because an accurate yield estimate can support farmers' decisions on harvesting or precision intervention. Robots can help to automate this process. To do so, they need to be able to perceive the surrounding environment to identify target objects such as trees and plants. In this paper, we introduce a novel approach to address the problem of hierarchical panoptic segmentation of apple orchards on 3D data from different sensors. Our approach is able to simultaneously provide semantic segmentation, instance segmentation of trunks and fruits, and instance segmentation of trees (a trunk with its fruits). This allows us to identify relevant information such as individual plants, fruits, and trunks, and capture the relationship among them, such as precisely estimate the number of fruits associated to each tree in an orchard. To efficiently evaluate our approach for hierarchical panoptic segmentation, we provide a dataset designed specifically for this task. Our dataset is recorded in Bonn, Germany, in a real apple orchard with a variety of sensors, spanning from a terrestrial laser scanner to a RGB-D camera mounted on different robots platforms. The experiments show that our approach surpasses state-of-the-art approaches in 3D panoptic segmentation in the agricultural domain, while also providing full hierarchical panoptic segmentation. Our dataset is publicly available at https://www.ipb.uni-bonn.de/data/hops/. The open-source implementation of our approach is available at https://github.com/PRBonn/hapt3D.

Why it matches plant phenotyping methodsリンゴ樹・果実・幹を3Dセグメンテーションし、樹ごとの果実数を推定する手法と専用データセットを中心に開発・評価しており、植物の器官形態・収量関連形質の取得に該当する。

abstractwe introduce a novel approach to address the problem of hierarchical panoptic segmentation of apple orchards on 3D data from different sensors.

Image dataset for classification of diseases in guava fruits and leaves. →

Guava (Psidium guajava) this is a tropical fruit and one of the common tropical fruits in Bangladesh. The economic and health value of this important crop is unmeasurable, but it quickly becomes infected with many diseases that can greatly reduce its yield and quality. Thus, the use of technology for automatic fruit and leaf disease detection is necessary in agriculture. The dataset provides us overall guava fruits & leaves image samples for detection of diseases in guava fruits and leaves. This dataset consists of images of healthy and diseased samples infected by fruit disease such as anthracnose, scab, styler end root and leaf disease such as canker, rust, anthracnose and dot. It consists of 3,432 real images obtained from different places in Bangladesh. It is also extended 20,344 augmented images ready to be used for machine learning purposes. This dataset serves as a fundamental building block for utilizing machine learning and computer vision techniques to develop automated detection systems of various diseases. It assists in the early detection of diseases affecting guava, and provides them with solutions to intervene there itself saving agricultural yield and nutritional losses while also promoting sustainable farming practices. This dataset will assist researchers for progressing guava detecting disease through the execution of computational models and application of better machine learning techniques.

Why it matches plant phenotyping methodsグアバ果実・葉の健全／罹病状態を画像で分類するデータセットであり、植物病害状態の画像ベース表現型取得と機械学習利用を中心とするため含める。

titleImage dataset for classification of diseases in guava fruits and leaves.

Deep Learning for Crop Yield Forcasting in Agriculture Using Multilayer Perceptron and Convolutional Neural Networks →

The primary challenge facing the agricultural sector, which is essential for ensuring global food security, is enhancing crop productivity while effectively addressing the challenges posed by plant diseases. Advanced technologies have the potential to completely transform agricultural methods, especially in the areas of computer vision and machine learning. This study uses meteorological as well as fruit and vegetables image datasets to create an integrated agricultural decision support system for crop yield estimation and disease prediction. By enabling early plant disease detection and precise crop yield estimates, the system seeks to improve precision agriculture techniques. To analyze and classify the images and predict the possibility of crop disease harming fruits and vegetables, a Convolutional Neural Network (CNN) deep learning model is used. The Multilayer Perceptron algorithm is used to train the model using a large dataset that contains historical meteorological data, allowing it to identify patterns and connections between environmental conditions. Finally, farmers receive an SMS notice with prediction specifics.

Why it matches plant phenotyping methods植物画像から病害状態を推定し、気象・画像データから収量を推定するCNN/MLP統合手法が研究の中心であり、単なる生物学的実験のルーチン測定ではない。

abstractThis study uses meteorological as well as fruit and vegetables image datasets to create an integrated agricultural decision support system for crop yield estimation and disease prediction.

Framework for smartphone-based grape detection and vineyard management using UAV-trained AI. →

Viticulture benefits significantly from rapid grape bunch identification and counting, enhancing yield and quality. Recent technological and machine learning advancements, particularly in deep learning, have provided the tools necessary to create more efficient, automated processes that significantly reduce the time and effort required for these tasks. On one hand, drone, or Unmanned Aerial Vehicles (UAV) imagery combined with deep learning algorithms has revolutionised agriculture by automating plant health classification, disease identification, and fruit detection. However, these advancements often remain inaccessible to farmers due to their reliance on specialized hardware like ground robots or UAVs. On the other hand, most farmers have access to smartphones. This article proposes a novel approach combining UAVs and smartphone technologies. An AI-based framework is introduced, integrating a 5-stage AI pipeline combining object detection and pixel-level segmentation algorithms to automatically detect grape bunches in smartphone images of a commercial vineyard with vertical trellis training. By leveraging UAV-captured data for training, the proposed model not only accelerates the detection process but also enhances the accuracy and adaptability of grape bunch detection across different devices, surpassing the efficiency of traditional and purely UAV-based methods. To this end, using a dataset of UAV videos recorded during early growth stages in July (BBCH77-BBCH79), the X-Decoder segments vegetation in the front of the frames from their background and surroundings. X-Decoder is particularly advantageous because it can be seamlessly integrated into the AI pipeline without requiring changes to how data is captured, making it more versatile than other methods. Then, YOLO is trained using the videos and further applied to images taken by farmers with common smartphones (Xiaomi Poco X3 Pro and iPhone X). In addition, a web app was developed to connect the system with mobile technology easily. The proposed approach achieved a precision of 0.92 and recall of 0.735, with an F1 score of 0.82 and an Average Precision (AP) of 0.802 under different operation conditions, indicating high accuracy and reliability in detecting grape bunches. In addition, the AI-detected grape bunches were compared with the actual ground truth, achieving an R 2 value as high as 0.84, showing the robustness of the system. This study highlights the potential of using smartphone imaging and web applications together, making an effort to integrate these models into a real platform for farmers, offering a practical, affordable, accessible, and scalable solution. While smartphone-based image collection for model training is labour-intensive and costly, incorporating UAV data accelerates the process, facilitating the creation of models that generalise across diverse data sources and platforms. This blend of UAV efficiency and smartphone precision significantly cuts vineyard monitoring time and effort.

Why it matches plant phenotyping methodsスマートフォン画像とUAVデータを用いてブドウ房を検出・計数するAIパイプラインを開発・評価し、実測値との比較も行っているため、植物器官形質の取得手法が中心である。

abstractAn AI-based framework is introduced, integrating a 5-stage AI pipeline combining object detection and pixel-level segmentation algorithms to automatically detect grape bunches in smartphone images of a commercial vineyard with vertical trellis training.

Micromechanical behavior of the apple fruit cuticle investigated by Brillouin light scattering microscopy. →

The cuticle is a polymeric membrane covering all plant aerial organs of primary origin. It regulates water loss and defends against environmental stressors and pathogens. Despite its significance, understanding of the micro-mechanical properties of the cuticle (cuticular membrane; CM) remains limited. In this study, non-invasive Brillouin light scattering (BLS) spectroscopy was applied to probe the micro-mechanics of native CM, dewaxed CM (DCM), and isolated cutin matrix (CU) of mature apple fruit. The BLS signal arises from the photon interaction with thermally induced pressure waves and allows for imaging with mechanical contrast. The derived loss tangent showed significant differences with wax extraction from the CM and further with carbohydrate extraction from the DCM, consistent with tensile test results. Spatial heterogeneity between anticlinal and periclinal regions was observed by BLS microscopy of CM and DCM, but not in CU. The key conclusions are: (1) BLS is sensitive to micro-mechanical variations, particularly the strain-stiffening effect of the cutin framework, offering insights into the CM's micro-mechanical behavior and underlying chemical structures; (2) CM and DCM exhibit spatial micro-mechanical heterogeneity between periclinal and anticlinal regions.

Why it matches plant phenotyping methodsリンゴ果実のクチクラの微力学特性を、BLS顕微鏡による非侵襲的イメージングで測定・比較しており、植物器官の物性形質取得が研究の中心である。

abstractnon-invasive Brillouin light scattering (BLS) spectroscopy was applied to probe the micro-mechanics of native CM, dewaxed CM (DCM), and isolated cutin matrix (CU) of mature apple fruit.

Cracking susceptibility of full-sibs of a cross of a cracking tolerant and cracking susceptible sweet cherry: Relation to cuticle characteristics, microcracking and calcium. →

Rain cracking compromises quality and quantity of sweet cherries worldwide. Cracking susceptibility differs among genotypes. The objective was to (1) phenotype the progeny of a cross between a tolerant and a susceptible sweet cherry cultivar for cuticle mass per unit area, strain release on cuticle isolation, cuticular microcracking and calcium/dry mass ratio and (2) relate these characteristics to cracking susceptibilities evaluated in laboratory immersion assays and published multiyear field observations. Mass of the dewaxed cuticle per unit area and strain release upon cuticle isolation were significantly related to cracking susceptibility in lab or field. Cuticular microcracking in the stylar end region as indexed by infiltration with acridine orange was more severe in susceptible than in tolerant genotypes and significantly correlated with susceptibility to cracking in lab and field. The Ca/dry mass ratio was lower (-8%) for susceptible than for tolerant genotypes. Fruit that cracked early had less Ca than those that cracked later. Only the Ca/dry mass ratio of the stylar end region was significantly correlated with cracking susceptibility in the field. Based on stepwise regression analyses microcracking of the cuticle accounted for most of the cracking susceptibilities in field and lab (partial r2 = 0.331 to 0.338 for field vs. r2 = 0.326 to 0.453 for lab). The variability in cracking susceptibility accounted for increased to a r2 = 0.571 (lab) when adding mass of dewaxed cuticle, up to r2 = 0.421 (field) when adding the Ca/dry mass ratio in the stylar end region or up to r2 = 0.478 (field) when entering the strain release on isolation into the model. A protocol for phenotyping is suggested that allows larger progenies to be phenotyped for microcracking, DCM mass and strain release.

Why it matches plant phenotyping methodsサクランボ果実の微細亀裂、クチクラ質量、ひずみ解放などを用いた表現型評価を扱い、大規模後代を評価するためのフェノタイピングプロトコルを提案しているため、方法が中心的である。

abstractThe objective was to (1) phenotype the progeny of a cross between a tolerant and a susceptible sweet cherry cultivar for cuticle mass per unit area, strain release on cuticle isolation, cuticular microcracking and calcium/dry mass ratio and (2) relate these characteristics to cracking susceptibilities evaluated in laboratory immersion assays and published multiyear field observations.

Unlocking the power of AI for phenotyping fruit morphology in Arabidopsis →

Abstract Deep learning can revolutionise high-throughput image-based phenotyping by automating the measurement of complex traits, a task that is often labour-intensive, time-consuming, and prone to human error. However, its precision and adaptability in accurately phenotyping organ-level traits, such as fruit morphology, remain to be fully evaluated. Establishing the links between phenotypic and genotypic variation is essential for uncovering the genetic basis of traits and can also provide an orthologous test of pipeline effectiveness. In this study, we assess the efficacy of deep learning for measuring variation in fruit morphology in Arabidopsis using images from a multiparent advanced generation intercross (MAGIC) mapping family. We trained an instance segmentation model and developed a pipeline to phenotype Arabidopsis fruit morphology, based on the model outputs. Our model achieved strong performance with an average precision of 88.0% for detection and 55.9% for segmentation. Quantitative trait locus analysis of the derived phenotypic metrics of the MAGIC population identified significant loci associated with fruit morphology. This analysis, based on automated phenotyping of 332,194 individual fruits, underscores the capability of deep learning as a robust tool for phenotyping large populations. Our pipeline for quantifying pod morphological traits is scalable and provides high-quality phenotype data, facilitating genetic analysis and gene discovery, as well as advancing crop breeding research.

Why it matches plant phenotyping methods深層学習による果実形態の画像ベース表現型抽出パイプラインを開発し、検出・セグメンテーション性能を評価しており、植物フェノタイピング手法が研究の中心である。

abstractWe trained an instance segmentation model and developed a pipeline to phenotype Arabidopsis fruit morphology, based on the model outputs.

Open-Source High-Throughput Phenotyping for Blueberry Yield and Maturity Prediction Across Environments: Neural Network Model and Labeled Dataset for Breeders →

Time to maturity and yield are important traits for highbush blueberry (Vaccinium corymbosum) breeding. Proper determination of the time to maturity of blueberry varieties and breeding lines informs the harvest window, ensuring that the fruits are harvested at optimum maturity and quality. On the other hand, high-yielding crops bring in high profits per acre of planting. Harvesting and quantifying the yield for each blueberry breeding accession are labor-intensive and impractical. Instead, visual ratings as an estimation of yield are often used as a faster way to quantify the yield, which is categorical and subjective. In this study, we developed and shared a high-throughput phenotyping method using neural networks to predict blueberry time to maturity and to provide a proxy for yield, overcoming the labor constraints of obtaining high-frequency data. We aim to facilitate further research in computer vision and precision agriculture by publishing the labeled image dataset and the trained model. In this research, true-color images of blueberry bushes were collected, annotated, and used to train a deep neural network object detection model [You Only Look Once (YOLOv11)] to detect mature and immature berries. Different versions of YOLOv11 were used, including nano, small, and medium, which had similar performance, while the medium version had slightly higher metrics. The YOLOv11m model shows strong performance for the mature berry class, with a precision of 0.90 and an F1 score of 0.90. The precision and recall for detecting immature berries were 0.81 and 0.79. The model was tested on 10 blueberry bushes by hand harvesting and weighing blueberries. The results showed that the model detects approximately 25% of the berries on the bushes, and the correlation coefficients between model-detected and hand-harvested traits were 0.66, 0.86, and 0.72 for mature fruit count, immature fruit count, and mature ratio, respectively. The model applied to 91 blueberry advance selections and categorized them into groups with diverse levels of maturity and productivity using principal component analysis (PCA). These results inform the harvest window and yield of these breeding lines with precision and objectivity through berry classification and quantification. This model will be helpful for blueberry breeders, enabling more efficient selection, and for growers, helping them accurately estimate optimal harvest windows. This open-source tool can potentially enhance research capabilities and agricultural productivity.

Why it matches plant phenotyping methodsブルーベリーの成熟度・収量 proxy を画像とニューラルネットワークで推定する高スループット表現型計測法を開発・検証し、モデルとラベル付きデータセットを共有しているため、方法が研究の中心である。

abstractwe developed and shared a high-throughput phenotyping method using neural networks to predict blueberry time to maturity and to provide a proxy for yield

LEHP-DETR: A model with backbone improved and hybrid encoding innovated for flax capsule detection. →

Flax, as a functional crop with rich essential fatty acids and nutrients, is important in nutrition and industrial applications. However, the current process of flax seed detection relies mainly on manual operation, which is not only inefficient but also prone to error. The development of computer vision and deep learning techniques offers a new way to solve this problem. In this study, based on RT-DETR, we introduced the RepNCSPELAN4 module, ADown module, Context Aggregation module, and TFE module, and designed the HWD-ADown module, HiLo-AIFI module, and DSSFF module, and proposed an improved model, called LEHP-DETR. Experimental results show that LEHP-DETR achieves significant performance improvement on the flax dataset and comprehensively outperforms the comparison model. Compared to the base model, LEHP-DETR reduces the number of parameters by 67.3%, the model size by 66.3%, and the FLOPs by 37.6%. the average detection accuracy mAP50 and mAP50:95 increased by 2.6% and 3.5%, respectively.

Why it matches plant phenotyping methodsアマ種子ではなくフラックスの莢という植物器官を画像から検出するモデルを新規設計し、比較実験で性能を検証しており、器官表現型の取得・抽出法が中心である。

titleLEHP-DETR: A model with backbone improved and hybrid encoding innovated for flax capsule detection.

Image dataset: UAV images and ground data of one 'Bingo' mandarin and two 'Valencia' orange rootstock trials conducted in Florida. →

The data are aerial images and ground tree measurement data of 3 citrus rootstock trials. Developing new citrus rootstock varieties requires field trials to test to identify selections with improved horticultural performance. A bud from a scion variety is grafted onto the rootstock and grown in a nursery until the grafted plant is ready to be planted in the field, which is in about one year. Trees in the field are assessed each year by measuring height, canopy diameter in 2 dimensions, overall health, and fruit number and quality factors when the trees begin to have a significant crop (∼3 years). Data collection of each tree is done manually. The image and ground data sets are of 3 rootstock trials that includes a 3-year-old Bingo mandarin hybrid trial of 206 trees, a 6-year-old Valencia orange trial of 643 trees, and a 7-year-old Valencia orange trials of 648 trees. Data for each trial includes aerial images and ground data of height, canopy diameters, and an overall health rating. The combination of ground validated measures and aerial images make this data set useful for building AI-based aerial image data collection applications. The data will be useful for 1) visualizing the effects of different rootstock selections and varieties on scion growth, effects that may not be fully captured with single measure metrics; and 2) development of image analysis applications and segmentation algorithms that can extract data from the images that are suitable for replacing some or all the ground measures.

Why it matches plant phenotyping methods柑橘樹の高さ、樹冠径、健康状態を対象とする航空画像・地上測定データセットで、画像解析やセグメンテーションによる形質抽出の開発用途が明示されており、表現型取得法が中心である。

abstractThe combination of ground validated measures and aerial images make this data set useful for building AI-based aerial image data collection applications.

A computer vision system for apple fruit sizing by means of low-cost depth camera and neural network application →

Fruit size is crucial for growers as it influences consumer willingness to buy and the price of the fruit. Fruit size and growth along the seasons are two parameters that can lead to more precise orchard management favoring production sustainability. In this study, a Python-based computer vision system (CVS) for sizing apples directly on the tree was developed to ease fruit sizing tasks. The system is made of a consumer-grade depth camera and was tested at two distances among 17 timings throughout the season, in a Fuji apple orchard. The CVS exploited a specifically trained YOLOv5 detection algorithm, a circle detection algorithm, and a trigonometric approach based on depth information to size the fruits. Comparisons with standard-trained YOLOv5 models and with spherical objects were carried out. The algorithm showed good fruit detection and circle detection performance, with a sizing rate of 92%. Good correlations (r > 0.8) between estimated and actual fruit size were found. The sizing performance showed an overall mean error (mE) and RMSE of + 5.7 mm (9%) and 10 mm (15%). The best results of mE were always found at 1.0 m, compared to 1.5 m. Key factors for the presented methodology were: the fruit detectors customization; the HoughCircle parameters adaptability to object size, camera distance, and color; and the issue of field natural illumination. The study also highlighted the uncertainty of human operators in the reference data collection (5–6%) and the effect of random subsampling on the statistical analysis of fruit size estimation. Despite the high error values, the CVS shows potential for fruit sizing at the orchard scale. Future research will focus on improving and testing the CVS on a large scale, as well as investigating other image analysis methods and the ability to estimate fruit growth.

Why it matches plant phenotyping methods果実サイズという植物器官形質を、深度カメラ・物体検出・円検出・三角測量で推定するコンピュータビジョン手法を開発・検証しており、フェノタイピング手法が中心である。

abstracta Python-based computer vision system (CVS) for sizing apples directly on the tree was developed

Early detection of plant leaf diseases using stacking hybrid learning →

The early identification of pests and diseases in crops now presents a significant challenge. Different methods have been used to resolve this problem. Sticky traps and black light traps, used to identify diseases and for field monitoring, are examples of a manual procedure for analysing the diseases. A lot of time is required, and it is less effective to manually inspect larger crop fields manually. To serve requires a professional, so it is, therefore, costly. The use of sticky traps, where by bugs stick to the material upon contact, is one method of disease monitoring. A camera is used to take a picture of the sticky trap. From the picture using the average disease count, this image is then processed to ascertain the pet density for a specific time period. Such manual methods, as well as providing an effective outcome also pose a danger to the environment. This is because farmers spray pesticides in large quantities as a preventative measure. Various approaches have been used to identify diseases, including image processing and sophisticated algorithms. The most effective method of disease identification from crops is automatic detection using methods of image processing and classification algorithms for the diseases to be categorised based on different picture attributes. With a stacking stacking hybrid learning with scratch and transfer learning strategies, which is utilised in this work, a model that has already been trained is used to learn on images of diverse fruit plant leaves from the Plant Village dataset, spanning both safe samples and various illnesses. This reasearch paper used ensemble CNN and we achieved accuracy between 99.75% to 100%.

Why it matches plant phenotyping methods植物葉の画像から病害状態を自動分類する画像解析・機械学習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 most effective method of disease identification from crops is automatic detection using methods of image processing and classification algorithms for the diseases to be categorised based on different picture attributes.

BerryPortraits: Phenotyping Of Ripening Traits cranberry (Vaccinium macrocarpon Ait.) with YOLOv8. →

Abstract BerryPortraits (Phenotyping of Ripening Traits) is open source Python-based image-analysis software that rapidly detects and segments berries and extracts morphometric data on fruit quality traits such as berry color, size, shape, and uniformity. Utilizing the YOLOv8 framework and community-developed, actively-maintained Python libraries such as OpenCV, BerryPortraits software was trained on 512 postharvest images (taken under controlled lighting conditions) of phenotypically diverse cranberry populations ( Vaccinium macrocarpon Ait.) from the two largest public cranberry breeding programs in the U.S. The implementation of CIELAB, an intuitive and perceptually uniform color space, enables differentiation between berry color and berry brightness, which are confounded in classic RGB color channel measurements. Furthermore, computer vision enables precise and quantifiable color phenotyping, thus facilitating inclusion of researchers and data analysts with color vision deficiency. BerryPortraits is a phenotyping tool for researchers in plant breeding, plant genetics, horticulture, food science, plant physiology, plant pathology, and related fields. BerryPortraits has strong potential applications for other specialty crops such as blueberry, lingonberry, caneberry, grape, and more. As an open source phenotyping tool based on widely-used python libraries, BerryPortraits allows anyone to use, fork, modify, optimize, and embed this software into other tools or pipelines.

Why it matches plant phenotyping methods植物果実の色・サイズ・形状・均一性を画像から抽出するオープンソースの表現型解析ソフトウェアを開発しており、植物フェノタイピング手法が研究の中心である。

abstractBerryPortraits (Phenotyping of Ripening Traits) is open source Python-based image-analysis software that rapidly detects and segments berries and extracts morphometric data on fruit quality traits such as berry color, size, shape, and uniformity.

Development of a Drone-Based Phenotyping System for European Pear Rust (Gymnosporangium sabinae) in Orchards →

Computer vision techniques offer promising tools for disease detection in orchards and can enable effective phenotyping for the selection of resistant cultivars in breeding programmes and research. In this study, a digital phenotyping system for disease detection and monitoring was developed using drones, object detection and photogrammetry, focusing on European pear rust (Gymnosporangium sabinae) as a model pathogen. High-resolution RGB images from ten low-altitude drone flights were collected in 2021, 2022 and 2023. A total of 16,251 annotations of leaves with pear rust symptoms were created on 584 images using the Computer Vision Annotation Tool (CVAT). The YOLO algorithm was used for the automatic detection of symptoms. A novel photogrammetric approach using Agisoft’s Metashape Professional software ensured the accurate localisation of symptoms. The geographic information system software QGIS calculated the infestation intensity per tree based on the canopy areas. This drone-based phenotyping system shows promising results and could considerably simplify the tasks involved in fruit breeding research.

Why it matches plant phenotyping methodsドローン画像、物体検出、写真測量を統合し、ナシ樹のさび病症状を検出・局在化して樹体ごとの感染強度を推定するデジタル表現型解析システムの開発が中心である。

abstracta digital phenotyping system for disease detection and monitoring was developed using drones, object detection and photogrammetry

A Comprehensive Hybrid Model for Apple Fruit Disease Detection using Multi-Architecture Feature Extraction →

Abstract The agriculture industry is critical to the global economy, with product quality having a direct impact on marketability and waste management. Apples, one of the most extensively produced fruits, are affected by a variety of diseases that can reduce productivity and quality. Accurate diagnosis of diseases is critical, but traditional manual approaches are time-consuming, error-prone, and ineffective. Inadequate labeled data and a wide range of disease symptoms make it necessary to design an automated, robust, and accurate system. This article describes a hybrid model for Apple Fruit Disease Detection (HMAFDD) that combines the strengths of three pre-trained convolutional neural network (CNN) models: ResNet50, DenseNet121, and EfficientNetB0. It accomplish this by using multi-architecture feature extraction. The hybrid system, which combines both models, is able to recognize a wide range of features, from simple textures to complex patterns unique to a certain diseases. Grad-CAM, or gradient-weighted class activation mapping, creates heatmaps that highlight significant regions for prediction, which enhances the interpretability of the model.To increase robustness and accuracy, techniques such as spectral-shifted adversarial perturbation for data augmentation and spectrally-weighted global average pooling for feature aggregation are used. This technique provides 99.75\% accuracy with minimal processing needs, making it acceptable for real-time applications in agricultural situations. This considerably improves apple disease management.

