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.
This study assessed the integration of Unmanned Aerial Vehicles (UAVs) and satellite images (Sentinel-1 and Sentinel-2) in advanced machine-learning techniques to monitor the ABV of quinoa crops (Jacha Grano variety) across the Bolivian Altiplano. The proposed method follows a two-step procedure. First, UAV RGB images were used in photogrammetric and deep-learning (Convolutional Neural Networks-CNN) models to estimate reference quinoa ABVs at a 10 m spatial resolution from the crop canopy 3D model and classification, respectively. Secondly, several spectral and polarization/texture indices derived from Sentinel-2 and -1 images were integrated into three decision-tree-based machine-learning models (Random Forest-RF, Gradient Boosting-GB, eXtreme Gradient Boosting-XGB), and one CNN-based machine-learning model to estimate ABV. Additionally, a Stacking Model (STM) build on top of the three decision-tree-based models was considered for comparison. Model evaluation was also performed in a two-step approach. First, a 10-fold cross-validation strategy was used to highlight ABV sensitivity to Sentinel-2 and Sentinel-1 alone and in combination. Secondly, a Leave-One-Plot-Out Cross-Validation (LOPOCV) strategy was used to avoid autocorrelation between the training and evaluation dataset and therefore provided more insight into ABV mapping potential. The results showed that the combination of Sentinel-1 and Sentinel-2 features in the CNN model achieved the best predictive performance with R2 and RMSE values of 0.64 and 0.39 m3 ∙ 100 m−2, respectively. These findings highlight the potential of integrating multi-source information in advanced artificial intelligence algorithms for quinoa ABV monitoring, offering new insights toward the identification of sustainable practices across remote regions with complex socio-economic contexts.
Why it matches plant phenotyping methodsUAV画像・衛星センサー・機械学習を統合し、キノアの地上部バイオマス体積という植物形質を推定する手法を開発・比較検証しており、フェノタイピング手法が中心である。
abstractUAV RGB images were used in photogrammetric and deep-learning (Convolutional Neural Networks-CNN) models to estimate reference quinoa ABVs
Automated fruit counting and yield estimation systems are necessary for efficient orchard management. This study presents a computer vision system based on video multi-object-tracking for fruit load estimation in apple orchards and provides a comprehensive analysis of the system performance under diverse scanning conditions. The system integrates fruit detection, tracking, localization within orchard, and fruit load map generation. Experiments were carried out in an experimental apple orchard containing 420 apple trees. Data was collected with two different RGB-D sensors (Azure Kinect DK and ZED 2) at three different scanning distances (125 cm, 175 cm, and 225 cm) on two different dates prior to the harvest. Comparing the two evaluated sensors, Azure Kinect provided more consistent performance across different dates. Results also show that the longer scanning distance improves accuracy due to seeing the full tree view gives better fruit counts than close partial views. Between the two dates, best results were achieved near harvest due to fruit color at this stage, achieving a Mean Absolute Percentage Error (MAPE) of 6.91 % and a determination coefficient (R 2 ) of 0.733 (using ZED2 sensor at 225 cm distance). Finally, a test comparing scanning from one or both sides of the tree row showed that bilateral scanning improved fruit load estimation at the stretch level by incorporating information from both sides of the canopy. The results of this work demonstrate the effectiveness of the video fruit tracking systems as a useful tool for automating fruit load estimation.
Why it matches plant phenotyping methods動画ベースの果実検出・追跡手法を開発・評価し、リンゴ樹の果実負荷量を推定することが研究の中心であるため、植物フェノタイピング手法として含める。
abstractThis study presents a computer vision system based on video multi-object-tracking for fruit load estimation in apple orchards and provides a comprehensive analysis of the system performance under diverse scanning conditions.
Background Olive ( Olea europaea L.) breeding initiatives rely heavily on the extensive and correct characterisation of genetic resources to successfully achieve their goals, such as addressing climate change and emerging diseases challenges. However, the historical lack of standardised phenotyping protocols across multi-environment trials has severely hindered data interoperability and large-scale comparative analyses. Methods Within the Horizon 2020 GEN4OLIVE project, five international olive germplasm banks established a consensus-based methodological framework to systematically evaluate over 500 olive cultivars. We harmonised 14 evaluation protocols covering six fundamental dimensions: phenological and agronomic traits, abiotic stress resilience, biotic stress resilience, olive oil yield and chemical quality, table olive quality assessment, and morphological characterisation and photography. While most protocols were adapted from previously published literature to ensure ease of implementation across different facilities, novel methodologies for frost tolerance and standardised photography were developed de novo. Results The implementation of these consensus methods across five countries proved highly successful. This methodological framework enabled the generation of the largest harmonised, publicly available dataset on olive genetic resources to date, effectively making possible the correct comparation and ranking of the olive cultivars based on their specific characteristics. Conclusions This compendium of methods provides a robust, highly replicable reference point for the standardisation of olive germplasm characterisation and use of shared benchmark cultivars as an effective way for data normalization and comparation. It facilitates future global pre-breeding efforts, ensures international data interoperability, and supports the discovery of resilient cultivars to secure the future of the olive sector.
Why it matches plant phenotyping methodsオリーブ遺伝資源の標準化フェノタイピングプロトコルを体系化し、複数機関で実装・検証して大規模データセットを生成した方法論中心の研究である。
abstractthe historical lack of standardised phenotyping protocols across multi-environment trials has severely hindered data interoperability and large-scale comparative analyses.
Reproduction assets foundThe article declares two paper-specific public assets: the GEN4OLIVE phenotypic dataset from evaluating over 500 olive accessions across five germplasm banks, hosted on the project's Olive Varieties Database, and a Zenodo-deposited methodological handbook (Extended Data) containing the 14 protocols, visual assessment, Dataset · publicData and software availability
The phenotypic dataset generated from the evaluation of over 500 olive varieties across the five Mediterranean
germplasm banks using this compendium of protocols and methodologies, is publicly available via the GEN4OLIVE
project repository.
• Repository: GEN4OLIVE Olive Varieties Database.
• Link: https://www.uco.es/ucolivo/gen4olive/olivevarieties (GEN4OLIVE Database, 2025).
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Open Research Europe 2026, 6:322 Last updated: 14 SEP 2026Open asset ↗GEN4OLIVE Olive Varieties Databasepdf-raw-page:8 lines:1-44Plant phenotyping relevance match · UnverifiedEurope PMC · checked 15 Sept 2026
Published2 Sept 2026TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik
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.
Accurate and efficient monitoring of tea plant growth parameters via remote sensing is essential for precision plantation management. However, spectral indices relying solely on reflectance often exhibit limited sensitivity in capturing complex tea canopy characteristics. This study developed a data-driven framework integrating spectral reflectance, frequency-domain harmonic components, and spatial texture features to construct tri-feature fusion indices (TFIs) and establish machine learning and deep learning models for tea growth monitoring. Ten-band multispectral imagery was acquired using a UAV alongside synchronous field measurements of leaf and plant biomass and nitrogen accumulation. TFIs were constructed through exhaustive feature combinations and optimized via a data-driven search strategy. Subsequently, random forest (RF), multilayer perceptron (MLP), convolutional neural network (CNN), and transformer models were evaluated using a leave-one-site-out cross-validation (LOSO-CV) strategy. The selected TFIs showed strong associations with tea growth parameters within the investigated dataset, with R2 values up to 0.63 and 0.62 for leaf dry matter and leaf nitrogen accumulation, respectively. Models incorporating selected TFIs achieved cross-validated R2 values of 0.56 for leaf dry matter (MLP), 0.59 for plant dry matter (MLP), 0.73 for leaf nitrogen accumulation (MLP), and 0.68 for plant nitrogen accumulation (CNN). These models exhibited competitive predictive performance comparable to RF, although no statistically significant differences in mean absolute error were observed under site-held-out evaluation. Furthermore, model-derived spatial maps provided insights into fine-scale spatial heterogeneity and potential interannual variations in tea growth parameters across representative plantations from 2024 to 2025. Overall, this study provides a UAV-based framework for tea growth parameter estimation by integrating multi-domain information without requiring additional environmental observations.
Why it matches plant phenotyping methodsUAVマルチスペクトル画像から茶植物の乾物量・窒素蓄積を推定する特徴量融合および機械学習・深層学習フレームワークを開発し、サイト外交差検証で評価しており、植物形質の取得・推定手法が中心である。
abstractThis study developed a data-driven framework integrating spectral reflectance, frequency-domain harmonic components, and spatial texture features to construct tri-feature fusion indices (TFIs) and establish machine learning and deep learning models for tea growth monitoring.
Aboveground biomass density (AGBD) is a key indicator in agricultural systems, directly reflecting crop carbon storage potential and yield levels. The World Food Studies (WOFOST) model is widely used for crop growth simulation due to its process-based interpretability. However, its application is limited by complex calibration demands and struggles with spatial heterogeneity. To address these limitations, this paper proposes an assimilation system that integrates Synthetic Aperture Radar (SAR) data into a modified WOFOST model, which requires simple calibration. WOFOST is run in potential production mode, which assumes ideal conditions to reduce input data requirements. Before assimilation, phenology-related temperature sums are aligned with phenology and meteorological data to match local growth stages. Two quantities are then estimated and updated in the model through data assimilation by minimizing the difference between SAR-derived and simulated AGBD. These quantities are the proposed yield reduction factor, which represents the proportional decrease in potential CO 2 assimilation under stresses, and the initial total dry weight at sowing. Validation experiments were conducted using multi-year cotton datasets from two farms in Georgia, USA, differing in whether irrigation was applied. Compared to WOFOST simulations and evaluated against in situ AGBD measurements, the assimilation results improve agreement and reduce error (approximately 43% RMSE reduction at the rainfed site and 15% at the irrigated site). It also delivers spatial maps of biomass, together with model-derived yield and harvest-index diagnostics, and remains operational under frequent cloud cover where optical observations are sparse. This SAR-based assimilation strategy reduces calibration demands, providing a novel and practical pathway to extend WOFOST applications to diverse agricultural scenarios.
Why it matches plant phenotyping methodsSARデータを作物成長モデルに同化して綿の地上部バイオマスを推定する手法を開発し、複数年・複数圃場データで検証しているため、植物形質取得が中心である。
abstractthis paper proposes an assimilation system that integrates Synthetic Aperture Radar (SAR) data into a modified WOFOST model
Grain yield is a central target in wheat breeding, yet accurately predicting it remains challenging because it depends on many genes and responds strongly to environmental variation. Genomic selection (GS) has improved breeding efficiency by enabling genome-based prediction of genetic merit, but predictability (PA) for grain yield is often limited under stress environments. At the same time, advances in high-throughput phenotyping (HTP) using unmanned aerial vehicles (UAVs) provide phenomic data that capture environment-responsive plant performance and may complement genomic information. In this study, we evaluated genomic and phenomic models for predicting grain yield in elite bread wheat lines across irrigated, drought, and heat-stress environments. Using a sparse phenotyping framework, we compared parametric and non-parametric models. PA was evaluated within environments and under cross-environment sparse phenotyping scenarios. Genomic models provided a stable baseline and enabled effective information sharing across environments when phenotypic data were incomplete. Phenomics-only models captured environment-specific plant responses but were more sensitive to environmental context. Multiomics models that integrated genomic and phenomic information consistently achieved the highest PA, with the largest gains observed under stress conditions. Overall, our results demonstrate that integrating genomics and UAV-based phenomics within sparse phenotyping designs offers a practical and scalable approach to improve grain yield prediction in wheat.
Why it matches plant phenotyping methodsUAV由来のフェノミクスを用いた疎な表現型取得と予測モデルを中心に、環境横断で評価しており、収量という植物形質の推定手法が主要な貢献である。
abstractadvances in high-throughput phenotyping (HTP) using unmanned aerial vehicles (UAVs) provide phenomic data that capture environment-responsive plant performance
Reproduction assets foundThe paper's grain yield BLUEs, spectral wavelength BLUEs, and genotypic data are publicly deposited in the CIMMYT data repository (https://doi.org/10.71682/10549399), directly reproducing this paper's phenotyping measurements. No author analysis code with a public URL is stated; other URLs are generic tools/services.Dataset · publicok.com.
Paolo Vitale, Email: p.vitale@cgiar.org.
DATA AVAILABILITY STATEMENT
The datasets generated and analyzed during this study, including best linear unbiased estimates (BLUEs) for grain yield and spectral wavelengths, as well as the corresponding genotypic information, are publicly available in the CIMMYT data repository ( https://doi.org/10.71682/10549399 ).
REFERENCES
Araus, J. L.
,
Kefauver, S. C.
,
Zaman‐Allah, M.
,
Olsen, M. S.
, &
Cairns, J. E.
(2018). Translating high‐throughput phenotyping into genetic gain. Trends in Plant Science, 23(5), 451–466. 10.1016/j.tplants.2018.02.001
Brault, C.
,
Lazerges, J.
,
Doligez, A.
,
Thomas, M.
,
Ecarnot, M.
,
Roumet, P.
,
Bertrand, Y.Open asset ↗CIMMYT data repository · 10.71682/10549399lines:280-433Plant phenotyping relevance match · UnverifiedEurope PMC · checked 14 Sept 2026
Year-to-year climate variability poses a challenge for agriculture by increasing crop yield variability; therefore, there is a need to identify genotypes that can withstand these fluctuations. With the right selection criteria, genotypes with yield stability across variable environmental conditions can be selected. Methods such as Finlay-Wilkinson random regression (FWRR) may allow us to use sparse datasets-common in plant breeding pipelines-and incorporate genomic data to leverage phenotypic information from related genotypes to predict yield stability. Our objective was to examine how the number of environments and the variance among those environments affect stability predictions. We also integrate FWRR as a genomic prediction tool for characterizing yield stability, comparing it to the traditional genomic prediction models as a reference. We used three datasets: one highly unbalanced dataset for oats (Avena sativa L.) and two completely balanced datasets with different numbers of environments for barley (Hordeum vulgare L.) and wheat (Triticum aestivum L.). We fit standard Finlay-Wilkinson (FW) and FWRR models to estimate grain yield and stability under various scenarios. We found that the estimated stability values obtained were similar using balanced datasets for FW or FWRR. FWRR also achieved moderate predictive ability for stability using unbalanced datasets under 10-fold cross-validation (CV1) with new genotypes. In terms of environmental representation, selecting the right set of environments for inclusion in the model was more important than adding more environments. Our results suggest the possibility of using FWRR to select stable genotypes earlier in line development, as well as to design resource-efficient stability-testing schemes.
Why it matches plant phenotyping methodsFWRRを用いて穀類の収量安定性を推定・予測する統計的手法を検討し、環境数やデータ構成による予測性能を評価しているため、収量形質の計算的フェノタイピング手法が中心です。
abstractMethods such as Finlay-Wilkinson random regression (FWRR) may allow us to use sparse datasets-common in plant breeding pipelines-and incorporate genomic data to leverage phenotypic information from related genotypes to predict yield stability.
Plant phenotyping relevance match · UnverifiedOpenAlex · Europe PMC · checked 14 Sept 2026
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.
Precision agriculture is becoming more and more of a challenge that requires the use of intelligent systems that are able to predict stress and prevent yield loss before it is too late. Traditional methods of agricultural surveillance are predominantly reactive with irrigation demands being based on thresholds or individual yield forecasts models that do not represent the intricate spatio-temporal interactions that exist between crop physiology, soil status, and environmental stresses. Besides, the majority of the current practices do not have an autonomous decision-making approach to preventive intervention which leads to inefficient use of water and slows down the response to stress. This paper suggests a cognitive UAV-assisted agro-surveillance system to predict yield vulnerability caused by crop stress and optimize adaptive irrigation with the help of spatio-temporal deep and reinforcement learning. The framework combines UAV-obtained RGB and multispectral and thermal imagery with measurements of soil sensors and meteorological data obtained with the Crop Health and Environmental Stress Dataset. A new GeoSpatio-TRiNet model is used to acquire long-range spatial relationship, time stress development, and diffusion of stresses across agricultural regions. The model predicts the vulnerability trajectories of the stress instead of the direct yield regression, and this allows early detection of yield risk. Such predictions serve to generate a cognitive environmental state of a Soft ActorCritic (SAC) reinforcement learning agent that autonomously computes zone-based irrigation behaviors to reduce the recurrence of stress at the minimum water usage cost. As shown by the results of the experiment, the proposed framework has a stress forecasting accuracy of 96.3% and performs much better than the traditional machine learning, CNN-based, and transformer-based baselines. The system also decreases the predicted yield vulnerability by 46.6 and enhances water-use efficiency by 41.1 as compared to irrigation strategies based on rules. The results confirm the usefulness of spatio-temporal intelligence with predictive control in terms of effectiveness, and the proposed framework is a scalable and sustainable solution to precision agriculture of the next generation.
Why it matches plant phenotyping methodsUAV画像とセンサーデータから作物ストレスの時系列状態および収量脆弱性を推定する計算・センシング手法が研究の中心であり、灌漑制御への応用も技術評価の一部として記述されている。
abstractThe framework combines UAV-obtained RGB and multispectral and thermal imagery with measurements of soil sensors and meteorological data
Reproduction assets foundThe paper uses the public Kaggle Crop Health and Environmental Stress Dataset (UAV RGB/multispectral/thermal imagery plus soil/weather measurements and stress labels) as its phenotyping data source, and the authors provide an explicit public GitHub repository for the analysis code.Dataset · publicThe current research is based on the Crop Health and Environmental Stress Dataset, which is a publicly available
dataset on Kaggle, specially created to help perform a spatio-temporal analysis of crop health in response to changing
environmental and water-stress factors [26].Open asset ↗pdf-raw-page:10 lines:1-62Code · publicturn: Final zone-wise stress predictions 𝐶
𝑡
𝑧, Yield vulnerability trajectories 𝑉𝑡
𝑧, Optimal adaptive irrigation policy
𝜋∗
End Algorithm
Code availability:
The data used to support the findings of this study are included in the article.
