Plant phenotyping methods.

WheatScoper: A lightweight organ-based framework for multi-view wheat phenotyping using time-series RGB images ↗

Accurate and dynamic monitoring of wheat phenotypes is essential for breeding decision-making and crop management. However, RGB image-based phenotyping still suffers from expensive pixel-level annotation, unstable organ-level segmentation across growth stages, and limited multi-trait extraction under complex field conditions. To address these issues, a high-throughput phenotyping framework (WheatScoper) was proposed, enabling organ-level segmentation and plot-level multi-trait extraction. To reduce annotation cost, a structure-aware geometry-assisted annotation (SAGA) algorithm was developed, yielding an approximately 7.6-fold improvement in annotation efficiency over fully manual annotation. To enable efficient organ-level segmentation, a lightweight semantic segmentation network (WheatScopeNet) was developed by integrating parallel hybrid spatial modeling with cross-scale feature fusion. On the held-out test set from the same site and growing season, WheatScopeNet achieved an mIoU of 0.869 and an mDice of 0.930. Leveraging the segmentation results, an automated system was established to extract 41 multi-view image-derived traits (I-traits) across four core phenotypic dimensions. The extracted I-traits supported the estimation of eight manually measured agronomic traits, with R 2 values ranging from 0.477 to 0.697. Notably, the correlations between stay-green-related-traits and yield varied distinctly with viewing-position. Only upper side-view indicators remained significantly correlated with yield, with Side-up final GPAR showing the strongest association, whereas top-view GPAR-derived indicators showed weak associations. Finally, a web-based platform integrating cascaded inference, segmentation visualization, and automatic I-trait extraction was developed. The platform provides an end-to-end solution for field wheat phenotyping and supports breeding decision-making and crop management.

Why it matches plant phenotyping methodsRGB画像から小器官を分割し、多数の植物形質を自動抽出・推定する手法とプラットフォームが研究の中心であるため、植物フェノタイピング手法として明確に採用。

abstracta high-throughput phenotyping framework (WheatScoper) was proposed, enabling organ-level segmentation and plot-level multi-trait extraction.

A C-repeat binding factor-salicylic acid (CBF-SA) module links wound-induced evaporative cooling to tissue repair in plants. ↗

Repairing damaged tissues is essential for the survival of all organisms. In plants, tissue injury rapidly triggers defense and repair programs. However, the molecular mechanisms linking early injury cues to the later stage of wound repair remain unclear. Here, we show that wounding of Arabidopsis leaves induces localized low temperature at the injury site, likely caused by evaporative cooling, which is accompanied by an activation of cold-responsive genes. Using thermal imaging combined with computer vision and deep learning, we developed a workflow to monitor the dynamics of wound healing in a quantitative, non-invasive, and real-time manner. Mechanistically, we show that C-repeat Binding Factor (CBF) transcription factors are required for the activation of the injury-associated cold response and downstream salicylic acid (SA) signaling. Our findings suggest that the CBF-SA pathway acts coordinately to promote lignin and callose deposition, thereby facilitating wound repair. Together, these findings reveal a link between a wound-induced biophysical cue and the tissue repair program.

Why it matches plant phenotyping methods熱画像とコンピュータビジョン・深層学習を組み合わせ、植物の創傷治癒を定量的・非侵襲的・リアルタイムに測定するワークフローを開発しており、表現型取得法が研究の中心である。

abstractUsing thermal imaging combined with computer vision and deep learning, we developed a workflow to monitor the dynamics of wound healing in a quantitative, non-invasive, and real-time manner.

Wheat biomass estimation across crop development using UAV LiDAR structure–intensity fusion alongside multispectral and thermal data ↗

This study systematically evaluated the contribution of UAV LiDAR structural features such as crop height (CH) and multi-layer gap fraction (GF) and the amplitude of the returning signal represented by normalized intensity (INT), together with multispectral (MS) and thermal infrared (TIR) observations for aboveground biomass (AGB) estimation in winter wheat using a common artificial neural network (ANN) framework. Among the evaluated single sensor approaches, LiDAR features consistently provided the strongest performance, demonstrating the complementary value of crop height, vertically distributed canopy density, and normalized LiDAR intensity for characterizing canopy structure and within-canopy variability. Multi-layer GF improved AGB estimation relative to conventional ground-based GF approaches, highlighting the importance of incorporating the vertical distribution of canopy density. Multi-sensor fusion produced only modest additional improvements, indicating limited benefits relative to the increased acquisition and processing requirements. Temporal analysis showed that structural LiDAR features were most informative during early crop development, whereas normalized intensity, spectral reflectance, and thermal observations became increasingly valuable during canopy maturation and senescence. Comparisons with destructively measured plant area index (PAI), leaf area index (LAI), green leaf area index (GLAI), and green fraction of LAI further demonstrated that normalized LiDAR intensity (903 nm) was more closely associated with green canopy components than purely structural LiDAR metrics. Overall, the results demonstrate that fully exploiting both the structural and spectral information contained within LiDAR observations can substantially improve UAV-based biomass estimation, while multispectral and thermal observations provide complementary information whose contribution varies with crop development and monitoring objectives.

Why it matches plant phenotyping methodsUAV LiDAR・マルチスペクトル・熱画像とANNを用いた小麦バイオマス推定手法を系統的に比較・評価しており、植物形質推定の取得・解析方法が研究の中心である。

abstractThis study systematically evaluated the contribution of UAV LiDAR structural features such as crop height (CH) and multi-layer gap fraction (GF) and the amplitude of the returning signal represented by normalized intensity (INT), together with multispectral (MS) and thermal infrared (TIR) observations for aboveground biomass (AGB) estimation in winter wheat using a common artificial neural network (ANN) framework.

Continuous monitoring of deficit irrigation in avocado across two contrasting rainfall years using sensor networks, telemetry, and machine learning ↗

Water scarcity and increasingly irregular rainfall threaten avocado production in Mediterranean regions, yet the long term physiological responses of mature trees to sustained deficit irrigation remain poorly understood. We conducted a two-year field study integrating continuous monitoring of the soil plant atmosphere continuum, drone-based multispectral imaging, canopy structural analysis, and fruit phenotyping in a mature avocado orchard subjected to three irrigation regimes. The two study years differed markedly in rainfall, providing a unique opportunity to evaluate how environmental conditions modulate tree responses to water limitation. Trees under severe deficit irrigation showed depletion of water in deeper soil layers and a flattened physiological profile, with near-zero diel variation in leaf thickness and trunk water potential, indicating minimal transpiration and decoupling of tree water status from environmental demand. Drone telemetry via NDVI detected stress during fruit growth and maturation, but not during flowering or the new summer leaf flush, revealing greater drought sensitivity at later maturation stages. Although canopy area did not differ among irrigation treatments, canopy surface roughness increased significantly under deficit irrigation, thereby identifying a novel structural indicator of drought stress. Despite large physiological differences among treatments, fruit number remained stable, while fruit weight decreased significantly under severe deficit irrigation, particularly in the wetter year, suggesting that annual rainfall modulates the trade-off between fruit retention and fruit growth. This study provides the first continuous, multi-scale characterization of avocado performance under sustained deficit irrigation in Mediterranean conditions. By integrating plant-based sensors, remote sensing, and artificial intelligence, we reveal previously undescribed stress dynamics and identify new indicators for precision irrigation management in fruit crops.

Why it matches plant phenotyping methods継続的な植物センサー、ドローン画像、樹冠構造解析、果実表現型計測を統合し、NDVIや樹冠表面粗さなどのストレス指標を抽出する方法が研究の主要部分であるため。

abstractWe conducted a two-year field study integrating continuous monitoring of the soil plant atmosphere continuum, drone-based multispectral imaging, canopy structural analysis, and fruit phenotyping

Multiplexed Nanosensors for Real-Time Monitoring of VOC-Mediated Signalling Response in Plants. ↗

To enhance crop performance, intercropping strategies leverage volatile organic compound (VOC)-driven interactions with companion plants that constitutively emit VOCs. Despite the agricultural importance, the mechanisms and kinetics of VOC-mediated sensory transduction in receiver plants eavesdropping on neighbouring non-kin emitters remain largely unknown due to a lack of appropriate non-destructive analytical tools. In this work, we employ multiplexed salicylic acid (SA) and H 2 O 2 nanosensors in Brassica rapa subsp. Chinensis (pak choy) plants to visualize, in real time, reactive oxygen species (ROS) and SA signal transduction following exposure to constitutively-released VOCs from neighbouring aromatic plants-namely sweet basil and spearmint. Unique emitter-specific temporal signatures of ROS and SA were observed in receiver pak choy: sweet basil VOCs induced concomitant generation of ROS and SA at 30 min, whereas spearmint VOCs triggered SA production at 30 min, followed by ROS accumulation. The temporal data enabled the formulation of a diffusion model that quantifies the VOC perception threshold that triggers the distinct early ROS and SA signalling. Transcriptomics analysis at 2 h revealed that both emitters evoke largely distinct changes in pak choy, likely stemming from variations in speed and sequence of the early signal transduction, leading to different phenotypic outcomes. Intercropping with sweet basil led to enhanced pak choy biomass, stress resilience and secondary metabolite accumulation, whereas spearmint as companions had a limited impact. Our study captures in real time, the VOC-induced rapid signalling in receiver plants and its ensuing effect on growth. These nanosensor-enabled findings represent an important advance in deciphering how emitter-specific volatile cues are integrated into plant responses, guiding rational selection of beneficial companion plants for improved yield and nutritional profiles in sustainable agriculture.

Why it matches plant phenotyping methods植物内のROSとSAシグナルをリアルタイム可視化する多重化ナノセンサーが研究の中心であり、植物の生理状態・応答を測定する方法として適用されている。

abstractdue to a lack of appropriate non-destructive analytical tools. In this work, we employ multiplexed salicylic acid (SA) and H 2 O 2 nanosensors in Brassica rapa subsp. Chinensis (pak choy) plants to visualize, in real time, reactive oxygen species (ROS) and SA signal transduction

Yield-graph: multi-stage growth-aware maize yield prediction via graph neural networks. ↗

Key message Yield-Graph enables accurate maize yield prediction from incomplete multi-stage phenotypic and environmental data by modeling higher-order environment-trait interactions, with robust applicability across growth stages, regions, and crop species. Accurate yield prediction before maize harvest is crucial for advancing agricultural management and ensuring food security. Unlike conventional approaches that rely on traits from a single growth stage, this study models multiple traits across different developmental stages, all targeting final yield, thereby uncovering their stage-specific contributions and demonstrating the feasibility of early yield prediction. We introduce Yield-Graph, an innovative framework that evaluates phenotypic data at distinct developmental stages for yield prediction. The method employs a bipartite graph structure to impute missing trait values at each stage and leverages a hypergraph attention mechanism to capture high-order sample relationships. Comprehensive benchmark experiments demonstrate that Yield-Graph matches the top-tier predictive accuracy of exhaustively optimized tree models. Moreover, the framework exhibits strong robustness across growth stages, high adaptability to regional variations, and effective generalization across datasets. These findings highlight the potential of graph-enhanced multi-stage modeling for early-stage yield prediction, offering a scalable solution for precision agriculture and intelligent crop management.

Why it matches plant phenotyping methods作物収量という植物形質を、複数時期の表現型データから推定するグラフニューラルネットワーク手法を開発し、ベンチマーク評価しているため、計算型フェノタイピング手法が中心である。

abstractWe introduce Yield-Graph, an innovative framework that evaluates phenotypic data at distinct developmental stages for yield prediction.

Destructive harvest validation of high-throughput measurements show that water use efficiency is unaffected by moderate drought in tobacco ↗

ABSTRACT Water-use efficiency (WUE), the ratio of accumulated plant biomass to water lost through transpiration has conventionally been determined using a destructive single-point measurement. Recent advances in high-throughput phenotyping now enable repeated, non-destructive estimation of biomass and WUE. However, these digital measurements must be statistically validated against conventional destructive methods to validate their use as reliable proxies. Therefore, we compared digital biomass determined point clouds produced from multispectral camera scanners with destructive harvests across eight harvests using Samsun tobacco grown under both drought and high-water conditions. WUE efficiency, calculated using the digital biomass estimated from a point cloud and gravimetric water use determinations, were compared to destructive harvest determinations. The coefficient of variation (CV) showed there were no significant differences in digital and destructive measurements for either biomass or WUE. Indicating that digital measurements can be used in place of destructive measurements. Drought plants used significantly less water and were significantly smaller than high-water plants from Harvests 4 through 8. However, there were no significant differences in the ratio of evapotranspiration to leaf area or WUE, indicating that drought plants were simply smaller and used less water than the high-water plants. This work validates that estimating plant biomass from a digital point coupled with continuous gravimetric determination of water use provides a reliable nondestructive measure of WUE in high-throughput measurements across the full plant life cycle. PLAIN LANGUAGE SUMMARY We grew tobacco plants under either a drought or high-water treatment and harvested a portion of the plants every few days for a total of eight harvests. Throughout the experiment, we collected 3D images of the plants and continuously measured pot weight to track plant growth and water use across different developmental stages. Destructive biomass served as the gold-standard measurement. We then compared biomass and water-use estimates generated from the digital measurements with the destructive measurements. The digital approach provided accurate estimates of plant biomass and water use while requiring little hands-on labor and no plant destruction. These nondestructive methods could help plant breeders identify water-efficient plants earlier in the breeding process, accelerating the development of crops that use water more efficiently.

Why it matches plant phenotyping methods3D画像による非破壊バイオマス推定と連続的な重量測定からWUEを推定する手法を、破壊収穫と比較して検証しており、植物表現型取得法が中心である。

abstractRecent advances in high-throughput phenotyping now enable repeated, non-destructive estimation of biomass and WUE. However, these digital measurements must be statistically validated against conventional destructive methods to validate their use as reliable proxies.

DualSlim-YOLO: A Lightweight Detection Model Based on Unmanned Aerial Vehicle Imagery for Cauliflower Seedling Identification and Growth Assessment ↗

Cauliflower emergence rate and seedling growth are key indicators of field conditions and varietal potential. Traditional manual surveys are unsuitable for continuous monitoring across multiple varieties. This study integrates UAV RGB imagery with the DualSlim-YOLO model to estimate cauliflower emergence rates and monitor seedling growth. Built on YOLOv11, the model incorporates a lightweight feature extraction structure and an optimized detection-scale configuration. It reduces computational complexity while maintaining detection accuracy, thereby improving the efficiency of cauliflower seedling detection. DualSlim-YOLO achieved P, R, F1-score, mAP@0.5, and mAP@0.5:0.95 of 95.35%, 96.75%, 96.05%, 98.55%, and 86.65%, respectively. The number of parameters was reduced by 38.61%, while the inference speed increased by 22.16%, demonstrating good lightweight performance. Based on this model, UAV images of 171 cauliflower varieties acquired at 7, 21, and 28 d after transplanting were used for seedling detection and emergence rate estimation. In addition, 18 time-series seedling phenotypic traits were extracted, enabling a comprehensive quantitative evaluation of emergence dynamics and early-growth performance across multiple cauliflower varieties. This method effectively screens cauliflower varieties for high emergence rates, rapid emergence, and excellent seedling growth performance. It provides technical support for high-throughput, nondestructive seedling phenotyping and early germplasm screening under field conditions.

Why it matches plant phenotyping methodsUAV画像と軽量YOLOモデルを用いて、カリフラワー苗の検出、出芽率推定、18種類の時系列表現型形質抽出を行う手法が中心であり、モデル性能も検証している。

abstractThis study integrates UAV RGB imagery with the DualSlim-YOLO model to estimate cauliflower emergence rates and monitor seedling growth.

PhenoStream: A Cyberinfrastructure for Automated and AI-Based Crop Trait Extraction from Aerial Imagery ↗

Abstract The integration of digital technologies for high-throughput field phenotyping is critical for accelerating crop improvement in agriculture. However, extracting traits from remote sensing data remains constrained by fragmented workflows, manual intervention, and limited interoperability among existing tools, resulting in delays that hinder timely biological insight and decision-making. To address these challenges, we present PhenoStream (Phenotyping Streaming), a scalable, end-to-end cyberinfrastructure designed to automate the full lifecycle of aerial imagery–based phenotyping, from data acquisition to plot-and genotype-level inference. The framework integrates automated data ingestion from distributed field sites, geospatial processing, and AI-enabled trait extraction within a unified, user-accessible graphical interface. Its modular and extensible architecture supports adaptable trait modeling and seamless integration of new data sources, enabling deployment across diverse crops, environments, and experimental designs. We demonstrate the system across a large multi-location field trial network of bioenergy crops, where it enables high-throughput characterization of spatiotemporal growth dynamics, genotype-by-environment (G×E) interactions, and predictive modeling of key agronomic traits. By significantly reducing processing latency and manual effort, the platform facilitates near-real-time analysis and reproducible workflows. This work establishes a generalizable and scalable pathway for operationalizing very-high-spatial resolution aerial phenotyping in agricultural research. By bridging data acquisition and analytics, the end-to-end cyberinfrastructure provides a foundation for integrating heterogeneous and unstructured data streams—including remote sensing, environmental, and management data—toward data-driven decision making in agriculture.

Why it matches plant phenotyping methods航空画像から作物形質を自動抽出するエンドツーエンドのフェノタイピング基盤を開発・実証しており、形質取得と解析ワークフローが研究の中心です。

abstracta scalable, end-to-end cyberinfrastructure designed to automate the full lifecycle of aerial imagery–based phenotyping, from data acquisition to plot-and genotype-level inference.

PhenoStream: a cyberinfrastructure for automated and AI-based crop trait extraction from aerial imagery. ↗

Abstract The integration of digital technologies for high-throughput field phenotyping is critical for accelerating crop improvement in agriculture. However, extracting traits from remote sensing data remains constrained by fragmented workflows, manual intervention, and limited interoperability among existing tools, resulting in delays that hinder timely biological insight and decision-making. To address these challenges, we present PhenoStream (Phenotyping Streaming), a scalable, end-to-end cyberinfrastructure designed to automate the full lifecycle of aerial imagery-based phenotyping, from data acquisition to plot- and genotype-level inference. The framework integrates automated data ingestion from distributed field sites, geospatial processing, and AI-enabled trait extraction within a unified, user-accessible graphical interface. Its modular and extensible architecture supports adaptable trait modeling and seamless integration of new data sources, enabling deployment across diverse crops, environments, and experimental designs. We demonstrate the system across a large multi-location field trial network of bioenergy crops, where it enables high-throughput characterization of spatiotemporal growth dynamics, genotype-by-environment (G×E) interactions, and predictive modeling of key agronomic traits. By significantly reducing processing latency and manual effort, the platform facilitates near-real-time analysis and reproducible workflows. This work establishes a generalizable and scalable pathway for operationalizing very-high-spatial resolution aerial phenotyping in agricultural research. By bridging data acquisition and analytics, the end-to-end cyberinfrastructure provides a foundation for integrating heterogeneous and unstructured data streams-including remote sensing, environmental, and management data - toward data-driven decision making in agriculture.

Why it matches plant phenotyping methods植物の航空画像から形質を自動抽出するエンドツーエンドのフェノタイピング基盤を開発・実証しており、形質取得ワークフローとプラットフォームが研究の中心である。

abstracta scalable, end-to-end cyberinfrastructure designed to automate the full lifecycle of aerial imagery-based phenotyping, from data acquisition to plot- and genotype-level inference.

Application of Remote Sensing Technologies in Crop Health Monitoring and Disease Surveillance ↗

The rapid detection and continuous monitoring of crop health and disease outbreaks are critical components of modern precision agriculture, essential for maintaining global food security. Traditional field-based scouting methods, while accurate, are often labor-intensive, time-consuming, and limited by spatial coverage, making them inadequate for large-scale agricultural operations. Remote sensing (RS) technologies—spanning satellite imagery, drone-based aerial platforms, and proximal sensors—offer a powerful, non-destructive, and scalable alternative for capturing high-resolution spectral and temporal data. This paper provides a comprehensive evaluation of current remote sensing applications in crop health monitoring and disease surveillance. We analyze how vegetation indices derived from multispectral and hyperspectral data, such as NDVI and red-edge parameters, serve as sensitive indicators of physiological stress and pathogen infection, often manifesting before visible symptoms appear. Furthermore, we explore the integration of machine learning and artificial intelligence algorithms in automating disease identification and severity mapping. By synthesizing recent advancements in sensor technology and data analytics, this paper demonstrates that remote sensing is indispensable for proactive, site-specific management. The findings emphasize that a multi-scale RS approach—integrating broad-scale satellite monitoring with high-resolution drone sorties—enables farmers to optimize input efficiency, minimize yield losses, and enhance the overall resilience of agro-ecosystems against biotic and abiotic stressors.

Why it matches plant phenotyping methods作物の健康・病害を対象に、リモートセンシング、センサー、植生指数、機械学習による状態・重症度推定を包括的に評価するレビューであり、フェノタイピング手法が中心です。

abstractThis paper provides a comprehensive evaluation of current remote sensing applications in crop health monitoring and disease surveillance.

IoT and Machine Learning for Crop Stress Assessment and Decision Support ↗

Precision agriculture increasingly requires intelligent systems capable of integrating multimodal sensing with transparent decision support to enable timely and reliable crop management. This study proposes a hybrid intelligent IoT framework integrating environmental monitoring, wearable plant physiological sensing, AI-based pest-monitoring, machine-learning-based prediction of crop physiological stress, and explainable fuzzy rule-based decision support into a unified architecture for crop stress assessment. A novel Physiological Stress Index (PSI) was developed by combining vapor pressure deficit, relative humidity, Delta-T, leaf capacitance, and relative irradiance to provide an interpretable indicator of crop physiological stress. The proposed framework was experimentally validated under real field conditions using a commercial environmental monitoring station, wearable leaf sensors, AI-enabled pest-monitoring devices, and cloud-based analytics. Correlation analysis confirmed strong relationships between PSI and the principal environmental variables (VPD: r = 0.980, Delta-T: r = 0.990, RH: r = −0.961), demonstrating the internal consistency and sensitivity of the proposed index. At the 15 min forecasting horizon, Linear Regression and Gradient Boosting demonstrated virtually identical performance: Gradient Boosting achieved a marginally lower RMSE and higher R2 (RMSE = 0.0273; R2 = 0.9810), whereas Linear Regression achieved a slightly lower MAE (MAE = 0.0186). At the 1 h forecasting horizon, Gradient Boosting achieved the strongest performance (R2 = 0.9034), indicating increasing relevance of nonlinear modelling at longer prediction horizons. The proposed framework demonstrates the feasibility of combining multimodal sensing, machine learning, explainable artificial intelligence, and edge-enabled IoT technologies to support proactive, transparent, and intelligent precision agriculture.

Why it matches plant phenotyping methods植物の生理的ストレス状態を多モーダルセンサーと機械学習で推定する方法を開発し、圃場で検証しており、フェノタイピング手法が中心である。

abstracta hybrid intelligent IoT framework integrating environmental monitoring, wearable plant physiological sensing, AI-based pest-monitoring, machine-learning-based prediction of crop physiological stress

Phenology-adaptive machine learning for early mapping of field-scale corn crop yield using fusion of Sentinel-2 satellite spectral imagery, and weather-based accumulated heat units ↗

Abstract Purpose Timely, accurate, and field-scale crop yield mapping is essential for precision crop management, yet most existing studies rely on late- or full-season data, limiting in-season decision-making. This study aims to develop a stage-aware earliest possible corn yield mapping framework that balances early data availability, predictive accuracy, and spatial fidelity by integrating Sentinel-2 imagery, vegetation indices (VIs), and accumulated growing degree days (AGDD). Methods Corn yield data were collected from a commercial farm over three growing seasons (2018–2020). The final modeling dataset included 51,794 Sentinel-2 10 m aggregated yield samples across three seasons: 2018 ( n = 16400), 2019 ( n = 18534), and 2020 ( n = 16860). Sentinel-2 raw spectral bands and derived VIs were organized for V4, V6, R1, R5, and R6 growth stages based on AGDD- and DAP-defined corn growth-stage windows, also confirmed visually on-ground, allowing observations from different planting and harvest dates across the three growing seasons to be aligned by crop developmental stage rather than calendar date. A stage-wise Pearson correlation and frequency-based selection identified informative and non-redundant VI subsets across crop development. Four machine learning models: Random Forest (RF), XGBoost (XGB), k-Nearest Neighbors (kNN), and a Neural Network (NNET; multi-layer perceptron) were trained using 13 input configurations, including individual growth stages and multi-stage combinations capturing phenological progression. Models were tuned via randomized search, trained on 2018–2019 data, and independently validated on the 2020 season. Yield predictions were mapped directly at 10 m Sentinel-2-pixel resolution without spatial interpolation to preserve fine-scale variability. Results Model performance was strongly influenced by phenological stage selection. Among single-stage inputs, R1 was the earliest stage where reliable yield mapping could be availed (RF: R² = 0.56, RMSE = 29.50%). While combining V6 with R1 stage inputs substantially improved predictive performance (RF: R² = 0.70, RMSE = 24.13%) for the yield mapping at the R1 stage, where V6-stage signals provided complementary yield-related information. The full-season combination (V4 + V6 + R1 + R5 + R6) produced the highest accuracy (RF: R² = 0.72, RMSE = 23.28%) but would be less suitable for early in-season decision-making. Early- or late-stage-only inputs (V4, R5, R6) showed weaker and less stable cross-year performance. Among algorithms, RF consistently generalized best to the independent 2020 dataset and is recommended for operational use. XGB showed strong training performance but reduced cross-year stability, kNN yielded moderate accuracy, and NNET achieved accuracy comparable to RF while closely reproducing observed spatial patterns such as center-pivot effects and edge gradients. Direct 10 m mapping preserved yield heterogeneity and avoided smoothing artifacts common in interpolation-based approaches. Conclusion Stage-aware feature selection and phenology-informed input combinations are critical for balancing yield prediction timeliness and accuracy. For operational in-season yield mapping, the RF model using the V6 + R1 stage combination provides a practical and reliable solution, enabling early, accurate, and spatially detailed yield estimates with robust cross-year performance. This study presents a deployable framework for integrating satellite time series and weather data into conventional (non-sequential) machine learning models to support proactive, within-season decision-making in precision agriculture.

Why it matches plant phenotyping methods衛星画像・気象データと機械学習を統合し、作物の収量という明示的な植物形質を圃場内10 m解像度で推定する手法を開発・独立年で検証しており、フェノタイピング手法が中心である。

abstractThis study aims to develop a stage-aware earliest possible corn yield mapping framework that balances early data availability, predictive accuracy, and spatial fidelity by integrating Sentinel-2 imagery, vegetation indices (VIs), and accumulated growing degree days (AGDD).

Long-term monitoring of winter wheat phenology using a 30 m Landsat framework integrating curve reconstruction and machine learning in northern Henan and southern Xinjiang ↗

Accurate long-term monitoring of winter wheat phenology is important for crop growth assessment and irrigation management, but 30 m Landsat-based phenology retrieval remains challenging because of sparse observations, cloud contamination and sensor differences. This study developed and evaluated an integrated Landsat-based workflow for monitoring winter wheat phenology in the People’s Victory Canal (PVC) Irrigation Area of northern Henan and the Alar Irrigation Area of southern Xinjiang from 2000 to 2024. Winter wheat areas were mapped using temporally stacked NDVI/EVI features and a CART classifier. Vegetation-index trajectories were reconstructed using locally adjusted cubic-spline capping combined with Savitzky–Golay filtering, and green-up, jointing, heading and maturity were extracted using threshold- and derivative-based detection. The CART-based mapping achieved an overall accuracy of 89.51%, with higher accuracy in Alar (91.45%) than in PVC (84.35%). Compared with S-G-only, Whittaker and TIMESAT-like approaches, LACC + S-G reduced phenological-date errors, especially for green-up and maturity, with RMSE values within 3.1 d against agro-meteorological observations. Phenological stages generally occurred later in Alar than in PVC, and spatial autocorrelation confirmed significant clustering. Agro-meteorological analysis suggested stronger thermal associations in PVC and stronger moisture-related associations in Alar. These results provide practical 30 m phenological information for regional winter wheat monitoring and irrigation scheduling analysis.

Why it matches plant phenotyping methodsLandsat時系列から冬コムギの生育ステージを抽出するワークフローを開発し、複数手法との比較および農業気象観測による精度検証を行っており、植物フェノタイピング手法が研究の中心である。

abstractThis study developed and evaluated an integrated Landsat-based workflow for monitoring winter wheat phenology

Temporal profiling of floret developmental asynchrony for wheat-fertility studies. ↗

Wheat grain number integrates fate of individual florets, strongly affected by environmental stress during sensitive stages like meiosis. Because development is asynchronous across tillers, spikelets, and florets, it is hard to distinguish stress tolerance from stress escape. Based on 2400 destructive measurements of spike and anther length together with non-destructive morphological measurements from 158 plants grown in four experiments in controlled-environment, we developed a framework to track individual floret developmental stages at plant level. We applied it in two case studies for connecting within-plant developmental asynchrony to reproductive success under favorable or heat conditions. All florets showed a common relative growth rate, producing additive delays across tillers (1-7 d), spikelets (1-5 d), and floret positions (1-6 d). This generated a developmental map for every floret based on external traits. Under control conditions, grain set probability at floret level combined both positional and developmental effects within a spike. Under heat stress, grain loss occurred only in florets at meiosis during the stress, allowing to quantify a true "stress response", while later florets escaped damage. This framework allows understanding and predicting floret development and linking it to grain set, clearly distinguishing timing effects from positional influences and separating tolerance from stress escape.

Why it matches plant phenotyping methods外部形態測定から個々の小花の発育段階を追跡する方法・発育マップを開発し、複数実験で適用しているため、表現型取得・推定が研究の中心である。

abstractwe developed a framework to track individual floret developmental stages at plant level

Climate change, water quality, and water diversion are associated with the shifts of aquatic vegetation structure and phenology in five temperate regulating lakes of eastern China. ↗

Aquatic plants are vital for lake ecosystem functioning and water-quality stability, yet their community dynamics and phenology rhythms remain insufficiently understood, due to the lack of effective strategies for fine-scale species mapping and phenology extraction. In this study, based on Sentinel-2 MSI imagery, we developed an integrated framework combining machine learning and a priori ecological knowledge to quantify the spatiotemporal changes in aquatic plant distribution, species composition and phenological dynamics for eight dominant species in five regulating lakes along the Eastern Route of the South-to-North Water Diversion Project in China. Results showed that the proposed framework enabled accurate aquatic plant identification, achieving an overall classification accuracy of 96.16% and over 90% accuracy for each species. Since 2016, aquatic vegetation coverage has substantially declined in most lakes, mainly due to the retreat of submerged vegetation. Community structure has shifted from submerged-plant dominance to emergent and floating-leaved dominance in two of them. Phenologically, we found that most aquatic vegetation exhibited a longer growing season, characterized by earlier growth onset (-0.28 days/year) and peak timing (-0.67 days/year) and delayed senescence (0.54 days/year). Correlation analysis indicated that aquatic vegetation dynamics was associated with climate variation, nutrient enrichment, turbidity, and water diversion, with warming and solar radiation likely promoting the growth of some emergent species, while nutrient enrichment and turbidity could be linked with submerged vegetation decline and earlier phenological shifts. Overall, this study provides an effective framework for species-level mapping and phenological monitoring of aquatic vegetation, offering valuable support for the management and conservation of lake ecosystems.

Why it matches plant phenotyping methodsSentinel-2画像と機械学習等を統合した、植物種分布・構成・フェノロジーを抽出する手法を開発し、精度検証と大規模適用を行っているため、植物フェノタイピング手法が中心である。

abstractwe developed an integrated framework combining machine learning and a priori ecological knowledge to quantify the spatiotemporal changes in aquatic plant distribution, species composition and phenological dynamics for eight dominant species in five regulating lakes

Time-Resolved Phenotyping Reveals Heterogeneous Rice Seed Germination Dynamics in Shallow-Water Culture ↗

Germination percentage is an endpoint measure and therefore does not describe when an individual seed begins visible growth or how rapidly its radicle and plumule expand. We developed a time-resolved phenotyping workflow to quantify rice seed germination continuously in shallow-water culture. A single industrial camera moved along a 1 m rail and imaged three culture boxes at 1 h intervals for up to 80 h. The archive comprised 1,062 full-frame images and 6,372 seed-level repeated observations under the six-seed field-of-view configuration. A physical grid maintained seed identity through time and enabled individual regions of interest to be extracted. Whole-seed foregrounds were obtained with a pretrained U 2 -Net, and a masked RGB intensity rule separated newly emerging tissue from the darker hull. For each tracked seed, projected emerging-tissue area and interval growth rate were calculated. Three representative normally germinating seeds first showed measurable tissue at 48 h, yet subsequently followed distinct trajectories: final projected areas ranged from 2,605 to 4,700 pixels and peak interval growth rates ranged from 106.88 to 287.92 pixels h −1 . B-1 accumulated 63.71% of its final visible area during 72–80 h, whereas B-3 accumulated 73.51% during 60–72 h. Thus, seeds with the same observed emergence interval can differ substantially in the timing and magnitude of post-emergence expansion. The workflow converts repeated images into biologically interpretable temporal phenotypes and provides a basis for nondestructive studies of rice seed vigor and germination heterogeneity.

Why it matches plant phenotyping methods連続画像から個々のイネ種子の発芽・組織面積・成長速度を抽出する時間分解フェノタイピングワークフローを開発しており、表現型取得と解析手法が研究の中心である。

abstractWe developed a time-resolved phenotyping workflow to quantify rice seed germination continuously in shallow-water culture.

Plant electrophysiological responses to drought and their association with live fuel moisture and flammability in Salvia rosmarinus . ↗

Live fuel moisture content is a key determinant of live fuel flammability, yet its destructive and discontinuous measurement limits high-temporal-resolution monitoring. This study evaluated whether leaf electrical potential can serve as a non-invasive proxy for LFMC and flammability-related traits under natural drought conditions. From February to July 2025, leaf and trunk electrical potentials were monitored weekly in Salvia rosmarinus individuals from a Mediterranean shrubland, while LFMC, essential oil yield, fatty-acid fraction, and laboratory-based flammability metrics-ignition time, combustion duration, and flame height-were assessed bi-weekly. Leaf electrical potential was strongly associated with LFMC (R 2 = 0.64, p < 0.001), decreasing as plants underwent seasonal drought-induced dehydration. Periods of high temperature and low rainfall reduced both LFMC and electrical potential, coinciding with shorter ignition times, which declined to approximately 20-30 s during the driest period. Based on the observed shifts in ignition time, combustion duration, and flame height, three empirical LFMC response zones were identified, with leaf electrical potential closely tracking transitions in plant hydration and flammability. These results suggest that plant electrophysiology may provide a promising non-invasive indicator of live fuel water status and seasonal flammability dynamics, with potential applications in wildfire risk monitoring when combined with conventional LFMC, meteorological, and remote-sensing approaches.

Why it matches plant phenotyping methods葉の電気的電位をLFMC（水分状態）および可燃性関連形質の非破壊・連続的な指標として評価しており、植物状態の取得方法の検証が研究の中心である。

abstractThis study evaluated whether leaf electrical potential can serve as a non-invasive proxy for LFMC and flammability-related traits under natural drought conditions.

Remote Sensing and Machine Learning for Monitoring Soil Nitrogen Dynamics and Crop Nitrogen Status in Field Conditions ↗

Efficient nitrogen (N) management is essential for sustaining crop productivity while minimizing environmental impacts associated with nitrogen losses. However, the high spatial and temporal variability of soil nitrogen dynamics and crop nitrogen status makes field-scale monitoring challenging, while conventional soil and plant sampling methods are labor-intensive, destructive, and provide limited spatial coverage. Recent advances in remote sensing technologies and machine learning (ML) offer promising alternatives for high-throughput, non-destructive monitoring of crop nitrogen status and related nitrogen dynamics in agroecosystems. This review synthesizes current progress in the use of proximal and remote sensing platforms, including unmanned aerial vehicles (UAVs), satellites, and ground-based sensors for assessing crop nitrogen status and inferring soil nitrogen availability. We examine spectral, thermal, and structural indicators, together with emerging sensor-fusion and time-series approaches. We also evaluate ML algorithms, including emerging foundation model approaches, for estimating crop nitrogen status and inferring soil nitrogen indicators, highlighting their performance, limitations, and transferability across environments. Particular emphasis is placed on field-scale applications in heterogeneous and water-limited systems, where nitrogen-water interactions critically influence crop responses. Finally, we discuss current challenges, including data scarcity, model generalization, and operational constraints, and outline future directions toward integrated, real-time decision support systems for precision nitrogen management. Overall, this review provides a comprehensive framework for leveraging remote sensing and data-driven approaches to improve nitrogen monitoring and enhance nitrogen use efficiency in diverse cropping systems.

Why it matches plant phenotyping methods作物の窒素状態という植物形質を対象に、リモートセンシングと機械学習による推定手法を体系的にレビューしており、フェノタイピング手法が中心である。

abstractThis review synthesizes current progress in the use of proximal and remote sensing platforms, including unmanned aerial vehicles (UAVs), satellites, and ground-based sensors for assessing crop nitrogen status and inferring soil nitrogen availability.

Dynamic Prediction of Maize Tasseling Stage Based on UAV LiDAR Time-Series Plant Height Growth Curves: A Framework Coupling UAV-CHM-POI ↗

Accurate identification and effective prediction of the maize tasseling stage are of great significance for guiding precision field management and ensuring stable crop yields. Conventional manual observation methods suffer from high labor intensity, poor timeliness, and strong subjectivity. In this study, based on an unmanned aerial vehicle (UAV) remote sensing platform, LiDAR point cloud data and RGB imagery were simultaneously acquired to construct digital surface models (DSMs) and digital terrain models (DTMs). Multi-dimensional statistical features were extracted to establish a high-precision plant height estimation method applicable to the entire growth cycle of maize. On this basis, the Logistic growth curve function was introduced to fit the dynamic changes in plant height, enabling the identification and early prediction of the maize tasseling stage based on the plant height growth curve. The research results indicate the following: (1) For maize plant height estimation, the LiDAR sensor outperforms RGB. The optimal accuracy is achieved by combining the 99th percentile of DSM with the minimum DTM, yielding a root mean square error (RMSE) of 0.17 m. (2) Based on the high-accuracy plant height time series, the point of inflection (POI) achieves the highest accuracy in tasseling stage identification, with an RMSE of 2.586 d under the reconstructed time series. (3) Prediction accuracy of the tasseling stage improves with increasing plant height threshold, and optimal performance is observed when the threshold is ≥1.6 m with a growth rate between 0.11 and 0.13. This study establishes a technical framework of "time-series perception-dynamic simulation-feature identification-early prediction", providing a scientific basis for automated monitoring and precision management of the maize tasseling stage. It holds significant theoretical and practical value for the advancement of smart agriculture and crop phenotyping research.

Why it matches plant phenotyping methodsUAV LiDAR/RGBによる草丈推定と時系列成長曲線から、トウモロコシの抽だい期を識別・予測する技術フレームワークが研究の中心であり、植物形質取得と検証を伴うため採用。

abstractMulti-dimensional statistical features were extracted to establish a high-precision plant height estimation method applicable to the entire growth cycle of maize.

Development and Validation of Minitron III: A System for Continuous Monitoring of Crop Gas Exchange in Controlled Environments ↗

Optimizing environmental inputs for indoor crop production by conducting a traditional endpoint growth analysis requires significant time and resources. The most common scientific approach to assessing crop response involves the accumulation of dry mass at the end of a cropping cycle. A growth dynamics analysis also results in the accurate estimation of the crop response to the growth environment through periodic destructive sampling. Measuring crop gas exchange in the same environment in which it is grown offers a powerful alternative to accelerating the environmental optimization process, especially for vegetative crops. This work introduces Minitron III, a third-generation technology advancement capable of continuous gas-exchange monitoring from seed to harvest for small specialty crop stands. For proof of concept, 24 ‘Rouxai’ red oakleaf lettuce plants were grown from seed to harvest over a 25-day cropping cycle. Instantaneous differences in the carbon dioxide (CO 2 ) and water vapor (H 2 O V ) mole fraction between sample/reference lines flowing through/around cuvette/growth space were measured using a differential infrared gas analyzer, allowing determination of net photosynthesis based on a 0.41-m 2 cropping area. Crop stand net photosynthesis was detectable 7 days after sowing seeds, increasing gradually from 0.13 to 0.60 µmol·m −2 ·s −1 over the following week. The crop net photosynthesis rate increased robustly on a daily basis from 15 days after sowing seeds. While the net photosynthesis rate at the beginning of the photoperiod was 0.68 µmol·m −2 ·s −1 on day 15, it increased to 7.7 µmol·m −2 ·s −1 by day 25 after sowing seeds. Crop dark respiration was detectable from 17 days after sowing seeds and ranged from −0.3 to −0.9 µmol·m −2 ·s −1 . Minitron III has potential for rapid optimization of multiple environmental inputs for indoor production of specialty crops based on the near-real-time crop response to environmental inputs.

Why it matches plant phenotyping methods作物のガス交換を連続測定して光合成・暗呼吸を推定するシステム自体の開発と概念実証が中心であり、植物生理状態のフェノタイピング手法に該当する。

titleDevelopment and Validation of Minitron III: A System for Continuous Monitoring of Crop Gas Exchange in Controlled Environments

Dynamic analysis of canopy coverage traits and their genetic basis in wheat under multiple environments ↗

The extent of canopy coverage (CC) prior to the booting stage is a useful indicator of environmental adaptation and may help anticipate key developmental events such as heading and flowering. We used UAV-based high-throughput phenotyping to monitor CC in a 262-line F 8 recombinant inbred line population grown under four irrigation-year environments across two seasons. To quantify CC dynamics, we fitted regression models using either days after sowing (DAS) or accumulated active temperature (AT). These models showed a high goodness-of-fit (overall coefficient of determination ( R 2 ) > 0.90 across environments; per-timepoint prediction R 2 = 0.60‒0.99 with root mean squared error (RMSE) = 0.00‒0.02) and were used to derive 31 CC-related traits. Principal component analysis (PCA) showed that the first two components explained 80.00% of total variance in CC traits, with PCA1 accounting for 48.88%‒62.51% of the variance for DAS-based traits and 50.26%‒54.93% for AT-based traits. PCA1 reflected early canopy vigor and rapid coverage increase, while PCA2 reflected canopy maintenance after jointing. Genotypes in the top 15% for PCA1 differed significantly in flowering time, heading time, and plant height from those in the bottom 15%. Cross-environment comparisons showed moderate to high consistency of CC traits (average correlation ( r ) = 0.41‒0.65 for DAS-standardized CC of 20‒160 DAS and 0.48‒0.67 for AT-standardized CC of 100‒1000 AT). Using CC features derived from both DAS and AT, we trained a random forest model to predict flowering time, highlighting the contribution of both temporal and thermal information to predictive accuracy. This model achieved an independent test set R 2 of 0.81 with an RMSE of 1.25 days within the current dataset. All 31 CC-derived traits were also used for QTL mapping. Inclusive composite interval mapping identified 156 QTL detection events across 15 chromosomes (0.80%‒27.70% phenotypic variance explained), which were consolidated into 26 QTL regions, including loci such as QCC.caas.7A (671.47‒680.09 Mb on 7A) and QCC.caas.5D2 (426.67‒459.42 Mb on 5D). Several of these regions co-localized with previously reported genes associated with tillering, flowering time, winter hardiness and plant height. These findings indicate that CC, characterized by DAS- and AT-based traits, is genetically tractable and predictive of flowering within the current dataset, supporting its potential as a phenology-related trait for wheat improvement. Further validation across broader environments, years, and genetic backgrounds will be needed before broader application.

Why it matches plant phenotyping methodsUAV高スループット表現型解析を用いて小麦のキャノピー被覆動態を定量化し、31形質を抽出・検証しているため、表現型取得と解析が研究の中心である。

abstractWe used UAV-based high-throughput phenotyping to monitor CC in a 262-line F 8 recombinant inbred line population grown under four irrigation-year environments across two seasons.

Rapid forage yield and growth rate measurement using a remotely controlled LiDAR sensor in perennial ryegrass field plots ↗

Biomass is a key trait in pasture plant breeding and agronomy, but measuring Dry Matter Yield or Fresh Weight across large numbers of samples is labour intensive and costly. Efficient biomass assessment systems must balance accuracy, speed, and cost, while ideally enabling non-destructive measurements. We developed a rapid, real-time, non-destructive, and remotely controlled LiDAR-based platform to estimate biomass in grass monocultures by measuring sward height at high spatial resolution. The system operates under ambient light conditions at a ground speed of 2.7 km per hour. It was evaluated in small-plot perennial ryegrass trials at two field sites in New Zealand, across two seasons at site A and one season at site B. At site A, correlations between LiDAR-derived height and fresh weight ranged from 0.33 to 0.74 across individual measurement cycles, with an overall multilevel R² of 0.72. At site B, the multilevel correlation increased to R² = 0.88. Weekly LiDAR scans at site B were used to estimate plot-level growth rates for 60 plots, demonstrating improved temporal resolution. Statistically significant differences in growth rate within regrowth cycles were detected among plots. The platform reliably differentiates perennial ryegrass plots based on biomass and offers higher temporal resolution than traditional methods.

Why it matches plant phenotyping methodsLiDARプラットフォームを開発し、草高から牧草バイオマスと成長率を非破壊推定・検証しており、植物形質取得手法が研究の中心です。

abstractWe developed a rapid, real-time, non-destructive, and remotely controlled LiDAR-based platform to estimate biomass in grass monocultures by measuring sward height at high spatial resolution.

A double-sigmoid approach for high-throughput phenotyping of winter wheat growth dynamics ↗

Multi-temporal data from unoccupied aerial systems (UAS) offer insights into growth parameters for winter wheat breeding decisions. Weekly UAS data were collected during the 2019 and 2020 growing seasons from dryland and irrigated nurseries at Bushland, Texas, within the Texas A&M Uniform Variety Trials. Canopy cover (CC) was extracted from orthomosaic images and modeled using a double-sigmoid function with a second-order derivative that captured genotypic variation in canopy growth and senescence with high coefficients of determination (R² > 0.99) and low root mean square error (RMSE) values ranging from 1.73 to 4.06. Analysis of variance (ANOVA) revealed highly significant genotypic effects (p<0.001) for yield, heading, and Green Leaf Area Duration (LAD) in all environments except 2020 dryland, where no significant differences among genotypes were detected. Extracted parameters showed positive correlations with agronomic traits, particularly under rainfed and stress-prone conditions. The end decrease stage (EDS) was correlated with grain yield (r=0.56 in 2019 dryland, and r=0.53 in 2020 irrigated, p<0.001), and the start decrease stage (SDS) was highly correlated with yield (r=0.53 in 2020 irrigated, p<0.001). The maximum decrease rate date (MDRD) was positively correlated with yield in 2019 dryland (r=0.55, p<0.001), while LAD had a correlation of r=0.56 in 2019 dryland and r=0.58 in 2020 irrigated (p<0.001). These findings demonstrate that double-sigmoid model provides a powerful, non-invasive framework for quantifying canopy development, senescence timing, and stress responses. By distinguishing genetics from environmental influences on canopy dynamics, this approach enhances selection accuracy and accelerates the development of stress-resilient winter wheat cultivars.

Why it matches plant phenotyping methodsUAS画像からキャノピー被覆を抽出し、二重シグモイドモデルで生育・老化動態を定量化する手法が研究の中心であり、精度評価と遺伝型・農業形質との検証も行っている。

titleA double-sigmoid approach for high-throughput phenotyping of winter wheat growth dynamics

An integrative high-throughput phenotyping framework for assessing canopy growth dynamics and light interception in potato ↗

Quantifying the canopy growth dynamics and light interception capacity under different management practices laid the physiological foundation for potato yield formation. However, the traditional manual measurement methods are labour-intensive, time-consuming, and incapable of capturing time-series dynamics. To address this, we proposed a novel high-throughput strategy that integrates UAV-based RGB imaging with a piecewise physiological model. Furthermore, how Nitrogen(N)-Potassium(K) interaction affects the temporal canopy growth dynamics, light interception, and tuber yield was determined. The results indicated that: (1) Among the 11 secondary indices extracted from the canopy growth dynamic curves, the interaction of N and K had the greatest effect on the maximum canopy duration and the total canopy growth curve integral. The direct path coefficients of N and K inputs on these two parameters were 0.847 and 0.805, and 0.234 and 0.148, respectively. (2) There was a strong linear relationship between the integral area under the curve (S∫) and the total plant dry weight, with R² at 0.90 in 2023-2024. A simplified net photosynthetically active radiation utilisation assessment framework that achieved high accuracy with minimal parameter was built. (3) Prolonging the maximum canopy continuous coverage time is the main way to improve potato yield. The overall effect of N input on yield was significantly higher than that of K fertiliser, with a total effect value of 1.428. Optimising the N-K interaction improves nutrient precision and light interception. The integration of UAV remote sensing and the crop physiological-ecological model enables the tracking of potato canopy dynamics, which is helpful for optimising management practices to improve potato yield.

Why it matches plant phenotyping methodsUAV RGB画像と生理モデルを統合した高スループット手法を開発し、ジャガイモのキャノピー成長動態と光 interception を時系列で推定することが中心である。

abstractTo address this, we proposed a novel high-throughput strategy that integrates UAV-based RGB imaging with a piecewise physiological model.

Machine Learning-Based Crop Growth Diagnosis System Using Spatiotemporal Relative Analysis of Vegetation Indices via a Quartile-Based Method ↗

Japanese agriculture faces pressing challenges, including a declining and aging farming population and the need to adapt to climate change. To address these issues, Smart Agriculture is being introduced to improve production efficiency. Among these, unmanned aerial vehicles (UAVs) have gained attention for their ability to rapidly monitor entire fields. We proposed a machine learning-based crop growth diagnosis system that generates spatiotemporal data for multiple vegetation indices (VIs) using the quartile method and diagnoses crop growth based on patterns of change in these values. The experimental site consisted of five paddy fields within an 80 m × 50 m plot in Iwate Prefecture, Japan, equipped with weather and water sensors. Ground-truth data (overall length, culm length, panicle number, and stem number) were collected approximately one week before harvest. UAV monitoring was conducted four times using a multispectral camera, and growth analysis was performed with six VIs. Correlation analysis revealed a positive relationship between crop growth and the daily average water level during the drainage period, and a negative relationship with the daily temperature range in mid-June. A combined cluster-label representation, constructed from clustering results of all VIs for each mesh, enabled integrated analysis and visualization of multi-index patterns. Grid size optimization showed no significant differences in correlation trends between 1 m × 1 m and 5 m × 5 m resolutions. For non-crop area removal, a comparison of three image segmentation methods demonstrated that the Otsu Method achieved the highest performance. Finally, to facilitate practical use in the field, we prototyped a report interface for the diagnosis system. Future work will focus on developing a comprehensive field diagnosis system to clarify field environments, with the aim of addressing fragmentation and enclaves in Japanese farms.

Why it matches plant phenotyping methodsUAVマルチスペクトル画像と植生指数、画像分割、クラスタリングを統合した作物生育診断システムの開発・評価が中心であり、作物形質との相関検証や実用インターフェースも扱っている。

abstractWe proposed a machine learning-based crop growth diagnosis system that generates spatiotemporal data for multiple vegetation indices (VIs) using the quartile method and diagnoses crop growth based on patterns of change in these values.

Field-scale potato yield prediction from sentinel-2 time series using lightweight deep learning models ↗

Accurate and timely crop yield prediction and forecasting are important for improving agricultural productivity and supporting informed management decisions. In this study, we developed and evaluated a framework for estimating in-season potato yield at the field scale using Sentinel-2 satellite time series. A Grouped TreeSHAP Stability Selection (GTSS) was first applied to identify a compact, phenology-aware subset of spectral bands and vegetation indices, thereby reducing redundancy and mitigating overfitting in small-data settings. Two deep learning architectures tailored for limited training data were then introduced: LiteTemporalConv, a lightweight temporal convolutional network, and MS-ConvBiGRU-Attn, a hybrid encoder combining multi-scale convolutions, bidirectional GRUs, and an attention mechanism. Both models were benchmarked against widely used machine learning methods, including Random Forest, Support Vector Machine, Extreme Gradient Boost, Partial Least Squares, as well as standard deep learning baselines (CNN and GRU). Results showed that the proposed models outperformed both machine learning and conventional deep learning baselines, with LiteTemporalConv achieving the highest accuracy under 10-fold cross-validation (R² = 0.84; RMSE = 3.18 t ha⁻¹; rRMSE = 6.36%) and MS-ConvBiGRU-Attn yielding similarly strong performance (R² = 0.82; RMSE = 3.53 t ha⁻¹; rRMSE = 7.03%). By comparison, the best baseline, XGB, achieved an R² of 0.79 with an rRMSE of 9.8%. The two best-performing models were further evaluated on an independent spatial dataset to assess their generalization beyond the training region. In an additional experiment, both deep learning models trained on mid-season observations showed predictive stability for late-season yield estimation. Overall, the results highlight the importance of targeted feature selection and lightweight encoders for yield modeling in data-scarce conditions.