Why it matches plant phenotyping methodsリンゴ果実の病徴を画像から推定するCNNベースの疾病検出手法を開発しており、植物の病害状態を直接評価する方法が研究の中心です。

abstractThis article describes a hybrid model for Apple Fruit Disease Detection (HMAFDD) that combines the strengths of three pre-trained convolutional neural network (CNN) models

Rape Yield Estimation Considering Non-Foliar Green Organs Based on the General Crop Growth Model. →

To address the underestimation of rape yield by traditional gramineous crop yield simulation methods based on crop models, this study used the WOFOST crop model to estimate rape yield in the main producing areas of southern Hunan based on 2 years of field-measured data, with consideration given to the photosynthesis of siliques, which are non-foliar green organs. First, the total photosynthetic area index (TPAI), which considers the photosynthesis of siliques, was proposed as a substitute for the leaf area index (LAI) as the calibration variable in the model. Two parameter calibration methods were subsequently proposed, both of which consider photosynthesis by siliques: the TPAI-SPA method, which is based on the TPAI coupled with a specific pod area, and the TPAI-Curve method, which is based on the TPAI and curve fitting. Finally, the 2 proposed parameter calibration methods were validated via 2 years of observed rape data. The results indicate that compared with traditional LAI-based crop model calibration methods, the TPAI-SPA and TPAI-Curve methods can improve the accuracy of rape yield estimation. The estimation accuracy ( R 2 ) for the total weight of storage organs (TWSO) and above-ground biomass (TAGP) increased by 9.68% and 49.86%, respectively, for the TPAI-SPA method and by 14.04% and 42.94%, respectively, for the TPAI-Curve method. Thus, the 2 calibration methods proposed in this study are of important practical importance for improving the accuracy of rape yield simulations. This study provides a novel technical approach for utilizing crop growth models in the yield estimation of oilseed crops.

Why it matches plant phenotyping methods非葉部器官の光合成を組み込んだTPAIを新たな校正変数として提案し、作物モデルによる収量・バイオマス推定法を開発・検証しているため、表現型推定手法が中心である。

abstractthe total photosynthetic area index (TPAI), which considers the photosynthesis of siliques, was proposed as a substitute for the leaf area index (LAI) as the calibration variable in the model.

Of buds and bits: a meta-QTL study identifies stable QTL for berry quality and yield traits in cranberry mapping populations ( Vaccinium macrocarpon Ait.). →

Introduction For nearly two centuries, cranberry (Vaccinium macrocarpon Ait.) breeders have improved fruit quality and yield by selecting traits on fruiting stems, termed “reproductive uprights.” Crop improvement is accelerating rapidly in contemporary breeding programs due to modern genetic tools and high-throughput phenotyping methods, improving selection efficiency and accuracy. Methods We conducted genotypic evaluation on 29 primary traits encompassing fruit quality, yield, and chemical composition in two full-sib cranberry breeding populations—CNJ02 (n = 168) and CNJ04 (n = 67)—over 3 years. Genetic characterization was further performed on 11 secondary traits derived from these primary traits. Results For CNJ02, 170 major quantitative trait loci (QTL; R2≥ 0.10) were found with interval mapping, 150 major QTL were found with model mapping, and 9 QTL were found to be stable across multiple years. In CNJ04, 69 major QTL were found with interval mapping, 81 major QTL were found with model mapping, and 4 QTL were found to be stable across multiple years. Meta-QTL represent stable genomic regions consistent across multiple years, populations, studies, or traits. Seven multi-trait meta-QTL were found in CNJ02, one in CNJ04, and one in the combined analysis of both populations. A total of 22 meta-QTL were identified in cross-study, cross-population analysis using digital traits for berry shape and size (8 meta-QTL), digital images for berry color (2 meta-QTL), and three-study cross-analysis (12 meta-QTL). Discussion Together, these meta-QTL anchor high-throughput fruit quality phenotyping techniques to traditional phenotyping methods, validating state-of-the-art methods in cranberry phenotyping that will improve breeding accuracy, efficiency, and genetic gain in this globally significant fruit crop.

Why it matches plant phenotyping methodsベリー形状・サイズ・色のデジタル形質および画像を用いた果実フェノタイピングをQTL解析で検証し、従来法との対応付けを行っており、手法の妥当性評価が研究の主要な成果に含まれる。

abstractdigital traits for berry shape and size (8 meta-QTL), digital images for berry color (2 meta-QTL)

CF-PRNet: Coarse-to-Fine Prototype Refining Network for Point Cloud Completion and Reconstruction →

In modern agriculture, precise monitoring of plants and fruits is crucial for tasks such as high-throughput phenotyping and automated harvesting. This paper addresses the challenge of reconstructing accurate 3D shapes of fruits from partial views, which is common in agricultural settings. We introduce CF-PRNet, a coarse-to-fine prototype refining network, leverages high-resolution 3D data during the training phase but requires only a single RGB-D image for real-time inference. Our approach begins by extracting the incomplete point cloud data that constructed from a partial view of a fruit with a series of convolutional blocks. The extracted features inform the generation of scaling vectors that refine two sequentially constructed 3D mesh prototypes - one coarse and one fine-grained. This progressive refinement facilitates the detailed completion of the final point clouds, achieving detailed and accurate reconstructions. CF-PRNet demonstrates excellent performance metrics with a Chamfer Distance of 3.78, an F1 Score of 66.76%, a Precision of 56.56%, and a Recall of 85.31%, and win the first place in the Shape Completion and Reconstruction of Sweet Peppers Challenge.

Why it matches plant phenotyping methods果実の部分RGB-D画像から3D形状を再構成する手法を開発・評価しており、植物器官の形態形質取得が研究の中心である。

abstractThis paper addresses the challenge of reconstructing accurate 3D shapes of fruits from partial views

Estimation of crop yield using deep learning for precision agriculture →

Precision agriculture is the application of correct amount of fertilizers and water pesticide to achieve higher agricultural productivity. Furthermore, under the framework of precision agriculture is the automated estimation of yield with advanced technologies including Artificial Intelligence (AI) and Remote Sensing (RS). The use of RS has advanced crop yield estimations and predictions in recent years. However, to validate RS-based models it is important to perform in-situ exercises such as fruit counting, which is a time-consuming task that increases the production costs. Drones, robots, and in-situ cameras in combination with AI algorithms are widely used to efficiently address these issues. The recent advancement in computational resources and power available has enabled the utilization of Deep Learning AI models. One of the best-performing models for object detection is the You-Only-Look-Once (YOLO). In this study, the YOLOv5s is used for object detection, which is the second smallest and fastest YOLOv5 architecture, on two different benchmark datasets collected from AgML. The first dataset consists of 1730 images of mango trees in Australia during night, and the second dataset consists of 6512 images of wheat heads collected from different regions around the world. The main objective of this work is to demonstrate the capabilities of light AI models for object detection and to evaluate their performance, which will serve as a benchmark for future comparison with the on-board environment.

Why it matches plant phenotyping methods植物器官の検出・カウントによる収量推定を対象とし、YOLOv5sの性能評価とベンチマーク化が主目的であるため、計算画像フェノタイピング手法として採用。

abstractIn this study, the YOLOv5s is used for object detection, which is the second smallest and fastest YOLOv5 architecture, on two different benchmark datasets collected from AgML.

FruitNeRF: A Unified Neural Radiance Field based Fruit Counting Framework →

We introduce FruitNeRF, a unified novel fruit counting framework that leverages state-of-the-art view synthesis methods to count any fruit type directly in 3D. Our framework takes an unordered set of posed images captured by a monocular camera and segments fruit in each image. To make our system independent of the fruit type, we employ a foundation model that generates binary segmentation masks for any fruit. Utilizing both modalities, RGB and semantic, we train a semantic neural radiance field. Through uniform volume sampling of the implicit Fruit Field, we obtain fruit-only point clouds. By applying cascaded clustering on the extracted point cloud, our approach achieves precise fruit count.The use of neural radiance fields provides significant advantages over conventional methods such as object tracking or optical flow, as the counting itself is lifted into 3D. Our method prevents double counting fruit and avoids counting irrelevant fruit.We evaluate our methodology using both real-world and synthetic datasets. The real-world dataset consists of three apple trees with manually counted ground truths, a benchmark apple dataset with one row and ground truth fruit location, while the synthetic dataset comprises various fruit types including apple, plum, lemon, pear, peach, and mango.Additionally, we assess the performance of fruit counting using the foundation model compared to a U-Net.

Why it matches plant phenotyping methods果実を対象に、画像・NeRF・点群クラスタリングを組み合わせて3D果実数を推定する手法を開発し、実データおよび合成データで評価しているため、植物表現型取得法が中心である。

abstractWe introduce FruitNeRF, a unified novel fruit counting framework that leverages state-of-the-art view synthesis methods to count any fruit type directly in 3D.

SPCN: An Innovative Soybean Pod Counting Network Based on HDC Strategy and Attention Mechanism →

Soybean pod count is a crucial aspect of soybean plant phenotyping, offering valuable reference information for breeding and planting management. Traditional manual counting methods are not only costly but also prone to errors. Existing detection-based soybean pod counting methods face challenges due to the crowded and uneven distribution of soybean pods on the plants. To tackle this issue, we propose a Soybean Pod Counting Network (SPCN) for accurate soybean pod counting. SPCN is a density map-based architecture based on Hybrid Dilated Convolution (HDC) strategy and attention mechanism for feature extraction, using the Unbalanced Optimal Transport (UOT) loss function for supervising density map generation. Additionally, we introduce a new diverse dataset, BeanCount-1500, comprising of 24,684 images of 316 soybean varieties with various backgrounds and lighting conditions. Extensive experiments on BeanCount-1500 demonstrate the advantages of SPCN in soybean pod counting with an Mean Absolute Error(MAE) and an Mean Squared Error(MSE) of 4.37 and 6.45, respectively, significantly outperforming the current competing method by a substantial margin. Its excellent performance on the Renshou2021 dataset further confirms its outstanding generalization potential. Overall, the proposed method can provide technical support for intelligent breeding and planting management of soybean, promoting the digital and precise management of agriculture in general.

Why it matches plant phenotyping methods大豆莢数という植物形質を画像から自動推定する手法を開発し、データセット上で性能評価しているため、植物フェノタイピング手法が研究の中心です。

abstractSoybean pod count is a crucial aspect of soybean plant phenotyping

High-throughput 3D shape completion of potato tubers on a harvester →

Potato yield is an important metric for farmers to further optimize their cultivation practices. Potato yield can be estimated on a harvester using an RGB-D camera that can estimate the three-dimensional (3D) volume of individual potato tubers. A challenge, however, is that the 3D shape derived from RGB-D images is only partially completed, underestimating the actual volume. To address this issue, we developed a 3D shape completion network, called CoRe++, which can complete the 3D shape from RGB-D images. CoRe++ is a deep learning network that consists of a convolutional encoder and a decoder. The encoder compresses RGB-D images into latent vectors that are used by the decoder to complete the 3D shape using the deep signed distance field network (DeepSDF). To evaluate our CoRe++ network, we collected partial and complete 3D point clouds of 339 potato tubers on an operational harvester in Japan. On the 1425 RGB-D images in the test set (representing 51 unique potato tubers), our network achieved a completion accuracy of 2.8 mm on average. For volumetric estimation, the root mean squared error (RMSE) was 22.6 ml, and this was better than the RMSE of the linear regression (31.1 ml) and the base model (36.9 ml). We found that the RMSE can be further reduced to 18.2 ml when performing the 3D shape completion in the center of the RGB-D image. With an average 3D shape completion time of 10 milliseconds per tuber, we can conclude that CoRe++ is both fast and accurate enough to be implemented on an operational harvester for high-throughput potato yield estimation. CoRe++'s high-throughput and accurate processing allows it to be applied to other tuber, fruit and vegetable crops, thereby enabling versatile, accurate and real-time yield monitoring in precision agriculture. Our code, network weights and dataset are publicly available at https://github.com/UTokyo-FieldPhenomics-Lab/corepp.git.

Why it matches plant phenotyping methodsRGB-D画像からジャガイモ塊茎の3D形状を補完し、体積・収量を推定する手法を開発・検証しており、植物フェノタイピング手法が研究の中心である。

abstractwe developed a 3D shape completion network, called CoRe++, which can complete the 3D shape from RGB-D images.

A Dataset and Benchmark for Shape Completion of Fruits for Agricultural Robotics →

As the world population is expected to reach 10 billion by 2050, our agricultural production system needs to double its productivity despite a decline of human workforce in the agricultural sector. Autonomous robotic systems are one promising pathway to increase productivity by taking over labor-intensive manual tasks like fruit picking. To be effective, such systems need to monitor and interact with plants and fruits precisely, which is challenging due to the cluttered nature of agricultural environments causing, for example, strong occlusions. Thus, being able to estimate the complete 3D shapes of objects in presence of occlusions is crucial for automating operations such as fruit harvesting. In this paper, we propose the first publicly available 3D shape completion dataset for agricultural vision systems. We provide an RGB-D dataset for estimating the 3D shape of fruits. Specifically, our dataset contains RGB-D frames of single sweet peppers in lab conditions but also in a commercial greenhouse. For each fruit, we additionally collected high-precision point clouds that we use as ground truth. For acquiring the ground truth shape, we developed a measuring process that allows us to record data of real sweet pepper plants, both in the lab and in the greenhouse with high precision, and determine the shape of the sensed fruits. We release our dataset, consisting of almost 7,000 RGB-D frames belonging to more than 100 different fruits. We provide segmented RGB-D frames, with camera intrinsics to easily obtain colored point clouds, together with the corresponding high-precision, occlusion-free point clouds obtained with a high-precision laser scanner. We additionally enable evaluation of shape completion approaches on a hidden test set through a public challenge on a benchmark server.

Why it matches plant phenotyping methods果実の3D形状という植物器官の形態形質を対象に、RGB-D画像・高精度点群・評価用ベンチマークを構築しており、形状取得と推定の方法論が中心である。

abstractWe provide an RGB-D dataset for estimating the 3D shape of fruits.

Fruit surface temperature data at different ripeness stages and ambient temperature provided as temperature-annotated 3D point clouds of apple trees. →

By means of a unique, low vibration circular conveyor system, plant sensors capturing light detection and ranging (LiDAR) unit and thermal camera were moved on the same route, around blocks of apple trees, with seven Malus x domestica Borkh. 'Gala' apple trees in each block. Measurements took place four times during the season. Additionally at harvest, diurnal courses were recorded with 18 readings during three days. The data are provided as [i] raw data (3D point clouds of 3 blocks of trees scanned from right and left sides and thermal images), [ii] processed 3D point clouds of canopies annotated with temperature data from the thermal camera, and [iii] manually segmented 3D point clouds of fruit, representing the spatially-resolved fruit surface temperature (FST). Manual FST readings are provided on each measuring date and during diurnal courses. The fruit data are capturing 1236 FST, providing temperature distribution as 3D point cloud and one manually recorded reference FST per fruit. Additionally, fruit size and colour were measured for each fruit, despite for the first date, when fruit were too small for colour readings. Weather data are provided from a station located in the orchard. Usage of data could be (a) in developing methodology for 3D point cloud processing based on raw data, accomplished with reference FST data. Furthermore, (b) the pre-processed point clouds of fruit surface temperature can be reused in ecophysiological studies related to global warming, optimizing fruit production systems, and other. Because the sensors and trees were measured from the same angle and distance, time series analysis of the canopies would be possible.

Why it matches plant phenotyping methodsLiDARと熱画像を統合し、果実表面温度を3D点群として取得・注釈化した再利用可能なデータセットであり、植物表現型取得手法とデータ提供が中心です。

abstractplant sensors capturing light detection and ranging (LiDAR) unit and thermal camera were moved on the same route, around blocks of apple trees

Development of a deep-learning phenotyping tool for analyzing image-based strawberry phenotypes. →

Introduction In strawberry farming, phenotypic traits (such as crown diameter, petiole length, plant height, flower, leaf, and fruit size) measurement is essential as it serves as a decision-making tool for plant monitoring and management. To date, strawberry plant phenotyping has relied on traditional approaches. In this study, an image-based Strawberry Phenotyping Tool (SPT) was developed using two deep-learning (DL) architectures, namely “YOLOv4” and “U-net” integrated into a single system. We aimed to create the most suitable DL-based tool with enhanced robustness to facilitate digital strawberry plant phenotyping directly at the natural scene or indirectly using captured and stored images. Methods Our SPT was developed primarily through two steps (subsequently called versions) using image data with different backgrounds captured with simple smartphone cameras. The two versions (V1 and V2) were developed using the same DL networks but differed by the amount of image data and annotation method used during their development. For V1, 7,116 images were annotated using the single-target non-labeling method, whereas for V2, 7,850 images were annotated using the multitarget labeling method. Results The results of the held-out dataset revealed that the developed SPT facilitates strawberry phenotype measurements. By increasing the dataset size combined with multitarget labeling annotation, the detection accuracy of our system changed from 60.24% in V1 to 82.28% in V2. During the validation process, the system was evaluated using 70 images per phenotype and their corresponding actual values. The correlation coefficients and detection frequencies were higher for V2 than for V1, confirming the superiority of V2. Furthermore, an image-based regression model was developed to predict the fresh weight of strawberries based on the fruit size (R2 = 0.92). Discussion The results demonstrate the efficiency of our system in recognizing the aforementioned six strawberry phenotypic traits regardless of the complex scenario of the environment of the strawberry plant. This tool could help farmers and researchers make accurate and efficient decisions related to strawberry plant management, possibly causing increased productivity and yield potential.

Why it matches plant phenotyping methods画像ベースでイチゴの複数形質を抽出・測定する深層学習ツールを開発し、精度と実測値との相関を検証しており、植物表現型取得手法が研究の中心である。

abstractIn this study, an image-based Strawberry Phenotyping Tool (SPT) was developed using two deep-learning (DL) architectures, namely “YOLOv4” and “U-net” integrated into a single system.

Bacterial-fungicidal vine disease detection with proximal aerial images. →

Vine disease detection is considered one of the most crucial components in precision viticulture. It serves as an input for several further modules, including mapping, automatic treatment, and spraying devices. In the last few years, several approaches have been proposed for detecting vine disease based on indoor laboratory conditions or large-scale satellite images integrated with machine learning tools. However, these methods have several limitations, including laboratory-specific conditions or limited visibility into plant-related diseases. To overcome these limitations, this work proposes a low-altitude drone flight approach through which a comprehensive dataset about various vine diseases from a large-scale European dataset is generated. The dataset contains typical diseases such as downy mildew or black rot affecting the large variety of grapes including Muscat of Hamburg, Alphonse Lavallée, Grasă de Cotnari, Rkatsiteli, Napoca, Pinot blanc, Pinot gris, Chambourcin, Fetească regală, Sauvignon blanc, Muscat Ottonel, Merlot, and Seyve-Villard 18402. The dataset contains 10,000 images and more than 100,000 annotated leaves, verified by viticulture specialists. Grape bunches are also annotated for yield estimation. Further, tests were made against state-of-the-art detection methods on this dataset, focusing also on viable solutions on embedded devices, including Android-based phones or Nvidia Jetson boards with GPU. The datasets, as well as the customized embedded models, are available on the project webpage.

Why it matches plant phenotyping methodsブドウ葉の病徴を低高度ドローン画像で検出する大規模データセットを構築し、葉アノテーションと手法比較・組込み機器での評価を行っており、植物状態の画像ベース計測が中心です。

abstractthis work proposes a low-altitude drone flight approach through which a comprehensive dataset about various vine diseases from a large-scale European dataset is generated.

Lightweight tomato ripeness detection algorithm based on the improved RT-DETR. →

Tomatoes, widely cherished for their high nutritional value, necessitate precise ripeness identification and selective harvesting of mature fruits to significantly enhance the efficiency and economic benefits of tomato harvesting management. Previous studies on intelligent harvesting often focused solely on identifying tomatoes as the target, lacking fine-grained detection of tomato ripeness. This deficiency leads to the inadvertent harvesting of immature and rotten fruits, resulting in economic losses. Moreover, in natural settings, uneven illumination, occlusion by leaves, and fruit overlap hinder the precise assessment of tomato ripeness by robotic systems. Simultaneously, the demand for high accuracy and rapid response in tomato ripeness detection is compounded by the need for making the model lightweight to mitigate hardware costs. This study proposes a lightweight model named PDSI-RTDETR to address these challenges. Initially, the PConv_Block module, integrating partial convolution with residual blocks, replaces the Basic_Block structure in the legacy backbone to alleviate computing load and enhance feature extraction efficiency. Subsequently, a deformable attention module is amalgamated with intra-scale feature interaction structure, bolstering the capability to extract detailed features for fine-grained classification. Additionally, the proposed slimneck-SSFF feature fusion structure, merging the Scale Sequence Feature Fusion framework with a slim-neck design utilizing GSConv and VoVGSCSP modules, aims to reduce volume of computation and inference latency. Lastly, by amalgamating Inner-IoU with EIoU to formulate Inner-EIoU, replacing the original GIoU to expedite convergence while utilizing auxiliary frames enhances small object detection capabilities. Comprehensive assessments validate that the PDSI-RTDETR model achieves an average precision mAP50 of 86.8%, marking a 3.9% enhancement over the original RT-DETR model, and a 38.7% increase in FPS. Furthermore, the GFLOPs of PDSI-RTDETR have been diminished by 17.6%. Surpassing the baseline RT-DETR and other prevalent methods regarding precision and speed, it unveils its considerable potential for detecting tomato ripeness. When applied to intelligent harvesting robots in the future, this approach can improve the quality of tomato harvesting by reducing the collection of immature and spoiled fruits.

Why it matches plant phenotyping methodsトマト果実の成熟度という植物状態を画像から推定する軽量検出モデルを開発し、精度・速度・計算量を評価しており、表現型取得手法が中心である。

abstractThis study proposes a lightweight model named PDSI-RTDETR to address these challenges.

DEKR-SPrior: An Efficient Bottom-Up Keypoint Detection Model for Accurate Pod Phenotyping in Soybean →

The pod and seed counts are important yield-related traits in soybean. High-precision soybean breeders face the major challenge of accurately phenotyping the number of pods and seeds in a high-throughput manner. Recent advances in artificial intelligence, especially deep learning (DL) models, have provided new avenues for high-throughput phenotyping of crop traits with increased precision. However, the available DL models are less effective for phenotyping pods that are densely packed and overlap in in situ soybean plants; thus, accurate phenotyping of the number of pods and seeds in soybean plant is an important challenge. To address this challenge, the present study proposed a bottom-up model, DEKR-SPrior (disentangled keypoint regression with structural prior), for in situ soybean pod phenotyping, which considers soybean pods and seeds analogous to human people and joints, respectively. In particular, we designed a novel structural prior (SPrior) module that utilizes cosine similarity to improve feature discrimination, which is important for differentiating closely located seeds from highly similar seeds. To further enhance the accuracy of pod location, we cropped full-sized images into smaller and high-resolution subimages for analysis. The results on our image datasets revealed that DEKR-SPrior outperformed multiple bottom-up models, viz., Lightweight-OpenPose, OpenPose, HigherHRNet, and DEKR, reducing the mean absolute error from 25.81 (in the original DEKR) to 21.11 (in the DEKR-SPrior) in pod phenotyping. This paper demonstrated the great potential of DEKR-SPrior for plant phenotyping, and we hope that DEKR-SPrior will help future plant phenotyping.