Code availability:
The code used in this research work is available in the following link.
https://github.com/replyvenugopal/Cognitive-UAV-Driven-Agro-Surveillance
4. Result and Discussion
The architectural agro-surveillance solution, which is proposed to be executed by UAVs, is executed through a
modular and scalable software framework to guarantee reproducibility and extensibility. The experiments are all
performed in Python as a main programming languageOpen asset ↗github.com/replyvenugopal/Cognitive-UAV-Driven-Agro-Surveillancepdf-raw-page:24 lines:1-55Plant phenotyping relevance match · UnverifiedCrossref · checked 5 Sept 2026
Faba bean yield reflects complex relationships among genotype, environment, and agronomic traits. This study evaluated an explainable Tabular Prior-data Fitted Network (TabPFN) framework for estimating plot-mean single-plant yield and prioritizing traits using 398 plot-level observations, 13 measured agronomic predictors, and six derived features. On the reference 80/20 split, TabPFN achieved the best values for all four test metrics (R2 = 0.8746, RMSE = 1.9132 g plant−1, MAE = 1.0819 g plant−1, and MAPE = 8.16%). The Friedman test detected differences among the six models (χ2(5) = 16.75, p = 0.005); Nemenyi comparisons distinguished TabPFN from HistGradientBoosting and SVR, whereas the Holm-corrected Wilcoxon analysis confirmed only the TabPFN–SVR difference. Across 10 repeated 80/20 splits, TabPFN obtained the highest mean test R2 (0.8614 ± 0.0691), ranked first in eight splits, and produced a higher R2 than every tuned baseline in at least eight splits. SHAP, permutation importance, and LOCO analyses emphasized pod-, seed-, and biomass-related predictors. Repeated-split ablation showed that derived features improved TabPFN consistently, whereas removing selected target-proximal yield variables reduced performance for every model. The framework is therefore a harvest-time trait-estimation and trait-prioritization tool rather than an early-season forecasting system. Notably, TabPFN achieved this performance without the 100-trial Optuna search used for each baseline; only n_estimators was screened over four prespecified values.
Why it matches plant phenotyping methods単一個体収量を推定し、形質優先順位付けを行う機械学習フレームワークを評価・比較しており、植物形質抽出手法が研究の中心である。
abstractThis study evaluated an explainable Tabular Prior-data Fitted Network (TabPFN) framework for estimating plot-mean single-plant yield and prioritizing traits
Accurate quantification of rice aboveground biomass (AGB) is critical for crop monitoring but remains challenging due to the complex nonlinearity arising from the coupling of plant density, spatial structure, and internal dry matter distribution. To address the limitations of single-source remote sensing, this study proposed a Three-Dimensional Dry Matter Distribution Integration (3D-DMI) model, which establishes a physically interpretable framework decomposing AGB into dry matter density ( ρ ), horizontal projection distribution ( S ), and vertical cumulative distribution ( h d ) components. Guided by this framework, a core subset of six features (Red_650, MTCI, G_correlation, R_correlation, LPI, and HPA0_99) was extracted from UAV-based multispectral, RGB, and LiDAR data using a dual-step feature selection approach combining Maximum Information Coefficient (MIC) and Distance Correlation (dCor). A Random Forest (RF) regression model was then developed to estimate AGB across the entire growth season. The results demonstrated that the 3D-DMI model achieved excellent performance with an R 2 of 0.920, an RMSE of 0.184 kg/m², and an RPD of 3.544, significantly outperforming any single-sensor approach. Single-feature analysis revealed that while LiDAR-derived structural features provided the fundamental basis for biomass estimation, they encountered inherent saturation bottlenecks during late growth stages. Feature contribution analysis based on SHAP further quantified that LiDAR-derived features dominated the estimation process (68.5% contribution), providing the volumetric basis, whereas RGB textures (18.3%) and multispectral features (13.3%) provided indispensable supplements. Ultimately, this study established a robust, physically grounded computational paradigm for high-precision UAV-based rice biomass monitoring across the entire growth cycle.
Why it matches plant phenotyping methodsUAVマルチスペクトル・RGB・LiDARデータからイネの地上部バイオマスを推定する3D-DMI計算手法を開発・評価しており、植物形質の取得・抽出が研究の中心である。
abstractthis study proposed a Three-Dimensional Dry Matter Distribution Integration (3D-DMI) model
Introduction Accurate estimation of aboveground biomass (AGB) is essential for monitoring pasture productivity and supporting sustainable management of integrated crop–livestock (ICL) systems. We hypothesized that integrating multispectral, thermal, and canopy-structural information derived from unmanned aerial vehicles (UAVs) would improve AGB prediction relative to spectral information alone, and that Generalized Additive Models for Location, Scale and Shape (GAMLSS) would accommodate seasonal heteroscedasticity while maintaining predictive performance comparable to Random Forest (RF) and Support Vector Machine (SVM) models. Methods We collected 280 destructive biomass samples from two ICL paddocks and one continuously grazed pasture in the Brazilian Cerrado between 2022 and 2024. Twenty-four UAV-derived predictors, including spectral bands, vegetation indices, canopy surface temperature, and canopy height, were evaluated using repeated five-fold cross-validation. Model transferability was assessed by withholding one management paddock at a time. Results and discussion Under repeated five-fold cross-validation, GAMLSS achieved the lowest prediction error (R² = 0.69 ± 0.01; RMSE = 2.15 ± 0.04 Mg ha⁻¹), followed closely by SVM (R² = 0.68 ± 0.01; RMSE = 2.19 ± 0.03 Mg ha -1 ); RF showed lower accuracy (R 2 = 0.53 ± 0.01; RMSE = 2.63 ± 0.02 Mg ha -1 ). In the paddock-transferability assessment, GAMLSS also showed the lowest error (R 2 = 0.63 ± 0.04; RMSE = 2.34 ± 0.26 Mg ha -1 ). For GAMLSS, the complete multisensor configuration reduced RMSE by 6.2% compared with the spectral-only configuration. The selected model was used to generate spatially explicit maps of AGB and standing aboveground biomass carbon, estimated from the mean measured carbon concentration of forage biomass. Integrating multispectral, thermal, and structural UAV data with distributional regression improves AGB estimation and enables spatial monitoring of tropical pastures under contrasting management conditions.
Why it matches plant phenotyping methodsUAVのマルチセンサーデータと統計モデルを用いて牧草の地上部バイオマスを推定し、交差検証と圃場間移 transferability 評価を行っており、植物形質の取得・推定手法が研究の中心である。
titleUAV multisensor data and GAMLSS improve forage biomass estimation in Cerrado integrated crop–livestock pastures
Abstract. In the face of escalating global food demand and increasing climate variability, precise and granular crop yield monitoring is indispensable for maintaining regional agricultural stability. However, current deep learning approaches for yield estimation are severely constrained by their heavy reliance on massive in situ labeled data, which limits their application in data-scarce regions. Furthermore, these models often overlook the essential temporal evolution logic of yield formation and lack a systematic discussion regarding the contribution patterns of different feature dimensions, resulting in a black-box nature of the underlying model mechanisms. To address these challenges, this study proposes a field-label-free training framework for maize yield estimation that couples mechanistic model with deep learning. The framework's core strength lies in a physiologically complete simulation database, using the WOFOST model to exhaustively cover 30 years of climate variability and habitat combinations across Northeast China (1.24 × 106 km2). A Gated Recurrent Unit (GRU) network was then introduced for end-to-end modeling, accurately capturing the energy accumulation trajectory from vegetative to reproductive growth. Validation against 458 independent ground points (2022–2024) demonstrated robust generalization with an R2 of 0.69, an RMSE of 1.21 t ha−1, and an RRMSE of 13.73 %, despite using no ground data for training. Our analysis revealed that integrating photosynthetic intensity (LAImean), duration (LAD) and peak features (LAImax) across growth stages is critical for accuracy, while omitting early-stage features significantly impairs the model's ability to capture cumulative growth effects. Furthermore, the model successfully captured the spatiotemporal yield anomalies caused by the 2023 typhoon and flooding events. Ultimately, this study generated a 10 m resolution maize yield dataset (2019–2024) for Northeast China. The dataset exhibits consistent interannual stability, with the RRMSE ranging from 7.98 % to 12.92 % and the R2 remaining above 0.44 at the city level. By deeply coupling mechanistic simulation with data mining, this dataset provides detailed support for optimizing agricultural production and guiding farming practices. The Northeast China Maize Yield 10 m dataset is openly available at https://doi.org/10.5281/zenodo.19547014 (Hu et al., 2026).
Why it matches plant phenotyping methodsトウモロコシ収量という植物・作物群落の形質を推定する計算フレームワークを開発し、独立地点で性能検証したうえで再利用可能な10 m解像度データセットを生成しており、単なる農業実験の routine measurement ではない。
abstractthis study proposes a field-label-free training framework for maize yield estimation that couples mechanistic model with deep learning.
Reproduction assets foundThe paper's core output, the NortheastChinaMaizeYield10m maize yield dataset (2019–2024) with accompanying uncertainty layers, is openly deposited on Zenodo with an explicit availability statement and DOI. No author analysis code or trained model checkpoints are stated as publicly available.Dataset · publicThe Northeast China Maize Yield 10 m dataset is openly available at https://doi.org/10.5281/zenodo.19547014 (Hu et al., 2026).Open asset ↗Zenodo · 10.5281/zenodo.19547014lines:158-191Plant phenotyping relevance match · UnverifiedEurope PMC · checked 5 Sept 2026
Abstract A systematic review based on 174 Scopus-records of studies using YOLO-type one-stage detectors for detecting citrus fruits, their count, and yield estimation followed PRISMA guidelines 2020. The title/abstract-screening process, done in duplicate (κ=0.920) yielded 90 included study-records, followed by two further post-hoc exclusions. Each study in the 80 reporting on fruit-level detection showed an average precision of 89.6%, recall of 85.9%, and mAP@0.5 of 91.0%. However, coverage for any individual metric rarely exceeded half of the studies, and only 13% were able to report the more stringent mAP@0.5:0.95. Both YOLOv8 and YOLOv5 were each utilized as the backbone architecture by approximately 22.2% of the studies. From 2025, YOLOv11 has also been emerging. Half of all studies modified architectural components including attention modules, lightweight architectures, and variants of IoU loss functions. Original contributions are generally concentrated in downstream tracking, sensor fusion, and yield modeling rather than the detector itself. A custom-made seven-domain risk of bias tool was developed and utilized by two reviewers who arbitrated discrepancies (91.5%). Results showed that all but one of the reviewed studies had a high level of risk due to almost universal lack of statistical validation and limited dataset diversity; a sensitivity analysis excluding the most risky studies left the performance profiles nearly identical. We conclude that the field has converged around a common technical toolkit but continues to lack standardized benchmarks, multispectral data, and rigorous field-deployment validation.
Why it matches plant phenotyping methods柑橘果実の検出・計数・収量推定に用いる画像解析手法を体系的にレビューし、性能評価、リスク・オブ・バイアス、標準化やベンチマーク不足を検討しており、植物フェノタイピング手法が中心である。
abstractA systematic review based on 174 Scopus-records of studies using YOLO-type one-stage detectors for detecting citrus fruits, their count, and yield estimation followed PRISMA guidelines 2020.
Abstract Purpose Timely, accurate, and field-scale crop yield mapping is essential for precision crop management, yet most existing studies rely on late- or full-season data, limiting in-season decision-making. This study aims to develop a stage-aware earliest possible corn yield mapping framework that balances early data availability, predictive accuracy, and spatial fidelity by integrating Sentinel-2 imagery, vegetation indices (VIs), and accumulated growing degree days (AGDD). Methods Corn yield data were collected from a commercial farm over three growing seasons (2018–2020). The final modeling dataset included 51,794 Sentinel-2 10 m aggregated yield samples across three seasons: 2018 ( n = 16400), 2019 ( n = 18534), and 2020 ( n = 16860). Sentinel-2 raw spectral bands and derived VIs were organized for V4, V6, R1, R5, and R6 growth stages based on AGDD- and DAP-defined corn growth-stage windows, also confirmed visually on-ground, allowing observations from different planting and harvest dates across the three growing seasons to be aligned by crop developmental stage rather than calendar date. A stage-wise Pearson correlation and frequency-based selection identified informative and non-redundant VI subsets across crop development. Four machine learning models: Random Forest (RF), XGBoost (XGB), k-Nearest Neighbors (kNN), and a Neural Network (NNET; multi-layer perceptron) were trained using 13 input configurations, including individual growth stages and multi-stage combinations capturing phenological progression. Models were tuned via randomized search, trained on 2018–2019 data, and independently validated on the 2020 season. Yield predictions were mapped directly at 10 m Sentinel-2-pixel resolution without spatial interpolation to preserve fine-scale variability. Results Model performance was strongly influenced by phenological stage selection. Among single-stage inputs, R1 was the earliest stage where reliable yield mapping could be availed (RF: R² = 0.56, RMSE = 29.50%). While combining V6 with R1 stage inputs substantially improved predictive performance (RF: R² = 0.70, RMSE = 24.13%) for the yield mapping at the R1 stage, where V6-stage signals provided complementary yield-related information. The full-season combination (V4 + V6 + R1 + R5 + R6) produced the highest accuracy (RF: R² = 0.72, RMSE = 23.28%) but would be less suitable for early in-season decision-making. Early- or late-stage-only inputs (V4, R5, R6) showed weaker and less stable cross-year performance. Among algorithms, RF consistently generalized best to the independent 2020 dataset and is recommended for operational use. XGB showed strong training performance but reduced cross-year stability, kNN yielded moderate accuracy, and NNET achieved accuracy comparable to RF while closely reproducing observed spatial patterns such as center-pivot effects and edge gradients. Direct 10 m mapping preserved yield heterogeneity and avoided smoothing artifacts common in interpolation-based approaches. Conclusion Stage-aware feature selection and phenology-informed input combinations are critical for balancing yield prediction timeliness and accuracy. For operational in-season yield mapping, the RF model using the V6 + R1 stage combination provides a practical and reliable solution, enabling early, accurate, and spatially detailed yield estimates with robust cross-year performance. This study presents a deployable framework for integrating satellite time series and weather data into conventional (non-sequential) machine learning models to support proactive, within-season decision-making in precision agriculture.
Why it matches plant phenotyping methods衛星画像・気象データと機械学習を統合し、作物の収量という明示的な植物形質を圃場内10 m解像度で推定する手法を開発・独立年で検証しており、フェノタイピング手法が中心である。
abstractThis study aims to develop a stage-aware earliest possible corn yield mapping framework that balances early data availability, predictive accuracy, and spatial fidelity by integrating Sentinel-2 imagery, vegetation indices (VIs), and accumulated growing degree days (AGDD).
Conventional breeding for ideotypes in target environments remains challenging due to genotype-by-environment interactions and the genetic complexity of key agronomic traits. Traditional multi-environment field trials are costly and time-consuming, limiting rapid genetic gain. These challenges highlight the need for digital tools to support rice breeding. However, two major approaches, genomic prediction (GP) and gene-based crop models (GBCMs), have distinct advantages. In this study, a dataset derived from a natural rice population comprising 210 genotypes, genotyped with about 650,000 markers, rice dry matter, and yield across three environments, was used to develop two genomic prediction models, genomic best linear unbiased prediction (GBLUP) and a convolutional neural network (CNN), together with a gene-based crop modeling framework. The effectiveness of these models in predicting rice traits and assisting in breeding selection was subsequently evaluated. Prediction results indicated that biomass and yield could be effectively predicted by all models, with Normalized Root Mean Square Error (NRMSE) values ranging from 10.60% to 18.59% and 9.93% to 18.19%, respectively. In terms of predictive accuracy, parameter-based crop models achieved the highest predictive accuracy, although it was confined to theoretical simulations. This was followed by the GBCM and CNN, whereas the GBLUP exhibited the lowest performance. Furthermore, GGE biplot analysis revealed the predictions of the GBCM aligned more closely with field observations than those of the CNN, emphasizing the potential of GBCM as a practical surrogate for digital breeding. These results provide valuable insights into modeling genotype-by-environment interactions and support the development of data-informed breeding strategies for future rice improvement.
Why it matches plant phenotyping methodsイネの乾物量・収量という植物形質を予測する複数の計算モデルを開発・比較評価しており、形質推定手法が研究の中心である。
abstractIn this study, a dataset derived from a natural rice population comprising 210 genotypes, genotyped with about 650,000 markers, rice dry matter, and yield across three environments, was used to develop two genomic prediction models, genomic best linear unbiased prediction (GBLUP) and a convolutional neural network (CNN), together with a gene-based crop modeling framework.
Field / plotLiDAR / point cloudWhole plant / canopy / plot / field2D/3D reconstructionYield / biomass estimationBiomass / plant weight
Reliable aboveground biomass (AGB) estimates for woody crops are essential for carbon accounting and for Measurement, Reporting and Verification (MRV) frameworks. However, it remains unclear how LiDAR modality and sampling geometry influence plot-scale and tree-scale AGB predictions in intensively managed Mediterranean orchards. In this study, we benchmarked four LiDAR modalities, namely open national airborne laser scanning from the Spanish National Aerial Orthophotography Plan (PNOA/ALS), a dedicated Riegl airborne laser scanner (ALS), unmanned laser scanning (ULS) and mobile laser scanning (MLS), across three woody-crop sites in Córdoba (southern Spain): IFAPA, Doña María, and Villaseca. Plot-level LiDAR metrics (mean height, 95th height percentile, maximum height, and canopy-cover proxies) were extracted from normalized point clouds and related to field AGB using Random Forest and XGBoost regression models, together with an ensemble predictor, under an 80/20 train–test split. In parallel, TreeQSM-based Quantitative Structure Models (QSMs) were evaluated as an independent tree-level three-dimensional reconstruction approach. XGBoost achieved the lowest errors at IFAPA (RMSE = 0.400 Mg ha−1; R2 = 0.994) and Villaseca (RMSE = 0.872 Mg ha−1; R2 = 0.995), whereas PNOA/ALS was competitive at Doña María (RMSE = 0.725 Mg ha−1; R2 = 0.994). TreeQSM closely matched the field inventory at the low-biomass IFAPA site but tended to overestimate biomass at Doña María and Villaseca, and only 28% of scanned trees yielded usable reconstructions. The results support the use of cross-platform LiDAR for orchard AGB and carbon mapping and identify the conditions under which open national LiDAR can enable scalable MRV of Mediterranean woody crops.