Why it matches plant phenotyping methodsSentinel-2時系列からジャガイモ収量を推定する特徴選択・深層学習手法を開発し、複数モデルとのベンチマークと独立データでの検証を行っており、植物形質取得が中心である。

abstractwe developed and evaluated a framework for estimating in-season potato yield at the field scale using Sentinel-2 satellite time series

From Seedling to Maturity: AI‐Based Mustard Crop Growth Tracking Using UAV Time‐Series Images ↗

ABSTRACT Accurate monitoring of plant phenology is essential for agricultural decision‐making, as deciding the right time of fertilizer application, the maturity of the plant, and climate variation. Traditional manual monitoring often fails to capture the temporal variations across large fields. UAV‐based imaging combined with deep learning can provide a solution for automated phenological assessment. In this study, we propose an AI‐driven framework on UAV‐captured Indian mustard plants to predict the phenological progress. We applied deep learning methods, EfficientNet‐B0, and a proposed hybrid model of a Vision Transformer + LSTM to predict phenological growth from UVV‐captured images of the Indian mustard plant. Both models were trained under a supervised regression setup with extensive augmentation and optimization strategies. The results of the study show that the ViT + LSTM outperforms the EfficientNet‐B0 model in terms of prediction accuracy for mustard plant phenology. The R 2 = 0.9974, minimal errors MSE = 0.0111, and RMSE = 0.149 indicate that the ViT + LSTM provides more accurate phenological predictions on temporal and spatial dependencies. Correlation Analysis confirmed a strong linear and monotonic relationship with the ground truth, with r = 0.9989 and ρ = 0.9946. Gram‐CAM visualization showed that the ViT + LSTM captures the meaning area of the plant. These results were further validated using statistical measures such as Pearson's r and Spearman's ρ , which confirmed the reliability and consistency of the model's predictions.

Why it matches plant phenotyping methodsUAV画像から植物の生育フェノロジーを推定する深層学習手法を開発し、複数モデルの精度比較と統計的検証を行っており、フェノタイピング手法が中心である。

abstractUAV‐based imaging combined with deep learning can provide a solution for automated phenological assessment.

A high-resolution (500 m) dataset for mapping key agronomic growth stages of maize in Northeast China. ↗

Accurate monitoring of agronomic phenology is essential for yield estimation and food security assessment. However, currently available maize phenology datasets usually represent only a limited number of growth stages, restricting their application in process-based crop modeling and stage-specific agricultural management. Here, we present a high-resolution maize phenology dataset for Northeast China spanning 2001-2024 at 500-m spatial resolution and daily temporal resolution. By coupling MODIS spectral information with meteorological drivers in an energy-driven XGBoost framework, we retrieved eight key agronomic stages: Emergence, Three-leaf, Seven-leaf, Jointing, Flowering, Silking, Milking, and Maturity. Validation against observations from 91 agrometeorological stations during 2009-2024 demonstrates robust performance, with an overall RMSE of less than 5 days and R² values greater than 0.63 across all stages. Beyond overall accuracy, the dataset shows strong spatial consistency and temporal stability, preserves coherent regional phenological gradients, and captures interannual variations over the 24-year period. This long-term, multi-stage dataset provides a valuable benchmark for crop model calibration, climate change impact assessment, and the development of adaptive agricultural strategies in one of the world's major maize-producing regions.

Why it matches plant phenotyping methodsMODISスペクトル情報と気象データ、XGBoostを組み合わせてトウモロコシの8つの生育段階を推定し、観測データで検証した高解像度フェノロジーデータセットであり、植物形質の取得・抽出手法とベンチマークが中心です。

abstractHere, we present a high-resolution maize phenology dataset for Northeast China spanning 2001-2024 at 500-m spatial resolution and daily temporal resolution.

A comparative analysis of 3D point clouds and crop surface models for rice plant height estimation using UAV-SfM ↗

Accurate estimation of crop plant height using unmanned aerial vehicles (UAVs) is essential for field-scale crop monitoring and phenotyping. Most previous studies using UAV-based structure-from-motion (SfM) photogrammetry have relied on raster-based crop surface models (CSMs) and have evaluated their performance using accuracy metrics such as the coefficient of determination ( R 2 ) and root mean square error (RMSE). However, such evaluations provide limited insight into how estimation behavior varies across space and time, particularly during dynamic crop growth stages. To address this gap, this study conducted a time-series comparison of rice plant height estimates derived from UAV-SfM-generated dense point clouds (DPCs) and raster-based CSMs in farmer-managed paddy fields in Cambodia, which are characterized by heterogeneous micro-environmental conditions. Rice plant height was measured throughout the growing season and UAV-derived estimates were evaluated using regression analysis, analysis of covariance, and canopy cover dynamics. In the pooled analysis, both approaches achieved high overall accuracy, with R 2 = 0.92 and RMSE = 7.2 cm for the CSM-based approach and R 2 = 0.90 and RMSE = 8.8 cm for the DPC-based approach. However, time-series analyses revealed that CSM-derived plant height estimates exhibited strong location-dependent variability and sensitivity to early-stage canopy development, whereas DPC-based estimates showed more consistent performance across locations and growth stages. Regression coefficients derived from CSM-based estimates varied significantly among locations, whereas those from DPC-based estimates did not, suggesting that point-based representations may provide more spatially consistent estimation behavior under heterogeneous field conditions. By explicitly considering temporal dynamics, canopy development, and data representation, this study highlights the limitations of current raster-based UAV-SfM workflows for structurally complex crop canopies and suggests that DPC-based approaches may offer a useful complementary representation for crop monitoring and phenotyping, particularly when spatial consistency across heterogeneous field conditions is important.

Why it matches plant phenotyping methodsUAV-SfMによるイネの草丈推定手法を、3D点群と作物表面モデルで時系列比較・検証しており、表現形式と技術性能の評価が研究の中心です。

titleA comparative analysis of 3D point clouds and crop surface models for rice plant height estimation using UAV-SfM

Assessing the suitability of a developed photogrammetric and multispectral method for detecting biostimulant effects on plants ↗

The present study validates a custom multi-sensor system for high-resolution, non-phenotyping. The photogrammetric workflow was optimised by evaluating image density, algorithms, and camera calibration. Beyond validation, a case study demonstrated the system’s capacity to monitor early plant development following biostimulant treatment. Technical assessment revealed that prior internal camera calibration was unnecessary for the optics used. A reduced dataset of 120 images yielded reconstruction accuracies statistically comparable to full 360-image sets ( p > 0.05), confirming potential for maximised throughput efficiency by reducing processing time by approximately 66% without compromising data integrity. Analysis demonstrated that algorithmic settings determined reconstruction accuracy. Active parameter tweaks were essential for maximising surface area precision across all plant species ( R 2 ≥ 0.98). Conversely, volumetric accuracy required deactivation of these tweaks to maintain mesh consistency. While surface area estimation remained robust, volumetric precision showed species-specific variability driven by morphological complexity. Baseline parameters for accurate plant health scaling were established by defining species-specific vegetation index ranges (e.g., 0.38–0.82 for C. sativus ). The platform’s robustness was validated through a longitudinal study evaluating four treatments: yeast autolysate (A), a fungal biostimulant (F), their combination (AF), and a control (C). The system captured distinct morpho-physiological responses, demonstrating that autolysate-based treatments (A and AF) significantly enhanced biomass growth. The developed multi-sensor system recorded surface area expansions of 122% and 102% relative to the control ( p < 0.001), alongside a 110% increase in biological height. Fidelity of these 3D reconstructions was substantiated by a strong correlation ( R 2 = 0.96) between the 3D-derived leaf area index and ground-truth measurements. A key innovation of the pipeline is the integration of vertical distribution metrics as descriptive statistical tools, enabling high-resolution characterisation of canopy architecture. The plant health status metric evidenced enhanced physiological resilience in variants A and AF. Gravimetric analysis corroborated the non-destructive findings, confirming significant increases ( p < 0.001) in dried shoot weight of 77% (A) and 79% (AF). The validated system decoupled structural biomass from physiological health, offering broad utility across diverse phenotyping tasks. Such functionality streamlines the valorisation of industrial by-products into biopreparations, driving progress in sustainable agriculture.

Why it matches plant phenotyping methodsフォトグラメトリとマルチスペクトル計測による植物表現型取得システムの最適化・技術検証が研究の中心であり、植物形態・生理状態の測定性能を評価している。

abstractThe present study validates a custom multi-sensor system for high-resolution, non-phenotyping.

A dual-branch perception and hybrid attention integrated framework for temporal remote estimation of wheat leaf biomass. ↗

Introduction Wheat leaf biomass is a key indicator of crop growth, nitrogen status, and yield potential, and its accurate estimation is essential for precision agriculture. Unmanned aerial vehicle (UAV) remote sensing provides multi-stage phenological observations for non-destructive biomass monitoring. However, existing approaches often fail to capture the superimposed temporal patterns inherent to crop phenology, including short-term physiological fluctuations driven by management events and long-term seasonal growth trends, as well as the cumulative causal effects of early-stage conditions on final biomass accumulation. Methods This study proposed a dual-branch perception and hybrid attention integrated framework (DBAFN) for temporal estimation of wheat leaf biomass from UAV multi-temporal observations across key growth stages. Results and discussion Experimental results demonstrated that the DBAFN achieved the best performance, with the coefficient of determination (R²) of 0.87, root mean square error (RMSE) of 38.41 g/m², mean absolute error (MAE) of 27.77 g/m², and relative RMSE (RRMSE) of 17.29%. Overall, the proposed framework provided an effective solution for temporal biomass estimation and demonstrated strong generalization capability, as further validated by independent experiments across different ecological regions and wheat genotypes (R² = 0.816-0.820). Compared with conventional machine learning models, the DBAFN showed consistently higher accuracy and lower prediction error. Multi-source feature analysis indicated that the combination of reflectance, vegetation indices, and canopy height provides the most accurate estimation. Ablation experiments further confirmed the effectiveness of each module in improving model performance. The SHapley Additive exPlanations (SHAP) analysis revealed that the canopy height and key spectral features contribute most to biomass prediction, highlighting the importance of integrating structural and physiological information. This study demonstrates that integrating multi-scale temporal dynamics, hybrid attention mechanisms, and transformer-based dependency modeling significantly improves the reliability of UAV-based biomass estimation. It offers a practical, data-driven pathway for intelligent crop monitoring and precision nitrogen management.

Why it matches plant phenotyping methodsUAVマルチ時期リモートセンシングから小麦葉バイオマスという植物形質を推定する手法を提案し、独立地域・遺伝子型で検証しているため、フェノタイピング手法が中心である。

abstractThis study proposed a dual-branch perception and hybrid attention integrated framework (DBAFN) for temporal estimation of wheat leaf biomass from UAV multi-temporal observations across key growth stages.

Development and validation of a low-cost imaging system for seedling germination kinetics through time-cumulative analysis ↗

The ready-to-eat lettuce industry is rapidly expanding, increasing the need for reliable, scalable methods to assess seed germination and early growth under realistic soil conditions. This study presents an automated imaging-based approach for quantifying germination dynamics and seedling vigor using a low-cost multi-camera system under greenhouse conditions. Lettuce seeds were grown in soil either inoculated or non-inoculated with the soil-borne pathogen Rhizoctonia solani. Top-view images were acquired using commercial surveillance cameras and processed through a calibrated pipeline including geometric correction, color normalization, vegetation segmentation, clustering, and temporal tracking of emergence events. Seedling vigor was quantified through projected leaf area estimation. The proposed method enables accurate estimation of germination kinetics and growth dynamics under field-like conditions. Automated counts were validated against manual measurements at both intermediate and final time points, achieving high agreement in both cases. At the final assessment, the method reached R² = 0.98 and RMSE = 1.12, while at the midterm evaluation it achieved improved performance with R² = 0.998 and RMSE = 0.5, reflecting the lower complexity of plant structure at earlier growth stages. Results showed that pathogen inoculation significantly reduced both germination rate and seedling vigor, with up to 70% reduction in biomass accumulation. The proposed framework provides a robust, low-cost solution for high-throughput phenotyping of early plant development in soil-based systems, supporting scalable agricultural experimentation.

Why it matches plant phenotyping methods低コスト多カメラ画像システムと画像解析パイプラインを開発・検証し、発芽動態と幼植物活力を定量化しているため、植物フェノタイピング手法が中心です。

abstractThis study presents an automated imaging-based approach for quantifying germination dynamics and seedling vigor using a low-cost multi-camera system under greenhouse conditions.

Phenology-Guided Early Prediction of Crop Damage Under Long-Duration Inundation Using Multi-Source SAR–Optical Imagery ↗

Long-duration flood inundation can substantially suppress crop growth and cause yield loss, particularly in semi-arid agricultural regions increasingly affected by extreme rainfall. Timely crop damage assessment is critical for disaster response and insurance-related decision-making, but direct yield-loss observations are often unavailable during or shortly after flooding. This study proposes a phenology-guided regression framework for early crop damage assessment using multi-source SAR–optical observations. The study was conducted on the Tumochuan Plateau, Inner Mongolia, China, where severe rainfall beginning on 23 July 2025 caused widespread cropland inundation. Sentinel-2 EVI time series from 2022 to 2025 were fitted using a Savitzky–Golay (SG) filter, and annual area under the EVI curve (AUC) loss in 2025 relative to the 2022–2024 historical mean was used as a proxy for flood-induced crop damage. Optical features from Landsat-8/9 and Sentinel-2, together with SAR backscatter features from Sentinel-1, Lutan-1, and Gaofen-3, were incorporated into machine learning regression models. SAR features improved pixel-wise prediction, with the Random Forest model achieving the highest R2 of 0.62 using early-period features and 0.77 using later-period features. Village-scale aggregation further improved performance, yielding an early-period R2 of 0.84 across 123 and 0.78 across 122 villages. These results demonstrate the feasibility of SAR–optical and phenology-guided regression for early crop damage assessment under long-duration inundation.

Why it matches plant phenotyping methodsSAR・光学画像とフェノロジー指標を用いて作物被害を推定する回帰手法が研究の中心であり、作物状態（洪水被害）を定量化・検証しているため。

abstractThis study proposes a phenology-guided regression framework for early crop damage assessment using multi-source SAR–optical observations.

Phenological growth stages of Finger millet (Eleusine coracana (L.)) using 3-D phenotyping with relevance to breeding applications ↗

Finger millet ( Eleusine coracana (L.) Gaertn.) is a small seeded cereal known for its health benefits and its ability to grow in water-limited and saline environments. Despite its health and adaptation advantages, there is no standardized BBCH scale developed for finger millet, precluding standardization of a defined growth and development scale. The initial step in any breeding program and related research, is the precise, consistent and standardized description of crop growth stages. Therefore, we present a standardized phenological scale to describe and compare different stages of growth and development. In this study, we used four-finger millet accessions from the U.S.D.A. National Plant Germplasm System (NPGS) collection. Using a standardized BBCH chart as the baseline, we describe nine main stages of development to provide a simplified and user-friendly phenological growth staging scale for finger millet. A novel feature of this study was the use of Neural Radiance Fields (NeRF) to generate three-dimensional (3-D) renderings that align growth stages with 3-D imaging, paving the way for future phenological staging studies to incorporate 3-D visualization as a tool for standardization, researcher training, and reduction of observer bias across environments.

Why it matches plant phenotyping methods指のキビの生育段階を標準化する手法を開発し、NeRFによる3D画像化を生育ステージ判定・標準化に組み込んでいるため、植物フェノタイピング手法が中心である。

titlePhenological growth stages of Finger millet (Eleusine coracana (L.)) using 3-D phenotyping with relevance to breeding applications

Bridging affordable phenomics with high-efficiency controlled environment agriculture for data-driven agriculture ↗

Controlled environment agriculture (CEA) is essential for resilient crop production but faces high energy demands and operational costs. While high-throughput phenotyping (HTP) provides critical biological feedback to optimize these systems, conventional HTP platforms remain prohibitively expensive, infrastructure-heavy, and technically complex for widespread adoption. This review examines the emerging shift toward “affordable phenomics”, an approach integrating low-cost, open-source microcontrollers and Internet-of-Things (IoT) devices to continuously capture dynamic plant physiological data. By utilizing customizable tools such as modular chlorophyll fluorometers and wearable sensors, researchers and commercial growers can non-destructively monitor key traits like photosynthetic efficiency and water status in real time. Coupling these accessible sensing networks with artificial intelligence (AI)-driven analytics allows static environmental controls to transition into dynamic, plant-centered feedback systems. We synthesize recent advancements in affordable sensor technologies and review how temporal AI modeling extracts biologically meaningful features from longitudinal datasets to direct adaptive lighting and irrigation strategies. Furthermore, we critically assess current technological limitations, including sensor calibration, signal noise, cross-platform data standardization, and edge-versus-cloud computation tradeoffs. Finally, we highlight essential future research directions, particularly the development of robust edge-computing frameworks and predictive crop digital twins, demonstrating how affordable phenomics offers a scalable, data-driven pathway to improve resource-use efficiency in modern agriculture.

Why it matches plant phenotyping methods植物フェノタイピングの低コストセンサー、IoT、AI解析、校正・標準化などを中心に扱うレビューであり、単なる農業応用ではなく手法・プラットフォームの評価が主題である。

abstractThis review examines the emerging shift toward “affordable phenomics”, an approach integrating low-cost, open-source microcontrollers and Internet-of-Things (IoT) devices to continuously capture dynamic plant physiological data.

Widespread Increase in Global Plant Water Stress Obscured by Greening ↗

Abstract Understanding the vulnerability of plants to more severe and frequent drought events and developing adaptive management strategies requires robust methods for quantifying long‐term changes in plant water stress (PWS). Most data‐driven explorations of long‐term trends in PWS have focused on alterations in canopy structure (e.g., leaf area index) or canopy structure‐dependent variables (e.g., gross primary productivity and evapotranspiration). This is largely because long‐term trends in canopy structure are relatively easy to detect from satellite observations. However, a focus on structural responses limits our ability to detect physiological stress due to challenges in isolating it from the effects of structural greening. Consequently, this difficulty hampers a comprehensive examination of long‐term PWS in the context of global greening trends. To address this gap, we developed a new process‐based metric for PWS to isolate physiological responses from structural greening, which we then used to detect global PWS trends over the past four decades. Combining site‐level and satellite observations at the half‐degree resolution across the globe, we found that accounting for greening‐related changes substantially alters the sign of long‐term PWS trends inferred from traditional approaches. Specifically, our study reveals a significant increase in PWS that is only detectable when accounting for structural greening trends. When greening trends are not accounted for, global PWS appears to have decreased over time. Overall, our results highlight the need to integrate structural dynamics and greening into PWS detection. Such an integration of observations and land models will improve our understanding of plant‐water‐energy interactions.

Why it matches plant phenotyping methods植物の生理的な水ストレスを定量化する新しいプロセスベース指標を開発し、衛星・地上観測で検証・適用しており、表現型測定法が研究の中心である。

abstractTo address this gap, we developed a new process‐based metric for PWS to isolate physiological responses from structural greening, which we then used to detect global PWS trends over the past four decades.

Spatio-Temporal Monitoring of the Invasive Plant Alternanthera philoxeroides in a Narrow River Using Sentinel-2 Time-Series Data ↗

Alternanthera philoxeroides, an invasive alien species, spreads rapidly in river systems via vegetative propagation from stem fragments, requiring river-system-scale monitoring to understand its expansion dynamics and habitat preferences. This study used multi-temporal Sentinel-2 data to analyze spatio-temporal variations in fractional vegetation cover (FVC) within a 3.5 km river reach. FVC estimates derived from vegetation indices were validated against high-resolution aerial images, with an EVI-based model achieving the highest accuracy (RMSE = 9.2%), enabling reliable monitoring even in narrow (~24 m) channels. Time-series analysis from 2019 to 2024 revealed downstream expansion beginning in 2022. Annual maximum FVC (Cmax) was used to assess relationships with removal records and bank structures, showing that removal effects were temporary and more pronounced in the first year, while steel sheet-pile banks limited vegetation growth compared to concrete revetments. These results demonstrate that Sentinel-2 data can provide an effective and accessible tool for evaluating invasive plant dynamics and management effectiveness in low-flow river systems where A. philoxeroides dominates the floating vegetation community.

Why it matches plant phenotyping methodsSentinel-2時系列から侵入植物の植生被覆率を推定し、航空画像で精度検証しており、植物状態の取得・評価手法が中心です。

abstractFVC estimates derived from vegetation indices were validated against high-resolution aerial images, with an EVI-based model achieving the highest accuracy (RMSE = 9.2%)

A multimodal geospatial foundation model anticipates crop stress and yield failure across climates and species ↗

Introduction Climate extremes increasingly threaten agricultural production, yet many artificial intelligence systems in agriculture remain local, reactive and narrowly trained for one crop, region or sensing modality. Methods We present AgriFM, a multimodal geospatial foundation model that combines satellite image time series, radar, thermal observations, weather trajectories, soil properties, topography and sparse management variables to estimate crop-stress and yield-failure risk across crops and regions. AgriFM was pretrained using self-supervised objectives on 2.4 million field-season sequences and evaluated on a curated benchmark spanning maize, wheat, soybean, rice and sorghum across five agroclimatic regions. Results In held-out geography and time-split evaluations, AgriFM improved early stress detection and yield-failure prediction over statistical, crop-model and deep-learning baselines. The largest gains occurred during compound drought and heat events, for which AgriFM produced alerts 18 to 24 days earlier than the satellite-only baseline while maintaining improved calibration. Phenology-conditioned fusion improved transfer across planting calendars, and uncertainty calibration reduced false alerts at fixed recall. Discussion Because the study is based on retrospective datasets, these findings establish cross-region retrospective performance rather than prospective field efficacy. The results support further field-based evaluation of multimodal foundation models for climate-resilient crop monitoring.

Why it matches plant phenotyping methods作物ストレス状態と収量失敗リスクを衛星・レーダー・熱画像等から推定する基盤モデルを開発し、複数作物・地域のベンチマークで評価しており、植物状態の取得・推定手法が中心である。

abstractWe present AgriFM, a multimodal geospatial foundation model that combines satellite image time series, radar, thermal observations, weather trajectories, soil properties, topography and sparse management variables to estimate crop-stress and yield-failure risk across crops and regions.

Image-based trait extraction of Chenopodium quinoa grown under salinity and drought stress. ↗

Above ground crop traits provide an early indication of a plant's capacity to tolerate stress, and are important for breeding programs aimed at improving stress tolerance. In this work, we present a high-throughput methodology to study morphological and physiological traits of individual quinoa plants over time under control, drought, and saline conditions. We used daily sideview imaging of individual plants, followed by segmentation of the panicle, leaf and stem using the deep learning U-Net++ segmentation model. The resulting segmentations were used in regression models to estimate leaf area, fresh and dry biomass, and leaf dry weight. The regression models showed high predictive accuracy. Using these estimates, we could calculate specific leaf area and leaf weight ratio. In addition, radiation use efficiency for above-ground biomass production was calculated, providing an independent physiological check on the consistency of these predictions. Finally, using automated measurements of plant transpiration we were able to determine daily averages of whole plant stomatal conductance. The results show that image-derived morphological traits can be used to accurately estimate biomass-related traits and to derive physiologically meaningful indicators of plant performance over time. This method provides a framework for non-destructive monitoring of quinoa responses to drought and salinity.

Why it matches plant phenotyping methods画像取得、深層学習セグメンテーション、回帰による植物形質推定を中核とする高スループット表現型解析手法であり、ストレス実験での単なるルーチン測定ではない。

abstractwe present a high-throughput methodology to study morphological and physiological traits of individual quinoa plants over time

DINO-Pheno-Cluster: Integrating few-shot foundation models and UAV time-series for spatiotemporal growth and functional characterization of alfalfa ↗

Precise characterization of alfalfa growth dynamics is essential for breeding accessions with superior regrowth capacity, persistence, and yield stability. However, traditional plot level and coarse scale observations suffer from low signal to noise ratios particularly before canopy closure when phenotypic data are strongly affected by weeds and soil background. Moreover, existing studies rarely capture the dynamic mechanisms of crop development across the entire growth cycle. To address this, the DINO-Pheno-Cluster framework is introduced as a foundation model driven and mechanism decomposed phenotyping approach. This decoupled framework first utilizes DINO-XMem, a few-shot individual plant segmentation network based on DINOv3 and a dual memory mechanism. It subsequently applies parameterized dynamic modeling guided by growth process knowledge. Validation utilized high frequency Unmanned Aerial Vehicle (UAV) imagery from 12 time points across three growing seasons covering 127 alfalfa accessions. DINO-XMem achieved an 89.54% mean Intersection over Union (mIoU) under a 10-shot setting and maintained 86.77% under extreme 1-shot conditions. It successfully resolved dense canopy oversegmentation outperforming fully supervised baselines by 4.08% to 11.97% in mIoU. Crucially, the extracted high purity time series trajectories were parameterized into specific biological indicators including maximum growth rate, comprehensive regeneration index, and seasonal stability index. Gaussian Mixture Model (GMM) clustering based on these mechanistic traits identified four distinct functional ideotypes comprising High yield/High regrowth, Upright/Sparse, High stability/Persistent, and Short/Dense, all validated by ground measured biomass. This workflow establishes a precision screening tool for multi harvest crops advancing crop phenomics toward process level analysis.

Why it matches plant phenotyping methods植物の時系列UAV画像から個体を分割し、成長・再生・安定性などの形質を抽出するフェノタイピング手法の開発と検証が中心である。

abstractthe DINO-Pheno-Cluster framework is introduced as a foundation model driven and mechanism decomposed phenotyping approach

Plant architecture reveals contrasting developmental strategies in two threatened West African timber species (Khaya senegalensisand Pterocarpus erinaceus): implications for conservation and sustainable forest management ↗

Abstract Architectural analysis provides a powerful analytical framework for understanding the ontogenetic trajectories of tree species and their adaptive responses to environmental constraints. Despite their ecological, economic, and cultural importance in West African agroforestry systems, the architectural development of Khaya senegalensis (Desr.) A. Juss. (Meliaceae) and Pterocarpus erinaceus Poir. (Fabaceae), two overexploited taxa classified as Vulnerable on the IUCN Red List, had never been formally described. This study presents the first complete characterization of their architectural development, from the seedling stage to senescence, based on architectural and retrospective analyses conducted on 360 individuals per species across seven localities along a south-north bioclimatic gradient in Côte d'Ivoire, covering contrasting vegetation zones ranging from dense humid forest to dry Sudanian savanna. Both species display well-defined ontogenetic trajectories comprising four phases: juvenile establishment, architectural construction, reproductive transition, and crown restructuring associated with ageing. Distinct architectural models were identified: K. senegalensis conforms to Rauh's model, characterized by a monopodial orthotropic trunk with indefinite growth and rhythmic acrotonic branching; P. erinaceus follows Troll's model, in which the orthotropic trunk progressively gives rise to a sympodial plagiotropic system with mixed terminal and lateral flowering. Architectural units, defined as the minimal structural organization enabling a species to reach reproductive maturity, were established at the adult stage: that of K. senegalensis comprises four axis categories and five branching orders, while that of P. erinaceus comprises three axis categories and up to six branching orders in old trees. Significant variation in growth-unit morphology among habitats and localities ( P ) revealed the architectural plasticity of both species in response to ecological gradients. The calculated Favourable Development indices ( FDi ) identified Bouaké and Katiola as optimal zones for K. senegalensis , and Bouaké and Toumodi for P. erinaceus , providing objective spatial criteria for reforestation planning. These findings demonstrate that architectural traits are robust indicators of development, adaptive strategies, and crown functioning. By linking structural organization to productivity, resilience, and regeneration potential, this study provides a scientific basis for integrating architectural analysis into reforestation programmes, sustainable forest management, and the design of agroforestry systems for threatened African tree species facing growing climatic and anthropogenic pressures. Complementary regression analyses further showed that phytomer number, rather than internode elongation, primarily governs growth-unit length in both species, and that growth unit diameter scales positively with growth unit length; a multivariate analysis of variance (MANOVA) confirmed that ontogenetic stage and locality, but not habitat alone, robustly structure growth-unit morphology.

Why it matches plant phenotyping methods樹木の成長段階・分枝構造・成長単位形態を対象に、建築学的および回顧的解析を中心的手法として適用し、植物構造形質と発達状態を定量・比較しているため。

abstractThis study presents the first complete characterization of their architectural development, from the seedling stage to senescence, based on architectural and retrospective analyses conducted on 360 individuals per species across seven localities

A Systematic Review of Dynamic Disease Phenotyping in Plant Pathology ↗

Plant disease phenotyping underpins resistance breeding, epidemiology and crop-loss management, yet it remains a recognised bottleneck. This review asked whether the two metrics that dominate the discipline, the disease severity index (DSI) and the area under the disease progress curve (AUDPC), adequately represent disease as a temporally unfolding process, and what the evidence says about dynamic alternatives. Reporting followed PRISMA 2020 and the Synthesis Without Meta-analysis (SWiM) guideline. Web of Science Core Collection, Scopus, PubMed and a Google Scholar grey-literature sweep were searched for records published between January 2020 and December 2025, retrieving 1,192 records; 874 remained after de-duplication, 128 full texts were assessed and 31 studies met the eligibility criteria. Citation chasing added 24 foundational works, giving 55 included studies. Records were dual-screened (Cohen's kappa = 0.86), appraised with an adapted Mixed Methods Appraisal Tool, and synthesised using vote counting by direction of effect, an evidence map and structured cross-study comparison; meta-analysis was inappropriate because outcomes were not commensurable. Thirty studies (54.5%) represented disease at a single assessment and eight (14.5%) collapsed the epidemic into one integrated area, whereas only twelve (21.8%) retained the full trajectory. Across six outcome domains, all 29 study-level comparisons favoured the temporally richer method and none reported a null or negative result, an asymmetry indicating probable reporting bias. Certainty was high for visual-assessment findings, moderate for sensing and dynamic modelling, and low for field-realised genetic gain. The phenotyping bottleneck has migrated from data acquisition to data representation.

Why it matches plant phenotyping methods植物病害フェノタイピング手法の動的評価を中心に、既存指標と代替手法を体系的に比較した方法論レビューである。

titleA Systematic Review of Dynamic Disease Phenotyping in Plant Pathology

3D Reconstruction of deciduous Trees using low-cost UAV - and Crane-based Photogrammetry for Monitoring Shoot Elongation across entire Canopies ↗

Abstract. Tree growth determines how much CO2 is sequestered from the atmosphere and temporarily stored in woody biomass. At the same time tree growth is affected by increasing temperatures, more frequent drought periods, late frosts and other extreme events associated with climate change. While continuous measurements of radial (secondary) tree growth using dendrometers are well established, monitoring of shoot elongation (primary growth) has largely been neglected because suitable measurement techniques are lacking. As a result, the effects of climate change on primary tree growth remain insufficiently understood. This work aims at reconstructing native deciduous trees in 3D as a basis for measuring and monitoring shoot elongation over entire tree canopies. Here we explored the use of low-cost UAV photogrammetry and of a multi-camera CraneCam system under real-world conditions. Data were collected in two study areas over an entire growing season. We present sensor evaluations, photogrammetric data acquisition and processing strategies. A special focus is placed on the analysis of the resulting photogrammetric 3D point clouds in terms of accuracy, resolution and completeness. Results demonstrate 3D point accuracies of 5-6 mm for entire trees using consumer-grade UAVs weighing less than 250 g and a 3D reconstruction completeness between 92% and 98% depending on the UAV type. The paper introduces a novel 3Dßprinted ground-truth branch to evaluate the capability to reconstructing fine-detail structures such as thin tree shoots. Finally, we discuss operational challenges and initial experiments towards a skeletonization of entire trees based on photogrammetric point clouds.

Why it matches plant phenotyping methods樹冠全体のシュート伸長という植物形質を取得するための3D再構成手法を開発・評価しており、精度・解像度・完全性の検証も中心的に扱っている。

abstractThis work aims at reconstructing native deciduous trees in 3D as a basis for measuring and monitoring shoot elongation over entire tree canopies.

LeafTip-RN: Generative AI-powered temporal interpolation for continuous phenotypic analysis of seedling establishment traits in wheat. ↗

Seedling establishment represents a critical phase in early crop growth and development, directly influencing biomass accumulation and yield potential. To characterise early growth dynamics under field conditions, both growth rate and uniformity of emergence need to be assessed continuously; however, manual quantification of these dynamic traits in large-scale trials remains impractical. Here, we present LeafTip-RN, an open-source and deep learning (DL)-powered pipeline for dynamically measuring wheat (Triticum aestivum L.) early establishment in the field. To enable flexible and scalable data collection, ultralow-altitude drone phenotyping was employed, followed by the development of an optimised DL model to automate leaf-tip-related feature extraction from complex backgrounds. Notably, to address data sparsity arising from eight phenotyping timepoints, we integrated an image-to-video generative AI (GenAI) module into the pipeline to interpolate keyframes between early and late seedling stages (i.e. 18-40 days after sowing), resulting in a training library comprising 353,019 labelled leaf tips. Using the pipeline, we successfully quantified multiple agronomically important establishment-related traits (e.g. plot-level leaf tips and seedling spatial uniformity), followed by deriving their growth curves for 51 wheat varieties across two growing seasons (2024-2026). After validating these LeafTip-RN-derived traits, we further computed varietal relative growth rates and uniformity indices, based on which the 51 varieties were classified into high-, medium-, and low-performance groups, revealing discrepancies between LeafTip-RN-derived classification (18-40 DAS) and manual assessment at 40 DAS when dynamic early performance was considered. Finally, to facilitate broad adoption by the plant research community, we developed an openly accessible graphical user interface (GUI) for non-expert users to visualise and analyse rapid seedling developmental changes. Taken together, our study provides a scalable GenAI-powered solution for evaluating seedling establishment in wheat, offering valuable tools for breeders and researchers to identify varieties with enhanced early growth vigour and emergence dynamics that are extensible to other cereal crops.

Why it matches plant phenotyping methodsLeafTip-RNは、ドローン画像と深層学習・生成AIによって小麦の葉先や出芽均一性などの形質を自動抽出・連続推定する手法およびGUIを開発し、導出形質を検証しているため、植物フェノタイピング手法が研究の中心である。

abstractHere, we present LeafTip-RN, an open-source and deep learning (DL)-powered pipeline for dynamically measuring wheat (Triticum aestivum L.) early establishment in the field.

Robot-based 3D-multispectral monitoring of soybean in a spatially heterogenous agrivoltaic environment ↗

Agrophotovoltaic (APV) systems provide a unique opportunity for improving agricultural land-use efficiency by combining crop production with solar energy capture via photovoltaic panels. In-depth information on plant growth patterns within the spatially heterogenous microclimate created by APVs would enable better planning and management within such unconventional systems. Thus, the present study demonstrates the implementation of a customized robot-mounted 3D-multispectral imaging system for monitoring the growth and spectral reflectance patterns of a conventional soybean cultivar "Eiko" (EK) and a chlorophyll-deficient mutant variety MinnGold (MG) under an APV system. Weekly trends in canopy morphometric features revealed significant variations in canopy height, surface area, light penetration, and volume across the APV field depending on the proximity with the overhead solar panels for both EK and MG, with plants receiving adequate rainfall and intermittent shade performing the best. Furthermore, although spectral indices exhibited variations between EK and MG due to intrinsic differences in pigmentation, symptoms of stress could be detected for both genotypes within rain-shaded areas of the APV plot. Hence, the present investigation depicts the potential for complementary usage of robotics and machine vision for high-precision high-throughput crop monitoring under APVs, which would help improve crop management within such non-homogenous cultivation systems.

Why it matches plant phenotyping methodsカスタマイズしたロボット搭載3Dマルチスペクトル画像システムを実装し、植物形態・スペクトル・ストレス状態を高精度に取得することが研究の中心である。

abstractthe present study demonstrates the implementation of a customized robot-mounted 3D-multispectral imaging system for monitoring the growth and spectral reflectance patterns

Temporal germination of lettuce under salinity and nano-silicon: A high-throughput phenomics framework with deep learning. ↗

Accurate high-throughput evaluation of seed germination under abiotic stress is often hindered by subjective manual scoring and insufficient temporal resolution. This study introduces an integrated phenomics framework leveraging an explainable deep learning model for real-time monitoring of lettuce (Lactuca sativa L.) germination dynamics under salinity stress and nano-silicon priming. Utilizing a custom X-Y motorized imaging system, we captured continuous time-lapse data across 16 treatment combinations (0-60 mM NaCl × 0-300 mg L⁻¹ nano-SiO₂). We developed an ultra-lightweight architecture, YOLO26n-Ghost-EMA, which integrates Ghost convolutions and Efficient Multi-scale Attention. This model achieved 99.46% mAP@50 with a 4.5 ms inference time, providing a high detection accuracy while maintaining a lightweight architecture and favorable accuracy-efficiency trade-off compared with standard YOLO variants. while reducing computational demand by 35-50%. To ensure biological validity, Explainable AI (XAI) via Grad-CAM confirmed that the model precisely targets radicle protrusion zones, eliminating 'black-box' opacity. Response Surface Methodology (RSM) quantified the potent ameliorative effect of nano-SiO₂, identifying 100 mg L⁻¹ as the optimal concentration to recover germination from 58.57% to 84.28% under severe salinity (60 mM NaCl). By bridging real-time computer vision and plant stress physiology, this framework provides a scalable, high-resolution solution for precision seed biology and rapid assessment of abiotic stress.

Why it matches plant phenotyping methods深層学習とカスタム撮像システムによる発芽動態の高スループット・リアルタイム定量が研究の中心であり、植物状態（発芽・幼根突出）を画像から抽出する手法を開発・検証している。

abstractThis study introduces an integrated phenomics framework leveraging an explainable deep learning model for real-time monitoring of lettuce (Lactuca sativa L.) germination dynamics under salinity stress and nano-silicon priming.

Real-Time Growth and Diurnal Thickness Variation of a Buried Solanum tuberosum (L.) Tuber ↗

Real-time measurement of belowground tuber growth has not been conducted in field crops. Here, a strain-gauge sensor was used to monitor potato tuber growth and estimate mean daily tuber water loss. Over the 13 days preceding harvest, tuber thickness increased by 0.90 mm, corresponding to a daily gain of 1.33 g, or a 4.8% increase. The greatest diurnal fluctuation was 0.453 mm, corresponding to a transpirational water loss of 9.4 ml, or 3% of the tuber’s water content. Daily transpiration showed a positive correlation with air temperature and vapor pressure deficit. This sensor will enable more precise input control and higher temporal resolution than current methods for below-ground crops, supporting improved crop management, yield prediction, and harvest decisions.

Why it matches plant phenotyping methods埋没ジャガイモ塊茎の成長・厚さ変動・水分損失をひずみゲージでリアルタイム測定する手法が研究の中心であり、植物器官形質の取得法として適格。

abstractHere, a strain-gauge sensor was used to monitor potato tuber growth and estimate mean daily tuber water loss.

SST-MAE: Learning Spectral-Spatio-Temporal Representations from Plant Hyperspectral Time Series to Discover Complex Genotype-Phenotype Relations ↗

Abstract Understanding the link between genetic variation and observable traits is key to crop breeding. Hyperspectral imaging captures physiological and biochemical profiles, but current supervised methods require costly trait annotations and treat each observation as a static snapshot, ignoring the temporal dynamics of plant development. We introduce SST-MAE, a self-supervised framework that learns genotype-discriminative representations from plant hyperspectral developmental trajectories, without requiring phenotypic labels. The model learns to reconstruct masked information, capturing multiple growth trajectories. Validated on 194 field-grown lettuce genotypes across eight time points, the frozen encoder serves as a feature extractor for downstream genotype classification. SST-MAE outperforms raw spectral and linear baselines, achieving AUROC > 0.89 for anthocyanin pigmentation SNPs and 0.77 for leaf serration. The learned features are highly label-efficient, attaining near-full performance with only 30–50% of labeled data, offering a scalable pathway toward high-throughput genetic screening from image-based phenotypes.

Why it matches plant phenotyping methods植物のハイパースペクトル時系列から表現型関連表現を抽出する自己教師あり手法を開発し、複数遺伝子型・時点で検証しているため、表現型取得・解析手法が中心です。

abstractWe introduce SST-MAE, a self-supervised framework that learns genotype-discriminative representations from plant hyperspectral developmental trajectories, without requiring phenotypic labels.

Apple Crop Health Detection Based on Vegetation Indices at Shalimar, Kashmir: North-Western Himalayas ↗

Apple orchard health monitoring is important for supporting timely crop management under the temperate conditions of Kashmir Valley. The present study evaluated the seasonal behaviour of four Sentinel-2-derived vegetation indices, namely the Normalized Difference Vegetation Index, Soil Adjusted Vegetation Index, Modified Soil Adjusted Vegetation Index and Enhanced Vegetation Index, in a 2 ha apple orchard at SKUAST-K, Shalimar, Kashmir, during the 2020 growing season. Sentinel-2 imagery acquired from April to September was processed using SNAP and QGIS, and mean vegetation index values were extracted for the orchard area. Monthly weather data, including average temperature and rainfall, were obtained from the on-campus meteorological observatory. Ground observations at 20 georeferenced points were used to support the interpretation of canopy development, phenological stage and visible plant health condition. All four vegetation indices showed a seasonal increase from April to July-August, followed by a decline during September-October, corresponding to canopy development, fruit maturation, harvest and senescence. Based on the monthly values presented in the study, temperature showed positive associations with the vegetation indices, with the strongest relationship observed for MSAVI, followed by NDVI and SAVI. Rainfall showed weak and non-significant associations with the indices during the study period. The results indicate that Sentinel-2-derived vegetation indices can reflect seasonal canopy dynamics in apple orchards under the studied conditions. MSAVI appeared particularly useful for representing canopy development, while field observations remained necessary for interpreting pest, disease and phenological effects.

Why it matches plant phenotyping methodsSentinel-2画像から植生指数を算出し、リンゴ樹冠の季節動態・健康状態を評価する測定ワークフローが研究の中心であり、植物状態の推定に直接用いられている。

abstractThe present study evaluated the seasonal behaviour of four Sentinel-2-derived vegetation indices

Tillering structures the genotypic variability of wheat vegetative growth and its plasticity under water deficit. ↗

Whole plant leaf expansion (shoot expansion) under drought drives the trade-off between water saving for later grain production and canopy photosynthesis. Fine-tuning shoot expansion could therefore become a target of genetic progress for drought-prone environments. However, its components (axis production, i.e. tillering, leaf production on each axis, and individual leaf elongation) may have their own genotypic variability and plasticity under drought, making hard to calibrate crop simulation models and specify breeding targets. In this study, we focused on the genetic diversity of bread wheat and durum wheat to determine the links and trade-offs between the underlying processes of shoot expansion under drought and how it translates at the whole plant and canopy level. For that, we used non-destructive imaging both in the field and controlled condition platforms to determine their dynamics and analyze their relative contribution to the genotypic variability of whole-plant shoot expansion under drought. Results show that shoot expansion measured at plant level in controlled environment was associated with that measured at canopy level in the field, indicating that controlled phenotyping platforms can capture the genotypic variability of growth in the field. Both whole-plant and canopy expansion were associated with tillering rate. In addition, the sensitivity of shoot growth and tillering to soil water deficit were correlated, indicating that both tillering ability and sensitivity to water deficit drive the genotypic variability of shoot expansion. Overall, dissecting shoot- expansion dynamics allowed determining the links between shoot expansion traits under drought, and provides key targets in phenotyping, modelling and breeding for drought environments.

Why it matches plant phenotyping methods非破壊画像と管理環境・圃場のフェノタイピングプラットフォームを用いて、シュート伸長・分げつの動態を測定し、環境間での性能を比較しているため、表現型取得法の応用が研究の中心的要素です。

abstractFor that, we used non-destructive imaging both in the field and controlled condition platforms to determine their dynamics and analyze their relative contribution to the genotypic variability of whole-plant shoot expansion under drought.

Modeling production curves in a strawberry breeding program to optimize early season productivity. ↗

Florida and California produce 98% of U.S. strawberries, with Florida growers' profitability depending on high yields early in the season (November-January), when prices are the highest in the U.S. market. This study aims to model the cumulative Marketable Yield and Delta Yield curves (difference in cumulative Marketable Yield between consecutive harvest time points) of strawberry genotypes to facilitate selection for greater early season productivity. The dataset comprised thirteen seasons (2013-14 to 2025-26) of advanced selection trial data. Marketable Yield trajectories were modeled using Legendre polynomial smoothing, with optimal degree selection balancing flexibility and noise reduction. The resulting coefficients served as surrogate phenotypes for genomic prediction. Forward prediction cross-validation was implemented for five seasons (2021-22, 2022-23, 2023-24, 2024-25, and 2025-26), with each season predicted using the information from all preceding seasons. For cumulative yield, across all five seasons, reconstructed curves from the Legendre models presented a clear temporal trend, with predictive ability increasing from low early-season values to peaks around Trait Dates (weeks) 7-8. In the 2021-22 and 2022-23 seasons, Legendre models showed higher predictive ability than single time-point predictions but were comparable to single-time point predictions for the other seasons. Legendre polynomial models utilizing Delta Yield achieved moderate predictive ability across five validation seasons, with consistent advantages over single time point models particularly in earlier seasons, indicating that genetic control extends beyond total yield to the trajectory of yield accumulation. Overall, Legendre modeling effectively captured the temporal dynamics of yield development while describing the trajectory with only a few parameters.

Why it matches plant phenotyping methodsイチゴの収量軌跡をLegendre多項式でモデル化し、少数の係数を代理表現型としてゲノム予測に利用・検証しており、収量表現型の計算的抽出が研究の中心である。

abstractMarketable Yield trajectories were modeled using Legendre polynomial smoothing, with optimal degree selection balancing flexibility and noise reduction.

Sector-Specific Machine Learning Models for Short-Term Sugarcane Yield Forecasting Using NDVI at Plot Level ↗

Abstract Accurate plot-level sugarcane yield forecasting is essential for optimizing agricultural management, resource allocation, and operational planning. Existing forecasting approaches are often limited by their inability to capture temporal crop dynamics and local biophysical variability, reducing their usefulness for real-time decision-making. To develop and evaluate a Machine Learning (ML)-based framework for short-term sugarcane yield forecasting at plot level using age-segmented Normalized Difference Vegetation Index (NDVI) derived from Sentinel-2 imagery, and to determine the earliest crop stage at which reliable yield predictions can be obtained. An integrated dataset was constructed by combining productivity records from 2,132 sugarcane plots across six harvest seasons (2016–17 to 2021–22) with NDVI time series derived from Sentinel-2 satellite imagery. NDVI observations were aggregated into phenology-based temporal intervals, from which statistical features were extracted. Ten ML regression algorithms were evaluated under two forecasting schemes: a global model trained with all observations and a sector-specific approach that developed localized models for individual production sectors. Model performance was assessed using RMSE and R² on an independent test set. The sector-specific approach outperformed the global model, achieving an RMSE of 12.48 TCH and an R² of 0.7840 on the independent test set, compared with an RMSE of 16.75 TCH and an R² of 0.5724 for the global model. Sparse Partial Least Squares (spls) and Support Vector Machines with Polynomial Kernel (svmPoly) were the most frequently selected algorithms. SHAP analysis revealed that Median NDVI was the dominant predictive feature, while the Elongation I stage was the most influential phenological period. Reliable forecasts were obtained from the fifth month of crop growth (RMSE = 14.13 TCH), and prediction accuracy improved progressively as the crop matured. The proposed framework also surpassed traditional expert estimations (RMSE = 15.47), providing earlier and more accurate yield forecasts. This study demonstrates that localized, sector-specific ML models combined with temporal NDVI dynamics can provide accurate and operationally useful plot-level sugarcane yield forecasts. The framework supports proactive agronomic management, improves planning and budgeting processes, and offers a scalable methodology for precision agriculture and sustainable sugarcane production systems.

Why it matches plant phenotyping methods圃場・区画レベルのサトウキビ収量という植物形質を、Sentinel-2 NDVI時系列と機械学習から推定する枠組みを開発・評価しており、予測手法が中心である。

abstractTo develop and evaluate a Machine Learning (ML)-based framework for short-term sugarcane yield forecasting at plot level using age-segmented Normalized Difference Vegetation Index (NDVI) derived from Sentinel-2 imagery

Integrating Crop Growth Models and Genomic Prediction to Improve Flowering Time Forecasting Across Novel Environments and Breeding Lines ↗

Abstract Genomic selection has accelerated genetic gain in many breeding programs worldwide but genotype-by-environment-by-management (GxExM) hampers further progress for systems where these interactions are important and not well represented in the training data. Process-based crop growth models (CGMs), which encode physiological relationships between plants and their environments, can extrapolate to novel conditions but cannot directly leverage genomic information. Coupling these complementary approaches in the Crop Growth Model–Whole Genome Prediction (CGM-WGP) framework addresses both limitations, yet applications in horticultural crops remain scarce. In this study, we apply CGM-WGP to predict flowering time in broccoli ( Brassica oleracea var. italica ) and common bean ( Phaseolus vulgaris L.), two horticultural species with contrasting physiological responses to temperature and photoperiod. Genotype-specific thermal time requirements and photoperiod parameters were jointly estimated with genome-wide marker effects and predictions were compared against a Reaction Norm Genomic Best Linear Unbiased Prediction (RN-GBLUP) benchmark across four cross-validation scenarios of increasing predictive difficulty. RN-GBLUP achieved the highest accuracy under sparse-testing scenarios where training data covered all target environments, while CGM-WGP outperformed RN-GBLUP when predicting untested environments and untested genotype-environment combinations (broccoli: Pearson r = 0.66, RMSE = 9.4 days; bean: r = 0.86, RMSE = 5.2 days). These results demonstrate that CGM-WGP can be applied to horticultural crops using genome-wide markers alone, but without requiring prior identification of quantitative trait loci. CGM-WGP also provides a modular foundation that can be extended to predict the timing of other developmental transitions and output traits such as biomass and yield.

Why it matches plant phenotyping methods開花期という植物形質を対象に、CGM-WGPによる予測手法を適用し、RN-GBLUPとの交差検証で精度比較・評価しており、形質推定ワークフローが研究の中心である。

abstractCoupling these complementary approaches in the Crop Growth Model–Whole Genome Prediction (CGM-WGP) framework addresses both limitations

Mathematical modeling with RGB data for comparative analysis of rice lineages and distribution of breaking points. ↗

Rice (Oryza sativa L.) is a crucial food crop, supplying a significant portion of the global population's caloric intake. With the shift from traditional breeding methods to digital approaches, image analysis is becoming essential for distinguishing between rice cultivars. However, the optimal growth stages for effectively utilizing image analysis to classify rice varieties remain uncertain. This study aimed to evaluate 102 rice cultivars through non-destructive image processing and RGB ratio analysis. Images were captured every two days throughout the growth period, and an RGB ratio formula was developed, excluding background pixels to focus on plant characteristics. Regression analysis identified critical time points for differentiation, with the red (R) channel being most effective at 55 and 75 days post-transplanting, and the green (G) channel at 60 and 80 days. Hierarchical clustering of slopes from piecewise regression categorized the 102 cultivars into three distinct clusters, representing their ecological types. These findings provide a precise and efficient method for classifying rice cultivars, offering breeders key insights into the most effective stages for variety differentiation. By optimizing image analysis techniques, this research enhances the efficiency of rice breeding programs and supports the targeted management of genetic resources for improved trait selection.

Why it matches plant phenotyping methodsイネの画像から背景を除去してRGB比を算出し、時系列画像解析と回帰・クラスタリングにより品種識別に有効な時点と特徴量を開発・評価しており、植物表現型取得・抽出手法が中心である。

abstractThis study aimed to evaluate 102 rice cultivars through non-destructive image processing and RGB ratio analysis.

Plant area index estimation from UAV LiDAR time-series over cherry orchards ↗

Purpose In recent years, there has been a growing use of unmanned aerial vehicle (UAV) based light detection and ranging (LiDAR) data for mapping plant area index (PAI) in orchards. However, using LiDAR time-series collected throughout the growing season to assess PAI variations in response to phenology, represents an understudied area of investigation. Furthermore, establishing the optimal spatial resolution for mapping biophysical variables of tree crops from LiDAR point cloud data remains poorly defined. Here, we assess the capability of a UAV-based LiDAR system to characterize cherry trees throughout the growing season, with a focus on monitoring PAI and the vertical structure of individual trees. Methods A time-series of 14 point cloud acquisitions with a density of 3300 points/m2 was collected between February and December 2022, covering all phenological stages of a cherry orchard in southern France. A voxel-based method was applied to create a three-dimensional grid within which PAI was estimated for each voxel. PAI was mapped by accumulating the individual voxel-based PAI values within each vertical voxel column. Results The results demonstrate that a voxel size of at least 0.7 m is required to retrieve reliable PAI estimates (RMSE = 0.58 m2.m−2, MAE = 0.48 m2.m−2, bias = 0.19 m2.m−2, rRMSE = 23%, and R2 = 0.51), while a voxel size of 1 m produced the most accurate PAI estimates (RMSE = 0.5 m2.m−2, MAE = 0.41 m2.m−2, bias = 0.07 m2.m−2, R2 = 0.59), when assessed against field-based PAI measurements obtained with a LAI-2200 Plant Canopy Analyzer. The temporal variation of canopy PAI illustrated the progression of key phenological stages, including flowering, leaf development, ripening and senescence, as well as the response of the canopy to drought stress (reduction in PAI due to leaf rolling) during the summer. The maps of PAI successfully described the variations in leaf canopy density for different cherry varieties and allowed assessment of the vertical PAI profile at the individual tree level, which provides valuable insight into tree condition. Conclusion This study confirms that seasonal UAV-LiDAR monitoring is a viable, informative approach for capturing orchard canopy dynamics at the individual tree and sub-canopy level, linking canopy structure to phenology, varietal differences, and stress responses across the growing season.