Why it matches plant phenotyping methods大豆の莢・種子数を高スループットに推定する画像解析モデルを開発し、既存モデルと比較検証しているため、植物表現型取得手法が研究の中心です。

abstractthe present study proposed a bottom-up model, DEKR-SPrior (disentangled keypoint regression with structural prior), for in situ soybean pod phenotyping

Segment Anything for Comprehensive Analysis of Grapevine Cluster Architecture and Berry Properties. →

Grape cluster architecture and compactness are complex traits influencing disease susceptibility, fruit quality, and yield. Evaluation methods for these traits include visual scoring, manual methodologies, and computer vision, with the latter being the most scalable approach. Most of the existing computer vision approaches for processing cluster images often rely on conventional segmentation or machine learning with extensive training and limited generalization. The Segment Anything Model (SAM), a novel foundation model trained on a massive image dataset, enables automated object segmentation without additional training. This study demonstrates out-of-the-box SAM's high accuracy in identifying individual berries in 2-dimensional (2D) cluster images. Using this model, we managed to segment approximately 3,500 cluster images, generating over 150,000 berry masks, each linked with spatial coordinates within their clusters. The correlation between human-identified berries and SAM predictions was very strong (Pearson's r 2 = 0.96). Although the visible berry count in images typically underestimates the actual cluster berry count due to visibility issues, we demonstrated that this discrepancy could be adjusted using a linear regression model (adjusted R 2 = 0.87). We emphasized the critical importance of the angle at which the cluster is imaged, noting its substantial effect on berry counts and architecture. We proposed different approaches in which berry location information facilitated the calculation of complex features related to cluster architecture and compactness. Finally, we discussed SAM's potential integration into currently available pipelines for image generation and processing in vineyard conditions.

Why it matches plant phenotyping methodsSAMを用いたブドウ房画像からの個別果粒セグメンテーション、検証、補正、および房構造・コンパクトネス形質の算出が研究の中心であるため。

abstractThis study demonstrates out-of-the-box SAM's high accuracy in identifying individual berries in 2-dimensional (2D) cluster images.

Designing and development of agricultural rovers for vegetable harvesting and soil analysis. →

To address the growing demand for sustainable agriculture practices, new technologies to boost crop productivity and soil health must be developed. In this research, we propose designing and building an agricultural rover capable of autonomous vegetable harvesting and soil analysis utilizing cutting-edge deep learning algorithms (YOLOv5). The precision and recall score of the model was 0.8518% and 0.7624% respectively. The rover uses robotics, computer vision, and soil sensing technology to perform accurate and efficient agricultural tasks. We go over the rover's hardware and software, as well as the soil analysis system and the tomato ripeness detection system using deep learning models. Field experiments indicate that this agricultural rover is effective and promising for improving crop management and soil monitoring in modern agriculture, hence achieving the UN's SDG 2 Zero Hunger goals.

Why it matches plant phenotyping methodsトマトの成熟度という植物器官の状態を深層学習で推定する画像ベース手法を、農業ローバーの主要機能として開発しているため。

abstractthe tomato ripeness detection system using deep learning models

Optimizing Strawberry Disease and Quality Detection with Vision Transformers and Attention-Based Convolutional Neural Networks. →

Machine learning and computer vision have proven to be valuable tools for farmers to streamline their resource utilization to lead to more sustainable and efficient agricultural production. These techniques have been applied to strawberry cultivation in the past with limited success. To build on this past work, in this study, two separate sets of strawberry images, along with their associated diseases, were collected and subjected to resizing and augmentation. Subsequently, a combined dataset consisting of nine classes was utilized to fine-tune three distinct pretrained models: vision transformer (ViT), MobileNetV2, and ResNet18. To address the imbalanced class distribution in the dataset, each class was assigned weights to ensure nearly equal impact during the training process. To enhance the outcomes, new images were generated by removing backgrounds, reducing noise, and flipping them. The performances of ViT, MobileNetV2, and ResNet18 were compared after being selected. Customization specific to the task was applied to all three algorithms, and their performances were assessed. Throughout this experiment, none of the layers were frozen, ensuring all layers remained active during training. Attention heads were incorporated into the first five and last five layers of MobileNetV2 and ResNet18, while the architecture of ViT was modified. The results indicated accuracy factors of 98.4%, 98.1%, and 97.9% for ViT, MobileNetV2, and ResNet18, respectively. Despite the data being imbalanced, the precision, which indicates the proportion of correctly identified positive instances among all predicted positive instances, approached nearly 99% with the ViT. MobileNetV2 and ResNet18 demonstrated similar results. Overall, the analysis revealed that the vision transformer model exhibited superior performance in strawberry ripeness and disease classification. The inclusion of attention heads in the early layers of ResNet18 and MobileNet18, along with the inherent attention mechanism in ViT, improved the accuracy of image identification. These findings offer the potential for farmers to enhance strawberry cultivation through passive camera monitoring alone, promoting the health and well-being of the population.

Why it matches plant phenotyping methodsイチゴ画像から病害と成熟度を分類する画像解析手法を開発・比較し、植物の状態推定が研究の中心であるため。

abstractthe analysis revealed that the vision transformer model exhibited superior performance in strawberry ripeness and disease classification.

Semantic segmentation of microbial alterations based on SegFormer. →

Introduction Precise semantic segmentation of microbial alterations is paramount for their evaluation and treatment. This study focuses on harnessing the SegFormer segmentation model for precise semantic segmentation of strawberry diseases, aiming to improve disease detection accuracy under natural acquisition conditions. Methods Three distinct Mix Transformer encoders - MiT-B0, MiT-B3, and MiT-B5 - were thoroughly analyzed to enhance disease detection, targeting diseases such as Angular leaf spot, Anthracnose rot, Blossom blight, Gray mold, Leaf spot, Powdery mildew on fruit, and Powdery mildew on leaves. The dataset consisted of 2,450 raw images, expanded to 4,574 augmented images. The Segment Anything Model integrated into the Roboflow annotation tool facilitated efficient annotation and dataset preparation. Results The results reveal that MiT-B0 demonstrates balanced but slightly overfitting behavior, MiT-B3 adapts rapidly with consistent training and validation performance, and MiT-B5 offers efficient learning with occasional fluctuations, providing robust performance. MiT-B3 and MiT-B5 consistently outperformed MiT-B0 across disease types, with MiT-B5 achieving the most precise segmentation in general. Discussion The findings provide key insights for researchers to select the most suitable encoder for disease detection applications, propelling the field forward for further investigation. The success in strawberry disease analysis suggests potential for extending this approach to other crops and diseases, paving the way for future research and interdisciplinary collaboration.

Why it matches plant phenotyping methodsイチゴ病害の画像から病斑・病害状態をセグメンテーションする手法を開発・比較しており、植物の病害表現型の取得が中心である。

abstractMiT-B0, MiT-B3, and MiT-B5 - were thoroughly analyzed to enhance disease detection

PlantSR: Super-Resolution Improves Object Detection in Plant Images →

Recent advancements in computer vision, especially deep learning models, have shown considerable promise in tasks related to plant image object detection. However, the efficiency of these deep learning models heavily relies on input image quality, with low-resolution images significantly hindering model performance. Therefore, reconstructing high-quality images through specific techniques will help extract features from plant images, thus improving model performance. In this study, we explored the value of super-resolution technology for improving object detection model performance on plant images. Firstly, we built a comprehensive dataset comprising 1030 high-resolution plant images, named the PlantSR dataset. Subsequently, we developed a super-resolution model using the PlantSR dataset and benchmarked it against several state-of-the-art models designed for general image super-resolution tasks. Our proposed model demonstrated superior performance on the PlantSR dataset, indicating its efficacy in enhancing the super-resolution of plant images. Furthermore, we explored the effect of super-resolution on two specific object detection tasks: apple counting and soybean seed counting. By incorporating super-resolution as a pre-processing step, we observed a significant reduction in mean absolute error. Specifically, with the YOLOv7 model employed for apple counting, the mean absolute error decreased from 13.085 to 5.71. Similarly, with the P2PNet-Soy model utilized for soybean seed counting, the mean absolute error decreased from 19.159 to 15.085. These findings underscore the substantial potential of super-resolution technology in improving the performance of object detection models for accurately detecting and counting specific plants from images. The source codes and associated datasets related to this study are available at Github.

Why it matches plant phenotyping methods植物画像向け超解像モデルとデータセットを開発・ベンチマークし、リンゴおよびダイズ種子の計数性能を評価しており、表現型取得・抽出法が中心である。

abstractwe built a comprehensive dataset comprising 1030 high-resolution plant images, named the PlantSR dataset.

Mango Fruit Diseases Severity Estimation based on Image Segmentation and Deep Learning →

Abstract Plant disease severity is the ratio between the surface area of disease symptoms and the total surface area of the plant unit (e.g. fruit, leaf). It is related to plant disease diagnosis and has several advantages for farmers. It is therefore a key element in the protection and management of plant diseases. In the literature, there are three proposed categories of plant disease severity determination solutions: those based on segmentation algorithms, those based on classical ML algorithms and those based on DL algorgorithms. Despite their many advantages, these solutions have a number of limitations, including i) subjectivity in data labeling, ii) loss of information on disease lesion contours during (manual) data labeling, and iii) the proposed solutions have focused on estimating plant disease severity from leaves, although diseases can also affect other parts of the plant, such as fruits. In this paper, we present a solution for estimating the severity of four mango fruit diseases, namely alternaria, anthracnose, aspergillus rot and stem rot. This solution is based on ResNet50 CNN and uses a dataset automatically labeled by a proposed algorithm based on two segmentation algorithms such as image color space segmentation and image thresholding. The solution has achieved an accuracy and a F1_score of 97.82% and 97.79%, respectively, on test data. It is then deployed in a mobile application with a diagnostic solution we previously proposed. This mobile application will help mango growers, particularly those in Sahelian countries like Senegal, to manage their mango diseases earlier.

Why it matches plant phenotyping methodsマンゴー果実の病斑面積に基づく病害重症度を、画像セグメンテーションと深層学習で推定する方法が中心であり、植物状態の定量的フェノタイピングに該当する。

abstractIn this paper, we present a solution for estimating the severity of four mango fruit diseases

FruitPhenoBox - a device for rapid and automated fruit phenotyping of small sample sizes. →

Background Fruit appearance of apple (Malus domestica Borkh.) is accession-specific and one of the main criteria for consumer choice. Consequently, fruit appearance is an important selection criterion in the breeding of new cultivars. It is also used for the description of older varieties or landraces. In commercial apple production, sorting devices are used to classify large numbers of fruit from a few cultivars. In contrast, the description of fruit from germplasm collections or breeding programs is based on only a few fruit from many accessions and is mostly performed visually by pomology experts. Such visual ratings are laborious, often difficult to compare and remain subjective. Results Here we report on a morphometric device, the FruitPhenoBox, for automated fruit weighing and appearance description using computer-based analysis of five images per fruit. Recording of approximately 100 fruit from each of 15 apple cultivars using the FruitPhenoBox was rapid, with an average handling and recording time of less than eleven seconds per fruit. Comparison of fruit images from the 15 apple cultivars identified significant differences in shape index, fruit width, height and weight. Fruit shape was characteristic for each cultivar, while fruit color showed larger variation within sample sets. Assessing a subset of 20 randomly selected fruit per cultivar, fruit height, width and weight were described with a relative margin of error of 2.6%, 2.2%, and 6.2%, respectively, calculated from the mean value of all available fruit. Conclusions The FruitPhenoBox allows for the rapid and consistent description of fruit appearance from individual apple accessions. By relating the relative margin of error for fruit width, height and weight description with different sample sizes, it was possible to determine an appropriate fruit sample size to efficiently and accurately describe the recorded traits. Therefore, the FruitPhenoBox is a useful tool for breeding and the description of apple germplasm collections.

Why it matches plant phenotyping methodsリンゴ果実の画像取得・コンピュータ解析・重量測定を統合した装置を開発し、測定速度、再現性、誤差、適切なサンプルサイズを評価しており、果実形態形質の取得法が研究の中心である。

abstractHere we report on a morphometric device, the FruitPhenoBox, for automated fruit weighing and appearance description using computer-based analysis of five images per fruit.

Image analysis and polyphenol profiling unveil red-flesh apple phenotype complexity. →

Background The genetic basis of colour development in red-flesh apples (Malus domestica Borkh) has been widely characterised; however, current models do not explain the observed variations in red pigmentation intensity and distribution. Available methods to evaluate the red-flesh trait rely on the estimation of an average overall colour using a discrete class notation index. However, colour variations among red-flesh cultivars are continuous while development of red colour is non-homogeneous and genotype-dependent. A robust estimation of red-flesh colour intensity and distribution is essential to fully capture the diversity among genotypes and provide a basis to enable identification of loci influencing the red-flesh trait. Results In this study, we developed a multivariable approach to evaluate the red-flesh trait in apple. This method was implemented to study the phenotypic diversity in a segregating hybrid F1 family (91 genotypes). We developed a Python pipeline based on image and colour analysis to quantitatively dissect the red-flesh pigmentation from RGB (Red Green Blue) images and compared the efficiency of RGB and CIEL*a*b* colour spaces in discriminating genotypes previously classified with a visual notation. Chemical destructive methods, including targeted-metabolite analysis using ultra-high performance liquid chromatography with ultraviolet detection (UPLC-UV), were performed to quantify major phenolic compounds in fruits' flesh, as well as pH and water contents. Multivariate analyses were performed to study covariations of biochemical factors in relation to colour expression in CIEL*a*b* colour space. Our results indicate that anthocyanin, flavonol and flavanol concentrations, as well as pH, are closely related to flesh pigmentation in apple. Conclustion Extraction of colour descriptors combined to chemical analyses helped in discriminating genotypes in relation to their flesh colour. These results suggest that the red-flesh trait in apple is a complex trait associated with several biochemical factors.

Why it matches plant phenotyping methodsリンゴ果肉の赤色形質をRGB画像と色解析で定量する手法を開発し、遺伝子型間の識別に実質的に適用しているため、植物フェノタイピング手法が中心である。

abstractWe developed a Python pipeline based on image and colour analysis to quantitatively dissect the red-flesh pigmentation from RGB (Red Green Blue) images

PlantSR: Super-Resolution Improves Object Detection in Plant Images →

Recent advancements in computer vision, especially deep learning models, have shown considerable promise in tasks related to plant image object detection. However, the efficiency of these deep learning models heavily relies on input image quality, with low-resolution images significantly hindering model performance. Therefore, reconstructing high-quality images through specific techniques will help extract features from plant images, thus improve model performance. In this study, we explored the value of super-resolution technology for improving object detection model performance on plant images. Firstly, we built a comprehensive dataset comprising 1030 high-resolution plant images, named the PlantSR dataset. Subsequently, we developed a super-resolution model using the PlantSR dataset and benchmarked it against several state-or-the-art models designed for general image super-resolution tasks. Our proposed model demonstrated superior performance on the PlantSR dataset, indicating its efficacy in enhancing the super-resolution of plant images. Furthermore, we explored the effect of super-resolution on two specific object detection tasks: apple counting and soybean seed counting. By incorporating super-resolution as a pre-processing step, we observed a significant reduction in mean absolute error. Specifically, on the YOLOv7 model employed for apple counting, the mean absolute error decreased from 13.085 to 5.71. Similarly, on the P2PNet-Soy model utilized for soybean seed counting, the mean absolute error decreased from 19.159 to 15.085. These findings underscore the substantial potential of super-resolution technology in improving the performance of object detection models for accurately detecting and counting specific plants from images. The source codes and associated datasets are available at https://github.com/SkyCol/PlantSR.

Why it matches plant phenotyping methods植物画像の超解像モデルとデータセットを開発・ベンチマークし、リンゴおよびダイズ種子のカウント性能を改善する手法を検証しており、植物器官数の画像ベース推定が中心である。

abstractwe built a comprehensive dataset comprising 1030 high-resolution plant images, named the PlantSR dataset.

High-throughput plant phenotyping analysis of Melon (Cucumis melo L.) germplasm resources using deep learning methods and computer vision →

Abstract Cucumis melo L., commonly known as melon, is a crucial horticultural crop. The selection and breeding of superior melon germplasm resources play a pivotal role in enhancing its marketability. However, current methods for melon appearance phenotypic analysis rely primarily on expert judgment and intricate manual measurements, which are not only inefficient but also costly. Therefore, to expedite the breeding process of melon, we analyzed the images of 117 melon varieties from two annual years utilizing artificial intelligence (AI) technology. By integrating the semantic segmentation model Dual Attention Network (DANet), the object detection model RTMDet, the keypoint detection model RTMPose, and the Mobile-Friendly Segment Anything Model (MobileSAM), a deep learning algorithm framework was constructed, capable of efficiently and accurately segmenting melon fruit and pedicel. On this basis, a series of feature extraction algorithms were designed, successfully obtaining 11 phenotypic traits of melon. Linear fitting verification results of selected traits demonstrated a high correlation between the algorithm-predicted values and manually measured true values, thereby validating the feasibility and accuracy of the algorithm. Moreover, cluster analysis using all traits revealed a high consistency between the classification results and genotypes. Finally, a user-friendly software was developed to achieve rapid and automatic acquisition of melon phenotypes, providing an efficient and robust tool for melon breeding, as well as facilitating in-depth research into the correlation between melon genotypes and phenotypes.

Why it matches plant phenotyping methodsメロン果実・果梗を画像から分割し、特徴抽出によって11形質を推定する深層学習フレームワークを開発・検証し、ソフトウェア化しているため、植物フェノタイピング手法が中心である。

abstractBy integrating the semantic segmentation model Dual Attention Network (DANet), the object detection model RTMDet, the keypoint detection model RTMPose, and the Mobile-Friendly Segment Anything Model (MobileSAM), a deep learning algorithm framework was constructed, capable of efficiently and accurately segmenting melon fruit and pedicel.

EscaYard: Precision viticulture multimodal dataset of vineyards affected by Esca disease consisting of geotagged smartphone images, phytosanitary status, UAV 3D point clouds and Orthomosaics. →

The "EscaYard" dataset comprises multimodal data collected from vineyards to support agricultural research, specifically focusing on vine health and productivity. Data collection involved two primary methods: (1) unmanned aerial vehicle (UAV) for capturing multispectral images and 3D point clouds, and (2) smartphones for detailed ground-level photography. The UAV used was DJI Matrice 210 V2 RTK, equipped with a Micasense Altum sensor, flying at 30 m above ground level to ensure detailed coverage. Ground-level data were collected using smartphones (iPhone X and Xiaomi Poco X3 Pro), which provided high-resolution images of individual plants. These images were geotagged, enabling location mapping, and included data on the phytosanitary status and number of grape clusters per plant. Additionally, the dataset contains RTK GNSS data, offering high-precision location information for each vine, enhancing the dataset's value for spatial analysis. Moreover, the dataset is structured to support various research applications, including agronomy, remote sensing, and machine learning. It is particularly suited for studying disease detection, yield estimation, and vineyard management strategies. The high-resolution and multispectral nature of the data allows for a detailed analysis of vineyard conditions. Potential reuse of the dataset spans multiple disciplines, enabling studies on environmental monitoring, geographic information systems (GIS), and precision agriculture. Its comprehensive nature makes it a valuable resource for developing and testing algorithms for disease classification, yield prediction, and plant phenotyping. For instance, the images of bunches and grape leaves can be used to train object detection algorithms for accurate disease detection and consequent precise spraying. Moreover, yield prediction algorithms can be trained by extracting the phenotypic traits of the grape bunches. The "EscaYard" dataset provides a foundation for advancing research in sustainable farming practices, optimising crop health, and improving productivity through precise agricultural technologies.

Why it matches plant phenotyping methodsブドウの病徴・生産性・房形質を対象とするマルチモーダル画像／UAVデータセットであり、植物フェノタイピングや病害・収量推定アルゴリズムの開発と評価を主目的としているため。

abstractThe "EscaYard" dataset provides a foundation for advancing research in sustainable farming practices, optimising crop health, and improving productivity through precise agricultural technologies.

The genetic basis of apple shape and size unraveled by digital phenotyping →

Great diversity of shape, size, and skin color is observed among the fruits of different apple genotypes. These traits are critical for consumers and therefore interesting targets for breeding new apple varieties. However, they are difficult to phenotype and their genetic basis, especially for fruit shape and ground color, is largely unknown. We used the FruitPhenoBox to digitally phenotype 525 genotypes of the apple reference population (apple REFPOP) genotyped for 303,148 single nucleotide polymorphism (SNP) markers. From the apple images, 573 highly heritable features describing fruit shape and size as well as 17 highly heritable features for fruit skin color were extracted to explore genotype-phenotype relationships. Out of these features, seven principal components (PCs) and 16 features with the Pearson's correlation r < 0.75 (selected features) were chosen to carry out genome-wide association studies (GWAS) for fruit shape and size. Four PCs and eight selected features were used in GWAS for fruit skin color. In total, 69 SNPs scattered over all 17 apple chromosomes were significantly associated with round, conical, cylindrical, or symmetric fruit shapes and fruit size. Novel associations with major effect on round or conical fruit shapes and fruit size were identified on chromosomes 1 and 2. Additionally, 16 SNPs associated with PCs and selected features related to red overcolor as well as green and yellow ground color were found on eight chromosomes. The identified associations can be used to advance marker-assisted selection in apple fruit breeding to systematically select for desired fruit appearance.

Why it matches plant phenotyping methodsFruitPhenoBoxを用いた画像ベースのデジタル表現型解析が、525遺伝子型から果実形状・サイズ・色の特徴を抽出する中心的方法として明示されている。

abstractWe used the FruitPhenoBox to digitally phenotype 525 genotypes of the apple reference population (apple REFPOP)

Toward Real Scenery: A Lightweight Tomato Growth Inspection Algorithm for Leaf Disease Detection and Fruit Counting. →

The deployment of intelligent surveillance systems to monitor tomato plant growth poses substantial challenges due to the dynamic nature of disease patterns and the complexity of environmental conditions such as background and lighting. In this study, an integrated cascade framework that synergizes detectors and trackers was introduced for the simultaneous identification of tomato leaf diseases and fruit counting. We applied an autonomous robot with smartphone camera to collect images for leaf disease and fruits in greenhouses. Further, we improved the deep learning network YOLO-TGI by incorporating Ghost and CBAM modules, which was trained and tested in conjunction with premier lightweight detection models like YOLOX and NanoDet in evaluating leaf health conditions. For the cascading with various base detectors, we integrated state-of-the-art trackers such as Byte-Track, Motpy, and FairMot to enable fruit counting in video streams. Experimental results indicated that the combination of YOLO-TGI and Byte-Track achieved the most robust performance. Particularly, YOLO-TGI-N emerged as the model with the least computational demands, registering the lowest FLOPs at 2.05 G and checkpoint weights at 3.7 M, while still maintaining a mAP of 0.72 for leaf disease detection. Regarding the fruit counting, the combination of YOLO-TGI-S and Byte-Track achieved the best R 2 of 0.93 and the lowest RMSE of 9.17, boasting an inference speed that doubles that of the YOLOX series, and is 2.5 times faster than the NanoDet series. The developed network framework is a potential solution for researchers facilitating the deployment of similar surveillance models for a broad spectrum of fruit and vegetable crops.

Why it matches plant phenotyping methodsトマト葉の病害状態と果実数という植物形質を、ロボット撮影画像から検出・計数する深層学習および追跡フレームワークを開発・評価しており、表現型取得手法が中心である。

abstractan integrated cascade framework that synergizes detectors and trackers was introduced for the simultaneous identification of tomato leaf diseases and fruit counting.

Detection of Apple Plant Diseases Using Leaf Images Through Convolutional Neural Network →

Plant diseases cause significant crop losses globally, posing challenges to agricultural productivity.Detecting these diseases is difficult due to the lack of expert knowledge.Deep learning-based models offer promising solutions using leaf images, but issues like the need for larger training sets and computational complexity persist.To address this, we propose a convolutional neural network (CNN) with fewer layers, reducing computational burden.Augmentation techniques such as shift, shear, scaling, zoom, and flipping are applied to expand the training set without capturing more images.As agriculture remains crucial for nourishing about half of the global population, increasing production by 50-60% is urgent, especially in regions with rapid population growth.Despite an expanding cultivation area, apple crop production in India faces challenges, with minimal growth in yield.In Himachal Pradesh, a major apple-producing state, fungal diseases significantly impact fruit quality.Our project addresses these challenges by employing deep learning models, including pre-trained ones, and utilizing YOLO series models for efficient disease detection in apples.By leveraging image processing and AI, timely and accurate disease diagnosis is ensured.This project has the potential to revolutionize disease detection in apple plants, enhancing food security globally.Farmers stand to benefit from prompt intervention, safeguarding their crops and ensuring increased yields, thereby contributing to overall food security for the growing global population.

Why it matches plant phenotyping methodsリンゴ葉画像から植物病害を検出するCNNを開発しており、病徴・病害状態の画像ベース推定が研究の中心である。

abstractwe propose a convolutional neural network (CNN) with fewer layers, reducing computational burden.