Why it matches plant phenotyping methodsLiDAR複数プラットフォームと3D再構成を比較・検証し、樹木・区画レベルの地上部バイオマスという植物形質を推定する手法が研究の中心である。
Accurate estimation of aboveground biomass (AGB) in dryland savanna woodlands is constrained by sparse field data, which has motivated widespread fusion of field plots with spaceborne LiDAR reference data from the Global Ecosystem Dynamics Investigation (GEDI). Here, we show that such fusion can substantially inflate apparent model accuracy when the two reference sources sample different spatial domains. Using 44 field plots from the Abu-Gadaf Natural Reserved Forest (AGNRF), Sudan, and 56 GEDI L4A footprints drawn from a 50 km buffer surrounding the reserve, we trained Random Forest (RF), Gradient Boosting (GB) and Classification and Regression Tree (CART) models on Sentinel-1, Sentinel-2, SRTM and Dynamic World predictors and evaluated them under 10-fold, 2 km block spatial cross-validation. The merged dataset yielded apparently moderate performance (RF: RMSE = 9.40 Mg ha−1, R2 = 0.33). However, GEDI-derived AGB was 2.1 times higher than field-measured AGB (18.71 vs. 8.89 Mg ha−1; Kolmogorov–Smirnov D = 0.53, p
Why it matches plant phenotyping methods圃場・GEDI・衛星データを統合して植物群落の地上部バイオマス（AGB）を推定し、空間交差検証でモデル精度と空間ドメイン不一致によるバイアスを評価している。植物形質の推定手法の検証が中心で、単なる生物学的実験の routine measurement ではない。
abstractAccurate estimation of aboveground biomass (AGB) in dryland savanna woodlands is constrained by sparse field data, which has motivated widespread fusion of field plots with spaceborne LiDAR reference data from the Global Ecosystem Dynamics Investigation (GEDI).
Sustainable wheat farming is challenging. Real-time information on crop health, disease transmission, and anticipated yields is essential for farmers. However, they frequently use slow, expensive, or non-communicative tools. This project develops a workable solution. There is no need for massive server farms because the entire system operates on a single graphics card. It incorporates images of wheat fields, Indian farming notes, greenhouse records, harvest statistics, and NASA meteorological data. Consider them as various “eyes” for crop photo analysis, and we tried several lightweight computer vision models. ConvNeXt-Tiny was slower but could operate on older equipment with 75% accuracy; EfficientNetB0 recognised wheat heads with 92% accuracy; and AgroMark, a hybrid solution that merged photo analysis with agricultural metadata (soil type, rainfall, increased to 87%, etc. Combining picture analysis with attention mechanisms (CBAM) allowed us to anticipate the amount of wheat that a field will yield based on these photo insights, and the results showed that our predictions were accurate, with an R 2 score of 0.97. Additionally, we developed a versatile detector that simultaneously detects disease, stress, head count, and pests. It is adjusted to deal with training data that is unbalanced (some diseases are common, while others are rare). As we packed everything into a 16-GB graphics card, we spent real time determining which strategies smaller training sets, removing weak features, and adjusting loss functions, work. We encounter real-world obstacles along the road, such as photographs from different locations not always match, mislabeled photographs from different locations not always match, mislabeled diseases, and neglected rare pests. Our step-by-step instructions, charts, and code are available.
Why it matches plant phenotyping methods小麦画像から病害・ストレス・穂数・収量などの植物形質・状態を推定するマルチモーダル手法を開発し、複数モデルの精度比較と実装上の検証を行っており、表現型取得・推定が研究の中心である。
abstractThis project develops a workable solution.
Reproduction assets foundThe paper builds its multimodal wheat phenotyping analysis on several explicitly cited public data assets: the Kaggle Wheat Plant Diseases image dataset (used for disease classification, Tables 2 and 9), the Global Wheat Head Detection dataset (used for head detection, Tables 1 and 6), FAOSTAT and India Open GovernmentDataset · publicAvailable online at: https://www.fao.org/faostat/ . FAOSTAT statistical database.Open asset ↗lines:1110-1162Plant phenotyping relevance match · UnverifiedOpenAlex · checked 15 Sept 2026
Accurate estimation of pasture biomass is essential for determining cattle stocking rates and grazing durations. The objective of this study was to comparatively evaluate five sensor-based systems for estimating aboveground Bermudagrass (Cynodon dactylon) biomass and identify the leading sensing approach for continued development and broader validation. The five systems included Structure-from-Motion (SfM), Ultrasound Sensor and Ski (US-Ski), Inertial Measurement Unit and Ski (IMU-Ski), Inertial Measurement Unit and Roller (IMU-Roller), and Depth Camera (DC). These systems were deployed on unmanned aerial and ground vehicles to measure crop height under identical field conditions. Regression models relating measured crop height to wet biomass yield (WBY) were developed as a common calibration framework for statistically comparing sensor performance. These empirical allometric equations were intended to support comparative benchmarking of the sensing systems and were not developed as final operational biomass prediction models for immediate field deployment. The influence of vegetation coverage on yield predictions generated by the crop height-based equations was also examined. The results indicated that the IMU-Ski system demonstrated the strongest overall comparative performance (R2 = 0.97; SeY = 1112 kg-wet/ha), followed by the DC system (R2 = 0.97; SeY = 1132 kg-wet/ha). Based on its overall benchmarking performance, including calibration accuracy, residual error and simplicity, the IMU-Ski system was identified as the leading sensing approach for continued development and broader validation among the five evaluated methods. The results also indicated that addition of vegetation coverage into the crop height-based regression models did not significantly improve prediction accuracy under the experimental conditions evaluated.
Why it matches plant phenotyping methods複数のセンサーシステムによる牧草バイオマス推定を比較・校正・ベンチマークしており、植物形質の取得法と技術性能の評価が研究の中心です。
abstractcomparatively evaluate five sensor-based systems for estimating aboveground Bermudagrass (Cynodon dactylon) biomass
Abstract In peanut ( Arachis hypogaea L.), plant stand establishment, seedling vigor, and canopy growth are key determinants of crop performance; yet traditional ground‐based assessment methods can be destructive, labor‐intensive, and limited in throughput. This study evaluated the potential of vegetation metrics derived from unmanned aerial vehicle (UAV)‐based red‐green‐blue (RGB) and multispectral (MS) imagery for high‐throughput, nondestructive assessment of plant stand establishment, seedling vigor, and light interception in peanut. Six runner‐type peanut cultivars were evaluated in 2024 and seven in 2025, with each cultivar represented by two seed size classes (small and large), to generate variation in these traits. Within‐row vegetation discontinuity‐based plant stand ratings for estimating plant stand count ( R 2 = 0.81–0.90), together with canopy coverage for assessing seedling biomass ( R 2 = 0.77–0.82) and light interception ( R 2 = 0.96–0.98), were the best‐performing vegetation metrics. These vegetation metrics provided similar or greater cultivar separation compared with ground‐based measurements. In contrast, several vegetation indices exhibited strong correlations with ground‐based measurements but provided inconsistent cultivar rankings and statistical groupings. MS imagery outperformed RGB imagery for plant stand and seedling biomass assessment. Overall, these results demonstrate that UAV‐derived canopy metrics provide reliable, high‐throughput tools for early‐ to mid‐season crop assessment and offer scalable alternatives to traditional ground‐based approaches for agronomic, crop physiological, and plant breeding research.
Why it matches plant phenotyping methodsUAV画像から植物体の出芽・苗勢・バイオマス・光 interception を推定する植 phenotyping 手法を開発・評価しており、取得指標の性能検証が研究の中心です。
abstractThis study evaluated the potential of vegetation metrics derived from unmanned aerial vehicle (UAV)‐based red‐green‐blue (RGB) and multispectral (MS) imagery for high‐throughput, nondestructive assessment of plant stand establishment, seedling vigor, and light interception in peanut.
Abstract Depth cameras measure the distance to a fruit's surface, whereas converting its silhouette into physical dimensions requires the depth of its center; corrections for this offset have so far been empirical, and therefore bound to the crop, sensor, and dataset they were fitted on. This paper derives the correction analytically. For a spherical fruit, integrating the surface-depth distribution over the visible hemisphere yields a closed-form sphere correction whose coefficient follows from sampling geometry, together with a theoretical justification of the median mask depth as the representative statistic. Combined with deep instance segmentation on RGB-D imagery of hydroponic melons, the empirically optimal coefficient coincided with the derived value, and the pipeline reached R 2 of 0.966 for fruit length (MAE 1.43 mm), 0.959 for width (1.84 mm), and 0.861 for end-to-end fresh weight (MAPE 4.6%). The analytical form made the measurement transferable. Applied unchanged to cylindrical mini-cucumbers, the pipeline held mm-level accuracy (width MAE 0.52 mm; fresh weight R 2 0.955 after coe cient refitting), with the correction's negligibility predicted in advance by an R / Z corollary; across active-stereo and time-of-flight cameras, the optimal coefficients proved non-interchangeable, identifying the coefficient as a physical parameter that absorbs geometry, sensor physics, and fruit shape. A field system that fuses and cross-verifies the two sensors, with an error-propagation confidence gate and parameterized grading logic, reproduced 2-3% fresh-weight error and 90.9% confirmed-judgment grading accuracy over four validation sessions in a commercial greenhouse unseen during development. Throughout, geometric components transferred unchanged while learned and regression components required recalibration - a boundary the model predicts and the system itself monitors.
Why it matches plant phenotyping methodsRGB-D画像と深度補正を用いて果実の寸法・重量を推定する手法を開発し、異なる果形・センサー・圃場で精度検証しており、植物表現型取得が中心である。
abstractThis paper derives the correction analytically.
Field / plotLiDAR / point cloudStem / branchYield / biomass estimationBiomass / plant weight
Integrating ground-based and aerial remote sensing for individual tree-level stem volume modeling remains underexplored in Mediterranean mixed forests, despite the growing need for cost-effective, automated forest inventory approaches. This study evaluated the combined use of Handheld Laser Scanning (HLS) and Unmanned Aerial Vehicle (UAV)-based Structure from Motion (SfM) photogrammetry for individual-tree stem volume modeling in a mixed stand in Castilla y León, Spain, dominated by Pinus halepensis, Pinus pinea, Quercus faginea, and Cupressus sempervirens. Two open-source HLS processing tools; the Forest Structural Complexity Tool (FSCT) and 3D Forest Inventory (3DFin), were compared for individual tree attribute extraction, with FSCT outperforming 3DFin across all species. Reference stem volumes were derived by applying species-specific Spanish National Forest Inventory (SNFI) allometric equations to FSCT-extracted diameter and height values. Random Forest models were then built using UAV-SfM crown metrics as predictors, testing two image overlap configurations: 80 × 80 F (80% front and side overlap) and 80 × 60 CF (80% front, 60% side, cross-flight). The 80 × 80 F configuration produced the best-performing model (R2 = 0.730), with 80 × 60 CF achieving comparable accuracy (R2 = 0.688), results confirmed by spatially independent leave-one-plot-out cross-validation (LOPO-CV R2 = 0.627 and 0.613, respectively). These results show that combining HLS and UAV-SfM through a predominantly open-source workflow offers a viable, reproducible approach to stem volume modeling in structurally complex Mediterranean mixed forests.
Why it matches plant phenotyping methodsHLSとUAV-SfMを用いて個体樹の直径・樹高から幹材積を推定する再現可能な計測・解析ワークフローを構築し、複数ツールと飛行条件を比較検証しているため、植物表現型取得が中心である。
abstractIntegrating ground-based and aerial remote sensing for individual tree-level stem volume modeling remains underexplored
Crop straw-to-grain ratio (SGR) estimation underpins regional straw resource assessment, yet national inventories rely on fixed coefficients that ignore structured variation across variety, environment, and phenotype. We introduce a Structured Multi-Kernel Heteroscedastic Gaussian Process (GP) framework that models SGR variation through three additive kernels heuristically motivated by the genotype–environment–phenotype (G+E+P) framework—capturing variety-associated variation, spatially structured variation, and environmental and management covariates—and employs an input-dependent noise model for prediction-specific uncertainty quantification. To prevent information leakage, target encoding and feature scaling are recomputed within each cross-validation fold. Evaluated via internal leave-one-out cross-validation on 80 rice samples (42 varieties, six Chinese provinces), the model achieves R2=0.541 with a prediction interval coverage probability of 0.95. Ablation identifies variety-associated variation as the largest contributor among the modeled factors (ΔR2=−0.024) and the multi-kernel design, by incorporating variety-specific information, substantially improves upon a covariate-only RBF GP (ΔR2=0.103). On point-prediction accuracy, Gradient Boosting achieves R2=0.58, slightly ahead of the Heteroscedastic GP (R2=0.54), underscoring that the primary advantage of the GP lies in its input-dependent uncertainty quantification. However, leave-one-county-out validation yields R2≈0 (with σ escalating to 24.4), confirming that the model does not yet generalize to unsampled counties; all reported performance is therefore internal to the nine sampled counties. The framework couples an agronomically motivated additive kernel structure with input-dependent uncertainty quantification, offering a path toward uncertainty-aware prediction from small field datasets.
Why it matches plant phenotyping methods作物のわら・穀粒比という植物関連形質を対象に、不確実性定量化を備えた予測手法を開発・検証しており、単なるルーチン測定ではなく計算的な形質推定が中心である。
abstractWe introduce a Structured Multi-Kernel Heteroscedastic Gaussian Process (GP) framework that models SGR variation
Semi-arid rangelands support livelihoods and key ecosystem services, yet sustainable management depends on accurate and scalable monitoring of herbaceous aboveground biomass (AGB). Field-based measurements are spatially limited, while satellite-derived vegetation indices often perform poorly in complex savanna systems such as the Kalahari. Using unoccupied aerial vehicle (UAV) structure-from-motion (SfM) photogrammetry, we evaluate the ability of fine-scale canopy height and spectral reflectance metrics to predict herbaceous biomass across a grazing intensity gradient. Canopy height consistently predicted AGB across all grazing levels, whereas normalised difference vegetation index (NDVI) effects were weak and grazing-dependent. The UAV-derived canopy height showed strong relationships with total herbaceous AGB, explaining up to 72% of observed variation, whereas vegetation greenness measured using NDVI showed limited predictive power. In contrast, predicting biomass of foraging importance proved challenging, with UAV-derived structural and spectral metrics explaining only a small proportion of variation. Together, these findings highlight the value of UAV-derived structural measurements over traditional spectral indices for fine-scale rangeland monitoring in semi-arid systems, while underscoring the limitations of current UAV-based spectral and structural metrics for assessing forage value across species and sites.
Why it matches plant phenotyping methodsUAV SfMフォトグラメトリから植物群落の canopy height を抽出し、地上部バイオマス予測性能を評価しており、植物形質取得法の技術的適用・検証が中心である。
abstractUsing unoccupied aerial vehicle (UAV) structure-from-motion (SfM) photogrammetry, we evaluate the ability of fine-scale canopy height and spectral reflectance metrics to predict herbaceous biomass across a grazing intensity gradient.
Semi-arid rangelands support livelihoods and key ecosystem services, yet sustainable management depends on accurate and scalable monitoring of herbaceous aboveground biomass (AGB). Field-based measurements are spatially limited, while satellite-derived vegetation indices often perform poorly in complex savanna systems such as the Kalahari. Using unoccupied aerial vehicle (UAV) structure-from-motion (SfM) photogrammetry, we evaluate the ability of fine-scale canopy height and spectral reflectance metrics to predict herbaceous biomass across a grazing intensity gradient. Canopy height consistently predicted AGB across all grazing levels, whereas normalised difference vegetation index (NDVI) effects were weak and grazing-dependent. The UAV-derived canopy height showed strong relationships with total herbaceous AGB, explaining up to 72% of observed variation, whereas vegetation greenness measured using NDVI showed limited predictive power. In contrast, predicting biomass of foraging importance proved challenging, with UAV-derived structural and spectral metrics explaining only a small proportion of variation. Together, these findings highlight the value of UAV-derived structural measurements over traditional spectral indices for fine-scale rangeland monitoring in semi-arid systems, while underscoring the limitations of current UAV-based spectral and structural metrics for assessing forage value across species and sites.
Why it matches plant phenotyping methodsUAV-SfMによるキャノピー高とスペクトル指標から植物群落のバイオマスを推定し、手法の予測性能を比較評価しており、植物形質取得が研究の中心です。
abstractUsing unoccupied aerial vehicle (UAV) structure-from-motion (SfM) photogrammetry, we evaluate the ability of fine-scale canopy height and spectral reflectance metrics to predict herbaceous biomass across a grazing intensity gradient.
Semi-arid rangelands support livelihoods and key ecosystem services, yet sustainable management depends on accurate and scalable monitoring of herbaceous aboveground biomass (AGB). Field-based measurements are spatially limited, while satellite-derived vegetation indices often perform poorly in complex savanna systems such as the Kalahari. Using unoccupied aerial vehicle (UAV) structure-from-motion (SfM) photogrammetry, we evaluate the ability of fine-scale canopy height and spectral reflectance metrics to predict herbaceous biomass across a grazing intensity gradient. Canopy height consistently predicted AGB across all grazing levels, whereas normalised difference vegetation index (NDVI) effects were weak and grazing-dependent. The UAV-derived canopy height showed strong relationships with total herbaceous AGB, explaining up to 72% of observed variation, whereas vegetation greenness measured using NDVI showed limited predictive power. In contrast, predicting biomass of foraging importance proved challenging, with UAV-derived structural and spectral metrics explaining only a small proportion of variation. Together, these findings highlight the value of UAV-derived structural measurements over traditional spectral indices for fine-scale rangeland monitoring in semi-arid systems, while underscoring the limitations of current UAV-based spectral and structural metrics for assessing forage value across species and sites.
Why it matches plant phenotyping methodsUAV-SfMによるキャノピー高とスペクトル指標を用いた植物バイオマス推定を比較・評価しており、植物形質の取得・推定手法が研究の中心である。
abstractUsing unoccupied aerial vehicle (UAV) structure-from-motion (SfM) photogrammetry, we evaluate the ability of fine-scale canopy height and spectral reflectance metrics to predict herbaceous biomass across a grazing intensity gradient.