Why it matches plant phenotyping methodsUAV-LiDARとボクセル法による樹冠PAI・垂直構造の推定手法を開発・検証し、時系列および個体レベルで評価しているため、植物フェノタイピング手法が中心である。

abstractHere, we assess the capability of a UAV-based LiDAR system to characterize cherry trees throughout the growing season, with a focus on monitoring PAI and the vertical structure of individual trees.

3D Reconstruction of deciduous Trees using low-cost UAV- and Crane-based Photogrammetry for Monitoring Shoot Elongation across entire Canopies ↗

Tree growth determines how much CO2 is sequestered from the atmosphere and temporarily stored in woody biomass. At the same time tree growth is affected by increasing temperatures, more frequent drought periods, late frosts and other extreme events associated with climate change. While continuous measurements of radial (secondary) tree growth using dendrometers are well established, monitoring of shoot elongation (primary growth) has largely been neglected because suitable measurement techniques are lacking. As a result, the effects of climate change on primary tree growth remain insufficiently understood. This work aims at reconstructing native deciduous trees in 3D as a basis for measuring and monitoring shoot elongation over entire tree canopies. Here we explored the use of low-cost UAV photogrammetry and of a multi-camera CraneCam system under real-world conditions. Data were collected in two study areas over an entire growing season. We present sensor evaluations, photogrammetric data acquisition and processing strategies. A special focus is placed on the analysis of the resulting photogrammetric 3D point clouds in terms of accuracy, resolution and completeness. Results demonstrate 3D point accuracies of 5-6 mm for entire trees using consumer-grade UAVs weighing less than 250 g and a 3D reconstruction completeness between 92% and 98% depending on the UAV type. The paper introduces a novel 3Dprinted ground-truth branch to evaluate the capability to reconstructing fine-detail structures such as thin tree shoots. Finally, we discuss operational challenges and initial experiments towards a skeletonization of entire trees based on photogrammetric point clouds.

Why it matches plant phenotyping methods樹冠全体のシュート伸長を測定するための3D再構成手法を開発・評価し、センサー評価、取得・処理戦略、精度・完全性の検証を中心に扱っているため。

abstractThis work aims at reconstructing native deciduous trees in 3D as a basis for measuring and monitoring shoot elongation over entire tree canopies.

Lodicule Isolation and Morphometric Analysis During Rice Floret Opening. ↗

Rice lodicules are specialized floral organs located at the base of the ovary that undergo dynamic morphological changes during the flowering period. Water uptake-driven swelling and subsequent dehydration-induced shrinkage of the lodicules trigger floret opening and closure, respectively. Although lodicules play a central role in floret movement, standardized methods for quantitatively monitoring their temporal morphological changes remain limited. Here, we describe a detailed and reproducible workflow for lodicule sampling, dissection, imaging, and quantitative morphometric analysis. Florets are collected at predefined clock time points during the flowering period, and lodicules are carefully isolated under a stereomicroscope. High-resolution imaging is performed under consistent acquisition settings, followed by precise measurement of lodicule length, width, and thickness using image analysis software. This protocol emphasizes positional consistency in sampling, uniform imaging parameters, and standardized data analysis to enhance reproducibility. This method is suitable for evaluating the effects of genetic background or environmental conditions on lodicule morphology. By providing a standardized analytical framework, this protocol enables accurate and quantitative morphometric analysis of rice lodicules during floret opening. Key features • Standardized time-point sampling minimizes variability caused by diurnal fluctuations and handling during lodicule morphometric analysis. • Enables reproducible isolation and imaging of rice lodicules while preserving native morphology and preventing dehydration-induced artifacts. • Time-resolved workflow enables analysis of rapid morphological changes associated with floret opening and closure. • Applicable for comparing genetic and environmental effects on lodicule morphology under controlled experimental conditions.

Why it matches plant phenotyping methodsイネ小花器官の形態を標準化された採取・撮像・画像解析で定量する再現可能な表現型測定プロトコルが中心である。

abstractwe describe a detailed and reproducible workflow for lodicule sampling, dissection, imaging, and quantitative morphometric analysis.

A Flexible, Top-Down Approach To Assays Of Leaf Movement Rhythms. ↗

A growing body of literature has illustrated the importance of understanding the circadian clock due to its connection to a wide array of molecular and physiological processes. Numerous methods have been developed in order to monitor the status of the circadian clock in living tissue; however, most methods are either costly or labor intensive, and often require precise conditions that lowers throughput and limits flexibility in the size, age, or type of plant to be assayed. Here, we present an affordable and adaptable methodology for assaying circadian period using the well-characterized circadian output of leaf movement. Employing fully automated time-lapse photography using Raspberry Pi cameras and predominantly automated image post-processing, this methodology minimizes manual input to expedite circadian analysis, thus improving throughput. Additionally, the top-down setup used in this method is appropriate for a wide range of sizes and ages of plants, allowing for an expansion of the scientific questions that can be assayed by this methodology.

Why it matches plant phenotyping methods葉の運動リズムを自動画像計測・解析して概日時計の周期を評価する、植物表現型取得法の開発が中心である。

abstractwe present an affordable and adaptable methodology for assaying circadian period using the well-characterized circadian output of leaf movement

GrowFields: Compositional 4D Neural Fields for Topology-Changing Plant Growth ↗

Quantifying plant growth dynamics from sparse longitudinal 3D observations is fundamental for agriculture and plant sciences. Yet, plants pose unique challenges: they undergo intricate non-rigid deformations, exhibit changing topology as new organs emerge, and often lack explicit temporal correspondences between consecutive data acquisitions due to newly formed tissue. Methods designed for general scenes struggle to model topology changes and asynchronous organ growth characteristic of plants. To address these challenges, we introduce GrowFields, a compositional dynamic neural field representation for organ-aware 4D plant growth modelling from point cloud time series. Our approach decomposes a plant into its constituent organs and aligns each organ into its own canonical coordinate frame, isolating intrinsic growth patterns from global plant motion. We then learn a shared continuous neural deformation field that models temporal dynamics across all organs, conditioned on learnable per-organ latent codes capturing organ identity and growth characteristics. The resulting modular yet unified representation naturally accommodates the asynchronous development of plant organs while remaining grounded in the practical setting of organ-level plant tracking. We evaluate GrowFields on growth sequences from four plant species, assessing geometric fitting and organ tracking accuracy using manually annotated leaf-tip trajectories. Results demonstrate consistent improvements in spatial precision, temporal coherence, and morphological fidelity over a range of existing representations.

Why it matches plant phenotyping methods植物の3D時系列観測から器官追跡と成長動態を抽出する、オルガン認識型4Dニューラルフィールド手法の開発・評価が中心である。

abstractwe introduce GrowFields, a compositional dynamic neural field representation for organ-aware 4D plant growth modelling from point cloud time series.

From Scalar Summaries to Functional Comparisons: A Framework for Analyzing Plant Disease Progress Curves. ↗

Disease progress curves (DPCs) are central to evaluating disease management strategies, including host plant resistance. Although widely used and often appropriate, scalar summaries such as the area under the disease progress curve (AUDPC) may obscure meaningful differences in epidemic timing and trajectory shape. Here, I introduce a curve-based framework for comparing plant disease epidemics that treats DPCs as epidemic phenotypes, enabling trajectory-based comparisons beyond conventional scalar summaries. Using a hierarchical generalized additive model, environment-adjusted mean epidemic curves were estimated for each treatment (corn hybrid) while accounting for repeated assessments and environmental heterogeneity. Similarity among hybrids was quantified using a functional distance defined over the epidemic time domain, and hierarchical clustering was used to identify epidemic phenotypes based on differences in curve shape. Applied to multi-environment field data (6 environments; 74 DPCs) for southern corn leaf blight in 13 hybrids, this approach identified distinct epidemic phenotypes that were not fully reflected by AUDPC-based comparisons, despite similar overall disease levels. In addition, a distance-based permutation test indicated that breeder-defined resistance classes (moderately resistant versus resistant), established independently of the curve analysis, were associated with systematic differences in epidemic trajectory shape across environments. By shifting emphasis from scalar summaries to curve-based epidemic representations, this framework provides a complementary tool for host resistance phenotyping and comparative epidemiology and establishes a foundation for hierarchical synthesis and trajectory-based inference across environments.

Why it matches plant phenotyping methods植物病害進展曲線を植物病害表現型として解析する統計的・計算的フレームワークを開発し、複数環境・ハイブリッドで適用しているため、方法が研究の中心である。

abstractHere, I introduce a curve-based framework for comparing plant disease epidemics that treats DPCs as epidemic phenotypes, enabling trajectory-based comparisons beyond conventional scalar summaries.

FewShotCropNet: Real-Time Detection of Emerging Crop Diseases with Limited Labels Using Spectral-Temporal Attention Prototypical Networks ↗

The acquisition of labelled data for new or emerging plant diseases is difficult due to the high cost and logistical complexity of ground-truth collection, challenges that are further compounded by the limited infrastructure available to smallholder farmers in sub-Saharan Africa. This study presents FewShotCropNet, a few-shot learning model based on Spectral-Temporal Attention Mechanisms and Prototypical Networks that utilises multispectral time-series data from Sentinel-2 to classify crop diseases. Two principal innovations are incorporated in the proposed model: (1) a spectral attention mechanism based on the Squeeze-and-Excitation approach to learn disease-relevant spectral band weights; and (2) a temporal attention pooling mechanism to identify the most discriminative growth stages for disease classification. The model employs a two-phase training strategy comprising supervised pre-training followed by episodic meta-learning, enabling the generation of optimal feature representations under extreme label scarcity. Crop disease detection experiments were conducted in Edo State, Nigeria on cassava and maize using monthly Sentinel-2 composites from 2024 (10 spectral bands and five vegetation indices across twelve temporal steps). Under a 4-way 5-shot classification scenario with 100 GPS-validated labelled samples (25 per-class), FewShotCropNet achieved a mean accuracy of 98.15% with a 95% confidence interval of ±0.58%. An equitable comparison was enabled by introducing a Pre-trained Simple Prototypical Network, a variant sharing the same two-phase training strategy as FewShotCropNet but without the attention modules—which achieved 97.75% (±0.63%). FewShotCropNet exceeded the Pre-trained Simple ProtoNet by +0.40 percentage points (t = 1.52, p = 0.13), with the attention module contribution verified as positive though not statistically significant on the current dataset. Statistically significant improvements over models trained without pre-training were observed: FewShotCropNet outperformed the Relation Network (94.40%), Matching Network (94.40%), and the Optimised Baseline Convolutional neural networks (CNN) (86.65%, pre-trained backbone with 5-shot linear probe), with p

Why it matches plant phenotyping methods植物病害状態を対象に、Sentinel-2時系列データから病害を分類するFewShotCropNetを開発し、比較評価しているため、病害フェノタイピング手法が中心である。

abstractThis study presents FewShotCropNet, a few-shot learning model based on Spectral-Temporal Attention Mechanisms and Prototypical Networks that utilises multispectral time-series data from Sentinel-2 to classify crop diseases.

Additively Manufactured in planta Integrated Microneedle–Microfluidic Sensing: Nondestructive Electrochemical Tracking of Glucose and Water Stress in Agricultural Crop Plants ↗

Abstract Timely quantification of crop stress physiology remains challenging because conventional assays are destructive, labor-intensive, and poorly suited for continuous monitoring and field deployment. Here, we report a microneedle-enabled electrochemical biosensing platform with smartphone-based data collection for the in planta monitoring of plant stress that integrates three design innovations in a single architecture: (i) a fully integrated hollow microneedle–microfluidic measurement pathway for sap access, (ii) physical isolation of the metal electrodes from direct tissue contact to reduce insertion-zone abrasion of the sensing interface, improving biocompatibility and potentially lowering fouling pathways, and (iii) lithography-free fabrication of a modular transducer on an additively manufactured substrate. The platform comprises a three-electrode gold (Au) transducer modified with a nanostructured reduced graphene oxide (rGO)–chitosan layer. The biosensing platform enabled dual sensing channels via functionalized glucose oxidase (GOx) and horseradish peroxidase (HRP) for the detection of glucose and water stress-associated hydrogen peroxide (H2O2), respectively. The glucose channel showed a strong linear calibration over the tested range, with Pearson’s r = 0.99, R2 = 0.98, sensitivity of 62.34 μA/mM, and a limit of detection (LOD) of 102.50 μM (∼1.85 mg/dL), while the H2O2 channel exhibited Pearson’s r = 0.99, R2 = 0.99, sensitivity of 3.65 μA/decade, and an LOD of 3.22 μM. Repeatability across measured standards remained high for both channels, with mean coefficients of variation of 1.31% for glucose and 1.16% for H2O2. Ex vivo measurements in plant sap, including standard-addition experiments and comparison with commercial benchmark assays, provided validation of analyte concentration determination in plant-derived samples. In planta measurements on maize plants (Zea mays L.) grown under graded watering treatments revealed statistically significant treatment-dependent glucose and H2O2 signatures over time (p

Why it matches plant phenotyping methods植物体内のグルコースとH2O2を非破壊・連続測定し、水ストレス状態を推定する電気化学センシング基盤の開発と検証が中心であり、植物フェノタイプ取得手法に該当する。

abstractwe report a microneedle-enabled electrochemical biosensing platform with smartphone-based data collection for the in planta monitoring of plant stress

Physiology-informed high-throughput phenotyping of grain moisture dynamics provides enhanced insights into rice grain weight formation. ↗

Grain filling is the decisive period for rice grain weight formation. However, traditional static traits fail to capture its complex, nonlinear dynamics, while direct panicle weighing is hindered by canopy occlusion. Given the intrinsic synchronization between grain filling and dehydration from anthesis to physiological maturity, monitoring grain moisture content (GMC) dynamics serves as a robust proxy for characterizing the filling process. Here, we propose a high-throughput, physiology-informed phenotyping framework to monitor dehydration. Leveraging a 4-year dataset across 135 cultivar-environment combinations, we demonstrate that the GMC threshold for physiological maturity is relatively stable (≈25%). Concurrently, we developed 2 image-based models for GMC estimation, achieving high accuracies (R2 = 0.82 and 0.86). Integrating this physiological threshold with GMC estimation models enabled the successful reconstruction of the dehydration process. Validation on 26 independent cultivars across 2 sowing dates predicted physiological maturity with a root mean square error of 2.4 to 3.3 d. Traits extracted from these dehydration profiles accounted for 42% of the variance in grain weight, doubling the explanatory power of traditional traits. These gains are largely attributed to a new integrated trait, the moisture maintenance index, which showed a higher and more stable correlation with thousand-grain weight (r = 0.6). This framework offers a scalable approach for monitoring large-scale dehydration dynamics to deepen our understanding of grain weight formation, facilitating the genetic improvement of the filling process to enhance crop yield.

Why it matches plant phenotyping methods穀粒含水率の画像推定モデルと生理学的閾値を統合し、脱水動態や成熟期などの植物形質を高スループットに抽出・検証する枠組みが研究の中心である。

abstractwe propose a high-throughput, physiology-informed phenotyping framework to monitor dehydration

Using UAV Multispectral Imagery to Predict Leaf SPAD Dynamics During Maize Growth Under Different Plant Densities ↗

Chlorophyll content represents a key growth indicator for maize. The traditional SPAD (Soil and Plant Analyzer Development) method, though easy to operate, is inefficient, destructive, and unsuitable for high-throughput field monitoring. UAV (Unmanned Aerial Vehicle) remote sensing technology is highly efficient and detects abundant indicators, enabling large-scale SPAD measurement. In this study, 18 vegetation indices and eight texture features were selected as the indicator system by combining prior knowledge and experimental analysis. In a two-year maize density experiment, multispectral images were collected in the growth period. The correlations among SPAD values, multispectral indices and texture features were analyzed using Pearson correlation coefficients. Then the detection accuracies of three algorithms, i.e., RF (Random Forest), PLSR (Partial Least Squares Regression), and SVR (Support Vector Regression), were compared under this indicator system. Compared with models constructed using single vegetation indices or single texture features, the estimation accuracy of the indicator system at the jointing stage was improved by 0.13 and 0.22, respectively. The results showed that SVR achieved the highest estimation accuracy among the three algorithms, with determination coefficients (R2) of 0.73, 0.77and 0.70 at the jointing, silking, and grain-filling stages, respectively. This study established a non-destructive monitoring framework for chlorophyll content during the entire maize growth stage based on UAV data.

Why it matches plant phenotyping methodsUAVマルチスペクトル画像と回帰モデルにより、トウモロコシの葉緑素量（SPAD）を非破壊推定する手法を構築し、複数アルゴリズムの精度比較も行っており、表現型取得手法が中心である。

abstractThis study established a non-destructive monitoring framework for chlorophyll content during the entire maize growth stage based on UAV data.

Thermal imaging as a tool for studying circadian rhythms in roots. ↗

Plants rely on the circadian clock to anticipate daily environmental fluctuations and to coordinate key physiological, metabolic, and developmental processes. Most if not all plant cells have semi-autonomous circadian oscillators. Roots possess a modified yet robust circadian oscillator that is entrained by external cues such as light and temperature to synchronize nutrient uptake, water transport, and metabolic activity. It has been shown that the root and shoot oscillators can communicate through long-distance signals including mobile proteins and carbon assimilates such as sucrose. Moreover, recent studies indicate root-microbe interactions; root-associated microbial communities exhibit diurnal oscillations structured by the host circadian system, while microbes can in turn modulate the circadian period and rhythmic outputs of the plant. However, in general, while the shoot circadian oscillator has been extensively characterized, much less is known about the root circadian system. Progress has been hampered by a lack of high-throughput, non-invasive methods to study root rhythmicity. Existing methods including luciferase reporters, quantitative RT-PCR, and microscopy remain limited by cost, destructive sampling, or require transgenic lines with reporter genes. We have developed a thermal infrared imaging platform that enables non-invasive, high resolution of circadian rhythms in roots across plant species and growth conditions. We show that our system can be used to analyse metabolite and microbial effects on root circadian regulation. This platform provides new opportunities to investigate below-ground circadian regulation and the possibilities of harnessing the root clock to enhance plant performance and resilience.

Why it matches plant phenotyping methods根の概日リズムという植物状態を、非破壊・高解像度の熱赤外画像で測定するプラットフォームを開発しており、フェノタイピング手法が研究の中心である。

abstractProgress has been hampered by a lack of high-throughput, non-invasive methods to study root rhythmicity.

Dynamic, adaptive and modular Digital Twin framework for resource-efficient Controlled Environment Agriculture. ↗

In Controlled Environment Agriculture (CEA), traditional fixed set-point control is replaced by dynamic control strategies. These strategies enable joint optimization of resource use efficiency and biomass output, leverage electricity price fluctuations to reduce energy costs, and employ targeted environmental stressors to enhance crop quality and physiological resilience. Implementation of dynamic control strategies, however, builds upon real-time monitoring, robust data integration and management, and high-fidelity predictive modeling. These capabilities can be effectively provided through a Digital Twin (DT). This study introduces a novel open-source DT framework designed to support dynamic control strategies in CEA, addressing challenges in scalability, generalizability and interoperability. The framework is centered on the IoT platform ThingsBoard, providing unified, scalable data acquisition and management across heterogeneous sensor and actuator networks through vendor-agnostic integration and standardized interfaces. A significant contribution is its physics-based modeling backend, built on ordinary differential equation models developed in Modelica and exported as Functional Mock-up Units (FMUs). To ensure model accuracy across varying biological conditions, a parameter estimation pipeline is developed to calibrate and adapt these FMUs against experimental data. Building on this, a dedicated simulation backend is implemented to leverage the calibrated FMUs, providing the dynamic predictive capabilities necessary for proactive system control. Furthermore, the framework incorporates a Multirate Moving Horizon Estimation (MMHE) state estimator to estimate critical unmeasured variables, such as plant biomass. This estimator is specifically designed to handle multirate data, maintaining continuous estimates even when certain sensors provide frequent data while others are sparse or infrequent. Demonstrated through a simulation-based case study modeling lettuce growth in a vertical hydroponic farm, the DT framework's architectural feasibility and virtual modeling capabilities are verified. Using synthetic data generated from a known true parameter set, the calibrated growth model achieved a low cross-validation prediction error, with an RMSE of 0.221g and an NRMSE of 6.62% on an independent test set. The MMHE-based state estimator effectively maintained continuous biomass estimates despite sparse synthetic measurements and model mismatch. These findings underscore the framework's potential as a robust and extensible foundation for future physical DT implementations in CEA, enabling a 31 transition toward dynamic, data-driven, and energy-aware operations.

Why it matches plant phenotyping methods植物バイオマスという観測可能な植物形質を、デジタルツインの状態推定器と動的モデルで継続的に推定する方法を開発・検証しており、単なる栽培制御や routine measurement ではない。

abstracta dedicated simulation backend is implemented to leverage the calibrated FMUs, providing the dynamic predictive capabilities necessary for proactive system control.

Phenomics-derived temporal maize health and environmental index enhance physiology-informed genomic prediction of yield across environments. ↗

Integrating multi-omics data, including phenomic, genomic, and environmental inputs, offers a powerful approach for enhancing maize performance and predicting grain yield. In this study, crop health was quantified using temporal NGRDI (Normalized Green Red Difference Index) trajectories collected from 16 unoccupied (unmanned) aerial vehicle or system (UAV or UAS, drones and sensors) flights (from 19 to 117 d after planting) in maize trials conducted in Texas. Crop health indices (CHIs) were calculated through area under the curve (CHIAUC) and functional principal component analysis (CHIFPCA), capturing dynamic plant health responses throughout the growing season. Heritability estimates of NGRDI fluctuated between 0.3 and 0.7, averaging 0.51 ± 0.02, reflecting consistent genetic contributions to growth dynamics. CHIs derived from a favorable (irrigated) trial in Texas effectively separated high- and low-yielding hybrids across 41 environment-tester combinations, achieving significant differentiation in 27 (CHIAUC ) and 28 (CHIFPCA1) environments. In comparison, only 21 environments were differentiated when using grain yield alone. Genomic mapping of temporal NGRDI revealed key quantitative trait loci (QTLs) linked to maize growth, containing candidate genes including br2, phyC1, wus1, mads69, cct1, rap2, miR172, and gl15, associated with canopy development, flowering regulation, and drought adaptation. Integrating multi-omics data into phenomic- and environment-informed genomic prediction models improved yield prediction accuracy by approximately 18.5%, particularly for untested genotypes in both tested and untested environments. These findings demonstrate that multi-omics integration provides a scalable framework for enhancing maize performance and advancing grain yield prediction across diverse agricultural systems.

Why it matches plant phenotyping methodsUAV画像から時系列NGRDIを抽出し、作物健康・生育動態の表現型指標を構築して検証・予測に利用しており、フェノタイピング手法の適用が研究の中心的要素です。

abstractCrop health indices (CHIs) were calculated through area under the curve (CHIAUC) and functional principal component analysis (CHIFPCA), capturing dynamic plant health responses throughout the growing season.

Unveiling the genetic control of repeat flowering in blueberry with a novel continuous quantitative phenotyping approach ↗

Flowering in perennial crops is a trait influenced by genetics, environmental cues and plant vigor. Here, we studied the genetic and environmental control of repeat flowering (RF) in blueberry ( Vaccinium corymbosum ). RF was measured in a full-sib population from a cross between repeat and non-repeat flowering cultivars (‘Hortblue Petite’ and ‘Nui’, respectively). Longitudinal phenotypes were used to model the area under the curve for the first and second flowering peaks. We found that RF was strongly influenced by bush size and vigor, which we then incorporated into the area under the flowering curve models. Quantitative trait loci linked to both first bloom and RF were detected at three hotspots on chromosomes 4 and 10, and genes of interest known to regulate flowering under both temperature and photoperiod control were discussed. The phenotyping protocol and statistical modelling method reported here are an effective strategy for the investigation of complex interactions between multiple genetic loci and environmental variables on developmental traits, such as flowering. Experimental designs with replicated multi-environment and multi-year measurements are now needed to corroborate our results and further elucidate the determinism of RF in blueberry.

Why it matches plant phenotyping methodsブルーベリーの反復開花を連続的・定量的に測定し、開花曲線のモデリングを組み合わせた新規フェノタイピング手法とプロトコルが明示され、開花形質の遺伝解析における方法論的貢献が中心的です。

titlewith a novel continuous quantitative phenotyping approach

A physics-informed neural network for continuous rice canopy thermal monitoring and forecasting from sparse UAV observations ↗

Continuous monitoring of canopy temperature (Tc), a key indicator of crop water-heat stress and physiological dynamics, using unmanned aerial vehicle (UAV) imagery is inherently limited by temporal discontinuity and the limited physical realism of purely data-driven models. This study develops a physics-informed neural network (PINN) framework to transform temporally sparse UAV thermal observations into continuous hourly rice Tc reconstruction and 48 h forecasting products. The model leverages sparse UAV thermal measurements as supervisory signals while integrating them with continuous meteorological forcing and daily UAV-derived crop phenotypic features. Validated through a comprehensive season-long rice field experiment using walk-forward cross-validation, the proposed PINN framework demonstrated superior performance. It achieved R 2 values of 0.92 for reconstruction and 0.90 for forecasting, with RMSE of 0.71 °C and 0.82 °C, respectively. Ablation analysis further showed that crop phenotypic variables contributed more strongly than temporal descriptors, reducing predictive uncertainty by approximately 4.8–14.3 %, while the integration of SEB physical constraints and uncertainty modeling improved R 2 by 8.4–9.5 % and reduced Total STD by 28.4–37.7 %. The model successfully captures diurnal dynamics, spatial variability, and canopy thermal hysteresis while maintaining physical consistency through improved energy closure. This framework bridges sparse aerial observations with continuous physiological monitoring and highlights its potential to support precision irrigation, early stress detection, and high-throughput phenotyping in smart agriculture.

Why it matches plant phenotyping methodsUAV熱画像による疎な観測からイネ群落温度を連続再構成・予測するPINNを開発し、交差検証とアブレーション分析で性能評価しており、表現型取得・推定手法が研究の中心である。

abstractThis study develops a physics-informed neural network (PINN) framework to transform temporally sparse UAV thermal observations into continuous hourly rice Tc reconstruction and 48 h forecasting products.

Hybrid CNN–GRU Architecture for Early Plant Disease Diagnosis Using Sequential Crop Images ↗

Agricultural productivity, crop quality, and food security worldwide can be highly impacted by plant diseases. Early detection and accurate diagnosis of disease in crops are vital for minimizing losses and sustaining precision farming practices. Regrettably, all modern disease diagnosis approaches based on deep learning techniques have concentrated on image classification, neglecting the time dependency of the disease process during different stages of the crops’ development cycle. Furthermore, traditional CNN-LSTM models have been associated with increased computational complexities and high memory costs. This research suggests a CNN-GRU hybrid model for early disease detection using sequential analysis of crop images. The suggested technique involves integrating the CNN and GRU, which helps the network develop the capability to learn spatiotemporal information on the crop plant disease. Datasets of sequential crop images that represent the progression stages of the diseases were collected from Plant Village and augmented crop images. The CNN portion of the model is responsible for extracting spatiotemporal characteristics of the diseases, including lesions, discolored parts, and texture changes. It is evident that the suggested Hybrid CNN-GRU method has higher accuracy (94.1%), precision (94.0%), recall (93.9%), and F1-score (94.0%) compared to CNN and CNN-LSTM models. The validation of efficacy and robustness of the suggested approach has been confirmed through standard deviation, paired t-test, and 5-fold cross-validation. Furthermore, the method demonstrated high scalability and strong tolerance to variations in light intensity, noise, and images from the fields of crop plants.

Why it matches plant phenotyping methods植物病害の病変・変色・テクスチャ変化を連続画像から抽出し、CNN-GRUモデルで病害状態を推定する手法の開発と検証が中心であるため。

abstractThis research suggests a CNN-GRU hybrid model for early disease detection using sequential analysis of crop images.

Beyond static snapshots: predicting dynamic, explainable intermediate phenotypes for climate-resilient crop breeding ↗

The convergence of multi-omics profiling, high-throughput phenotyping (HTP), and artificial intelligence (AI) has expanded our ability to characterize crop stress responses at unprecedented resolution (Danilevicz et al., 2025;Pacheco-Ruiz et al., 2025;Tsega and Mullualem, 2026). Researchers can now routinely identify candidate genes, construct gene regulatory networks, and train machine learning models to predict terminal phenotypes, such as yield under drought, biomass under salinity, and disease severity scores. Yet the practical impact remains limited: delivering a single improved crop variety to market still requires approximately one decade and more than 14 million euros, a timeline that has barely changed in 30 years despite the exponential growth in data generation (Pacheco-Ruiz et al., 2025). We argue that a fundamental cause of this translational gap is what we call the temporal poverty of current GP: models often predict static endpoints rather than the dynamic processes that determine them.Classical GP models, including multi-omics-informed variants, are overwhelmingly trained on traits measured at single time points, such as final yield or end-of-season stress scores. However, stress tolerance is inherently temporal, reflecting a cascade of physiological decisions whose sequence and timing ultimately determine field survival: when to close stomata, how rapidly to accumulate osmolytes, and whether to prioritize root extension or shoot preservation. A model that predicts terminal drought tolerance without distinguishing whether it arises from early water conservation, sustained photosynthesis, or post-stress recovery offers limited support for rational gene stacking or knowledge transfer across environments and crops (Danilevicz et al., 2025). Based on these observations, we hypothesize that making the dynamic trajectories of intermediate physiological traits the direct targets of GP, rather than treating them as auxiliary variables, will substantially improve prediction accuracy, mechanistic interpretability, and the rate of genetic gain for stress resilience in crop breeding.To bridge this temporal gap, we propose a dynamic explainable genomic prediction framework centered on intermediate physiological trajectories (Figure 1). The framework integrates dynamic phenotyping, environmental information, and mechanistic multi-omics anchors to support trajectory-aware prediction and climate-resilient breeding.Conventional genomic prediction focuses on static endpoint prediction, whereas the proposed framework targets dynamic intermediate phenotypes and integrates environmental and multi-omics information to enable trajectory-aware, interpretable prediction for climate-resilient crop breeding.This reframing is becoming increasingly feasible. The recent dynamicGP model combines GP with dynamic mode decomposition (DMD) to predict full temporal trajectories of multiple morphometric and colorimetric traits scored by HTP in maize and Arabidopsis thaliana (Hobby et al., 2025). DynamicGP was also shown to predict traits at time points beyond the training period. It was the only model tested with this capability and showed superior longitudinal accuracy in capturing developmental dynamics (Hobby et al., 2026). The model further revealed that traits with more temporally stable heritability can be predicted with higher accuracy, providing practical guidance on which dynamic intermediates to prioritize (Hobby et al., 2025).Mechanistic modeling offers a complementary line of evidence: computational models of grass inflorescence morphodynamics recently guided the discovery of the duo2 mutant allele in wheat, which accelerates developmental progression and improved yield by 7-11% under field conditions (Wang et al., 2026b). These two independent advances, one data-driven and one mechanism-driven, converge on the same insight: incorporating time as a central dimension in prediction can provide predictive power and mechanistic understanding that are inaccessible to static models, thereby connecting prediction with actionable breeding decisions.A realistic view of current data availability shapes this strategy. The current and near-future foundation for dynamic intermediate phenotype prediction is largely HTP.The marginal cost of repeated phenotyping with automated platforms, UAVs, and low-cost sensors has decreased substantially, and public time-series datasets covering wheat, sorghum (LeBauer et al., 2020), soybean, and several other crops are rapidly expanding. This supports a pragmatic, asymmetric integration strategy: HTP provides the dense temporal skeleton of dynamic trait trajectories, while multi-omics is deployed selectively at a small number of mechanistically critical time windows, such as the onset of stress signaling, the transition from alarm to acclimation, or the peak of a known physiological trade-off. These sparse but information-rich omics snapshots serve as "explainability anchors." When explainable AI approaches are used to link these molecular profiles to parameterized dynamic modes extracted from HTP, the resulting model can reveal which genes, transcripts, or metabolites modulate specific phases of the dynamic response and when. For instance, SHAP-based interpretation of Random Forest models applied to soybean multi-omics data revealed that the isoflavone derivative daidzin and specific drought-tolerant microbes are major contributors to phenotypic variation under drought stress, while SHAP-based interaction networks uncovered cross-omics links between metabolites and microbial taxa (Yoshioka et al., 2026). Extracting biologically meaningful signals from such comparisons requires specialized computational tools. The MODAS2 pipeline, for example, uses contrastive principal component analysis, a machine learning algorithm, to disentangle stress-responsive molecular QTLs from background genetic effects in multi-omics data, enabling the identification of salt-responsive genetic variants in maize (Liu et al., 2025). Such tools are essential for implementing the explainability-anchor strategy at the stress-transition windows targeted by our framework.Advocating for dynamic intermediate phenotypes as prediction targets does not mean abandoning terminal agronomic traits. The two approaches serve complementary roles at different stages of the breeding pipeline. In early-generation selection, when thousands of lines must be evaluated and resources for multi-environment yield trials are limited, dynamic intermediates, which are often measurable earlier, at lower cost per data point, and with higher heritability, can help enrich populations for stress-resilient candidates (Melsen et al., 2025). In later-stage trials, direct prediction of yield under target stress environments remains indispensable for final variety release decisions. In practice, the central question is not which target is superior in isolation, but whether their combined use can accelerate genetic gain for stress tolerance.Dynamic intermediate phenotypes can contribute to genetic gain through three main routes. First, many dynamic intermediates show higher heritability and earlier measurability than terminal yield under stress, enabling more accurate early-generation selection and shorter breeding cycles. Second, a dynamic physiological module, such as rapid osmotic adjustment within 48 hours of soil drying, can become a reusable building block once it has been genetically dissected and validated. Such modules could then be stacked, introgressed, or transferred across genetic backgrounds and crop species. Third, selecting on the shape of a response curve rather than a single terminal value can reduce environmental noise, because temporal patterns are often more genetically determined than absolute end-point values (Hobby et al., 2025). This framework is also inherently cross-crop: a conserved physiological module such as "stomatal response speed to soil drying" is unlikely to be restricted to a single species. Orthologous genes and conserved pathways can inform candidate selection in legumes, vegetables, and under-researched crops, extending advanced breeding methodologies beyond the major cereals (Kundu and Tanti, 2026;Wang et al., 2026b).The dynamic GP framework we advocate remains incomplete without explicit environmental inputs. At present, many AI-driven prediction models treat the environment as a categorical label or a set of static summary statistics. This approach can conflate genetic and environmental effects and limit performance forecasting across mega-environments or novel climatic scenarios. To support the development of climate-resilient varieties, models should instead incorporate environmental data as an explicit, dynamic data layer, including time series of temperature, soil moisture, and vapor pressure deficit, that co-determines the trajectory of intermediate phenotypes.Recent advances suggest that this is increasingly feasible. Enviromics and reaction-norm approaches that incorporate high-dimensional environmental covariates through penalized regression can now approach the accuracy of deep learning while retaining interpretability and an explicit description of genotype-by-environment interactions (Avagyan et al., 2025). In parallel, hybrid frameworks that couple crop growth models with whole-genome prediction can link genetic, environmental, and management inputs to dynamic physiological outputs (Laurent et al., 2025). Building on these developments, embedding environmental time series into the temporal kernels of dynamic models such as dynamicGP could, in principle, enable prospective, environment-aware forecasting of genotype-specific response curves. This would shift selection from retrospective mega-environment classification toward forward-looking prediction across single or multiple target mega-environments. However, robust extrapolation to untested environments and stress combinations remains a key open challenge. Careful envirotyping and cross-environment validation will therefore be essential before such models can guide variety deployment decisions in practice.The framework proposed here has important implications for future crop production.By shifting the breeding target from terminal yield to the temporal architecture of stress responses, breeders could develop selection strategies that are both physiologically informed and operationally efficient. Dynamic intermediate phenotypes, captured through increasingly affordable HTP platforms, can serve as early indicators of resilience, allowing breeders to discard susceptible lines long before harvest. This could shorten the breeding cycle, especially when combined with genomic selection and speed breeding, while also enabling the deliberate assembly of stress-resilience modules that are robust across environments. Empirical evidence already shows that integrating HTP-derived spectral data with genomic information can substantially improve cross-environment prediction accuracy (McBreen et al., 2025;Nannuru et al., 2025). As climate variability intensifies, the ability to design varieties with predictable temporal behavior under drought, heat, or salinity will become increasingly important for enhancing yield stability and food security.Challenges remain. Dynamic GP models have yet to be systematically validated across radically different environments, and their ability to predict trait dynamics under novel stress combinations remains unproven. Data from controlled HTP platforms must also be calibrated against field conditions. In addition, the integration of heterogeneous multi-omics datasets creates persistent bottlenecks that constrain practical application beyond proof-of-concept studies (Pacheco-Ruiz et al., 2025;Tsega and Mullualem, 2026). Multi-omics time series, even at the sparse sampling density we advocate, remain limited by high technology costs and scalability challenges that restrict their routine deployment in breeding programs (Syeda, 2025;Younas et al., 2025). However, pilot-scale time-series multi-omics studies demonstrate both feasibility and value. For example, transcriptomic and ionomic profiling of Sorghum bicolor across a 21-day micronutrient stress time course revealed iron-zinc regulatory crosstalk and conserved gene regulatory networks (Mishra et al., 2025), while high-resolution time-series transcriptomic and metabolomic profiling of salt-tolerant and salt-sensitive maize inbred lines identified the hub gene ZmGLN2 and constructed dynamic regulatory networks governing salt-responsive metabolite biosynthesis (Zhang et al., 2025). Furthermore, the MODAS2 pipeline, which uses contrastive principal component analysis to extract stress-responsive signals from multi-omics comparisons, illustrates that the computational methods needed to integrate heterogeneous omics layers are already under active development (Liu et al., 2025).Equally important is the ability of AI models to capture the non-linear genetic interactions that underpin complex stress responses. Linear mixed models, the backbone of classical GP, primarily model additive effects and therefore have limited capacity to capture epistasis, gene-by-environment interactions, and threshold-type responses (Wang et al., 2026a). In contrast, deep learning architectures can learn hierarchical, non-linear mappings from high-dimensional input spaces. When applied to dynamic intermediate phenotypes, these models could learn not only which genomic regions influence the temporal shape of a trait, but also how those regions interact with each other and with environmental triggers over time. For example, convolutional neural networks have outperformed classical methods such as LASSO and Bayes C in predicting integrative traits, with the combination of CNNs and crop model parameters further enhancing prediction accuracy (Larue et al., 2024). Fully harnessing non-linear interactions for dynamic trait prediction will likely require hybrid approaches that embed mechanistic constraints into flexible AI architectures, ensuring that predictions remain both powerful and biologically plausible.As outlined in the preceding section, integrating environmental time series into dynamic GP models remains a frontier, but the computational tools and conceptual frameworks are now within reach. The integration of environmental data with multiple omics layers for genotype-by-environment prediction has been identified as a major emerging frontier, although it is currently addressed in fewer than 20% of studies (Tsega and Mullualem, 2026). This gap underscores the urgency of the framework we advocate. These are not sequential prerequisites, but parallel investments that reinforce one another. We therefore call on the crop science community to: (i) prioritize the generation of time-series phenotypic data in multi-environment stress trials, leveraging increasingly affordable HTP platforms; (ii) adopt explainable AI as standard practice, not merely reporting prediction accuracy but also elucidating which features drive predictions, when, and through which physiological mechanisms (Danilevicz et al., 2025); and (iii) develop selection indices that explicitly reward favorable dynamic trajectories alongside terminal trait values.Multi-omics and AI should not merely describe how stress resistance appears at harvest; they must reveal how it unfolds over time and how it can be rationally assembled. Bridging this temporal gap will connect current data abundance with the practical goal of delivering climate-resilient crops to farmers' fields.In

Why it matches plant phenotyping methods動的HTP phenotypingと軌跡予測を中核とする概念・方法論的枠組みを提案し、既存モデル、環境データ統合、検証課題を体系的に論じているため。

abstractThe recent dynamicGP model combines GP with dynamic mode decomposition (DMD) to predict full temporal trajectories of multiple morphometric and colorimetric traits scored by HTP in maize and Arabidopsis thaliana

A hyperbolic topological atlas reveals polyamine steering of a shared developmental manifold in Arabidopsis ↗

Abstract High-throughput plant phenotyping captures development at scale, yet image-rich screens are still often reduced to static trait summaries. We tested whether nutrient availability, polyamine priming, concentration, and their transport reshape Arabidopsis rosette development by generating distinct morphologies or by changing residence along a common trajectory. We analyzed 138,223 time-resolved rosette images from Col-0 and five mutants involved in polyamine transport ( put1-5 ) primed to putrescine, spermidine, spermine, dose, and nutrient regimes using a self-supervised vision backbone, Poincaré embedding, hyperbolic Mapper, and manifold straightening. The data form a single connected developmental manifold with 410 nodes and 746 edges, organized from an early, low-nutrient-biased hub through high-betweenness transition corridors to two late, nutrient-enriched terminal regions. Polyamine identity stratifies this manifold by developmental phase: putrescine enriches early states, spermidine occupies transition corridors, and spermine marks late compact rosettes. Nutrient richness and dose change distal occupancy, whereas put genotypes alter dwell time within shared regions rather than producing separate topologies. Manifold straightening resolves these effects into a short early lateral deflection followed by convergence, yielding two scalar readouts, early transverse offset and distal occupancy, that summarize treatment action on a common morphodynamic scale. The framework converts large image screens into interpretable developmental geometry for image-based phenomics.

Why it matches plant phenotyping methods大規模なロゼット画像から発達形態を抽出し、自己教師あり視覚モデルとトポロジー解析で再利用可能な表現型指標を開発・適用しており、表現型取得・解析手法が研究の中心である。

abstractHigh-throughput plant phenotyping captures development at scale, yet image-rich screens are still often reduced to static trait summaries.

Genetic dissection of dynamic leaf area index variation in maize using UAV-based phenotyping and time-series genome-wide association studies ↗

Abstract The leaf area index (LAI) is a key determinant of canopy architecture and yield potential in maize, primarily through its influence on photosynthetic efficiency. Although unmanned aerial vehicle (UAV) technology has greatly advanced field-based phenotyping, its potential for deciphering the genetic mechanisms underlying dynamic and complex trait development remains underexplored. In this study, multispectral UAV images were collected from a diverse maize panel across eight developmental stages in four environments over two consecutive years. Using multi-temporal data, a random forest model accurately predicted LAI (R² = 0.82–0.83), significantly outperforming models based on single time-point data. By integrating high-throughput phenotypic predictions with time-series genome-wide association studies (GWAS), 36 dynamic SNPs associated with LAI variation were identified. Principal component analysis (PCA) of temporal LAI data revealed two principal components that together explained 84.2–86.5% of the total phenotypic variance. GWAS based on these components identified an additional 51 SNPs, seven of which overlapped between the two analytical approaches. Among the 72 candidate genes identified, Zm00001d048615 exhibited significant variation in both phenotype and expression among different inbred lines. The heterologous overexpression of Zm00001d048615 in Arabidopsis induced leaf curling and a significant reduction in leaf size, indicating its potential role in regulating leaf development. Collectively, these findings establish a robust framework that integrates UAV-based phenomics with temporal GWAS to identify key genes regulating complex dynamic traits. This approach provides valuable insights and genetic targets for improving maize canopy architecture and yield potential through molecular breeding.

Why it matches plant phenotyping methodsUAVマルチスペクトル画像と時系列データからLAIを推定するモデルを開発・評価し、高スループット表現型解析に中核的に用いているため。

abstractmultispectral UAV images were collected from a diverse maize panel across eight developmental stages in four environments over two consecutive years.

Automated, high-throughput hyperspectral imaging enables early detection of grapevine downy mildew and monitoring of vineyard spray program performance. ↗

Grapevine downy mildew (GDM), caused by Plasmopara viticola, is managed largely through repeated fungicide applications, yet evaluating spray-program performance is difficult because field infections are spatially heterogeneous. However, host physiological changes can precede visible symptom development. We tested whether standardized, high-throughput VNIR hyperspectral imaging of field-grown grapevine leaf discs can capture early optical changes associated with infection and discriminate program-linked mitigation. Leaves were collected from a 2025 vineyard trial in Geneva, NY (cv. La Crescent) managed under three spray programs (conventional fungicides, biofungicides, and untreated control). Leaf discs (≈87 per program) were excised, inoculated with P. viticola, and imaged at 0.5, 1.5, and 3.5 days post inoculation (dpi) using a custom built, automated, hyperspectral imaging microscopy platform (400-980 nm). No visible sporulation occurred at 0.5 or 1.5 dpi; sporulation was first observed at 3.5 dpi and occurred only in the untreated control, whereas no discs from either treated program sporulated. Multivariate spectral analyses showed significant separation by spray program and dpi, and disease-related spectral indices exhibited program-dependent trajectories, with treated discs showing attenuated optical change relative to the control. A random-forest classifier trained on pre-sporulation spectra (0.5 and 1.5 dpi; N = 169) predicted subsequent sporulation with 0.78 accuracy and 0.77 ROC-AUC (95% CI 0.68-0.85), highlighting informative bands across visible, red-edge, and near-infrared regions. Together, these results support outcome-linked, replicate-rich hyperspectral phenotyping of vineyard spray programs using field-derived material under standardized acquisition conditions.

Why it matches plant phenotyping methods自動化VNIRハイパースペクトル撮像で、発病前のブドウ葉の光学的変化と将来の胞子形成を推定する手法を中心に検証しており、植物病害状態の表現型取得・分類に該当する。

abstractWe tested whether standardized, high-throughput VNIR hyperspectral imaging of field-grown grapevine leaf discs can capture early optical changes associated with infection and discriminate program-linked mitigation.

Multimodal Deep Learning for Pest and Disease Recognition and Crop Growth Assessment in Open-Field Agricultural Environments ↗

Against the backdrop of the rapid development of smart agriculture, pest and disease monitoring and crop growth assessment for large-scale farmlands are of substantial importance for precision management and risk early warning. However, traditional unimodal visual methods are highly susceptible to illumination variation, canopy occlusion, scale differences, and background interference in real field environments, and thus fail to make full use of environmental sensing information and spatial priors. To address these issues, a multimodal target perception framework for intelligent farmland inspection is proposed in this study. By jointly integrating UAV imagery, time-series data from ground Internet of Things sensors, and spatial positional information, joint modeling of pest and disease recognition and crop growth assessment is achieved through cross-modal alignment and collaborative encoding, multi-scale target perception, and dynamic multimodal fusion and decision-making. Experimental results demonstrate that, in the pest and disease recognition task, the proposed method achieved a Precision of 91.63%, a Recall of 90.27%, an F1-score of 90.94%, and an mAP of 93.15%, significantly outperforming comparison models such as Faster R-CNN with ResNet50 backbone, YOLOv8-m, Swin Transformer-Tiny, and Multimodal Transformer. In the crop growth assessment task, an Accuracy of 89.96%, a Precision of 89.11%, a Recall of 88.74%, and a Macro-F1 of 88.92% were achieved, again clearly exceeding those of ResNet50, EfficientNet-B3, ViT-B/16, and conventional multimodal fusion models. The ablation study further verified the effectiveness of the cross-modal alignment module, the multi-scale target perception module, and the dynamic fusion module, with the complete model reaching 90.94%, 93.15%, and 88.92% in Pest F1, Pest mAP, and Growth Macro-F1, respectively. Furthermore, the net economic return regression experiment at the unit-area level further demonstrates that the proposed method can effectively connect state information with economic outcomes, showing strong application potential in return prediction, performance evaluation, and resource allocation optimization. These findings indicate that the proposed method can effectively improve perception accuracy and robustness in complex farmland environments, thereby providing reliable technical support for intelligent inspection, pest and disease early warning, and precision management in agricultural scenarios.

Why it matches plant phenotyping methodsUAV画像、IoT時系列データ、空間情報を統合したマルチモーダル手法を開発し、作物生育状態の評価を技術的に検証している。害虫認識単独ではなく、植物の生育評価を含む取得・推定手法が中心である。

abstracta multimodal target perception framework for intelligent farmland inspection is proposed in this study.

Rapid rice seed vigor assessment: A machine learning and deep learning framework with multi-time-point image analysis. ↗

Automated rice seed vigor classification provides a non-invasive and scalable solution for improving agricultural decision-making. This study proposed an image-based framework to compare traditional machine learning and deep learning approaches for classifying individual rice seed vigor using standard RGB images. Machine learning models were developed using hand-crafted morphological and color features, while convolutional neural networks were employed to automatically extract visual patterns related to seed quality. Both single-time-point and multi-time-point image analysis strategies were investigated. Models trained on images captured at individual growth stages were compared with a multi-time-point ensemble approach that integrated visual information across multiple developmental stages. The ensemble approach achieved superior performance, highlighting the importance of incorporating temporal growth dynamics into vigor classification. Notably, traditional machine learning models performed comparably to deep learning models when informative features were carefully engineered. To improve transparency and reliability, interpretability techniques were applied to better understand model decisions. Overall, the findings demonstrate the practical potential of data-driven, image-based seed vigor assessment.

Why it matches plant phenotyping methodsRGB画像と機械学習・深層学習を用いてイネ種子の活力を自動推定する枠組みを開発・比較しており、表現型取得・抽出手法が研究の中心である。

abstractThis study proposed an image-based framework to compare traditional machine learning and deep learning approaches for classifying individual rice seed vigor using standard RGB images.

Sat-Crop transformer: integrating temporal satellite imagery and GAN-based synthesis for vegetation health monitoring ↗

Monitoring vegetation health is vital for environmental management, agriculture, and land use planning. We introduce an innovative approach that integrates satellite imagery analysis and predictive modeling to predict vegetation indices and generate synthetic field images. We propose the Sat-Crop Transformer, a transformer-based model specifically designed for satellite crop monitoring for the prediction of crop health. Historical satellite imagery data, including vegetation indices such as the modified soil-adjusted vegetation index and environmental parameters, are used to predict future vegetation indices. The Sat-Crop Transformer demonstrates better performance in capturing long-range dependencies in temporal satellite data. A generative adversarial network–based approach is used to generate synthetic field images corresponding to the predicted vegetation indices, thereby enhancing the data visualization and model training. This integration of advanced predictive modeling and image generation provides a deeper understanding of environmental processes and supports decision-making in various domains.

Why it matches plant phenotyping methods衛星時系列画像から作物の植生指数・健康状態を推定するモデルを中心的に開発しており、植物状態の定量的推定手法に該当する。

abstractWe introduce an innovative approach that integrates satellite imagery analysis and predictive modeling to predict vegetation indices and generate synthetic field images.

Forest biometrics in the 21 century special issue ↗

Abstract Forest biometrics has evolved from a measurement-driven discipline focused on field efficiency and statistical rigor to a data-rich, technology-enabled science integrating multisensor information and advanced modeling approaches. This special issue, inspired by the Second North American Forest Mensurationists Conference held in 2022, highlights this transformation through nine studies that collectively span scales from individual branches to regional forest dynamics. Together, they emphasize a shift from identifying single optimal models to developing integrated, uncertainty-aware model systems that support operational decision-making. At the finest scale, advances in terrestrial laser scanning enable improved characterization of branch geometry under challenging conditions, yielding robust taper and form factor estimates for volume. At the tree level, extensive benchmarking of height–diameter relationships demonstrates that model form and stand origin strongly influence predictive performance, with generalized additive models often outperforming traditional approaches. Complementary work shows that calibration strategies are not universally transferable across model forms, underscoring the need for careful alignment of function choice and calibration design. Addressing biases in young stands, Bayesian model averaging offers a practical interim solution where traditional volume models trained on mature cohorts fail. At broader scales, studies demonstrate the operational potential of integrating public and low-cost remote sensing data. Freely available USGS 3DEP LiDAR supports highly accurate dominant height and site index estimation, while bias-corrected digital aerial photogrammetry provides a viable alternative in areas lacking LiDAR coverage. Landscape-level analyses using Landsat time series and permanent plots enable mapping of basal area growth, revealing spatial variability and temporal trends driven largely by stand dynamics. Collectively, these studies define a cohesive framework for modern forest biometrics: combining multiple data sources, selecting model families deliberately, applying light but effective calibration, and explicitly quantifying uncertainty. This integrated approach supports scalable, reliable predictions tailored to the needs of forest managers and policymakers. The special issue thus outlines a forward-looking research agenda that prioritizes resilient modeling systems over isolated solutions, enabling forestry to meet contemporary challenges across scales from tree components to landscapes.