Geographic-Scale Coffee Cherry Counting with Smartphones and Deep Learning. →

Deep learning and computer vision, using remote sensing and drones, are 2 promising nondestructive methods for plant monitoring and phenotyping. However, their applications are infeasible for many crop systems under tree canopies, such as coffee crops, making it challenging to perform plant monitoring and phenotyping at a large spatial scale at a low cost. This study aims to develop a geographic-scale monitoring method for coffee cherry counting, supported by an artificial intelligence (AI)-powered citizen science approach. The approach uses basic smartphones to take a few pictures of coffee trees; 2,968 trees were investigated with 8,904 pictures in Junín and Piura (Peru), Cauca, and Quindío (Colombia) in 2022, with the help of nearly 1,000 smallholder coffee farmers. Then, we trained and validated YOLO (You Only Look Once) v8 for detecting cherries in the dataset in Peru. An average number of cherries per picture was multiplied by the number of branches to estimate the total number of cherries per tree. The model's performance in Peru showed an R 2 of 0.59. When the model was tested in Colombia, where different varieties are grown in different biogeoclimatic conditions, the model showed an R 2 of 0.71. The overall performance in both countries reached an R 2 of 0.72. The results suggest that the method can be applied to much broader scales and is transferable to other varieties, countries, and regions. To our knowledge, this is the first AI-powered method for counting coffee cherries and has the potential for a geographic-scale, multiyear, photo-based phenotypic monitoring for coffee crops in low-income countries worldwide.

Why it matches plant phenotyping methodsスマートフォン画像と深層学習でコーヒー果実数を推定する方法を開発・検証しており、植物形質の取得が研究の中心です。

abstractThis study aims to develop a geographic-scale monitoring method for coffee cherry counting, supported by an artificial intelligence (AI)-powered citizen science approach.

EyeHex toolbox for complete segmentation of ommatidia in fruit fly eyes →

Variation in Drosophila compound eye size is studied across research fields, from evolutionary biology to biomedical studies, requiring the collection of large datasets to ensure robust statistical analyses. To address this, we present EyeHex, a tool for automatic segmentation of fruit fly compound eyes from brightfield and scanning electron microscopy (SEM) images. EyeHex features two integrated modules: the first utilizes machine learning to generate probability maps of the eye and ommatidia locations, while the second, a hard-coded module, leverages the hexagonal organization of the compound eye to map individual ommatidia. This iterative segmentation process, which adds one ommatidium at a time based on registered neighbors, ensures robustness to local perturbations. EyeHex also includes an analysis tool that calculates key metrics of the eye, such as ommatidia count and diameter distribution across the eye. With minimal user input for training and application, EyeHex achieves exceptional accuracy (>99.6% compared to manual counts on SEM images) and adapts to different fly strains, species, and image types. EyeHex offers a cost-effective, rapid, and flexible pipeline for extracting detailed statistical data on Drosophila compound eye variation, making it a valuable resource for high-throughput studies.

Why it matches plant phenotyping methods昆虫（ショウジョウバエ）の眼を対象としており植物ではないため、植物フェノタイピング文献の対象外です。

abstractautomatic segmentation of fruit fly compound eyes from brightfield and scanning electron microscopy (SEM) images

Maturity Recognition and Fruit Counting for Sweet Peppers in Greenhouses Using Deep Learning Neural Networks →

This study presents an approach to address the challenges of recognizing the maturity stage and counting sweet peppers of varying colors (green, yellow, orange, and red) within greenhouse environments. The methodology leverages the YOLOv5 model for real-time object detection, classification, and localization, coupled with the DeepSORT algorithm for efficient tracking. The system was successfully implemented to monitor sweet pepper production, and some challenges related to this environment, namely occlusions and the presence of leaves and branches, were effectively overcome. We evaluated our algorithm using real-world data collected in a sweet pepper greenhouse. A dataset comprising 1863 images was meticulously compiled to enhance the study, incorporating diverse sweet pepper varieties and maturity levels. Additionally, the study emphasized the role of confidence levels in object recognition, achieving a confidence level of 0.973. Furthermore, the DeepSORT algorithm was successfully applied for counting sweet peppers, demonstrating an accuracy level of 85.7% in two simulated environments under challenging conditions, such as varied lighting and inaccuracies in maturity level assessment.

Why it matches plant phenotyping methods深層学習による果実の成熟段階認識と計数が研究の中心であり、植物器官の状態（成熟度）を画像から抽出・評価しているため、植物フェノタイピング手法として含める。

abstractThis study presents an approach to address the challenges of recognizing the maturity stage and counting sweet peppers of varying colors

Empowering agricultural research: A comprehensive custard apple ( Annona squamosa ) disease dataset for precise detection. →

The Custard Apple, known as sugar apple or sweetsop, spans diverse regions like India, Portugal, Thailand, Cuba, and the West Indies. This dataset holds 8226 images of Custard Apple (Annona squamosa) fruit and leaf diseases, categorized into six types: Athracnose, Blank Canker, Diplodia Rot, Leaf Spot on fruit, Leaf Spot on leaf, and Mealy Bug. It's a key resource for refining machine learning algorithms focused on detecting and classifying diseases in Custard Apple plants. Utilizing methods like deep learning, feature extraction, and pattern recognition, this dataset sharpens automated disease identification precision. Its extensive range suits testing and training disease identification techniques. Public access fosters collaboration, fast-tracking plant pathology advancements and supporting Custard Apple plant sustainability. This dataset fosters collaborative efforts, aiding disease prevention techniques to boost Custard Apple yield and refine farming. It enhances disease identification, monitoring, and management in Custard Apple production, aiming to elevate agricultural practices and crop yields.

Why it matches plant phenotyping methodsカスタードアップルの果実・葉の病害画像を収録したデータセットで、植物病害状態の画像ベース表現型評価と検出・分類手法の訓練および検証が中心です。

abstractThis dataset holds 8226 images of Custard Apple (Annona squamosa) fruit and leaf diseases, categorized into six types

Orchid fruit and root movement analyzed using 2D photographs and a bioinformatics pipeline for processing sequential 3D scans. →

Premise Most studies of the movement of orchid fruits and roots during plant development have focused on morphological observations; however, further genetic analysis is required to understand the molecular mechanisms underlying this phenomenon. A precise tool is required to observe these movements and harvest tissue at the correct position and time for transcriptomics research. Methods We utilized three-dimensional (3D) micro-computed tomography (CT) scans to capture the movement of fast-growing Erycina pusilla roots, and built an integrated bioinformatics pipeline to process 3D images into 3D time-lapse videos. To record the movement of slowly developing E. pusilla and Phalaenopsis equestris fruits, two-dimensional (2D) photographs were used. Results The E. pusilla roots twisted and resupinated multiple times from early development. The first period occurred in the early developmental stage (77-84 days after germination [DAG]) and the subsequent period occurred later in development (140-154 DAG). While E. pusilla fruits twisted 45° from 56-63 days after pollination (DAP), the fruits of P. equestris only began to resupinate a week before dehiscence (133 DAP) and ended a week after dehiscence (161 DAP). Discussion Our methods revealed that each orchid root and fruit had an independent direction and degree of torsion from the initial to the final position. Our innovative approaches produced detailed spatial and temporal information on the resupination of roots and fruits during orchid development.

Why it matches plant phenotyping methods3DマイクロCT、2D画像、画像処理パイプラインを用いてランの根・果実のねじれ運動を時空間的に抽出する手法が研究の中心であり、植物形態表現型の取得に該当する。

abstractWe utilized three-dimensional (3D) micro-computed tomography (CT) scans to capture the movement of fast-growing Erycina pusilla roots, and built an integrated bioinformatics pipeline to process 3D images into 3D time-lapse videos.

AmodalAppleSize_RGB-D dataset: RGB-D images of apple trees annotated with modal and amodal segmentation masks for fruit detection, visibility and size estimation. →

The present dataset comprises a collection of RGB-D apple tree images that can be used to train and test computer vision-based fruit detection and sizing methods. This dataset encompasses two distinct sets of data obtained from a Fuji and an Elstar apple orchards. The Fuji apple orchard sub-set consists of 3925 RGB-D images containing a total of 15,335 apples annotated with both modal and amodal apple segmentation masks. Modal masks denote the visible portions of the apples, whereas amodal masks encompass both visible and occluded apple regions. Notably, this dataset is the first public resource to incorporate on-tree fruit amodal masks. This pioneering inclusion addresses a critical gap in existing datasets, enabling the development of robust automatic fruit sizing methods and accurate fruit visibility estimation, particularly in the presence of partial occlusions. Besides the fruit segmentation masks, the dataset also includes the fruit size (calliper) ground truth for each annotated apple. The second sub-set comprises 2731 RGB-D images capturing five Elstar apple trees at four distinct growth stages. This sub-set includes mean diameter information for each tree at every growth stage and serves as a valuable resource for evaluating fruit sizing methods trained with the first sub-set. The present data was employed in the research paper titled "Looking behind occlusions: a study on amodal segmentation for robust on-tree apple fruit size estimation" [1].

Why it matches plant phenotyping methodsリンゴ果実のRGB-D画像、アノテーション、サイズ正解値を含む公開データセットで、果実サイズ推定法の開発・評価を直接支援するため、植物フェノタイピング手法のデータ資源として中心的です。

abstractenabling the development of robust automatic fruit sizing methods and accurate fruit visibility estimation

Coffee and cashew nut dataset: A dataset for detection, classification, and yield estimation for machine learning applications. →

Conventional methods of crop yield estimation are costly, inefficient, and prone to error resulting in poor yield estimates. This affects the ability of farmers to appropriately plan and manage their crop production pipelines and market processes. There is therefore a need to develop automated methods of crop yield estimation. However, the development of accurate machine-learning methods for crop yield estimation depends on the availability of appropriate datasets. There is a lack of such datasets, especially in sub-Saharan Africa. We present curated image datasets of coffee and cashew nuts acquired in Uganda during two crop harvest seasons. The datasets were collected over nine months, from September 2022 to May 2023. The data was collected using a high-resolution camera mounted on an Unmanned Aerial Vehicle . The datasets contain 3000 coffee and 3086 cashew nut images, constituting 6086 images. Annotated objects of interest in the coffee dataset consist of five classes namely: unripe, ripening, ripe, spoilt, and coffee_tree. Annotated objects of interest in the cashew nut dataset consist of six classes namely: tree, flower, premature, unripe, ripe, and spoilt. The datasets may be used for various machine-learning tasks including flowering intensity estimation, fruit maturity stage analysis, disease diagnosis, crop variety identification, and yield estimation.

Why it matches plant phenotyping methodsコーヒーとカシューナッツの画像データセットを構築し、開花強度、成熟段階、収量などの植物形質・状態推定に利用する方法基盤を提供しており、表現型取得用データセットが研究の中心である。

abstractWe present curated image datasets of coffee and cashew nuts acquired in Uganda during two crop harvest seasons.

Sunflower Disease detection using Ensemble Deep Learning Models →

Plant diseases, such as fungi and parasites, disrupt or alter the plant’s essential functions. In order to prevent potential economic losses from these plant diseases, early diagnosis of these diseases is crucial. The use of Deep Learning models for the detection and classification of plant diseases has been found to dramatically increase the speed of diagnosis while at the same time minimizing the amount of error involved. Taking advantage of a variety of tools and techniques, including transfer learning and ensemble learning, we have experimented with different deep-learning models and pre-existing architectures to find out which combination would best fit the data we gathered from the Sun Flower Fruits and Leaves dataset. Moreover, our best model has the ability to classify and detect sunflower disease with an accuracy of 97.91%, which is a considerable improvement over state-of-the-art models currently used for the classification and detection of sunflower disease.

Why it matches plant phenotyping methodsヒマワリ葉・果実画像から病害状態を分類・検出する深層学習手法を比較・評価しており、植物病害表現型の取得・推定が中心である。

abstractwe have experimented with different deep-learning models and pre-existing architectures to find out which combination would best fit the data we gathered from the Sun Flower Fruits and Leaves dataset.

Free and open-source software for object detection, size, and colour determination for use in plant phenotyping →

BACKGROUND: Object detection, size determination, and colour detection of images are tools commonly used in plant science. Key examples of this include identification of ripening stages of fruit such as tomatoes and the determination of chlorophyll content as an indicator of plant health. While methods exist for determining these important phenotypes, they often require proprietary software or require coding knowledge to adapt existing code. RESULTS: We provide a set of free and open-source Python scripts that, without any adaptation, are able to perform background correction and colour correction on images using a ColourChecker chart. Further scripts identify objects, use an object of known size to calibrate for size, and extract the average colour of objects in RGB, Lab, and YUV colour spaces. We use two examples to demonstrate the use of these scripts. We show the consistency of these scripts by imaging in four different lighting conditions, and then we use two examples to show how the scripts can be used. In the first example, we estimate the lycopene content in tomatoes (Solanum lycopersicum) var. Tiny Tim using fruit images and an exponential model to predict lycopene content. We demonstrate that three different cameras (a DSLR camera and two separate mobile phones) are all able to model lycopene content. The models that predict lycopene or chlorophyll need to be adjusted depending on the camera used. In the second example, we estimate the chlorophyll content of basil (Ocimum basilicum) using leaf images and an exponential model to predict chlorophyll content. CONCLUSION: A fast, cheap, non-destructive, and inexpensive method is provided for the determination of the size and colour of plant materials using a rig consisting of a lightbox, camera, and colour checker card and using free and open-source scripts that run in Python 3.8. This method accurately predicted the lycopene content in tomato fruit and the chlorophyll content in basil leaves.

Why it matches plant phenotyping methods植物画像からサイズ・色を抽出し、果実リコピンや葉クロロフィルを推定するオープンソース手法と撮像系を開発・検証しており、表現型取得が研究の中心である。

abstractWe provide a set of free and open-source Python scripts that, without any adaptation, are able to perform background correction and colour correction on images using a ColourChecker chart.

GenoDrawing: An Autoencoder Framework for Image Prediction from SNP Markers →

Advancements in genome sequencing have facilitated whole-genome characterization of numerous plant species, providing an abundance of genotypic data for genomic analysis. Genomic selection and neural networks (NNs), particularly deep learning, have been developed to predict complex traits from dense genotypic data. Autoencoders, an NN model to extract features from images in an unsupervised manner, has proven to be useful for plant phenotyping. This study introduces an autoencoder framework, GenoDrawing, for predicting and retrieving apple images from a low-depth single-nucleotide polymorphism (SNP) array, potentially useful in predicting traits that are difficult to define. GenoDrawing demonstrates proficiency in its task using a small dataset of shape-related SNPs. Results indicate that the use of SNPs associated with visual traits has substantial impact on the generated images, consistent with biological interpretation. While using substantial SNPs is crucial, incorporating additional, unrelated SNPs results in performance degradation for simple NN architectures that cannot easily identify the most important inputs. The proposed GenoDrawing method is a practical framework for exploring genomic prediction in fruit tree phenotyping, particularly beneficial for small to medium breeding companies to predict economically substantial heritable traits. Although GenoDrawing has limitations, it sets the groundwork for future research in image prediction from genomic markers. Future studies should focus on using stronger models for image reproduction, SNP information extraction, and dataset balance in terms of phenotypes for more precise outcomes.

Why it matches plant phenotyping methodsSNPからリンゴ画像を予測・再構成するGenoDrawingフレームワークを提案しており、果樹の視覚形質を推定する計算手法が研究の中心である。

abstractThis study introduces an autoencoder framework, GenoDrawing, for predicting and retrieving apple images from a low-depth single-nucleotide polymorphism (SNP) array

An extensive real-world in field tomato image dataset involving maturity classification and recognition of fresh and defect tomatoes. →

Tomato, a fruiting plant species within the Solanaceae family, is a widely used ingredient in culinary dishes due to its sweet and acidic flavor profile, as well as its rich nutritional content. Recognized for its potential health benefits, including reducing the risk of coronary artery disease and specific types of cancer, tomatoes have become a staple in global cuisine. Traditional methods for tomato maturity assessment, harvesting, quality grading, and packaging are often labor-intensive and economically inefficient. This paper introduces an extensive dataset of high-resolution tomato images collected over an eight-month period from the demonstration fields of Sher-E-Bangla Agricultural University in Dhaka, Bangladesh, in collaboration with plant breeding experts of the same university. The dataset was meticulously curated to ensure precision and consistency, encompassing various stages of tomato maturity, including images of both fresh and defective tomatoes. This dataset is a valuable resource for researchers, stakeholders, and individuals interested in tomato production in Bangladesh, providing a robust foundation for leveraging computer vision and deep learning techniques in the agriculture sector. The dataset's potential applications extend to automating tasks such as robotic harvesting, quality assessment, and packaging systems, ultimately enhancing the efficiency of tomato production processes.

Why it matches plant phenotyping methodsトマト果実の成熟段階と欠陥を対象とする大規模画像データセットを構築しており、植物状態の画像ベース評価が研究の中心です。

abstractThis paper introduces an extensive dataset of high-resolution tomato images

ShinyFruit: interactive fruit phenotyping software and its application in blackberry →

Introduction: Horticultural plant breeding programs often demand large volumes of phenotypic data to capture visual variation in quality of harvested products. Increasing the throughput potential of phenomic pipelines enables breeders to consider data-hungry molecular breeding strategies such as genome-wide association studies and genomic selection. Methods: We present an R-based web application called ShinyFruit for image-based phenotyping of size, shape, and color-related qualities in fruits and vegetables. Here, we have demonstrated one potential application for ShinyFruit by comparing its estimates of fruit length, width, and red drupelet reversion (RDR) with ImageJ and analogous manual phenotyping techniques in a population of blackberry cultivars and breeding selections from the University of Arkansas System Division of Agriculture Fruit Breeding Program. Results: = 0.62 - 0.70). Neither phenotyping method detected genotypic differences in blackberry fruit width, suggesting that this trait is unlikely to be heritable in the population observed. Discussion: It is likely that implementing a treatment to promote RDR expression in future studies might strengthen the documented correlation between phenotyping methods by maximizing genotypic variance. Even so, our analysis has suggested that ShinyFruit provides a viable, open-source solution to efficient phenotyping of size and color in blackberry fruit. The ability for users to adjust analysis settings should also extend its utility to a wide range of fruits and vegetables.

Why it matches plant phenotyping methodsShinyFruitは果実のサイズ・形状・色を画像から推定するソフトウェアであり、ImageJおよび手動測定との比較検証も行っているため、植物表現型取得法が中心である。

abstractWe present an R-based web application called ShinyFruit for image-based phenotyping of size, shape, and color-related qualities in fruits and vegetables.

Climatic records and within field data on yield and harvest quality over a whole vineyard estate. →

Detailed and precise knowledge of production parameters (yield, quality, health status, etc.) in agriculture is the basis for analyzing the effect of any agricultural practice. Fine mapping of production parameters makes it possible to identify the origin of observed variability, whether associated with environmental factors or with agricultural practices. In viticulture, in real commercial context, these data are rare because monitoring systems embedded on harvesting machines for grape yield and quality are not yet available. As a result, they are costly and/or cumbersome to acquire manually. As an alternative, a research project has been proposed to test low-cost methods using GNSS tracking devices for yield and harvest quality mapping in viticulture. The data set was acquired as part of this research. The methodology was applied on a commercial vineyard of 30 ha during the whole 2022 harvest season. The method has identified harvest sectors (HS) associated to measured production parameters (grape mass and harvest quality parameters: sugar content, total acidity, pH, yeast assimilable nitrogen, organic nitrogen) and calculated production parameters (potential alcohol of grapes, yield, yield per plant, percentage of unproductive plants) over the entire vineyard. The grape mass was measured at the vineyard cellar or at the wine-growing cooperative by calibrated scales. The harvest quality parameters were measured from samples on grape must at a commercial laboratory specialized in oenological analysis (Institut Coopératif du Vin, Montpellier, France) with standardized protocols. The percentage of unproductive plants of a harvest sector was calculated from the manually geolocation of each unproductive plants (dead plants + missing plants) over the entire vineyard, the plantation density of blocks, and the geolocalization of the harvest sector. The mean area of these harvest sectors is 0.3 ha. The data set is supplemented by climatic data from a weather station deployed in the center of the vineyard. It provided three climatic parameters (relative humidity, rainfall, air temperature) every 15 min, for the 2020, 2021 and 2022 years. It was also supplemented by a complete description of the vineyard blocks (grape variety, plantation year, area, inter-row distance and vine distance). The proposed data set constitutes a unique and interesting resource for research in agronomy, vine ecophysiology and remote sensing. It can be used for any research in vine ecophysiology aimed at identifying potential relationships between yield and harvest quality parameters for different grape varieties. The data set only covers one year, which is a limitation for studying inter-annual variability of the parameters measured. Another limitation of the method concerns the footprint (0.3 ha on average) of the parameters measured.

Why it matches plant phenotyping methodsGNSSを用いた低コストのブドウ収量・収穫品質マッピング手法と、その大規模データセットが研究の中心であり、収量や不生産株割合などの植物・圃場形質を抽出している。

abstracta research project has been proposed to test low-cost methods using GNSS tracking devices for yield and harvest quality mapping in viticulture.

Quasi Real-Time Apple Defect Segmentation Using Deep Learning. →

Defect segmentation of apples is an important task in the agriculture industry for quality control and food safety. In this paper, we propose a deep learning approach for the automated segmentation of apple defects using convolutional neural networks (CNNs) based on a U-shaped architecture with skip-connections only within the noise reduction block. An ad-hoc data synthesis technique has been designed to increase the number of samples and at the same time to reduce neural network overfitting. We evaluate our model on a dataset of multi-spectral apple images with pixel-wise annotations for several types of defects. In this paper, we show that our proposal outperforms in terms of segmentation accuracy general-purpose deep learning architectures commonly used for segmentation tasks. From the application point of view, we improve the previous methods for apple defect segmentation. A measure of the computational cost shows that our proposal can be employed in real-time (about 100 frame-per-second on GPU) and in quasi-real-time (about 7/8 frame-per-second on CPU) visual-based apple inspection. To further improve the applicability of the method, we investigate the potential of using only RGB images instead of multi-spectral images as input images. The results prove that the accuracy in this case is almost comparable with the multi-spectral case.

Why it matches plant phenotyping methodsリンゴ果実の欠陥を画像から画素単位で抽出する深層学習手法を開発・評価しており、植物器官の状態（欠陥）取得が中心的な方法論的貢献である。

abstractwe propose a deep learning approach for the automated segmentation of apple defects using convolutional neural networks (CNNs)

Simultaneous fruit detection and size estimation using multitask deep neural networks →

The measurement of fruit size is of great interest to estimate the yield and predict the harvest resources in advance. This work proposes a novel technique for in-field apple detection and measurement based on Deep Neural Networks. The proposed framework was trained with RGB-D data and consists of an end-to-end multitask Deep Neural Network architecture specifically designed to perform the following tasks: 1) detection and segmentation of each fruit from its surroundings; 2) estimation of the diameter of each detected fruit. The methodology was tested with a total of 15,335 annotated apples at different growth stages, with diameters varying from 27 mm to 95 mm. Fruit detection results reported an F1-score for apple detection of 0.88 and a mean absolute error of diameter estimation of 5.64 mm. These are state-of-the-art results with the additional advantages of: a) using an end-to-end multitask trainable network; b) an efficient and fast inference speed; and c) being based on RGB-D data which can be acquired with affordable depth cameras. On the contrary, the main disadvantage is the need of annotating a large amount of data with fruit masks and diameter ground truth to train the model. Finally, a fruit visibility analysis showed an improvement in the prediction when limiting the measurement to apples above 65% of visibility (mean absolute error of 5.09 mm). This suggests that future works should develop a method for automatically identifying the most visible apples and discard the prediction of highly occluded fruits.

Why it matches plant phenotyping methodsRGB-D画像と深層学習を用いて果実の検出・セグメンテーションおよび直径推定法を開発し、アノテーションデータで性能評価しているため、果実形質の取得手法が中心である。

abstractThis work proposes a novel technique for in-field apple detection and measurement based on Deep Neural Networks.