Ground-level ozone (O 3 ) adversely affects rice physiology and is associated with yield reductions. This study developed a high-resolution assessment framework integrating multi-source satellite remote sensing with econometric methods to quantify the impacts of O 3 on rice production in China's primary rice-growing region-the Middle and Lower Reaches of the Yangtze River (MLYR)-from 2019 to 2023. We fused Sentinel-5P TROPOMI total ozone column (TOC) data, a harmonized multi-satellite solar-induced chlorophyll fluorescence (SIF) product (LHSIF), high-precision rice distribution maps, and ERA5 meteorological reanalysis data. In addition to SIF, we examined multiple vegetation indicators (chlorophyll content, leaf area index, and vegetation indices) to capture broad physiological responses. A bidirectional fixed-effects panel model was employed to control for spatiotemporal confounders, revealing a significant inhibitory effect of O 3 on photosynthesis (β = -1.334 × 10 -5 , p 3 concentrations would increase regional SIF by 36.36%, while a commensurate 10% reduction in annual exposure could elevate rice yields by approximately 8.4%. This spaceborne remote sensing approach provides a robust and transferable methodology for the precise regional monitoring of ozone stress and for informing targeted mitigation strategies to safeguard crop productivity.
Why it matches plant phenotyping methods衛星リモートセンシングによるSIF等の植物生理指標を用いてイネのオゾンストレスを地域スケールで推定する評価フレームワークが研究の中心であり、単なる生物学的実験の routine 測定ではない。
abstractThis study developed a high-resolution assessment framework integrating multi-source satellite remote sensing with econometric methods to quantify the impacts of O 3 on rice production
Phenotyping high-biomass perennial crops is laborious and the rate of genetic gain in conventional perennial crop breeding programs is typically low. So, it is especially important to identify methods that produce efficiency gains in the breeding process. Miscanthus is a C4 perennial grass with favorable characteristics for producing biomass as a feedstock for biofuels and diverse bio-based products. Increasing biomass yield will increase profitability and environmental benefits, so it is a key target for Miscanthus breeding. In addition, the identification of well-adapted genotypes across a wide range of environmental conditions requires the establishment of multi-environment trials (METs). Sparse testing is a genomic prediction-based strategy that reduces the phenotyping costs in METs by selecting a subset of genotypes to evaluate in a subset of environments and then predicts the performance of the unobserved genotype-environment combinations. A Miscanthus sacchariflorus (MSA) population comprising 336 genotypes observed across three environments was analyzed implementing sparse testing designs. Three prediction models considering main effects (environments, genotypes, genomic) and interaction effects (genotype-by-environment; G×E interaction) were implemented for forecasting dry biomass yield (YDY), total culm (TCM), average internode length (AIL), and culm node number (CNN). Multiple calibration sets based on different compositions and sizes were considered to evaluate performance in terms of the predictive ability (PA) and the mean square error (MSE) for a fixed testing set size. The training set size ranged from 52 to 112 to predict a fixed set of 224 unobserved genotypes across all three environments. The results showed that the model accounting for G×E interaction consistently presented the highest PA and the lowest MSE: for CNN (PA: ~0.77, MSE: ~0.5) and YDY (PA: ~0.70, MSE: ~1.3) while for TCM and AIL these ranged from ~0.28 to 0.41 and ~1.3 to 4.3, respectively. Overall, varying training sets and allocation strategies did not affect PA and MSE, with 52 non-overlapping and 0 overlapping genotypes per environment as the optimal cost-effective allocation framework. This suggests that implementing sparse testing designs could significantly reduce phenotyping costs by fivefold, without compromising PA in breeding programs for perennial crops such as Miscanthus .
Why it matches plant phenotyping methodsスパーステスト設計とゲノム予測を用いて、複数環境での植物形質予測と表現型測定コスト削減を評価しており、表現型取得・予測手法が研究の中心である。
abstractSparse testing is a genomic prediction-based strategy that reduces the phenotyping costs in METs by selecting a subset of genotypes to evaluate in a subset of environments and then predicts the performance of the unobserved genotype-environment combinations.
Reproduction assets foundThe paper's data availability statement points to a public figshare deposit (DOI 10.6084/m9.figshare.31796794) containing the datasets analyzed in this Miscanthus sparse-testing genomic prediction study, including the phenotypic and genotypic data used for the models.Dataset · publicThe datasets analyzed for this study can be found in the figshare repository at https://doi.org/10.6084/m9.figshare.31796794 .Open asset ↗figshare · 10.6084/m9.figshare.31796794lines:603-621Plant phenotyping relevance match · UnverifiedCrossref · OpenAlex · checked 14 Sept 2026
Spike count and spatial arrangement are among the strongest determinants of grain yield in wheat, yet reliable spike-level phenotyping under field conditions remains challenging. Field-acquired images are often affected by occlusion, heterogeneous illumination, and dense canopy overlap. In addition to these visual complexities, the effort required to generate large-scale instance-level annotations makes it difficult to build the extensive labeled datasets typically needed for robust segmentation models. This paper addresses both problems. The core methodological contribution is a semi-automated iterative annotation workflow: a YOLOv11x-seg model trained on a small manually annotated set is applied to unlabeled field images, and its predictions, after post-processing to remove duplicated, fragmented, and merged detections, are incorporated back into training. To prevent augmentation from distorting the training distribution, we introduce a distribution-aware augmentation strategy guided by Fréchet Inception Distance (FID), which retains only those augmented samples that remain within an acceptable distance from the original data distribution. Together, these components allowed us to build an effective training set from 3,899 high-resolution RGB images (4000 × 3000 pixels) of durum wheat collected at the CREA Research Centre for Cereal and Industrial Crops, with substantially reduced manual annotation effort. On the independent test set(242 images), the final YOLOv11x-seg model (M5 model) achieved a mask-level precision of 86.73%, recall of 83.02%, F1-score of 84.83%, mAP@50 of 89.42%, and mAP@50:95 of 60.51%. Spike masks were used to derive image-based traits including spike count, spike density, canopy coverage, spike area, spatial distribution, and vegetation indices. Their relationships with measured grain yield were explored through statistical analysis and machine-learning-based yield estimation.Both statistical and machine-learning analyses demonstrated that image-derived spike traits provided meaningful information for grain yield estimation, with canopy coverage showing the strongest positive association with yield. Using repeated nested cross-validation with out-of-fold (OOF) predictions, XGBoost achieved the highest yield estimation performance ( R OOF 2 = 0.312 , RMSE = 106.61 g/plot), supporting the potential of near-image phenotyping for late-stage yield estimation in wheat. These results show that semi-automated iterative annotation can enable practical wheat spike segmentation and image-based phenotyping under realistic open-field conditions. While grain yield estimation should be interpreted within the context of the experimental setting, the proposed framework highlights the value of image-derived spike traits for late-stage phenotyping and yield assessment in breeding experiments rather than for early-season yield forecasting.
Why it matches plant phenotyping methods半自動アノテーション、YOLOv11x-segによる小麦穂の画像セグメンテーション、分布認識型データ拡張、形質抽出と検証が中心的な方法論的貢献である。
abstractThe core methodological contribution is a semi-automated iterative annotation workflow
Finger millet is an important cereal crop widely cultivated worldwide for food and fodder. Breeding programs aim to select genotypes with desirable architectural traits to develop new varieties with higher yields. In this effort, accurate high-throughput plant phenotyping is essential for accelerating crop improvement. To overcome the time-consuming and labor-intensive process of manual measurements, this study presents a comprehensive 3D imaging pipeline that leverages neural radiance fields (NeRF), 3D gaussian splatting (3DGS), and its advanced extensions (e.g., Feature 3DGS and Gaussian Grouping) to reconstruct, segment, and analyze finger millet yield component traits using multi-view 2D images. First, multiple-view RGB images of a single finger millet plant were captured, and COLMAP was then utilized to estimate the camera poses of the images and reconstruct the sparse point cloud, followed by advanced 3D reconstruction through 3DGS and NeRF. Second, feature 3DGS and gaussian grouping models were used to generate the 3D gaussian representation of finger millet panicles. This single-process framework enabled the generation of high-fidelity 3D point clouds and semantic feature fields without the need for expensive depth sensors or manual annotations. Our results demonstrated the effectiveness of these models in capturing morphological variations across different panicle phenotypes, including compact versus open panicle architectures. In addition, the 3D point clouds of the panicles were utilized to extract structural traits for yield prediction, achieving biologically meaningful correlations with grain productivity. This work highlights the potential of 3DGS-based phenotyping pipelines as a low-cost, near real-time, photorealistic solution for trait quantification, segmentation, and yield estimation in real-world agricultural settings.
Why it matches plant phenotyping methods3D画像再構成・セグメンテーション・形質抽出を統合した植物フェノタイピング手法の開発が中心であり、収量関連形質の定量と予測まで技術的に評価している。
abstractthis study presents a comprehensive 3D imaging pipeline that leverages neural radiance fields (NeRF), 3D gaussian splatting (3DGS), and its advanced extensions (e.g., Feature 3DGS and Gaussian Grouping) to reconstruct, segment, and analyze finger millet yield component traits using multi-view 2D images.
• Development of yellow color index (YCI) for yield estimation at flowering stage • Development of web-based interface (YCPM-UAV) for canola yield prediction using UAVs • Global application capability for UAVs datasets to predict canola yield using YCPM-UAV • Multi-sensor and multi-spectrum data fusion to find most suited indices for canola • Multiple and stepwise regression analysis for selection of most influencing VIs Canola ( Brassica napus L.) is a globally significant oilseed crop, yet accurate yield estimation remains challenging due to the complex and unique nature of the crop, especially at the flowering stage. Traditional field-based yield estimation methods are labor-intensive, time-consuming, and destructive, necessitating innovative approaches for early and non-destructive yield prediction. The main objective of the study is to develop a novel web-based platform, YCPM-UAV (Yellow Color Prediction Model using Unmanned Aerial Vehicles), for early and accurate canola yield estimation using high-resolution multi-sensor datasets acquired through low-altitude UAVs (LA-UAVs). To achieve this objective, a comprehensive two-year field study (2022-2024) was conducted across ten farmers’ fields in different geographical locations. Multisensor data (RGB, multispectral, and thermal) were acquired using UAVs at seven growth stages. Several vegetation indices (VIs), yellow color-based indices, and a thermal index were calculated. Linear, multiple, and stepwise regression analyses were performed to evaluate relationships of remote sensing indices with ground-truth yield data collected from 1200 sampling points. Multiple and stepwise regression analyses indicated that the newly developed Yellow Color Index (YCI) exhibited the strongest correlation with actual canola yield at the flowering stage across both years (Year 1: R 2 = 0.84, RMSE = 39.30 g m⁻²; Year 2: R² = 0.88, RMSE = 31.57 g m⁻²). Based on proposed predictive modeling, the YCPM-UAV web interface was developed, featuring automated data processing and spatial analysis with a testing accuracy of 88%. The YCPM-UAV platform provides farmers, researchers, and policymakers with a timely, user-friendly, and actionable decision-support tool for canola yield estimation at the field scale, contributing to improved crop management and food security. Future studies should incorporate additional canola varieties, irrigated and non-irrigated fields, and deep learning algorithms to further improve model robustness.
Why it matches plant phenotyping methodsUAVマルチセンサー画像からカノーラ収量を推定する指標・回帰モデル・Webプラットフォームを開発し、複数年データで検証しており、植物形質取得・推定が中心である。
titleDevelopment of web-based YCPM-UAV interface for early yield prediction of canola crop using UAV multi-sensor data
Plant height (PH) and aboveground biomass (AGB) are critical agronomic traits that determine the yield potential of maize ( Zea mays L . ). However, the application of genomic selection (GS) and genome-wide association studies (GWAS) in maize breeding is often hindered by the limitations of phenotypic data collection, which is typically characterized by low throughput and inadequate accuracy. To address this challenge, we employed an unmanned aerial vehicle (UAV) equipped with LiDAR and RGB cameras for high-throughput assessment of pH and AGB in a panel of 817 maize hybrids derived from 364 inbred lines over two growing seasons. Our results demonstrated that the integration of UAV-derived LiDAR point clouds with crop surface models (CSMs) enabled robust estimation of pH across multiple years ( R 2 > 0.90). Furthermore, a three-dimensional AGB estimation model was developed using UAV-derived PH and canopy coverage (CC), achieving high estimation accuracy ( R 2 > 0.83). Subsequently, the UAV-derived PH and AGB were utilized for GS and GWAS analyses. Replicated 10-fold cross-validation showed that the mean predictability was 0.504 for PH and 0.402 for AGB across eight commonly used GS models. Moreover, of the 66,066 potential crosses derived from the 364 inbred lines, the top 200 crosses selected for AGB showed up to twice the AGB of the bottom 200 crosses. Field validation demonstrated that the mean ear weight (EW) in the AGB top group was 39.0% higher than that in the bottom group. A total of 16 and 11 significant SNPs were identified by at least two GWAS methods for PH and AGB, respectively. Based on these SNPs, 81 candidate genes were functionally annotated, six of which were simultaneously associated with both traits. The candidate gene association analysis suggested that variations in the promoter region of ZmFLA9 may affect both traits. Overall, our study highlights the potential of UAV-based high-throughput phenotyping to accelerate maize genomic breeding by enabling rapid, precise, and large-scale trait assessment.
Why it matches plant phenotyping methodsUAVのLiDAR・RGBデータから草丈と地上部バイオマスを推定する高スループット表現型測定モデルを開発・検証しており、フェノタイピング手法が研究の中心です。
abstractwe employed an unmanned aerial vehicle (UAV) equipped with LiDAR and RGB cameras for high-throughput assessment of pH and AGB
Cover crops offer essential agroecosystem benefits, including reduced soil erosion, weed suppression, and improved soil health. Aboveground biomass (AGB) is a key indicator of these benefits; however, field-based quantification is often limited, which hinders effective cover crop management decisions. This study integrated unmanned aerial vehicle (UAV)-based multispectral imagery with machine learning (ML) models to estimate AGB in cover crops across two water-limited regions of Texas. Ground-truth and imagery data were collected over three years (2023–2025) for winter rye ( Secale cereale L.) in Lamesa and two years (2023–2024) for winter wheat ( Triticum aestivum L.) in Chillicothe under varying irrigation regimes. Five ML algorithms, random forest, support vector regression, extreme gradient boosting, partial least squares regression (PLSR), and artificial neural network (ANN), were evaluated across four individual and eleven feature fusion datasets. The ANN model consistently achieved the highest predictive accuracy, particularly when vegetation indices were combined with structural features (R² = 0.87, RMSE = 9.08 g m - ²), while PLSR showed the weakest performance. Grouped validation (leave-one-year-out, leave-one-species-out, and leave-one-treatment-out) revealed reduced model performance compared to random (70/30) splitting of pooled data, yet the ANN maintained moderate predictive ability, indicating reasonable generalizability across years, species, and management conditions. Shapley additive explanations (SHAP) revealed key predictors in the ANN model, including plant height, chlorophyll vegetation index, chlorophyll sensitive index, blue band reflectance, modified chlorophyll absorption in reflectance index, dissimilarity, correlation, and enhanced green vegetation index. These findings demonstrate the effectiveness of UAV-ML integration for accurate AGB estimation and highlight the potential for scalable, data-driven cover crop monitoring in water-limited environments and beyond.
Why it matches plant phenotyping methodsUAVマルチスペクトル画像と機械学習を統合し、植物の地上部バイオマスを推定する手法を開発・比較検証しており、表現型取得が研究の中心である。
abstractThis study integrated unmanned aerial vehicle (UAV)-based multispectral imagery with machine learning (ML) models to estimate AGB in cover crops across two water-limited regions of Texas.
Shoot apical meristem (SAM) homeostasis integrates environmental and genetic cues to regulate growth dynamics that drive biomass accumulation and crop yield; however, no robust, non-destructive, quantitative proxy has been established for modeling or monitoring SAM-homeostasis-associated dynamics. Here, we developed a novel robot-based 3D imaging system and a custom pot-chamber gas exchange system to non-destructively measure plant occupation volume (POV) and whole-plant photosynthetic rate in wild-type Arabidopsis plants and nine mutants with disrupted SAM homeostasis. We demonstrate that POV robustly captures 3D plant architecture, whereas whole-plant photosynthetic rate serves as a superior proxy for optimal growth dynamics and final biomass associated with SAM homeostasis, outperforming conventional traits such as leaf number, leaf size, total leaf area, and rosette diameter. The strong positive correlations among POV, whole plant photosynthesis, and biomass accumulation establish a powerful new framework for quantitative studies of SAM homeostasis and data-driven evaluation of plant architecture.
Why it matches plant phenotyping methodsロボット3D画像とカスタムガス交換による非破壊的な植物形態・光合成表現型測定系を開発し、従来形質との比較検証も行っており、方法が研究の中心である。
abstractwe developed a novel robot-based 3D imaging system and a custom pot-chamber gas exchange system to non-destructively measure plant occupation volume (POV) and whole-plant photosynthetic rate
Reproduction assets foundThe paper's authors explicitly state that the Python source code for whole-plant leaf-area segmentation, 3D point cloud processing, POV calculation, and Mask3D-based segmentation is publicly available on GitHub at https://github.com/songqingfeng/AtPOVcalculator. This is a paper-specific, public, actionable analysis/PhDCode · publicThe Python source code for whole-plant leaf-area segmentation and calculation is publicly available on GitHub ( https://github.com/songqingfeng/AtPOVcalculator ).Open asset ↗songqingfeng/AtPOVcalculatorlines:224-233Plant phenotyping relevance match · UnverifiedCrossref · checked 15 Sept 2026
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.
Accurate prediction of foxtail millet yield is essential for effective field management and high-throughput breeding. Despite advances in UAV-based yield prediction for major crops, existing studies predominantly rely on single-temporal features (SFs) extracted at noon, overlooking significant diurnal dynamic signals that characterize crop responses to water stress. To address this research gap, we propose a novel approach utilizing diurnal cross-temporal features (CFs) derived from UAV-based multispectral and thermal imagery to enhance yield prediction accuracy under different irrigation regimes. During the flowering and grain-filling stages, UAV images were acquired across eight time slots (T1–T8) within a single day to capture the complete diurnal trajectory of canopy physiological responses. SFs were extracted at each time slot, and CFs were derived through summation, averaging, and range operations across multiple slots. A systematic four-step workflow was developed to determine the optimal UAV flight frequency and timing by balancing prediction accuracy with operational costs. Three ensemble learning algorithms (Random Forest (RF), Adaptive Boosting (AdaBoost), and Extreme Gradient Boosting (XGBoost)) were evaluated using multiple feature sets incorporating SFs, CFs, and their integration. Results demonstrated that CFs more comprehensively captured dynamic crop responses to water stress than SFs. Canopy features from afternoon combinations generally exhibited stronger yield correlations than morning combinations. The [T5, T8] combination was identified as optimal, providing a practical balance between prediction accuracy and operational cost. Model comparison revealed that RF exhibited greater robustness across different water treatments, whereas AdaBoost achieved higher accuracy on the test set. Feature importance analysis confirmed the dominance of CFs, with ∑VSWI ranking first across both models and growth stages. This study provides a systematic framework for utilizing diurnal dynamic signals in crop yield prediction, offering new methodological insights for precision agriculture and high-throughput phenotyping of foxtail millet and other dryland crops.