Why it matches plant phenotyping methods森林の枝形状、樹高、林分指標などの植物形質を、レーザースキャン、航空写真、LiDAR、時系列衛星データ、統計モデルで推定・検証する方法群を中心に扱う特集概説であり、測定・推定手法が中心である。

abstractAt the finest scale, advances in terrestrial laser scanning enable improved characterization of branch geometry under challenging conditions, yielding robust taper and form factor estimates for volume.

Integrated assessment of drought-driven vegetation declines in Olive and Citrus Orchards of Semi-Arid Morocco: A Multi-Index Remote Sensing Framework ↗

Abstract In the era of climate change, drought is defined as one of the most severe natural catastrophes that affects the environment, crop growth, and water resources, leading to economic losses, migration, and risks to human life. Since 2019, Morocco has suffered one of the most severe droughts in its recording history, coinciding with a broader period of precipitation deficit across the Mediterranean basin, resulting in a significant reduction in reservoir storage levels and the suspension of irrigation provided by dams in some areas due to low or absent rainfall, making drought a serious challenge to natural resources in this country. This study focused on semi-arid regions, especially on the Tensift basin in Morocco, and was conducted between 2018 and 2024. The effects of drought on arboriculture were analyzed thanks to remote sensing by using the normalized difference vegetation index (NDVI), while NDVI, TCI (temperature condition index), VCI (vegetation condition index), VHI (vegetation health index), and SPI (standardized precipitation index) were employed to assess and evaluate the health of the vegetation area, especially the arboriculture area, and the effective water stress conditions in our agricultural study area. The analyses indicated that arboriculture cover decreased markedly, from 11.17% in 2020 to 7.40% in 2023. From the analyses, it was evident that the cover of this culture had significantly declined from 11.17% in 2020 to 7.40% in 2023. From 2018 to 2024, more than half of the area suffered from drought in the agriculture of varying intensity levels, from moderate to severe. The meteorology of the evaluations confirmed the above observations by showing that there was a considerable decline in precipitation levels from about 350 mm in 2019 to less than 50 mm in 2024, coupled with continuously negative SPI-6 indices. Moreover, it was established that there was a significant effect on tree crops such as olives and citrus. Degradation of land was at its worst during 2021 when it affected more than 3,000 hectares of olives and 2,250 hectares of citrus. Similarly, 80% of farmers engaged in the production of citrus registered a decline in yield from 37% to 41%. Consequently, this study provides new information concerning the need for comprehensive evaluation and monitoring of agricultural drought in Morocco, thereby emphasizing the importance of essential factors.

Why it matches plant phenotyping methodsリモートセンシングと複数の植生・水ストレス指数を中核に、オリーブ・柑橘樹の植生健康状態や干ばつ影響を評価しており、植物状態の抽出手法の実質的応用に該当する。

abstractThe effects of drought on arboriculture were analyzed thanks to remote sensing by using the normalized difference vegetation index (NDVI), while NDVI, TCI (temperature condition index), VCI (vegetation condition index), VHI (vegetation health index), and SPI (standardized precipitation index) were employed to assess and evaluate the health of the vegetation area, especially the arboriculture area, and the effective water stress conditions in our agricultural study area.

Spatiotemporal Canopy Temperature Forecasting for Precision Irrigation Management ↗

Abstract Canopy temperature (Tc) is a critical physiological indicator of water and heat stress in cotton. Although weather-driven Tc forecasting is used by 60% of Australian cotton growers for irrigation scheduling, current methods typically rely on a single in situ sensor to represent an entire management area. This uniform assumption overlooks substantial spatial variability in Tc and can lead to suboptimal water application. We propose UAV-linear, a novel spatio-temporal forecasting model that integrates high-accuracy in-situ sensors with weekly Unmanned Aerial Vehicle (UAV) thermal imagery to generate high-resolution hourly spatial Tc forecasts. Experimental results show that UAV-linear forecast stress conditions at unmeasured locations as effectively as models trained on exhaustive historical data, achieving a 25-35% improvement over the standard uniform-forecast assumption. Furthermore, in a large-scale validation across 50,000 hectares of commercially active farms (practical dataset), UAV-linear improved stress-hour prediction by 22% relative to the uniform assumption while maintaining accuracy comparable to historical benchmarks. These findings show that the proposed spatio-temporal framework provides the spatial detail needed for differentiated precision management, with potential to improve crop yield and water-use efficiency.

Why it matches plant phenotyping methods綿花のキャノピー温度という植物の生理状態を、UAV熱画像とセンサーから推定・予測する手法を開発し、大規模に検証しているため、灌漑管理への応用でもフェノタイピング手法が中心です。

abstractWe propose UAV-linear, a novel spatio-temporal forecasting model that integrates high-accuracy in-situ sensors with weekly Unmanned Aerial Vehicle (UAV) thermal imagery to generate high-resolution hourly spatial Tc forecasts.

SeedMatExplorer: the transcriptome atlas of Arabidopsis seed maturation. ↗

Background Seed maturation is a critical developmental phase during which seeds acquire traits essential for nutritional value, desiccation tolerance, and long-term survival. Abscisic acid (ABA) signalling is a key regulator of this process, coordinating gene expression programs underlying the acquisition of seed quality traits. However, the molecular regulation of many of these traits remains poorly understood. To address this, we performed a comprehensive analysis of seed maturation in Arabidopsis thaliana, combining physiological and transcriptomic approaches across wild-type plants and mutants affected in ABA biosynthesis, signalling, and catabolism. Results We generated a high-resolution transcriptome dataset covering seed development from 12 days after pollination to the dry seed stage in wild-type and ten mutant lines. In parallel, we characterized the temporal acquisition of multiple seed traits, including germination capacity, dormancy, chlorophyll fluorescence, longevity and desiccation tolerance. Integration of these datasets using weighted gene co-expression network analysis (WGCNA) identified gene modules associated with specific trait acquisition patterns. This approach enabled the identification of coordinated transcriptional programs linked to distinct seed quality traits, extending beyond individual gene-level analyses. Notably, modules associated with desiccation tolerance and longevity were enriched for genes involved in stress responses and ABA-regulated pathways, highlighting the complex and multifactorial regulation of these traits. Conclusions This study provides a comprehensive physiological and transcriptomic framework for understanding seed maturation and the acquisition of key seed quality traits in Arabidopsis thaliana. By linking gene expression dynamics to trait development, our work offers new insights into the regulatory networks underlying seed resilience and storage capacity. The dataset is made accessible through SeedMatExplorer (https://www.bioinformatics.nl/SeedMatExplorer), an open-access web platform that enables interactive exploration and supports hypothesis generation. Together, this resource represents a valuable tool for advancing research on seed biology and improving seed performance in agricultural contexts.

Why it matches plant phenotyping methods種子成熟に伴う複数の植物形質を体系的に取得し、トランスクリプトームと統合した再利用可能なデータセットおよび探索プラットフォームを提供しており、単なる生物学的実験の routine 測定を超える。

abstractIn parallel, we characterized the temporal acquisition of multiple seed traits, including germination capacity, dormancy, chlorophyll fluorescence, longevity and desiccation tolerance.

Machine learning-assisted non-destructive prediction of root architecture in early-stage tomato rootstocks. ↗

The architecture of the root system is a primary factor in determining rootstock performance, affecting water and nutrient uptake, biomass accumulation, and overall vigor. However, direct root phenotyping is destructive, labor-intensive, and difficult to do routinely in breeding programs. The present study investigated early root morphological variation among developed interspecific tomato rootstock candidates (Solanum lycopersicum x S. habrochaites). The ability of linear regression and machine learning models to predict root traits from easily measured plant growth parameters was assessed. Nineteen interspecific hybrid rootstock candidates, two commercial rootstocks, and one scion were grown under optimal greenhouse conditions and evaluated at 0, 10, 20, and 30 days after planting. Root length, root surface area, root diameter, and root volume were determined by digital image analysis. In contrast, genotype, plant length, and stem diameter were used as input variables. Significant genotype x sampling date effects were observed for most morphological and biomass traits, indicating dynamic changes in root and shoot development during the first 30 days of growth. The rootstock candidates RSH-17 and RSH-6 generally showed relatively higher root length, surface area, root volume, and biomass accumulation than the commercial rootstocks and scion. XGBoost and OLR were the best predictive models, with R 2 values as high as 0.95 for root length, surface area, and volume. Root diameter was predicted less accurately than root length, surface area, and volume, suggesting that it might be a more independent or less variable root trait during early development. Overall, results suggest that vigor-related traits can serve as useful proxies for estimating major root architectural traits in early-stage tomato rootstock selection. Both XGBoost and OLR performed well, suggesting that root and shoot development were highly coordinated under optimal (non-stress) conditions. Hence, predictive modeling may help prioritize promising rootstock candidates before destructive root analysis. However, more validation under stress conditions and for longer periods of development is needed to determine the greater applicability of these models.

Why it matches plant phenotyping methods根系形態形質をデジタル画像解析で取得し、線形回帰・機械学習による非破壊予測モデルを評価・比較しており、植物フェノタイピング手法が研究の中心である。

abstractThe ability of linear regression and machine learning models to predict root traits from easily measured plant growth parameters was assessed.

Monitoring Forest Landscape Restoration Success Using Sentinel-2 NDVI and Field Measurements in Timor-Leste ↗

Abstract Forest Landscape Restoration (FLR) has become an important strategy for reversing land degradation and improving ecosystem resilience in tropical drylands. However, quantitative evaluations of restoration effectiveness remain scarce in Timor-Leste, particularly those integrating satellite-based monitoring with field observations. This study assessed vegetation recovery following reforestation activities within a 148-ha restoration site in Balak, Manatuto, Timor-Leste, using multi-temporal Sentinel-2 imagery and field-based ecological measurements. Vegetation dynamics were evaluated using the Normalized Difference Vegetation Index (NDVI) derived from Sentinel-2 images acquired in May 2022 and May 2026. NDVI differencing was applied to quantify vegetation change, while field data collected from 29 monitoring plots were used to assess seedling survival and growth performance. Pearson correlation and linear regression analyses were employed to examine relationships between vegetation growth indicators and restoration performance. The results indicated substantial vegetation improvement across the restoration area. Mean NDVI increased from 0.288 in 2022 to 0.475 in 2026, representing a 65% increase in vegetation greenness. Approximately 77.6% of the sites experienced moderate to significant vegetation recovery based on ΔNDVI analysis, whereas only 2.3% showed vegetation decline. Field assessments revealed that 62.1% of monitoring plots were classified as high-recovery sites and only 6.9% as low-recovery sites. A significant positive relationship was observed between average plant height and growth percentage ( r = 0.423, R ² = 0.179, p = 0.022), indicating that vegetation structural development was associated with restoration performance. These findings demonstrate that the AFoCO-supported reforestation programme has effectively accelerated vegetation establishment and improved ecosystem condition within a degraded tropical dryland landscape. The integration of Sentinel-2-derived NDVI indicators with field measurements provides a practical, cost-effective, and scalable framework for monitoring FLR outcomes in data-limited regions and offers valuable evidence to support restoration planning and evaluation in Timor-Leste and comparable tropical dryland environments.

Why it matches plant phenotyping methodsSentinel-2 NDVIと圃場測定を統合し、植生回復・成長という植物状態を定量評価する監視フレームワークを中心的に適用しているため。

abstractusing multi-temporal Sentinel-2 imagery and field-based ecological measurements

Integrating UAV-based dynamic phenotyping and GWAS to decipher the genetic basis of cotton defoliation ↗

Upland cotton (Gossypium hirsutum L.) is a critical economic crop, yet the efficiency of mechanized harvesting is heavily contingent upon effective pre-harvest defoliation. Traditional manual assessment of defoliation is labor-intensive and subjective, posing a significant bottleneck for large-scale genetic dissection of this dynamic trait. In this study, we established an integrated “high-throughput phenotyping-to-gene discovery” framework by utilizing UAV-based multispectral imaging to monitor 306 cotton cultivars across 4 environments. A Partial Least Squares Regression (PLSR) model was optimized to accurately estimate Leaf Area Index (LAI), and Gaussian curve fitting was employed to standardize LAI time series (ΔLAI) into a comparable dynamic phenotypic dataset. Genome-wide association studies (GWAS) based on these dynamic phenotypes identified 472 significant SNPs and 39 candidate genes. By integrating GWAS signals with transcriptome profiling of the petiole abscission zone and haplotype analysis, we identified 3 core regulatory genes: Ghi_A01G08401 (GhPIN3a), Ghi_D08G10716, and Ghi_D11G03091. Functional validation via virus-induced gene silencing (VIGS) and qRT-PCR demonstrated that Ghi_D08G10716 (encoding oxalyl-CoA synthetase) and Ghi_D11G03091 (encoding a VQ motif-containing protein) act as negative regulators in the defoliation process. These results provide a scalable technical paradigm and critical genetic resources for the precision breeding of cotton cultivars optimized for mechanized harvesting.

Why it matches plant phenotyping methodsUAVマルチスペクトル画像からLAIを推定し、時系列を動的表現型データへ変換する高スループット表現型解析手法が研究の中心であり、GWASへの実質的適用も行っている。

abstractwe established an integrated “high-throughput phenotyping-to-gene discovery” framework by utilizing UAV-based multispectral imaging to monitor 306 cotton cultivars across 4 environments.

Canopy Structure and Water Use Efficiency Variations Between Short- and Long-Day Strawberry Cultivars Revealed by Non-Destructive 3D Phenotyping ↗

Cultivars of strawberry (Fragaria × ananassa) differ in photoperiodic responses, which influence the balance between vegetative and reproductive growth, shaping canopy development, biomass production, and water use efficiency (WUE). Using 3D point-cloud phenotyping, this study compared the canopy structure and WUE of the short-day cultivar ‘Sonata’ and long-day cultivar ‘Favori’ grown under identical greenhouse conditions. Cultivar-specific growth and water use traits were quantified using daily non-destructive 3D point cloud phenotyping combined with continuous whole-plant gravimetry, supported by manual and destructive measurements. Non-destructive estimates of plant height and digital biomass corresponded moderately to measurements (height: R2 = 0.628; biomass: R2 = 0.579; mean absolute percentage error (MAPE) = 13.86%). Growth analysis indicated similar relative growth rates between the two cultivars, whereas the crop growth rate was higher in ‘Sonata’ than in ‘Favori’. Integration of growth estimates with gravimetric records revealed higher period average WUE in ‘Sonata’ (3.1 mg g−1) than in ‘Favori’ (2.5 mg g−1). These results highlight the distinctive growth strategies of a canopy-driven pattern in ‘Sonata’ and a reproduction-driven pattern in ‘Favori’. The combined 3D phenotyping–gravimetry framework provides a high-resolution, non-destructive approach to quantify cultivar-specific growth and water use traits.

Why it matches plant phenotyping methods3D点群による非破壊フェノタイピングと連続重量計測を組み合わせ、植物形態・バイオマス・水利用形質を定量化し、測定精度も検証しているため、手法が研究の中心である。

abstractUsing 3D point-cloud phenotyping, this study compared the canopy structure and WUE

Editorial: Plant phenotyping for agriculture ↗

Modern agriculture operates at an unprecedented crossroads, it must simultaneously accelerate crop yields to feed an expanding global population and adapt to the severe, fluctuating pressures of climate change, structural soil degradation, abiotic water deficits, and evolving biological threats. Historically, selecting resilient crop varieties and implementing field-scale management strategies relied extensively on destructive, labor-intensive, and fundamentally subjective visual metrics. This manual processing approach has long been recognized as the primary operational bottleneck in agricultural advancement.To bridge the gap between rapidly expanding genomic data and actual field performance, the systematic, non-destructive quantification of structural and functional plant traits, plant phenotyping, has emerged as a transformative frontier. By integrating high-throughput engineering, multi-scale remote sensing, deep learning, and advanced molecular biology, modern phenotyping transitions crop science away from qualitative estimation toward highly reproducible, multidimensional data frameworks. This Research Topic presents new advances in advanced 3D reconstruction and deep semantic segmentation at the seedling stage; amodal fruit segmentation, morphological extraction, and early water-stress diagnostics; high-throughput in-field seedling counting and dynamic density modeling; multimodal foundation models, network pruning, and intelligent phytoprotection; aerial and spaceborne remote sensing for canopy analysis and weed monitoring; plant physiology, functional spectroscopy, and functional genomics under abiotic stress; and automated diagnostics for real-time orchard scouting and vineyard management.Automating the characterization of complex spatial layouts under controlled or greenhouse environments is essential for early variety selection and early-stage structural evaluation. Several contributions within this volume provide key breakthroughs in navigating overlapping tissues, severe occlusions, and low-contrast edge regions. showcases how substituting standard convolutions with deformable convolutions enables deep neural networks to accurately isolate the main stem of mature, high-density crops like soybeans. This architecture overcomes the traditional challenges of color mimicry and severe occlusion by pods and leaves, achieving an outstanding mIoU of 90.58% and providing reliable indices for lodging resistance and structural yield modeling (R 2 = 0.9746).Accurately extracting fruit morphology under commercial greenhouse conditions remains heavily constrained by overlapping crop structures, foliage cover, and variable shadows. Simple semantic masks typically fail when a target fruit is partially blocked, leading to a loss of key volumetric data.To resolve the challenge of hidden boundaries, Li, Yin, et al. (2025) developed CGA-ASNet, a specialized RGB-D amodal segmentation network driven by a Contextual and Global Attention (CGA) module designed to restore occluded tomato regions. Trained on a high-fidelity synthetic greenhouse dataset (Tomato-sim) generated via NVIDIA Isaac Sim's Replicator Composer and optimized with a mean coordinate fusion algorithm for real-world validation, this architecture expands the network's receptive field to predict the complete, hidden circular forms of occluded tomatoes, achieving an F@0.75 score of 94.2 and an amodal mIoU of 82.4%. This proves that simulation-to-real (Sim2Real) domain pathways can successfully decode full physical volumes under dense commercial canopies.Complementing this structural restoration, Yang, Li, et al. (2025) designed an integrated diagnostic framework to identify early water stress dynamics in greenhouse tomatoes. Built upon an optimized YOLOv11n core, their system integrates adaptive kernel convolutions (AKConv) into the network backbone's C3k2 modules and implements a recalibration feature pyramid detection head based on the specialized P2 small-target layer. This combination achieved a 5.4% increase in mAP50-95 for identifying fine phenotypic parts. By applying automated geometric analysis to the extracted bounding boxes, the system extracts plant heights and petiole count with low relative errors, feeding these phenotypic parameters into a Random Forest classification routine that flags water-stressed plants with 98% accuracy to guide targeted, automated drip irrigation.Accurate plant stands during early vegetative stages represent the foundational metric required to establish true field emergence rates, validate seed vigor across diverse breeding blocks, and perform early yield predictions.To solve the challenges of small targets, extreme spatial density, and adjacent leaf overlap, Zang et al. (2025) designed DM_IOC_fpn, a wheat seedling counting framework that balances local and global contextual features. By structuring a point-annotated dataset and embedding a densityenhanced encoder module, their network balances micro-scale spatial limits with macro-scale canopy structures. Optimized through a combined loss function tracking counting, classification, and regression parameters, this architecture achieved low error scores (RMSE = 2.91; MAE = 2.23), outperforming standard object-detection benchmarks in complex field environments.At the same time, scaling up to real-time aerial monitoring required major reductions in model complexity to support resource-constrained edge computers on autonomous aerial platforms. Feng, Nie, and Li (2025) engineered an ultra-lightweight YOLOv8n variant tailored for real-time maize seedling counting from high-speed UAV RGB overflights. By reparametrizing RepConv with HGNetV2, they constructed a lean Rep_HGNetV2 backbone, integrated a Bidirectional Feature Pyramid Network (BiFPN) for multi-scale feature alignment, and implemented a Task Dynamically Aligned Detection Head (TDADH). This architecture compressed total model parameters by 47% and reduced weight sizes to 3.5 MB while maintaining a 96.5% detection accuracy and an ultra-fast processing speed of 146.3 FPS, paving the way for low-cost, real-time field scouting.Automated phytoprotection requires machine-vision architectures capable of generalizing across highly diverse species, complex field conditions, and varying computational boundaries. A significant subset of the published papers addresses these challenges through foundation model adaptation, multi-modal alignment, and efficient network compression.A major paradigm shift presented in this collection involves moving away from task-specific training and toward foundation model adaptation. Chen, Ruan, et al. (2026) introduce a novel architecture integrating the DinoV3 foundation model with a Unet framework to achieve robust leaf lesion segmentation across diverse species (such as coffee and black gram). By incorporating a Spatial Prior Module (SPM), their approach surpassed standard benchmark networks by over 10.5% in IoU while reducing inference times by approximately 93.6%, demonstrating that highparameter foundation models can be highly optimized for resource-constrained edge devices in real-time scouting.To solve the perennial problem of limited training data for rare or emerging crop diseases, Cooper et al. ( 2026) developed an ingenious synthetic data generation pipeline. Combining 3D procedural leaf modeling in Blender with diffusion-based disease synthesis (Stable Diffusion fine-tuned with LoRA and ControlNet), they synthesized highly accurate plant disease images with perfect groundtruth annotation masks. When deployed in low-resource data settings, combining these synthetic pipelines with restricted real-world datasets consistently drives significant improvements in downstream segmentation tasks. To tackle specific, complex pathologies, Xu, Chang, et al. (2025) developed the TSSC deep learning model, which embeds three-neighbor channel attention paired with a complementary squeeze-and-excitation mechanism. This specific architecture minimizes structural degradation risks while pushing classification accuracy to 99.61% for highly complex pea leaf pathologies. Similarly, Feng, Liu, et al. (2025) tackled overlapping leaf occlusions and small lesion footprints in citrus groves with YOLO-Citrus, an optimized framework integrating C3K2-STA, ADown modules, and a Wise-Inner-MPDIoU loss function to strike a balance between edge computational constraints and field deployment.UAVs and high-resolution satellite imagery have expanded the operational scale of phenotyping from individual pots to vast breeding blocks and commercial fields, allowing researchers to capture macro-dynamic parameters over time.In complex canopy systems that defy standard top-down aerial sensing, such as single-staked white Guinea yams, Iseki et al. (2026) demonstrated the distinct advantage of utilizing multi-angle (combined nadir and oblique) UAV imaging configurations. When coupled with support vector regression, this method captures complementary canopy-structure information to model shoot biomass trajectories (R 2 = 0.79) across multiple years and management zones. These nondestructive, time-series datasets enabled the fitting of genotype-specific Richard's growth curves using Bayesian inference, isolating valuable genetic variations in early growth allocation.To capture full-season vertical physiological changes over large scales, Li, Yue, and Luo (2025) developed a hybrid CNN-LSTM-Attention (CLA) model designed to estimate the full-period Leaf Area Index (LAI) in rice using multi-temporal UAV multispectral imagery. By using the CNN layer to extract instantaneous spatial features, the LSTM block to process seasonal time-series intervals, and a self-attention mechanism to weight critical growth transitions, their platform achieved a high coefficient of determination (R 2 = 0.92) and kept relative root mean square errors (RRMSE) below 9%. This network minimized soil background noise during early vegetative stages (LAI values 1-

Why it matches plant phenotyping methods植物フェノタイピングの技術動向を扱うEditorialであり、画像解析、UAVセンシング、深層学習、形質抽出などの方法が中心的に整理されている。

titleEditorial: Plant phenotyping for agriculture

Improving Nitrogen Use Efficiency in Wheat: Integrating Agronomic, Genomics, and Remote Sensing for Sustainable Production. ↗

Improving nitrogen use efficiency (NUE) in wheat is critical for addressing the dual challenges of global food security and environmental sustainability. Globally, only 42%-47% of applied nitrogen (N) fertilisers taken up by crops, with remainder lost to the environment, driving soil and water pollution, greenhouse gas emissions, and ecological imbalances. This review provides a comprehensive synthesis and integrative framework- integrating agronomic practices, advanced remote sensing and genomic approaches to enhance wheat NUE. We first examine the physiological basis of NUE, emphasising the synergy between photosynthetic carbon assimilation and N metabolism, the critical role of Rubisco in carbon-nitrogen coupling, and the temporal dynamics of N uptake, transport, and remobilisation throughout the wheat growth cycle. The temporal mismatch between source-sink N partitioning during grain filling emerges as a major physiological constraint limiting NUE in modern high-yielding varieties. We then explore transformative advances in remote sensing technologies, highlighting the paradigm shift from traditional vegetation indices to physiological sensing approaches. Through integration of multispectral imaging, LiDAR, thermal infra-red sensing, and solar-induced chlorophyll fluorescence, coupled with three-dimensional radiative transfer models and machine learning algorithms, these technologies enable non-destructive, real-time monitoring of crop N status while overcoming spectral-structural ambiguity and saturation limitations. From a genomic perspective, we synthesise recent progress in quantitative trait loci mapping and genome-wide association studies (GWAS), identifying key genetic loci controlling root architecture, N uptake transporters (NRT/AMT families), and grain filling efficiency. Multi-omics integration-spanning genomics, transcriptomics, and metabolomics-reveals temporal genetic networks distinguishing short-term nitrogen signalling responses from long-term adaptive remodelling, with genes such as TaNAC2-5A, TaNPF6.2, and QMrl-7B emerging as promising targets for molecular breeding. High-throughput phenotyping platforms enable time-series GWAS analysis, capturing developmental dynamics and genotype × environment interactions that traditional approaches miss. Finally, we discuss sustainable N management strategies, including enhanced efficiency fertilisers, precision application technologies, and soil health optimisation. By integrating these multidisciplinary approaches within a Genotype × Environment × Management framework, this review provides a roadmap for developing climate-smart, N-efficient wheat varieties and precision N management systems that simultaneously enhance productivity, reduce environmental footprints, and ensure sustainable agricultural intensification.

Why it matches plant phenotyping methods小麦の窒素状態を非破壊・時系列に測定するリモートセンシングと高スループット表現型解析を、技術的課題や統合手法とともにレビューしており、表現型取得法が実質的に扱われている。

abstractWe then explore transformative advances in remote sensing technologies, highlighting the paradigm shift from traditional vegetation indices to physiological sensing approaches.

Coupled quantity–structure fluctuations of riparian vegetation under geomorphic constraints: the integration of field surveys and unmanned aerial vehicle mapping ↗

Introduction Riparian vegetation is critical to river stability, but quantity–structure risk under geomorphic constraints remains poorly quantified. Methods Using the Chishui River Basin as a case study, this study combined quarterly field surveys from 25 riparian transects with high-resolution unmanned aerial vehicle imagery to develop an integrated framework for identifying coupled fluctuations in vegetation quantity and community structure and their spatiotemporal risk patterns. Results A total of 263 plant species from 185 genera and 65 families were recorded. The results showed that riparian vegetation in the Chishui River exhibited pronounced spatial fluctuation at the basin scale. Biomass peaked upstream in autumn at 425 g m -2 and in the middle–lower reaches in summer at 522 g m -2 , but remained below 400 g m -2 downstream year-round. UAV-derived FVC mean and Texture std were significantly correlated with field-based vegetation-quantity and community-structure indicators, respectively (R 2 = 0.72, p 2 = 0.48, p RI values generally above 0.45, and maximum RI values reached 0.793 and 0.788 in two typical high- RI sections associated with observed human activity and possible engineering-related disturbance. Discussion This integrated framework provides a quantitative basis for cross-scale vegetation monitoring and ecological restoration prioritization in complex basins.

Why it matches plant phenotyping methodsUAV画像から植生量・群落構造を推定し、現地調査指標との相関で検証する統合的な植物状態測定フレームワークが研究の中心であるため。

abstractcombined quarterly field surveys from 25 riparian transects with high-resolution unmanned aerial vehicle imagery to develop an integrated framework for identifying coupled fluctuations in vegetation quantity and community structure

Stable Seasonal Trends in Satellite-Derived Vegetation Indices over Vineyards: Preliminary Results from Trinity Canyon, Armenia ↗

Continuous monitoring of vineyard dynamics is essential for optimizing viticultural practices and assessing plant health. While the seasonal behaviors of satellite-derived vegetation indices are widely studied, robust parametric modeling of these temporal trends remains underexplored. Building upon initial clues derived from Italian vineyards, this study proposes a novel analytical framework based on the consistent parabolic temporal signature of optical and Synthetic Aperture Radar (SAR) indices. Focusing on the elevated Trinity Canyon Vineyards in Armenia, we model the yearly evolution and temporal aggregations of these indices using a parabolic fitting approach. Our results suggest that the parabola vertex, which we hypothesize corresponds to the absolute maximum of vegetative activity, remains remarkably stable across diverse vine types, satellite orbits, and years. While this stable behavior suggests an underlying phenological or structural consistency, distinct exceptions to this trend have also been identified and considered. Furthermore, to bridge the gap between remote sensing observables and agronomic traits, we investigated the relationship between the fitted parabolic parameters and the Winkler index, which is used here as an estimator of above-ground biomass (AGB). By correlating the vegetation indices’ temporal dynamics with biomass growth and by isolating specific anomalies driven by environmental or anthropogenic factors, this work offers a basis for a predictive methodology that enables tracking vineyard structural development.

Why it matches plant phenotyping methods衛星画像の植生指数を放物線フィッティングし、ブドウ園の植生活動・地上部バイオマス・構造発達を推定する分析手法が研究の中心であるため。

abstractthis study proposes a novel analytical framework based on the consistent parabolic temporal signature of optical and Synthetic Aperture Radar (SAR) indices

Quantifying Canopy Closure Dynamics Using UAV Imagery and Semantic Segmentation in Rice Breeding Trials. ↗

The canopy closure stage is a critical phase of rice ( Oryza sativa L.) development that influences canopy structure and final grain yield. Accurate and continuous monitoring of canopy closure dynamics is therefore essential for variety screening and cultivation optimization. This study combines unmanned aerial vehicle (UAV) remote sensing technology with deep learning-based semantic segmentation to establish an efficient framework for quantifying rice canopy closure dynamics. UAV RGB images were acquired for 198 hybrid rice varieties during early growth stages and used to build a canopy segmentation dataset. Three semantic segmentation models, i.e., DeepLabv3+, U-Net, and PSPNet, were systematically evaluated. Results show that DeepLabv3+ performed the best and enabled precise extraction of rice canopy features, obtaining a mean intersection over union (mIoU) of 0.86. Based on the extracted canopy coverage, the Gompertz model was utilized to characterize temporal canopy closure trajectories for all varieties, achieving an average R 2 of 0.978. Subsequently, five key dynamic indicators were derived, including canopy closure limit value ( K ), initial growth coefficient ( a ), growth rate coefficient ( b ), maximum instantaneous growth rate ( MGR ), and days to maximum growth rate ( Tm ). K-means clustering analysis was performed on these indicators to categorize all rice varieties into three clusters, disclosing pronounced differences in early-stage canopy development characteristics. Correlation analysis further demonstrated that canopy closure dynamics were closely associated with grain yield. Overall, while acknowledging the limitations of a single-season and single-site dataset, this study provides a scalable and objective framework for quantifying rice canopy closure dynamics, offering valuable support for variety selection, cultivation optimization, and high-yield rice production.

Why it matches plant phenotyping methodsUAV画像と深層学習セマンティックセグメンテーションを用いてイネのキャノピー閉鎖動態を定量化する手法を構築・評価しており、植物形質抽出が研究の中心である。

abstractThis study combines unmanned aerial vehicle (UAV) remote sensing technology with deep learning-based semantic segmentation to establish an efficient framework for quantifying rice canopy closure dynamics.

Continuous monitoring of plant transpiration dynamics with a leaf-mounted sensor across environmental conditions ↗

O_LITranspiration plays a central role in plant water relations and strongly influences plant growth. Continuous monitoring is essential for understanding responses to environmental conditions and improving water management in both natural and agricultural systems. Gas-exchange techniques such as infrared gas analysers (IRGAs) and porometers are widely used but are challenging for long-term or large-scale monitoring. On the other hand, the FylloClip is a low-cost, leaf-mounted capacitance sensor developed previously to monitor transpiration by detecting condensation of water vapour near the leaf surface. Here, we evaluated the potential of the FylloClip for monitoring transpiration dynamics and assessed environmental conditions that may affect its performance. C_LIO_LIThe FylloClip was tested under growth chamber, greenhouse, and tropical field conditions. We evaluated how its capacitance measurements respond to rainfall, temperature and humidity, and compared FylloClip measurements with transpiration measured with an IRGA. C_LIO_LIThere was a strong correlation (r = 0.85) between FylloClip and IRGA data. Both systems captured similar diurnal transpiration patterns, with transpiration declining simultaneously under water deficit. Rainfall and very high relative humidity produced FylloClip signals that could be misinterpreted as high transpiration, although transpiration is negligible under these conditions. C_LIO_LIOur results revealed that FylloClips capture temporal patterns of transpiration with high accuracy and resolution, providing a reliable tool for long-term, large-scale monitoring of transpiration dynamics in ecophysiological studies and precision agriculture. C_LI

Why it matches plant phenotyping methods葉面センサーによる蒸散動態測定法を開発・評価し、IRGAとの比較検証および環境条件による性能評価を行っており、植物生理形質の取得が中心である。

abstractHere, we evaluated the potential of the FylloClip for monitoring transpiration dynamics and assessed environmental conditions that may affect its performance.

Dual-signal MOF nanozyme microneedle patch for on-site monitoring of hydrogen peroxide in postharvest lettuce. ↗

Real-time monitoring of H 2 O 2 in plant tissues is useful for evaluating oxidative changes during postharvest storage, but direct on-site detection in vegetables remains difficult because most assays still require tissue disruption and laboratory instruments. In this study, a dual-signal microneedle biosensor was developed by integrating polydopamine-coated Fe/Zr-MOF nanozyme (PDA@Fe/Zr-MOF) into a gelatin/sodium alginate microneedle patch for H 2 O 2 detection in lettuce. The polydopamine coating improved the peroxidase-like response of Fe/Zr-MOF through •OH generation and also contributed to photothermal conversion under 808 nm near-infrared (NIR) irradiation. After contact with lettuce leaves, the microneedles extracted interstitial fluid and allowed H 2 O 2 -triggered TMB oxidation to be read by both colorimetric imaging and thermal imaging. The two outputs were not independent recognition mechanisms, but they provided mutually supportive information and helped reduce the influence of sample color and environmental fluctuations. The sensor achieved detection limits of 0.42 μM for the colorimetric mode and 0.34 μM for the photothermal mode. During 15 days of storage at 4°C, the sensor tracked H 2 O 2 accumulation in lettuce and showed a clear relationship with spoilage progression. These results indicate that PDA@Fe/Zr-MOF-based microneedle sensing is a feasible approach for monitoring oxidative freshness changes in postharvest vegetables.

Why it matches plant phenotyping methodsレタス組織内H2O2という植物の生理状態を、マイクロニードルとカラー・熱画像で現場測定するセンサーを開発しており、取得手法が研究の中心である。

abstracta dual-signal microneedle biosensor was developed by integrating polydopamine-coated Fe/Zr-MOF nanozyme (PDA@Fe/Zr-MOF) into a gelatin/sodium alginate microneedle patch for H 2 O 2 detection in lettuce.

Species responses to nutrient loading promote resistance but not temporal stability in floating macrophyte communities ↗

Determining the drivers of ecological stability amid accelerating global environmental change is a critical goal of contemporary ecology. Various candidate drivers have been suggested, with recent attention turning to response diversity—the variation among organism-environment responses. However, despite conceptual interest in response diversity as a driver of stability, there remain few field tests of this relationship. Using multi-species competitive communities of floating aquatic macrophytes as an experimental model for measuring temporal stability and response diversity to nutrient loading, we show that response diversity does not promote temporal stability of total macrophyte cover, but that communities with an uneven distribution of species responses were more resistant to an exogenous shock. To quantify macrophyte composition and growth dynamics from photographic time series of our experimental communities, we developed an open-source, scalable, machine learning workflow ( LeafMosaic ) capable of classifying four species from noisy field data including variable lighting, resolution, and plant morphology. We measured response diversity as the balance of positive and negative biomass growth responses to dissolved nitrate concentration, weighted by species’ relative contributions to biomass, and tested its effect on temporal stability and resistance to an unexpected pulse disturbance (a large typhoon that disrupted our outdoor mesocosms). Response imbalance predicted typhoon resistance, but species asynchrony and mean population stability best predicted community stability, with no direct or indirect effect of species responses. Overall, our results provide new experimental evidence for how the structure of species responses promotes stability, and we aim our LeafMosaic workflow to empower future field experiments using floating macrophytes to study response diversity and ecological stability.

Why it matches plant phenotyping methods浮遊水生植物の写真時系列から種組成と成長動態を抽出する、オープンソースでスケーラブルな機械学習ワークフローを開発しており、植物表現型取得・解析法が中心的です。

abstractTo quantify macrophyte composition and growth dynamics from photographic time series of our experimental communities, we developed an open-source, scalable, machine learning workflow ( LeafMosaic ) capable of classifying four species from noisy field data including variable lighting, resolution, and plant morphology.

AGIcam: An open‐source Internet of Things–based camera system for automated in‐field phenotyping and yield prediction ↗

Abstract Continuous, high‐frequency monitoring is essential to capture rapid phenological transitions and dynamic crop responses to the environment. However, most phenotyping platforms lack the temporal resolution and automation required for consistent, season‐long trait assessment. This study introduces AGIcam, an open‐source Internet of Things (IoT) camera system for automated and continuous in‐field plant phenotyping and yield prediction. The platform integrates solar‐powered Raspberry Pi units with a modular software stack, comprising Node‐RED, InfluxDB, Grafana, and Microsoft Azure, for automated data acquisition, transfer, and visualization. In the 2022 growing season, 18 AGIcam systems were deployed in spring and winter wheat ( Triticum aestivum ) breeding trials, maintaining an uptime of over 85% while capturing frequent red‐green‐blue and no‐infrared imagery. Time‐series vegetation indices derived from these images were used to predict yield using random forest and long short‐term memory (LSTM) models. The LSTM approach achieved the highest accuracy approximately one week after heading, with mean prediction errors of 3.41% for spring wheat and 1.62% for winter wheat. These results highlight the potential of IoT‐based platforms such as AGIcam to enable real‐time, scalable, and effective phenotyping solutions for data‐driven crop improvement. The presented work provides open‐source resources for the development and time‐series analysis of IoT data for phenotyping and precision agricultural applications.

Why it matches plant phenotyping methods植物フェノタイピング用のIoTカメラ基盤を開発・実証し、画像由来の時系列形質から収量を予測する方法が研究の中心である。

abstractThis study introduces AGIcam, an open‐source Internet of Things (IoT) camera system for automated and continuous in‐field plant phenotyping and yield prediction.

3D measurement of cell thickness and its dynamics in plants. ↗

Main conclusion A novel and efficient method was developed to accurately measure thickness in 3D of many cells from a confocal stack, as well as to track changes in cell thickness overtime. Plant cells and organs are three-dimensional objects with a certain thickness. Among basic geometric parameters (length, width, depth/thickness), cell thickness is less accurately and comprehensively measured, probably because it cannot be directly seen. The current methods of cell thickness quantification have some limitations, such as measuring only from a cross-section, not accounting for the directionality of biological thickness, or not offering a way to track changes in thickness of individual cells over time. This research is an attempt to bridge the gap, by making the quantification of thickness and tracking its changes in many cells easier and more accurate. We devised a novel method to efficiently measure average cell thickness in 3D from cells imaged with confocal microscopy, the most popular technique to image live samples over many days. The method, in combination with the popular software MorphoGraphX, also allows accurate and efficient tracking of changes in thickness between different time points. We tested the method on various organs of the model plant Arabidopsis thaliana such as the shoot apical meristem, the hypocotyl, the cotyledon, and the sepal. We demonstrated that this new method can reliably measure the thickness of hundreds of cells at once in a short amount of time to reveal new biological insights. We believe this would be a useful tool for plant researchers to accurately characterize this hidden morphological dimension.

Why it matches plant phenotyping methods植物細胞の3D厚みと経時変化を効率・高精度に測定する手法を開発し、複数器官で検証しているため、植物形態フェノタイピング手法が中心である。

abstractA novel and efficient method was developed to accurately measure thickness in 3D of many cells from a confocal stack, as well as to track changes in cell thickness overtime.

An Interpretable Multimodal Transfer Learning Decision-Support Framework for Multi-Crop, Multi-Disease Detection in Precision Agriculture ↗

Despite the widespread use of image-only convolutional models for plant disease diagnosis to provide global food security, image variability at the field level, visually similar symptoms, and stress due to soil nutrients or moisture conditions, can cause loss of accuracy. This paper compares classical machine learning classification models to custom convolutional neural networks and pretrained transfer-learning models for multi-crop and multi-disease classification and also introduces a late-fusion multimodal decision support model that could integrate data about images, soil, and weather. Experiments were conducted on the PlantVillage dataset which had 54,305 RGB images belonging to 38 different crop-condition classes (43,456 training, 10,849 validation, and 10,849 test images) across 14 different crops. The accuracy, macro-precision, macro-recall and macro-F1 score were computed for the five classical classifiers (KNN, Random Forest, Extra Trees, SGD-linear SVM, and SVC-RBF using PCA-reduced features), three custom CNN variants, and four pretrained models (ResNet50, MobileNetV2, GoogleNet, and EfficientNetB7). Of the classical models, SVC with RBF kernel yielded the highest accuracy (83.58%) and MacroF1 (82.96%). In the case of the custom CNN models, the deeper they became and the more dropout the higher accuracy they gained, with CNN-V3 attaining 95.71% accuracy and 95.66% macro-F1. Transfer learning yielded the best results with MobileNetV2 (99.30% accuracy and macro-F1) outperforming ResNet50 (98.60% accuracy and macro-F1) and GoogleNet (97.83% accuracy and 97.46% macro-F1). The findings serve as the basis for the introduction of a multimodal system for soil forecasting integrating a MobileNetV2 image encoder, a residual MLP for soil features, and two dual LSTMs for 48-hour and 168-hour time-series of the weather. The interpretability, modularity and the sufficient resistance towards loss of sensor information for probability-level late fusion with 0.80, 0.10, 0.05 and 0.05 respectively make the framework appropriate for precision-agriculture advisory systems, until it is tested in the field.

Why it matches plant phenotyping methods植物画像から病害状態を推定する分類手法を複数比較し、マルチモーダル意思決定フレームワークを構築・評価しており、病害表現型の取得・推定が中心である。

abstractThis paper compares classical machine learning classification models to custom convolutional neural networks and pretrained transfer-learning models for multi-crop and multi-disease classification

The Spatiotemporal Genetic Architecture of Seed Vigor in Upland Cotton. ↗

Seed vigor underpins uniform crop establishment, but its dynamic genetics are understudied. Combining high-resolution temporal phenotyping and genomics in upland cotton, we used the SeedRanger platform to record 17 image-based traits every 30 min over 120 h, revealing stage-specific heritability and identifying 541 seed-vigor loci. These loci show extensive pleiotropy and temporal coordination, forming a genetic network that preserves developmental continuity; 8.9% overlap regions under domestication selection, indicating concurrent optimization with fiber yield. Functional validation of FLA2, a candidate gene underlying a dynamic QTL, implicates auxin-mediated control of radicle elongation and cotyledon development. This temporal framework exposes dynamic genetic architecture and breeding targets for high-vigor crops.

Why it matches plant phenotyping methodsSeedRangerによる高頻度画像計測と17形質の抽出が研究の主要なデータ取得基盤であり、時間的な種子活力表現型を解析する実質的なフェノタイピング応用である。

abstractCombining high-resolution temporal phenotyping and genomics in upland cotton, we used the SeedRanger platform to record 17 image-based traits every 30 min over 120 h

Dynamic monitoring of rice plant height during the early growth stage using UAV-LiDAR and GWAS analysis of growth rate ↗

Plant height during the early growth stage of rice is a key indicator reflecting canopy establishment rate, tillering potential, and overall growth vigor, all of which critically determine final yield formation. Conventional manual measurements fail to capture high-frequency, continuous, and non-destructive monitoring of plant height dynamics, limiting the understanding of early growth vigor and its genetic mechanisms. In this study, a UAV-based LiDAR system was employed to acquire canopy point clouds of 211 rice accessions across ten time points within 40 days after transplanting. High-resolution canopy height models (CHMs) were generated, and continuous plant height trajectories H(t) were reconstructed using piecewise cubic Hermite interpolation (PCHIP). The first derivative V(t) quantified growth rate dynamics and identified the timing of maximum growth (T max ), enabling precise differentiation of early growth patterns among geno-types. Genome-wide association analysis (GWAS) using a mixed linear model (MLM, Q+K) detected 604 significant SNPs, among which 33 were stably expressed across environments. Five candidate genes were identified within ±200 kb windows, mainly encoding proteins related to cell elongation, hormone signaling, and photosynthetic metabolism. The results highlight that LiDAR-based dynamic monitoring of plant height, coupled with genomic association analysis, provides a robust framework for quantifying rice early growth vigor and elucidating its molecular basis, offering valuable guidance for breeding high-vigor “early-establishing” rice cultivars.

Why it matches plant phenotyping methodsUAV-LiDARによるイネ草丈の時系列取得・CHM生成・成長率推定が研究の中心であり、GWASはその測定形質の応用分析。

abstractConventional manual measurements fail to capture high-frequency, continuous, and non-destructive monitoring of plant height dynamics

Individual plant-level (IPL) soybean biomass estimation and spatial mapping through UAV multisource feature-driven machine learning framework ↗

Abstract Rapid and accurate quantification of crop biomass using multisource UAV imagery–derived features, such as plant height, vegetation indices, and texture indices demonstrates strong potential for soybean high-throughput phenotyping. The indeterminate growth habit of soybean, alongside extensive nodulation and intense inter-plant competition, necessitates individual plant level (IPL) monitoring to quantify plant-specific nitrogen fixation and competitive vigor. However, most studies aggregate measurements at multi-plants at the plot level, thereby masking these soybean-specific traits. This study aims to develop and evaluate a UAV imagery-based framework for estimating soybean biomass at the IPL, with the objective of characterizing high-resolution spatial variability and supporting high-throughput phenotyping. Regions of interest (ROIs) for IPL data acquisition were defined as rectangular plots based on planting density and were generated from early-stage imagery before canopy overlap occurred. Using these ROIs, structural information (SIs) including plant height (PH) and vegetation fraction (VF)), vegetation indices (VIs), and texture indices (TIs) were derived for each individual plant from RGB and multispectral imagery and organized into sensor-specific feature groups. Recursive feature elimination was applied to select optimal features, which were then used as inputs for machine learning architectures including support vector regression (SVR) with a linear kernel, Random Forest (RF), and XGBoost (XGB). Among them, the SVR model using fused multisource features (SIs + VIs + Tis) achieved the best performance, with R² = 0.88, RMSE = 55.34 g, and rRMSE = 8.50% on an independent test dataset. The results show that: (1) tree-based models, including XGB and RF may suffer from overfitting due to limited sample size and feature redundancy, whereas linear SVR showed better generalization; (2) fusing RGB and multispectral features consistently improved biomass estimation accuracy. Inparticular, near-infrared and red-edge-based indices such as RECI and NDRE, along with VF and PH, were identified as important predictors, while texture indices were not selected as significant features; and (3) the proposed framework enabled spatially explicit IPL biomass mapping and time-series analysis, revealing variability in growth conditions and distinct growth trajectories. The framework provides a reliable solution for IPL soybean biomass estimation with practical potential for UAV-based agricultural decision-making.

Why it matches plant phenotyping methodsUAV画像由来の特徴量と機械学習により個体レベルのダイズ biomass を推定・評価する枠組みが研究の中心であり、植物表現型の取得・抽出手法に該当する。

abstractThis study aims to develop and evaluate a UAV imagery-based framework for estimating soybean biomass at the IPL

Construction of a Virtual Sensor-Driven Digital Twin System for Plant Growth Monitoring on Rooftop Farms ↗

Rooftop farms are urban green infrastructure integrating food production, ecological regulation, and public services, and their management increasingly relies on data-driven approaches. However, open built environments, microclimatic heterogeneity, and limited sensor deployment challenge continuous monitoring and short-term prediction of rooftop plant growth. This study proposes and validates a virtual sensor-driven digital twin system using a rooftop tomato case in Xiamen, China. The system adopts a five-layer architecture comprising data acquisition, transmission, modeling, processing, and application service layers. By coupling a Long Short-Term Memory (LSTM) weather prediction model with the Decision Support System for Agrotechnology Transfer (DSSAT) crop growth model, a predictive virtual sensor module was developed to forecast leaf area index (LAI), aboveground biomass, phenology, and yield for seven days. Results show that the system links environmental data acquisition, LSTM–DSSAT prediction, database storage, and three-dimensional visualization, transforming rooftop plant growth into an updatable, predictable, and visualized digital twin object. The coupled model showed high predictive accuracy, with R2 values of 0.9814 for LAI and 0.9966 for aboveground biomass, while supporting phenology and yield prediction. The system supports irrigation optimization, landscape management, and activity planning in sensor-constrained rooftop farms.

Why it matches plant phenotyping methods植物成長のLAI、地上部バイオマス、フェノロジー、収量を予測する仮想センサー・デジタルツインを開発し、精度検証しており、表現型推定手法が研究の中心である。

abstractThis study proposes and validates a virtual sensor-driven digital twin system using a rooftop tomato case in Xiamen, China.

Repeatability and Heritability of UAV-Derived Canopy Traits in a Cassava Breeding Population Using Time-Series Data from Two Consecutive Growing Seasons ↗

Cassava is a major staple crop in tropical regions, particularly in Sub-Saharan Africa, yet its productivity remains constrained by genetic and agronomic limitations. A major bottleneck in cassava breeding is the difficulty of accurately phenotyping agronomic traits under field conditions using conventional, labor-intensive methods. Here, we evaluated the potential of uncrewed aerial vehicle (UAV)-based phenotyping to quantify canopy growth traits and assess their genetic relevance under realistic field conditions. For this, multi-temporal UAV imagery was collected over two growing seasons (2018-2019 and 2019-2020) in a panel of 46 cassava genotypes planted in fields of the International Institute for Tropical Agriculture (IITA), Nigeria. Canopy height, canopy volume, and their relative growth rates (RGRh and RGRv) were extracted at the plot-level, and their seasonal dynamics and canopy-yield relationships were further assessed across developmental stages and environmental conditions. Repeatability (R) and broad-sense heritability (H2) were estimated using a linear mixed model (LMM) that partitioned genetic, genotype-by-year, and residual variance components, enabling the evaluation of both measurement reliability and genetic signal. Overall, UAV-derived growth dynamics were found to exhibit comparable patterns across genotypes, reflecting shared seasonal growth trajectories, while canopy-yield relationships varied with developmental stage and environmental conditions. In terms of genetic metrics, R was high for all UAV-derived traits (R = 0.68-0.69), indicating reliable genotype-level assessment across replicates and seasons. In contrast, H2 differed substantially among traits. Canopy volume (H2 = 0.64) and canopy height (H2 = 0.58) exhibited moderate-to-high heritability, reflecting strong genotype effects and comparatively moderate genotype-by-year interactions. However, their relative growth rates showed near-zero H2 values, driven primarily by genotype-by-year interaction, indicating a dominant environmental influence. These results demonstrate that UAV-derived canopy height and volume provide a consistent basis for genetic differentiation of cassava genotypes across environments, supporting their use in selection, whereas growth-rate traits are better suited for characterizing growth plasticity and genotype-by-environment interactions.

Why it matches plant phenotyping methodsUAV画像からキャッサバの樹冠高さ・体積・相対成長率を抽出し、再現性と遺伝率を検証することが研究の中心であり、実質的な植物フェノタイピング手法の評価に該当する。

abstractwe evaluated the potential of uncrewed aerial vehicle (UAV)-based phenotyping to quantify canopy growth traits and assess their genetic relevance under realistic field conditions.

The Sykes tree: Changes in the architecture of Fouquieria columnaris after six decades on the coast of Sonora, Mexico ↗

Estimating the age and growth of long-lived desert succulents is challenging due to the absence of annual growth rings. This study utilizes Single-Image Photogrammetry (SIP) and a historical photograph taken by G. Sykes in 1965 and two replicated photographs obtained in 2016 and 2025 to analyze architectural changes over six decades in an iconic “Boojum tree” ( Fouquieria columnaris ) and an adjacent columnar cactus ( Pachycereus pringlei ) from a relictual population in Sonora, Mexico. Results indicate that F. columnaris exhibited a slow mean vertical growth rate of 1.71 cm yr −1 during the 1965-2016 interval which increased to 3 cm yr −1 for the recent 2016-2025 period. This acceleration aligned with values recorded at more favorable sites (i.e. 3.3 to 3.6 cm yr −1 ). Conversely, P. pringlei exhibited a minimal growth rate (1.01 cm yr −1 ), which is much lower than rates reported from repeat photography (5-10 cm yr −1 ) or radiocarbon dating of spines (3-23 cm yr −1 ). Together, these species demonstrate high ecological resilience near their physiological limits in the Sonoran Desert through divergent morphofunctional pathways. F. columnaris favors architectural stability and sustained growth, whereas P. pringlei relies on mechanical robustness and structural redundancy. These findings highlight the efficacy of SIP and historical records for long-term demographic monitoring in extreme arid environments.