The genetic basis of apple shape and size unraveled by digital phenotyping →

Abstract Great diversity of shape, size, and skin color is observed among the fruits of different apple genotypes. These traits are critical for consumers and therefore interesting targets for breeding new apple varieties. However, they are difficult to phenotype and their genetic basis, especially for fruit shape and ground color, is largely unknown. We used the fruit FruitPhenoBox to digitally phenotype 506 genotypes of the apple reference population (apple REFPOP) genotyped for 303,148 single nucleotide polymorphism (SNP) markers. From the apple images, 573 highly heritable features describing fruit shape and size as well as 17 highly heritable features for fruit skin color were extracted to explore genotype-phenotype relationships. Out of these features, nine and four principal components (PCs) as well as 16 and eight uncorrelated features were chosen to carry out genome-wide association studies for fruit shape, size, and fruit skin color, respectively. In total, 69 SNPs scattered over all 17 apple chromosomes were significantly associated with round, conical, cylindrical, or symmetric fruit shapes and fruit size. Novel associations with major effect on round or conical fruit shapes and fruit size were identified on chromosomes 1 and 2. Additionally, 16 SNPs associated with PCs and uncorrelated features related to red over color as well as green and yellow ground color were found on eight chromosomes. The identified associations can be used to advance marker-assisted selection in apple fruit breeding to systematically select for desired fruit appearance.

Why it matches plant phenotyping methodsFruitPhenoBoxを用いた画像ベースのデジタル表現型計測が研究の中心で、リンゴ果実の形状・サイズ・色の特徴抽出を大規模に実施しているため、表現型手法の実質的応用に該当する。

abstractWe used the fruit FruitPhenoBox to digitally phenotype 506 genotypes of the apple reference population (apple REFPOP)

An efficient convolutional neural network-based diagnosis system for citrus fruit diseases. →

Introduction: Fruit diseases have a serious impact on fruit production, causing a significant drop in economic returns from agricultural products. Due to its excellent performance, deep learning is widely used for disease identification and severity diagnosis of crops. This paper focuses on leveraging the high-latitude feature extraction capability of deep convolutional neural networks to improve classification performance. Methods: The proposed neural network is formed by combining the Inception module with the current state-of-the-art EfficientNetV2 for better multi-scale feature extraction and disease identification of citrus fruits. The VGG is used to replace the U-Net backbone to enhance the segmentation performance of the network. Results: Compared to existing networks, the proposed method achieved recognition accuracy of over 95%. In addition, the accuracies of the segmentation models were compared. VGG-U-Net, a network generated by replacing the backbone of U-Net with VGG, is found to have the best segmentation performance with an accuracy of 87.66%. This method is most suitable for diagnosing the severity level of citrus fruit diseases. In the meantime, transfer learning is applied to improve the training cycle of the network model, both in the detection and severity diagnosis phases of the disease. Discussion: The results of the comparison experiments reveal that the proposed method is effective in identifying and diagnosing the severity of citrus fruit diseases identification.

Why it matches plant phenotyping methods柑橘果実の病害識別と重症度診断を対象に、CNN、セグメンテーション、転移学習を組み合わせた画像解析手法を開発・比較しており、感染植物の状態を推定する方法が中心である。

abstractThe proposed neural network is formed by combining the Inception module with the current state-of-the-art EfficientNetV2 for better multi-scale feature extraction and disease identification of citrus fruits.

CAM-YOLO: tomato detection and classification based on improved YOLOv5 using combining attention mechanism. →

Background One of the key elements in maintaining the consistent marketing of tomato fruit is tomato quality. Since ripeness is the most important factor for tomato quality in the viewpoint of consumers, determining the stages of tomato ripeness is a fundamental industrial concern with regard to tomato production to obtain a high quality product. Since tomatoes are one of the most important crops in the world, automatic ripeness evaluation of tomatoes is a significant study topic as it may prove beneficial in ensuring an optimal production of high-quality product, increasing profitability. This article explores and categorises the various maturity/ripeness phases to propose an automated multi-class classification approach for tomato ripeness testing and evaluation. Methods Object detection is the critical component in a wide variety of computer vision problems and applications such as manufacturing, agriculture, medicine, and autonomous driving. Due to the tomato fruits' complex identification background, texture disruption, and partial occlusion, the classic deep learning object detection approach (YOLO) has a poor rate of success in detecting tomato fruits. To figure out these issues, this article proposes an improved YOLOv5 tomato detection algorithm. The proposed algorithm CAM-YOLO uses YOLOv5 for feature extraction, target identification and Convolutional Block Attention Module (CBAM). The CBAM is added to the CAM-YOLO to focus the model on improving accuracy. Finally, non-maximum suppression and distance intersection over union (DIoU) are applied to enhance the identification of overlapping objects in the image. Results Several images from the dataset were chosen for testing to assess the model's performance, and the detection performance of the CAM-YOLO and standard YOLOv5 models under various conditions was compared. The experimental results affirms that CAM-YOLO algorithm is efficient in detecting the overlapped and small tomatoes with an average precision of 88.1%.

Why it matches plant phenotyping methodsトマト果実の成熟度という植物器官の状態を画像から自動推定する改良YOLO手法を開発し、標準手法と性能比較しているため、植物フェノタイピング手法が中心である。

abstractThis article explores and categorises the various maturity/ripeness phases to propose an automated multi-class classification approach for tomato ripeness testing and evaluation.

A Novel Approach to Pod Count Estimation Using a Depth Camera in Support of Soybean Breeding Applications. →

Improving soybean ( Glycine max L. (Merr.)) yield is crucial for strengthening national food security. Predicting soybean yield is essential to maximize the potential of crop varieties. Non-destructive methods are needed to estimate yield before crop maturity. Various approaches, including the pod-count method, have been used to predict soybean yield, but they often face issues with the crop background color. To address this challenge, we explored the application of a depth camera to real-time filtering of RGB images, aiming to enhance the performance of the pod-counting classification model. Additionally, this study aimed to compare object detection models (YOLOV7 and YOLOv7-E6E) and select the most suitable deep learning (DL) model for counting soybean pods. After identifying the best architecture, we conducted a comparative analysis of the model's performance by training the DL model with and without background removal from images. Results demonstrated that removing the background using a depth camera improved YOLOv7's pod detection performance by 10.2% precision, 16.4% recall, 13.8% mAP@50, and 17.7% mAP@0.5:0.95 score compared to when the background was present. Using a depth camera and the YOLOv7 algorithm for pod detection and counting yielded a mAP@0.5 of 93.4% and mAP@0.5:0.95 of 83.9%. These results indicated a significant improvement in the DL model's performance when the background was segmented, and a reasonably larger dataset was used to train YOLOv7.

Why it matches plant phenotyping methods深度カメラと物体検出モデルを用いてダイズ莢数という植物形質を非破壊推定する手法を開発・比較・評価しており、表現型取得が中心的である。

abstractwe explored the application of a depth camera to real-time filtering of RGB images, aiming to enhance the performance of the pod-counting classification model.

Low-Cost Sensor for Lycopene Content Measurement in Tomato Based on Raspberry Pi 4. →

Measuring lycopene in tomatoes is fundamental to the agrifood industry because of its health benefits. It is one of the leading quality criteria for consuming this fruit. Traditionally, the amount determination of this carotenoid is performed using the high-performance liquid chromatography (HPLC) technique. This is a very reliable and accurate method, but it has several disadvantages, such as long analysis time, high cost, and destruction of the sample. In this sense, this work proposes a low-cost sensor that correlates the lycopene content in tomato with the color present in its epicarp. A Raspberry Pi 4 programmed with Python language was used to develop the lycopene prediction model. Various regression models were evaluated using neural networks, fuzzy logic, and linear regression. The best model was the fuzzy nonlinear regression as the RGB input, with a correlation of R 2 = 0.99 and a mean error of 1.9 × 10 -5 . This work was able to demonstrate that it is possible to determine the lycopene content using a digital camera and a low-cost integrated system in a non-invasive way.

Why it matches plant phenotyping methodsトマト果皮画像の色からリコペン含量を非破壊推定する低コストセンサーと予測モデルの開発が中心であり、植物器官の形質測定法に該当する。

abstractthis work proposes a low-cost sensor that correlates the lycopene content in tomato with the color present in its epicarp.

A Self-Supervised Anomaly Detector of Fruits Based on Hyperspectral Imaging. →

Hyperspectral imaging combined with chemometric approaches is proven to be a powerful tool for the quality evaluation and control of fruits. In fruit defect-detection scenarios, developing an unsupervised anomaly detection framework is vital, as defect sample preparation is labor-intensive and time-consuming, especially for exploring potential defects. In this paper, a spectral-spatial, information-based, self-supervised anomaly detection (SSAD) approach is proposed. During training, an auxiliary classifier is proposed to identify the projection axes of principal component (PC) images that were transformed from the hyperspectral data cubes. In test time, the fully connected layer of the learned classifier was used as a 'spectral-spatial' feature extractor, and the feature similarity metric was adopted as the score function for the downstream anomaly evaluation task. The proposed network was evaluated with two fruit data sets: a strawberry data set with bruised, infected, chilling-injured, and contaminated test samples and a blueberry data set with bruised, infected, chilling-injured, and wrinkled samples as anomalies. The results show that the SSAD yielded the best anomaly detection performance (AUC = 0.923 on average) over the baseline methods, and the visualization results further confirmed its advantage in extracting effective 'spectral-spatial' latent representation. Moreover, the robustness of SSAD is verified with the data pollution experiment; it performed significantly better than the baselines when a portion of anomalous samples was involved in the training process.

Why it matches plant phenotyping methods果実の病害・損傷・低温障害などの状態をハイパースペクトル画像から検出する手法を開発・評価しており、植物器官の状態推定が研究の中心です。

abstractIn this paper, a spectral-spatial, information-based, self-supervised anomaly detection (SSAD) approach is proposed.

TomatoDIFF: On-plant Tomato Segmentation with Denoising Diffusion Models →

Artificial intelligence applications enable farmers to optimize crop growth and production while reducing costs and environmental impact. Computer vision-based algorithms in particular, are commonly used for fruit segmentation, enabling in-depth analysis of the harvest quality and accurate yield estimation. In this paper, we propose TomatoDIFF, a novel diffusion-based model for semantic segmentation of on-plant tomatoes. When evaluated against other competitive methods, our model demonstrates state-of-the-art (SOTA) performance, even in challenging environments with highly occluded fruits. Additionally, we introduce Tomatopia, a new, large and challenging dataset of greenhouse tomatoes. The dataset comprises high-resolution RGB-D images and pixel-level annotations of the fruits.

Why it matches plant phenotyping methods植物上のトマト果実を画像からセグメンテーションする手法を開発・比較し、RGB-D画像と画素アノテーションのデータセットも提供しており、植物器官の状態・位置推定に関わる方法が中心である。

abstractwe propose TomatoDIFF, a novel diffusion-based model for semantic segmentation of on-plant tomatoes

Fruit Detection and Counting in Apple Orchards Based on Improved Yolov7 and Multi-Object Tracking Methods. →

With the increasing popularity of online fruit sales, accurately predicting fruit yields has become crucial for optimizing logistics and storage strategies. However, existing manual vision-based systems and sensor methods have proven inadequate for solving the complex problem of fruit yield counting, as they struggle with issues such as crop overlap and variable lighting conditions. Recently CNN-based object detection models have emerged as a promising solution in the field of computer vision, but their effectiveness is limited in agricultural scenarios due to challenges such as occlusion and dissimilarity among the same fruits. To address this issue, we propose a novel variant model that combines the self-attentive mechanism of Vision Transform, a non-CNN network architecture, with Yolov7, a state-of-the-art object detection model. Our model utilizes two attention mechanisms, CBAM and CA, and is trained and tested on a dataset of apple images. In order to enable fruit counting across video frames in complex environments, we incorporate two multi-objective tracking methods based on Kalman filtering and motion trajectory prediction, namely SORT, and Cascade-SORT. Our results show that the Yolov7-CA model achieved a 91.3% mAP and 0.85 F1 score, representing a 4% improvement in mAP and 0.02 improvement in F1 score compared to using Yolov7 alone. Furthermore, three multi-object tracking methods demonstrated a significant improvement in MAE for inter-frame counting across all three test videos, with an 0.642 improvement over using yolov7 alone achieved using our multi-object tracking method. These findings suggest that our proposed model has the potential to improve fruit yield assessment methods and could have implications for decision-making in the fruit industry.

Why it matches plant phenotyping methodsリンゴ果実を画像から検出・追跡して収量（果実数）を推定する手法を開発・評価しており、植物表現型取得が研究の中心です。

titleFruit Detection and Counting in Apple Orchards Based on Improved Yolov7 and Multi-Object Tracking Methods.

An expertized grapevine disease image database including five grape varieties focused on Flavescence dorée and its confounding diseases, biotic and abiotic stresses. →

The grapevine is vulnerable to diseases, deficiencies, and pests, leading to significant yield losses. Current disease controls involve monitoring and spraying phytosanitary products at the vineyard block scale. However, automatic detection of disease symptoms could reduce the use of these products and treat diseases before they spread. Flavescence dorée (FD), a highly infectious disease that causes significant yield losses, is only diagnosed by identifying symptoms on three grapevine organs: leaf, shoot, and bunch. Its diagnosis is carried out by scouting experts, as many other diseases and stresses, either biotic or abiotic, imply similar symptoms (but not all at the same time). These experts need a decision support tool to improve their scouting efficiency. To address this, a dataset of 1483 RGB images of grapevines affected by various diseases and stresses, including FD, was acquired by proximal sensing. The images were taken in the field at a distance of 1-2 meters to capture entire grapevines and an industrial flash was ensuring a constant luminance on the images regardless of the environmental circumstances. Images of 5 grape varieties (Cabernet sauvignon, Cabernet franc, Merlot, Ugni blanc and Sauvignon blanc) were acquired during 2 years (2020 and 2021). Two types of annotations were made: expert diagnosis at the grapevine scale in the field and symptom annotations at the leaf, shoot, and bunch levels on computer. On 744 images, the leaves were annotated and divided into three classes: 'FD symptomatic leaves', 'Esca symptomatic leaves', and 'Confounding leaves'. Symptomatic bunches and shoots were, in addition of leaves, annotated on 110 images using bounding boxes and broken lines, respectively. Additionally, 128 segmentation masks were created to allow the detection of the symptomatic shoots and bunches by segmentation algorithms and compare the results to those of the detection algorithms.

Why it matches plant phenotyping methodsブドウ病害の症状を画像から抽出するための専門家アノテーション付きデータセットであり、植物体・葉・枝・果房の病徴状態を対象とするフェノタイピング手法・ベンチマークとして中心的です。

abstractTo address this, a dataset of 1483 RGB images of grapevines affected by various diseases and stresses, including FD, was acquired by proximal sensing.

CocoaMFDB: A dataset of cocoa pod maturity and families in an uncontrolled environment in Côte d'Ivoire. →

Cocoa cultivation is the basis for chocolate production; it has a unique aroma that makes it useful in the production of snacks and usable for cooking or baking. The maximum harvest period of cocoa is normally once or twice a year and spread over several months, depending on the country. Determining the best harvesting period for cocoa pods plays a major role in the export process and the pods quality. The degree of ripening of the pods affects the quality of the resulting beans. Also, unripe pods do not have enough sugar and may prevent proper bean fermentation. As for too-mature pods, they are usually dry, and their beans may germinate inside the pods, or they may develop a fungal disease and cannot be used. Computer-based determination of the ripeness of cocoa pods throughout image analysis could facilitate massive cocoa ripeness detection. Recent technological advances in computing power, communication systems, and machine learning techniques provide opportunities for agricultural engineering and computer scientists to meet the demands of the manual. The need for diverse and representative sets of pod images is essential for developing and testing automatic cocoa pod maturity detection systems. In this perspective, we collected images of cocoa pods to set up a database of cocoa pods of the Côte d'Ivoire named CocoaMFDB. We performed a pre-processing step using the CLAHE algorithm to improve the quality of the images since the effect of the light was not controlled on our data set. CocoaMFDB allows the characterization of cocoa pods according to their maturity level and provides information on the pod family for each image. Our dataset comprises three large families, namely Amelonado, Angoleta, and Guiana, grouped into two maturity categories: the ripe and unripe pods. It is, therefore, perfect for developing and evaluating image analysis algorithms for future research.

Why it matches plant phenotyping methodsカカオ果実の成熟度という植物器官形質を対象とする画像データセットを構築し、画像解析アルゴリズムの開発・評価用に提供しているため、フェノタイピング手法・データセットが中心です。

abstractwe collected images of cocoa pods to set up a database of cocoa pods of the Côte d'Ivoire named CocoaMFDB.

Leaf Disease Classification in Bell Pepper Plant using VGGNet →

In the era of artificial intelligence, deep learning, and computer vision play a vital role in leaf-based disease identification and categorization. Leaf diseases are the most dangerous calamity that has direct detrimental effects on farmers’ lives, and consequently on gross yield production and the world economy. Nutritious food for all is a great challenge faced by the farmer and agricultural research community. Bell peppers can be categorized as fruit or vegetable that is universally available and full of various nutrients like carbs, vitamins, and fat. Leaves of bell pepper plants infected by bacterial spot diseases affect their yield significantly. The aim of this study is to classify bacterial spots and healthy images of bell peppers’ leaf images taken from the PlantVillage dataset using CNN-based pre-trained architecture. Two CNN architectures, i.e., VGG16 and VGG19 are applied through transfer learning in the binary classification of leaf-based disease. A total of 2475 images are used for training, validation, and testing purposes, with 1478 healthy images and 997 images with bacterial disease spots. Although both VGG16 and VGG19 achieved good performances, VGG16 architecture performs slightly better than VGG19.

Why it matches plant phenotyping methodsベルペッパー葉の病斑という植物の病態を画像から分類するCNN手法が研究の中心であり、植物病害フェノタイピングの方法適用に該当する。

abstractThe aim of this study is to classify bacterial spots and healthy images of bell peppers’ leaf images taken from the PlantVillage dataset using CNN-based pre-trained architecture.

Looking behind occlusions: A study on amodal segmentation for robust on-tree apple fruit size estimation →

The detection and sizing of fruits with computer vision methods is of interest because it provides relevant information to improve the management of orchard farming. However, the presence of partially occluded fruits limits the performance of existing methods, making reliable fruit sizing a challenging task. While previous fruit segmentation works limit segmentation to the visible region of fruits (known as modal segmentation), in this work we propose an amodal segmentation algorithm to predict the complete shape, which includes its visible and occluded regions. To do so, an end-to-end convolutional neural network (CNN) for simultaneous modal and amodal instance segmentation was implemented. The predicted amodal masks were used to estimate the fruit diameters in pixels. Modal masks were used to identify the visible region and measure the distance between the apples and the camera using the depth image. Finally, the fruit diameters in millimetres (mm) were computed by applying the pinhole camera model. The method was developed with a Fuji apple dataset consisting of 3925 RGB-D images acquired at different growth stages with a total of 15,335 annotated apples, and was subsequently tested in a case study to measure the diameter of Elstar apples at different growth stages. Fruit detection results showed an F1-score of 0.86 and the fruit diameter results reported a mean absolute error (MAE) of 4.5 mm and R2 = 0.80 irrespective of fruit visibility. Besides the diameter estimation, modal and amodal masks were used to automatically determine the percentage of visibility of measured apples. This feature was used as a confidence value, improving the diameter estimation to MAE = 2.93 mm and R2 = 0.91 when limiting the size estimation to fruits detected with a visibility higher than 60%. The main advantages of the present methodology are its robustness for measuring partially occluded fruits and the capability to determine the visibility percentage. The main limitation is that depth images were generated by means of photogrammetry methods, which limits the efficiency of data acquisition. To overcome this limitation, future works should consider the use of commercial RGB-D sensors. The code and the dataset used to evaluate the method have been made publicly available at https://github.com/GRAP-UdL-AT/Amodal_Fruit_Sizing.

Why it matches plant phenotyping methods果実の遮蔽に頑健な画像ベースのアモーダル分割と、リンゴ果径という植物形質の推定手法を開発・検証しており、方法が研究の中心である。

abstractThe predicted amodal masks were used to estimate the fruit diameters in pixels.

ASPEN study case: real time in situ tomato detection and localization for yield estimation →

As human population continue to increase, our food production system is challenged. With tomatoes as the main indoor produced fruit, the selection of adapter varieties to each specific condition and higher yields is an imperative task if we wish to supply the growing demand of coming years. To help farmers and researchers in the task of phenotyping, we here present a study case of the A gro s cope ph en otyping tool (ASPEN) in tomato under indoor conditions. We prove that using the ASPEN pipeline it is possible to obtain real time in situ yield estimation not only in a commercial-like greenhouse level but also within growing line. To discuss our results, we analyse the two main steps of the pipeline in a desktop computer: object detection and tracking, and yield prediction. Thanks to the use of YOLOv5, we reach a mean average precision for all categories of 0.85 at interception over union 0.5 with an inference time of 8 ms, who together with the best multiple object tracking (MOT) tested allows to reach a 0.97 correlation value compared with the real harvest number of tomatoes and a 0.91 correlation when considering yield thanks to the usage of a SLAM algorithm. Moreover, the ASPEN pipeline demonstrated to predict also the sub following harvests. Confidently, our results demonstrate in situ size and quality estimation per fruit, which could be beneficial for multiple users. To increase accessibility and usage of new technologies, we make publicly available the required hardware material and software to reproduce this pipeline, which include a dataset of more than 850 relabelled images for the task of tomato object detection and the trained YOLOv5 model[1] [1]https://github.com/camilochiang/aspen

Why it matches plant phenotyping methodsASPENはトマト果実の検出・追跡から収量、果実サイズ、品質を推定する画像ベースの表現型解析パイプラインであり、手法の評価と再現可能なソフトウェア・データセット提供が中心です。

abstractwe here present a study case of the A gro s cope ph en otyping tool (ASPEN) in tomato under indoor conditions.

GrapesNet: Indian RGB & RGB-D vineyard image datasets for deep learning applications. →

In most of the countries, grapes are considered as a cash crop. Currently huge research is going on in development of automated grape harvesting systems. Speedy and reliable grape bunch detection is prime need for various deep learning based automated systems which deals with object detection and object segmentation tasks. But currently very few datasets are available on grape bunches in vineyard, because of which there is restriction to the research in this area. In comparison to the vineyard in outside countries, Indian vineyard structure is more complex, so it becomes hard to work in real-time. To overcome these problems and to make vineyard dataset for suitable for Indian vineyard scenarios, this paper proposed four different datasets on grape bunches in vineyard. For creating all datasets in GrapesNet, natural environmental conditions have been considered. GrapesNet includes total 11000+ images of grape bunches. Necessary data for weight prediction of grape cluster is also provided with dataset like height, width and real weight of cluster present in image. Proposed datasets can be used for prime tasks like grape bunch detection, grape bunch segmentation, and grape bunch weight estimation etc. of future generation automated vineyard harvesting technologies.

Why it matches plant phenotyping methodsブドウ果房画像データセットを構築し、果房の検出・セグメンテーションに加えて重量推定用の寸法と実重量を提供することが中心で、再利用可能な植物表現型データセットに該当する。

abstractthis paper proposed four different datasets on grape bunches in vineyard.

GenoDrawing: An autoencoder framework for image prediction from SNP markers →

Abstract Advancements in genome sequencing have facilitated whole genome characterization of numerous plant species, providing an abundance of genotypic data for genomic analysis. Genomic selection and neural networks, particularly deep learning, have been developed to predict complex traits from dense genotypic data. Autoencoders, a neural network model to extract features from images in an unsupervised manner, has proven to be useful for plant phenotyping. This study introduces an autoencoder framework, GenoDrawing, for predicting and retrieving apple images from a low-depth single nucleotide polymorphism (SNP) array, potentially useful in predicting traits that are difficult to define. GenoDrawing demonstrated proficiency in its task while using a small dataset of shape-related SNPs, and multiple experiments were conducted to evaluate the impact of SNP selection and shape relation. Results indicated that the correct relationship of SNPs with visual traits had a significant impact on the generated images, consistent with biological interpretation. While using significant SNPs is crucial, incorporating additional, unrelated SNPs results in performance degradation for simple NN architectures that cannot easily identify the most important inputs. The proposed GenoDrawing method is a practical framework for exploring genomic prediction in fruit tree phenotyping, particularly beneficial for small to medium breeding companies to predict economically significant heritable traits. Although GenoDrawing has limitations, it sets the groundwork for future research in image prediction from genomic markers. Future studies should focus on using stronger models for image reproduction, SNP information extraction, and improved dataset balance in terms of shape for more precise outcomes.