Why it matches plant phenotyping methodsUAVマルチスペクトル・熱画像から作物特徴量を抽出し、収量という植物形質を推定する手法と、撮影頻度・時刻を最適化するワークフローが研究の中心であるため。
abstractwe propose a novel approach utilizing diurnal cross-temporal features (CFs) derived from UAV-based multispectral and thermal imagery to enhance yield prediction accuracy
Citrus fruit cracking causes substantial yield and economic losses, yet its relationship with plant water status (PWS) and irrigation management remains insufficiently characterized. Unlike previous UAV-based irrigation studies that focused on water-stress detection or yield estimation, this study introduces a dynamic, physiology-based framework that links temporal PWS trajectories during key phenological stages to fruit-cracking risk at the individual-tree scale. UAV-based multispectral, thermal, and LiDAR data, combined with field physiological measurements and machine-learning models, were evaluated in an irrigation management experiment in an ‘Ori’ mandarin orchard (Israel) across three contrasting growing seasons (2023–2025). Several irrigation treatments with different irrigation timings and water inputs were applied during the growing season to evaluate their effects on temporal PWS dynamics and fruit cracking. Trunk growth (TG), stem water potential (SWP), stomatal conductance (SC), and plant area index (PAI) were measured throughout the two seasons and estimated using Random Forest models (R 2 > 0.783). These indicators were subsequently used to predict yield and fruit cracking with high accuracy (yield: R² = 0.896; cracking: R² = 0.845). Cracking was lowest in 2023 (∼3%), with ∼25% lower irrigation, suggesting reduced irrigation may reduce cracking risk. Higher cracking in 2024 (∼14%, vs ∼8% in 2025) coincided with intense heat events. Mid-season SWP and SC were strongly associated with yield formation and cracking patterns. These findings demonstrate that monitoring temporal PWS dynamics can support precision irrigation management by identifying high-risk zones and enabling irrigation strategies that stabilize PWS, reduce the incidence of cracking, and improve yield under variable climatic conditions.
Why it matches plant phenotyping methodsUAVマルチセンサーと機械学習により、樹体水分状態などの植物形質を推定し、収量・果実裂果を予測する技術的枠組みが研究の中心である。
abstractthis study introduces a dynamic, physiology-based framework that links temporal PWS trajectories during key phenological stages to fruit-cracking risk at the individual-tree scale.
Accurate estimation of forest aboveground biomass (AGB) is critical for carbon accounting, ecosystem monitoring, and climate change mitigation. While remote sensing offers broad spatial coverage, standard deterministic models often struggle to capture the complex relationship between spectral information and structural forest attributes, and they frequently lack reliable quantification of uncertainty. This study presents a novel probabilistic framework that integrates convolutional neural networks (CNNs) and transformer architectures for AGB estimation using a multi-sensor fusion of Sentinel-1/2 imagery. The framework employs a customized, adaptive version of the Swin Transformer-reconfigured specifically for regression tasks and streamlined to a single-stage architecture-and implements a Gaussian Mixture Modeling (GMM) approach to ensemble model outputs. This framework enables the decomposition of predictive uncertainty into epistemic (model-related) and aleatoric (data-inherent) components. Evaluated across heterogeneous forest regions in Montana and Idaho, the CNN-transformer integration achieved superior performance, with R 2 =0.83, RMSE=19.16 Mg/ha, and MAE=13.37 Mg/ha, outperforming standalone CNNs (R 2 =0.81) and vision transformers (R 2 =0.80). Transfer learning and fine-tuning experiments demonstrated high model robustness, improving prediction accuracy in independent test regions by 39% in RMSE. Spatially explicit analysis revealed that while CNNs provide stable local feature extraction, the Swin Transformer’s self-attention mechanism significantly mitigates errors on topographically complex slopes by leveraging non-local spectral cues to compensate for shadowing and geometric distortions. The results highlight that an ensemble approach leveraging the complementary strengths of CNNs and customized transformers provides the transparency and precision required for operational carbon monitoring and high-resolution, trustworthy biomass mapping.
Why it matches plant phenotyping methods森林の地上部バイオマスという植物群落形質を、マルチセンサー画像とCNN・Transformer・GMMで推定する手法を開発し、比較評価と独立地域での検証を行っており、形質推定法が研究の中心である。
abstractThis study presents a novel probabilistic framework that integrates convolutional neural networks (CNNs) and transformer architectures for AGB estimation using a multi-sensor fusion of Sentinel-1/2 imagery.
Accurate and timely crop yield prediction and forecasting are important for improving agricultural productivity and supporting informed management decisions. In this study, we developed and evaluated a framework for estimating in-season potato yield at the field scale using Sentinel-2 satellite time series. A Grouped TreeSHAP Stability Selection (GTSS) was first applied to identify a compact, phenology-aware subset of spectral bands and vegetation indices, thereby reducing redundancy and mitigating overfitting in small-data settings. Two deep learning architectures tailored for limited training data were then introduced: LiteTemporalConv, a lightweight temporal convolutional network, and MS-ConvBiGRU-Attn, a hybrid encoder combining multi-scale convolutions, bidirectional GRUs, and an attention mechanism. Both models were benchmarked against widely used machine learning methods, including Random Forest, Support Vector Machine, Extreme Gradient Boost, Partial Least Squares, as well as standard deep learning baselines (CNN and GRU). Results showed that the proposed models outperformed both machine learning and conventional deep learning baselines, with LiteTemporalConv achieving the highest accuracy under 10-fold cross-validation (R² = 0.84; RMSE = 3.18 t ha⁻¹; rRMSE = 6.36%) and MS-ConvBiGRU-Attn yielding similarly strong performance (R² = 0.82; RMSE = 3.53 t ha⁻¹; rRMSE = 7.03%). By comparison, the best baseline, XGB, achieved an R² of 0.79 with an rRMSE of 9.8%. The two best-performing models were further evaluated on an independent spatial dataset to assess their generalization beyond the training region. In an additional experiment, both deep learning models trained on mid-season observations showed predictive stability for late-season yield estimation. Overall, the results highlight the importance of targeted feature selection and lightweight encoders for yield modeling in data-scarce conditions.
Why it matches plant phenotyping methodsSentinel-2時系列からジャガイモ収量を推定する特徴選択・深層学習手法を開発し、複数モデルとのベンチマークと独立データでの検証を行っており、植物形質取得が中心である。
abstractwe developed and evaluated a framework for estimating in-season potato yield at the field scale using Sentinel-2 satellite time series
In-season fine-scale (i.e., within-field experiment plot scale) crop grain yield (GY) prediction is critical for optimizing inputs, minimizing environmental impacts, and supporting sustainable food production. Traditional approaches, such as field surveys, are often costly and inefficient over large areas. As an alternative, remote sensing combined with crop simulation models (CSMs) has been increasingly applied for in-season GY prediction. This study investigates the potential of integrating Uncrewed Aircraft Systems (UAS)-based remote sensing data, deep learning, and CSMs to predict maize and soybean GY using a data assimilation approach. UAS multispectral imagery was collected, along with field-measured maize above-ground biomass (AGB) and soybean leaf area index (LAI) during the 2022 and 2023 growing seasons at experimental fields in Brookings, South Dakota. Maize AGB was measured at two growth stages, while soybean LAI was collected across four stages. One-dimensional convolutional neural networks (1D-CNNs) were used to estimate maize AGB and soybean LAI from canopy spectral, textural, and structural features derived from UAS imagery. These UAS and deep learning–derived crop traits were assimilated into DSSAT-Maize and DSSAT-Soybean models to optimize parameters, and the optimized models were subsequently used to predict GY. For maize, the DSSAT-Maize model achieved an R² of 0.62, an RMSE of 717.8 kg ha⁻¹, and an rRMSE of 6.7% for GY prediction. For soybean, the DSSAT-Soybean model achieved an R² of 0.81, an RMSE of 207.3 kg ha⁻¹, and an rRMSE of 4.9%. Overall, these results highlight the potential of combining high-resolution UAS data and deep learning–derived crop traits within a CSM framework through data assimilation, enabling fine-scale, in-season yield predictions and supporting precise agricultural management.
Why it matches plant phenotyping methodsUAS画像と深層学習により、作物のAGBおよびLAIという植物形質を推定する取得・解析手法が研究の中心であり、作物モデルへの同化と性能評価も行っている。
abstractOne-dimensional convolutional neural networks (1D-CNNs) were used to estimate maize AGB and soybean LAI from canopy spectral, textural, and structural features derived from UAS imagery.
• DL model trained on MS data achieved the highest accuracy with an R 2 of 75.29% • Linear Regression Coefficient-Based feature selection with SVM and PCA with Linear Regression significantly improved model performance. • NIR and red-edge bands in the MS dataset consistently outperformed the RGB dataset • More represented rice variety (Sona) achieved a strong R 2 of 80.21% on MS data Accurate crop yield prediction is critical for agricultural planning, food security assessment, and farm-level decision-making. In Nepal, however, rice yield estimation is still predominantly based on traditional approaches, where local agricultural extension offices collect field-level observations that are subsequently aggregated at district, provincial, and national scales, often limiting spatial detail and timeliness. This study aims to develop a field-scale rice yield estimation framework by integrating Unmanned Aerial Vehicle (UAV)-derived remote sensing data with machine learning (ML) and deep learning (DL) techniques. High-resolution multispectral (MS) and RGB UAV imagery were used to evaluate the influence of Vegetation Indices (VIs), including HUE and VNDVI from RGB data and RGBVI and Simple Ratio (SR) from MS data, along with plant characteristics and farm management practices (e.g., application of Zyme and Zinc Potash) on rice yield. The predictive performance of Support Vector Machines (SVM), Linear Regression (LR), Decision Trees (DT), Random Forests (RF), and deep neural network models were systematically assessed. Data preprocessing included feature selection based on importance ranking, Yeo–Johnson power transformation, and Principal Component Analysis (PCA) to improve model stability and performance. Among conventional ML models, LR combined with PCA achieved a coefficient of determination (R²) of 69.09% using MS data, while SVM yielded the best performance using RGB data (R² = 68.27%). Overall, deep neural networks outperformed other models, achieving R² values of 75.29% and 64.60% for MS and RGB data, respectively. Model performance varied notably across rice varieties; the Sona variety (n = 127) achieved the highest coefficient of determination (R² = 80.21% for MS and 76.34% for RGB), whereas varieties with fewer samples exhibited lower predictive performance. Results further indicate that ranking features by importance, rather than eliminating them, enhances predictive accuracy, particularly when using LR-derived feature importance, which proved critical for improving the performance of both LR and SVM models.
Why it matches plant phenotyping methodsUAV画像からイネ収量を推定する手法・フレームワークの開発と、複数の機械学習モデルの系統的評価が研究の中心であり、単なる収量のルーチン測定ではない。
abstractThis study aims to develop a field-scale rice yield estimation framework by integrating Unmanned Aerial Vehicle (UAV)-derived remote sensing data with machine learning (ML) and deep learning (DL) techniques.
Accurate and timely crop yield estimation is fundamental for global food security, agricultural policy, and farm management. The Copernicus Sentinel-2 constellation has catalyzed a paradigm shift in Earth observation for agriculture, enabling field and sub-field scale monitoring. This review synthesizes recent advances in crop yield estimation that leverage Sentinel-2 data. A dominant theme is the transition from regional-scale to high-resolution field-level assessments, driven by three approaches: (i) empirical models using vegetation indices coupled with machine and deep learning (e.g., Random Forest, Convolutional Neural Networks); (ii) integration of process-based crop growth models (e.g., WOFOST, SAFY) through data assimilation of Sentinel-2 derived biophysical variables such as Leaf Area Index; and (iii) data fusion of Sentinel-2 with Sentinel-1 Synthetic Aperture Radar to overcome cloud cover. The synthesis shows that Sentinel-2-based frameworks can explain a large fraction of within-field yield variability, while performance remains constrained by limited ground-truth data, cloud gaps, and model transferability. Looking ahead, knowledge-guided models, self-supervised foundation-model pre-training, lightweight edge workflows, improved ground observations, and multi-sensor fusion are key pathways toward robust, operational decision-support tools for precision agriculture.
Why it matches plant phenotyping methods圃場・圃場内スケールの作物収量という植物形質を対象に、Sentinel-2等による推定手法、モデル統合、データ融合、性能制約を体系的にレビューしており、方法論が中心である。
abstractThis review synthesizes recent advances in crop yield estimation that leverage Sentinel-2 data.
Crop residues support soil health by reducing erosion, improving water retention, and contributing to carbon sequestration. Accurate estimation of crop residue biomass is essential for understanding residue distribution patterns and improving sustainable land management practices. Remote sensing, especially high-resolution UAV-based imaging, is a powerful tool for monitoring residue over agricultural fields, and many studies use remote sensing datasets for mapping residue cover (a 2D metric). However, few studies have evaluated residue biomass using remote sensing, despite biomass being more ecologically informative. This study uses high-resolution UAV multispectral imagery to predict crop residue biomass using feature selection and machine learning. Candidate predictors included raw bands, spectral indices, texture metrics, and digital-surface-model-derived topographic variables. Three feature selection methods—recursive feature elimination with cross-validation, Pearson correlation screening, and least absolute shrinkage and selection operator regression, were applied on the training set to identify informative predictors. Four machine learning models (Random Forest Regression, Support Vector Regression, CatBoost, and k-Nearest Neighbors [kNN]) were evaluated individually and in combination using simple averaging, weighted averaging, and stacked ensemble strategies. Results show that Pearson-selected features paired with kNN achieved the best performance (R 2 = 0.61, RMSE = 188.71 g m -2 ). Ensemble approaches did not outperform the best individual model, suggesting limited benefit from meta-learning under small-sample conditions. Across selection methods, red- and blue-band-related predictors were consistently retained, while textural and topographic variables were selected more selectively, indicating context-dependent contributions. Overall, simpler models with targeted feature selection can outperform more complex ensembles for UAV-based crop residue biomass estimation.
Why it matches plant phenotyping methodsUAVマルチスペクトル画像から作物残渣バイオマスを推定し、特徴選択法と複数の機械学習モデルを比較・評価することが中心で、植物由来バイオマスという明示的な状態量を技術的に推定している。
abstractThis study uses high-resolution UAV multispectral imagery to predict crop residue biomass using feature selection and machine learning.
With the rapid development of artificial intelligence, UAV remote sensing, and agricultural Internet of Things technologies, crop growth monitoring is evolving from manual inspection and single-source analysis toward intelligent decision-making based on multisource perception. However, existing methods still suffer from limited robustness under environmental variations, insufficient integration between UAV imagery and sparse ground sensor observations, and weak capability for transforming predictions into practical agricultural management recommendations. This study proposes a UAV–ground sensor collaborative lightweight framework for crop growth assessment and agricultural decision support. The proposed framework integrates UAV RGB and multispectral imagery with ground sensor observations through a region-level aerial–ground alignment mechanism and a sensor-guided attention fusion module, enabling environmental conditions to enhance visual feature interpretation. Furthermore, a fact-constrained decision module is developed to generate management recommendations based on crop status, environmental risks, and field information. Experimental results demonstrate that the proposed method achieves superior performance in crop growth classification and yield-trend prediction, reaching Accuracy, Precision, Recall, and F1-score values of 92.47%, 91.86%, 91.39%, and 91.62%, respectively, with an RMSE of 0.381 and an R2 of 0.902. The lightweight framework requires only 6.18M parameters and 0.91G FLOPs, achieving 39.56 ms inference latency and 25.28 FPS on edge devices. The proposed framework also improves decision reliability, achieving an expert agreement rate of 89.34% and a risk identification accuracy of 90.18%. Economic analysis indicates that the proposed framework reduces labor cost, water consumption, and fertilizer input by 49.7%, 26.7%, and 23.0%, respectively, while increasing net benefit by 46.1% compared with conventional field management practices. These results demonstrate that the proposed method provides an accurate, interpretable, and deployable AI-driven solution for intelligent crop management in smallholder and medium-sized farming systems.
Why it matches plant phenotyping methodsUAV画像と地上センサーを融合し、作物生育状態を評価する取得・推定フレームワーク自体を開発しており、植物状態の推定方法が中心的です。
abstractThis study proposes a UAV–ground sensor collaborative lightweight framework for crop growth assessment and agricultural decision support.
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.
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.
Timely forecasting of maize productivity is essential to support precision agriculture and optimize management practices. In this study, we analyzed the potential of integrating ground-based measurements and UAV-derived spectral data for predicting maize grain yield (GY) under different fertilization conditions. Field data were collected at two key phenological stages: early vegetative stage (V7) and pre-harvest (R4). Ground-based measurements included SPAD, above-ground biomass (AGB), and leaf area index (LAI), while multispectral and hyperspectral imagery was acquired by drone. A series of Ordinary Least Squares (OLS) models was developed to evaluate the predictive performance of individual variables and their combinations. Model robustness was assessed using two validation strategies: Leave-One-Treatment-Out (LOTO) to assess model performance across the treatments included in the experimental design and random sampling to assess performance within the dataset. The results showed that yield prediction was less accurate during the early growth stages, where data fusion significantly improved the model’s accuracy (R2 = 0.82; MAE = 6.36 q ha−1; MAPE≈7 %). The predictive performance of VIs alone increased substantially in the pre-harvest stage, with the combination of red-edge indices and LAI proving to be the best model for late yield prediction (R2 = 0.86; MAE = 6.56 q ha−1; MAPE≈7%). Comparison of multispectral and hyperspectral data revealed comparable predictive performance, suggesting that multispectral sensors may already capture the key spectral information needed for yield forecasting. Furthermore, random validation consistently produced more optimistic results than the LOTO method, highlighting the importance of using validation strategies that explicitly account for the experimental design when evaluating model performance across the treatments included in the study. Overall, the present study demonstrates that yield prediction is highly dependent on the phenological stage and validation approach, and that integrating complementary data sources can improve model performance, particularly during the early growth stages. These findings should be interpreted as a proof-of-concept based on a single-site, single-season experiment with a limited sample size (n = 12), and therefore require further validation across multiple environments and growing seasons.