Why it matches plant phenotyping methods単一画像フォトグラメトリを用いて植物の建築構造変化と成長速度を定量化することが研究の中心であり、植物表現型の実質的な測定法適用に該当する。

abstractThis study utilizes Single-Image Photogrammetry (SIP) and a historical photograph taken by G. Sykes in 1965 and two replicated photographs obtained in 2016 and 2025 to analyze architectural changes over six decades

Developing a sinusoidal-polynomial fitting model for deriving the structural and biochemical circadian rhythms for different parts of Birch from hyperspectral LiDAR data. ↗

A deeper understanding of circadian rhythms in plants, especially trees, is crucial for uncovering how structural and physiological processes align with daily environmental cycles. However, most studies analyze biochemical changes and positional variations separately, with limited exploration of their coordination within the whole-plant system. Hyperspectral light detection and ranging (HSL) integrates three-dimensional (3D) structural mapping with hyperspectral reflectance, enabling non-destructive assessment of plant biochemistry. Previous work showed that HSL can detect nocturnal vertical canopy displacements with centimeter accuracy, but organ-level rhythmic patterns (e.g., branches vs. leaves) remain poorly studied. Here, we developed a hyperspectral point cloud classification method combining spectral and spatial data to separate branches from leaves and analyze their sleep movements independently. A novel sinusoidal-polynomial fitting model was then proposed to characterize circadian rhythms in both sleep movements and reflectance variations. We applied HSL data from a single birch tree (Betula pendula) collected at 30 distinct HSL measurement times over 24 h to develop a 3D canopy partitioning approach that divides the canopy into nine grids (3 × 3) and ten vertical layers per grid. Results revealed near-24-hour rhythmic patterns (max R² = 0.5841, P < 0.05) and stratified sleep movements: branches exhibited larger amplitudes than the corresponding canopy layers, with the overall maximum movement amplitude occurring shortly before sunrise (04:00-06:30) and recovering after sunrise. The model also effectively characterized diurnal reflectance variations (max R² = 0.5812, P < 0.05). In addition, chlorophyll-related spectral indices exhibited a sinusoidal variation, reaching a minimum around 03:00. These findings highlight the potential of HSL for the joint analysis of structural and biochemical circadian rhythms, providing a non-destructive approach to investigate plant rhythmicity in both structural and physiological domains.

Why it matches plant phenotyping methods hyperspectral LiDARによる植物の構造・生理形質の取得と、葉・枝の分類および概日リズム推定モデルの開発が研究の中心である。

abstractHere, we developed a hyperspectral point cloud classification method combining spectral and spatial data to separate branches from leaves and analyze their sleep movements independently.

Minimally invasive quantitative tracking of minerals, sugars, amino acids, and hormones in the leaf apoplast of Arabidopsis thaliana and Vicia faba. ↗

The apoplast of leaves is involved in nutrient transport, microbe-host interactions, systemic signaling, cell wall dynamics, and serves as an interface for various other physiological processes. The composition of the apoplastic solute pool, which supports many of these functions, is dynamic and shaped by developmental and environmental cues. However, due to the complexity and compartmentalization of the apoplast, analysing these fluids - and thus the associated physiological processes - remains technically challenging. This study introduces a minimally invasive method for extracting apoplastic fluids from leaves of selected dicots (e.g. Arabidopsis thaliana, Vicia faba, and many more), offering two key advantages: (i) repeated extractions from the same leaves to generate time-series data, such as every 24 hours, over consecutive days, and (ii) high spatial resolution, enabling identification of macrodomains within the leaf apoplast. For example, abscisic acid macrodomains were revealed along the leaf axis, providing insight into apoplastic hormone regulation. The method also reveals other previously unrecognized aspects, such as the accumulation of kaempferol glycosides in the apoplast after plants experienced salt stress. Finally, the method addresses the distortion of apoplast compound levels caused by dilution bias that results from the inconsistent recovery of infiltration fluid. Adding pyranine enables correction, ensuring accurate and comparable data. By integrating spatial and temporal precision, this new tool will promote a deeper understanding of plant apoplastic processes and their physiological relevance in various biological contexts.

Why it matches plant phenotyping methods葉のアポプラスト液を反復・高空間分解能で抽出し、植物の生理状態を定量する新規手法の開発が中心である。

abstractThis study introduces a minimally invasive method for extracting apoplastic fluids from leaves of selected dicots

Diagnostic system for tebuthiuron soil ecotoxicity using morphophysiological indicators of Mucuna pruriens validated by Lactuca sativa. ↗

This study developed an integrated diagnostic system for tebuthiuron-induced soil ecotoxicity based on morphophysiological indicators of Mucuna pruriens, using the germination index (GI) of Lactuca sativa as a sensitive ecotoxicological validation endpoint. The experiment was conducted under greenhouse conditions using a completely randomized design with 12 treatments and 360 individual pots (independent samples evaluated via destructive sampling), which were distributed across five evaluation periods at 14, 28, 42, 56, and 70 days after sowing. Morphophysiological variables, including plant height, root length, shoot and root dry mass, chlorophyll content, nodule number, and visual phytotoxicity, were quantified and integrated with multivariate and probabilistic modeling approaches. Given the multifactorial nature of the germination index, Principal Component Analysis (PCA) was applied to identify ecological and physiological gradients associated with plant vigor, stress, and symbiotic functioning. The PCA outputs were subsequently used as inputs for Probabilistic Neural Networks (PNNs), enabling the classification and prediction of bioindicator-based ecotoxicological levels using mathematically defined low, medium, and high GI classes. Model performance was internally assessed using training and validation datasets, confusion matrices, overall accuracy, sensitivity, specificity, and ROC curves. Because no independent external dataset was available, the predictive performance should be interpreted as evidence of internal consistency rather than definitive generalizability across different soils, climates, herbicide doses, or field conditions. Multivariate analyses revealed that ecotoxicological attenuation trajectories in tebuthiuron-contaminated soils are inherently nonlinear, being structured by coordinated shifts in morphophysiological traits rather than isolated responses of individual variables. The integrated PCA-PNN framework demonstrated that aboveground traits. Particularly plant height, chlorophyll content, and shoot dry mass, were more sensitive indicators of tebuthiuron-induced stress than root traits alone. Higher GI values were associated with PCA regions characterized by increased shoot biomass, greater plant height, reduced phytotoxicity, and improved physiological performance, whereas lower GI classes corresponded to suppressed growth and multidimensional stress signatures. The progressive convergence between plant vigor and GI across evaluation periods suggests a gradual mitigation of ecotoxicological stress signals on the indicator plants, indicating transitions from acute injury to physiological adaptation states. These findings confirm that M. pruriens functions as an effective bioindicator for diagnosing soil ecotoxicological status and monitoring tebuthiuron-induced impacts. However, as tebuthiuron residues were not chemically quantified, these responses should not be interpreted as direct evidence of herbicide degradation, dissipation, or removal. These findings confirm that M. pruriens functions as an effective bioindicator for diagnosing soil ecotoxicological status and monitoring tebuthiuron-induced impacts. However, as tebuthiuron residues were not chemically quantified, the observed improvements should be interpreted as evidence of physiological adaptation and/or ecological attenuation rather than definitive proof of herbicide degradation or removal. Overall, this approach provides a robust framework for early detection of soil contamination and supports its application in monitoring and guiding soil rehabilitation processes, with potential for future validation under field conditions.

Why it matches plant phenotyping methods植物の形態・生理形質を統合し、PCA-PNNで植物ストレスおよび土壌生態毒性レベルを診断する手法の開発・内部検証が中心であり、単なる生物学的測定ではない。

abstractThis study developed an integrated diagnostic system for tebuthiuron-induced soil ecotoxicity based on morphophysiological indicators of Mucuna pruriens

A Measurement-Driven Digital Twin Architecture for Plant-Level Biomass Estimation and Growth Forecasting in Hydroponic Systems ↗

Alternatives to soil-based horticulture, such as hydroponics, have been developed to respond to food distribution concerns for dense urban centers. A new system was developed to track an individual lettuce plant's growth in a hydroponic environment, utilizing streams of measured information and available models to continuously update the growth trajectory estimates for a plant. These "digital twin" models were integrated into an operating hydroponic greenhouse, with custom horticultural and sensor hardware to grow and measure relevant information. To aid in updating model parameters, plant yield was continuously measured with a custom neural network, using RGB-D images of the plants as an input. The network, trained on a collected dataset of 1300 images, was able to estimate mass within 1.5 g of the ground-truth value. After integration into the custom system, digital twin growth projections could approximate future yield between one and four days in the future, maintaining around a 2 g forecasting error.

Why it matches plant phenotyping methodsRGB-D画像から個体レタスの収量・質量を推定するニューラルネットワークと、センサー統合型の成長追跡基盤が研究の中心であり、植物形質の取得・予測手法を実質的に開発・検証している。

abstractA new system was developed to track an individual lettuce plant's growth in a hydroponic environment, utilizing streams of measured information and available models to continuously update the growth trajectory estimates for a plant.

A novel approach to assessing the tracking accuracy of crop phenology for multi-orbit and multi-feature Sentinel-1 time series ↗

: This study presents a novel framework for quantifying uncertainties and variabilities related to the monitoring of crop phenology via Synthetic Aperture Radar (SAR) time series at the field scale. Therefore, the study investigated multi-orbit, multi-feature time series derived from Sentinel-1 (S1) VV/VH polarizations. This multi-feature approach encompasses backscatter intensity, interferometric coherence and alpha/entropy decomposition features. Crop phenology tracking is crucial for assessing agricultural resilience under climate change, yet existing approaches face challenges due to uncertainties and variability in SAR signal interpretation as well as in situ data. Building on previous landscape-level analyses, this work introduces the concept of trackability, defined as the temporal range during which SAR-derived time-series metrics (TSM), such as breakpoints in backscatter intensity or interferometric coherence, align with key phenological stages (e.g., stem elongation in winter wheat). A growing degree day (GDD)-based normalization contextualizes field-specific deviations relative to landscape averages, enabling quantification of uncertainties inherent in both SAR signals and ground observations. The framework captures the spatio-temporally variable nature of crop development by estimating the first and last phenologically relevant TSM occurrence within a defined uncertainty window, thus providing relational and relative indicators of phenological tracking. This approach reduces dependencies of extensive in situ data and enhances comparability across studies with differing SAR processing methods and their acquisition geometries. Results reproduce known feature-stage relationships (e.g., tracking for stem elongation by interferometric coherence) and reveal inter-seasonal variability influenced by weather conditions and acquisition parameters. On average relevant TSM occurrences were found at approximately 90% of GDD progression of in situ reported phenological stages, while systematic differences of around 5% by relative orbit were discovered. The study highlights the potential of integrating multiple S1 features and orbits without optimization-induced information loss, producing quality masks that identify optimal tracking performance at the field level. This framework advances SAR-based phenology monitoring by offering scalable, transferable insights for precision agriculture, while practical implementation still requires detailed field boundaries and early-season crop management information.

Why it matches plant phenotyping methodsSAR時系列から作物フェノロジーを追跡・定量化する不確実性評価フレームワークが研究の中心であり、圃場レベルの植物状態測定法として開発・検証されている。

abstractThis study presents a novel framework for quantifying uncertainties and variabilities related to the monitoring of crop phenology via Synthetic Aperture Radar (SAR) time series at the field scale.

Hyperspectral imaging meets 3D Gaussian Splatting: A novel approach beyond 3D plant morphology ↗

Accurate acquisition of plant phenotypes is crucial for elucidating plant growth and development, underlying genetic mechanisms, and responses to environmental stimuli. Traditional three-dimensional (3D) phenotyping mainly captures geometric traits such as height, leaf area, and canopy volume, while overlooking physiological and biochemical information. Here, we present a hyperspectral point clouds generation method based on PlantGaussian (a 3D Gaussian Splatting technique) that integrates structural and spectral information, extending 3D phenotyping beyond geometry to include physiology. High-quality plant point clouds were first reconstructed using PlantGaussian, and hyperspectral images(HSI) were mapped onto them to produce hyperspectral point clouds. In potted soybean experiments, we built predictive models linking hyperspectral reflectance to SPAD (chlorophyll content) and EWT (equivalent water thickness), and visualized their 3D distributions. The hyperspectral point clouds achieved strong predictive performance for SPAD ( R 2 = 0.78, RMSE = 2.05) and EWT ( R 2 = 0.80, RMSE = 1.07), thereby validating the approach. It further revealed clear vertical stratification within the canopy, highlighting significant spatial heterogeneity of SPAD and EWT in individual plants. Temporal monitoring from August 6 to 21, 2025, captured a sharp increase in EWT after heavy rainfall on August 11. Overall, our results demonstrate that hyperspectral point clouds enable accurate, non-destructive trait estimation and provide a powerful tool for exploring plant function, monitoring stress responses, and advancing precision agriculture.

Why it matches plant phenotyping methods植物の3D形態とハイパースペクトル情報を統合してSPAD・EWTを推定する手法を開発し、予測性能を検証しているため、植物フェノタイピング手法が中心である。

abstractHere, we present a hyperspectral point clouds generation method based on PlantGaussian (a 3D Gaussian Splatting technique) that integrates structural and spectral information, extending 3D phenotyping beyond geometry to include physiology.

Synthesizing crop modelling and deep learning for remote estimation of wheat biomass dynamics from multispectral and weather observations ↗

Improving crop productivity while maintaining low environmental impact is essential for sustainable food production under increasing population pressure and irreversible climate changes. Dynamic biomass prediction is critical for effective crop growth monitoring and management, yet existing approaches struggle to provide consistent and reasonable predictions across diverse environments in a rapid, economic, and practical manner. Here, we propose SpecWeaNet, a biophysics-informed neural network framework that integrates explicit biophysical principles governing biomass accumulation with implicit mechanisms learned from representative training data. The framework enables dynamic prediction of wheat biomass from sowing to harvest using daily weather data and limited in-season spectral observations, without requiring model recalibration. From a systematic perspective, SpecWeaNet is designed as a flexible framework, from which we further developed three ready-to-use pre-trained variants with different input configurations tailored to commonly used sensors. Our comprehensive evaluation demonstrates the robustness and generalizability of pre-trained models for seasonal prediction of biomass dynamics from non-daily spectral observations (with random interval between two consecutive observations) and daily weather data, with coefficient of determination (R 2 ) higher than 0.99, relative mean absolute error (RMAE) within 26% and relative root mean square error (RRMSE) within 35% on more than 250,000 in-silico simulation scenarios across diverse environmental conditions, including different years, geographical locations, and crop varieties. Furthermore, validation on multiple field experiments showcases the capability of pre-trained models to provide reliable predictions at both trial (R 2 = 0.77–0.88, RMAE = 20–26%, RRMSE = 29–40%) and plot (R 2 = 0.83–0.93, RMAE = 12–19%, RRMSE = 15–26%) scales, utilizing daily weather observations and available satellite or drone-based imagery. This work demonstrates how integrating crop modelling with artificial intelligence can enable scalable estimation of crop biomass dynamics, advancing remote sensing–based crop phenotyping and monitoring for sustainable agricultural systems.

Why it matches plant phenotyping methodsSpecWeaNetは気象・スペクトル観測からコムギのバイオマス動態を推定する計算フェノタイピング手法であり、モデル開発、シミュレーション評価、複数圃場での検証が中心である。

abstractwe propose SpecWeaNet, a biophysics-informed neural network framework that integrates explicit biophysical principles governing biomass accumulation with implicit mechanisms learned from representative training data.

ARTIFICIAL INTELLIGENCE FOR PLANT DISEASE DETECTION, MONITORING, AND FORECASTING: ADVANCES, CHALLENGES, AND FUTURE GAPS ↗

Plant diseases are one of the main limiting factors in global agricultural productivity, causing significant losses and compromising food security. The increasing complexity of production systems and the limitations of traditional diagnostic methods, based mainly on visual assessment and laboratory analyses, have driven the incorporation of artificial intelligence (AI) in plant pathology. In this context, the present study aimed to synthesize the advances, challenges, and gaps related to the application of AI in the detection, monitoring, and forecasting of plant diseases. This is an integrative literature review, conducted through systematic searches in national and international scientific databases, encompassing studies that addressed machine learning techniques, deep learning, and hybrid models applied to plant pathology. Approaches based on RGB images, multispectral and hyperspectral data, integration with unmanned aerial vehicles (UAVs), and forecasting models based on climatic variables were analyzed. The results show that convolutional neural networks and temporal architectures, such as LSTM, have substantially increased the diagnostic accuracy and forecasting potential of the systems, especially when integrated with environmental data. However, challenges persist related to the generalization of the models, scarcity of representative databases, field variability, and high computational cost. It is concluded that AI represents a strategic tool for the transition from a from a reactive phytopathology to a predictive and decision-support approach. However, its consolidation under real cultivation conditions depends on robust agronomic validation, methodological standardization, and multidisciplinary integration, aiming at more precise, sustainable systems applicable to precision agriculture.

Why it matches plant phenotyping methods植物病害の画像・マルチスペクトル・ハイパースペクトル観測とAIによる検出・予測を主題とするレビューであり、植物状態（病害）の取得・推定手法が中心です。

abstractthe present study aimed to synthesize the advances, challenges, and gaps related to the application of AI in the detection, monitoring, and forecasting of plant diseases.

Image-based phenotyping of faba bean genetic resources for water deficit responses under controlled conditions ↗

Abstract Faba bean ( Vicia faba L.) has great potential to contribute to sustainable agriculture and protein security globally but is known to be very sensitive to drought stress. Uncovering drought-adapted germplasm is critical for developing resilient cultivars and advancing our understanding of the mechanisms underlying stress adaptation. However, high-throughput plant phenotyping under stress conditions remain a major bottleneck in crop genetics and breeding programs. In this study, a multi-sensor indoor phenotyping platform was used to assess 44 faba bean genotypes under water deficit conditions. Standardized, monitored stress conditions were achieved by watering-by-weighing for drought onset, duration, and intensities allowing genotype-level comparisons. The genotypes showed a range of stress responses in growth and physiology, including traits such as plant height, biomass, water use efficiency (WUE), and chlorophyll fluorescence parameters. Digital biomass, derived from combined top- and side-view plant imaging, was strongly correlated with biological biomass at the experimental endpoint, validating its use as a non-destructive proxy for growth assessment in faba bean. Time-resolved generalized additive modelling further revealed genotype-specific differences in the timing and magnitude of water deficit response. Genotypes that maintained growth and WUE under water deficit conditions may serve as valuable pre-breeding materials for development of drought-adapted faba bean.

Why it matches plant phenotyping methods多センサー表現型プラットフォームを用いた画像ベースのデジタル biomass 推定を検証し、植物形質評価への利用可能性を示しており、表現型取得法が中心的です。

abstractIn this study, a multi-sensor indoor phenotyping platform was used to assess 44 faba bean genotypes under water deficit conditions.

WaveST-Yield: a novel spatio-temporal deep learning framework with frequency-domain refinement for UAV-based maize yield prediction. ↗

Accurate and generalizable plot-scale maize yield prediction is critical for precision agriculture and food security. While UAV-based multispectral remote sensing provides rich phenotyping data, existing yield prediction models often struggle with insufficient mining of complex spatio-temporal dynamics, ineffective separation of spatial details from background noise, and inadequate focus on yield-sensitive features throughout the crop growth cycle. To address these limitations, this study proposes WaveST-Yield, a novel hybrid deep learning framework tailored for multi-temporal multispectral data. The proposed model integrates three core modules: a Spatio-Temporal Phenology Encoder (SPE) based on ConvLSTM to capture the temporal dynamic patterns and spatio-temporal correlations across the entire growth period; a Multiscale Frequency-Spatial Refiner (MFSR) utilizing Haar Wavelet Downsampling (HWD) to preserve image details and decouple noise without early loss of key physiological features; and an Adaptive Yield-Sensitive Re-calibrator (AYSR) leveraging a 3D-CBAM attention mechanism to enhance the extraction of critical yield-related traits while suppressing background interference. The model was rigorously evaluated on two independent maize experimental fields using 5-fold cross-validation and cross-plot external validation. Results demonstrate that WaveST-Yield consistently outperforms traditional machine learning algorithms and single-structure deep learning models, achieving the highest prediction accuracy (Overall R² of 0.883 and 0.775 in Field 1 and Field 2, respectively) with superior error control. Extensive ablation and multi-model comparison experiments confirm that the synergistic integration of spatio-temporal encoding, frequency-domain refinement, and 3D attention mechanisms significantly improves model robustness and cross-regional generalization ability. This study provides a highly accurate, robust, and generalizable methodological framework for high-throughput crop yield monitoring.

Why it matches plant phenotyping methodsUAVマルチスペクトル時系列からトウモロコシ収量を推定する深層学習フレームワークの開発と、独立圃場・交差検証による技術評価が研究の中心である。

abstractthis study proposes WaveST-Yield, a novel hybrid deep learning framework tailored for multi-temporal multispectral data.

Estimation of Ramie Key Phenotypic Traits Based on UAV Remote Sensing ↗

UAV-based phenotyping enables efficient high-throughput measurement of field crops. Phenotypic monitoring of ramie is critical for its cultivation management and variety breeding. However, ramie exhibits characteristics including multiple annual harvests, short growth cycles and rapid dynamic growth change, all of which increase the difficulty of growth monitoring and yield estimation. This study aims to utilize UAV-based multispectral remote sensing to estimate ramie plant height (PH), leaf area index (LAI), and above-ground biomass (AGB) over multiple time series, and to assess the influence of seasonal effects and different data processing strategies on the accuracy of ramie digital phenotyping. Over three ramie growth cycles, a total of 15 UAV flights were conducted over an experimental field consisting of 72 plots. The structure from motion (SfM) algorithm was applied to estimate PH. Remote sensing features derived from UAV imagery were used with background segmentation and machine learning to estimate LAI. The AGB was estimated by combining remote sensing-derived PH, LAI, and climate data. The results showed that the estimated and measured phenotypes were highly correlated, with optimal coefficients of determination of 0.961 for PH and 0.873 for LAI. Background segmentation improved LAI accuracy. Integrating climate data, remote sensing-derived PH and LAI significantly enhanced the accuracy of AGB estimation. In conclusion, this study provides a feasible method for extracting ramie phenotypes from UAV remote sensing imagery, providing methodological support for large-scale management of the crop industry and intelligent, precise monitoring of crop growth.

Why it matches plant phenotyping methodsUAVマルチスペクトル画像、SfM、背景分割、機械学習を用いてラムーの草丈・LAI・地上部バイオマスを推定し、精度評価まで行う手法研究であり、表現型取得・抽出が中心である。

abstractThis study aims to utilize UAV-based multispectral remote sensing to estimate ramie plant height (PH), leaf area index (LAI), and above-ground biomass (AGB) over multiple time series, and to assess the influence of seasonal effects and different data processing strategies on the accuracy of ramie digital phenotyping.

Towards Accurate Crop Yield Prediction: Integrating Sentinel-2 Remote Sensing with AI-Based Modelling ↗

Abstract. Accurate monitoring of vegetation health and canopy structure is essential for optimizing agricultural productivity and managing natural resources. Remote sensing technologies, combined with artificial intelligence (AI) and advanced satellite data, have revolutionized the capacity to assess crop conditions at large scales with high temporal and spatial resolution. This study leverages Sentinel-2 multispectral imagery and a novel AI-driven model approach to estimate Leaf Area Index (LAI) across multiple fields for canola. By integrating spectral reflectance data with view and solar geometry parameters, the model effectively captures the complex interactions between canopy structure and environmental factors. The methodology employs a two-layer neural network calibrated with physically based normalization to translate Sentinel-2 spectral and angular inputs into accurate LAI estimates. Validation against observed field measurements demonstrates strong agreement, underscoring the model’s robustness and reliability. Spatial analysis reveals distinct LAI patterns among the crop types, highlighting differences in canopy density and growth dynamics. Temporal profiling further illustrates crop-specific development trends, with canola showing extended canopy expansion. The results confirm that the fusion of remote sensing data with AI modelling provides a powerful tool for precision agriculture, enabling detailed monitoring of crop growth and facilitating informed decision-making. This approach offers significant potential for enhancing yield prediction, resource management, and sustainable farming practices, ultimately supporting global food security efforts.

Why it matches plant phenotyping methodsSentinel-2画像とニューラルネットワークにより、作物のLAIという明示的な植物形質を推定し、実測値で検証する手法が研究の中心である。

abstractThis study leverages Sentinel-2 multispectral imagery and a novel AI-driven model approach to estimate Leaf Area Index (LAI) across multiple fields for canola.

Predicting wheat yield and grain quality with UAV multispectral imagery and deep learning. ↗

Bread wheat ( Triticum aestivum L.) is a major staple crop, and timely, in-season prediction of grain yield (GY) and grain quality traits, grain protein content (GP), and grain test weight (TW), is critical for informed management and field-based high-throughput phenotyping (HTP). Unmanned Aerial Vehicle (UAV) remote sensing, coupled with artificial intelligence and deep learning (DL), offers a practical pathway for rapid, plot-scale trait estimation. Here, we investigate the value of multitemporal, multispectral UAV imagery for predicting winter wheat GY, GP, and TW, and we systematically compare two modeling paradigms: (1) handcrafted feature-based workflows that use plot-aggregated spectral and texture descriptors derived from UAV imagery, and (2) image-based, end-to-end workflows that learn directly from plot-level reflectance image chips. During the 2022 growing season, multispectral UAV data were collected repeatedly over seven experimental wheat sites in South Dakota, USA. For handcrafted feature-based modeling, we evaluated Support Vector Regression (SVR) and Random Forest Regression (RFR), along with DL models including a feedforward Deep Neural Network (DNN) and a one-dimensional Convolutional Neural Network (1D-CNN). For end-to-end image-based modeling, we implemented 2D-CNN, 3D-CNN, and a hybrid 2D-CNN–LSTM architecture to leverage both spatial information and multi-date dependencies. Our results show that: 1) the image-based modeling workflow yielded comparable to slightly better performance than the handcrafted feature-based modeling workflow across wheat GY, GP, and TW predictions; 2) 3D-CNN outperformed all other methods with R 2 of 0.65, 0.61 and 0.69 for GY, GP and TW estimations, respectively; 3) multitemporal UAV data outperformed the data collected from a single growth stage; and UAV data from wheat Feekes 10 (booting) stage yielded slightly better estimation results compared to the data collected from other growing stages, with R 2 of 0.62, 0.55, and 0.62 for GY, GP, and TW estimations, respectively. The results indicate that DL applied to high-resolution multitemporal and multispectral UAV imagery holds strong promise for predicting winter wheat yield and grain quality during the growing season, while also informing HTP efforts and site-specific management.

Why it matches plant phenotyping methodsUAVマルチスペクトル画像から収量・品質形質を推定するワークフローを開発・比較・評価しており、植物表現型取得が研究の中心である。

abstractwe systematically compare two modeling paradigms: (1) handcrafted feature-based workflows that use plot-aggregated spectral and texture descriptors derived from UAV imagery, and (2) image-based, end-to-end workflows that learn directly from plot-level reflectance image chips.

Explainable Deep Learning for Greenhouse Horticulture: Feature and Temporal Interpretability in Crop Yield and Energy Optimization ↗

Optimizing crop yield while minimizing energy consumption remains a central challenge in greenhouse horticulture. This study introduces an integrated deep learning framework that couples multi-horizon time-series forecasting with dual-layered explainability to address the critical need for spatiotemporal transparency in optimizing greenhouse crop yield and energy efficiency. Four deep learning architectures, including the One-Dimensional Convolutional Neural Network (1D-CNN), Long Short-Term Memory Network (LSTM), Bidirectional Long Short-Term Memory Network (BiLSTM), and TinyTimeMixer (TTM), were evaluated across two varieties of capsicum. LSTM and BiLSTM achieved the highest accuracy for incremental yield prediction, whereas TTM outperformed other models in forecasting daily energy usage, reflecting the distinct temporal characteristics of biological growth and environment-driven energy demand. To uncover the factors driving these predictions, two complementary explainability methods were applied: Gradient SHapley Additive exPlanations (SHAP) for feature-level attribution and a Temporal Convolutional Network with Convolutional Block Attention Module (TCN–CBAM) attention mechanism for joint temporal-feature interpretation. Radiation and drainage-related variables consistently emerged as the dominant contributors to yield, whereas external temperature, and humidity were the primary determinants of energy usage. Temporal attention further showed that yield is influenced by both recent irrigation responses and longer-term developmental dynamics, while energy consumption is driven mainly by short-term climatic fluctuations. These findings provide actionable insights for irrigation scheduling, climate-control strategies, and energy optimization, supporting more transparent and sustainable greenhouse management.

Why it matches plant phenotyping methods温室作物の収量という植物形質を深層学習で予測し、複数モデル比較と説明可能性解析を行う計算的形質推定手法が研究の中心である。

abstractThis study introduces an integrated deep learning framework that couples multi-horizon time-series forecasting with dual-layered explainability

Multi-Context Validation of Global Fractional Vegetation Cover Products in Croplands Using Multi-Source Crop FVC References ↗

Fractional Vegetation Cover of Crops (CropFVC) is a critical canopy parameter for monitoring crop growth, yet the behavior of widely used global FVC products (GLASS, GEOV1, GEOV2, and GEOV3) over croplands remains insufficiently understood due to fragmented validation references and limited crop-specific assessments. This study compiled a multi-source global CropFVC reference dataset (2000–2024) by integrating five international validation networks, the literature-derived samples, and newly acquired UAV and Jilin-1 satellite-derived CropFVC samples from China in 2024. The references were organized into three complementary validation contexts (V1~V3) to examine product behavior under different temporal coverage, crop purity, and reference conditions, together with spatio-temporal observations at the KONZ site. Results show that (1) across validation contexts, the evaluated products showed consistent behavior patterns, including shared overestimation under dense canopy conditions and reduced differences at low FVC levels; (2) spatio-temporal analysis at the KONZ site confirmed that peak-season deviations reflect shared response behavior rather than site-specific reference uncertainties; (3) historical mixed references (V1~V2) showed similar bias structures, whereas crop-specific validation (V3) preliminary revealed clearer crop-dependent responses, with predictive difficulty following winter wheat > maize > rice > soybean and improved stability after integrating 2024 observations. The integration of recent high-resolution crop observations expands existing global CropFVC references and enables behavior-oriented interpretation of global FVC products beyond simple accuracy ranking, providing an updated validation perspective for future development and application of global CropFVC products in agricultural monitoring.

Why it matches plant phenotyping methods作物キャノピーのFVCという植物形質を対象に、複数の全球FVC推定プロダクトを多様な参照データで体系的に検証し、UAV・衛星観測を含むCropFVC参照データセットを構築している。形質取得・検証が研究の中心である。

titleMulti-Context Validation of Global Fractional Vegetation Cover Products in Croplands Using Multi-Source Crop FVC References

Validation and application of high-throughput 3D multispectral phenotyping platform for evaluating seasonal adaptation in Chinese cabbage ↗

Climate change poses increasing challenges to Chinese cabbage ( Brassica rapa L. ssp. pekinensis ) production through unpredictable weather patterns that induce premature bolting and physiological disorders. Traditional breeding programs rely on labor-intensive visual assessment that cannot capture continuous developmental dynamics or precisely quantify stress responses across variable environments. This study validated and applied an automated high-throughput phenotyping system for evaluating seasonal adaptation in 134 Chinese cabbage genotypes across contrasting autumn (favorable) and spring (stressful) seasons in Taiwan. The system, based on a FieldScan gantry platform equipped with multispectral 3D scanners, operated autonomously 2-3 times daily, continuously monitoring morphological parameters (3D leaf area, digital biomass, plant height) and spectral indices (NDVI, PSRI) throughout the growth cycle. The system’s automated components -continuous data acquisition and real-time parameter extraction – generated approximately 100,000 data points from 63 morphological, spectral, and structural parameters during 6-week pre-harvest period. Subsequent quality and statistical analysis enabled objective genotype classification and breeding decisions. Automated measurements showed season-dependent associations with visual assessment scores (R² = 0.37-0.56 in autumn; R² = 0.73-0.80 in spring), with spring models substantially outperforming autumn models due to enhanced physiological differentiation under stress. Spring cultivation induced severe stress responses, evidenced by 71% increase in PSRI (0.12 vs. 0.07) and 26% increase in plant height, with bolting resistance emerging as the critical determinant of adaptation. A quantile-based multi-dimensional classification framework integrating seasonal composite scores and Euclidean distances stratified germplasm into actionable breeding categories: stable genotypes (3.7%), spring-specific types (0.7%), poor performers (13.4%), and intermediate materials (82.1%). Continuous temporal monitoring enabled early stress detection, with binned PSRI measurements predicting subsequent morphological development one week in advance (R² = 0.62). This integrated phenotyping framework provides efficient tools for accelerating climate-resilient breeding through objective genotype classification, early stress detection, and data-driven decision support, with potential adaptation to other vegetable crops and integration with IoT-based collaborative breeding network.

Why it matches plant phenotyping methods高スループット3D・マルチスペクトル表現型計測プラットフォームの検証と応用が研究の中心であり、形態・スペクトル形質の自動取得、抽出、予測性能、遺伝子型分類を評価している。

abstractThis study validated and applied an automated high-throughput phenotyping system for evaluating seasonal adaptation in 134 Chinese cabbage genotypes

Advances in root phenotyping: high-throughput imaging, computational tools, and integrative approaches for crop improvement. ↗

Abstract Climate change increasingly threatens global agriculture by intensifying abiotic stresses and destabilizing crop productivity, necessitating a deeper understanding of root-mediated traits governing resource acquisition and stress resilience. Here, we synthesize recent advances in root-centred plant phenomics, emphasizing how high-throughput phenotyping enables high-resolution, scalable characterization of complex root traits and robust comparative analysis across diverse genotypes and environments. Innovations in multimodal imaging, notably X-ray computed tomography, MRI, and machine learning-integrated rhizotrons, facilitate detailed reconstruction of root system architecture and its temporal dynamics under both controlled and semi-field conditions. Furthermore, root phenotyping is increasingly interpreted within an integrated whole-plant framework. The integration of organ-specific assessments with physiological phenomics leveraging spectral and thermal data enables the characterization of developmental plasticity and root-mediated processes, including water-use dynamics, nutrient acquisition, and canopy stress responses under heterogeneous field conditions. These approaches link root traits such as rooting depth and spatial distribution to canopy-level physiological responses under stress. Despite these advances, significant bottlenecks persist in data interoperability, analytical scalability, and protocol standardization. Future progress will require integration of root phenomics with genomics, predictive modelling, and digital twin frameworks to improve resource-use efficiency, yield stability, and climate resilience in global cropping systems.

Why it matches plant phenotyping methods根系フェノタイピングの高スループット画像化、計算ツール、機械学習統合、データ標準化を中心に扱う方法論レビューであり、植物形質の取得・解析手法が主題である。

titleAdvances in root phenotyping: high-throughput imaging, computational tools, and integrative approaches for crop improvement.

Heliocot: A Field RGB Imaging Approach for Diurnal Canopy Orientation Dynamics in Early-Season Cotton ↗

Understanding diurnal canopy orientation in crops is important for interpreting plant responses to light and environmental conditions, yet field-based quantification remains limited. In this study, we present Heliocot, a field RGB imaging approach that converts time-resolved images into reference-area standardized projected leaf area (PLA) time series to quantify within-day canopy orientation dynamics in early-season cotton. Leaf instance segmentation was performed using YOLOv8m-seg and refined through a 144-combination post-processing optimization. On the held-out early-stage validation/tuning set, the selected workflow showed strong agreement with manual ground truth (R2 = 0.948; NRMSE = 0.082) and destructive leaf area measurements (R2 = 0.836). Derived diurnal metrics, including Daily Orientation Amplitude (DOA) and Peak Orientation Index (POI), consistently revealed a midday maximum (13:15) in canopy projection. Exploratory genotype-level analysis suggested negative associations between orientation indices and selected plant traits, including specific leaf area (SLA) versus DOA (r = −0.71, p = 0.021, R2 = 0.508), destructive leaf area (LA) versus DOA (r = −0.69, p = 0.028, R2 = 0.471), and stem dry weight (SDW) versus POI (r = −0.74, p = 0.014, R2 = 0.554), while plant height was not significantly associated with POI and DOA (p > 0.05). Although currently limited to early-season conditions and two field-imaging dates, this approach provides a practical workflow for field-based monitoring of canopy projection dynamics in cotton, while broader temporal and environmental validation remains necessary.

Why it matches plant phenotyping methods圃場RGB画像から葉面積と日周キャノピー配向動態を推定する手法を開発・検証しており、植物形質取得が研究の中心である。

abstractwe present Heliocot, a field RGB imaging approach that converts time-resolved images into reference-area standardized projected leaf area (PLA) time series to quantify within-day canopy orientation dynamics in early-season cotton.

Multisource Grapevine Phenology Dataset for Smart Farming and AI Modeling ↗

Abstract Artificial Intelligence and Machine Learning rely on large, high-quality datasets for accurate and robust models, yet data scarcity remains a major challenge, especially in smart farming. Phenology modeling, a key application, studies how plant biological events relate to climate and seasons. Accurate phenology models improve crop quality, support climate adaptation, and guide decisions such as pesticide use and harvesting, enhancing environmental and economic sustainability. However, agricultural data are highly diverse and heterogeneous, complicating model development. This study presents a proposed georeferenced dataset for Machine Learning-based grapevine phenology prediction across 3 Protected Designations of Origin in Aragón, Spain. Developed by a multidisciplinary team, the dataset combines 9 datasets from 8 sources (including meteorological time series, field phenology observations, and Copernicus Sentinel-2 multispectral imagery) covering the period 2016–2022. It supports both physical and Machine Learning-based phenology modeling and facilitates knowledge extraction in agronomy and plant biology. Its relevance lies in its comprehensive scope, the inclusion of 9 phenological stages, and a rigorous methodology ensuring reproducibility. This framework enables the creation of similar datasets for other regions or crops, advancing smart farming through scalable, data-driven solutions. The open publication of the code further supports this objective. We further anticipate its potential contribution to developing foundation models as well as to the creation of new knowledge in biology and agronomy.

Why it matches plant phenotyping methodsブドウの9段階のフェノロジーを対象に、圃場観測と衛星画像などを統合した再利用可能な地理参照データセットを構築しており、植物形質取得・モデル化の方法論が中心である。

abstractThis study presents a proposed georeferenced dataset for Machine Learning-based grapevine phenology prediction across 3 Protected Designations of Origin in Aragón, Spain.

Phenological growth phases of dwarf apple trees: coding and description based on the BBCH scale. ↗

Background The BBCH scale (Biologische Bundesanstalt, Bundessortenamt und Chemieindustrie) is a fundamental tool for standardizing plant phenological observations. As apple production shifts towards high-density dwarf orchard systems to enhance yield and facilitate mechanization, a significant gap exists in a unified phenological description framework for dwarfing rootstock apple trees, particularly under desert climate conditions. This study aims to systematically characterize the phenological growth stages of dwarf-rootstock apple using an extended BBCH scale to support precision orchard management. Result In our study, phenological monitoring was carried out systematically through the utilization of optical observation equipment and manual observations throughout the entire growth cycles. The extended BBCH scale with a three-digit coding system was applied, where the first digit indicates the principal growth stage (0-9), the second digit represents a mesostage (1 for spring, 2 for autumn growth), and the third digit describes secondary stages (0-9). We described and illustrated eight main growth stages: bud development (stage 0), leaf development (stage 1), shoot development (stage 3), inflorescence emergence (stage 5), flowering (stage 6), fruit development (stage 7), fruit ripening period (stage 8), and senescence and beginning of dormancy (stage 9). A total of 43 secondary stages were defined. Crucially, mesostages were introduced to differentiate the distinct spring and autumn vegetative growth flushes characteristic of the bimodal growth pattern observed under desert conditions. Conclusions The developed three-digit BBCH scale offers a standardized and refined framework for monitoring apple phenology in high-density dwarf orchards. It serves as a vital tool for optimizing the timing of key agronomic practices like irrigation, fertilization, pruning, and pest control, thereby supporting the intelligent implementation of precision agriculture. This framework effectively standardizes phenological observations across diverse environments, laying a foundation for improved yield, fruit quality, and sustainable orchard management.

Why it matches plant phenotyping methodsリンゴの生育段階を標準化・細分類するBBCHスケールを開発し、光学観察と手動観察によるフェノロジー取得を中心的に扱っているため、植物フェノタイピング手法として含める。

abstractThe BBCH scale (Biologische Bundesanstalt, Bundessortenamt und Chemieindustrie) is a fundamental tool for standardizing plant phenological observations.

Crop Yield Prediction using Hyperspectral Imagery and Machine Learning Algorithms Deployed on Edge Computing Nodes ↗

This research work proposed the precision agriculture is supported by accurate future crop yield forecasting which allows optimal use of resources automated use of crops and planning production of food. The problems that conventional predictive systems basing on cloud computing are likely to face include longer latency unreliable network connectivity and heavy processing power requirements which are especially troublesome in the rural farm environment. To deal with these drawbacks the study proposes an Edge-AI-driven framework of crop yield estimation which entails the integration of hyperspectral imaging with real-time measurements of agricultural sensors of soil moisture, pH level, temperature, and humidity. it is based on an STM32 Edge-AI microcontroller and a hybrid deep learning architecture Conv LSTM-ViT (Convolutional Long Short-Term Memory embedded with Vision Transformer) to process spectral changes and environmental changes over time and identify the factors that influence crop growth. The model is able to make decisions in a short time track continuously and lessen cloud reliance by executing inference at the edge. The proposed Conv LSTM-ViT Edge AI model outperforms Random Forest, XG Boost, CNN, and Conv LSTM with up to 14% higher accuracy and 70–80% lower inference latency, demonstrating strong suitability for real-time smart agriculture deployments. Metadata and prediction outcomes are safely uploaded to the Blynk IoT cloud to be visualized and offer decision support to the farm levels. Field testing applications with UAVs further support that the system is energy-saving scalable and able to assist real-time smart farming processes which creates a sustainable system of future farming technologies.

Why it matches plant phenotyping methodsハイパースペクトル画像とエッジAIによって作物収量を推定する取得・解析手法を開発し、既存モデルとの性能比較と実地検証を行っており、収量推定法が中心である。

abstractthe study proposes an Edge-AI-driven framework of crop yield estimation which entails the integration of hyperspectral imaging

Airborne ion charge kinetics reveal circadian-range periodicity in detached plant fruits: a continuous, noncontact, and noninvasive measurement system ↗

Abstract Background Understanding temporal regulation in plant systems requires measurement approaches that capture physiological kinetics with minimal tissue perturbation. Here, we present a magnetically levitated electrode ionization chamber (MALIC) system for monitoring airborne ion charge kinetics in a continuous, noncontact, and noninvasive manner, enabling the continuous physicochemical observation of plant-derived signals without genetic modification or optical readouts. Results Using detached fruits of two apple cultivars (Yoko and Akibae), Lomb-Scargle periodogram analysis identified dominant periodic components within the circadian range (~ 24–25 h) in airborne ion charge. Phase drift analysis revealed cultivar-dependent differences in temporal stability, with Yoko exhibiting relatively consistent peak timing across successive cycles, whereas Akibae showed greater variability. These differences were further supported by phase coherence analysis, which demonstrated the tighter clustering of phase values in Yoko compared with Akibae. Quantitative analysis showed that Akibae exhibited larger amplitude and a higher coefficient of variation, indicating greater relative variability. Because the MALIC system detects net ion-related signals in the surrounding air rather than intracellular processes directly, the observed oscillations should be interpreted as a proxy for integrated physiological activity. These rhythms are consistent with temporally organized physiological processes but do not establish a direct link to endogenous circadian clock mechanisms. Conclusions The MALIC system enables the continuous, noncontact, and noninvasive measurement of airborne ion charge kinetics exhibiting reproducible circadian-range periodicity in detached plant tissues. This work establishes airborne ion charge as a previously unrecognized temporal signal at the plant–environment interface. Rather than replacing established circadian assays, the MALIC system should be considered a complementary approach that captures signals distinct from transcriptional and photosynthetic readouts. Further validation across species, cultivars, and environmental conditions, together with integrated environmental, molecular, and physiological measurements, will be essential to determine whether airborne ion charge kinetics can serve as reliable indicators of endogenous biological rhythms in plants.

Why it matches plant phenotyping methodsMALICシステムによる植物由来の空中イオン荷電動態を、非接触・連続的に測定する手法の提示と、リンゴ果実での技術的適用・解析が中心である。

abstractHere, we present a magnetically levitated electrode ionization chamber (MALIC) system for monitoring airborne ion charge kinetics in a continuous, noncontact, and noninvasive manner

AI-Driven Plant Disease and Pest Surveillance: Deep Learning, IoT, and Next-Generation Crop Protection ↗

Plant disease and pest surveillance is undergoing a profound technological transition. Conventional crop protection has historically depended on episodic field scouting, expert visual inspection, and broad-spectrum preventative spraying, all of which are constrained by labour intensity, uneven diagnostic accuracy, and weak temporal resolution. In contrast, recent advances in artificial intelligence, deep learning, the Internet of Things, remote sensing, and edge computing have enabled crop-health monitoring systems that are more continuous, data-rich, and spatially explicit. This review analyses the evolution of AI-driven plant disease and pest surveillance, with particular attention to how image-based deep learning, connected environmental sensing, unmanned aerial vehicle platforms, cloud-edge infrastructures, and multimodal analytics are reshaping next-generation crop protection. The article argues that the central innovation is not merely automated diagnosis, but the emergence of surveillance ecosystems capable of recognising symptoms, estimating risk, localising hotspots, and informing more selective intervention. The review synthesises major developments in convolutional neural networks, object detection, semantic segmentation, transfer learning, domain adaptation, transformer-based computer vision, anomaly detection, environmental time-series modelling, and multimodal analytics. It also evaluates the practical obstacles that still limit real-world deployment, including dataset bias, annotation uncertainty, poor cross-domain generalisation, limited interoperability, energy and connectivity constraints, weak model explainability, and uneven economic accessibility. The article further considers how AI-based surveillance may strengthen integrated pest management by supporting earlier warning, more precise treatment timing, reduced blanket pesticide use, and stronger alignment between biological risk and management action. It concludes that the future of crop protection will depend less on isolated improvements in benchmark accuracy and more on the development of trustworthy, scalable, and biologically meaningful surveillance systems that can support sustainable decisions under real agricultural conditions.

Why it matches plant phenotyping methods植物病害の症状認識・リスク推定・ホットスポット局在化を行う画像解析、センサー、UAV、マルチモーダル手法を中心にレビューしており、植物の病害状態を推定するフェノタイピング手法レビューに該当する。

abstractThis review analyses the evolution of AI-driven plant disease and pest surveillance, with particular attention to how image-based deep learning, connected environmental sensing, unmanned aerial vehicle platforms, cloud-edge infrastructures, and multimodal analytics are reshaping next-generation crop protection.

Characterization of Rhizosphere Oxidation Associated with Root Development in Rice Using Planar Oxygen Optodes ↗

Rhizosphere oxidation is a key adaptive mechanism in reductive soil environments, in which oxygen released from roots alters rhizosphere redox conditions and regulates biogeochemical processes. Rice plants possess an internal oxygen transport system, and radial oxygen loss (ROL) from roots is closely associated with root development. However, the spatial patterns of ROL in soil and their relationships with root traits remain poorly characterized. In this study, we developed a multimodal imaging system that integrates planar oxygen optodes with X-ray computed tomography to simultaneously visualize rhizosphere oxidation and root development in rice. Daily time-course tracking of individual crown roots revealed dynamic changes in the spatial distribution and magnitude of rhizosphere oxygen in relation to root elongation and aging. Root thickness was positively correlated with dissolved oxygen levels near root tips. Genotypic comparisons further identified a cultivar with reduced rhizosphere oxidation despite possessing thicker roots among the tested genotypes, thereby indicating the involvement of additional physiological processes. Overall, these findings demonstrate that rhizosphere oxidation is regulated by root growth stage and thickness and dynamically modulated during root development.

Why it matches plant phenotyping methods平面酸素オプトードとX線CTを統合したマルチモーダル画像システムを開発し、イネ根の発達と根圏酸化を時系列・空間的に測定しているため、植物フェノタイピング手法が研究の中心である。

abstractwe developed a multimodal imaging system that integrates planar oxygen optodes with X-ray computed tomography to simultaneously visualize rhizosphere oxidation and root development in rice.

Improved leaf area index estimation in Jujube trees by fusing spatial-temporal features from UAV RGB time-series with a deep learning framework. ↗

To achieve high-precision and high-efficiency estimation of the Leaf Area Index (LAI) of jujube trees using drone remote sensing, and to overcome the limitations of traditional vegetation index methods, such as saturation in the later stages of crop growth, sensitivity to background noise, and difficulty in capturing temporal dynamics, this study proposes a parallel hybrid deep learning framework using CNN-GRU. The model adaptively extracts spatial-spectral local features from drone RGB images through a convolutional neural network (CNN) branch, while a gated recurrent unit (GRU) branch learns the sequential evolution of LAI during key phenological periods. Finally, a meta-learner integrates spatial-temporal information for decision-making. To verify the model's effectiveness and prediction performance, the study systematically collected multi-temporal ground-measured LAI data and synchronized drone remote sensing images during critical growth stages of jujube trees in two independent years: 2024 (Bachu, Xinjiang) and 2025 (Alaer, Xinjiang). A series of spectral and texture indices were extracted as model inputs. The experimental results show that the proposed CNN-GRU model exhibits excellent learning and fitting capabilities on the training set, with an R 2 value of 0.839. On the test set, after optimization with data augmentation strategies, the model's prediction accuracy is significantly improved, with prediction accuracy reaching its best level, with an R 2 of 0.83 and an RMSE of 0.150. All error metrics outperform mainstream comparative models such as Transformer, KNN, MLP, and CNN. This study demonstrates that the hybrid deep learning architecture, combining spatial feature extraction and time-series modeling, is an effective approach for accurate and robust remote sensing inversion of crop LAI in complex agricultural scenarios, providing a reliable technical tool for the digital management of smart orchards and precise agricultural decision-making.

Why it matches plant phenotyping methodsUAV RGB画像からナツメ樹のLAIを推定するCNN-GRU手法を開発し、複数年データと比較モデルで性能検証しており、植物形質取得が中心である。

abstractthis study proposes a parallel hybrid deep learning framework using CNN-GRU

Image-based phenotyping of faba bean genetic resources for water deficit responses under controlled conditions ↗

Abstract Faba bean ( Vicia faba L.) has great potential to contribute to sustainable agriculture and protein security globally but is known to be very sensitive to drought stress. Uncovering drought-resilient germplasm is critical for developing resilient cultivars and advancing our understanding of the mechanisms underlying stress adaptation. However, high-throughput plant phenotyping under stress conditions remain a major bottleneck in crop genetics and breeding programs. In this study, a multi-sensor indoor phenotyping platform was used to assess 44 faba bean genotypes under water deficit conditions. Standardized, monitored stress conditions were achieved by watering-by-weighing for drought onset, duration, and intensities allowing genotype-level comparisons. The genotypes showed a range of stress responses in growth and physiology, including traits such as plant height, biomass, water use efficiency (WUE), and chlorophyll fluorescence parameters. Digital biomass, derived from combined top- and side-view plant imaging, was strongly correlated with biological biomass at the experimental endpoint, validating its use as a non-destructive proxy for growth assessment in faba bean. Time-resolved generalized additive modelling further revealed genotype-specific differences in the timing and magnitude of water deficit response. Genotypes that maintained growth and WUE under water deficit conditions may serve as valuable pre-breeding materials for development of drought-adapted faba bean.

Why it matches plant phenotyping methods多センサー表現型プラットフォームを用いた画像由来バイオマスの抽出と生物量との検証が研究の中心であり、表現型取得・検証に該当する。

abstractIn this study, a multi-sensor indoor phenotyping platform was used to assess 44 faba bean genotypes under water deficit conditions.

High-throughput phenotypic analysis of plant and curd growth dynamics during the whole growth period of cauliflower based on instance segmentation ↗

Efficient phenotyping monitoring of cauliflower is crucial for its breeding and production. However, traditional manual measurement methods are time-consuming and labor-intensive, and existing deep learning (DL) methods mostly focus on the seedling stage, lacking systematic research covering the entire growth period. In this study, RGB images of cauliflower from seedling to harvest were collected. Through systematic screening and evaluation of instance segmentation models, accurate segmentation of plants and curds was achieved, and plant canopy width, leaf area, and curd traits were automatically extracted to track their dynamic changes. Evaluation results showed that YOLO12s-seg was the optimal model. It can achieved a segmentation mask mAP 50 of 99.4% for plants and curds in sparsely planted images and showed an advantage in identifying partially occluded early curds beneath inner leaves. Traits such as plant canopy width and curd diameter automatically extracted from segmentation results were highly consistent with manual measurements (R 2 > 0.90). Furthermore, the Richards model and Sine model were used to accurately fit the growth dynamics of leaf area and curd area, respectively. Based on growth kinetics, curds were classified into three types: mature and compact type, peak-burst type, and steady-increase type. Cluster analysis of 47 germplasms based on high-throughput phenotyping data revealed four groups and their growth characteristics: comprehensively coordinated type, mid-maturity compact type, large high-yield type, and curd-dominant type. Integrating the above functions, a platform for cauliflower growth monitoring and phenotypic analysis was developed. It provided full-process support from automatic image processing to growth dynamic analysis. This work provides an effective automated solution for high-throughput phenotyping analysis and growth dynamic monitoring of cauliflower, and offers a referable analytical framework for crop growth pattern research and intelligent breeding decision-making.