Why it matches plant phenotyping methodsSNPからリンゴ画像を予測・再構成するオートエンコーダ手法自体が中心であり、果実形状などの植物表現型推定に直接関係する。

abstractThis study introduces an autoencoder framework, GenoDrawing, for predicting and retrieving apple images from a low-depth single nucleotide polymorphism (SNP) array

A hierarchical dataset of vegetative and reproductive growth in apple tree organs under conventional and non-limited carbon resources. →

A monitoring of apple fruit, shoot and trunk growth was performed on 15 trees, equally split according to three treatments, which determined heavily contrasting carbon assimilate availability: unmanipulated trees (FRU), thinned trees (THI) and defruited trees (DEF). Several variables describe the vegetative growth on FRU and DEF trees (shoot length, base diameter, number of fruits on shoot, and height, diameter, pruning intensity and number of fruits of the branch carrying the shoot; trunk circumference), as well as the fruit growth on FRU and THI trees (3 fruit diameters). Additional measurements from ancillary shoots (apical diameter, number of leaves, leaf dry weight, stem dry weight, fresh mass, volume) and fruits (3 diameters, dry weight) from trees undergoing the same treatments, provide a more complete (destructive) characterization of organs growth, thanks to several measurements performed across the growing season. Organs are provided with categorical variables indicating the treatment, tree, canopy height, orientation (for both shoots and fruit), as well as branch and shoot identifiers, so that hierarchical modeling of the dataset can be performed. The dataset is completed with dates and day of the year of the measurements and the accumulated growing degree days from full bloom. Data can be used to calculate apple tree absolute and relative growth rates, maximum potential growth rates, as well as shoot growth responses to thinning and pruning. The dataset can also be used to calibrate allometric relationships, estimate structural apple tree growth parameters and their variability.

Why it matches plant phenotyping methodsリンゴ器官の成長形質を階層的・反復的に収録した再利用可能なデータセットであり、成長率やアロメトリーの推定・モデル較正に用いるデータ資源として方法論的価値がある。

titleA hierarchical dataset of vegetative and reproductive growth in apple tree organs under conventional and non-limited carbon resources.

Free and open-source software for object detection, size, and colour determination for use in plant phenotyping →

Abstract Background Object detection, size determination, and colour detection of optical images are tools commonly used in plant science. Key examples of this include identification of ripening stages of fruit such as tomatoes and the determination of chlorophyll content as an indicator of plant health. While methods exist for determining these important phenotypes, they often require proprietary software or require coding knowledge to adapt existing code. Results We provide a set of free and open-source Python scripts that, without any adaptation, are able to perform background correction and colour correction on images using a ColourChecker chart. Further scripts identify objects, use an object of known size to calibrate for size, and extract the average colour of objects in RGB, Lab, and YUV colour spaces. We use two examples to demonstrate the use of these scripts. We show the consistency of these scripts by imaging in four different lighting conditions, and then we use two examples to show how the scripts can be used. In the first example, we estimate the lycopene content in tomatoes (Solanum lycopersicum) var. Tiny Tim using fruit images and an exponential model to predict lycopene content. We demonstrate that three different cameras (a DSLR camera and two separate mobile phones) are all able to model lycopene content. The models that predict lycopene or chlorophyll need to be adjusted depending on the camera used. In the second example, we estimate the chlorophyll content of basil (Ocimum basilicum) using leaf images and an exponential model to predict chlorophyll content. Conclusion A fast, cheap, non-destructive, and inexpensive method is provided for the determination of the size and colour of plant materials using a rig consisting of a lightbox, camera, and colour checker card and using free and open-source scripts that run in Python 3.8. This method accurately predicted the lycopene content in tomato fruit and the chlorophyll content in basil leaves.

Why it matches plant phenotyping methods植物画像からサイズ・色を抽出し、リコペンおよびクロロフィル含量を推定するオープンソース手法と画像取得系を開発・実証しており、植物フェノタイピング手法が中心である。

abstractWe provide a set of free and open-source Python scripts that, without any adaptation, are able to perform background correction and colour correction on images using a ColourChecker chart.

Three-dimensional fruit growth analysis clarifies developmental mechanisms underlying complex shape diversity in persimmon fruit →

How fruit size and shape are determined is of research interest in agriculture and developmental biology. Fruit typically exhibits three-dimensional structures with genotype-dependent geometric features. Although minor developmental variations have been recognized, little research has fully visualized and measured these variations throughout fruit growth. In this study, a high-resolution 3D scanner was used to investigate the fruit development of 51 persimmon ( Diospyros kaki ) cultivars with various complex shapes. We obtained 2,380 3D fruit models that fully represented fruit appearance, and enabled precise and automated measurements of unique geometric features throughout fruit development. The 3D fruit model analysis identified key stages that determined the shape attributes at maturity. Typically, genetic diversity in vertical groove development was found, and such grooves can be filled by tissue expansion in the carpal fusion zone during fruit development. Furthermore, transcriptome analysis of fruit tissues from groove/non-groove tissues revealed gene co-expression networks that were highly associated with groove depth variation. The presence of YABBY homologs was most closely associated with groove depth and indicated the possibility that this pathway is a key molecular contributor to vertical groove depth variation. These results demonstrate the validity of fruit 3D growth analysis, which is a powerful tool for identifying the developmental mechanisms of fruit shape variation and the molecular basis of this diversity.

Why it matches plant phenotyping methods高解像度3Dスキャナと自動3Dモデル解析により、果実形状を発達期間 boyunca定量化する方法が研究の中心であり、果実形状の表現型解析手法として妥当です。

abstracta high-resolution 3D scanner was used to investigate the fruit development of 51 persimmon ( Diospyros kaki ) cultivars with various complex shapes

Feature Reduction for the Classification of Bruise Damage to Apple Fruit Using a Contactless FT-NIR Spectroscopy with Machine Learning. →

Spectroscopy data are useful for modelling biological systems such as predicting quality parameters of horticultural products. However, using the wide spectrum of wavelengths is not practical in a production setting. Such data are of high dimensional nature and they tend to result in complex models that are not easily understood. Furthermore, collinearity between different wavelengths dictates that some of the data variables are redundant and may even contribute noise. The use of variable selection methods is one efficient way to obtain an optimal model, andthis was the aim of this work. Taking advantage of a non-contact spectrometer, near infrared spectral data in the range of 800-2500 nm were used to classify bruise damage in three apple cultivars, namely 'Golden Delicious', 'Granny Smith' and 'Royal Gala'. Six prominent machine learning classification algorithms were employed, and two variable selection methods were used to determine the most relevant wavelengths for the problem of distinguishing between bruised and non-bruised fruit. The selected wavelengths clustered around 900 nm, 1300 nm, 1500 nm and 1900 nm. The best results were achieved using linear regression and support vector machine based on up to 40 wavelengths: these methods reached precision values in the range of 0.79-0.86, which were all comparable (within error bars) to a classifier based on the entire range of frequencies. The results also provided an open-source based framework that is useful towards the development of multi-spectral applications such as rapid grading of apples based on mechanical damage, and it can also be emulated and applied for other types of defects on fresh produce.

Why it matches plant phenotyping methodsリンゴ果実の打撲損傷という植物器官の状態を、非接触FT-NIR分光と機械学習で分類し、波長選択とモデル性能を評価しているため、植物フェノタイピング手法が中心です。

abstractTaking advantage of a non-contact spectrometer, near infrared spectral data in the range of 800-2500 nm were used to classify bruise damage in three apple cultivars

Dataset on UAV RGB videos acquired over a vineyard including bunch labels for object detection and tracking. →

Counting the number of grape bunches at an early stage of development offers relevant information to the winegrower about the potential yield to be harvested. However, manual counting on the fields is laborious and time-consuming. Remote sensing, and more precisely unmanned aerial vehicles mounted with RGB or multispectral cameras, facilitate this task rapidly and accurately. This dataset contains 40 RGB videos from a 1.06-ha vineyard located in northern Spain. Moreover, the dataset includes mask labels of visible grape bunches. The videos were acquired throughout four UAV flights with an RGB camera tilted at 60 degrees. Each flight recorded one side of a row of the vineyard. The grape berries were between pea-size (BBCH75) and bunch closure (BBCH79) stage, which is two months before harvesting. No operations other than those usual in a commercial vineyard, such as pruning, cane tying, fertilization, and pest treatment, have been carried out, hence, the dataset presents leaf occlusion. The dataset was gathered and labelled to train object detection and tracking algorithms for grape bunch counting. Furthermore, it eases the work of winegrowers to check the sanitary status of the vineyard.

Why it matches plant phenotyping methodsブドウ房数という植物の収量関連形質をUAV画像から推定するための、ラベル付き動画データセットであり、物体検出・追跡手法の開発を支援する中心的な成果である。

abstractThis dataset contains 40 RGB videos from a 1.06-ha vineyard located in northern Spain. Moreover, the dataset includes mask labels of visible grape bunches.

In-Orchard Sizing of Mango Fruit: 1. Comparison of Machine Vision Based Methods for On-The-Go Estimation →

Estimation of fruit size on-tree is useful for yield estimation, harvest timing and market planning. Automation of measurement of fruit size on-tree is possible using RGB-depth (RGB-D) cameras, if partly occluded fruit can be removed from consideration. An RGB-D Time of Flight camera was used in an imaging system that can be driven through an orchard. Three approaches were compared, being: (i) refined bounding box dimensions of a YOLO object detector; (ii) bounding box dimensions of an instance segmentation model (Mask R-CNN) applied to canopy images, and (iii) instance segmentation applied to extracted bounding boxes from a YOLO detection model. YOLO versions 3, 4 and 7 and their tiny variants were compared to an in-house variant, MangoYOLO, for this application, with YOLO v4-tiny adopted. Criteria developed to exclude occluded fruit by filtering based on depth, mask size, ellipse to mask area ratio and difference between refined bounding box height and ellipse major axis. The lowest root mean square error (RMSE) of 4.7 mm and 5.1 mm on the lineal length dimensions of a population (n = 104) of Honey Gold and Keitt varieties of mango fruit, respectively, and the lowest fruit exclusion rate was achieved using method (ii), while the RMSE on estimated fruit weight was 113 g on a population weight range between 180 and 1130 g. An example use is provided, with the method applied to video of an orchard row to produce a weight frequency distribution related to packing tray size.

Why it matches plant phenotyping methodsRGB-D画像と物体検出・インスタンスセグメンテーションを用いて樹上マンゴー果実のサイズ・重量を推定し、複数手法を比較検証しているため、植物表現型取得法が研究の中心である。

abstractThree approaches were compared, being: (i) refined bounding box dimensions of a YOLO object detector; (ii) bounding box dimensions of an instance segmentation model (Mask R-CNN) applied to canopy images, and (iii) instance segmentation applied to extracted bounding boxes from a YOLO detection model.

In-field hyperspectral imaging dataset of Manzanilla and Gordal olive varieties throughout the season. →

Because spectral technology has exhibited benefits in food-related applications, an increasing amount of effort is being dedicated to develop new food-related spectral technologies. In recent years, the use of remote sensing or unmanned aerial vehicles for precision agriculture has increased. As spectral technology continues to improve, portable spectral devices become available in the market, offering the possibility of realising in-field monitoring. This study demonstrates hyperspectral imaging and spectral olive signatures of the Manzanilla and Gordal cultivars analysed throughout the table-olive season from May to September. The data were acquired using an in-field technique and sampled via a non-destructive approach. The olives were monitored periodically during the season using a hyperspectral camera. A white reference was used to normalise the illumination variability in the spectra. The acquired data were saved in files named raw, normalised, and processed data. The normalised data were calculated by the sensor by correcting the white and black levels using the acquired reflectance values. The olive spectral signature of the images is saved in the processed data files. The images were labelled and processed using an algorithm to retrieve the olive spectral signatures. The results were stored as a chart with 204 columns and 'n' rows. Each row represents the pixel of an olive in the image, and the columns contain the reflectance information at that specific band. These data provide information about two olive cultivars during the season, which can be used for various research purposes. Statistical and artificial intelligence approaches correlate spectral signatures with olive characteristics such as growth level, organoleptic properties, or even cultivar classification.

Why it matches plant phenotyping methodsオリーブ果実を対象とした圃場ハイパースペクトル画像データセットであり、画像取得、正規化、アルゴリズムによるスペクトル特徴抽出、データ保存が中心的に記述されているため、植物フェノタイピング手法・データセットとして収録する。

abstractThis study demonstrates hyperspectral imaging and spectral olive signatures of the Manzanilla and Gordal cultivars analysed throughout the table-olive season from May to September.

Automatic Classification Service System for Citrus Pest Recognition Based on Deep Learning. →

Plant diseases are a major cause of reduction in agricultural output, which leads to severe economic losses and unstable food supply. The citrus plant is an economically important fruit crop grown and produced worldwide. However, citrus plants are easily affected by various factors, such as climate change, pests, and diseases, resulting in reduced yield and quality. Advances in computer vision in recent years have been widely used for plant disease detection and classification, providing opportunities for early disease detection, and resulting in improvements in agriculture. Particularly, the early and accurate detection of citrus diseases, which are vulnerable to pests, is very important to prevent the spread of pests and reduce crop damage. Research on citrus pest disease is ongoing, but it is difficult to apply research results to cultivation owing to a lack of datasets for research and limited types of pests. In this study, we built a dataset by self-collecting a total of 20,000 citrus pest images, including fruits and leaves, from actual cultivation sites. The constructed dataset was trained, verified, and tested using a model that had undergone five transfer learning steps. All models used in the experiment had an average accuracy of 97% or more and an average f1 score of 96% or more. We built a web application server using the EfficientNet-b0 model, which exhibited the best performance among the five learning models. The built web application tested citrus pest disease using image samples collected from websites other than the self-collected image samples and prepared data, and both samples correctly classified the disease. The citrus pest automatic diagnosis web system using the model proposed in this study plays a useful auxiliary role in recognizing and classifying citrus diseases. This can, in turn, help improve the overall quality of citrus fruits.

Why it matches plant phenotyping methods柑橘の葉・果実画像から病害状態を分類するデータセット、深層学習モデル、診断Webシステムを構築・検証しており、植物状態の取得・推定手法が中心である。

abstractIn this study, we built a dataset by self-collecting a total of 20,000 citrus pest images, including fruits and leaves, from actual cultivation sites.

Tracing Back the History of Pepper (Capsicum annuum) in the Iberian Peninsula from a Phenomics Point of View →

The Iberian Peninsula was the place where pepper (Capsicum annuum) entered Europe and dispersed to other continents but was also an important secondary center for its diversification. The current work evaluated the phenotypic diversity existing in this region and investigated how that evolved from Capsicum native areas (Mexico and Andean Region). For that purpose, the high-throughput phenotyping tool Tomato Analyzer was employed. Descriptors related to size and shape were the most distinctive among fruit types, reflecting a broad diversity for Iberian peppers. These traits likely reflected those suffering from more intensive human selections, driving the worldwide expansion of C. annuum. Iberian peppers maintained close proximity to the American accessions in terms of fruit phenomics. The highest similarities were observed for those coming from the southeastern edge of the Peninsula, while northwestern accessions displayed more significant differences. Common fruit traits (small, conical) suggested that Portuguese and Spanish landraces may have arisen from an ancient American population that entered the south of Spain and promptly migrated to the central and northern territories, giving rise to larger, elongated, and blocky pods. Such lineages would be the result of adaptations to local soil–climate factors prevailing in different biogeographic provinces.

Why it matches plant phenotyping methodsTomato Analyzerを用いた高スループット表現型解析が、ペッパー果実のサイズ・形状多様性を評価する研究の中心であり、方法の実質的な適用に該当する。

abstractFor that purpose, the high-throughput phenotyping tool Tomato Analyzer was employed.

Optimal plant part segmentation using 3D neural architecture search →

The automatic, and accurate plant phenotyping plays important role to improve the crop yield through enabling efficient plant analysis and plant breeding studies. The 3d deep learning has allows automatic segmentation of plant parts from point cloud data. However, the network architecture is designed manually and performance is limited to prior experience. The aim of this study is to search for optimal 3d deep networks to perform the plant part segmentation. We perform the 3d neural architecture search by training a super network composed of candidate networks. Using the trained super network, the evolutionary searching is used to search for top performing architecture. The results demonstrate the searched architecture outperforms manually designed architectures by attaining mean IoU and accuracy of more than 90% and 96%, respectively. The searched architecture achieves more than 83% class-wise IoU for all main stem, branches, and boll class. These plant part segmentation method shows promising results and holds potential to be utilized by plant breeders for enhancing the production quality.

Why it matches plant phenotyping methods植物点群から茎・枝・ボールなどの器官を自動分割する3Dニューラルネットワーク探索手法を開発・評価しており、植物表現型取得が研究の中心です。

abstractThe aim of this study is to search for optimal 3d deep networks to perform the plant part segmentation.

Computer generation of fruit shapes from DNA sequence →

The generation of realistic plant and animal images from marker information could be a main contribution of artificial intelligence to genetics and breeding. Since morphological traits are highly variable and highly heritable, this must be possible. However, a suitable algorithm has not been proposed yet. This paper is a proof of concept demonstrating the feasibility of this proposal using ‘decoders’, a class of deep learning architecture. We apply it to Cucurbitaceae, perhaps the family harboring the largest variability in fruit shape in the plant kingdom, and to tomato, a species with high morphological diversity also. We generate Cucurbitaceae shapes assuming a hypothetical, but plausible, evolutive path along observed fruit shapes of C. melo . In tomato, we used 353 images from 129 crosses between 25 maternal and 7 paternal lines for which genotype data were available. In both instances, a simple decoder was able to recover expected shapes with large accuracy. For the tomato pedigree, we also show that the algorithm can be trained to generate offspring images from their parents’ shapes, bypassing genotype information. Data and code are available at https://github.com/miguelperezenciso/dna2image .

Why it matches plant phenotyping methodsDNA配列や親の形状から植物果実形状画像を生成する深層学習手法の概念実証であり、植物形態の取得・推定が研究の中心です。

titleComputer generation of fruit shapes from DNA sequence

Intelligent yield estimation for tomato crop using SegNet with VGG19 architecture →

Yield estimation (YE) of the crop is one of the main tasks in fruit management and marketing. Based on the results of YE, the farmers can make a better decision on the harvesting period, prevention strategies for crop disease, subsequent follow-up for cultivation practice, etc. In the current scenario, crop YE is performed manually, which has many limitations such as the requirement of experts for the bigger fields, subjective decisions and a more time-consuming process. To overcome these issues, an intelligent YE system was proposed which detects, localizes and counts the number of tomatoes in the field using SegNet with VGG19 (a deep learning-based semantic segmentation architecture). The dataset of 672 images was given as an input to the SegNet with VGG19 architecture for training. It extracts features corresponding to the tomato in each layer and detection was performed based on the feature score. The results were compared against the other semantic segmentation architectures such as U-Net and SegNet with VGG16. The proposed method performed better and unveiled reasonable results. For testing the trained model, a case study was conducted in the real tomato field at Manapparai village, Trichy, India. The proposed method portrayed the test precision, recall and F1-score values of 89.7%, 72.55% and 80.22%, respectively along with reasonable localization capability for tomatoes.

Why it matches plant phenotyping methodsトマト果実の検出・局在化・計数による収量推定手法を開発し、複数モデルと比較・実地検証しており、植物フェノタイピング手法が中心である。

abstractan intelligent YE system was proposed which detects, localizes and counts the number of tomatoes in the field using SegNet with VGG19

Photogrammetric reconstruction of 3D carpological collection in high resolution for plants authentication and species discovery →

This study provides an accurate and efficient method to reconstruct detailed and high-resolution digital 3D models of carpological materials by photogrammetric method, in which only about 100 to 150 images are required for each model reconstruction. The 3D models reflect the realistic morphology and genuine color of the carpological materials. The 3D models are scaled to represent the true size of the materials even as small as 3 mm in diameter. The interfaces are interactive, in which the 3D models can be rotated in 360° to observe the structures and be zoomed to inspect the macroscopic details. This new platform is beneficial for developing a virtual herbarium of carpological collection which is thus the most important to botanical authentication and education.

Why it matches plant phenotyping methods植物の果実・種子等の形態を高解像度3D再構成するフォトグラメトリ手法とインタラクティブ基盤が中心であり、観察可能な植物形態を取得する方法論研究である。

abstractThis study provides an accurate and efficient method to reconstruct detailed and high-resolution digital 3D models of carpological materials by photogrammetric method

Detection and localization of citrus fruit based on improved You Only Look Once v5s and binocular vision in the orchard. →

Intelligent detection and localization of mature citrus fruits is a critical challenge in developing an automatic harvesting robot. Variable illumination conditions and different occlusion states are some of the essential issues that must be addressed for the accurate detection and localization of citrus in the orchard environment. In this paper, a novel method for the detection and localization of mature citrus using improved You Only Look Once (YOLO) v5s with binocular vision is proposed. First, a new loss function (polarity binary cross-entropy with logit loss) for YOLO v5s is designed to calculate the loss value of class probability and objectness score, so that a large penalty for false and missing detection is applied during the training process. Second, to recover the missing depth information caused by randomly overlapping background participants, Cr-Cb chromatic mapping, the Otsu thresholding algorithm, and morphological processing are successively used to extract the complete shape of the citrus, and the kriging method is applied to obtain the best linear unbiased estimator for the missing depth value. Finally, the citrus spatial position and posture information are obtained according to the camera imaging model and the geometric features of the citrus. The experimental results show that the recall rates of citrus detection under non-uniform illumination conditions, weak illumination, and well illumination are 99.55%, 98.47%, and 98.48%, respectively, approximately 2-9% higher than those of the original YOLO v5s network. The average error of the distance between the citrus fruit and the camera is 3.98 mm, and the average errors of the citrus diameters in the 3D direction are less than 2.75 mm. The average detection time per frame is 78.96 ms. The results indicate that our method can detect and localize citrus fruits in the complex environment of orchards with high accuracy and speed. Our dataset and codes are available at https://github.com/AshesBen/citrus-detection-localization.

Why it matches plant phenotyping methods収穫ロボット向けの位置検出が主目的だが、果実形状・姿勢・3D直径を画像から抽出し、精度を検証する技術開発が中心であり、再利用可能な植物器官形質の推定に該当する。

abstracta novel method for the detection and localization of mature citrus using improved You Only Look Once (YOLO) v5s with binocular vision is proposed.

Exploring Soybean Flower and Pod Variation Patterns During Reproductive Period Based on Fusion Deep Learning. →

The soybean flower and the pod drop are important factors in soybean yield, and the use of computer vision techniques to obtain the phenotypes of flowers and pods in bulk, as well as in a quick and accurate manner, is a key aspect of the study of the soybean flower and pod drop rate (PDR). This paper compared a variety of deep learning algorithms for identifying and counting soybean flowers and pods, and found that the Faster R-CNN model had the best performance. Furthermore, the Faster R-CNN model was further improved and optimized based on the characteristics of soybean flowers and pods. The accuracy of the final model for identifying flowers and pods was increased to 94.36 and 91%, respectively. Afterward, a fusion model for soybean flower and pod recognition and counting was proposed based on the Faster R-CNN model, where the coefficient of determination R 2 between counts of soybean flowers and pods by the fusion model and manual counts reached 0.965 and 0.98, respectively. The above results show that the fusion model is a robust recognition and counting algorithm that can reduce labor intensity and improve efficiency. Its application will greatly facilitate the study of the variable patterns of soybean flowers and pods during the reproductive period. Finally, based on the fusion model, we explored the variable patterns of soybean flowers and pods during the reproductive period, the spatial distribution patterns of soybean flowers and pods, and soybean flower and pod drop patterns.

Why it matches plant phenotyping methodsダイズの花・莢数という植物形質を画像から自動認識・計数する深層学習手法を比較、改良、検証しており、表現型取得法が研究の中心である。

abstractthe use of computer vision techniques to obtain the phenotypes of flowers and pods in bulk, as well as in a quick and accurate manner, is a key aspect of the study

wGrapeUNIPD-DL: An open dataset for white grape bunch detection. →

National and international Vitis variety catalogues can be used as image datasets for computer vision in viticulture. These databases archive ampelographic features and phenology of several grape varieties and plant structures images (e.g. leaf, bunch, shoots). Although these archives represent a potential database for computer vision in viticulture, plant structure images are acquired singularly and mostly not directly in the vineyard. Localization computer vision models would take advantage of multiple objects in the same image, allowing more efficient training. The present images and labels dataset was designed to overcome such limitations and provide suitable images for multiple cluster identification in white grape varieties. A group of 373 images were acquired from later view in vertical shoot position vineyards in six different Italian locations at different phenological stages. Images were then labelled in YOLO labelling format. The dataset was made available both in terms of images and labels. The real number of bunches counted in the field, and the number of bunches visible in the image (not covered by other vine structures) was recorded for a group of images in this dataset.

Why it matches plant phenotyping methodsブドウ房を対象とする画像・ラベル dataset の構築と公開が中心で、房の検出・可視数の記録という植物器官の表現型取得に直接関係するため。

abstractThe present images and labels dataset was designed to overcome such limitations and provide suitable images for multiple cluster identification in white grape varieties.