Why it matches plant phenotyping methodsUAVマルチ／ハイパースペクトル画像と地上測定を統合し、トウモロコシ収量を予測する方法を開発・比較・検証しており、植物形質の取得・推定が研究の中心である。
abstractA series of Ordinary Least Squares (OLS) models was developed to evaluate the predictive performance of individual variables and their combinations.
Plant phenotyping relevance match · UnverifiedCrossref · Europe PMC · checked 5 Sept 2026
Introduction Climate extremes increasingly threaten agricultural production, yet many artificial intelligence systems in agriculture remain local, reactive and narrowly trained for one crop, region or sensing modality. Methods We present AgriFM, a multimodal geospatial foundation model that combines satellite image time series, radar, thermal observations, weather trajectories, soil properties, topography and sparse management variables to estimate crop-stress and yield-failure risk across crops and regions. AgriFM was pretrained using self-supervised objectives on 2.4 million field-season sequences and evaluated on a curated benchmark spanning maize, wheat, soybean, rice and sorghum across five agroclimatic regions. Results In held-out geography and time-split evaluations, AgriFM improved early stress detection and yield-failure prediction over statistical, crop-model and deep-learning baselines. The largest gains occurred during compound drought and heat events, for which AgriFM produced alerts 18 to 24 days earlier than the satellite-only baseline while maintaining improved calibration. Phenology-conditioned fusion improved transfer across planting calendars, and uncertainty calibration reduced false alerts at fixed recall. Discussion Because the study is based on retrospective datasets, these findings establish cross-region retrospective performance rather than prospective field efficacy. The results support further field-based evaluation of multimodal foundation models for climate-resilient crop monitoring.
Why it matches plant phenotyping methods作物ストレス状態と収量失敗リスクを衛星・レーダー・熱画像等から推定する基盤モデルを開発し、複数作物・地域のベンチマークで評価しており、植物状態の取得・推定手法が中心である。
abstractWe present AgriFM, a multimodal geospatial foundation model that combines satellite image time series, radar, thermal observations, weather trajectories, soil properties, topography and sparse management variables to estimate crop-stress and yield-failure risk across crops and regions.
The use of a combined assessment of the informational significance of vegetation indices for predicting the yield of spring wheat, taking into account varietal specificity and agrotechnical factors, has been studied. The test site was the field experience in the forest-steppe zone of the Novosibirsk Priobye. In the experiment, spring wheat of the Suenga and Novosibirsk 41 varieties was cultivated using intensive agricultural technology. For the analysis, data obtained using the DJI Phantom 4 Multispectral Phantom unmanned aerial vehicle during the crop growing period in 2023–2025 were used. Vegetation index values were calculated using five spectral channels: blue (B, 450 ± 16 nm), green (G, 560 ± 16), red (R, 650 ± 16), red edge (RE, 730 ± 16) and near-infrared (NIR, 840 ± 26 nm). For the analysis of informational importance, the following indices were used as predictors of crop yield: NDVI, NDWI, GNDVI, LAI, CVI, GCI, and ChlRE. For assessing the informativeness of the indices, independent methods were used: the F-statistic of one-way regression (ANOVA F-test), evaluation of mutual information (Mutual Information, MI), and feature importance of the random forest algorithm (Random Forest, RF). Each of the scores was normalized in the range [0; 1] using the min-max normalization method, after which a combined score was calculated as a weighted sum. For the Suenga variety, the stable predictors regardless of the experimental variants were CVI (tillering) and ChlRE (stem elongation and heading), while for Novosibirsk 41, the set of informative predictors significant ly depended on the combination of plant protection and fertilizer systems. It was found that chlorophyll content indices (GCI, ChlRE) increased the predictive relationship with yield under fertilization, while the water status index (NDWI) lost informativeness when fertilizers were applied.
Why it matches plant phenotyping methodsUAVマルチスペクトル画像から植生指数を抽出し、複数の統計・機械学習手法を統合して小麦収量予測における指標の有用性を評価しており、植物形質推定ワークフローが中心です。
abstractThe use of a combined assessment of the informational significance of vegetation indices for predicting the yield of spring wheat
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
Accurate estimation of crop water requirements is essential to improve irrigation efficiency for forage maize production. This study compared satellite- and UAV-derived normalized difference vegetation index (NDVI) models for estimating crop coefficients (K c ) and evaluated their operational performance for irrigation scheduling. K c -NDVI models were developed during the 2023 growing season and subsequently validated under field conditions during the 2024 season in two forage maize hybrids (N83N5 and Matador) under three irrigation strategies: conventional producer irrigation (ID1), satellite-based irrigation scheduling (ID2), and UAV-based irrigation scheduling (ID3). Both NDVI sources exhibited strong relationships with K c , with higher calibration accuracy for the UAV model (R 2 = 0.9414) than for the satellite model (R 2 = 0.8278). The UAV-based model applied 23-30% less irrigation water, maintaining high water productivity but also reducing crop growth, forage yield, and nutritional quality. In contrast, satellite-based irrigation scheduling promoted greater crop growth and produced the highest forage yield, reaching 59.8 t ha -1 in hybrid N83N5 while maintaining efficient water use. This treatment also improved forage quality by increasing dry matter and starch concentrations while reducing fiber fractions. The findings highlight the complementary potential of satellite and UAV imagery in precision irrigation and underscore the trade-offs between spatial detail, temporal resolution, and operational scalability. Furthermore, the results demonstrate that a stronger K c -NDVI relationship does not necessarily translate into improved irrigation scheduling performance. Under the conditions evaluated, the satellite-based model provided the best balance between water use, forage yield, and nutritional quality.
Why it matches plant phenotyping methods衛星・UAV画像からNDVIを用いて作物係数を推定する手法を開発し、別年・圃場条件で検証しており、植物群落状態の取得・推定が研究の中心である。
abstractK c -NDVI models were developed during the 2023 growing season and subsequently validated under field conditions during the 2024 season
Plant phenotyping relevance match · UnverifiedOpenAlex · Europe PMC · Crossref · checked 5 Sept 2026
Abstract Quantifying blueberry fruit yield and maturity is important for evaluating yield potential in breeding trials, but manual measurement remains slow, labor-intensive, and costly. Object detection and classification networks offer a high-throughput solution, yet few studies validate image-based counts against hand-harvested ground truth while explicitly accounting for canopy occlusion. Hence, this study developed a multi-class berry detection pipeline for immature and mature berries and validated image-based estimates against hand-harvest counts across 32 diverse southern highbush blueberry genotypes. Among the models evaluated, YOLOv8x achieved the highest detection performance, with an mAP50 of 0.82 and an mAP50–95 of 0.66. External validation produced F1 scores ranging from 0.74 to 0.91 for berry maturity classes. However, image-based detections systematically underestimated hand-harvested fruit counts, with R² values ranging from 0.40 to 0.61. Fruit occlusion varied widely among genotypes, from 42% to 90%, indicating that canopy structure strongly affects berry visibility. Incorporating image-derived canopy architecture, color, and texture features improved predictions of berry counts and maturity. Partial Least Squares regression provided the best performance, increasing R² values of hand-harvested fruit counts, ranging from 0.52 to 0.74. These results show that accounting for canopy occlusion improves image-based estimation of blueberry yield and supports more accurate high-throughput phenotyping.
Why it matches plant phenotyping methodsブルーベリーの収量・成熟度を画像から推定する検出パイプラインを開発し、手収穫値との外部検証および樹冠遮蔽・構造を考慮した改良を行っており、植物表現型取得法が中心である。
abstractthis study developed a multi-class berry detection pipeline for immature and mature berries and validated image-based estimates against hand-harvest counts
Introduction Accurate and non-destructive estimation of wheat biomass is essential for crop growth monitoring, yield prediction, and precision agriculture. Unmanned aerial vehicle (UAV)-based remote sensing, integrating both spectral and structural information, has shown great potential for biomass estimation. However, the mechanisms by which different types of variables contribute to biomass prediction remain poorly understood, especially when using machine learning models. Methods In this study, we fused spectral reflectance, vegetation indices, and canopy height data derived from a UAV multispectral camera to estimate wheat biomass across four growth stages (jointing, booting, heading, and filling). Four machine learning algorithms-XGBoost, Random Forest Regressor (RFR), Support Vector Regressor (SVR), and LASSO-were employed and compared. Results and discussion The results showed that XGBoost achieved the highest accuracy (R 2 = 0.919, RMSE = 102.43 g/m², MAE = 77.43 g/m², RRMSE = 19.71%). Furthermore, SHAP (SHapley Additive exPlanations) analysis revealed that canopy height (CH) was the most important variable, followed by spectral indices such as R842 and GNDVI. The univariate and global contribution analyses demonstrated that structural and spectral variables played complementary roles in biomass estimation. This study provides a mechanistic understanding of variable contributions and offers a robust framework for UAV-based wheat biomass estimation.
Why it matches plant phenotyping methodsUAVスペクトル・キャノピー高データから小麦バイオマスを推定し、複数機械学習法を比較・評価する方法論的研究であり、植物形質取得が中心である。
abstractwe fused spectral reflectance, vegetation indices, and canopy height data derived from a UAV multispectral camera to estimate wheat biomass across four growth stages
Abstract Blanket-rate agrochemical scheduling — a practice wherein the same quantity of fertilizer or pesticide is spread uniformly across an entire field irrespective of spatial or temporal crop need — persists as the dominant farm management paradigm across rural India and large parts of South Asia. This approach generates cascading inefficiencies: excess nitrogen drains into waterways, off-target pesticide deposits devastate pollinators, input costs erode thin profit margins, and wide-scale greenhouse gas release from soil microbial activity accelerates climate change. The study documented here addresses this challenge through a purpose-built, four-layer intelligent field management platform. The platform ingests continuous data from drone-mounted multispectral cameras, in-field IoT soil probes, a wireless weather station, and cloud-sourced Sentinel-2 satellite imagery, then passes these inputs through a cascaded AI inference stack. A fine-tuned YOLOv8-L network performs real-time pest and foliar disease localisation; a ResNet-50 backbone quantifies canopy health across five stress gradients; a two-layer stacked LSTM projects short-horizon yield trajectories; and a Deep Q-Network autonomously plans drone spray routes weighted by field-specific prescription maps. Field validation spanned two consecutive growing seasons (Rabi 2022–23 and Kharif 2023–24) across six georeferenced plots covering 4.8 ha at Baramati, Maharashtra. Outcome metrics recorded during head-to-head comparison with conventional practice included a disease detection score of 95.6% mAP, a 47.3% reduction in total nitrogen applied, a 38.1% decrease in pesticide volume, and a 22.4% uplift in harvested grain weight. Together, these field-verified numbers substantiate the operational readiness of integrated AI precision agriculture for smallholder deployment.
Why it matches plant phenotyping methodsマルチスペクトル画像・深層学習による病害局在化とキャノピー健康状態の定量化を中核機能とする統合プラットフォームであり、植物の病害状態・生育状態を直接推定して現地検証している。
abstractThe platform ingests continuous data from drone-mounted multispectral cameras, in-field IoT soil probes, a wireless weather station, and cloud-sourced Sentinel-2 satellite imagery, then passes these inputs through a cascaded AI inference stack.
Reproduction assets found保存済みの本文根拠を更新済みルールで再検証し、公開資産1件を確認しました。Code · publicData Availability The annotated image dataset (14,300 images, 23 classes), trained YOLOv8-L and ResNet-50 weights, LSTM model files, DQN policy checkpoint, and all analysis scripts are archived at https://github.com/precision-agri-ai (Zenodo DOI: 10.5281/zenodo.XXXXXXX).Open asset ↗precision-agri-ailines:161-182Plant phenotyping relevance match · UnverifiedCrossref · checked 5 Sept 2026
Remote sensing has become an important tool for crop monitoring and precision agriculture, yet its applications in sugar beet production remain fragmented across sensing platforms, target traits and modelling strategies. This review synthesises the development, current applications and future directions of remote sensing in sugar beet production, with particular attention to the transition from crop monitoring to precision management. A structured search was conducted in Scopus and the Web of Science Core Collection for publications from 2003 to 2025, and 181 relevant peer-reviewed articles were retained for thematic analysis. The literature shows a clear increase in sugar beet remote sensing studies, particularly after 2015, coinciding with the availability of Sentinel-2 imagery and, from 2016 onwards, the growing use of unmanned aerial vehicle-based sensing. It also indicates a gradual shift from crop mapping and canopy monitoring towards disease detection, weed mapping, yield prediction and management-oriented applications. Current studies demonstrate the value of satellite, unmanned aerial vehicle and proximal sensing for retrieving canopy traits, assessing biotic stresses, estimating root yield and supporting field-scale management. However, sugar beet presents specific challenges because its economic value depends not only on canopy development or root biomass, but also on sucrose concentration, recoverable sugar yield, and processing quality. These quality-related traits remain less studied and are difficult to infer directly from canopy observations. Modelling approaches have evolved from vegetation-index-based empirical models towards machine learning, deep learning, multi-temporal analysis, data fusion and crop model assimilation, but issues of model transferability, ground-truth availability and operational decision support remain unresolved. Future research should strengthen multi-source observations, external validation, quality-oriented prediction and decision-support workflows to promote robust, scalable and economically meaningful remote sensing applications in sugar beet production.
Why it matches plant phenotyping methodsサトウダイコンのリモートセンシングによるキャノピー形質、ストレス、根収量などの推定手法を体系的にレビューしており、センシング基盤とモデル化・検証課題が中心的に扱われている。
abstractThis review synthesises the development, current applications and future directions of remote sensing in sugar beet production, with particular attention to the transition from crop monitoring to precision management.
Strawberry production in hydroponic systems requires precise and spatially explicit information on fruit load, maturity, and size to support harvest planning and quality control. This study presents an integrated computer vision and GNSS RTK framework that detects individual strawberries, estimates their maturity and physical dimensions, assigns fruits to operational size–maturity categories, and generates high-resolution yield maps in an open-field hydroponic system. RGB-D images are processed with YOLOv8-seg and a BoT-SORT-based tracking module to obtain instance-level masks, from which a color-based ripeness index and 3D point clouds are derived. After DBSCAN-based filtering, fruit length and width are computed in metric space and combined with ripeness percentage to assign each strawberry to one of nine operational size–maturity categories using predefined threshold rules. The system was evaluated in a commercial hydroponic crop in Arcabuco, Boyacá, Colombia, achieving accurate segmentation, with median IoU values up to 0.83 for bounding boxes and 0.71 for masks, and mean absolute errors of 2.51 mm in length and 1.85 mm in width with respect to Vernier caliper measurements. Yield maps aggregated in 1 m2 cells and by crop row revealed marked spatial variability in fruit density, maturity state, and size–maturity composition, allowing the identification of zones with a high concentration of fruits ready for harvest versus areas dominated by immature fruits. The proposed framework provides a practical and low-cost decision support tool for hydroponic strawberry management and may be adapted to other high-value horticultural crops after recalibration under different crop architectures, cultivars, and environmental conditions.
Why it matches plant phenotyping methodsRGB-D画像と追跡・3D解析により、イチゴ果実の成熟度、寸法、果実密度および収穫状態を個体レベルで推定し、精度検証も行う中心的なフェノタイピング手法研究である。
abstractThis study presents an integrated computer vision and GNSS RTK framework that detects individual strawberries, estimates their maturity and physical dimensions, assigns fruits to operational size–maturity categories, and generates high-resolution yield maps in an open-field hydroponic system.
Plant phenotyping relevance match · UnverifiedOpenAlex · Europe PMC · checked 5 Sept 2026
Fall dormancy (FD) and forage yield (FY) are two key traits in alfalfa ( Medicago sativa L.) breeding programs. However, genetic progress has remained limited over the past decades, largely due to the complexity of alfalfa breeding and the reliance on labor-intensive phenotyping methods. High-throughput phenotyping (HTP) using unmanned aerial vehicles (UAVs) represents a promising alternative for rapid and non-destructive crop evaluation. The objectives of this study were to i) estimate FD using UAV-derived canopy height and RGB vegetation indices and ii) evaluate the predictive performance of machine learning (ML) models for FY estimation. A total of 210 alfalfa populations with diverse genetic backgrounds were evaluated over two growing seasons (2023 to 2025) across seven harvests under Mediterranean conditions in central Chile. FY was measured manually, while FD was estimated using both manual and UAV-based approaches. A total of 19 RGB-derived indices (VIs) including plant height (PH) were extracted and used as predictor variables. Five complex predictive ML models were evaluated: PLS, PCR, SVM, ANN, and MLR. The results showed that UAV-derived FD was significantly correlated with FD obtained through conventional methods ( R 2 = 0.88). The automated UAV-based FD phenotyping framework demonstrated slightly higher precision ( R 2 = 0.92) and broad-sense heritability ( H 2 = 0.69) compared to manual measurements ( R 2 = 0.87–0.89; H 2 = 0.64), providing a more reliable selection tool for breeders. Among the tested ML models, SVM and ANN achieved the highest accuracy ( R 2 ≈ 0.73) for FY prediction. These findings demonstrate that integrating low-cost RGB imagery with complex modeling offers a promising avenue that could assist in refining future selection strategies for this genetically complex species.
Why it matches plant phenotyping methodsUAV画像からアルファルファの休眠性と収量関連形質を推定する高スループット表現型解析手法を開発・検証し、手動測定との比較と機械学習モデル評価を行っているため、方法が研究の中心である。
abstractHigh-throughput phenotyping (HTP) using unmanned aerial vehicles (UAVs) represents a promising alternative for rapid and non-destructive crop evaluation.