Why it matches plant phenotyping methods植物のインスタンスセグメンテーションから葉面積・草冠幅・花蕾形質を自動抽出し、手動測定との技術検証と成長動態解析、統合プラットフォーム開発を行っており、フェノタイピング手法が研究の中心である。

abstractThrough systematic screening and evaluation of instance segmentation models, accurate segmentation of plants and curds was achieved, and plant canopy width, leaf area, and curd traits were automatically extracted to track their dynamic changes.

Spatio-Temporal Reconstruction of MODIS LAI Using a Self-Supervised Framework for Vegetation Dynamics Monitoring Across China ↗

Leaf Area Index (LAI) is a key biophysical parameter for characterizing terrestrial vegetation dynamics and land surface processes. Time-series MODIS LAI products are widely used in ecological and land-related research, but cloud contamination and sensor noise lead to widespread spatio-temporal gaps, limiting their ability to support long-term, consistent vegetation monitoring over large areas. To address this issue, this study proposes a novel self-supervised LAI reconstruction framework (SSLAI) for generating gap-free and ecologically consistent LAI datasets across China. The framework integrates cross-modal environmental fusion, multi-scale spatio-temporal modeling, and adaptive phenological constraints to ensure the reconstructed LAI aligns with realistic vegetation growth rhythms. SSLAI outperforms seven traditional and state-of-the-art deep learning methods, maintaining a root mean square error (RMSE) below 0.20 even with 16 missing time windows. Field validation confirms its high accuracy, with a coefficient of determination (R2) of 0.885 and an RMSE of 0.477. Furthermore, SSLAI’s response to meteorological changes aligns with ecological principles, demonstrating favorable physical interpretability and ecological rationality. The reconstructed LAI exhibits superior spatial completeness and temporal consistency compared with MODIS, VIIRS, and GLASS products, and performs robustly under variable climatic conditions. This study provides an effective self-supervised solution for MODIS LAI gap-filling over large regions, and the generated high-quality LAI dataset can serve as a reliable data foundation for vegetation dynamics monitoring, land surface modeling, and global change research.

Why it matches plant phenotyping methods植物群落のLAIという明示的な植物形質を対象に、欠測補完の計算手法を開発し、既存手法との比較および野外検証を行っているため、方法開発・検証が中心である。

abstractthis study proposes a novel self-supervised LAI reconstruction framework (SSLAI) for generating gap-free and ecologically consistent LAI datasets across China.

A Public-Data-Based Multimodal Framework for Plant Growth State Analysis Toward Future Filter-Free Aquaponic Validation ↗

This study proposes the Hydroponic Plant Growth Analysis System (HPGAS), a public-data-based preliminary framework for multimodal plant growth state analysis toward future filter-free aquaponic validation. The HPGAS integrates plant images, water quality signals, and environmental signals to estimate an image-centered growth index, growth stage, and proxy abnormal state probability. Because no public dataset jointly provides plant images, direct growth labels, fish metabolic variables, suspended solids, and nitrification-related measurements from a real filter-free aquaponic system, this study is not a direct operational validation. A two-stage evaluation was conducted using the Autonomous Greenhouse Challenge (AGC), HydroGrowNet, and two aquaponic Internet of Things (IoT) water quality datasets. Stage 1 implemented dataset loaders, image–sensor alignment, proxy label generation, and unimodal and fusion baselines. Stage 2 expanded handcrafted image and sensor-context features and adopted month-wise hold-out evaluation. The image-only model achieved the best growth index regression performance, with a root mean square error (RMSE) of 0.0492 ± 0.0187, whereas the fusion model showed a RMSE of 0.0837 ± 0.0196. Conversely, the fusion model achieved the best proxy abnormal state classification performance, with a F1 score of 0.9695 ± 0.0057 under the clean condition, decreasing to 0.9232 ± 0.0263 under sensor dropout and 0.9132 ± 0.0169 under image noise. Under sensor dropout, the fusion model was more stable than the sensor-only model, whereas under image noise it degraded more than the image-only model. These results indicate that multimodal fusion is most useful for proxy abnormal state classification and robust state interpretation, rather than universally superior scalar growth regression. The HPGAS provides a reproducible baseline for future real filter-free aquaponic experiments, while its operational validity remains to be tested using real filter-free aquaponic data.

Why it matches plant phenotyping methods植物画像とセンサーデータを統合し、成長指数・成長段階・異常状態確率を推定する再現可能な解析フレームワークを開発・評価しており、植物表現型の取得・推定手法が中心である。

abstractThis study proposes the Hydroponic Plant Growth Analysis System (HPGAS), a public-data-based preliminary framework for multimodal plant growth state analysis

Generation of Spatially and Temporally Fine-Resolution Imagery Using STF Algorithms and CACAO Post-Processing ↗

Abstract Spatio-temporal fusion (STF) has been widely used across various remote sensing applications, including environmental monitoring, land cover change detection, and water resource management by integrating multi-sensor data with different spatial and temporal resolutions. The objective of this study was to generate spatially and temporally fine-resolution imagery and to evaluate the performance of multiple STF algorithms and Consistent Adjustment of the Climatology to Actual Observations (CACAO) post-processing for parcel-level crop monitoring. The study was conducted in a soybean field located in Anseong, South Korea, using Planet SuperDove satellite imagery which has 3 m spatial resolution and near-daily temporal resolution, and Phantom 4 Multispectral Unmanned Aerial Vehicle (UAV) data which has 0.05 m spatial resolution, downscaled to target resolution 0.5 m, and 1–4 week irregular temporal resolution. Relative radiometric normalization was applied, followed by the implementation and comparison of four STF algorithms— Enhanced Spatial and Temporal Adaptive Reflectance Fusion Model (ESTARFM), Fitting, spatial Filtering and residual Compensation (FitFC), Flexible Spatiotemporal Data Fusion (FSDAF), and Variation-based Spatiotemporal Data Fusion (VSDF)—within a 4-fold cross-validation framework. CACAO post-processing was then employed to reconstruct temporally continuous NDVI trajectories, from which growth metrics such as Vegetation Growth Metrics (VGM)85 and VGMmax were derived. The validation results indicated that ESTARFM achieved the highest Normalized Difference Vegetation Index (NDVI) performance among the evaluated algorithms, with an Root Mean Square Error (RMSE) of 0.113 and the Universal Image Quality Index (UIQI) of 0.697, and CACAO further improved the results, with CA-ESTARFM providing the highest NDVI accuracy, with an RMSE of 0.108 and a UIQI of 0.740. NDVI histogram and spatial analyses demonstrated that CA-ESTARFM achieved the most consistent agreement with UAV observations while preserving fine-scale spatial heterogeneity. In addition, intra-field vegetation assessment using VGM85 and VGMmax confirmed that CA-ESTARFM enhanced the reliability of crop growth evaluation compared to simple linear interpolation of UAV observations. The proposed framework demonstrates strong potential for applications in comprehensive crop monitoring, precision agriculture management, and yield forecasting.

Why it matches plant phenotyping methods衛星・UAV画像の時空間融合アルゴリズムを比較検証し、NDVI軌跡から作物生育指標を抽出する方法が研究の中心であるため、植物フェノタイピング手法として採択する。

abstractThe objective of this study was to generate spatially and temporally fine-resolution imagery and to evaluate the performance of multiple STF algorithms and Consistent Adjustment of the Climatology to Actual Observations (CACAO) post-processing for parcel-level crop monitoring.

Proactive Irrigation Timing Decision-Making for Greenhouse Tomatoes via STL-LSTM Deep Learning and Plant–Soil Dual-Threshold Sensing ↗

Traditional irrigation management for tomatoes in solar greenhouses relies heavily on empirical manual experience and single soil moisture indicators, often leading to irrigation scheduling that lacks crop-specific physiological evidence and results in suboptimal water-use efficiency. To address these challenges, this study developed an intelligent, plant-centric irrigation decision-making framework for greenhouse tomatoes in the arid region of Xinjiang. Central to this framework is the precise identification of irrigation timing—the most critical first step and a fundamental prerequisite for achieving true on-demand irrigation. By monitoring the high-frequency dynamics of stem diameter (SD) and integrating soil moisture data, the physiological responsiveness of tomatoes to water stress was systematically analyzed. A hybrid predictive model, STL-LSTM, was constructed by coupling Seasonal-Trend decomposition using Loess (STL) with Long Short-Term Memory (LSTM) networks to forecast 24-h SD trends. Furthermore, an innovative dual-threshold irrigation mechanism was established, utilizing a physiological trigger (Maximum Daily Shrinkage, MDS > 70 μm) and a soil moisture constraint (Volumetric Water Content, VWC ≤ 17%). Results demonstrated that tomato SD exhibited distinct diurnal rhythms, with MDS and Daily Increment (DI) identified as highly sensitive indicators of plant water status. The proposed STL-LSTM model achieved superior predictive performance during the peak fruiting stage, with a coefficient of determination (R2) of 0.9184, representing an improvement of 14.8% and 27.56% over standalone LSTM and ARIMA models, respectively. The validation of the dual-threshold mechanism confirms its ability to balance real-time crop water demand with conservation requirements, effectively mitigating the risks of premature or delayed irrigation inherent in traditional methods. This research provides scientific rationale and technical support for the transition of greenhouse agriculture in arid regions towards precision irrigation and optimised water resource management.

Why it matches plant phenotyping methodsトマト茎径を植物の水分状態指標として高頻度センシングし、STL-LSTMによる予測と二重閾値の検証を行うことが中心であり、単なる灌漑実験ではない。

abstractCentral to this framework is the precise identification of irrigation timing—the most critical first step and a fundamental prerequisite for achieving true on-demand irrigation.

Phenotypic analysis method for 3D reconstruction of eggplant seedlings fused with background purification — based on the improved EggplantPointNet++ model and DBSCAN clustering ↗

Eggplant (Solanum melongena L.) is a widely cultivated vegetable crop worldwide, occupying an important position in the agricultural industries of Asia, the Middle East, and Southern Europe. Its significance extends beyond agricultural economics to diverse dimensions such as dietary nutrition, rendering it of considerable research and application value. Traditional crop phenotyping methods suffer from low efficiency, substantial manual errors, and a tendency to damage tender seedlings, while existing three-dimensional phenotyping techniques face challenges including strong background interference and large data volumes. These dual constraints limit the accuracy and application feasibility of seedling phenotyping. To address these issues, this study proposes a non-destructive phenotyping method for eggplant seedlings, with the improvement of the PointNet++ architecture as its core and point cloud background purification as a key preprocessing step, aiming to enhance eggplant breeding efficiency and seedling screening accuracy. The raw point clouds first undergo background purification to actively remove seedling tray points, thereby improving point cloud purity and reducing data size. Concurrently, based on the PointNet++ model, we develop an improved point cloud segmentation model, EggplantPointNet++, by introducing multi-scale residual blocks, integrating channel attention mechanisms, incorporating a global context module, and refining the feature propagation layer. In conjunction with the DBSCAN clustering algorithm, this approach achieves semantic and instance segmentation of eggplant seedling point clouds, with certain improvements in segmentation accuracy and model efficiency under small-scale and occluded scenarios. To validate the technical effectiveness, multiple comparative experiments and ablation studies were conducted. The results demonstrate that EggplantPointNet++ outperforms the original model, background purification preprocessing provides positive gains, and each improved module contributes positively. The final model achieves improvements in core metrics including Recall and F1-score. Based on the segmented point cloud data, this study calculates core phenotypic parameters including plant height, stem diameter, cotyledon angle, and cotyledon area. Using the technical system established in this study, we completed the time-series measurement of three-dimensional morphological changes in eggplant seedlings during the cotyledon stage, providing quantitative references for seedling growth assessment and superior plant selection.

Why it matches plant phenotyping methodsナス幼苗の3D点群から形質を抽出する非破壊フェノタイピング手法を開発し、比較実験・アブレーションで技術性能を検証しているため、方法が中心的である。

abstractthis study proposes a non-destructive phenotyping method for eggplant seedlings

Wearable Plant Electronics Enables Early Detection of Salt Stress by Tracking K + /Na + Homeostasis and Salicylic Acid Accumulation. ↗

Soil salinization threatens global food security by disrupting plant ion homeostasis and triggering complex hormonal signaling cascades. Early detection of salt stress and real-time tracking of stress-responsive physiological dynamics remain major technical bottlenecks, as current methods rely on destructive sampling or single-parameter sensing that obscure the crosstalk between ionic and hormonal networks. Here, we report a wearable plant electronic system that enables noninvasive, in situ monitoring of K + /Na + homeostasis and salicylic acid (SA) accumulation, two key indicators of plant salt stress adaptation. The integrated platform combines flexible laser-induced graphene (LIG) ion-selective electrodes enhanced with a SnS 2 -MoS 2 heterostructure for stable potentiometric sensing, a reverse iontophoresis module for noninvasive analyte extraction, and a biocompatible flexible zinc-air battery for long-term power supply. Deployed on tobacco plants, the wearable device detected salt stress within 24 h by capturing the initial disruption of the K + /Na + ratio and the subsequent accumulation of SA, far preceding visible symptoms. The temporally resolved data revealed a dynamic correlation where SA accumulation coincided with a partial recovery of the K + /Na + ratio, suggesting an active role of SA in modulating ion homeostasis. This wearable plant electronic system transcends the limitations of conventional single-parameter detection, providing a powerful tool for early stress diagnosis, deciphering plant adaptive mechanisms, and advancing precision agriculture to mitigate the impact of soil salinization.

Why it matches plant phenotyping methods植物の塩ストレス状態を非破壊・リアルタイムに測定するウェアラブルセンサー基盤の開発が研究の中心であり、K+/Na+恒常性とサリチル酸蓄積という生理表現型を直接取得している。

abstractHere, we report a wearable plant electronic system that enables noninvasive, in situ monitoring of K + /Na + homeostasis and salicylic acid (SA) accumulation, two key indicators of plant salt stress adaptation.

From plots to commercial fields: scalable, transferable cotton morphology and productivity estimation using functional growth proxies from UAV and PlanetScope time series. ↗

Product demand and climate variability are progressively increasing the need for real-time, scalable crop monitoring to support varietal selection and in-season input optimisation. However, producers still have limited information on the temporal and spatial variability of cotton health and performance beyond point-scale field surveying. In addition, given cotton's high phenotypic plasticity, near real-time derived metrics are essential to improve input efficiency and strengthen long-term sustainability of the cotton industry in Australia. Therefore, we proposed a functional integrated predictive sensing framework to estimate and predict cotton canopy morphological (i.e., height) and productivity traits (i.e., dry matter and lint yield) across large plots (12m × 6m). Scalability was validated by applying the proposed framework to estimate and map cotton yield across commercial fields. To do this, we explored the accuracy of high-resolution multispectral imagery from two platforms (unmanned aerial vehicle (UAV) and PlanetScope (PS)) collected across two 144-plot trials for two cotton seasons. These were designed with a large range in nitrogen rates (N), shading, and two growth-regulator doses, thus, creating variable environments. Sensing metrics were obtained from UAV imagery (1.3-1.6 cm pixel size) acquired once in 2022/23 and eight times in 2023/24, while PS composites (3 m pixel size) provided near-daily coverage in both seasons. Time-series gaps were imputed using Savitzky-Golay smoothing in thermal time (GDD), enabling extraction of growth dynamic metrics (GDMs) as single-date (SD; e.g., peak canopy) and multi-date (MD; e.g., daily average growth rate) metrics. After reducing collinearity and dimensionality, random forest (RF), support vector regression (SVR), and gaussian process regression (GPR) were trained and interpreted with SHAP, for feature contribution. UAV single-date models (SD_ UAV) achieved strong accuracy for height (R 2 = 0.77), biomass (R 2 = 0.73), and yield (R 2 = 0.81). Incorporating UAV time-series metrics (MD_UAV) improved the performance R 2 = 0.87, 0.86, and 0.85 for height, biomass and yield, respectively. Application of the derived models using high resolution satellite data (MD_PS) for different farming systems showed highly significant accuracy (R 2 = 0.67) to predict cotton yield at aggregated field scale. As such, enabling the detailed spatial prediction of cotton yield within a field. It is anticipated that the proposed functional sensing framework will improve the estimation of key cotton production traits, supporting field- and within-field decision-making, ultimately contributing to more resilient and sustainable cotton production in Australia.

Why it matches plant phenotyping methodsUAV・衛星時系列画像から綿花の形態・生産性形質を推定するセンシング／予測フレームワークを開発・検証し、商業圃場へ適用しており、表現型取得手法が中心である。

abstractwe proposed a functional integrated predictive sensing framework to estimate and predict cotton canopy morphological (i.e., height) and productivity traits (i.e., dry matter and lint yield) across large plots (12m × 6m).

Mapping California's Urban Forest at Scale: An Error-Adjusted Canopy Time Series for Monitoring Change ↗

Statewide tracking of urban tree canopy change is essential for evaluating progress toward policy targets, but detecting real change requires both high-resolution mapping and rigorous uncertainty estimation. We produced a four-year canopy cover time series for all California census-designated places using 60-cm NAIP aerial imagery and a U-Net deep learning model trained with semi-automated LiDAR-derived labels and manually annotated tiles. Canopy cover and change were estimated using stratified, error-adjusted area estimation, enabling comparisons across years. Statewide canopy cover showed a modest negative trend from 2016 to 2022 (Sens slope: -0.60% per year), but confidence intervals included zero across all groups and climate zones, indicating that trends were not statistically distinguishable from no change. Urban canopy cover was consistently lower than non-urban canopy by approximately six percentage points, and canopy cover was highest in the Northern California Coast and lowest in the Southwest Desert. Residential parcels accounted for 55-56% of canopy within incorporated urban areas across all years, indicating that statewide canopy increase goals will require engagement with private landowners. Error adjustment substantially altered canopy estimates relative to raw pixel-count totals, with direct implications for AB 2251 canopy tracking where baselines and targets drawn from unadjusted maps may not reflect true canopy extent. This open-source workflow is transferable to future NAIP acquisition years and other U.S. states, providing a scalable framework for long-term urban forest monitoring.

Why it matches plant phenotyping methods航空画像とU-Netにより都市樹冠被覆率を推定し、誤差調整と不確実性評価を行う再利用可能なワークフローを中心に扱っているため、植物状態の測定手法として採用。

abstractWe produced a four-year canopy cover time series for all California census-designated places using 60-cm NAIP aerial imagery and a U-Net deep learning model trained with semi-automated LiDAR-derived labels and manually annotated tiles.

Research on maize growth simulation and organ morphology co-modeling driven by multimodal data fusion. ↗

Introduction Addressing the core bottleneck in traditional crop models-the disconnect between morphology and physiological function at the organ scale and their limited dynamic response to environmental changes-this study aimed to construct a multi-source data fusion maize growth model for simultaneous organ-scale simulation. Methods We developed a closed-loop Environment-Driven-Functional Response-Morphological Feedback (EDFM) architecture. By integrating environmental time-series data, RGB images, and 3D point clouds, we created a multimodal fusion model based on a gated attention network. This approach adaptively weights multi-source features and pioneers a bidirectional morphology-physiology feedback loop based on physiological development time (PDT) and NURBS surfaces. The WOFOST moisture response function was also improved. Results The model significantly enhanced the simulation accuracy of organ-scale growth, reducing the root mean square error (RMSE) for plant height by 74.6% through a morphology-physiology dynamic weighting mechanism. More fundamentally, it resolved the disconnect between morphological and physiological processes. The improved plant height prediction validates the model's effectiveness at the organ scale. Discussion The pioneering "physiology-morphology" parallel simulation architecture provides an interpretable theoretical model and robust quantitative tools for designing high-photosynthetic-efficiency plant architecture and enabling precision water-fertilizer management.

Why it matches plant phenotyping methodsRGB画像・3D点群・環境データを統合し、器官スケールの形態と生長をシミュレーションする手法を開発しており、植物形質（草丈など）の推定が中心的な技術貢献である。

abstractWe developed a closed-loop Environment-Driven-Functional Response-Morphological Feedback (EDFM) architecture.

Artificial Intelligence Technologies in Plant Factories over the Last Decade: Machine Vision, Nutrient Intelligence, Control, and Digital Twins ↗

Plant factories have evolved from automated cultivation facilities into data-driven crop production systems. Over the last decade, artificial intelligence has been applied to non-destructive crop monitoring, sensor correction, nutrient-solution diagnosis, growth prediction, environmental control, digital twins, and product-level inspection. This review summarizes AI technologies for plant factories, focusing on machine vision, deep learning, nutrient-solution intelligence, reinforcement learning, and digital-twin interfaces. The main argument is that plant-factory AI should not be understood only as image-based phenotyping; practical systems require an integrated intelligence stack connecting visual perception, sensor calibration, nutrient modeling, control, remote operation, and industrial inspection. Remaining challenges include dataset scarcity, model generalization, sensor drift, explainability, energy-aware control, and closed-loop decision-making.

Why it matches plant phenotyping methods植物工場における機械視覚・センサー補正・作物モニタリングなどのフェノタイピング関連技術を中心に扱うレビューであり、方法論的役割が明確。

abstractThis review summarizes AI technologies for plant factories, focusing on machine vision, deep learning, nutrient-solution intelligence, reinforcement learning, and digital-twin interfaces.

High-Resolution UAV-Based NDVI Monitoring Method for Sustainable Post-Mining Land Management ↗

The transition of coal regions under the European Green Deal and Just Transition Fund creates a need for quantitative, transparent monitoring of ecological recovery on post-mining land. This study presents an autonomous UAV-based methodology for high-resolution monitoring of vegetation dynamics on a reclaimed coal waste heap in Upper Silesia, Poland. A DJI Mavic 3 Multispectral platform with RTK positioning conducted approximately biweekly flights from August 2024 to October 2025 over three study plots acquiring RGB and multispectral imagery at approximately 4 cm/pixel. Photogrammetric processing in DJI Terra produced radiometrically corrected orthomosaics and NDVI maps, which were analyzed using an automated QGIS workflow for reprojection, clipping, NDVI-based classification, and quantification of vegetation area across three different reclamation variants. The results indicate that intensive soil conditioning through the application of compost derived from bio-waste achieved a maximum vegetation cover of 94.4%. This treatment consistently maintained the highest level of cover during periods of environmental stress and significantly surpassed both seeding-only treatments and those combining seeding with irrigation. Baseline vegetation cover below 6% confirmed the necessity of active reclamation. This workflow provides rapid and reproducible metrics that are suitable for adaptive management and regulatory reporting. It also offers a scalable template for monitoring coal waste heaps across Europe undergoing SDG-aligned reclamation.

Why it matches plant phenotyping methodsUAVマルチスペクトル画像と自動QGISワークフローにより、植生被覆を plot レベルで定量化する再現可能な計測手法が研究の中心であるため、植物状態の画像ベース表現型計測として採用。

abstractThis study presents an autonomous UAV-based methodology for high-resolution monitoring of vegetation dynamics on a reclaimed coal waste heap

Research on the Application of Agricultural Big Data in Plant Growth Prediction ↗

The intelligent transformation of agriculture places plant growth prediction as a critical component for ensuring food security, optimizing resource allocation, and enhancing sustainable productivity. Traditional methods reliant on empirical or simplified mechanistic models struggle with the nonlinearity, high dimensionality, and spatiotemporal heterogeneity inherent in agro-ecological systems. This study investigates the paradigm shift enabled by agricultural big data integrating multi-source, real-time streams from IoT sensors, satellites, UAVs, and farm management systems. We propose a ``Multi-source Data Assimilation and Hybrid Intelligence'' (MDA-HI) framework that synergistically couples process-based crop models with ensemble machine learning algorithms---including Transformer-based architectures and Physics-Informed Neural Networks---within a holistic pipeline encompassing multi-modal data fusion, hybrid modeling, and scalable deployment. Empirical validation across major crops (rice, wheat, maize, tomato) in diverse eco-regions of China (2023--2025) demonstrates significant improvements: the MDA-HI model achieved average RMSE reductions of 42.7% for yield prediction and 38.1% for key phenological stage prediction relative to best-in-class standalone models. A large-scale case study on rice-wheat rotation systems showed that data-driven prescriptions reduced nitrogen fertilizer use by 22.5% and irrigation water by 18.3% while increasing yield by 5.1%. The study further establishes a five-dimensional evaluation system covering accuracy, robustness, interpretability, scalability, and economic benefit. Remaining challenges include edge computing for real-time inference, federated learning for privacy-preserving collaboration, and explainability of complex ``black-box'' models. This research concludes that agricultural big data constitutes a foundational catalyst for predictive, precise, and proactive cognitive agriculture, with profound implications for global food system resilience.

Why it matches plant phenotyping methods農業ビッグデータを用いて生育・収量・フェノロジーを推定するMDA-HI手法を提案し、複数作物・地域で性能検証しており、植物形質推定手法が研究の中心である。

abstractWe propose a ``Multi-source Data Assimilation and Hybrid Intelligence'' (MDA-HI) framework that synergistically couples process-based crop models with ensemble machine learning algorithms---including Transformer-based architectures and Physics-Informed Neural Networks---within a holistic pipeline encompassing multi-modal data fusion, hybrid modeling, and scalable deployment.

Artificial Intelligence Technologies in Plant Factories over the Last Decade: Machine Vision, Nutrient Intelligence, Control, and Digital Twins ↗

Plant factories have evolved from automated cultivation facilities into data-driven crop production systems. Over the last decade, artificial intelligence has been applied to non-destructive crop monitoring, sensor correction, nutrient-solution diagnosis, growth prediction, environmental control, digital twins, and product-level inspection. This review summarizes AI technologies for plant factories, focusing on machine vision, deep learning, nutrient-solution intelligence, reinforcement learning, and digital-twin interfaces. The main argument is that plant-factory AI should not be understood only as image-based phenotyping; practical systems require an integrated intelligence stack connecting visual perception, sensor calibration, nutrient modeling, control, remote operation, and industrial inspection. Remaining challenges include dataset scarcity, model generalization, sensor drift, explainability, energy-aware control, and closed-loop decision-making.

Why it matches plant phenotyping methods植物工場におけるAI技術レビューで、非破壊的な作物モニタリング、機械視覚、深層学習、センサー補正など、植物形質取得に関わる方法を中心的に扱っている。

abstractThis review summarizes AI technologies for plant factories, focusing on machine vision, deep learning, nutrient-solution intelligence, reinforcement learning, and digital-twin interfaces.

Continuous monitoring of plant water potential: sensor‐based approaches and best practices ↗

Summary Plant water potential is a central integrator of plant water status, linking hydraulic function with physiological performance and ecosystem water dynamics across species and systems. This review is motivated by the need to capture these dynamics under rapidly changing environmental conditions, which are often missed by discrete measurements. We evaluate the main approaches for continuous monitoring of plant water potential, including direct in situ sensors, indirect methods based on plant water content, and remote‐sensing proxies. We discuss the principles, measurement mechanisms, practical constraints, and environmental sensitivities of each approach. Relative to traditional methods, such as pressure chambers, continuous measurements offer major advantages by resolving rapid variation in water status and strengthening inference on plant–soil–atmosphere interactions. These approaches are especially valuable under dynamic field conditions, where temporal variability in vapor pressure deficit, soil moisture, temperature, and radiation strongly shapes hydraulic behavior. We conclude that continuous monitoring has substantial potential to advance plant and ecosystem science, but wider application will depend on careful interpretation and greater harmonization across comparable methodologies. By synthesizing core principles, methodological challenges and best practices, this review provides a practical framework for researchers and practitioners applying continuous water potential measurements.

Why it matches plant phenotyping methods植物の水ポテンシャルという生理形質を連続測定するセンサー手法を比較・整理し、測定原理、制約、標準化、実践指針を扱う方法論レビューであり、フェノタイピング手法が中心である。

abstractWe evaluate the main approaches for continuous monitoring of plant water potential, including direct in situ sensors, indirect methods based on plant water content, and remote‐sensing proxies.

Stomatal setpoints and environmental responsiveness are sculpted by developmental trajectories ↗

Efficient gas and water exchange between plants and their environment largely depends on the number and distribution of stomata, cellular valves in leaf epidermis. Core genetic regulators of stomatal cell identity and pattern along with asymmetric stem-cell like divisions in stomatal precursors are hypothesized to customize stomatal production for optimal leaf performance. How these regulators work in concert and how division dynamics are modified and adjusted in different environments, however, are poorly understood. Here, we leveraged the variation in stomatal patterning in Arabidopsis thaliana accessions from diverse environments to define developmental rules and constraints in the stomatal lineage. The accessions subtle and quantitative variation enables us to identify which cellular parameters are flexible, revealing how developmental plasticity generates phenotypic plasticity. By developing live-cell imaging tools to track cellular behaviors during leaf growth under varying environmental conditions in these accessions, we could decompose stomatal density variation into its developmental origins. Variation in final stomatal numbers is driven by differences in the relative contributions of stomatal initiation, cell size-based fate thresholds, general proliferative capacity, and coordination between sister and neighbor cell behaviors. Overall, diverse accessions converge toward two lineage regimes: one dominated by autonomous decisions with loose cell-cell coordination, the other by extensive cell-cell coordination. Challenging accessions with environmental fluctuations revealed regime-specific flexibility, with plasticity primarily mediated by a single division-related parameter. Our results show how cellular parameters integrate into alternative developmental strategies that shape environmental responsiveness.

Why it matches plant phenotyping methods葉の成長中の細胞挙動を追跡するライブセルイメージングツールを開発し、気孔密度の発生的起源を定量化しており、植物フェノタイピング手法が研究の中心である。

abstractBy developing live-cell imaging tools to track cellular behaviors during leaf growth under varying environmental conditions in these accessions, we could decompose stomatal density variation into its developmental origins.

Monitoring Carbon Stock Change at the Individual-Plant Scale: A Methodological Review and Integrative Framework ↗

With increasing demand for fine-scale ecological management under carbon neutrality frameworks, multi-temporal assessment of carbon stock change (ΔC) at the individual-plant scale has become essential for understanding plant-level carbon dynamics and supporting management decisions. However, methodologies for repeated monitoring at this scale remain fragmented, showing limited cross-temporal comparability, weak cross-scale consistency, and insufficient integration across methods. Existing approaches can be grouped into three pathways: (i) process-based methods derived from CO2 exchange measurements, (ii) state-based approaches estimating biomass and ΔC, and (iii) sensing-based approaches using structural, spectral, thermal, and fluorescence signals. These approaches offer complementary strengths, yet none simultaneously achieve high accuracy, temporal continuity, and operational scalability for multi-temporal ΔC estimation. Among these, stock-based and structural approaches form the primary estimation pathways, while flux-based and functional sensing methods provide complementary constraints. This review synthesizes and compares these approaches in terms of their theoretical basis, spatial support, temporal characteristics, and uncertainty structures. To address the lack of methodological integration, we propose a structure–function–scale framework that links heterogeneous observations across spatial and temporal domains and emphasizes cross-scale consistency as a prerequisite for reliable ΔC estimation. Within this framework, we further examine how multi-source integration can connect structural and functional observations through segmentation, co-registration, scaling, temporal alignment, and uncertainty propagation. By integrating traditional measurement logic with emerging remote sensing technologies, this review provides a unified methodological framework for ΔC estimation and identifies key directions for advancing fine-scale carbon monitoring, spatiotemporally consistent data fusion, uncertainty-aware inference, and MRV-oriented verification systems.

Why it matches plant phenotyping methods個体植物スケールの炭素蓄積変化を推定するための測定・センシング・統合手法を体系的に比較し、セグメンテーションや不確実性伝播を含む統合枠組みを提案する方法論レビューであり、植物状態の取得・推定が中心である。

abstractmethodologies for repeated monitoring at this scale remain fragmented

Mechanosensory Coupling Between Human Cardiac Activity and Plant Bioelectric Potentials: A Naturalistic Self-Study with Spectral Validation ↗

We report a single-subject proof-of-concept naturalistic longitudinal within-office study (n ≈ 93,000 one-Hz observations from a single participant across seven daytime sessions; n here refers to time-series samples, not biological replicates) testing whether human emotional states couple to the bioelectric potentials of a co-located Kalanchoe dai-gremontiana plant through measurable physical intermediaries. Using a custom IoT platform comprising two complementary AD8232 bioelectric plant sensors (Plant1: RC lowpass, 5-second averages; Plant2: 0.1–20 Hz bandpass at 1 Hz), a Sensirion SCD41 CO₂/temperature/humidity sensor, an SGP40 volatile organic compound (VOC) sensor, a Polar H10 heart rate monitor, and HSEmotion facial expression recognition, we recorded simultaneous human emotion (valence, arousal), physiology (heart rate HR, heart rate variability RMSSD), and environmental chemistry (CO₂, VOC index) at 1 Hz alongside plant bioelectric voltage. Lagged mediation analysis confirmed partial mediation of the valence→plant relationship through heart rate (Δa = 8 s for valence→HR, r = +0.067, p < 0.001; 30% partial mediation with Plant1). Critically, a novel spectral mediation analy-sis—using short-time Fourier transform (STFT) band powers of Plant2 as outcome vari-ables—reveals that the valence→HR coupling (Δa = 8 s) is invariant across all eight plant frequency bands, while the HR→plant coupling (path b) is frequency-specific: full sta-tistical mediation occurs only in the 44–75 second oscillation band (Δb = 34 s), with partial mediation across five other bands. This frequency specificity rules out broadband me-chanical coupling and points toward a frequency-selective biological transduction mechanism analogous to Venus flytrap mechanosensory integration. HRV-derived emotion (RMSSD-based valence, independent of the camera system) provides convergent validation. VOC index is the strongest cross-session predictor of emotional state in random forest models.

Why it matches plant phenotyping methods植物のバイオ電位をセンサーで取得し、STFTによる周波数解析とスペクトル媒介分析で評価する技術的手法が研究の中心であるため、植物の生理状態を対象とするフェノタイピング手法として含める。

abstractUsing a custom IoT platform comprising two complementary AD8232 bioelectric plant sensors

Machine vision RGB phenotyping reveals divergent and real‐time responses to different watering regimes in near‐isogenic wheat genotypes ↗

Abstract This study assesses high‐throughput red, green, and blue (RGB) imaging as an approach for detecting subtle phenotypic differences under well‐watered and reduced watering conditions in genetically uniform wheat ( Triticum aestivum L.) populations. It aims to support the design of breeding populations by identifying parents with complementary coping mechanisms that can be combined in crosses to produce superior progeny. We used RGB imaging to monitor side‐projected area (SPA) in BC 2 F 6 wheat progenies under well‐watered, pre‐anthesis, and post‐anthesis reduced watering conditions. SPA was modeled with logistic growth curves per genotype to extract dynamic canopy traits, which, together with the area under the SPA‐based growth curve, were then correlated with yield, straw biomass, harvest index, and spike traits measured at maturity. Despite genetic similarity, RGB‐based imaging revealed distinct phenotypes under normal conditions and stress response strategies among wheat lines, highlighting the value of dynamic, non‐destructive phenotyping for identifying complementary response patterns. Under well‐watered conditions ( n = 36), area under the curve was strongly associated with grain weight ( R 2 = 0.76, 95% confidence interval [CI]: 0.59–0.87), but relationships weakened under reduced watering, especially post‐anthesis, indicating a reduced association of canopy size with reproductive output. The data revealed contrasting response patterns among breeding lines based on characteristics of the logistic growth curve under normal conditions, their recovery slope after pre‐flowering reduced watering, or conversion of their straw biomass into harvestable grains. RGB imaging enables real‐time, non‐destructive detection of reduced watering responses in genetically similar wheat lines and provides complementary in‐season data to design next‐generation breeding populations for climate‐resilient cultivars.

Why it matches plant phenotyping methodsRGB画像で動的なキャノピー形質を抽出し、育種利用に向けた非破壊・リアルタイム表現型解析を実質的に評価しているため。

abstractThis study assesses high‐throughput red, green, and blue (RGB) imaging as an approach for detecting subtle phenotypic differences

Hyperspectral Imaging-Based Evaluation of Seasonal Growth Characteristics in Turfgrass. ↗

Efficient phenotyping is essential for accelerating genetic improvement in turfgrass breeding, where manual measurements are labor-intensive. This study evaluated hyperspectral imaging (HSI) as a high-throughput tool for assessing Zoysia spp. breeding populations consisting of 464 genotypes. HSI data (400-1000 nm) were processed through a user-in-the-loop hybrid segmentation pipeline integrating UMAP dimensionality reduction, DBSCAN clustering, Random Forest classification, and pseudo-RGB refinement. To independently assess vegetation classification performance, 10,000 manually annotated reference points from 50 pseudo-RGB images were compared with the automated module, yielding an overall accuracy of 0.9697, a precision of 0.8830, a recall of 0.9240, a specificity of 0.9779, an F1-score of 0.9030, and Cohen's kappa of 0.8851. A Combined Ranking Score (CRS) integrating five vegetation indices and vegetation pixel count was significantly associated with aerial shoot count ( r = -0.445, p r = -0.207, p < 0.001). The highest-ranked genotype showed a 9370.3-pixel increase in vegetation area between 6 and 16 weeks after transplanting, compared with 1417.7 pixels for the lowest-ranked genotype. Classification performance declined under high-coverage conditions, indicating increased mixed-pixel ambiguity in dense canopies. These results suggest that HSI-based CRS can support rapid, objective, and non-destructive relative ranking of density-related vegetative growth in turfgrass breeding. Because the study was conducted at a single location and season and correlations with manual traits were moderate, the framework is best interpreted as a screening and ranking tool rather than a direct predictive model.

Why it matches plant phenotyping methodsHSI画像と解析パイプラインを用いて、芝草の植生面積・密度関連成長形質を高スループットに推定・検証することが研究の中心であり、育種集団の表現型スクリーニング手法に該当する。

abstractThis study evaluated hyperspectral imaging (HSI) as a high-throughput tool for assessing Zoysia spp. breeding populations consisting of 464 genotypes.

A cytological framework of female meiosis in Arabidopsis. ↗

Female and male meiosis often differ in many aspects, such as their duration and the frequency as well as the positioning of crossovers. However, studying female meiosis is often very challenging and thus, much less is known about female versus male meiosis in many species including plants, where meiosis occurs deep within the ovules. To approach this gap, we developed a live-cell imaging system for female meiocytes in Arabidopsis (Arabidopsis thaliana) in this study. This allowed us to obtain a temporally resolved cytological framework of female meiosis in the wild type that serves as a guiding system for future studies. Subsequently, we have applied this imaging system here to study mutants in cyclin-dependent kinase inhibitors, in which a designated female meiocyte undergoes several mitotic divisions before entering meiosis. This mutant context enabled us to address when a meiocyte is committed to meiosis, a key question during reproductive development and in particular for the analysis of apomictic species in which meiosis is skipped.

Why it matches plant phenotyping methodsシロイヌナズナの雌性減数分裂を対象とするライブセルイメージングシステムを開発し、時間分解された細胞学的表現型の取得に用いており、フェノタイピング手法が研究の中心である。

abstractwe developed a live-cell imaging system for female meiocytes in Arabidopsis (Arabidopsis thaliana) in this study.

Tracking Recovery: Temporally-Matched 3D Gaussian Splatting of Ecosystems after Prescribed Burns ↗

Land management and stewardship teams continue to lack the tools to capture 3D spatiotemporal insights of the ecosystems they oversee. For wildfire management at the wildland-urban interface, teams face challenges in capturing vegetation growth over time after a fuel reduction program and connecting seasonal changes to the vegetation distribution across the treated area. Current approaches rely on triangle meshes or point clouds generated from photogrammetry or LiDAR surveys on drones or hiked traverses. However, the difficulties in optimizing these meshes lead to large triangles that inadequately approximate the bulk vegetation shape, and the point cloud data is often too sparse for local plant-scale understanding. To address this gap, we extend recent machine learning-based computer graphics techniques in 3D Gaussian Splatting (3DGS) to reconstruct scenes at the wildland-urban interface from handheld imagery with sufficient detail to identify species, capture individual leaves, recover plant stature, and disambiguate overhanging plant individuals. We develop a new method to match the 3DGS reconstruction of these scenes across months, associating plant growth across seasons interactively in 3D. To achieve the centimeter-level matching, we adapt the Umeyama algorithm and the iterative closest point algorithm from point cloud maps to the 3DGS scene, leveraging the probabilistic interpretation of the 3D Gaussian data structure and robustly handling visual and geometric changes associated with vegetation phenology over time. We have applied our method to recent pile burns at Stanford’s Jasper Ridge ’Ootchamin ’Ooyakma Biological Preserve at monthly intervals. We demonstrate differences in ecological response where some piles featured the unexpected return of a rare and threatened bushmallow, and others remained more barren. This pile burn microcosm implicates the need for plant-level 3D spatiotemporal models to understand ecosystem recovery to fire mitigation practices. Please visit the project page for the spatiotemporal alignment video and more information: https://danineamati.github.io/burn-ecorecovery.github.io/ Please visit the Stanford Data Repository for the field data: https://doi.org/10.25740/ws901xs0162

Why it matches plant phenotyping methods植物の3D画像再構成と時系列位置合わせ手法を開発し、植物の個体・葉・草丈・成長を抽出することが中心であるため、植物フェノタイピング手法研究に該当します。

abstractwe extend recent machine learning-based computer graphics techniques in 3D Gaussian Splatting (3DGS) to reconstruct scenes at the wildland-urban interface from handheld imagery with sufficient detail to identify species, capture individual leaves, recover plant stature, and disambiguate overhanging plant individuals.

Diversity of photosynthesis-related and high-throughput phenotyping traits in indica rice ↗

Manual phenotyping of photosynthesis-related traits in rice is labor-intensive and limits the scale and temporal resolution of genetic analysis under field conditions. Here, we integrated unmanned aerial vehicle (UAV)-based high-throughput phenotyping (HTP) with genome-wide association studies (GWAS) to dissect the diversity and genetic architecture of photosynthesis-related traits in a large indica rice diversity panel (>300 accessions) evaluated across three dry seasons. A total of 45 traits, including UAV-derived NDVI, canopy height, and canopy temperature, together with leaf gas-exchange, stomatal, anatomical, and agronomic traits, were quantified. UAV-derived traits captured temporal growth and senescence dynamics and showed strong and consistent correlations with leaf photosynthetic rate, stomatal conductance, flowering time, biomass, and grain yield. GWAS identified multiple QTLs for photosynthetic and HTP traits, including a cross-year stable transpiration-rate QTL (qTRMMOL-2-2) and a photosynthetic-rate QTL (qPHOTO-1-2). Haplotype analyses revealed that the wall-associated receptor-like kinase gene OsWAK6 and the potassium transporter gene OsHAK1 were strongly associated with variation in photosynthetic rate and transpiration, respectively. Several elite accessions with consistently high photosynthetic performance carried superior haplotypes at multiple qPHOTO loci, suggesting their potential value for breeding. Together, our results demonstrate that UAV-based HTP provides reliable field-scale proxies for physiological performance, and that integrating HTP with GWAS can enable the identification of genetic targets for improving photosynthesis, water use, and yield potential in rice. • Forty-five traits, including HTP, photosynthesis, and leaf morphology, were measured across three dry seasons in diverse Indica rice. • GWAS identified genes linked to photosynthesis and stomatal density, aiding in breeding resilient, high-yield rice. • UAV-based HTP data effectively tracked plant growth and senescence, correlating with photosynthetic rate. • GWAS co-localization revealed shared QTLs, suggesting multi-trait regulation by common genes.

Why it matches plant phenotyping methodsUAVベースのHTPによる植物形質取得と生理性能の推定が研究の中心であり、45形質を大規模・反復的に測定し、信頼性や他の生理形質との相関も評価している。

abstractwe integrated unmanned aerial vehicle (UAV)-based high-throughput phenotyping (HTP) with genome-wide association studies (GWAS)

Enhancing WorldCereal crop calendars with land surface phenology and machine learning ↗

Accurate crop calendars are critical for understanding global agricultural phenology, mapping crop types, improving yield forecasts, and addressing food security challenges in the context of climate variability. This study presents significant advancements in crop calendar modeling, building upon the WorldCereal system by integrating Land Surface Phenology (LSP) metrics derived from MODIS AQUA NDVI time series with ERA5-Land climate parameters and machine learning algorithms, particularly XGBoost. Our new approach introduces key enhancements, including densification of training data in underrepresented regions, explicit modeling of dormancy periods for winter cereals, and the synergistic use of climate and phenological predictors to refine Start of Season (SOS) and End of Season (EOS) estimates across diverse agro-ecological zones for eleven crops types explicitly excluding rice, which falls outside the scope of the WorldCereal project. The model was validated against harmonized ground-truth data, remote sensing-based phenology retrievals, and expert assessments from agricultural monitoring institutions, achieving R 2 values of 0.94 (SOS) and 0.92 (EOS) for summer crops, with an RMSE of 18 and 22 days, respectively. For winter crops, the model reached R 2 values of 0.90 (SOS) and 0.92 (EOS), with RMSE values of 29 and 28 days. The inclusion of dormancy modeling significantly improved the representation of winter cereal cycles, reducing previous overestimations in high-latitude regions such as Canada, Northern Europe, and Central Asia. Additionally, enhanced spatial resolution addressed gaps in South America, Africa, and Asia, refining SOS and EOS timing in monsoon-driven cropping systems. Expert validation from institutions such as INPE (Brazil), NASA Harvest, and the Chinese Academy of Sciences further refined estimates, correcting anomalies in China and southern Brazil, ensuring alignment with observed agricultural cycles. The findings demonstrate the added value of combining remote sensing-derived phenology and climate data with XGBoost-based machine learning to improve crop calendar precision, optimize planting and harvesting schedules, and mitigate risks from climate variability. This study establishes a robust, data-driven tool for agricultural monitoring, supporting yield forecasting and global food security initiatives. • Enhanced WorldCereal global crop calendars using MODIS NDVI and ERA5-Land. • Modeled winter crop dormancy to improve phenological accuracy at scale. • Used XGBoost to fuse climate and phenology features for SOS/EOS prediction. • Validated against expert assessments and external geo-referenced datasets. • Achieved R 2 > 0.90 and RMSE <30 days across crop types and regions.

Why it matches plant phenotyping methodsMODIS NDVIと気候データをXGBoostで統合し、作物のSOS/EOS（生育季節）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が研究の中心である。

abstractintegrating Land Surface Phenology (LSP) metrics derived from MODIS AQUA NDVI time series with ERA5-Land climate parameters and machine learning algorithms, particularly XGBoost

Integrating Satellite Remote Sensing and Artificial Intelligence for the Presymptomatic Detection of Crop Diseases and Nutrient Deficiencies: A Comprehensive Narrative Review ↗

ABSTRACT Global food security is threatened by crop diseases and nutrient deficiencies. Traditional detection methods—visual scouting, molecular diagnostics and soil testing—are reactive and only identify problems once visible symptoms appear, which often misses intervention windows. This narrative review synthesizes 173 peer‐reviewed articles (from 2012 to 2025) to critically evaluate the synergistic potential of artificial intelligence (AI) and multisensor satellite remote sensing (RS) for presymptomatic detection. We propose a four‐principal framework: (1) sensor choice must align with pathogen infection strategy; (2) detection becomes actionable when spectral deviation exceeds twice baseline noise; (3) spectral time series can estimate epidemiological parameters (e.g., latent period, Area Under the Disease Progress Curve); and (4) explainable AI (XAI) converts black‐box predictions into interpretable diagnostics. Key findings uncovered were that multispectral sensors detect biotrophic pathogens 5–10 days pre‐symptomatically via red‐edge sensitivity; hyperspectral platforms offer 7–14 days warning and that thermal sensors detect vascular wilts 1–7 days earlier. Key challenges remain, including trade‐offs between resolution and revisit frequency, atmospheric interference causing 60%–80% optical data loss in tropical regions, spectral confusion between biotic and abiotic stresses, and limited scalability for smallholder farms (

Why it matches plant phenotyping methods衛星リモートセンシングとAIによる作物病害・栄養欠乏の早期検出手法を体系的に評価するレビューであり、植物の病害状態を推定するセンシング手法が中心です。

abstractThis narrative review synthesizes 173 peer‐reviewed articles (from 2012 to 2025) to critically evaluate the synergistic potential of artificial intelligence (AI) and multisensor satellite remote sensing (RS) for presymptomatic detection.

Turning Mediterranean Farmlands Into Priority Habitats: Natural Expansion of Juniper Woodlands After Agricultural Abandonment ↗

ABSTRACT Aims Natural woodland expansion into former agricultural land contributes to conservation and global reforestation goals. However, tree colonisation and woodland persistence depend on interactions among vegetation, land‐use history and suitable microclimatic conditions. Understanding these drivers is essential for anticipating woodland expansion outcomes over large spatial and temporal scales. Methods We combined airborne photogrammetry with field measurements to assess the long‐term success of Juniperus thurifera woodlands—a Natura 2000 priority habitat—across a 20‐km 2 region of central Spain. A canopy height model, calibrated with field biomass data, was used to map juniper biomass, while time series land‐cover maps estimated woodland age. This novel approach enabled evaluation of colonisation success using a space‐for‐time substitution along the expansion frontier. Results Over the past 34 years, land cover has changed markedly, with agricultural land declining by 75% and open woodland tripling. Juniper stands have expanded from steep slopes onto flatter terrain and into areas with lower irradiance. Increasing dwarf‐shrub density within stands reduced juniper biomass by up to 25% in the oldest woodlands. Higher solar exposure promoted faster biomass accumulation through time but limited biomass in younger stands. Contrarily, new stands under lower insolation showed greater biomass for their age, suggesting positive land‐use legacies where drought stress was reduced. Conclusion Overall, J. thurifera woodlands have expanded substantially over recent decades, yet growth constraints differ across the expansion front. With our innovative framework integrating high‐resolution photogrammetry and field‐based biomass models, our study underscores the interplay between local competition and abiotic factors in shaping woodland dynamics across space and time. This framework offers a valuable, scalable and transferable tool for monitoring and managing long‐term ecosystem dynamics across larger spatial and temporal scales and informing habitat restoration and conservation planning under changing environmental conditions.

Why it matches plant phenotyping methods航空写真測量とフィールド biomass データで樹木バイオマスを推定・地図化する手法が研究の中心であり、植物群落の形質を大規模に測定する実質的なフェノタイピング応用である。

abstractA canopy height model, calibrated with field biomass data, was used to map juniper biomass

How to Monitor Growth and Identify Developmental Stages of Maize ( Zea mays ). ↗

Properly characterizing the stages of corn growth is critical to conducting successful experiments in maize genetics and breeding. Specifically, accurately identifying stages of growth is required to perform developmentally dependent sampling or data collection, to predict time to flowering and seed maturation, and to allow for comparisons between different lines and populations based on developmental time. In this protocol, we summarize previous knowledge about maize development and describe how to monitor these stages in the reference inbred line B73, a yellow dent corn.

Why it matches plant phenotyping methodsトウモロコシの発育段階という植物状態を、実験・育種で再現可能にモニタリングするプロトコルが中心であり、発育ステージ測定法として収録対象と判断します。

titleHow to Monitor Growth and Identify Developmental Stages of Maize ( Zea mays ).

Development of a Spatiotemporal Estimation Method for Rice Plant Height Using Pattern Matching Based on Time-Series Satellite-Derived Vegetation Indices and In Situ Measurements ↗

Rice plant height is a key indicator of crop growth and phenology, yet continuous daily estimation remains challenging under limited field observations. This study proposes an interpretable Bayesian LUT-based framework to estimate rice plant height from time-series, satellite-derived GCVI, and sparse in situ measurements. Daily plant height was estimated as a posterior-weighted ensemble of multiple LUT-derived heights, together with uncertainty reflecting ambiguity among plausible growth trajectories. Applied to rice paddies in Ryugasaki City, Japan, using Harmonized Landsat–Sentinel-2 data from the 2025 growing season, the method achieved R2=0.85 and RMSE = 7.08 cm on the validation dataset, outperforming simple baseline approaches. The estimated daily height time series also enabled evaluation of the timing at which plant height reached 70 cm, revealing clear spatial variability among fields and an associated uncertainty of approximately 10 days. Although this threshold was discussed with reference to previous studies on L-band SAR sensitivity, the present study relied solely on optical observations. Overall, the proposed framework provides a data-efficient and explainable approach for daily, spatially explicit rice growth monitoring, while current limitations include the single-region, single-year LUT construction and the simplified statistical assumptions used in the Bayesian weighting framework.

Why it matches plant phenotyping methods衛星由来時系列データからイネの草丈を推定する手法を開発し、検証データで性能評価しているため、植物フェノタイピング手法が中心です。

abstractThis study proposes an interpretable Bayesian LUT-based framework to estimate rice plant height from time-series, satellite-derived GCVI, and sparse in situ measurements.