PSFD-Musa: A dataset of banana plant, stem, fruit, leaf, and disease. →

In recent times, the classification and identification of different fruits and food crops have become a necessity in the field of agricultural science; for sustainable growth. Probable processes have been developed worldwide to improve the production of food crops. Problem-specific, clean and crisp datasets are also lagging in the sector. This article introduces an image dataset of varieties of banana plants and the diseases related to them. The varieties of Banana plants that we have considered in the dataset are the Malbhog ( Musa assamica ), Jahaji ( Musa chinensis ), Kachkol ( Musa paradisiaca L. ), Bhimkol ( M. Balbisiana Colla ). And the diseases and pathogens that we have considered here are the Bacterial Soft Rot, Banana Fruit Scarring Beetle, Black Sigatoka, Yellow Sigatoka, Panama disease, Banana Aphids, and Pseudo-Stem Weevil. A dataset of Potassium deficiency has been also considered in this article. A total of 8000+ processed images are present in the dataset. The purpose of this article is to provide the Researchers and Students in getting access to our dataset that would help them in their research and in developing some machine learning models.

Why it matches plant phenotyping methodsバナナ植物の器官・品種・病害・カリウム欠乏を画像化した大規模データセットを提供しており、植物の状態推定に再利用できるデータ基盤が中心である。

abstractThis article introduces an image dataset of varieties of banana plants and the diseases related to them.

Introducing Three-Dimensional Scanning for Phenotyping of Olive Fruits Based on an Extensive Germplasm Survey →

Morphological characterization of olive (Olea europaea L.) varieties to detect desirable traits has been based on the training of expert panels and implementation of laborious multiyear measurements with limitations in accuracy and throughput of measurements. The present study compares two- and three-dimensional imaging systems for phenotyping a large dataset of 50 olive varieties maintained in the National Germplasm Depository of Greece, employing this technology for the first time in olive fruit and endocarps. The olive varieties employed for the present study exhibited high phenotypic variation, particularly for the endocarp shadow area, which ranged from 0.17−3.34 cm2 as evaluated via 2D and 0.32−2.59 cm2 as determined by 3D scanning. We found significant positive correlations (p < 0.001) between the two methods for eight quantitative morphological traits using the Pearson correlation coefficient. The highest correlation between the two methods was detected for the endocarp length (r = 1) and width (r = 1) followed by the fruit length (r = 0.9865), mucro length (r = 0.9631), fruit shadow area (r = 0.9573), fruit width (r = 0.9480), nipple length (r = 0.9441), and endocarp area (r = 0.9184). The present study unraveled novel morphological indicators of olive fruits and endocarps such as volume, total area, up- and down-skin area, and center of gravity using 3D scanning. The highest volume and area regarding both endocarp and fruit were observed for ‘Gaidourelia’. This methodology could be integrated into existing olive breeding programs, especially when the speed of scanning increases. Another potential future application could be assessing olive fruit quality on the trees or in the processing facilities.

Why it matches plant phenotyping methodsオリーブ果実・内果皮の形態形質を対象に、2D/3Dイメージングを比較・検証し、3Dスキャンによる新規形質を抽出しており、フェノタイピング手法が中心である。

abstractThe present study compares two- and three-dimensional imaging systems for phenotyping a large dataset of 50 olive varieties

Supervised and Weakly Supervised Deep Learning for Segmentation and Counting of Cotton Bolls Using Proximal Imagery. →

The total boll count from a plant is one of the most important phenotypic traits for cotton breeding and is also an important factor for growers to estimate the final yield. With the recent advances in deep learning, many supervised learning approaches have been implemented to perform phenotypic trait measurement from images for various crops, but few studies have been conducted to count cotton bolls from field images. Supervised learning models require a vast number of annotated images for training, which has become a bottleneck for machine learning model development. The goal of this study is to develop both fully supervised and weakly supervised deep learning models to segment and count cotton bolls from proximal imagery. A total of 290 RGB images of cotton plants from both potted (indoor and outdoor) and in-field settings were taken by consumer-grade cameras and the raw images were divided into 4350 image tiles for further model training and testing. Two supervised models (Mask R-CNN and S-Count) and two weakly supervised approaches (WS-Count and CountSeg) were compared in terms of boll count accuracy and annotation costs. The results revealed that the weakly supervised counting approaches performed well with RMSE values of 1.826 and 1.284 for WS-Count and CountSeg, respectively, whereas the fully supervised models achieve RMSE values of 1.181 and 1.175 for S-Count and Mask R-CNN, respectively, when the number of bolls in an image patch is less than 10. In terms of data annotation costs, the weakly supervised approaches were at least 10 times more cost efficient than the supervised approach for boll counting. In the future, the deep learning models developed in this study can be extended to other plant organs, such as main stalks, nodes, and primary and secondary branches. Both the supervised and weakly supervised deep learning models for boll counting with low-cost RGB images can be used by cotton breeders, physiologists, and growers alike to improve crop breeding and yield estimation.

Why it matches plant phenotyping methods綿花ボール数という植物表現型を画像からセグメンテーション・計数する深層学習手法を開発し、教師あり・弱教師ありモデルの精度とアノテーションコストを比較しており、表現型取得手法が研究の中心である。

abstractThe goal of this study is to develop both fully supervised and weakly supervised deep learning models to segment and count cotton bolls from proximal imagery.

Cotton Yield Estimation From Aerial Imagery Using Machine Learning Approaches. →

Estimation of cotton yield before harvest offers many benefits to breeding programs, researchers and producers. Remote sensing enables efficient and consistent estimation of cotton yields, as opposed to traditional field measurements and surveys. The overall goal of this study was to develop a data processing pipeline to perform fast and accurate pre-harvest yield predictions of cotton breeding fields from aerial imagery using machine learning techniques. By using only a single plot image extracted from an orthomosaic map, a Support Vector Machine (SVM) classifier with four selected features was trained to identify the cotton pixels present in each plot image. The SVM classifier achieved an accuracy of 89%, a precision of 86%, a recall of 75%, and an F1-score of 80% at recognizing cotton pixels. After performing morphological image processing operations and applying a connected components algorithm, the classified cotton pixels were clustered to predict the number of cotton bolls at the plot level. Our model fitted the ground truth counts with an R 2 value of 0.93, a normalized root mean squared error of 0.07, and a mean absolute percentage error of 13.7%. This study demonstrates that aerial imagery with machine learning techniques can be a reliable, efficient, and effective tool for pre-harvest cotton yield prediction.

Why it matches plant phenotyping methods航空画像と機械学習による綿花の収量・果球数推定パイプラインを開発し、画素分類と地上計数で性能検証しており、植物表現型の取得・抽出が研究の中心である。

abstractThe overall goal of this study was to develop a data processing pipeline to perform fast and accurate pre-harvest yield predictions of cotton breeding fields from aerial imagery using machine learning techniques.

The shape of aroma: measuring and modeling citrus oil gland distribution →

O_LICitrus come in diverse sizes and shapes, and play a key role in world culture and economy. Citrus oil glands in particular contain essential oils which include plant secondary metabolites associated with flavor and aroma. Capturing and analyzing nuanced information behind the citrus fruit shape and its oil gland distribution provides a morphology-driven path to further our insight into phenotype-genotype interactions. C_LIO_LIWe investigated the shape of citrus fruit of 51 accessions based on 3D X-ray CT scan reconstructions. Accessions include all three ancestral citrus species, accessions from related genera, and several interspecific hybrids. We digitally separate and compare the size of fruit endocarp, mesocarp, exocarp, and oil gland tissue. Based on the centers of the oil glands, overall fruit shape is approximated with an ellipsoid. Possible oil gland distributions on this ellipsoid surface are explored using directional statistics. C_LIO_LIThere is a strong allometry along fruit tissues; that is, we observe a strong linear relationship between the volume of any pair of major tissues. This suggests that the relative growth of fruit tissues with respect to each other follows a power law. We also observe that on average, glands distance themselves from their nearest neighbor following a square root relationship, which suggests normal diffusion dynamics at play. C_LIO_LIThe observed allometry and square root models point to the existence of biophysical developmental constraints that govern novel relationships between fruit dimensions from both evolutionary and breeding perspectives. Understanding these biophysical interactions prompt an exciting research path on fruit development and breeding. C_LI Societal Impact StatementCitrus are intrinsically connected to human health and culture, including preventing human diseases like scurvy, and inspiring sacred rituals. Citrus fruits come in a stunning number of different sizes and shapes, ranging from small clementines to oversized pummelos, and fruits display a vast diversity of flavors and aromas. These qualities are key in both traditional and modern medicine and the production of cleaning and perfume products. By quantifying and modeling overall fruit shape and oil gland distribution, we can gain further insight into citrus development and the impacts of domestication and improvement on multiple characteristics of the fruit.

Why it matches plant phenotyping methods3D X線CT再構成とデジタル分離により、柑橘果実の形状・組織体積・油腺分布を定量化しモデル化しており、植物表現型の取得・解析が研究の中心です。

abstractCapturing and analyzing nuanced information behind the citrus fruit shape and its oil gland distribution provides a morphology-driven path to further our insight into phenotype-genotype interactions.

High‐throughput measurement of plant fitness traits with an object detection method using Faster R‐CNN →

Summary Revealing the contributions of genes to plant phenotype is frequently challenging because loss‐of‐function effects may be subtle or masked by varying degrees of genetic redundancy. Such effects can potentially be detected by measuring plant fitness, which reflects the cumulative effects of genetic changes over the lifetime of a plant. However, fitness is challenging to measure accurately, particularly in species with high fecundity and relatively small propagule sizes such as Arabidopsis thaliana . An image segmentation‐based method using the software I mage J and an object detection‐based method using the Faster Region‐based Convolutional Neural Network (R‐CNN) algorithm were used for measuring two Arabidopsis fitness traits: seed and fruit counts. The segmentation‐based method was error‐prone (correlation between true and predicted seed counts, r 2 = 0.849) because seeds touching each other were undercounted. By contrast, the object detection‐based algorithm yielded near perfect seed counts ( r 2 = 0.9996) and highly accurate fruit counts ( r 2 = 0.980). Comparing seed counts for wild‐type and 12 mutant lines revealed fitness effects for three genes; fruit counts revealed the same effects for two genes. Our study provides analysis pipelines and models to facilitate the investigation of Arabidopsis fitness traits and demonstrates the importance of examining fitness traits when studying gene functions.

Why it matches plant phenotyping methodsFaster R-CNNによる種子・果実数という植物形質の画像ベース測定法を開発・比較検証し、解析パイプラインとモデルを提示しているため、フェノタイピング手法が中心的です。

abstractAn image segmentation‐based method using the software I mage J and an object detection‐based method using the Faster Region‐based Convolutional Neural Network (R‐CNN) algorithm were used for measuring two Arabidopsis fitness traits: seed and fruit counts.

Vegetable Size Measurement Based on Stereo Camera and Keypoints Detection →

This work focuses on the problem of non-contact measurement for vegetables in agricultural automation. The application of computer vision in assisted agricultural production significantly improves work efficiency due to the rapid development of information technology and artificial intelligence. Based on object detection and stereo cameras, this paper proposes an intelligent method for vegetable recognition and size estimation. The method obtains colorful images and depth maps with a binocular stereo camera. Then detection networks classify four kinds of common vegetables (cucumber, eggplant, tomato and pepper) and locate six points for each object. Finally, the size of vegetables is calculated using the pixel position and depth of keypoints. Experimental results show that the proposed method can classify four kinds of common vegetables within 60 cm and accurately estimate their diameter and length. The work provides an innovative idea for solving the vegetable's non-contact measurement problems and can promote the application of computer vision in agricultural automation.

Why it matches plant phenotyping methods野菜の長さ・直径という植物器官形質を、ステレオカメラ、深度画像、キーポイント検出で非接触推定する手法が研究の中心であるため。

abstractThis work focuses on the problem of non-contact measurement for vegetables in agricultural automation.

Deep-learning-based in-field citrus fruit detection and tracking. →

Fruit yield estimation is crucial for establishing fruit harvest and marketing strategies. Recently, computer vision and deep learning techniques have been used to estimate citrus fruit yield and have exhibited notable fruit detection ability. However, computer-vision-based citrus fruit counting has two key limitations: inconsistent fruit detection accuracy and double-counting of the same fruit. Using oranges as the experimental material, this paper proposes a deep-learning-based orange counting algorithm using video sequences to help overcome these problems. The algorithm consists of two sub-algorithms, OrangeYolo for fruit detection and OrangeSort for fruit tracking. The OrangeYolo backbone network is partially based on the YOLOv3 algorithm, which has been improved upon to detect small objects (fruits) at multiple scales. The network structure was adjusted to detect small-scale targets while enabling multiscale target detection. A channel attention and spatial attention multiscale fusion module was introduced to fuse the semantic features of the deep network with the shallow textural detail features. OrangeYolo can achieve mean Average Precision (mAP) values of 0.957 in the citrus dataset, higher than the 0.905, 0.911, and 0.917 achieved with the YOLOv3, YOLOv4, and YOLOv5 algorithms. OrangeSort was designed to alleviate the double-counting problem associated with occluded fruits. A specific tracking region counting strategy and tracking algorithm based on motion displacement estimation were established. Six video sequences taken from two fields containing 22 trees were used as the validation dataset. The proposed method showed better performance (Mean Absolute Error (MAE) = 0.081, Standard Deviation (SD) = 0.08) than video-based manual counting and produced more accurate results than the existing standards Sort and DeepSort (MAE = 0.45 and 1.212; SD = 0.4741 and 1.3975).

Why it matches plant phenotyping methods柑橘果実の検出・追跡により樹上果実数（収量推定に使う形質）を定量する画像解析手法を開発し、既存手法および手動計数と検証・比較しており、植物フェノタイピング手法が中心です。

abstractthis paper proposes a deep-learning-based orange counting algorithm using video sequences to help overcome these problems.

Metabolomic selection for enhanced fruit flavor. →

Although they are staple foods in cuisines globally, many commercial fruit varieties have become progressively less flavorful over time. Due to the cost and difficulty associated with flavor phenotyping, breeding programs have long been challenged in selecting for this complex trait. To address this issue, we leveraged targeted metabolomics of diverse tomato and blueberry accessions and their corresponding consumer panel ratings to create statistical and machine learning models that can predict sensory perceptions of fruit flavor. Using these models, a breeding program can assess flavor ratings for a large number of genotypes, previously limited by the low throughput of consumer sensory panels. The ability to predict consumer ratings of liking, sweet, sour, umami, and flavor intensity was evaluated by a 10-fold cross-validation, and the accuracies of 18 different models were assessed. The prediction accuracies were high for most attributes and ranged from 0.87 for sourness intensity in blueberry using XGBoost to 0.46 for overall liking in tomato using linear regression. Further, the best-performing models were used to infer the flavor compounds (sugars, acids, and volatiles) that contribute most to each flavor attribute. We found that the variance decomposition of overall liking score estimates that 42% and 56% of the variance was explained by volatile organic compounds in tomato and blueberry, respectively. We expect that these models will enable an earlier incorporation of flavor as breeding targets and encourage selection and release of more flavorful fruit varieties.

Why it matches plant phenotyping methods果実の風味という植物器官形質を、メタボロームから予測する統計・機械学習モデルを開発し、交差検証で性能評価している。育種に利用可能な風味表現型推定法が中心であり、単なる代謝測定ではない。

abstractwe leveraged targeted metabolomics of diverse tomato and blueberry accessions and their corresponding consumer panel ratings to create statistical and machine learning models that can predict sensory perceptions of fruit flavor.

A Data Driven Approach to Assess Complex Colour Profiles in Plant Tissues. →

The ability to quantify the colour of fruit is extremely important for a number of applied fields including plant breeding, postharvest assessment, and consumer quality assessment. Fruit and other plant organs display highly complex colour patterning. This complexity makes it challenging to compare and contrast colours in an accurate and time efficient manner. Multiple methodologies exist that attempt to digitally quantify colour in complex images but these either require a priori knowledge to assign colours to a particular bin, or fit the colours present within segment of the colour space into a single colour value using a thresholding approach. A major drawback of these methodologies is that, through the process of averaging, they tend to synthetically generate values that may not exist within the context of the original image. As such, to date there are no published methodologies that assess colour patterning using a data driven approach. In this study we present a methodology to acquire and process digital images of biological samples that contain complex colour gradients. The CIE (Commission Internationale de l'Eclairage/International Commission on Illumination) ΔE2000 formula was used to determine the perceptually unique colours (PUC) within images of fruit containing complex colour gradients. This process, on average, resulted in a 98% reduction in colour values from the number of unique colours (UC) in the original image. This data driven procedure summarised the colour data values while maintaining a linear relationship with the normalised colour complexity contained in the total image. A weighted ΔE2000 distance metric was used to generate a distance matrix and facilitated clustering of summarised colour data. Clustering showed that our data driven methodology has the ability to group these complex images into their respective binomial families while maintaining the ability to detect subtle colour differences. This methodology was also able to differentiate closely related images. We provide a high quality set of complex biological images that span the visual spectrum that can be used in future colorimetric research to benchmark colourimetric method development.

Why it matches plant phenotyping methods植物組織・果実画像の複雑な色彩パターンを取得・定量化・分類する画像解析手法の開発が中心であり、植物器官の色という表現型を直接扱うため。

abstractIn this study we present a methodology to acquire and process digital images of biological samples that contain complex colour gradients.

A Crop Modelling Strategy to Improve Cacao Quality and Productivity. →

Cacao production systems in Colombia are of high importance due to their direct impact in the social and economic development of smallholder farmers. Although Colombian cacao has the potential to be in the high value markets for fine flavour, the lack of expert support as well as the use of traditional, and often times sub-optimal technologies makes cacao production negligible. Traditionally, cacao harvest takes place at exactly the same time regardless of the geographic and climatic region where it is grown, the problem with this strategy is that cacao beans are often unripe or over matured and a combination of both will negatively affect the quality of the final cacao product. Since cacao fruit development can be considered as the result of a number of physiological and morphological processes that can be described by mathematical relationships even under uncontrolled environments. Environmental parameters that have more association with pod maturation speed should be taken into account to decide the appropriate time to harvest. In this context, crop models are useful tools to simulate and predict crop development over time and under multiple environmental conditions. Since harvesting at the right time can yield high quality cacao, we parameterised a crop model to predict the best time for harvest cacao fruits in Colombia. The cacao model uses weather variables such as temperature and solar radiation to simulate the growth rate of cocoa fruits from flowering to maturity. The model uses thermal time as an indicator of optimal maturity. This model can be used as a practical tool that supports cacao farmers in the production of high quality cacao which is usually paid at a higher price. When comparing simulated and observed data, our results showed an RRMSE of 7.2% for the yield prediction, while the simulated harvest date varied between +/-2 to 20 days depending on the temperature variations of the year between regions. This crop model contributed to understanding and predicting the phenology of cacao fruits for two key cultivars ICS95 y CCN51.

Why it matches plant phenotyping methodsカカオ果実の成熟・生育（フェノロジー）を気象変数と熱時間から推定する作物モデルを構築・パラメータ化し、観測値と比較検証しており、植物状態の推定手法が研究の中心である。

abstractwe parameterised a crop model to predict the best time for harvest cacao fruits in Colombia

PFuji-Size dataset: A collection of images and photogrammetry-derived 3D point clouds with ground truth annotations for Fuji apple detection and size estimation in field conditions. →

The PFuji-Size dataset is comprised of a collection of 3D point clouds of Fuji apple trees ( Malus domestica Borkh. cv. Fuji) scanned at different maturity stages and annotated for fruit detection and size estimation. Structure-from-motion and multi-view stereo techniques were used to generate the 3D point clouds of 6 complete Fuji apple trees containing a total of 615 apples. The resulting point clouds were 3D segmented by identifying the 3D points corresponding to each apple (3D instance segmentation), obtaining a single point cloud for each apple. All segmented apples were labelled with ground truth diameter annotations. Since the data was acquired in field conditions and at different maturity stages, the set includes different fruit diameters -from 26.9 mm to 94.8 mm- and different fruit occlusion percentages due to foliage. In addition, 25 apples were photographed 360° in laboratory conditions, obtaining high resolution 3D point clouds of this sub-set. To the best of the authors' knowledge, this is the first publicly available dataset for apple size estimation in field conditions. This dataset was used to evaluate different fruit size estimation methods in the research article titled "In-field apple size estimation using photogrammetry-derived 3D point clouds: comparison of 4 different methods considering fruit occlusion" (Gené-Mola et al., 2021).

Why it matches plant phenotyping methodsリンゴ果実の3D画像・点群から果径を推定するための公開データセットであり、アノテーション、3Dセグメンテーション、サイズ推定評価が中心的な方法論的貢献である。

abstractThe PFuji-Size dataset is comprised of a collection of 3D point clouds of Fuji apple trees ( Malus domestica Borkh. cv. Fuji) scanned at different maturity stages and annotated for fruit detection and size estimation.

Region-aggregated attention CNN for disease detection in fruit images. →

Background Diseases and pests have a profound effect on a yearly harvest and productivity in agriculture. A precise and accurate detection of the diseases and pests could facilitate timely treatment and management of the diseases and pests and lessen the resultant loss in economy and health. Herein, we propose an improved design of the disease detection system for plant images. Methods Built upon the two-stage framework of object detection neural networks such as Mask R-CNN, the proposed network involves three types of extensions, including the addition of additional level of feature pyramids to improve the exploration and proposal of candidate regions, the aggregation of feature maps from all levels of feature pyramids per candidate region to fully exploit the information from feature pyramids, and the introduction of a squeeze-and-excitation block to the construction of feature pyramids and the aggregated feature maps to improve the representation of feature maps. Results The proposed network was evaluated using 74 images of infected apple fruits. In 3-fold cross-validation, the proposed network achieved averaged precision (AP) of 72.26, AP at 0.5 threshold of 88.51 and AP at 0.75 threshold of 82.30. In the comparative experiments, the proposed network outperformed the other competing networks. The utility of the three extensions was also demonstrated in comparison to Mask R-CNN. Conclusions The experimental results suggest that the proposed network could identify and localize the symptom of the disease with high accuracy, leading to an early diagnosis and treatment of the disease, and thus holding the potential for improving crop yield and quality.

Why it matches plant phenotyping methods植物画像から病徴を識別・局在化するCNN手法を開発し、Mask R-CNNとの比較検証も行っており、植物病害状態の表現型抽出が中心である。

abstractwe propose an improved design of the disease detection system for plant images.

Central Object Segmentation by Deep Learning to Continuously Monitor Fruit Growth through RGB Images. →

Monitoring fruit growth is useful when estimating final yields in advance and predicting optimum harvest times. However, observing fruit all day at the farm via RGB images is not an easy task because the light conditions are constantly changing. In this paper, we present CROP (Central Roundish Object Painter). The method involves image segmentation by deep learning, and the architecture of the neural network is a deeper version of U-Net. CROP identifies different types of central roundish fruit in an RGB image in varied light conditions, and creates a corresponding mask. Counting the mask pixels gives the relative two-dimensional size of the fruit, and in this way, time-series images may provide a non-contact means of automatically monitoring fruit growth. Although our measurement unit is different from the traditional one (length), we believe that shape identification potentially provides more information. Interestingly, CROP can have a more general use, working even for some other roundish objects. For this reason, we hope that CROP and our methodology yield big data to promote scientific advancements in horticultural science and other fields.

Why it matches plant phenotyping methodsRGB画像から果実をセグメンテーションし、画素数で果実サイズと成長を時系列推定する手法開発が中心である。

abstractIn this paper, we present CROP (Central Roundish Object Painter). The method involves image segmentation by deep learning, and the architecture of the neural network is a deeper version of U-Net.

DiaMOS Plant: A Dataset for Diagnosis and Monitoring Plant Disease →

The classification and recognition of foliar diseases is an increasingly developing field of research, where the concepts of machine and deep learning are used to support agricultural stakeholders. Datasets are the fuel for the development of these technologies. In this paper, we release and make publicly available the field dataset collected to diagnose and monitor plant symptoms, called DiaMOS Plant, consisting of 3505 images of pear fruit and leaves affected by four diseases. In addition, we perform a comparative analysis of existing literature datasets designed for the classification and recognition of leaf diseases, highlighting the main features that maximize the value and information content of the collected data. This study provides guidelines that will be useful to the research community in the context of the selection and construction of datasets.