Abstract Purpose of Review Ground-based 3D point cloud technologies, including static terrestrial laser scanning (TLS), mobile laser scanning (MLS), and close-range photogrammetry, are increasingly used for estimation of aboveground vegetation biomass as they provide detailed structural representations across vegetation types; however, a comprehensive synthesis of how point-cloud data are translated into biomass estimates remains lacking. This review evaluates current approaches, performance patterns, and methodological gaps in biomass estimation using 3D ground-based point clouds. Recent Findings We systematically reviewed and analyzed 160 research articles (comprising 171 device-specific studies) published until the end of 2025 (first appearing in 2010). Research was dominated by tree-based applications (74%), with limited attention to shrubs, grasslands or crops. TLS was the prevailing acquisition technology (78%), although MLS adoption is growing. Biomass estimation primarily relied on allometric equations, volume-based reconstructions (e.g., quantitative structure models, voxelizations, convex hull), and parametric regression models. Reported model performance was generally high in tree- and shrub-based studies (median R 2 > 0.8), but more variable in non-woody vegetation types. Despite rapid advances in 3D sensing, point-cloud-native deep-learning approaches remain rarely implemented in biomass estimation workflows. Summary Ground-based 3D sensing is maturing technically, yet methodological heterogeneity persists. Many workflows still depend on destructive calibration data, semi-manual preprocessing, and non-standardized modelling strategies, limiting reproducibility and cross-study comparability. Multi-sensor integration is emerging but lacks consistent upscaling frameworks. Future research should expand coverage of underrepresented vegetation types, promote standardized and automated processing pipelines, and systematically evaluate point-cloud-native deep learning architectures, both for extracting structural proxies and for assessing their capacity to estimate biomass directly.
Why it matches plant phenotyping methods3Dセンシングによる植物バイオマス推定手法を体系的にレビューし、取得技術、推定ワークフロー、性能、再現性、標準化を評価しており、表現型測定法が中心である。
abstractThis review evaluates current approaches, performance patterns, and methodological gaps in biomass estimation using 3D ground-based point clouds.
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.
Abstract Accurate plot-level sugarcane yield forecasting is essential for optimizing agricultural management, resource allocation, and operational planning. Existing forecasting approaches are often limited by their inability to capture temporal crop dynamics and local biophysical variability, reducing their usefulness for real-time decision-making. To develop and evaluate a Machine Learning (ML)-based framework for short-term sugarcane yield forecasting at plot level using age-segmented Normalized Difference Vegetation Index (NDVI) derived from Sentinel-2 imagery, and to determine the earliest crop stage at which reliable yield predictions can be obtained. An integrated dataset was constructed by combining productivity records from 2,132 sugarcane plots across six harvest seasons (2016–17 to 2021–22) with NDVI time series derived from Sentinel-2 satellite imagery. NDVI observations were aggregated into phenology-based temporal intervals, from which statistical features were extracted. Ten ML regression algorithms were evaluated under two forecasting schemes: a global model trained with all observations and a sector-specific approach that developed localized models for individual production sectors. Model performance was assessed using RMSE and R² on an independent test set. The sector-specific approach outperformed the global model, achieving an RMSE of 12.48 TCH and an R² of 0.7840 on the independent test set, compared with an RMSE of 16.75 TCH and an R² of 0.5724 for the global model. Sparse Partial Least Squares (spls) and Support Vector Machines with Polynomial Kernel (svmPoly) were the most frequently selected algorithms. SHAP analysis revealed that Median NDVI was the dominant predictive feature, while the Elongation I stage was the most influential phenological period. Reliable forecasts were obtained from the fifth month of crop growth (RMSE = 14.13 TCH), and prediction accuracy improved progressively as the crop matured. The proposed framework also surpassed traditional expert estimations (RMSE = 15.47), providing earlier and more accurate yield forecasts. This study demonstrates that localized, sector-specific ML models combined with temporal NDVI dynamics can provide accurate and operationally useful plot-level sugarcane yield forecasts. The framework supports proactive agronomic management, improves planning and budgeting processes, and offers a scalable methodology for precision agriculture and sustainable sugarcane production systems.
Why it matches plant phenotyping methods圃場・区画レベルのサトウキビ収量という植物形質を、Sentinel-2 NDVI時系列と機械学習から推定する枠組みを開発・評価しており、予測手法が中心である。
abstractTo develop and evaluate a Machine Learning (ML)-based framework for short-term sugarcane yield forecasting at plot level using age-segmented Normalized Difference Vegetation Index (NDVI) derived from Sentinel-2 imagery
Plant phenotyping relevance match · UnverifiedOpenAlex · Crossref · Europe PMC · checked 5 Sept 2026
In recent decades, global weather patterns have shifted dramatically, introducing greater unpredictability into agriculture. A major challenge in plant breeding is developing selection strategies that remain accurate under such uncertainty. Sparse testing is a well-established approach to increase the number of genotypes evaluated in field trials while keeping costs manageable. However, incorporating image-based data into sparse testing remains challenging. We developed a strategy to integrate high-throughput phenotyping data into sparse testing in potato breeding to improve predictive performance in multi-environment trials. Our approach involved constructing an environmental kernel derived from the covariance matrix of image-based data. We assessed the predictive performance of several regression models under sparse testing, including those based on genomic or phenomic data alone and in combination. Models using only the proposed environmental kernel achieved predictive accuracies comparable to, or exceeding, those of genomic prediction models in various sparse testing scenarios. The best results were observed for tuber yield, a key trait in potato breeding. These findings highlight the potential of image-based environmental kernels to improve the efficiency and accuracy of sparse testing. This approach is cost-effective and scalable, particularly useful for breeding programs with limited resources.
Why it matches plant phenotyping methods画像ベースの高スループット表現型データを環境カーネルとして構築し、ジャガイモ育種の疎試験に統合する方法が研究の中心であるため、表現型予測手法として収載する。
abstractWe developed a strategy to integrate high-throughput phenotyping data into sparse testing in potato breeding to improve predictive performance in multi-environment trials.
Accurate yield prediction for major grain and oilseed crops, including soybean, corn, wheat, and rice, is essential for food-security assessment and precision field management. This study presents a structured integrative review of UAV-based crop yield prediction and follows PRISMA-guided procedures for literature search, screening, and evidence synthesis. Seventy peer-reviewed studies published between 2018 and 2025 were synthesized within a "Data-Ground Truth-Model-Decision" framework. Beyond summarizing UAV platforms, sensor configurations, feature-engineering strategies, and model architectures, the review explicitly distinguishes among microplot, field, and regional prediction scales, and evaluates the characteristics and limitations of yield-label acquisition methods, including manual harvest, plot-combine harvest, and combine yield-monitor data. Existing evidence indicates that the reliability of UAV-based yield prediction depends not only on optimal image acquisition windows, multi-source feature fusion, and model architecture, but also on scale-consistent yield labels, spatially aware validation strategies, and clearly defined model outputs, such as plot-level scalar yield, field-scale yield maps, and regional yield estimates. Major bottlenecks include scale mismatch between UAV imagery and yield labels, error propagation during yield-map generation, limited cross-year and cross-region transferability, weak causal interpretability, and difficulties in deploying models under complex operational field conditions. Future research should emphasize scale-explicit benchmark datasets, quality-controlled ground-truth yield acquisition, UAV-satellite-ground data fusion, spatiotemporal deep learning, and edge-cloud collaborative systems that can translate prediction outputs into agronomic decisions. This review provides a practical pathway for developing robust, interpretable, and deployable UAV-based yield prediction systems for major grain and oilseed crops.
Why it matches plant phenotyping methodsUAV画像から作物の収量という植物形質を推定する手法を中心に、プラットフォーム、特徴量、モデル、検証尺度、グラウンドトゥルースを体系的にレビューしているため、方法レビューとして収載。
abstractThis study presents a structured integrative review of UAV-based crop yield prediction and follows PRISMA-guided procedures for literature search, screening, and evidence synthesis.
Plant phenotyping relevance match · UnverifiedOpenAlex · Crossref · Europe PMC · checked 5 Sept 2026
Here, we present a single-operator push-cart platform equipped with a 16-beam LiDAR. A push-button interface controls data acquisition, and the data processing pipeline removes ground points, filters noise, performs 5-cm voxelization, and produces plot-level canopy metrics. We validated biomass estimation in hairy vetch (Vicia villosa) and corn (Zea mays) leaf- and whole-plant thinning experiments. In vetch, voxelized estimation of plant volume correlated strongly with destructively measured biomass (r2 = 0.88), showing that the multi-beam LiDAR can produce biomass estimates comparable to previously reported methods. In corn, comparisons of perpendicular (0°) and multi-angle LiDAR beams showed significantly greater voxel counts in the upper canopy when angled beams were used (beam angle × height interaction, p < 0.001), demonstrating that multi-beam scanning provides greater penetration into the upper canopy than a single perpendicular scan plane. We also extended the suite of LiDAR-derived traits to include apparent leaf area index (LAI), mean tilt angle (MTA), persistent homology-based stand density, and plot-bounded foliage area density (FAD). The persistent homology algorithm distinguished between leaf-removal and plant-removal treatments (removal type × removal amount, p = 0.0039). LiDAR-derived LAI has been used to estimate canopy leaf area, but gap-fraction approaches do not fully exploit the ability of LiDAR to resolve distance. Plot-bounded FAD used ray length and interception distance within defined plot volumes and was more sensitive to plot-level treatments than apparent LAI or MTA, detecting differences associated with both the removal amount and removal type. These results show that a robust, portable, multi-beam LiDAR cart can reproduce plot-level canopy measurements and improve trait especially in research-sized plots.
Why it matches plant phenotyping methods携帯型マルチビームLiDARプラットフォームと処理パイプラインを開発・検証し、バイオマス、LAI、葉面積密度などの作物形質を推定しているため、フェノタイピング手法が研究の中心である。
titleA Single-Operator Push-Cart Multi-Beam LiDAR Platform for Multi-Trait Field Phenotyping
Context Precision agriculture can benefit from within-field boundary line analysis (BLA) to identify the most limiting factors impacting crop yield. In this study, the BLA was applied at the within-field scale using yield monitor data and key environmental factors, including evapotranspiration (ET), elevation, and the apparent soil electrical conductivity (ECa). Aims We aimed to develop and evaluate a novel BLA method to estimate Yp and quantify Yg at the within-field scale, and to assess the diagnostic potential of freely available proxy variables for identifying spatially variable yield-limiting factors in dryland wheat production. Methods We combined Mahalanobis distance-based filtering for data denoising with 2Dl kernel density estimation (KDE) and percentile thresholding to select high-density, high-yield points that define the upper yield envelope. A generalised additive model (GAM) was then used to produce the boundary line through these selected points to represent the Yp. Key results Results from the two case studies showed that this approach was robust and less sensitive to noise and outliers in fine-scale datasets. Freely available ET and elevation could be proxies to highlight the impact of some limiting factors, such as frost events or waterlogging. The ECa could identify areas where some potential soil-related factors (e.g. lower clay content reducing plant available water capacity) could be the limiting factors. Conclusions While the proxy variables effectively indicated potential limiting factors, ground-truth validation is required to confirm the underlying causal mechanisms. Implications Growers could benefit from the BLA approach to identify local yield constraints, estimate site-specific Yp and Yg, and fine-tune their inputs, leading to more efficient resource use and improved profitability.
Why it matches plant phenotyping methods作物収量という植物形質を推定する境界線分析法を開発・評価し、ノイズ除去、KDE、GAMによるワークフローを中心的に提示しているため。
abstractWe aimed to develop and evaluate a novel BLA method to estimate Yp and quantify Yg at the within-field scale
0. Morphological traits such as floral area and body size are fundamental to ecological research, serving as inputs for studies of pollinator–plant interactions, habitat quality, and biodiversity monitoring. However, accurately measuring these traits from images remains challenging, particularly in complex field conditions where existing tools exhibit reduced accuracy and limited generalizability across taxa. We present EcoMorph, a modular morphological measurement system that leverages the Segment Anything Model 3 (SAM3) to quantify traits across diverse ecological contexts. Unlike task-specific segmentation models requiring domain-specific training data, SAM3’s prompt-based architecture enables segmentation of arbitrary biological structures from natural-language prompts, using the same underlying model across flowers, insects, and other targets without retraining. From the resulting segmentations, EcoMorph extracts three classes of measurement: area, linear dimensions, and object counts. We validated EcoMorph across two ecological scales. At the intermediate scale, EcoMorph-derived floral area agreed closely with manual ImageJ measurements (R 2 = 0.935, n = 74) under simple-background conditions and (R 2 = 0.928, n = 58) under complex-background conditions, with valid predictions for 95% of images. At the fine scale, EcoMorph-derived insect body area was strongly correlated with hand-measured intertegular distance (r = 0.810, n = 349), capturing body-size variation across species from the small Bombus impatiens to the large Xylocopa virginica . Object counts matched manual counts almost exactly for well-separated insects in an insect box (R 2 = 0.9997, n = 12). By combining prompt-based segmentation with modular measurement, EcoMorph enables high-throughput quantification of area, size, and abundance from heterogeneous image sources without taxon-specific training. This generality supports a broad range of ecological applications, including pollinator and plant trait research, biodiversity and abundance monitoring, and allometric biomass estimation.
Why it matches plant phenotyping methods画像から花の面積など植物形態形質を抽出する汎用システムを開発し、手動測定との一致で検証しており、植物フェノタイピング手法が中心である。
abstractWe present EcoMorph, a modular morphological measurement system that leverages the Segment Anything Model 3 (SAM3) to quantify traits across diverse ecological contexts.
Reproduction assets foundThe paper's Data and code availability statement provides a public Zenodo deposit containing the validation datasets and code used for the EcoMorph phenotyping measurements (floral area, insect morphometrics, counts), plus a public web deployment of the EcoMorph software itself.Code · publicValidation datasets and code are available here on Zenodo
https://zenodo.org/records/20980236.Open asset ↗Zenodo · 20980236pdf-page:2 lines:1-54Plant phenotyping relevance match · UnverifiedOpenAlex · Europe PMC · Crossref · checked 5 Sept 2026
Abstract Precision field management and high-throughput plant phenotyping increasingly rely on remote sensing to capture spatial and temporal variability in crop performance. Unmanned aerial vehicle (UAV) – based sensing offers unique advantages for field-scale data collection, including high spatial resolution, flexible deployment, and scalable throughput. However, the full potential of UAV platforms remains constrained by labor-intensive operations across flight execution, data transfer, and processing workflows. This study presents a systematic evaluation of an automatic UAV-based crop sensing platform through a season-long, multi-crop field experiment. Data acquisition was conducted over a maize irrigation trial and a soybean breeding experiment, resulting in 176 completed flights over 28 days during the growing season. High-frequency flights on selected days captured diurnal dynamics in key canopy traits, including maize leaf rolling under drought stress and genotype-dependent plot temperature variation in soybean. In the maize irrigation experiment, significant differences in diurnal canopy cover ratio (CCR) were observed among irrigation treatments. The predictive relationship between CCR and final grain yield strengthened throughout the day, with the coefficient of determination (R 2 ) increasing from 0.05 in the early morning (RMSE = 3.05 Mg ha − 1 ) to 0.65 at midday (RMSE = 1.87 Mg ha − 1 ), highlighting the importance of temporal optimization in UAV-based sensing. Temperature measurements from the onboard thermal infrared camera showed a strong overall linear correlation with ground truth measurements (R 2 = 0.85). In the soybean trial, the highest plot temperature was observed on the fast-wilting genotype. Additionally, regression models were developed to estimate key crop traits, including canopy height (CH) and leaf area index (LAI), demonstrating the platform’s quantitative sensing capability. Overall, this study demonstrates that automatic UAV systems enable high-temporal-resolution crop monitoring while substantially reducing operational cost. The results highlight their potential for precise crop management and scalable field phenotyping. Future work will focus on integrating automated data processing pipelines to support near-real-time analytics and decision-making.
Why it matches plant phenotyping methods自動UAVのRGB・熱画像センシング platform を圃場で系統的に評価し、温度・キャノピー被覆率・高さ・LAIなどの植物形質を定量化しているため、フェノタイピング手法が研究の中心である。
abstractThis study presents a systematic evaluation of an automatic UAV-based crop sensing platform through a season-long, multi-crop field experiment.
Abstract Multispectral three‐dimensional (3D) imaging offers substantial potential for plant phenotyping, yet manual segmentation of plant organs remains a bottleneck in breeding programs. We developed a color‐based filtering workflow for faba bean ( Vicia faba L.) point clouds that optimizes lower and upper thresholds of spectral indices and broadband brightness via Bayesian optimization. Rather than maximizing geometric segmentation accuracy, thresholds are selected to maximize correlations between retained points and yield‐related traits, outperforming manual filtering, reducing user effort, and standardizing decisions. Across multispectral 3D point clouds, Bayesian optimization recovered index‐specific threshold ranges that yielded strong in‐sample correlations with grain yield ( r = 0.72), bean number ( r = 0.61), pod number ( r = 0.53), and straw biomass ( r = 0.72). Peak associations occurred at harvest for straw biomass, at 41 days before harvest (DBH) for seed yield, 33 DBH for bean number, and 34 DBH for pod number. Across the season, greenness‐based indices and broadband brightness metrics consistently showed stronger links with seed yield than pigment ratio or water status indices. For straw biomass and pod number, pigment ratio indices showed consistently lower correlations. Targeting trait‐relevant canopy signals via Bayesian optimization enables reliable, nondestructive assessment of relationships between spectral signals and yield‐related traits in faba bean. By optimizing thresholds to maximize trait correlations rather than geometric accuracy, the workflow can support earlier, more cost‐efficient identification of high‐performing genotypes under drought stress and contribute to strengthening high‐throughput phenotyping in breeding programs. This enables faster identification of canopy signals most relevant to target traits.
Why it matches plant phenotyping methods植物の3D点群画像から表現型を抽出するセグメンテーション手法を開発し、ベイズ最適化による閾値選択と性能評価を行っており、フェノタイピング手法が研究の中心である。
abstractWe developed a color‐based filtering workflow for faba bean ( Vicia faba L.) point clouds that optimizes lower and upper thresholds of spectral indices and broadband brightness via Bayesian optimization.