Plant Disease Detection ↗

Agriculture remains a critical pillar of economic sustainability, particularly in developing countries where crop productivity directly impacts food security and farmer income. However, plant diseases significantly reduce crop yield and quality, leading to substantial economic losses. Traditional disease detection techniques rely on manual inspection and expert consultation, which are time-consuming, subjective, and often inaccessible in rural areas. This paper presents an advanced deep learning-based system for plant disease detection, severity classification, and outbreak prediction. The proposed framework integrates Convolutional Neural Networks (CNNs) for image-based disease identification, clustering techniques for severity classification, and Long Short-Term Memory (LSTM) models for time-series-based prediction. The system also incorporates feature importance analysis using Random Forest to enhance interpretability. A web-based interface enables real-time interaction, allowing users to upload images and receive immediate diagnostic feedback. Experimental results demonstrate high accuracy and robustness across diverse datasets. The integration of multiple learning paradigms ensures improved performance, scalability, and adaptability, making the system suitable for real-world agricultural applications

Why it matches plant phenotyping methods植物画像から病害の有無と重症度を推定する深層学習手法が研究の中心であり、病害状態のフェノタイピングに該当する。

abstractThis paper presents an advanced deep learning-based system for plant disease detection, severity classification, and outbreak prediction.

Evaluation of SAR C-band radar vegetation indices for rice crop monitoring in Tamil Nadu, India ↗

Rice (Oryza sativa) cultivation plays a critical role in food security across Asia, where smallholder farmers depend heavily on timely information about crop development and field conditions. Monitoring these changes using optical remote sensing is constrained by persistent cloud cover during monsoon-driven growing seasons, underscoring the necessity of Synthetic Aperture Radar (SAR) for continuous observation. This study evaluates the capability of Sentinel-1 C-band SAR for tracking rice phenology in two smallholder fields in Mayiladuthurai District, Tamil Nadu, during the Late Samba season (September to January). Field-scale analysis of VV, VH, and NDVI time series for 2023–2024 captured key phenological transitions, with polarization showing a strong correlation with NDVI (Farm 1: r = 0.75; Farm 2: r = 0.73). Radar Vegetation Indices (RVI, mRVI, and RVI4S1) were computed from multi-year Sentinel-1 data (2018–2023) and compared with MODIS NDVI. Although the radar indices showed high inter-correlation (r > 0.90), their relationship with NDVI remained weak (0.15–0.30). Machine learning experiments over a 1.5 × 1.5 km region (2018–2022) demonstrated that a Linear Regression model (6.92 × 10−5) outperformed Random Forest Regression (0.000258) in predicting RVI4S1 from VV and VH, indicating linear relationship between radar channels and the index. The study highlights the suitability of Sentinel-1 SAR-particularly VH polarization – for phenology tracking in smallholder contexts, especially where optical data are limited by cloud cover.

Why it matches plant phenotyping methodsSARセンシングとレーダー植生指数を用いてイネの生育・フェノロジーを推定し、光学指標との比較および機械学習による技術評価を行っており、表現型取得法が中心である。

abstractThis study evaluates the capability of Sentinel-1 C-band SAR for tracking rice phenology in two smallholder fields in Mayiladuthurai District, Tamil Nadu, during the Late Samba season (September to January).

Assessment of Temporal Variations in Crop Growth Dynamics Using UAV Imagery ↗

Abstract. Effective crop monitoring is essential for optimizing agricultural practices and promoting sustainable production. This study explores the use of temporal Unmanned Aerial Vehicle (UAV) imagery to assess variations in crop growth dynamics across different developmental stages. UAV images were captured at five-day intervals, enabling the analysis of temporal changes in phenological parameters and plant health. Key vegetation indices and canopy height were derived at multiple time points and statistically evaluated to determine their effectiveness in monitoring crop development. The multi-temporal analysis identified the most informative vegetation indices and image processing techniques for assessing crop conditions. Results demonstrate that UAV-based temporal imaging offers valuable insights into crop growth patterns that are difficult to obtain through conventional monitoring approaches. The findings highlight the potential of UAV imagery as a practical tool for improving crop management by enabling timely and informed decision-making, ultimately contributing to enhanced yield and resource use efficiency.

Why it matches plant phenotyping methodsUAV画像を用いて作物の生育動態を時系列で評価し、植生指数と群落高を抽出・比較することが研究の中心であり、植物形質の取得手法として実質的です。

abstractUAV images were captured at five-day intervals, enabling the analysis of temporal changes in phenological parameters and plant health.

Quantifying the dynamic recovery of plants through stress memory and physiological attractors. ↗

Climate change-induced weather variability poses a growing threat to global food security, yet plant resilience is still interpreted through static and reductionist models that treat stress as independent and transient. Here, we introduce a unified quantitative framework grounded in dynamical systems theory. We formalize three novel metrics: (1) the Phenological Weather Memory Index (PWMI), that quantifies exponentially decaying stress memory across developmental stages (with a decay constant α = 0.10 determined by cross‑validation); (2) the Treatment-Weather Resonance Coefficient (TWRC), which measures the alignment of agronomic interventions with favorable weather conditions; and (3) the Physiological State-Space Trajectory (PSST), which maps multi-trait plant physiology into low dimensional attractor basins. Analyzing 288 tomato plants across 24 cultivars under hot, sub-tropical conditions (mean VPD: 2.53 kPa, 65 heat days > 35 °C), we discovered that stress memory is strongly phase-dependent, remaining minimal during vegetative growth (PWMI = 0.009) but increasing sharply during reproductive phase (PWMI = 0.574). Despite the prolonged thermal stress, 97.9% of plants converged into a stable high-yield attractor basin, revealing a fundamental nonlinearity in plant performance. This convergence was driven by dynamic recovery, defined as the capacity of certain cultivars to rapidly forget the stress memory while maintaining internal physiological flexibility. Cultivars such as 'Pony Express', combined low PWMI with effective treatment-weather synchronization, enabling stable productivity under extreme conditions. Together, these results demonstrate that resilience is not a static trait of endurance, but an emergent property arising from temporal synchronization, rapid stress recovery and stable physiological organization. By quantifying stress "forgetting curves" and attractor dynamics, this framework provides a predictive, systems-based foundation for breeding and management strategies that prioritize dynamic recovery over stress tolerance alone.

Why it matches plant phenotyping methods植物のストレス記憶・回復・生理状態を定量化する新規指標と状態空間フレームワークを中心に提示しており、単なる生理測定ではなく表現型抽出・解析手法の開発に該当する。

abstractHere, we introduce a unified quantitative framework grounded in dynamical systems theory.

Integrating Multi-Source and Multi-Temporal UAV Observations to Improve Wheat Yield Prediction Using Machine Learning. ↗

Accurate yield estimation is vital for precision wheat management and breeding. Traditional methods based on single growth stages or single-source data cannot capture cumulative growth effects, limiting prediction accuracy. UAV remote sensing provides high-resolution, multi-source, and multi-temporal data, enabling improved non-destructive yield estimation. In this study, UAV-based multispectral and RGB imagery were collected at six key growth stages, and vegetation indices, texture, and color features were extracted to develop yield prediction models using RF, XGBoost, and KNN under single- and multi-temporal scenarios. The results showed that red-edge-based vegetation indices were highly sensitive to wheat yield and outperformed texture- and color-based features. Multi-feature fusion further improved prediction accuracy at key growth stages, particularly during booting and flowering (R 2 = 0.53-0.67). Compared with single-temporal models, multi-temporal data fusion significantly enhanced yield estimation accuracy, achieving a maximum R 2 of 0.72 by integrating data from the late-jointing, booting and flowering stages. Among the algorithms, XGBoost and KNN exhibited superior accuracy and stability across most growth stages. Overall, these results demonstrate that integrating UAV-based multi-source and multi-temporal remote sensing data effectively improves the accuracy and robustness of wheat yield estimation, providing valuable technical support for precision agriculture and phenotyping-assisted breeding.

Why it matches plant phenotyping methodsUAV画像から特徴量を抽出し、機械学習でコムギ収量を推定する手法が研究の中心であり、マルチソース・マルチテンポラル統合の技術評価も行っている。

abstractUAV remote sensing provides high-resolution, multi-source, and multi-temporal data, enabling improved non-destructive yield estimation.

A thermal time framework drives coordinated below- and above-ground development in temperate cereal crops ↗

Summary Cereal architecture is underpinned by the coordinated development of modular phytomer units. While above-ground phenology is well characterized by metrics such as the phyllochron, an equivalent framework for root system development is lacking. Because each phytomer node initiates both leaves and adventitious roots, root and shoot development are inherently linked. Here, we quantified this coordination in wheat, barley, and rye across contrasting temperature regimes and validated the results under field conditions. We introduce the rhizochron, defined as the thermal time (growing degree-days, °C d) period between the emergence of nodal roots on successive stem nodes, and the root appearance interval, describing the emergence rate of individual root axes. Root development followed a highly conserved thermal sequence synchronized with shoot phenology. Across species and environments, the rhizochron averaged 146.1°C d, closely matching the phyllochron (126.6°C d). We also identified a consistent thermal offset, with nodal roots emerging approximately 185.3°C d after the corresponding leaf on the same phytomer node. The root appearance interval averaged 45.3°C d, reflecting continuous root deployment across active nodes. By integrating root phenology into a node-based framework, the rhizochron provides a predictive tool for crop modeling, trait-based breeding, and more target phenotyping aimed at improving resource acquisition and climate resilience.

Why it matches plant phenotyping methods根系と地上部の発達を定量化する新しい熱時間指標（rhizochron等）を導入し、複数種・環境および圃場条件で検証しており、表現型測定法が研究の中心である。

abstractWe introduce the rhizochron, defined as the thermal time (growing degree-days, °C d) period between the emergence of nodal roots on successive stem nodes, and the root appearance interval, describing the emergence rate of individual root axes.

Field Phenotyping of Triticale Overwintering Dynamics Under Varied Sowing Practices Using Spectral Indices ↗

This study aims to enhance the early warning and monitoring of frost damage in triticale (×Triticosecale Wittmack), as well as to identify frost-tolerant materials. To this end, this work focused on phenotyping the dynamics of triticale under different damage intensities using spectral indices. Sixteen triticale genotypes were planted under three sowing date (SD) treatments, with three sowing rate (SR) gradients set for each SD. The multispectral data of triticale under six frost damage intensities were acquired using an unmanned aerial vehicle (UAV) platform. A total of eight spectral indices (SIs) were extracted from samples under each intensity. In general, for each combination of SD and SR, all SIs decreased monotonically with increasing damage intensity. These indices are therefore suitable for monitoring frost damage in triticale under complex sowing scenarios. Under early frost damage, the relative decline rates (RDRs) of the SRI (Simple Ratio Vegetation Index), EVI2 (Enhanced Vegetation Index 2), NIRv (Near-Infrared Reflectance of Vegetation), and GLI (Green Leaf Index) were higher than those of other indices, indicating that they are more sensitive to early frost damage and thus more suitable for frost warning. Under frost stress, the RDRs of the indices were higher in early-sown samples than in late-sown samples. SD plays a more significant role than SR in determining the response of triticale indices to frost damage. Models were developed to detect triticale under varying damage intensities with SIs and classification algorithms—XGBoost, Quadratic Discriminant Analysis (QDA), Random Forest (RF), and Support Vector Machine (SVM). The SVM classifier demonstrated the best generalization performance (overall accuracy: 98.03%; F1-score: 0.98). The detection contributions of indices within the optimal model were evaluated by their respective SHAP (Shapley Additive Explanations) values. The GLI, NIRv, NDVI (Normalized Difference Vegetation Index), and GNDVI (Green Normalized Difference Vegetation Index) were identified as key indices, as they exhibit higher cumulative SHAP values. Identification models for triticale with different frost tolerance levels were established based on the time-series data of these key indices and the above four algorithms. The optimal model based on the SVM algorithm achieved an identification accuracy exceeding 90%. The average overwintering dynamics and frost damage responses of the key indices were analyzed for triticale with different frost tolerance levels under all treatments. Under frost stress, these indices and their RDRs in frost-tolerant triticale were generally higher and lower, respectively, than those in frost-sensitive triticale. These four key indices can thus assist in the identification of frost tolerance in triticale. This study aids in the early warning and monitoring of frost damage in triticale under complex planting scenarios and the evaluation of overwintering performance in triticale germplasm.

Why it matches plant phenotyping methodsUAVマルチスペクトル画像とスペクトル指標を用いて、コムギライムギの凍害強度・耐凍性を推定するモデルを開発・評価しており、植物表現型取得と解析手法が研究の中心である。

abstractThe multispectral data of triticale under six frost damage intensities were acquired using an unmanned aerial vehicle (UAV) platform.

Dynamics and Crosstalks of H 2 S and H 2 O 2 Signaling in Plant Abiotic Stress Response Deciphered by a Disposable SERS Sensing Patch. ↗

Abiotic stresses caused by climate change pose a serious threat to global crop productivity, making the early detection of plant stress responses crucial. Hydrogen sulfide (H 2 S) and hydrogen peroxide (H 2 O 2 ), as key signaling molecules, their dynamic synergistic effects are central to understanding the mechanisms of plant stress adaptation. However, real-time tracking of the dynamic changes of these molecules remains challenging. This study developed a wearable plasmonic nanoarray sensor integrated with metal-organic frameworks (MOFs), which cleverly combines the high sensitivity of surface-enhanced Raman scattering (SERS) with the gas enrichment capacity of the MOF, incorporates 2D plasmonic membrane assembly technology and 4-mercaptophenylboronic acid (4-MPBA) conjugation strategy, and successfully achieves real-time and synchronous detection of H 2 S and H 2 O 2 in plants. The 24 h dynamic monitoring results showed that under different stress conditions, H 2 S and H 2 O 2 in tomatoes and rice both had specific dynamic change rules, and there was a complex cross-regulation mechanism between them. By combining sensor data with partial least squares discriminant analysis (PLS-DA), the classification accuracy of stress types exceeds 95%. This non-destructive and highly sensitive detection system can provide real-time dynamic data of stress signals, bringing a breakthrough to the in-situ monitoring of plant physiological states.

Why it matches plant phenotyping methods植物内のストレスシグナルをリアルタイム測定するウェアラブルSERSセンサーの開発が研究の中心であり、植物の生理状態の表現型取得に直接結び付いている。

abstractThis study developed a wearable plasmonic nanoarray sensor integrated with metal-organic frameworks (MOFs)

Genetically Encoded Fluorescent Biosensors Enable Noninvasive Real-Time Visualization of Nitrate Dynamics in Intact Living Plants. ↗

Nitrate (NO 3 - ) serves as a pivotal molecule with dual functions in nutrient supply and signaling during plant growth and development. Precise monitoring of its spatiotemporal dynamics in planta is therefore essential for dissecting the regulatory mechanisms underlying plant nitrogen metabolism. However, conventional nitrate detection methods suffer from inherent limitations, including destructive sampling, insufficient spatiotemporal resolution, and an inability to achieve real-time whole-plant monitoring. Here, we report a genetically encoded nitrate biosensor, designated NitNRCL1, constructed using a split firefly luciferase complementation system. Functional validation in both prokaryotic and eukaryotic systems demonstrates that NitNRCL1 responds to changes in nitrate availability and generates stable chemiluminescent signals in bacteria and diverse plant species. Importantly, NitNRCL1 enables non-invasive, real-time, and whole-plant monitoring of nitrate levels in living plants. Using NitNRCL1, we successfully imaged the spatiotemporal dynamics of nitrate signaling in Arabidopsis thaliana . Collectively, our findings establish NitNRCL1 as a robust and novel tool for investigating nitrate transport, signaling, and metabolic pathways in plants. This biosensor advances our mechanistic understanding of plant nitrate biology and provides a technical foundation for breeding nitrogen-use-efficient crops and developing precision fertilization strategies.

Why it matches plant phenotyping methods植物体内の硝酸動態を非破壊・リアルタイム・全身的に可視化する遺伝子コード型バイオセンサーを開発し、複数の生物・植物種で機能検証しているため、植物生理状態の取得手法が中心です。

abstractHere, we report a genetically encoded nitrate biosensor, designated NitNRCL1, constructed using a split firefly luciferase complementation system.

GrowScreen-Rhizo 3 - automated large-scale high throughput greenhouse phenotyping of plant root and shoot development. ↗

Roots play a pivotal role for plant performance, but they are difficult to access, which hampers quantitative measurements. Repeated imaging of rhizotrons, flat growth containers with a transparent side, has proven suitable to assess dynamics of root traits in indoor experiments. However, measuring hundreds of soil-grown plants with high temporal resolution remains a laborious challenge. We introduce a novel whole-plant phenotyping platform with a capacity of almost 900 rhizotrons, which we named GrowScreen-Rhizo 3. This platform was designed to image shoots and roots of individual plants simultaneously and derive digital proxy traits for biomass and growth. In addition, built-in weighing and watering stations deliver water use data for each rhizotron. To achieve the desired throughput (image all 896 plants once a day) a high degree of automatization and standardization was required. We realized a modular plant-to-sensor solution, using a fleet of automated guided vehicles (AGVs) to transport large rhizotrons (80x40x5 cm) to four measurement chambers for daily imaging, weighing, and watering. Simultaneous imaging of the root system with a high-resolution camera (116 μm per px) and the shoot from six different viewing angles allows to monitor plant growth with high spatial and temporal accuracy. First, we verified that moving plants to the measurement chambers did not significantly affect above- or belowground plant growth. Next, we measured phenotypic variation in root and shoot traits of 24 barley genotypes, parents of a nested association mapping population. Our analysis revealed that heritability of root traits such as root system depth and seminal root length was moderate to high (r 2 =0.52 and r 2 =0.93, respectively), enabling further assessment of increasing numbers of recombinant genotypes. The results demonstrate the suitability of GrowScreen-Rhizo 3 to phenotype a range of plant species characterized by various growth habits, including crop, niche, and wild plant species. We conclude that GrowScreen-Rhizo 3 will contribute significantly to the development of phenotyping pipelines for the identification of candidate genotypes with improved resource use efficiency and to pre-breeding processes of climate-resilient crops.

Why it matches plant phenotyping methods根とシュートを自動撮像し、バイオマス・成長などの形質を抽出する大規模フェノタイピング platform の開発・検証が中心である。

abstractWe introduce a novel whole-plant phenotyping platform with a capacity of almost 900 rhizotrons, which we named GrowScreen-Rhizo 3.

Turning Mediterranean Farmlands Into Priority Habitats: Natural Expansion of Juniper Woodlands After Agricultural Abandonment ↗

ABSTRACT Aims Natural woodland expansion into former agricultural land contributes to conservation and global reforestation goals. However, tree colonisation and woodland persistence depend on interactions among vegetation, land‐use history and suitable microclimatic conditions. Understanding these drivers is essential for anticipating woodland expansion outcomes over large spatial and temporal scales. Methods We combined airborne photogrammetry with field measurements to assess the long‐term success of Juniperus thurifera woodlands—a Natura 2000 priority habitat—across a 20‐km 2 region of central Spain. A canopy height model, calibrated with field biomass data, was used to map juniper biomass, while time series land‐cover maps estimated woodland age. This novel approach enabled evaluation of colonisation success using a space‐for‐time substitution along the expansion frontier. Results Over the past 34 years, land cover has changed markedly, with agricultural land declining by 75% and open woodland tripling. Juniper stands have expanded from steep slopes onto flatter terrain and into areas with lower irradiance. Increasing dwarf‐shrub density within stands reduced juniper biomass by up to 25% in the oldest woodlands. Higher solar exposure promoted faster biomass accumulation through time but limited biomass in younger stands. Contrarily, new stands under lower insolation showed greater biomass for their age, suggesting positive land‐use legacies where drought stress was reduced. Conclusion Overall, J. thurifera woodlands have expanded substantially over recent decades, yet growth constraints differ across the expansion front. With our innovative framework integrating high‐resolution photogrammetry and field‐based biomass models, our study underscores the interplay between local competition and abiotic factors in shaping woodland dynamics across space and time. This framework offers a valuable, scalable and transferable tool for monitoring and managing long‐term ecosystem dynamics across larger spatial and temporal scales and informing habitat restoration and conservation planning under changing environmental conditions.

Why it matches plant phenotyping methods航空写真測量と現地 biomass データで樹冠高モデルを較正し、ジュニパー biomass を広域推定する手法が研究の中心であり、植物群落の形態・生長形質を測定する実質的なフェノタイピング手法に該当する。

abstractA canopy height model, calibrated with field biomass data, was used to map juniper biomass

Deep learning technology in multimodal remote sensing data fusion to analyze crop growth and economic forecast ↗

This paper integrated multimodal remote sensing (RS) data with deep learning to develop a maize growth analysis and income prediction model based on CNN (Convolutional Neural Network)-Attention and Bi-LSTM (Bidirectional Long Short-Term Memory). Utilsing Landsat 8, Sentinel-2, and Sentinel-1 satellite data, the CNN-Attention network extracts vegetation features such as NDVI (Normalised Difference Vegetation Index), EVI (Enhanced Vegetation Index), and canopy density for corn growth stage identification and prediction. The study combined these features with meteorological, soil, and market data and fed them into a Bi-LSTM model for time series analysis to forecast corn income. The method achieved 98.3% accuracy in growth stage classification, with an RMSE (Root Mean Squared Error) of 0.04 and R² of 0.94 for canopy coverage prediction under 10-fold cross-validation, and an RMSE of 0.13 and R² of 0.94 for income prediction, showing high stability over time. Overall, this research supports data-driven precision agriculture through real-time monitoring and reliable economic forecasting.

Why it matches plant phenotyping methods衛星リモートセンシングと深層学習による作物生育段階・キャノピー密度の推定手法が中心的に開発・検証されており、植物状態の定量化を含むため。収益予測も扱うが、植物フェノタイプ推定部分が明示されている。

abstractintegrated multimodal remote sensing (RS) data with deep learning to develop a maize growth analysis and income prediction model

Unmanned aerial vehicle–based spatiotemporal phenotyping and growth modeling for forecasting potato yield ↗

Abstract Monitoring spatial variations in plant growth and forecasting yield before harvest provides valuable insights for optimizing agronomic decision‐making in potato ( Solanum tuberosum L.) cultivation. Although unmanned aerial vehicle (UAV)‐based remote sensing has recently enabled the development of tuber fresh weight (TW) estimation models, their integration into practical yield‐forecasting systems remains limited. In this study, we developed machine learning models to estimate tuber weights at multiple preharvest time points using RGB and multispectral UAV imagery. Image‐derived features were extracted from the orthomosaic and digital surface model images for each plot, and a random forest regression model was trained for TW estimation. The estimated values were subsequently used to fit the Gompertz growth curves, which were then used to forecast the yield at the expected harvest time. The correlation between the estimated and observed values was strong in the UAV‐based TW estimation, with correlation coefficients exceeding 0.8 and coefficients of determination ( R 2 ) above 0.6 at all time points. Yield forecasts based on fitted growth curves achieved a correlation of 0.78 and an R 2 of −0.17 in 2023 and 0.70 and an R 2 of 0.47 in 2024. These results demonstrate that UAV‐based sampling combined with machine learning is a feasible approach for monitoring spatiotemporal variations in tuber growth and forecasting potato yield at the plot level prior to harvest.

Why it matches plant phenotyping methodsUAV画像からジャガイモ塊茎重量を推定し、機械学習と成長曲線で収量を予測する手法が研究の中心であり、推定精度も検証している。

abstractwe developed machine learning models to estimate tuber weights at multiple preharvest time points using RGB and multispectral UAV imagery.

Predictive Modeling of Crop Growth Using a Smart Agriculture Measurement Module Composed of Multipoint Soil Moisture Sensor and Environmental Sensors ↗

In this study, we addressed agricultural labor shortages by developing a smart farming sensor module that integrated low-cost environmental sensors with a multipoint soil moisture sensor to predict broccoli growth, plant height ( PH ), and leaf count (L n ). Multivariable regression confirmed that integrated solar radiation ( S ) was the most dominant factor, although broccoli growth involved a complex interplay of solar radiation, optimal temperature, humidity, and soil moisture. More importantly, the analysis revealed that the middle layer soil moisture (u m ) exhibited the strongest positive contribution to PH . This finding indicated that water availability in the main root zone was essential for vertical growth and highlighted the indispensability of multipoint sensing over conventional single-depth measurements to accurately model the intricate relationship between soil moisture and crop development. Moving forward, we aim to leverage the superiority of multipoint data to construct a sophisticated growth prediction model, thereby contributing to the optimization of irrigation and temperature management in smart farming systems.

Why it matches plant phenotyping methods環境・土壌水分センサーを統合した測定モジュールを開発し、植物高や葉数などの作物形質を予測する手法が研究の中心である。

abstractdeveloping a smart farming sensor module that integrated low-cost environmental sensors with a multipoint soil moisture sensor to predict broccoli growth, plant height ( PH ), and leaf count (L n ).

Evaluating SAR-Derived Phenological Metrics for Monsoon (Kharif) Crop Monitoring in Diversified Agricultural Systems: Insights from Central India ↗

Effective crop monitoring during monsoon growing seasons in Central India faces challenges from persistent cloud cover that limits optical remote sensing during critical agricultural periods. This study presents the first attempt to develop a novel set of SAR-derived phenological metrics organized into five thematic categories for monsoon crop discrimination in smallholder agricultural systems. Five major monsoon crops (cotton, rice, maize, soybean, and urad) were analyzed across five different agroclimatic zones in Central India using Sentinel-1 data for the 2021 growing season. Phenological features were extracted from VV, VH polarizations, and their ratio, including seasonal extrema, threshold crossings, duration measures, curve shape descriptors, and area under the curve. Distinct crop-specific signatures were observed, with cotton showing extended phenology and cereal–legume crops displaying compressed, overlapping growth patterns. VV polarization achieved the highest statistical discrimination for intensity-based metrics, with 75% thresholds (VV_HP75V: F = 1287) providing higher separability than other thresholds by capturing near-peak biomass differences. VH performed best for duration and integration-based metrics, while VH/VV provided limited additional separability across metric types. For area-under-the-curve metrics, AUC25 outperformed AUC50 and AUC75 by capturing cumulative backscatter across the broader growing season while remaining robust to soil- and residue-dominated backscatter variability at sowing and harvest. Multiclass classification achieved 48.3% overall accuracy with systematic cereal–legume confusion, reflecting fundamental phenological convergence among monsoon-aligned crops. Cotton achieved the highest performance (F1: 0.79), with VH polarization dominating feature importance (65% of top 20 features). Binary classification revealed crop-specific discrimination patterns: cotton was best separated using VV intensity metrics, maize using the VH/VV ratio, and rice using timing-based features. Cross-district transferability showed the highest mean overall accuracy for rice (74%) and cotton (72%), while the remaining crops showed lower accuracy due to their phenological similarity. These findings highlight both the potential and limitations of SAR phenological metrics for monsoon crop discrimination, with effective results for structurally distinct crops but persistent cereal–legume confusion, requiring further investigation with multi-sensor approaches.

Why it matches plant phenotyping methodsSAR時系列から作物のフェノロジー指標を抽出・評価し、識別性能や転移性を検証することが研究の中心であるため、植物フェノタイピング手法として含める。

abstractThis study presents the first attempt to develop a novel set of SAR-derived phenological metrics organized into five thematic categories for monsoon crop discrimination in smallholder agricultural systems.

UAV-Based Multispectral Phenotyping and Machine-Learning Modeling Reveals Early Canopy Traits as Strong Predictors of Yield and Weed Competitiveness in Oat (Avena sativa L.) ↗

Understanding how oat (Avena sativa L.) cultivars differ in canopy development and competitive ability is essential for improving yield stability under increasing weed pressure. This study used unmanned aerial vehicle (UAV)-based multispectral imaging to characterize the temporal spectral and structural traits of sixteen oat cultivars grown under weed-free and weedy conditions across two locations for two years. Weedy conditions involved natural weed populations and pseudo-weeds where canola (Brassica napus) seeded as a weed. Weekly drone imaging was carried out using a multispectral sensor, which provided vegetation indices (NDVI, NDRE, ExG) and canopy metrics (ground cover, height, volume). Logistic and Gompertz models were fitted to cultivar traits to describe growth trajectories and obtain dynamic growth parameters. Cultivars showed clear differences in early canopy expansion, maximum NDVI, and canopy volume, with forage types expressing aggressive growth and several grain types combining high early growth rate with high yield potential. Machine-learning models integrating static and dynamic UAV-derived plant traits identified early ground cover and NDRE at three weeks after planting as the strongest predictors of grain yield. Models accurately predicted both weed-free (MAE = 262, R2 = 0.90) and weedy yield (MAE = 258, R2 = 0.90), demonstrating that early-season UAV traits capture the physiological and structural characteristics associated with competitive ability and grain yield. These findings show that high-throughput UAV phenotyping can reliably identify traits linked to yield formation and weed tolerance, providing a scalable approach for selecting competitive oat cultivars without relying solely on labor-intensive weedy field trials.

Why it matches plant phenotyping methodsUAVマルチスペクトル画像からキャノピー形質を高スループットに抽出し、機械学習による予測性能も評価することが研究の中心であるため、植物フェノタイピング手法の実質的応用・検証に該当する。

abstractThis study used unmanned aerial vehicle (UAV)-based multispectral imaging to characterize the temporal spectral and structural traits of sixteen oat cultivars

Rhizo-PET: A Dedicated PET System for 4D Imaging of Carbon Dynamics in the Rhizosphere ↗

Imaging carbon movements in the rhizosphere is fundamentally limited by high soil heterogeneity, low signal levels, and lack of methodology. We present Rhizo-PET, a dedicated positron emission tomography (PET) imaging and analysis framework designed to characterize the 4D spatiotemporal patterns of tracer distribution in intact plant–soil systems. The system achieved a global energy resolution of 11.93 ± 0.02% FWHM at 511 keV and maintained stable performance over 8 h of continuous acquisition, with a coincidence rate variation of only 0.7%. Spatial resolution reached 1.06 mm near the center of the field of view, establishing a high-fidelity region for root-scale analysis. Dynamic datasets were acquired from live Phaseolus vulgaris plants ( N = 3) over 180 min following 11 CO 2 pulse labeling and reconstructed into 3 min temporal frames. Quantitative analysis across 243 independent regions of interest (ROI) revealed that cumulative tracer accumulation decreases monotonically with radial distance from the root axis, while axial transport delays increase systematically in lower root segments ( p < 0.001). Hierarchical variability analysis showed that within-plant spatial organization ( CV TTP = 0.03) is significantly more stable than inter-plant variation ( CV TTP = 0.14), proving that the observed heterogeneity reflects biological spatial organization rather than experimental instability. These results establish Rhizo-PET as a robust, reproducible platform for the non-invasive, time-resolved analysis of carbon dynamics in the rhizosphere under realistic soil conditions.

Why it matches plant phenotyping methods植物根圏における炭素動態を非侵襲・時系列で測定する専用PETシステムを開発し、性能・再現性・空間解析能力を検証した研究であり、植物状態の取得方法が中心である。

abstractWe present Rhizo-PET, a dedicated positron emission tomography (PET) imaging and analysis framework designed to characterize the 4D spatiotemporal patterns of tracer distribution in intact plant–soil systems.

In-Planta Tattoo and Kirigami Sensors for Moisture-Powered Monitoring of Vapor Pressure Deficit and Growth Dynamics. ↗

We report a scalable, moisture-powered in-planta sensor platform for the continuous monitoring of plant hydration and growth. The system integrates two components: a leaf-mounted tattoo sensor for estimating vapor pressure deficit (VPD) and a kirigami-inspired strain sensor for tracking radial stem growth. Uniquely, the tattoo sensor serves a dual function: measuring temperature and humidity beneath the leaf surface while simultaneously harvesting power from ambient moisture via a vanadium pentoxide (V 2 O 5 ) nanosheet membrane. This moist-electric-generator (MEG) configuration enables energy-autonomous operation, delivering a power density of 0.1114 μW/cm 2 . The V 2 O 5 -based sensor exhibits high sensitivity to humidity (4.2 mV/% RH) and temperature (1.02%/°C), enabling accurate VPD estimation for over 10 days until leaf senescence. The eutectogel-based kirigami strain sensor, wrapped around the stem, offers a gauge factor of 1.5 and immunity to unrelated mechanical disturbances, allowing for continuous growth tracking for more than 20 days. Both sensors are fabricated via cleanroom-free, roll-to-roll compatible methods, underscoring their potential for large-scale agricultural deployment to monitor abiotic stress and improve crop management.

Why it matches plant phenotyping methods植物の水分状態（VPD）と茎の成長を連続測定するセンサー基盤を開発・性能評価しており、植物表現型の取得が中心的な技術貢献である。

abstractWe report a scalable, moisture-powered in-planta sensor platform for the continuous monitoring of plant hydration and growth.

Deep learning-based phenology extraction and crop classification in arid oasis using Sentinel-2 time series ↗

Multi-temporal remote sensing data in large-scale crop phenology identification and classification have become increasingly utilized, particularly for precision management in arid oasis agricultural regions with complex cropping systems. In this study, we developed a deep learning framework integrating Sentinel-2 multi-temporal imagery and normalized difference vegetation index (NDVI) time series for mapping cotton, winter jujube, and tiger nut crops in Tumushuke City, Xinjiang Uygur Autonomous Region, China. We employed the minimum redundancy maximum relevance (mRMR) algorithm for spectral and vegetation index feature selection, followed by Savitzky-Golay (S-G) filtering and double logistic function fitting, to automatically extract the key phenological parameters (start of season (SOS), peak of season (POS), and end of season (EOS)), significantly improving phenological feature extraction accuracy. By incorporating multi-temporal Sentinel-2 data and a multi-scale feature fusion approach, we could systematically compare five classification models (multi-layer perceptron (MLP), residual network-18 (ResNet-18), convolutional long short-term memory (ConvLSTM), Transformer, and random forest classifier (RFC)), demonstrating that high-resolution spatial details substantially enhance crop boundary delineation and classification consistency in complex environments. Further optimization of Transformer's spatial representation through multi-scale window analysis revealed that the use of 1×1+3×3+5×5 convolutional windows achieves an optimal balance between accuracy and computational efficiency. Independent validation on unseen areas confirmed robust model transferability, with F1 scores of 94.37%, 87.75%, and 86.35% for the three crops (winter jujube, cotton, and tiger nut), respectively. This study validates the high-precision identification potential of Sentinel-2 temporal data and deep neural networks for multi-crop environments, enabling the precise spatial mapping of crop distributions and providing methodological support for smart agricultural decision-making in arid oasis regions.

Why it matches plant phenotyping methodsSentinel-2時系列から植物の生育季節性（SOS、POS、EOS）を自動抽出し、その精度向上と独立地域での検証を行っており、作物分類を含む解析ワークフローにおける植物フェノタイプ抽出が中心的です。

abstractto automatically extract the key phenological parameters (start of season (SOS), peak of season (POS), and end of season (EOS)), significantly improving phenological feature extraction accuracy.

Exploring the optimal timing for detecting maize growth differences using unmanned aerial vehicle-derived crop surface models ↗

Unmanned aerial vehicle (UAV)-based remote sensing is useful to understand crop growth conditions or grain yield potential, and monitoring forage maize (Zea mays L.) is particularly advantageous because its tall canopy makes manual measurements time-consuming. This study aimed to identify the optimal timing for effectively detecting maize growth variability using aerial photogrammetry with a UAV. We conducted weekly aerial photography of a maize field under variable nitrogen conditions to produce artificial growth differences. The results showed that the crop surface model (CSM) could effectively visualize maize growth differences after exceeding approximately 1.0 m, which corresponded to the internode elongation stage. Moreover, the determination coefficient between temporal CSM values and grain yield reached a peak of 0.7 approximately one week before silking. These results suggest that approximately one week before silking is the optimal time for CSM-based observations and the early detection of within-field maize growth differences and yield variability.

Why it matches plant phenotyping methodsUAV空撮とフォトグラメトリによる作物表面モデル（CSM）を用いたトウモロコシ生育差・収量変動の検出時期を検証しており、表現型取得法が研究の中心である。

abstractThis study aimed to identify the optimal timing for effectively detecting maize growth variability using aerial photogrammetry with a UAV.

Exploring the optimal timing for detecting maize growth differences using unmanned aerial vehicle-derived crop surface models ↗

Unmanned aerial vehicle (UAV)-based remote sensing is useful to understand crop growth conditions or grain yield potential, and monitoring forage maize (Zea mays L.) is particularly advantageous because its tall canopy makes manual measurements time-consuming. This study aimed to identify the optimal timing for effectively detecting maize growth variability using aerial photogrammetry with a UAV. We conducted weekly aerial photography of a maize field under variable nitrogen conditions to produce artificial growth differences. The results showed that the crop surface model (CSM) could effectively visualize maize growth differences after exceeding approximately 1.0 m, which corresponded to the internode elongation stage. Moreover, the determination coefficient between temporal CSM values and grain yield reached a peak of 0.7 approximately one week before silking. These results suggest that approximately one week before silking is the optimal time for CSM-based observations and the early detection of within-field maize growth differences and yield variability.

Why it matches plant phenotyping methodsUAV航空写真から作成した作物表面モデル（CSM）によるトウモロコシの生育差・収量変動の検出時期を評価しており、植物表現型の取得方法の技術的適用と評価が中心である。

abstractThis study aimed to identify the optimal timing for effectively detecting maize growth variability using aerial photogrammetry with a UAV.

Phenological modeling for ecological double-cropping of grapes with rain and pest resilience strategies based on MobileNet developed by Augmented Dream Optimizer. ↗

Double-cropping grape systems offer enhanced land productivity but face significant challenges from climate variability, particularly rain stress and pest outbreaks during critical phenological stages. Accurate phenological prediction is essential to synchronize management practices with crop development and improve ecological resilience. This study presents a novel deep learning framework that integrates MobileNet with an augmented version of Dream Optimizer [Augmented Dream Optimizer (ADO)] to model grape phenology using satellite-derived time series of Normalized Difference Vegetation Index (NDVI), Enhanced Vegetation Index (EVI), and rainfall from the CropHarvest dataset. The model transforms temporal data into pseudo-images for efficient spatiotemporal feature extraction, achieving 93% classification accuracy and a 6.1-day mean absolute error in stage prediction. ADO enhances convergence and generalization by optimizing key hyperparameters through a hybrid metaheuristic search. The system further identifies high-risk periods for rain damage and pest infestation, enabling proactive interventions. The model statistically significantly outperforms machine learning and deep learning baselines (p< 0.01) across three different agroecological zones [Mediterranean (California, USA, and southern Europe), subtropical (South Australia), and temperate (central Europe)] through spatially stratified fivefold cross-validation on 3,000 held-out test samples of the CropHarvest dataset. This work demonstrates the potential of optimized lightweight neural networks in sustainable viticulture, providing a scalable tool for precision management in climate-resilient double-cropping systems.

Why it matches plant phenotyping methods衛星時系列からブドウの生育ステージを推定する深層学習手法を開発し、交差検証とベースライン比較で性能を検証しており、植物フェノタイピング手法が中心である。

abstractThis study presents a novel deep learning framework that integrates MobileNet with an augmented version of Dream Optimizer [Augmented Dream Optimizer (ADO)] to model grape phenology using satellite-derived time series of Normalized Difference Vegetation Index (NDVI), Enhanced Vegetation Index (EVI), and rainfall from the CropHarvest dataset.

CNN-Assisted Growth Monitoring and Stress Management of Cucumber in Semi-Transparent PV Greenhouses for Agrivoltaics ↗

Currently operating commercial photovoltaics (PV) systems integrated with agricultural production (Agrivoltaics) offer immense potential for the dual harvest of renewable energy and agro-products. Within controlled-environment agriculture (CEA), the use of semi-transparent photovoltaics (ST-PV) and the ability to control the microclimate and shading are beneficial for the production of high-value crops such as cucumbers. The objective of this research was to commence the cultivation of cucumbers under evolving CEA-PV systems by combining greenhouse experiments with computer vision (CV) based driven phenotyping to create an analytical framework and system control framework for the cultivation of cucumbers in an evolving CEA-PV system. The method involved using the monitored plant vigor to control in real time the irrigation and shading of the cucumber plants. The control of irrigation and shading was based on the monitored plant vigor as determined by a U-Net++ implementation for canopy segmentation, an EfficientNet-B3 implementation for stress detection, and a CNN regressor for growth trait estimation. Within the greenhouse, uniform environmental and fertigation conditions were established to evaluate the effect of four shading regimes (0%, 20%, 40%, 60%) on the cucumbers. Simulated, yet representative results predicted cucumber yields to be stable (within ±4% of full yield) with a 20% shading and a 15-20% reduction in water use compared to full sun. Yield was also observed to drop by 10-14% under higher shading of 40 to 60% due to insufficient photosynthetic activity for fruiting. The CNN based models were robust, (segmentation IoU 0.91, stress-class F1 0.92, LAI regression R²≈0.93), allowing for precise and comprehensive monitoring in an annual non-invasive fashion. The greenhouse's annual photovoltaic (PV) output was estimated to be 1,550 to 1,750 kWh/kWp which is able to exceed the energy demand resulting to a net energy surplus. The outcome demonstrates that the cucumber crop can be successfully combined with controlled environment agrovoltaic systems with moderate shading for optimum cucumber yield. Moreover, informed supervision through Artificial Intelligence (AI) helps to navigate closed-loop systems and enhance the water-use efficiency and yield stability.

Why it matches plant phenotyping methodsCNNによるキャノピー分割、ストレス検出、成長形質推定を中核とする植物フェノタイピングおよび閉ループ制御フレームワークであり、性能指標も報告されているため。

abstractcombining greenhouse experiments with computer vision (CV) based driven phenotyping to create an analytical framework and system control framework for the cultivation of cucumbers

Fully-printed microneedles meet plants: a pathway towards easy-to-use NFC monitoring of total ionic conductivity in precision agriculture. ↗

This study showcases and validates a fully-printed, low-cost microneedles (MNs) device integrated with environmental sensors and NFC wireless readout for real-time monitoring of changes in plant total ionic conductivity. The Aerosol-Jet printed MNs patch enabled minimally invasive impedance measurements for the monitoring of leaf hydration and ion uptake. Inkjet-printed temperature and humidity sensors provided complementary environmental and leaf's microclimate data. Both sensing platforms were integrated in a cost-effective, easy-to-use wooden clip assembly, granting adhesion and reproducible MNs insertion. Dehydration and ions uptake tests demonstrated that the devices can detect ionic variations in different cellular compartments of the leaves, with distinct responses across plant species reflecting their physiological and anatomical differences. The NFC system validation confirmed that wireless, battery-free readout can be used to observe similar impedance trends with respect to the ones observed with conventional potentiostat measurements. Overall, the presented platform establishes a scalable approach toward simple, field-deployable plant monitoring systems, supporting future development of species-tailored and functionally enhanced sensors for precision agriculture.

Why it matches plant phenotyping methods植物の葉の水分状態・イオン吸収を測定する低侵襲センサーとNFC読出しプラットフォームの開発・検証が研究の中心であり、植物状態の表現型を直接取得している。

abstractThis study showcases and validates a fully-printed, low-cost microneedles (MNs) device integrated with environmental sensors and NFC wireless readout for real-time monitoring of changes in plant total ionic conductivity.

A ROBUST MULTI-SENSOR DEEP REGRESSION FRAMEWORK FOR PREDICTIVE PLANT GROWTH MODELLING IN CONTROLLED ENVIRONMENTS ↗

The analysis of plant growth and development in controlled agricultural environments has become increasingly important to ensure sustainable and efficient food production. Traditionally, plant monitoring relied on manual observations and basic statistical approaches, which provided limited insights into the complex interactions between environmental factors and plant physiology. To address these challenges, this study proposes a machine learning–driven analytical framework designed for comprehensive plant development analysis. The system integrates data preprocessing, exploratory data analysis, classification, regression, and hybrid deep learning approaches within a unified pipeline. Classification algorithms such as Support Vector Classifier (SVC), Bernoulli Naive Bayes (BNC), and Multinomial Naive Bayes (MNC) are employed to identify plant growth stages. Regression models, including Decision Tree Regressor (DTR), Support Vector Regressor (SVR), and Ridge Regressor (RR), are utilized to estimate growth-related parameters. Furthermore, two hybrid models are introduced to enhance predictive performance. The Deep Feature Probabilistic Classifier (DFPC) combines Feed Forward Neural Networks (FFNN) with Gaussian Naive Bayes (GNB) for improved classification accuracy, while the Hybrid Deep Ridge Predictor (HDRP) integrates FFNN with Ridge Regressor to achieve precise regression outcomes. Experimental results demonstrate that the DFPC model attains an accuracy of 94.42%, whereas the HDRP model achieves an R² score of 0.999. These findings highlight the effectiveness of combining deep learning and machine learning techniques for accurate plant growth analysis and informed decision-making in controlled agricultural systems.

Why it matches plant phenotyping methods植物の成長段階と成長関連パラメータを推定する機械学習・深層学習パイプラインが研究の中心であり、表現型推定手法の開発に該当する。

abstractClassification algorithms such as Support Vector Classifier (SVC), Bernoulli Naive Bayes (BNC), and Multinomial Naive Bayes (MNC) are employed to identify plant growth stages.

Unraveling the Dynamics of Tar Spot Epidemics in Corn Fields: A Data-Driven Framework for Disease Development and Surveillance. ↗

Tar spot, caused by Phyllachora maydis Maubl, has significantly impacted U.S. corn production since its first detection in 2015. The elusive nature of this fungus has hindered advancement in disease characterization, especially pertaining to its spatiotemporal development. This study provides an in-depth analysis of field-scale epidemics by considering both temporal and vertical dynamics to ascertain the spatiotemporal intensification of this disease. The analysis involved generating high-resolution severity data across four growing seasons (2021 to 2024) in two production-style corn fields in northwest Indiana. We then applied population growth models and Markov chains to parameterize the temporal and vertical dynamics of tar spot progression within the corn canopy. From this, we found three distinct epidemiological phases: an establishment phase characterized by sporadic onset with <0.5% severity, a lag phase with widespread low severity (0.5 to 1%), and an exponential phase with rapid severity increases exceeding 40% in some cases. Beyond the conventional "bottom-up" paradigm, we observed diverse infection-like patterns influenced by canopy position, onset timing, and corn growth stage. Exponential growth models described severity intensification with an average apparent infection rate of 0.20/day, which was applicable across canopy positions, locations, and years. An aggregated Markov chain model, built from the 2021-2023 data, accurately estimated the 2024 epidemic's vertical-temporal progression and thus validated the framework developed from this study. Ultimately, this approach supports improved surveillance for targeted management by establishing a foundation for real-time detection and probabilistic modeling to aid in the enhancement of crop production.

Why it matches plant phenotyping methodsトウモロコシ葉のタールスポット病 severity という植物病害状態を高解像度データで定量化し、時空間モデルとMarkov連鎖による進展推定・検証を行う枠組みが研究の中心であるため。

abstractThis study provides an in-depth analysis of field-scale epidemics by considering both temporal and vertical dynamics to ascertain the spatiotemporal intensification of this disease.

Applicability of the StatFaRmer time series analysis tool in soybean (Glycine max) digital phenotyping. ↗

Contemporary agrobiotechnology research increasingly relies on automated methods for capturing and interpreting morphophysiological and spectral plant characteristics - a field known as digital phenotyping. This approach aims to identify stable differences between genotypes cultivated under non-identical environmental conditions. We previously introduced StatFaRmer, an open-source tool that we further develop here for comprehensive analysis of temporal phenotypic datasets, with a primary focus on crops such as soybean (Glycine max). The tool implements automated data preprocessing procedures, including synchronization of timestamps across samples and removal of noise artifacts and outliers. These features are particularly relevant for multi-month experiments involving assessments of growth parameters, fluctuations in photosynthetic apparatus area, or other biometric indicators. Support for standardized data formats (XLSX, CSV) ensures compatibility with common phenotyping systems, simplifying cross-platform integration. Thus, the tool can integrate with widely used HTPP platforms (e. g., Traitmill, HyperAIxpert, Plant Accelerator), enabling data from diverse sources to be analyzed within a single pipeline. For soybean experiments, StatFaRmer provides customizable analysis of variance (ANOVA) with visualization of diagnostic parameters (normality of distribution, homogeneity of variances) and evaluation of effect significance between user-defined groups. An example application compares growth parameters across 20 soybean cultivars under controlled stress: the tool automatically aggregated data with uneven measurement frequencies (from 1 hour to 3 days), identified anomalies in hypocotyl elongation dynamics, and computed statistical significance between groups (p < 0.01).The tool has been tested on large-scale datasets (over 2,000 measurements per experiment). StatFaRmer is implemented as a Shiny-based web application, with step-by-step deployment guides for Windows and Linux. All processing stages - from raw data to final plots - are documented to ensure transparency and compliance with research reproducibility standards. Thus, StatFaRmer offers a specialized solution for statistical hypothesis testing in soybean digital phenotyping, reducing data preparation time and minimizing risks of error when handling non-stationary time series.

Why it matches plant phenotyping methods植物デジタルフェノタイピング用の時系列解析ツールを開発・拡張し、前処理、異常値除去、統計解析、再現可能なワークフローを提供しているため、フェノタイピング手法が中心である。

abstractWe previously introduced StatFaRmer, an open-source tool that we further develop here for comprehensive analysis of temporal phenotypic datasets

Exploring the optimal timing for detecting maize growth differences using unmanned aerial vehicle-derived crop surface models ↗

Unmanned aerial vehicle (UAV)-based remote sensing is useful to understand crop growth conditions or grain yield potential, and monitoring forage maize (Zea mays L.) is particularly advantageous because its tall canopy makes manual measurements time-consuming. This study aimed to identify the optimal timing for effectively detecting maize growth variability using aerial photogrammetry with a UAV. We conducted weekly aerial photography of a maize field under variable nitrogen conditions to produce artificial growth differences. The results showed that the crop surface model (CSM) could effectively visualize maize growth differences after exceeding approximately 1.0 m, which corresponded to the internode elongation stage. Moreover, the determination coefficient between temporal CSM values and grain yield reached a peak of 0.7 approximately one week before silking. These results suggest that approximately one week before silking is the optimal time for CSM-based observations and the early detection of within-field maize growth differences and yield variability.

Why it matches plant phenotyping methodsUAV航空写真から作成した作物表面モデル（CSM）によるトウモロコシの生育差・収量変動検出について、観測時期と技術性能を評価しており、植物表現型取得法が中心である。

abstractThis study aimed to identify the optimal timing for effectively detecting maize growth variability using aerial photogrammetry with a UAV.

Cobalt oxide based microneedle sensor for direct detection of glucose from plant leaves ↗

Glucose is a crucial biomarker reflecting plant metabolism and growth. While glucose sensing is well-established in human healthcare, continuous in situ measurement in living plants remains challenging. In this study, we developed a non-enzymatic microneedle (MN) electrochemical sensor for the direct, real-time monitoring of glucose in plant leaves. To achieve this, we utilized a highly customizable and cost-effective fabrication strategy. A three-electrode MN system was fabricated by combining SU-8 micromolding with 3D printing of a carbon paste circuit, significantly reducing the reliance on complex cleanroom processes. The working electrode was then functionalized via a single-step co-electrodeposition of Co 3 O 4 catalysts and multiwall carbon nanotubes in a chitosan matrix. This co-deposition effectively compensated for the inherently low electrical conductivity of Co 3 O 4 . The optimized sensor exhibited reliable in vitro analytical performance. Furthermore, the MN sensor was inserted into living leaves to monitor glucose levels under varying light and dark conditions. The sensor successfully recorded dynamic real-time current signals, showing an average of 71.5 ± 11.0 nA in the dark and 9.6 ± 2.8 nA in the light. This customizable MN platform provides a practical diagnostic tool for continuous plant health monitoring.

Why it matches plant phenotyping methods植物葉内のグルコースをリアルタイム測定するマイクロニードル電気化学センサーを開発し、生葉での連続モニタリングまで実証しており、植物生理状態の取得方法が研究の中心である。

abstractwe developed a non-enzymatic microneedle (MN) electrochemical sensor for the direct, real-time monitoring of glucose in plant leaves.

Biomass prediction and shoot growth characterization of single-staked yam plants using UAV imagery. ↗

This study presents an unmanned aerial vehicle (UAV)-based approach for estimating shoot biomass and characterizing growth patterns in single-staked white Guinea yams ( Dioscorea rotundata ). Multi-angle aerial images from nadir and oblique views were used to extract vegetation- and height-related indices that served as predictors in machine learning models. Support vector regression using combined-view imagery provided the highest prediction accuracy (R² = 0.79) and remained robust across growth stages, years, fertilizer treatments, and genotypes. Notably, the combined-view configuration outperformed single-view imaging, demonstrating the advantage of capturing complementary canopy-structure information in complex staked-vine canopies. Time-series biomass estimates enabled the fitting of genotype-specific Richards growth curves using Bayesian inference. Significant genotypic variations were observed in parameters associated with maximum biomass and early growth rate, whereas phenology-related parameters showed comparatively minimal differences. These parameter differences may reflect variation in canopy architecture and growth allocation among genotypes. Overall, this integrated workflow provides a scalable tool for nondestructive monitoring of yam growth dynamics and for summarizing biomass trajectories with interpretable parameters, supporting breeding efforts aimed at improving yam productivity and yield stability across diverse cultivation conditions.