Why it matches plant phenotyping methods植物病徴を画像で診断・モニタリングする公開データセットの構築と既存データセット比較が中心であり、植物病害状態の画像ベース表現型解析に該当する。

abstractwe release and make publicly available the field dataset collected to diagnose and monitor plant symptoms, called DiaMOS Plant

An Advanced Photogrammetric Solution to Measure Apples →

This work presents an advanced photogrammetric pipeline for inspecting apple trees in the field, automatically detecting fruits from videos and quantifying their size and number. The proposed approach is intended to facilitate and accelerate farmers’ and agronomists’ fieldwork, making apple measurements more objective and giving a more extended collection of apples measured in the field while also estimating harvesting/apple-picking dates. In order to do this rapidly and automatically, we propose a pipeline that uses smartphone-based videos and combines photogrammetry, deep learning and geometric algorithms. Synthetic, laboratory and on-field experiments demonstrate the accuracy of the results and the potential of the proposed method. Acquired data, labelled images, code and network weights, are available at 3DOM-FBK GitHub account.

Why it matches plant phenotyping methodsリンゴ果実の数とサイズを動画から自動抽出するフォトグラメトリ手法を開発し、実験で精度を検証しており、植物フェノタイピング手法が中心である。

abstractThis work presents an advanced photogrammetric pipeline for inspecting apple trees in the field, automatically detecting fruits from videos and quantifying their size and number.

Diagnosis of Typical Apple Diseases: A Deep Learning Method Based on Multi-Scale Dense Classification Network. →

Disease has always been one of the main reasons for the decline of apple quality and yield, which directly harms the development of agricultural economy. Therefore, precise diagnosis of apple diseases and correct decision making are important measures to reduce agricultural losses and promote economic growth. In this paper, a novel Multi-scale Dense classification network is adopted to realize the diagnosis of 11 types of images, including healthy and diseased apple fruits and leaves. The diagnosis of different kinds of diseases and the same disease with different grades was accomplished. First of all, to solve the problem of insufficient images of anthracnose and ring rot, Cycle-GAN algorithm was applied to achieve dataset expansion on the basis of traditional image augmentation methods. Cycle-GAN learned the image characteristics of healthy apples and diseased apples to generate anthracnose and ring rot lesions on the surface of healthy apple fruits. The diseased apple images generated by Cycle-GAN were added to the training set, which improved the diagnosis performance compared with other traditional image augmentation methods. Subsequently, DenseNet and Multi-scale connection were adopted to establish two kinds of models, Multi-scale Dense Inception-V4 and Multi-scale Dense Inception-Resnet-V2, which facilitated the reuse of image features of the bottom layers in the classification neural networks. Both models accomplished the diagnosis of 11 different types of images. The classification accuracy was 94.31 and 94.74%, respectively, which exceeded DenseNet-121 network and reached the state-of-the-art level.

Why it matches plant phenotyping methodsリンゴ葉・果実の病害画像と病害グレードを深層学習で診断する画像ベースの植物状態推定法が研究の中心であり、データ拡張、モデル構築、精度比較まで実施している。

abstracta novel Multi-scale Dense classification network is adopted to realize the diagnosis of 11 types of images, including healthy and diseased apple fruits and leaves.

Combining Local and Global Viewpoint Planning for Fruit Coverage →

Obtaining 3D sensor data of complete plants or plant parts (e.g., the crop or fruit) is difficult due to their complex structure and a high degree of occlusion. However, especially for the estimation of the position and size of fruits, it is necessary to avoid occlusions as much as possible and acquire sensor information of the relevant parts. Global viewpoint planners exist that suggest a series of viewpoints to cover the regions of interest up to a certain degree, but they usually prioritize global coverage and do not emphasize the avoidance of local occlusions. On the other hand, there are approaches that aim at avoiding local occlusions, but they cannot be used in larger environments since they only reach a local maximum of coverage. In this paper, we therefore propose to combine a local, gradient-based method with global viewpoint planning to enable local occlusion avoidance while still being able to cover large areas. Our simulated experiments with a robotic arm equipped with a camera array as well as an RGB-D camera show that this combination leads to a significantly increased coverage of the regions of interest compared to just applying global coverage planning.

Why it matches plant phenotyping methods果実の位置・サイズ推定に必要な3Dセンサデータ取得を対象に、局所遮蔽回避と大域的視点計画を組み合わせる視点計画法を開発・評価しており、植物表現型取得が中心である。

abstractespecially for the estimation of the position and size of fruits, it is necessary to avoid occlusions as much as possible and acquire sensor information of the relevant parts

A dataset of fortunella margarita images for object detection of deep learning based methods. →

Crops require appropriate planting techniques at different growth stages. Judgments on crop maturity affect the yield of crops. The planting and management of crops rely heavily on experienced farmers, which can reduce planting costs and increase yields. With the advancement of smart agriculture [1], images of crops can be used to accurately determine the growth stage of crops and estimate crop yields [2]. This can be combined with drones or smartphones to predict the growth stage and yield of Fortunella margarita for farmers in the future. This article presents an F. margarita image dataset. We classified F. margarita into three growth stages: mature, immature, and growing. In this dataset, an image may contain plants in several growth stages. The images were divided into seven categories according to growth stage. The dataset contains a total of 1031 original images. The total number of images was increased to 6611 through data augmentation. In addition, the dataset includes 6611 annotations with 7 categories of manually marked positions of F. margarita . Field images were captured in Jiaoxi, Yilan County, Taiwan, using smartphones. The dataset can serve as a resource for researchers who use different algorithms of machine learning or deep learning for object detection, image segmentation, and multiclass classification.

Why it matches plant phenotyping methods植物の生育段階を画像から判定するための注釈付きデータセットを提供しており、植物状態の画像取得・分類基盤が中心です。

abstractThis article presents an F. margarita image dataset.

Modeling Carbon Balance and Sugar Content of Vitis vinifera under Two Different Trellis Systems. →

Environmental factors might influence the carbon balance and sugar content in grapevine. In this two-year research, the STELLA software was employed to predict dry matter accumulation in Sangiovese vines, comparing the traditional vertical shoot positioning (VSP) and the single high wire (SHW) trellis systems. Every week, vegetative, eco-physiological and grape quality parameters were collected for 15 tagged vines per trellis system to set up the software. Significant differences in photosynthesis were recorded in 2014, with higher values in VSP (23-25% more). Shoot growth was significantly higher in VSP (20-25% more), whereas higher dry matter (30%) and yield (9-11% more) were detected for SHW. At harvest, berry composition suggested a slower ripening in SHW compared to VSP, which was linked to the shading of clusters in SHW. Finally, for the first time, linear regressions were found between measured berry sugar content and STELLA-estimated dry matter (R 2 = 0.96 in VSP; R 2 = 0.95 in SHW). This latter evidence allowed the estimation of berry sugar content, showing this software to be a practical tool to support winegrowers in decision making. Other studies are already underway to calibrate and validate the model for other varieties, training systems and environments.

Why it matches plant phenotyping methodsSTELLAモデルによるブドウの乾物蓄積・果実糖含量の推定と、実測値との回帰による検証が研究の中心であり、植物形質の計算推定手法として扱える。

abstractthe STELLA software was employed to predict dry matter accumulation in Sangiovese vines

MFCIS: an automatic leaf-based identification pipeline for plant cultivars using deep learning and persistent homology →

Recognizing plant cultivars reliably and efficiently can benefit plant breeders in terms of property rights protection and innovation of germplasm resources. Although leaf image-based methods have been widely adopted in plant species identification, they seldom have been applied in cultivar identification due to the high similarity of leaves among cultivars. Here, we propose an automatic leaf image-based cultivar identification pipeline called MFCIS (Multi-feature Combined Cultivar Identification System), which combines multiple leaf morphological features collected by persistent homology and a convolutional neural network (CNN). Persistent homology, a multiscale and robust method, was employed to extract the topological signatures of leaf shape, texture, and venation details. A CNN-based algorithm, the Xception network, was fine-tuned for extracting high-level leaf image features. For fruit species, we benchmarked the MFCIS pipeline on a sweet cherry (Prunus avium L.) leaf dataset with >5000 leaf images from 88 varieties or unreleased selections and achieved a mean accuracy of 83.52%. For annual crop species, we applied the MFCIS pipeline to a soybean (Glycine max L. Merr.) leaf dataset with 5000 leaf images of 100 cultivars or elite breeding lines collected at five growth periods. The identification models for each growth period were trained independently, and their results were combined using a score-level fusion strategy. The classification accuracy after score-level fusion was 91.4%, which is much higher than the accuracy when utilizing each growth period independently or mixing all growth periods. To facilitate the adoption of the proposed pipelines, we constructed a user-friendly web service, which is freely available at http://www.mfcis.online .

Why it matches plant phenotyping methods葉画像から形態・形状・質感・葉脈特徴を抽出して品種を識別するパイプラインを開発・ベンチマークし、ウェブサービス化しており、植物表現型取得・解析手法が中心である。

abstractHere, we propose an automatic leaf image-based cultivar identification pipeline called MFCIS (Multi-feature Combined Cultivar Identification System), which combines multiple leaf morphological features collected by persistent homology and a convolutional neural network (CNN).

High throughput measurement of Arabidopsis thaliana fitness traits using transfer learning →

Summary Revealing the contributions of genes to plant phenotype is frequently challenging because the effects of loss of gene function may be subtle or be masked by genetic redundancy. Such effects can potentially be detected by measuring plant fitness, which reflects the cumulative effects of genetic changes over the lifetime of a plant. However, fitness is challenging to measure accurately, particularly in species with high fecundity and relatively small propagule sizes such as Arabidopsis thaliana . An image segmentation-based (ImageJ) and a Faster Region Based Convolutional Neural Network (R-CNN) approach were used for measuring two Arabidopsis fitness traits: seed and fruit counts. Although straightforward to use, ImageJ was error-prone (correlation between true and predicted seed counts, r 2 =0.849) because seeds touching each other were undercounted. In contrast, Faster R-CNN yielded near perfect seed counts (r 2 =0.9996) and highly accurate fruit counts (r 2 =0.980). By examining seed counts, we were able to reveal fitness effects for genes that were previously reported to have no or condition-specific loss-of-function phenotypes. Our study provides models to facilitate the investigation of Arabidopsis fitness traits and demonstrates the importance of examining fitness traits in the study of gene functions.

Why it matches plant phenotyping methods画像分割とFaster R-CNNを用いて種子数・果実数という植物形質を高スループット測定し、精度比較・検証を行うことが中心であるため。

titleHigh throughput measurement of Arabidopsis thaliana fitness traits using transfer learning

Parts-per-Object Count in Agricultural Images: Solving Phenotyping Problems via a Single Deep Neural Network →

Solving many phenotyping problems involves not only automatic detection of objects in an image, but also counting the number of parts per object. We propose a solution in the form of a single deep network, tested for three agricultural datasets pertaining to bananas-per-bunch, spikelets-per-wheat-spike, and berries-per-grape-cluster. The suggested network incorporates object detection, object resizing, and part counting as modules in a single deep network, with several variants tested. The detection module is based on a Retina-Net architecture, whereas for the counting modules, two different architectures are examined: the first based on direct regression of the predicted count, and the other on explicit parts detection and counting. The results are promising, with the mean relative deviation between estimated and visible part count in the range of 9.2% to 11.5%. Further inference of count-based yield related statistics is considered. For banana bunches, the actual banana count (including occluded bananas) is inferred from the count of visible bananas. For spikelets-per-wheat-spike, robust estimation methods are employed to get the average spikelet count across the field, which is an effective yield estimator.

Why it matches plant phenotyping methods植物器官の可視パーツ数を画像から検出・計数する深層学習手法を開発し、複数作物データセットで評価しているため、表現型取得・推定法が中心です。

abstractWe propose a solution in the form of a single deep network, tested for three agricultural datasets pertaining to bananas-per-bunch, spikelets-per-wheat-spike, and berries-per-grape-cluster.

Linking Tissue Damage to Hyperspectral Reflectance for Non-Invasive Monitoring of Apple Fruit in Orchards. →

Reflected light carries ample information about the biochemical composition, tissue architecture, and physiological condition of plants. Recent technical progress has paved the way for affordable imaging hyperspectrometers (IH) providing spatially resolved spectral information on plants on different levels, from individual plant organs to communities. The extraction of sensible information from hyperspectral images is difficult due to inherent complexity of plant tissue and canopy optics, especially when recorded under ambient sunlight. We report on the changes in hyperspectral reflectance accompanying the accumulation of anthocyanins in healthy apple (cultivars Ligol, Gala, Golden Delicious) fruits as well as in fruits affected by pigment breakdown during sunscald development and phytopathogen attacks. The measurements made outdoors with a snapshot IH were compared with traditional "point-type" reflectance measured with a spectrophotometer under controlled illumination conditions. The spectra captured by the IH were suitable for processing using the approaches previously developed for "point-type" apple fruit and leaf reflectance spectra. The validity of this approach was tested by constructing a novel index mBRI (modified browning reflectance index) for detection of tissue damages on the background of the anthocyanin absorption. The index was suggested in the form of mBRI = ( R 640 -1 + R 800 -1 ) - R 678 -1 . Difficulties of the interpretation of fruit hyperspectral reflectance images recorded in situ are discussed with possible implications for plant physiology and precision horticulture practices.

Why it matches plant phenotyping methodsリンゴ果実のハイパースペクトル画像から組織損傷を検出する指標を開発・検証しており、植物状態の取得手法が研究の中心である。

abstractThe validity of this approach was tested by constructing a novel index mBRI (modified browning reflectance index) for detection of tissue damages on the background of the anthocyanin absorption.

GANana: Unsupervised Domain Adaptation for Volumetric Regression of Fruit →

3D reconstruction of fruit is important as a key component of fruit grading and an important part of many size estimation pipelines.Like many computer vision challenges, the 3D reconstruction task suffers from a lack of readily available training data in most domains, with methods typically depending on large datasets of high-quality image-model pairs.In this paper, we propose an unsupervised domain-adaptation approach to 3D reconstruction where labelled images only exist in our source synthetic domain, and training is supplemented with different unlabelled datasets from the target real domain.We approach the problem of 3D reconstruction using volumetric regression and produce a training set of 25,000 pairs of images and volumes using hand-crafted 3D models of bananas rendered in a 3D modelling environment (Blender).Each image is then enhanced by a GAN to more closely match the domain of photographs of real images by introducing a volumetric consistency loss, improving performance of 3D reconstruction on real images.Our solution harnesses the cost benefits of synthetic data while still maintaining good performance on real world images.We focus this work on the task of 3D banana reconstruction from a single image, representing a common task in plant phenotyping, but this approach is general and may be adapted to any 3D reconstruction task including other plant species and organs.

Why it matches plant phenotyping methods果実の3D再構成と体積回帰を対象とする教師なしドメイン適応手法を開発しており、植物器官の形態・サイズ推定に用いるフェノタイピング手法が研究の中心である。

abstractIn this paper, we propose an unsupervised domain-adaptation approach to 3D reconstruction

Convolutional Neural Network for Automatic Identification of Plant Diseases with Limited Data →

Automated identification of plant diseases is very important for crop protection. Most automated approaches aim to build classification models based on leaf or fruit images. These approaches usually require the collection and annotation of many images, which is difficult and costly process especially in the case of new or rare diseases. Therefore, in this study, we developed and evaluated several methods for identifying plant diseases with little data. Convolutional Neural Networks (CNNs) are used due to their superior ability to transfer learning. Three CNN architectures (ResNet18, ResNet34, and ResNet50) were used to build two baseline models, a Triplet network and a deep adversarial Metric Learning (DAML) approach. These approaches were trained from a large source domain dataset and then tuned to identify new diseases from few images, ranging from 5 to 50 images per disease. The proposed approaches were also evaluated in the case of identifying the disease and plant species together or only if the disease was identified, regardless of the affected plant. The evaluation results demonstrated that a baseline model trained with a large set of source field images can be adapted to classify new diseases from a small number of images. It can also take advantage of the availability of a larger number of images. In addition, by comparing it with metric learning methods, we found that baseline model has better transferability when the source domain images differ from the target domain images significantly or are captured in different conditions. It achieved an accuracy of 99% when the shift from source domain to target domain was small and 81% when that shift was large and outperformed all other competitive approaches.

Why it matches plant phenotyping methods植物画像から病害状態を推定するCNN手法の開発と比較評価が研究の中心であり、植物病害フェノタイピング手法に該当する。

titleConvolutional Neural Network for Automatic Identification of Plant Diseases with Limited Data

Real-time plant health assessment via implementing cloud-based scalable transfer learning on AWS DeepLens →

The control of plant leaf diseases is crucial as it affects the quality and production of plant species with an effect on the economy of any country. Automated identification and classification of plant leaf diseases is, therefore, essential for the reduction of economic losses and the conservation of specific species. Various Machine Learning (ML) models have previously been proposed to detect and identify plant leaf disease; however, they lack usability due to hardware sophistication, limited scalability and realistic use inefficiency. By implementing automatic detection and classification of leaf diseases in fruit trees (apple, grape, peach and strawberry) and vegetable plants (potato and tomato) through scalable transfer learning on Amazon Web Services (AWS) SageMaker and importing it into AWS DeepLens for real-time functional usability, our proposed DeepLens Classification and Detection Model (DCDM) addresses such limitations. Scalability and ubiquitous access to our approach is provided by cloud integration. Our experiments on an extensive image data set of healthy and unhealthy fruit trees and vegetable plant leaves showed 98.78% accuracy with a real-time diagnosis of diseases of plant leaves. To train DCDM deep learning model, we used forty thousand images and then evaluated it on ten thousand images. It takes an average of 0.349s to test an image for disease diagnosis and classification using AWS DeepLens, providing the consumer with disease information in less than a second.

Why it matches plant phenotyping methods植物葉の病害状態を画像から自動推定する深層学習・クラウド実装を開発・評価しており、植物フェノタイピング手法が中心です。

abstractAutomated identification and classification of plant leaf diseases is, therefore, essential

Assessing the Performance of RGB-D Sensors for 3D Fruit Crop Canopy Characterization under Different Operating and Lighting Conditions →

The use of 3D sensors combined with appropriate data processing and analysis has provided tools to optimise agricultural management through the application of precision agriculture. The recent development of low-cost RGB-Depth cameras has presented an opportunity to introduce 3D sensors into the agricultural community. However, due to the sensitivity of these sensors to highly illuminated environments, it is necessary to know under which conditions RGB-D sensors are capable of operating. This work presents a methodology to evaluate the performance of RGB-D sensors under different lighting and distance conditions, considering both geometrical and spectral (colour and NIR) features. The methodology was applied to evaluate the performance of the Microsoft Kinect v2 sensor in an apple orchard. The results show that sensor resolution and precision decreased significantly under middle to high ambient illuminance (>2000 lx). However, this effect was minimised when measurements were conducted closer to the target. In contrast, illuminance levels below 50 lx affected the quality of colour data and may require the use of artificial lighting. The methodology was useful for characterizing sensor performance throughout the full range of ambient conditions in commercial orchards. Although Kinect v2 was originally developed for indoor conditions, it performed well under a range of outdoor conditions.

Why it matches plant phenotyping methodsRGB-Dセンサーの性能を、果樹キャノピーの3D形状・色・NIR特徴の取得という植物フェノタイピング用途で、照明・距離条件下で評価する方法論が中心である。

abstractThis work presents a methodology to evaluate the performance of RGB-D sensors under different lighting and distance conditions, considering both geometrical and spectral (colour and NIR) features.

Maturity Prediction in Yellow Peach ( Prunus persica L.) Cultivars Using a Fluorescence Spectrometer. →

Technology for rapid, non-invasive and accurate determination of fruit maturity is increasingly sought after in horticultural industries. This study investigated the ability to predict fruit maturity of yellow peach cultivars using a prototype non-destructive fluorescence spectrometer. Collected spectra were analysed to predict flesh firmness (FF), soluble solids concentration (SSC), index of absorbance difference (I AD ), skin and flesh colour attributes (i.e., a* and H°) and maturity classes (immature, harvest-ready and mature) in four yellow peach cultivars-'August Flame', 'O'Henry', 'Redhaven' and 'September Sun'. The cultivars provided a diverse range of maturity indices. The fluorescence spectrometer consistently predicted I AD and skin colour in all the cultivars under study with high accuracy (Lin's concordance correlation coefficient > 0.85), whereas flesh colour's estimation was always accurate apart from 'Redhaven'. Except for 'September Sun', good prediction of FF and SSC was observed. Fruit maturity classes were reliably predicted with a high likelihood ( F1 -score = 0.85) when samples from the four cultivars were pooled together. Further studies are needed to assess the performance of the fluorescence spectrometer on other fruit crops. Work is underway to develop a handheld version of the fluorescence spectrometer to improve the utility and adoption by fruit growers, packhouses and supply chain managers.

Why it matches plant phenotyping methods蛍光分光計を用いてモモ果実の成熟度や品質関連形質を非破壊推定し、複数品種で精度評価しているため、植物フェノタイピング手法が中心です。

abstractusing a prototype non-destructive fluorescence spectrometer

High-Throughput Phenotyping of Morphological Seed and Fruit Characteristics Using X-Ray Computed Tomography. →

Traditional seed and fruit phenotyping are mainly accomplished by manual measurement or extraction of morphological properties from two-dimensional images. These methods are not only in low-throughput but also unable to collect their three-dimensional (3D) characteristics and internal morphology. X-ray computed tomography (CT) scanning, which provides a convenient means of non-destructively recording the external and internal 3D structures of seeds and fruits, offers a potential to overcome these limitations. However, the current CT equipment cannot be adopted to scan seeds and fruits with high throughput. And there is no specialized software for automatic extraction of phenotypes from CT images. Here, we introduced a high-throughput image acquisition approach by mounting a specially-designed seed-fruit container onto the scanning bed. The corresponding 3D image analysis software, 3DPheno-Seed&Fruit, was created for automatic segmentation and rapid quantification of eight morphological phenotypes of internal and external compartments of seeds and fruits. 3DPheno-Seed&Fruit is a graphical user interface designed and user-friendly software with an excellent phenotype result visualization function. We described the software in detail and benchmarked it based upon CT image analyses in seeds of soybean, wheat, peanut, pine nut, pistacia nut and dwarf Russian almond fruit. R2 values between the extracted and manual measurements of seed length, width, thickness, and radius ranged from 0.80 to 0.96 for soybean and wheat. High correlations were found between the 2D (length, width, thickness, and radius) and 3D (volume and surface area) phenotypes for soybean. Overall, our methods provide robust and novel tools for phenotyping the morphological seed and fruit traits of various plant species, which could benefit crop breeding and functional genomics.

Why it matches plant phenotyping methodsCT画像取得法と3D解析ソフトウェアを開発し、種子・果実形態形質の自動抽出をベンチマークしており、フェノタイピング手法が中心である。

abstractHere, we introduced a high-throughput image acquisition approach by mounting a specially-designed seed-fruit container onto the scanning bed.

Automatic fruit morphology phenome and genetic analysis: An application in the octoploid strawberry →

ABSTRACT Automatizing phenotype measurement is needed to increase plant breeding efficiency. Morphological traits are relevant in many fruit breeding programs, as appearance influences consumer preference. Often, these traits are manually or semi-automatically obtained. Yet, fruit morphology evaluation can be boosted by resorting to fully automatized procedures and digital images provide a cost-effective opportunity for this purpose. Here, we present an automatized pipeline for comprehensive phenomic and genetic analysis of morphology traits extracted from internal and external strawberry images. The pipeline segments, classifies and labels the images, extracts conformation features, including linear (area, perimeter, height, width, circularity, shape descriptor, ratio between height and width) and multivariate (Fourier Elliptical components and Generalized Procrustes) statistics. Internal color patterns are obtained using an autoencoder to smooth out the image. In addition, we develop a variational autoencoder to automatically detect the most likely number of underlying shapes. Bayesian modeling is employed to estimate both additive and dominant effects for all traits. As expected, conformational traits are clearly heritable. Interestingly, dominance variance is higher than the additive component for most of the traits. Overall, we show that fruit shape and color can be quickly and automatically evaluated and is moderately heritable. Although we study the strawberry species, the algorithm can be applied to other fruits, as shown in the GitHub repository https://github.com/lauzingaretti/DeepAFS .

Why it matches plant phenotyping methodsイチゴ果実の画像から形態・色彩形質を自動抽出するパイプラインの開発が研究の中心であり、遺伝解析はその応用である。

abstractHere, we present an automatized pipeline for comprehensive phenomic and genetic analysis of morphology traits extracted from internal and external strawberry images.

Image-based Phenotyping Identifies Quantitative Trait Loci for Cluster Compactness in Grape →