Why it matches plant phenotyping methodsUAV画像からヤムのシュートバイオマスと生育を推定する画像解析・機械学習ワークフローが研究の中心であり、複数視点画像の比較検証と時系列形質推定を行っている。

abstractThis study presents an unmanned aerial vehicle (UAV)-based approach for estimating shoot biomass and characterizing growth patterns

Computer vision and IoT based plant phenotyping and growth monitoring with 3D point clouds ↗

Computer vision and Internet of Things (IoT) technologies offer robust solutions for plant phenotyping, but traditional mainstream segmentation methods often fail in high-density plantings with overlapping foliage. This study introduces an integrated phenotyping system combining automated data capture and high-temporal RGB-D imaging using off-the-shelf hardware (Intel RealSense D435 and Raspberry Pi) to generate 3D point clouds of lettuce under controlled greenhouse conditions. While recent agricultural applications have shown limited success and required domain-specific adaptations, Segment Anything Model (SAM) and FastSAM were demonstrated to achieve exceptional zero-shot segmentation performance for individual lettuce plants in high-density arrangements without additional training. This capability effectively addresses the traditional challenges of species-specific parameter tuning and extensive training data requirements and fine-tuning. By mapping 2D segmentation masks to corresponding 3D point clouds, the system accurately extracted key phenotypic traits, namely plant height, length, and width, from which area and volume were subsequently estimated, showing strong correlations with manual measurements for Rex and Rouxai lettuce cultivars. This high-temporal, non-destructive monitoring provided unique insights into plant growth dynamics. The study highlights distinct growth patterns among these cultivars, underscoring the importance of tailored phenotyping approaches to optimise crop management strategies. By addressing the limitations of existing phenotyping methods, this work advances precision agriculture technologies, offering a cost-effective and efficient solution for monitoring dynamic crop growth with potential applications across various crops and growing conditions.

Why it matches plant phenotyping methodsRGB-D撮像、3D点群、セグメンテーションを統合した植物表現型取得システムを開発し、草丈・長さ・幅などを抽出して手測定と検証しているため、方法が中心的である。

abstractThis study introduces an integrated phenotyping system combining automated data capture and high-temporal RGB-D imaging using off-the-shelf hardware (Intel RealSense D435 and Raspberry Pi) to generate 3D point clouds of lettuce under controlled greenhouse conditions.

HTPRootSlides: A high-throughput phenotyping platform for crop root germination dynamic screening ↗

Root phenotyping is crucial for advancing our understanding of plant development and adaptation. However, existing platforms often face challenges in balancing high-throughput capacity with long-term, high-frequency monitoring. To overcome this limitation, we present HTPRootSlides, an integrated root phenotyping platform designed for dynamic and scalable trait analysis. Its design features a circulating zone that accommodates 141 specialized root boxes for high-throughput operation synchronously. Root boxes follow a continuous S-shaped trajectory step by step, facilitating repetitive imaging for high-throughput, time-series data acquisition. To address challenges such as water vapor condensation and fine root entanglement, we developed a dedicated segmentation algorithm, achieving 89.56 % accuracy in root isolation. Combining morphological and skeleton-based feature extraction techniques, the platform ensures comprehensive and efficient phenotypic trait quantification. We validated HTPRootSlides by dynamically monitoring root development in four staple crops (soybean, maize, wheat, and rice) during early-stage germination (<14 d). The results demonstrate the capability of HTPRootSlides for high-frequency, high-precision and large-scale root phenotyping (< 1h with 141 root boxes per run), offering researchers a powerful tool to investigate root dynamics and optimize crop performance through trait selection.

Why it matches plant phenotyping methods根の動態を高スループットで撮像・分割・特徴抽出し、形態・骨格形質を定量するプラットフォームの開発と検証が中心である。

abstractwe present HTPRootSlides, an integrated root phenotyping platform designed for dynamic and scalable trait analysis

Computer vision and IoT based plant phenotyping and growth monitoring with 3D point clouds ↗

Computer vision and Internet of Things (IoT) technologies offer robust solutions for plant phenotyping, but traditional mainstream segmentation methods often fail in high-density plantings with overlapping foliage. This study introduces an integrated phenotyping system combining automated data capture and high-temporal RGB-D imaging using off-the-shelf hardware (Intel RealSense D435 and Raspberry Pi) to generate 3D point clouds of lettuce under controlled greenhouse conditions. While recent agricultural applications have shown limited success and required domain-specific adaptations, Segment Anything Model (SAM) and FastSAM were demonstrated to achieve exceptional zero-shot segmentation performance for individual lettuce plants in high-density arrangements without additional training. This capability effectively addresses the traditional challenges of species-specific parameter tuning and extensive training data requirements and fine-tuning. By mapping 2D segmentation masks to corresponding 3D point clouds, the system accurately extracted key phenotypic traits, namely plant height, length, and width, from which area and volume were subsequently estimated, showing strong correlations with manual measurements for Rex and Rouxai lettuce cultivars. This high-temporal, non-destructive monitoring provided unique insights into plant growth dynamics. The study highlights distinct growth patterns among these cultivars, underscoring the importance of tailored phenotyping approaches to optimise crop management strategies. By addressing the limitations of existing phenotyping methods, this work advances precision agriculture technologies, offering a cost-effective and efficient solution for monitoring dynamic crop growth with potential applications across various crops and growing conditions.

Why it matches plant phenotyping methodsRGB-D画像、3D点群、セグメンテーションを統合して植物形質を抽出するフェノタイピングシステムの開発・評価が中心であり、手動測定との相関検証も行っているため。

abstractThis study introduces an integrated phenotyping system combining automated data capture and high-temporal RGB-D imaging using off-the-shelf hardware (Intel RealSense D435 and Raspberry Pi) to generate 3D point clouds of lettuce under controlled greenhouse conditions.

Robot-based 3D-multispectral monitoring of soybean in a spatially heterogenous agrivoltaic environment ↗

Agrophotovoltaic (APV) systems provide a unique opportunity for improving agricultural land-use efficiency by combining solar energy capture via photovoltaic panels with crop production. However, in-depth information on plant growth patterns within the spatially heterogenous microclimate created by the intermittent shading of APVs is largely missing. In the present study, we implement a customized robot-mounted 3D-multispectral imaging system to closely monitor the growth and spectral reflectance patterns of a conventional soybean cultivar “Eiko” (EK) and a chlorophyll-deficient mutant variety MinnGold (MG) under an APV system. Weekly trends in canopy morphometric features revealed significant variations in plant height, 3D leaf area, light penetration, and canopy volume across the APV field depending on the proximity with the overhead solar panels for both EK and MG, with plants receiving adequate rainfall and intermittent shade performing the best. Furthermore, although spectral indices exhibited variations between EK and MG due to intrinsic differences in pigmentation, symptoms of stress could be detected for both genotypes within rain-shaded areas of the APV plot. Hence, the present investigation depicts the potential for complementary usage of robotics and machine vision for high-precision high-throughput crop monitoring under APVs, which would enable better crop management within such non-homogenous cultivation systems.

Why it matches plant phenotyping methodsロボット搭載の3D・マルチスペクトル画像システムを構築・適用し、作物の形態形質とストレス状態を高精度・高スループットに取得しており、表現型取得手法が研究の中心である。

abstractwe implement a customized robot-mounted 3D-multispectral imaging system to closely monitor the growth and spectral reflectance patterns

Insights into biomass accumulation and challenges in grain yield prediction of elite breeding materials using UAV‐based vegetation indices in soft red winter wheat ↗

Abstract High‐throughput phenotyping (HTP) techniques have brought new opportunities to understand and evaluate key traits in plant breeding programs. Combining multiple measures through time and random regression models permits a more comprehensive understanding of the genetic and environmental effects on trait expression over time. This study aims to understand the genetic basis of biomass accumulation in winter wheat and how this biomass is related to grain yield using unmanned aerial vehicle (UAV)‐based vegetation indices. A large panel of 596 soft red winter wheat genotypes was evaluated for agronomic performance in six environments to verify the ability of HTPs to predict grain yield using multivariate genomic prediction and random regression with Legendre polynomials to model growth through time. An additional set of 22 breeding lines was directly measured for above‐ground biomass, serving as a ground truth for the HTP‐derived biomass estimates. Cumulative vegetation indices were found to be a reliable method to infer biomass accumulation. Vegetation indices capture reliable phenotypes but exhibit low and inconsistent genetic correlation to grain yield, especially when incorporating residual covariance between traits. Predictive abilities of grain yield increased when using vegetation indices as a secondary trait in a multi‐trait genomic prediction model, but increases were highly variable across environments and growing stages, which may be confounded by micro‐environmental variation and lead to biased estimates of true genetic merit. Our results suggest that UAV‐based vegetation indices can be used to understand genetic parameters of biomass accumulation, but wheat breeders should use caution in their use as proxies for grain yield.

Why it matches plant phenotyping methodsUAV植生指数によるバイオマス推定を中心に、実測値を用いて検証し、遺伝解析・収量予測への利用可能性を評価しているため、植物フェノタイピング手法の実質的な適用・検証に該当する。

abstractCumulative vegetation indices were found to be a reliable method to infer biomass accumulation.

A Precise Reproductive Calendar of Sexual and Apomictic Genotypes of Eragrostis curvula . ↗

Eragrostis curvula serves as a valuable model for studying diplosporous apomixis due to its unique reproductive mode, wide ploidy range, and extensive genomic resources. A major limitation for reproductive studies in this species is the difficulty of isolating female tissues at precise developmental stages, for example, for transcriptomics studies, since different floral tissues can introduce expression noise from non-target tissues. To overcome this, we performed a detailed cytoembryological and morphometric characterization of male and female development in seven E. curvula genotypes with different ploidy levels (2X-7X) and reproductive modes (sexual, facultative apomictic, and obligate apomictic). Using differential interference contrast microscopy and methyl salicylate clarification, we described key cytological stages of male and female development. These stages were then correlated with external floral parameters, including pistil, ovary, style, and anther length, to generate genotype-specific developmental calendars. Pistil length showed the strongest association with female developmental stage, particularly during the early phases of ovule development, enabling more precise staging. Synchrony between male and female development was also evaluated, revealing no consistent differences among reproductive modes or ploidy levels. This genotype-informed framework provides a practical tool for stage prediction and tissue selection, supporting future reproductive, developmental, and comparative studies in E. curvula and related grasses.

Why it matches plant phenotyping methods花器官の形態計測を細胞発生段階の推定に体系的に対応付け、遺伝子型別の発達カレンダーと再利用可能なステージ予測手法を構築しており、表現型取得が中心である。

abstractThese stages were then correlated with external floral parameters, including pistil, ovary, style, and anther length, to generate genotype-specific developmental calendars.

AI-Driven Predictive Plant Disease Diagnosis and Treatment Recommendation System using IoT ↗

In precision farming, plant diseases destroy 20-40% of crops worldwide every year, threatening global food security. Our project delivers a working prototype that combines IoT sensors with deep learning to catch diseases early and prevent losses. The system uses CNN models to analyze leaf images and LSTM to predict how diseases will spread over time. Real-time IoT data (soil moisture, temperature, humidity) feeds a hybrid CNN-LSTM model that spots trouble 7-14 days ahead and calculates exact pesticide/nutrient doses needed. Tested on PlantVillage dataset (54,000+ images, 14 crops), it hits 97.2% disease detection accuracy and 95.8% prediction accuracy – beating standalone CNN (94.1%) and LSTM (89.5%). F1-scores stay above 0.96. This shifts farming from "react when plants die" to "predict and prevent". Farmers cut losses by 30%, use fewer chemicals, and grow more sustainably. Smallholder farmers win big – affordable, scalable, climate-proof agriculture. Future plans: drone integration + federated learning.1][2].

Why it matches plant phenotyping methods葉画像から植物病害を推定するCNNベースの診断手法と、IoTデータを統合した予測モデルの開発・比較評価が中心であり、植物の病害状態を直接推定するため含める。

abstractThe system uses CNN models to analyze leaf images and LSTM to predict how diseases will spread over time.

A Plant-Level Survival Modeling Framework for Spatiotemporal Strawberry Canopy Decline Using UAV Multispectral Time Series ↗

Timely identification of canopy decline in commercial strawberry production is challenging because visual scouting often misses subtle or spatially heterogeneous symptoms. We developed a plant-level UAV-based monitoring framework that integrates repeated multispectral imagery, canopy-derived metrics, unsupervised clustering, and Random Survival Forest (RSF) time-to-event modeling. The framework was applied across three commercial strawberry fields in Oxnard, California using nine UAV surveys collected from December 2022 to June 2023, yielding 159,220 plant-level monitoring units. NDRE- and Redness Index-based classifications quantified proportional and absolute canopy dieback within standardized hexagonal units and supported survival-based modeling of canopy decline progression. Across withheld test plants from all survey dates, overall concordance indices ranged from 0.88 to 0.95 across fields, indicating strong ability to rank plants by time-to-decline risk under heterogeneous field conditions. Spatial risk maps revealed localized high-risk clusters that expanded over time in fields with greater canopy deterioration, while fields with minimal visible decline exhibited diffuse but stable risk distributions. Post-hoc comparison with operational fumigation rates (280, 336, and 392 kg Pic-Clor 60/ha) showed no consistent association with predicted canopy decline risk. These results demonstrate that framing repeated UAV observations as a time-to-event process enables fine-scale spatiotemporal modeling of canopy decline dynamics and supports risk stratification for targeted field monitoring in commercial strawberry systems.

Why it matches plant phenotyping methodsUAVマルチスペクトル画像から植物体レベルのキャノピー衰退・枯死を抽出し、時系列解析と生存モデルで評価するフレームワークが研究の中心であり、性能検証も行っている。

abstractWe developed a plant-level UAV-based monitoring framework that integrates repeated multispectral imagery, canopy-derived metrics, unsupervised clustering, and Random Survival Forest (RSF) time-to-event modeling.

AN INTEGRATED DEEP LEARNING AND TIME-SERIES FRAMEWORK FOR MONITORING BARK BEETLE STRESS IN NORWAY SPRUCE USING UAV IMAGERY ↗

Climate change-driven bark beetle outbreaks pose severe threats to Norway spruce forests across Europe, yet early detection of infested trees remains difficult with conventional field surveys or satellite imagery. Existing detection methods, such as traditional and deep learning-based methods, require extensive time, training data, and computational resources while underutilizing dense temporal observations. We present an integrated UAV framework that merges deep learning-based tree detection with multitemporal spectral analysis for early, tree-level identification of bark beetle stress. A key novelty of this research is the use of high-frequency UAV time series to enable temporal change-detection methods such as CUSUM, providing scalable early-warning capabilities previously unattainable at individual-tree resolution. Firstly, a novel Fused YOLO-SAM pipeline was developed to automatically detect and delineate Norway spruce trees using UAV imagery collected over the mixed forests. Three YOLO v12 models were trained separately on summer (June), fall (November), and combined seasonal datasets acquired with a DJI Phantom drone having 5-band camera. The fall-trained model achieved the highest detection performance (F1 = 0.827, mAP50 = 0.916) and demonstrated superior cross-seasonal generalization, producing accurate and transferable crown segmentations when integrated with the Segment Anything Model (SAM). These automatically delineated spruce canopies provided a consistent and scalable base for individual tree-level spectral analysis. To discriminate between healthy and bark beetle-infested Norway spruce trees at the individual tree level, the delineated crowns were subsequently used to extract per-tree spectral time series for stress analysis. Radiometrically calibrated multispectral bands and vegetation indices were evaluated using cumulative sum (CUSUM)-based Receiver Operating Characteristic (ROC)-Area under Curve (AUC) and effect size metrics. The results demonstrated that calibration significantly improves early-season discrimination, with near-infrared and red-edge bands achieving stable performance (mean AUC ≈ 0.75-0.80; Cohen’s d ≈ 0.9-1.2). In contrast, vegetation indices such as NDRE and MSR-RE exhibited lower discrimination and greater temporal variability. This research also performed comparisons of calibrated multispectral features with uncalibrated RGB features. The analysis indicated that selected RGB indices (notably ExG and GCC) is comparable to the performance of the multispectral bands (REG, NIR), showing positive early discrimination and mean AUC values around 0.70-0.75 which can provide operational benefit for forest monitoring and management when the expensive multispectral cameras are unavailable. Overall, this research demonstrates a scalable and operationally feasible pipeline that integrates automated tree delineation with robust spectral stress diagnostics, supporting early bark beetle detection and informed forest management under resource and data constraints.

Why it matches plant phenotyping methodsUAV画像による樹冠抽出と時系列スペクトル解析を統合し、個体レベルのトウヒの樹皮甲虫ストレスを推定する手法が研究の中心であるため。

abstractWe present an integrated UAV framework that merges deep learning-based tree detection with multitemporal spectral analysis for early, tree-level identification of bark beetle stress.

A Three-Year Multimodal Holistic Dataset For Horticultural Tomato Cultivation. ↗

Existing tomato datasets often focus on short-term experiments or lack integrated environmental and agronomic data. We present Horti-M3-Tomato, a comprehensive three-year dataset collected in Northeast China's greenhouse, including high-resolution RGB images, environmental sensor data (recorded every 30 minutes), soil conditions, and detailed agronomic records such as yield data and management practices. Spanning three growing seasons (2023-2025), the dataset integrates temporal imaging, environmental monitoring, soil data, and manual phenotypic and yield records. Horti-M3-Tomato supports research on growth dynamics, genotype-environment interactions, and provides a benchmark for AI-based phenotyping and precision horticulture. The dataset is openly available for further research in controlled-environment agriculture.

Why it matches plant phenotyping methodsトマトの画像・環境センサーデータ・手動表現型記録を統合したデータセットであり、AIベースの表現型解析のベンチマークとして明示されているため、表現型データ基盤が中心です。

abstractincluding high-resolution RGB images, environmental sensor data (recorded every 30 minutes), soil conditions, and detailed agronomic records such as yield data and management practices.

BioOS: A Gene-Driven Digital Twin Runtime for Emergent Plant Development ↗

Predicting plant phenotypes from genomic data requires models that bridge molecular regulation and organ-scale morphogenesis. We introduce BioOS, a computational runtime in which plant behavior - cell division, differentiation, and elongation - emerges from the execution of a gene regulatory network rather than from hardcoded rules. The system is built on the Formal Cell abstraction: a minimal signal-processing unit analogous to the McCulloch-Pitts formal neuron, whose transfer function is gene expression. Each Formal Cell evaluates promoters, transcribes mRNA, translates proteins, and derives its entire behavioral repertoire from the resulting protein concentrations - without a single hardcoded rule in the simulator code. A multi-scale architecture with level-of-detail switching enables real-time simulation of Arabidopsis thaliana primary root development. On the current official five-case primary-root auxin benchmark, BioOS achieves 75.4% mean score, 5/5 qualitative matches, 5/5 cases passing all current gates, and Spearman severity correlation ρ = 0.70. The current root-auxin runtime is driven by a curated 35-gene registry with explicit promoter logic, kinetic parameters, and epigenetic state; for readability, this manuscript details a core 18-gene subnetwork that carries the main auxin benchmark logic. We describe the architecture, the gene expression runtime, the epigenetic memory model, the completed transition to post-hoc (non-causal) zone classification, and candidate benchmark extensions for persistent plasmodesmata and intracellular auxin compartmentalization within a broader six-suite, 63-case benchmark framework. Beyond the root-auxin slice, the current codebase also closes the official flowering (5/5), photosynthesis (7/7), and cytokinin (5/5) gates, while root-patterning remains a passing candidate panel.

Why it matches plant phenotyping methods植物の発生表現型を遺伝子制御モデルから予測する計算ランタイムの開発と、根の発生ベンチマークによる評価が中心であり、単なる生物学的測定ではない。

abstractPredicting plant phenotypes from genomic data requires models that bridge molecular regulation and organ-scale morphogenesis.

High-Resolution Plant Area Index Estimation in Cherry Orchards Using UAV LiDAR for Agroecosystem Monitoring ↗

Monitoring crop conditions is crucial for effective crop management and provides valuable insights into soil-plant-atmosphere interactions. While some studies have used unmanned aerial vehicle (UAV)-based light detection and ranging (LiDAR) data for mapping plant area index (PAI) in orchards, LiDAR-based time-series analysis to assess PAI variations with phenology throughout the growing season represents a significant gap in knowledge. Tracking PAI dynamics across phenological stages reflects canopy development and leaf expansion, which are directly linked to yield formation. Furthermore, the optimal spatial resolution for mapping biophysical variables of tree crops from LiDAR point clouds is yet to be determined. This study aimed to demonstrate the potential of UAV-derived LiDAR time-series to monitor the PAI and tree vertical profiles at high spatial resolution throughout the growing season of a cherry orchard located in southeastern France. A time series of 14 point cloud acquisitions with a density of 3300 points/m² was collected between February and December 2022, with at least one acquisition per month, covering all phenological stages of the cherry orchard. Field measurements were collected on May 30, and October 6, to measure the PAI at twilight using an LAI-2200C Plant Canopy Analyzer (LI-COR Biosciences, Lincoln, NE, USA), with 248 trees sampled. A voxel-based method was applied on the LiDAR point cloud data to create a three-dimensional grid within which PAI was estimated for each voxel. The results showed that a voxel size of at least 70 cm is required to retrieve reliable PAI estimates, while a voxel size of 100 cm produced the most accurate PAI estimates (RMSE = 0.5 m2.m-2, bias = 0.07, R2 = 0.59), when assessed against in-situ PAI measurements. The temporal variation of canopy PAI illustrated the progression of the phenological stages, including flowering, leaf development, ripening and senescence, and the response of the canopy to drought stress (reduction in PAI due to leaf rolling) during the summer. The maps of PAI successfully described the variations in leaf canopy density for different cherry varieties and allowed assessment of the vertical PAI profile at the individual tree level. The LiDAR-derived PAI maps and vertical profiles were able to detect trees exhibiting poor leaf development, which is an important health indicator for effective crop management in orchard settings. Future work should focus on applying UAV-derived observations to optimize crop models to enhancing decision-making tools for effective orchard management.

Why it matches plant phenotyping methodsUAV LiDARとボクセル解析により、樹木レベルのPAIおよび垂直プロファイルを推定し、実測値で精度検証しているため、植物表現型取得手法が研究の中心である。

abstractA voxel-based method was applied on the LiDAR point cloud data to create a three-dimensional grid within which PAI was estimated for each voxel.

Real-time monitoring of plant CO2 exchange using a direct absorption-based optical sensor ↗

Understanding CO2 plant exchange is essential for quantifying its role in the global carbon cycle, predicting ecosystem responses to environmental change, and evaluating long-term growth under varying environmental conditions across several types of photosynthesis[1,2]. Plants exchange carbon dioxide with the atmosphere through three primary physiological processes: photosynthesis, which assimilates CO₂ during daylight to produce glucose and release O2 as a byproduct; photorespiration, a light-dependent process that recycles harmful byproducts of photosynthesis while releasing excess energy and CO2; mitochondrial respiration, which releases CO₂ and consume O2 to produce energy, occurring both day and night. These CO₂ fluxes are coupled with transpiration that facilitates the loss of water vapor from leaves through stomata[1]. These processes can be accurately quantified using gas-exchange techniques, in which a gas analyzer measures the exchange of CO₂ and H₂O between leaves and the atmosphere. In this study, we employed a self-calibrated, optical sensor based on tunable diode laser spectroscopy to monitor plant CO₂ exchange in real time. The sensor consists of a quantum cascade laser emitting at 4.234 μm as the light source and a photodetector to measure CO2 absorption along an open optical path of 10 cm. Measurements were performed using an amplitude modulation approach with first-harmonic detection at 10 kHz, employing a phase-sensitive lock-in amplifier. The optical sensor was placed inside a transparent plexiglass enclosure (525x375x300 mm3) containing a plant to monitor CO₂ exchange with the surrounding environment. A temperature and humidity sensor was also installed inside the enclosure, while a non-dispersive infrared CO₂ sensor (SEFRAM 9825) outside the enclosure was used to track ambient CO₂, temperature, and humidity. Continuous measurements were performed over approximately 20 days, covering both daytime and nighttime periods outside the laboratory, in a dedicated open area to minimize disturbances from nearby activity. Measured CO₂ concentrations inside the enclosure reflected both plant exchange and diffusive transport driven by the concentration gradient with the external environment. A differential equation model accounting for these processes was developed and applied to the experimental data to quantitatively determine the plant’s net CO₂ exchange rate.ReferencesNiu, Z., Ye, Z. W. Y., Huang, Q., Peng, C. & Kang, H. Accuracy of photorespiration and mitochondrial respiration in the light fitted by CO2 response model for photosynthesis. Front. Plant Sci. 16, 1455533 (2025).Busch, F. A., Ainsworth, E. A., Amtmann, A., Cavanagh, A. P., Driever, S. M., et al. A guide to photosynthetic gas exchange measurements: Fundamental principles, best practice and potential pitfalls. Plant Cell Environ. 47, 3344–3364 (2024).

Why it matches plant phenotyping methods植物のCO₂交換率をリアルタイムに定量する光学センサーと解析モデルが研究の中心であり、植物の生理状態を測定するフェノタイピング手法に該当する。

abstractIn this study, we employed a self-calibrated, optical sensor based on tunable diode laser spectroscopy to monitor plant CO₂ exchange in real time.

Expanding DWD phenology monitoring through crowdsourced plant reports and AI-enabled data partnership ↗

Phenology at the Deutscher Wetterdienst (DWD) involves the observation and analysis of recurring, seasonally driven development stages of plants, such as flowering, leaf unfolding, fruit ripening, and leaf fall. These phenological phases are closely linked to weather and climate conditions and therefore serve as biologically based indicators of climate variability and long-term change. The DWD phenological observations are used in multiple contexts, including climate monitoring and diagnostics, agrometeorological services, and scientific studies that analyse shifts in phase timing in relation to temperature trends. Phenological information also supports operational applications, for example in agricultural modelling and other environment-related services.A key element of DWD’s phenological activities is its long-running observation network, which is based on standardized and quality-controlled field observations. In recent years, DWD has started to complement this classical network with additional digital data sources in order to improve spatial coverage and temporal resolution. One important development is the crowdsourcing feature “Pflanzenmeldungen” in the DWD WarnWetter app, which allows citizens to submit geo-referenced reports of plant development stages via smartphone. These reports can help capture regional differences, extreme-year signals, and near-real-time vegetation responses, particularly in areas with fewer traditional observations. By integrating these app-based reports with established phenological datasets and expert workflows, DWD aims to extend and enrich its national phenology record while maintaining scientific usability.Further expansion of digital data sources is planned through a collaboration with Flora Incognita, a machine-learning-based plant identification platform. This cooperation aims to link phenological monitoring with scalable species recognition and user-driven reporting. The combination of supported plant identification and structured phenological input is expected to improve data consistency, encourage participation, and increase the volume and resolution of phenological information.Overall, DWD’s phenology programme is developing toward a hybrid monitoring system that integrates long-term standardized observations with crowdsourced app data and AI-supported plant identification. This approach enhances spatial and temporal coverage and strengthens the basis for monitoring climate impacts on vegetation and for providing robust phenology-based climate services.

Why it matches plant phenotyping methods植物の開花・葉展開・果実成熟・落葉などの表現型を、市民参加型アプリとAI植物同定を統合して取得・拡張する監視基盤が中心であり、単なる生物学的実験での routine 測定ではない。

abstractOne important development is the crowdsourcing feature “Pflanzenmeldungen” in the DWD WarnWetter app, which allows citizens to submit geo-referenced reports of plant development stages via smartphone.

Linking aggregate-scale pore structure to plant water acquisition: A 4D X-ray CT study of wheat roots in Chernozem ↗

Soil structure creates spatial heterogeneity that shapes ecosystem functions, including water retention and root colonization. Chernozems – soils characterized by exceptionally stable aggregation resulting from millennia of root-soil co-evolution – offer a unique model to investigate how aggregate-scale pore architecture controls plant responses to drought. Using soil microcosms (4 × 10 cm, ~80 g soil) with aggregates from Native Steppe and Arable Chernozems, we established six experimental treatments (3 aggregate sizes × 2 soil types) with three replicates each. Root-soil dynamics were tracked through repeated X-ray computed tomography (Neoscan N80, Belgium) at 16 µm resolution. Imaging was synchronized with plant developmental stages – germination, first leaf, and third leaf stage at permanent wilting point – yielding a total of 54 soil tomograms for analysis.Preliminary processing of the data reveals distinct pore network architectures across aggregate size classes. Small aggregates exhibited low CT-visible porosity (24%) with high solid phase connectivity (6.60 mm⁻³), while medium aggregates showed moderate porosity (39%) with lower connectivity (0.64 mm⁻³), and large aggregates had the highest porosity (49%) but the lowest connectivity (0.51 mm⁻³). This structural gradient directly controlled root colonization: solid phase connectivity showed a strong negative correlation with root volume growth (r = −0.76), suggesting that matrix mechanical cohesion, rather than pore characteristics alone, limits root expansion. Medium aggregates – which naturally dominate in undisturbed steppe soils – provided optimal conditions for root development, with 90% greater root surface expansion compared to small aggregates. Root sphericity decreased 3–4 times more in medium aggregates (−0.14) than in small aggregates (−0.04), indicating greater architectural plasticity critical for water acquisition. Importantly, our preliminary results also show that medium aggregates provided the greatest drought resistance: plants in these microcosms reached the permanent wilting point latest, suggesting that this aggregate fraction optimizes both root development and water availability over time.These findings demonstrate that native Chernozem aggregate structure represents an optimized spatial configuration balancing root accessibility with water retention. The strong coupling between aggregate-scale heterogeneity and root response suggests that tillage-induced disruption of natural aggregate distributions may compromise this evolutionary optimization. Our approach – combining high-resolution CT with growth stage-synchronized imaging – offers a framework for quantifying how spatial heterogeneity translates into ecosystem-relevant soil functions. Data processing is ongoing, and final results will include expanded replication and additional root morphometric parameters.

Why it matches plant phenotyping methods高解像度X線CTを用いて根の体積成長、表面拡大、球形度などの形態形質を反復取得・定量する手法が研究の中心であり、植物フェノタイピングへの実質的応用に該当する。

abstractRoot-soil dynamics were tracked through repeated X-ray computed tomography (Neoscan N80, Belgium) at 16 µm resolution.

Field-Aware and Explainable Modelling for Early-Season Crop Yield Prediction Using Satellite-Derived Phenology ↗

Accurate and early prediction of crop yield at the sub-field scale is essential for precision-agriculture and food-system planning. This study evaluates a phenology-based machine learning framework for winter wheat yield prediction using Sentinel-2 satellite imagery, climate reanalysis data, and field-level yield data. Phenological metrics derived from the normalised difference vegetation index (NDVI), the normalised difference water index (NDWI), and the normalised difference red-edge index (NDRE) were combined with accumulated seasonal rainfall and seasonal potential evapotranspiration, and multiple modelling strategies were assessed using a leave-one-field-out cross-validation (LOFO CV) scheme to ensure spatial generalisation. Among the evaluated models, the Random Forest (RF) algorithm achieved the highest overall performance, explaining up to 73% of the yield variability with a root mean square error (RMSE) of 0.88 t ha−1 at optimal prediction timing (day of year 160–175). Integrating phenological and climatic covariates consistently improved prediction accuracy compared to models based only on phenological variables, while the inclusion of soil properties provided limited additional benefit at the examined spatial scale. Phenological metrics based on red-edge data, particularly the maximum NDRE, were the most influential predictors, highlighting the added value of red-edge spectral information beyond traditional red–near-infrared indices. Uncertainty analysis revealed spatially heterogeneous prediction uncertainty, particularly near field boundaries and in areas of complex spatial patterns. Overall, the proposed framework enables robust, early, and interpretable yield prediction at the sub-field scale, supporting uncertainty-aware decision-making in precision agriculture and offering a scalable foundation for regional crop monitoring.

Why it matches plant phenotyping methods衛星画像から抽出した作物フェノロジー指標を用いて圃場内の収量を推定する機械学習フレームワークを構築・交差検証しており、植物形質の取得・推定手法が中心である。

abstractThis study evaluates a phenology-based machine learning framework for winter wheat yield prediction using Sentinel-2 satellite imagery

Characterizing plant hydraulic behaviour under drought stress using vegetation modelling ↗

Droughts have emerged as the primary driver of forest disturbances across Europe in the 21st century, significantly impacting both tree growth dynamics and mortality rates. Tree species are differently affected under drought, and these differences are related to species-specific plant hydraulic traits that govern water storage, hydraulic conductivity, and stomatal regulation. However, quantifying variability in these hydraulic traits across sites, species, and time remains challenging, as site measurements have historically rarely been comprehensive enough to assess the evolution of plant hydraulic behavior under drought stress. New continuous, high temporal resolution observational plant hydraulic data paired with process-based plant hydraulic modelling opens an opportunity to address this gap, by providing a framework to test and quantify theories based on first principles across species and sites.In this study, we apply the terrestrial biosphere model QUINCY, augmented by a recently developed plant hydraulic architecture module, across three eddy covariance sites in Germany covering broadleaved forest species (Aplern, Hainich, and Hartheim). The model is parameterized for three common temperate tree species present at the aforementioned sites. We constrain QUINCY across these species and sites using 30-minute resolution stem water potential measurements collected during the summer and autumn of 2023. Our results show that two groups of model parameters explain most of the simulated plant water potentials: parameters controlling plant water uptake from soil (plant ability to extract water from soil and the root distribution), and parameters regulating stomatal sensitivity to pre-dawn leaf water potential. Across species, we find ash to be more drought resistant than beech and hornbeam, as it closes its stomata earlier than other species under similar levels of drought stress, and it is characterised by a higher hydraulic capacitance per unit stem volume. Our study demonstrates how integrating the new generation of in situ plant hydraulic observations into vegetation models can facilitate the quantification of species-specific hydraulic parameters, effectively reducing uncertainty in, and providing robust constraints on, modelled responses to drought.

Why it matches plant phenotyping methods植物の水理状態・水理形質を連続観測と拡張モデルで定量化する手法の適用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。

abstractOur study demonstrates how integrating the new generation of in situ plant hydraulic observations into vegetation models can facilitate the quantification of species-specific hydraulic parameters

Evaluating Spectral Resolution Effects on Crop Monitoring: A Comparison of UAV-based Multispectral, Hyperspectral and handheld Greenseeker sensor ↗

Spectral sensors have become an integral part of modern precision agriculture. It enables fast, non-destructive and map-based crop monitoring of key crop physiological parameters. The spectral resolution of a sensor plays an important role in determining its ability to detect subtle changes in the crop, nutrient status and canopy development. Sensor’s comparison based on spectral resolution remains limited particularly in the context of field-level agronomic monitoring. This study aims to address this gap by using three sensors UAV-based multispectral (MS), UAV-based hyperspectral (HS) and handheld Greenseeker (GS) NDVI measurements. Hyperspectral sensors provide continuous high-resolution data from visible to near infrared; MS use fewer broad bands; GS limits to two bands for quick NDVI field checks. The experimental study was conducted in the arid region of Uttar Pradesh, India. The experimental setup consisted of plots with same irrigation (100% ETc) and varying nitrogen dosage i.e. 150,120 and 90 kg/ha (Plot 1, Plot 2 and Plot 3, respectively) with three replications. Plots 4 and 5, representing farmer-field conditions with 120 kg ha⁻¹ nitrogen and no nitrogen respectively, followed regional irrigation practices, whereas Plot 6 (rainfed) was irrigated only once initially. A series of UAV-flights were conducted across critical phenological stages, and the reflectance was used to generate Normalized Difference Vegetation Index (NDVI) representing canopy density.The results showed that NDVI rapidly increased during early vegetative stage (61-75) DAS, saturated around (75-85) DAS, followed by a decline during (101-117) DAS. NDVI peaked around flowering stage for all the sensors. GS-NDVI varied between (0.46-0.78), MS-NDVI displayed (0.52-0.86), whereas HS- NDVI varied between (0.55-0.90). The mean NDVI values were (0.570 ± 0.085) for GS, (0.608 ± 0.075) for MS, and (0.664 ± 0.087) for the HS, with HS exceeding others by 16.5% (vs. GS) and 9.3% (vs. MS). Pearson correlation coefficients confirm strong inter-sensor agreement: Greenseeker-Hyperspectral r = 0.96, Multispectral-Hyperspectral r = 0.91, Greenseeker-Multispectral r = 0.87 (all p

Why it matches plant phenotyping methods複数のセンサーによる作物キャノピーNDVI測定を比較し、スペクトル分解能とセンサー間一致度を評価することが研究の中心であるため、植物フェノタイピング手法の技術比較・検証に該当する。

abstractThis study aims to address this gap by using three sensors UAV-based multispectral (MS), UAV-based hyperspectral (HS) and handheld Greenseeker (GS) NDVI measurements.

Evaluating SAM3 and Conventional Image Processing Method for Potato Canopy Cover Estimation as an Indicator of Crop Health ↗

Precise monitoring of crop canopy cover (CC) is crucial for evaluating growth and health under diverse water and nutrient conditions. Although nano liquid urea has been promoted in India as an eco-friendly alternative to conventional nitrogen (N) fertilizers. Its effectiveness in potato cultivation, particularly for canopy development and yield, remains unclear. To address this gap, a field experiment was conducted during the 2024–25 winter season using three N treatments under a micro-irrigation system: T1-recommended granular urea (46% N), T2-without N, and T3-IFFCO nano liquid urea (4% w/v). Images were captured using a downward-looking smartphone camera positioned 2.5 meters above the crop near each treatment, serving as the primary input for estimating canopy cover. The images were processed using both a prompt-based segmentation model (SAM3) and an image-processing pipeline (Modified Excess Green Index + Otsu thresholding) to estimate CC. The SAM3 occasionally overestimated or failed to detect the potato canopy with the prompt “Green plants, leaves, vegetations, canopy cover”, whereas the image-processing approach consistently provided accurate CC estimates and was therefore used for subsequent analysis. The result revealed that the CC clearly showed differentiation among the treatments after 25 days after sowing (DAS). With this most of the treatment comparisons depict the CC peaking after 45 DAS, where the T1 recorded the highest canopy cover (~71%), indicating a healthy crop, while the pairwise comparisons showed CC values of ~55% (T1–T2), ~66% (T1–T3), ~33% (T2–T2), ~36% (T3–T3), and ~36% (T2–T3), depicting the nitrogen deficit. Similarly, the yield followed the same trend, with T1 producing the highest yield (26.78 t/ha), compared to 10.89 t/ha in T2 and 11.90 t/ha in T3. The results indicate that nano liquid urea does not supply sufficient nitrogen to support optimal potato canopy growth and productivity, resulting almost similar response to the no nitrogen application treatment. Increasing the nitrogen concentration in nano liquid urea formulations may improve their effectiveness. This study provides evidence to guide farmers in selecting appropriate nitrogen fertilizers for potato cultivation. In the future, such fertilizers should be evaluated across different crops to ensure their efficacy and to prevent farmers from adopting products that may not meet crop nutrient requirements.

Why it matches plant phenotyping methodsジャガイモのキャノピー被覆率という植物形質を、SAM3と画像処理パイプラインで推定し、両手法の性能を比較・評価しているため、施肥試験を含むがフェノタイピング手法が中心的です。

titleEvaluating SAM3 and Conventional Image Processing Method for Potato Canopy Cover Estimation as an Indicator of Crop Health

Deep roots through time and crops: insight from five seasons at DeepRootLab. ↗

Deep-rooted crops accessing water and nutrients from deep soil layers enhance the resource base for crop production. However, studying these roots in field conditions is labour-intensive, limiting research scope. We established a field root research facility with 48 plots for replicated experiments. The facility includes 144 6-metre-long minirhizotron tubes and an AI-based pipeline for rapid root trait analysis. We also attempted to install access tubes and customized ingrowth core production for less-invasive root activity determination. Our study revealed significant differences in deep root density among species, particularly at depths of 2.5 to 4.5 m, over 5 years. The less-invasive studies using ingrowth cores reached depths of 4.2 m. Nutrient tracer 15 N analysis showed marked differences in deep root activity among crop species. Time domain reflectometry sensors indicated varying water depletion in deeper soil layers, influenced by crop species and root growth patterns. We established a field facility for studying deep root growth and function, demonstrating its effectiveness in analysing diverse deep-rooted plant species. This facility provides an ideal platform for conducting meaningful research in deep soil layers, yielding statistically and biologically significant results for agricultural applications.

Why it matches plant phenotyping methods深根研究施設とAIによる根形質解析パイプラインの構築・有効性評価が中心的に記述されており、根密度などの植物形質を取得するフェノタイピング基盤に該当する。

abstractThe facility includes 144 6-metre-long minirhizotron tubes and an AI-based pipeline for rapid root trait analysis.

Developing and deploying an unmanned aerial system–based phenotyping program for maturity to support soybean breeding ↗

Abstract Soybean [ Glycine max (L.) Merr.] varieties are categorized into different relative maturity groups (MGs) that correspond to the approximate region that the variety is best adapted. Maturity is an important trait that growers consider when deciding which varieties to plant and for breeders as a covariate to compare genotypes. Accurate phenotyping of maturity is an important task during line development but is labor‐intensive. High‐throughput phenotyping (HTP) of soybean maturity using unmanned aerial systems can reduce the labor and error associated with manual maturity notes. An HTP program for maturity will provide higher quality maturity data that will improve breeders’ ability to evaluate the performance of breeding lines on a large scale. The objective of this study was to develop an intuitive, accessible, and precise HTP program to determine the maturity of soybean varieties in the field that can be deployed in soybean breeding programs. In this study, “Matti,” a QGIS plugin, was developed to track the average green leaf index (GLI) of soybean research plots during the senescence period. Piecewise and local polynomial regression models monitor the senescence curve and provide maturity estimates when the GLI values are near or below a user‐specified threshold. This algorithm resulted in moderate to high correlations ( r = 0.52–0.97) between the ground truth and estimated maturity of soybean lines in both early and late maturity MGs. Similar correlations ( r = 0.43–0.72) were found for early generation materials. Results indicate that Matti can be easily implemented by soybean breeding programs to provide timely estimates of relative maturity.

Why it matches plant phenotyping methodsUAV画像から大豆の成熟度を推定するHTPプログラムとQGISプラグインを開発し、地上真値との相関で検証しており、植物表現型取得・推定手法が中心である。

abstractThe objective of this study was to develop an intuitive, accessible, and precise HTP program to determine the maturity of soybean varieties in the field that can be deployed in soybean breeding programs.

Potato yield can be predicted by using drone-captured and environmental measurements early in the growing season ↗

Abstract Accurate pre-harvest prediction of crop yield informs variety selection, optimizes management, and accelerates breeding. As potato is the world’s leading non-grain staple, here we evaluate a diverse panel of varieties in a three-year field trial across five European locations. Canopy development and environmental parameters are monitored throughout the growing season using drone-based imaging, in-field sensors and gene expression measurements, while tuber yield and quality traits are quantified at harvest. We show that these data enable the identification of climate-resilient, high-yielding genotypes and support the development of machine learning models that explain over 80% of yield variation in independent test sets. Strikingly, measurements collected within the first two months after planting achieve predictive performance comparable to models trained on full-season data. Model interrogation further shows that over 70% of yield variation can already be predicted based on a simple five-parameter linear equation. Our framework thus demonstrates the potential of integrative field phenotyping and data-driven modeling to improve variety selection across heterogeneous environments.

Why it matches plant phenotyping methodsドローン画像と圃場センサーによる作物表現型取得、および収量予測モデルの開発が研究の中心であり、単なる収量測定ではない。

abstractCanopy development and environmental parameters are monitored throughout the growing season using drone-based imaging, in-field sensors and gene expression measurements

Imaging and genetic toolbox to study Arabidopsis embryogenesis ↗

Embryogenesis in the model plant Arabidopsis thaliana provides a framework for understanding how cell polarity and patterning coordinate with hormonal signalling to establish the plant body plan. Following fertilisation, the zygote divides asymmetrically to generate apical and basal lineages, establishing the apical-basal axis that defines future shoot and root poles. Genetic and molecular analyses of classical mutants including gnom, monopteros (mp), bodenlos (bdl) and topless revealed that localised auxin biosynthesis, directional transport and downstream transcriptional responses are central to apical-basal axis establishment and organ initiation. The main components of this regulation are polarly localised PIN auxin transporters and downstream modules involving MONOPTEROS and WUSCHEL-RELATED HOMEOBOX transcription factors. Advances in microscopy have transformed the study of Arabidopsis embryogenesis: fluorescence-compatible clearing reagents and three-dimensional reconstructions now permit quantitative analyses of cell geometry, division orientation, and cytoskeletal dynamics. Live ovule imaging setups with confocal laser scanning and multiphoton microscopes enable real-time observation of embryo development, while laser-assisted cell ablation can be used to probe cell-to-cell communication and fate plasticity. Together, these methodological breakthroughs position Arabidopsis embryos as a prime model for dissecting the chemical and biophysical cues that shape plant development.

Why it matches plant phenotyping methods胚発生を解析するための蛍光イメージング、三次元再構成、ライブ撮像などの方法論と定量的な細胞形態・分裂方向測定が中心であり、植物フェノタイピング手法に該当する。

abstractAdvances in microscopy have transformed the study of Arabidopsis embryogenesis: fluorescence-compatible clearing reagents and three-dimensional reconstructions now permit quantitative analyses of cell geometry, division orientation, and cytoskeletal dynamics.

ALPHA: A High Throughput System for Quantifying Growth in Aquatic Plants ↗

The need for more sustainable agricultural systems is becoming increasingly apparent. The global demand for agricultural products—food, feed, fuel and fiber—will continue to increase as the global population continues to grow. This challenge is compounded by climate change. Not only does a changing climate make it difficult to maintain stable yields but current agricultural systems are a major source of greenhouse gas emissions and continue to drive the problem further. Therefore, future agricultural systems must not only increase production but also significantly decrease negative environmental impacts. One approach to addressing this is to begin breeding and cultivating new plant species that have fundamental sustainability advantages over our existing crops. The Lemnaceae, commonly known as duckweeds, are one family of plants that have potential to increase output and reduce the negative environmental impacts of agricultural production. Herein we describe the Automated Lab‐scale PHenotyping Apparatus, ALPHA, for high‐throughput phenotyping of Lemnaceae. ALPHA is being used for selective breeding of one species, Lemna gibba , toward the goal of creating a new crop for use in sustainable agricultural systems. ALPHA can be used on many small aquatic plant species to assess growth rates in different environmental conditions. A proof of principle use case is demonstrated where ALPHA is used to determine saltwater tolerance of six different clones of L. gibba .

Why it matches plant phenotyping methods水生植物の成長率をハイスループットに定量するフェノタイピング装置を開発・適用しており、表現型取得システムが研究の中心である。

abstractHerein we describe the Automated Lab‐scale PHenotyping Apparatus, ALPHA, for high‐throughput phenotyping of Lemnaceae.

Improving plant diversity prediction in revegetated grasslands using compact Sentinel-2 time series descriptors ↗

Previous studies have shown that multitemporal data can strengthen the relationship between grassland diversity and spectral reflectance. However, most studies used interpolated Sentinel-2 time series as such. This study investigated whether species richness models can be improved using fitted Sentinel-2 temporal features describing the overall plant growth patterns.We measured plant species richness in 77 quadrats (1m x 1m) from revegetated alpine grasslands located around an open pit mine in Hochfilzen, Austria, characterized by a high range of species richness. Several multi-year Sentinel-2 vegetation index time series were used as inputs for fitting temporal features such as phenology descriptors, harmonic decomposition, frequency decomposition and functional principal components. Those features were compared to interpolated time series of Sentinel-2 bands used in state of the art baseline models (Fauvel et al., 2020; Muro et al., 2022).The feature sets were inserted into a Random Forest regression model pipeline, first selecting the best performing features in a nested cross-validation, then applying the final model over the grassland areas to produce species richness maps. Lastly, SHAP feature analysis was performed to improve model interpretability.Our best model, using fitted CIRE time series features, achieved coefficient of determination R2 = 0.19 in cross-validation and R2 = 0.36 on holdout set (16 quadrats). Features describing events around peak growing season were found especially important. Our model clearly outperformed all baseline models on holdout set across all metrics: R2 (+0.15 to +0.33), absolute Root Mean Squar Error RMSE (-0.35 to -0.91) and relative RMSE (-0.02 to -0.05).All models highlighted similar areas of high or low richness. Differences were observed for most extreme species richness, or less densely vegetated pixels. Results suggest our features are better suited to small datasets. The comparison of models will also be carried out on larger field inventories.Future steps will include extension to species abundance metrics, and a comparison to spectral variation features extracted from multi-scale hyperspectral imagery from Hyspex Mjölnir VS-620 drone and EnMAP satellite.This research is part of the MultiMiner project funded by the European Union’s Horizon Europe research and innovations actions programme under Grant Agreement No. 101091374.

Why it matches plant phenotyping methodsSentinel-2時系列から植物種多様性（種数）を推定する特徴抽出・機械学習パイプラインを開発・比較し、交差検証とホールドアウトで評価しているため、植物形質推定法が中心です。

abstractThis study investigated whether species richness models can be improved using fitted Sentinel-2 temporal features describing the overall plant growth patterns.

Investigating plant functional traits, taxonomy and phenology as drivers of leaf spectral variation ↗

Mitigation of the ongoing biodiversity crisis requires thorough understanding of species dynamics across scales. However, monitoring plant species and their functional traits is time-consuming and challenging to implement across larger spatial scales and through time. Spectroscopy is emerging as a promising tool for monitoring plant functional and taxonomic diversity within and between ecosystems. This relies on the presence of a functional and taxonomic signal in leaf optical properties, which in turn depends on the spectral similarity of species, intra- and interspecific trait variation, and the timing of the measurements. In order to address these relations in natural and semi-natural ecosystems in Denmark, we are compiling a spectral library of plants. An important methodological aspect of this work is to assess how leaf degradation, and the phenological stage of the plant, affect leaf optical properties. This was assessed by measuring leaf spectra from 350 – 2500 nm of four plant species, representing different plant functional types, from the same site over five months. We measured leaves at the time of sampling, and repeatedly after detachment from the plant to test how sampling strategy, potential leaf degradation after detachment and phenological stage influence leaf optical properties. Furthermore, we collected spectral and functional trait data of dominant plant species in 100 vegetation plots across the Store Åmose nature area in July and August. We present results of the spectral and functional differences among species and taxonomic levels, and the significance of leaf degradation and phenology on measured spectra. Leaf water and chorophyll content are expected to be the major drivers of spectral variation over time. However, subtle spectral signals may reflect other biochemical traits or leaf biophysical changes during the growing season. These dynamics are expected to depend on plant ecology, functional types, and environmental conditions such as wet and dry habitats. Our results will demonstrate the potential (and challenges) of using spectroscopy for taxonomic and functional identification of plants. We will provide insights into the role of leaf sampling strategy and phenology on spectral signals of plant species, which can inform the planning of future remote sensing and field campaigns.

Why it matches plant phenotyping methods葉の分光計測を用いた植物機能形質・分類情報の取得を中心に、葉の劣化、採取方法、フェノロジーが光学特性へ与える影響を評価しており、表現型取得手法の方法論的検討が実質的に含まれる。

abstractSpectroscopy is emerging as a promising tool for monitoring plant functional and taxonomic diversity within and between ecosystems.

Computer Vision-Based Monitoring and Data Integration in a Multi-Trophic Controlled-Environment Agriculture Demonstrator ↗

Controlled-environment agriculture (CEA) and circular production systems require coordinated monitoring of biological and physicochemical processes across trophic levels. This project report presents the implementation of a multi-trophic controlled-environment agriculture demonstrator that integrates computer-vision-based monitoring with established sensor infrastructure for aquaculture, poultry, plants, microalgae, duckweed, and insect modules. Stereo imaging and RGB-D systems are deployed for non-invasive quantification of fish biomass and plant growth, while continuous water-quality and environmental measurements (e.g., pH, dissolved oxygen, nitrate, ammonium, temperature, CO2) provide complementary process data. These data streams are synchronized within a shared database architecture to enable cross-module evaluation of nutrient dynamics, growth progression, and operational stability under real facility conditions. The implemented framework demonstrates how computer vision can extend conventional sensor-based monitoring by directly capturing biological performance indicators across aquatic, terrestrial, and microbial domains. While advanced predictive modeling and full digital twin simulation remain future development steps, the realized data-integration architecture establishes a structural foundation for the systematic evaluation of circular indoor food-production systems. The demonstrator illustrates how multimodal monitoring can support nutrient recirculation, transparency of biological variability, and data-driven assessment within controlled multi-trophic environments.

Why it matches plant phenotyping methodsステレオ画像およびRGB-Dによる植物生長の非破壊定量と、データ統合型モニタリング基盤の実装が中心的に記述されており、植物フェノタイピング基盤として収載対象です。

abstractStereo imaging and RGB-D systems are deployed for non-invasive quantification of fish biomass and plant growth

UAV-Based Remote Sensing and Artificial Intelligence for Climate-Smart Agriculture: A Systematic Review of Technologies, Analytics, and Applications in Smallholder Systems ↗