Sweet potato is a nutritionally valuable crop that contributes to food security, owing to its storage roots rich in starch, sugars, and antioxidants, while requiring minimal cultivation inputs. Estimating its yield based on visible above-ground traits remains challenging due to weak and inconsistent correlations between shoot biomass and storage root development. Therefore, direct assessment of underground biomass is essential. In this study, we demonstrate the field application of ground penetrating radar (GPR) for non-destructive detection and yield estimation of sweet potato. GPR is a geophysical technique that typically transmits ultra high frequency radio waves into the soil and records reflections from subsurface objects. Electromagnetic wave simulations within the soil-root system revealed GPR signals that strongly correlate with root length, forming the basis for yield quantification. We developed an image-processing pipeline comprising static correction, gain adjustment, noise filtering, and hyperbola segmentation via the Hough transform to enable semi-automated storage root detection from GPR data. By integrating detection and quantification approaches, a linear regression model predicting sweet potato yield from GPR signals achieved moderate accuracy ( R 2 = 0.567, normalized RMSE 0.190). We established a non-destructive and low-labor approach for monitoring root systems, providing a foundation for rapid, scalable, and field-ready yield estimation in sweet potato and other root and tuber crops.
Why it matches plant phenotyping methodsGPRによる地下貯蔵根の検出・定量化と収量推定を中心に、信号処理および画像処理パイプラインを開発・評価しているため、植物フェノタイピング手法として収載する。
abstractWe developed an image-processing pipeline comprising static correction, gain adjustment, noise filtering, and hyperbola segmentation via the Hough transform to enable semi-automated storage root detection from GPR data.
Reproduction assets found保存済みの本文根拠を更新済みルールで再検証し、公開資産1件を確認しました。Code · publicThe datasets analyzed during the current study consist of GPR line scans of the field at ALRC and list of sweet potato storage root weights. These data are available together with the analysis scripts on GitHub under open access. All data and scripts are the property of NARO and are distributed under the Creative Commons Attribution-NonCommercial 4.0 International License (CC BY-NC 4.0). The repository can be accessed at: https://github.com/mtei1/GPRScript.Open asset ↗mtei1/GPRScripthtml-lines:240-264Plant phenotyping relevance match · UnverifiedEurope PMC · Crossref · checked 15 Sept 2026
Introduction Accurate and transferable rice yield prediction is essential for precision agriculture and food security, yet existing remote sensing-based models often suffer from limited generalization across regions, cultivars, and field scales. Methods This study developed an interpretable automated machine learning framework for rice yield prediction using UAV-based multispectral imagery collected at the maturity stage. A total of 143 rice samples, including 79 experimental plots and 64 production fields across 15 counties in Sichuan Province, China, were investigated. 20 vegetation indices and 36 gray-level co-occurrence matrix texture features were extracted from multispectral orthomosaics, and three feature selection strategies: Pearson correlation coefficient (PCC), Random Forest feature importance (RF-I), and AutoGluon feature importance(AutoGluon-I), were systematically compared. Four regression approaches, including CatBoost, ExtraTrees, Random Forest, and an AutoGluon stacked ensemble, were evaluated using R 2 , RMSE, and MAE. Results The results showed that the AutoGluon ensemble consistently outperformed individual machine learning models, improving testset R 2 from 0.403-0.670 to 0.528-0.736. The best performance was achieved by combining Pearson correlation-based feature selection with AutoGluon, yielding a training R 2 of 0.821 and a test R 2 of 0.736, with RMSE and MAE values of 0.749 and 0.568 t ha -1 , respectively. Shapley Additive Explanations (SHAP) analysis further revealed that texture features, particularly red-band contrast and angular second moment features, contributed substantially to yield prediction, indicating the importance of canopy structural heterogeneity at maturity. Discussion Overall, the proposed PCC-AutoGluon-SHAP framework provides a lightweight, accurate, and interpretable approach for UAV-based rice yield estimation across heterogeneous field conditions, offering practical potential for scalable precision agriculture and regional yield monitoring.
Why it matches plant phenotyping methodsUAVマルチスペクトル画像からイネの収量を推定する画像・特徴抽出・機械学習フレームワークを開発し、複数モデルと特徴選択法を比較検証しており、植物表現型取得・推定が研究の中心である。
abstractThis study developed an interpretable automated machine learning framework for rice yield prediction using UAV-based multispectral imagery collected at the maturity stage.
Accurate estimation of crop yield and biomass using UAV-based remote sensing is influenced by flight altitude, plant density, canopy structure, vegetation index (VI) selection, and crop growth stage. This study evaluated how the joint optimization of these factors influences biomass and yield prediction in common buckwheat (Fagopyrum esculentum Moench var. 'Yangjeol'). Field experiments were conducted using broadcast seeding and drill seeding at four row spacings (12.5, 20, 30, and 40 cm) following the complete Latin square design. UAV RGB imagery was acquired at the third-leaf and full-flowering stages from 30, 50, and 60 m altitudes, and vegetation indices Excess Green Index (ExG), Green Leaf Index (GLI), and Normalized Green-Red Difference Index (NGRDI)were extracted. ANOVA with Tukey's HSD revealed significant variations in biomass and yield traits among sowing treatments (p < 0.005). The highest fresh weight was recorded under drill seeding at 12.5 cm spacing, while seed weight was consistently higher under all drill seeding treatments compared with broadcast seeding. The number of seeds per plant peaked under 40 cm spacing, indicating a trade-off between planting density and reproductive output. Strong and significant correlations between vegetation indices and ground-measured traits were observed (r = 0.82-0.98), but these relationships were highly dependent on growth stage, sowing configuration, and UAV altitude. The third-leaf stage under broadcast seeding and full flowering stage under drill seeding at 20 cm spacing showed the strongest and most consistent VI-trait associations. Among UAV altitudes, 50 m provided the most stable predictive performance across traits. ExG and GLI exhibited more consistent relationships with biomass and yield parameters than NGRDI. These findings demonstrate that no single UAV altitude, vegetation index, or growth stage is universally optimal. Instead, coordinated optimization of UAV operational parameters and sowing configurationsubstantially improves the reliability of UAV-based yield and biomass estimation in buckwheat.
Why it matches plant phenotyping methodsUAV RGB画像と植生指数を用いたバイオマス・収量推定の条件最適化と精度評価が研究の中心であり、植物形質の取得手法を実質的に検証している。
abstractAccurate estimation of crop yield and biomass using UAV-based remote sensing is influenced by flight altitude, plant density, canopy structure, vegetation index (VI) selection, and crop growth stage.
Operational satellite monitoring of pasture biomass demands models that extrapolate beyond the range of properties on which they were calibrated. We show that the dominant failure mode of Sentinel-2 pasture-biomass models in tropical Australian rangelands is the saturation and phenological inversion of greenness-based vegetation indices across sites, and that this failure can be substantially repaired with open climate and topsoil covariates from public archives. The work builds on a hierarchical pipeline that scales clip-and-weigh ground truth (n=1120 tare-corrected samples across eleven sites on five Queensland properties) through UAV digital-surface-model imagery to Sentinel-2 predictions, using TabPFN – a pre-trained transformer foundation model for small tabular data – as the regressor at all three nested spatial scales, and a seven-class deep-learning pasture mask (overall accuracy 98.6 %) to suppress mixed-pixel noise. Under a leave-one-site-out (LOSO) cross-validation protocol on twenty site-date aggregates across nine sites, spectral-only models failed to transfer across sites (R2=−0.21, RMSE=4.79 t ha-1). Appending open climate (Open-Meteo ERA5) and soil (SoilGrids 2.0) covariates, and switching to a gradient-boosted regressor on log-transformed biomass, lifted LOSO R2 to +0.07 and reduced RMSE to 4.19 t ha-1. A leaf-nitrogen growth trajectory, predicted by the TabPFN nitrogen regressor developed in our earlier pasture chemistry work, reduced LOSO error by a further 11 % relative to greenness-only growth features. Three additional covariate classes – BARRA-R2 reanalysis climate, three independent fractional-cover products, and Sentinel-1 C-band SAR backscatter – were tested and rejected, all hitting the same RMSE floor. The symmetric negative results suggest that the residual LOSO ceiling at the current nine-property footprint is a sample-size and sensor-saturation limit rather than a feature-engineering one, and that the most tractable operational path forward is to stratify the production model by climatic zone and Queensland Land Type rather than pursue further covariates within a single global learner. Expanding UAV calibration footprints and integrating open climate, soil and plant-chemistry data are complementary, not competing, investments for operational rangeland remote sensing.
Why it matches plant phenotyping methodsUAV・衛星画像、マスク処理、回帰モデルを組み合わせて牧草バイオマスを推定する測定パイプラインを構築し、サイト外交差検証で性能評価しているため、植物形質取得手法が中心である。
abstractThe work builds on a hierarchical pipeline that scales clip-and-weigh ground truth (n=1120 tare-corrected samples across eleven sites on five Queensland properties) through UAV digital-surface-model imagery to Sentinel-2 predictions
Plant phenotyping relevance match · UnverifiedCrossref · Europe PMC · checked 5 Sept 2026
Assessing tools for rapid evaluation of new cultivars across large fields is essential for improving crop yields and ensuring future food security. Current phenotyping approaches remain labor-intensive and imprecise at the field scale, particularly for traits determining light interception and the light extinction coefficient ( K ). While robotic phenotyping and three-dimensional (3D) models have gained interest in estimating light interception in plant canopies, primarily at the single-plant scale or using single-plant-derived virtual canopies, applications at the field-scale canopy level remain limited. In this study, a semi-automated robotic phenotyping platform, PhenoLinc, was deployed to obtain canopy-level multispectral 3D data across 200 diverse wheat genotypes grown under field conditions over two years. 3D canopy architecture revealed substantial genotype-specific variation in inclination angle and K , which influenced radiation use efficiency (RUE), contrasting with the constant K commonly assumed in conventional approaches. This architectural variation was classified as two distinct architectural phenotypes, erectophiles (median angle 65°) and planophiles (59°) at pre-anthesis stages, which converged toward being homogenous by the anthesis stage. Erectophile phenotypes exhibited higher RUE (33.1%) than planophile phenotypes, leading to a higher yield. In yield prediction analyses, 3D-derived architectural traits provided comparable predictive performance to conventional measurements, however, architectural phenotype information reduced prediction error. Together, these findings highlight the value of field-scale robotic canopy phenotyping for characterizing genotype-specific canopy architectural traits and their relationship with yield.
Why it matches plant phenotyping methodsフィールド規模のロボット型3D・マルチスペクトル計測プラットフォームを用いて、コムギ群落の建築形質を取得・評価することが研究の中心である。
abstracta semi-automated robotic phenotyping platform, PhenoLinc, was deployed to obtain canopy-level multispectral 3D data across 200 diverse wheat genotypes grown under field conditions over two years.
Abstract Mangroves play a critical role in coastal ecosystem services, particularly through their capacity to sequester large amounts of atmospheric carbon, contributing to climate change mitigation. Developing accurate mangrove carbon models is therefore essential for monitoring ecosystem condition and carbon stocks at relevant scales. This study aimed to estimate mangrove Above-Ground Carbon (AGC) in Baluran National Park by integrating field measurements and remote sensing data within a Machine Learning (ML) framework. The study utilised an extensive field data collection programme of 60 sampling plots of girth at breast height, canopy cover, tree height, and tree density. Mangrove AGC was estimated using allometric equations. AGC was also modelled by processing satellite images, conducting statistical analyses, developing models with five ML algorithms (Random Forest (RF), Support Vector Machine (SVM), Decision Tree (DT), k-Nearest Neighbour (k-NN), and Gradient Boost (GB)), and checking accuracy using 5-fold cross-validation (CV) of Root Mean Square Error (RMSE). The RF model, using field-measured tree height, Ratio Vegetation Index (RVI), and Transformed Soil-Adjusted Vegetation Index (TSAVI), achieved the best performance ( R² training = 0.93, R² testing = 0.84, 5-fold CV RMSE = 12.20 Mg C ha⁻¹). Predicted AGC ranged from 5.39 to 57.18 Mg C ha⁻¹ (mean ± Standard Deviation (SD) = 30.43 ± 16.09 Mg C ha⁻¹) and showed improved accuracy compared to the global mangrove biomass dataset of (Simard et al., 2019). A key contribution of this study is the integration of field-measured tree height within a satellite-based ML framework, which enhances the accuracy and ecological relevance of AGC estimation compared to approaches relying solely on spectral predictors or remotely sensed canopy height products, offering a practical and cost-effective alternative for sites where UAV or LiDAR data are unavailable. This approach provides a practical method for regional mangrove carbon monitoring, national carbon accounting and supports climate change mitigation efforts.
Why it matches plant phenotyping methodsマングローブの樹高・樹冠情報と衛星データを統合し、機械学習で個体・プロットレベルの地上部炭素量という植物状態を推定する手法を開発・交差検証しており、単なる生態系測定ではなく表現型取得手法が中心である。
abstractAGC was also modelled by processing satellite images, conducting statistical analyses, developing models with five ML algorithms (Random Forest (RF), Support Vector Machine (SVM), Decision Tree (DT), k-Nearest Neighbour (k-NN), and Gradient Boost (GB)), and checking accuracy using 5-fold cross-validation (CV) of Root Mean Square Error (RMSE).
Reproduction assets foundThe authors state that all analysis code (model development, hyperparameter configuration, diagnostics, accuracy assessment) is publicly available in their GitHub repository Mangroves-AGC-Baluran, which reproduces this paper's mangrove AGC machine-learning analysis.Code · publicThe Python codes were available on
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Mangroves-AGC-Baluran.git.Open asset ↗Mangroves-AGC-Baluran.git · Mangroves-AGC-Baluran.gitpdf-raw-page:17 lines:1-379Plant phenotyping relevance match · UnverifiedEurope PMC · checked 5 Sept 2026
Accuracy crop distribution mapping and reliable yield estimation are essential for overcoming fragmentation and decentralization in smallholder farming systems of the Loess Plateau gully region. Multi-source remote sensing data, ancillary datasets, and machine learning techniques were integrated to map maize distribution and estimate yield. First, Sentinel-2 temporal spectral features, vegetation indices, and topographic variables were integrated to identify the optimal maize mapping model by a comparing machine learning algorithms: Random Forest (RF), Extra Trees (ET), Gradient Boosting Decision Tree (GBDT), and Histogram-Based Gradient Boosting Decision Tree (HGBDT). Subsequently, Sentinel-2 optical data and ERA5-Land meteorological data were dynamically resampled and spatiotemporally fused. A maize yield estimation model was then developed by integrating these fused predictors with in-situ measured maize yield samples. Finally, SHapley Additive exPlanations (SHAP) analysis was applied to quantify the feature contribution to both crop mapping and yield estimation, improving model transparency and interpretability. The results indicate that RF model achieved superior performance for maize identification in heterogeneous agricultural landscapes, with an overall Accuracy of 0.825, Precision of 0.849, Recall of 0.933, and F1-Score of 0.889. In the multi-source fusion-based yield estimation task, the HGBDT model yielded the highest predictive accuracy, with an R² of 0.6, RMSE of 1.07 t/ha, relative RMSE (rRMSE) of 11.49%, and MAE of 0.86 t/ha. Here, a methodological advancement is presented toward accurate and interpretable crop mapping and yield estimation in the ecologically complex and topographically fragmented Loess Plateau.
Why it matches plant phenotyping methodsトウモロコシの収量という植物形質を、リモートセンシング・気象データ融合と機械学習で推定する手法を開発・評価しており、単なる農業実験の routine 測定ではない。
abstractA maize yield estimation model was then developed by integrating these fused predictors with in-situ measured maize yield samples.
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.
Accurate yield estimation and crop load monitoring are essential for precision orchard management, supporting targeted fertilization, pruning, thinning, harvest planning, and marketing decisions. However, reliable in-situ monitoring remains challenging because commercial orchards are characterized by severe canopy occlusion, fruit overlap, heterogeneous tree architecture, variable illumination, and complex backgrounds. This review synthesizes advances in multi-modal sensing and deep learning for orchard yield estimation, breaking down the paradigm into intermediate fruit-counting or crop-load monitoring steps and supplementary spectral quality-assessment dimensions. First, yield-related indicators are summarized, including direct phenotypic traits such as fruit number, size, volume, and spatial distribution, as well as indirect structural and physiological proxies such as canopy volume, vegetation indices, flowering intensity, and spectral maturity attributes. Second, representative sensing devices and carrying platforms are reviewed, including red-green-blue (RGB) cameras, red-green-blue-depth (RGB-D) sensors, light detection and ranging (LiDAR), hyperspectral and multispectral systems, unmanned ground vehicles (UGVs), and unmanned aerial vehicles (UAVs). Third, the evolution of estimation methods is discussed, from traditional image processing and machine learning to object detection, instance segmentation, multi-object tracking, point-cloud analysis, remote-sensing regression, and multi-modal fusion. The review shows that no single sensor or algorithm can satisfy all orchard monitoring requirements. Ground-based vision and depth sensing are more suitable for fine-scale fruit counting and sizing, whereas UAV and spectral sensing provide advantages for regional yield mapping and quality-enhanced assessment. Future research should emphasize occlusion-aware perception, robust cross-environment generalization, lightweight edge deployment, standardized benchmarks, and integrated quantity-quality monitoring frameworks for actionable crop load management.
Why it matches plant phenotyping methods果実数・サイズ・体積・空間分布などの植物形質を対象に、センシング機器と画像解析・深層学習による収量推定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 advances in multi-modal sensing and deep learning for orchard yield estimation, breaking down the paradigm into intermediate fruit-counting or crop-load monitoring steps and supplementary spectral quality-assessment dimensions.
Accurate crop yield estimation is essential for food-security planning, supply-chain logistics and crop-insurance indexing. However, field-level forecasting in rainfed cotton systems can be affected by human bias, spatial error and seasonal variability. This study evaluated the comparative accuracy, statistical efficiency and predictive reliability of three field sampling protocols for cotton yield estimation under actual farming conditions. Primary data were collected from 31 commercial cotton plots in Sanglud, Morgaon Sadijan and Ural villages in Akola district, Maharashtra. The evaluated methods were the 5 x 5 m crop-cut experiment, plant-based estimation at the open-boll stage and area-based quadrat sampling, assessed across the first and second picking phases. Predictive performance was compared with ground-truth harvested yields using mean actual yield, percentage error, standard deviation and root mean square error (RMSE). The 5 x 5 m crop-cut method showed the closest agreement with actual yield, with low dispersion (s = 2.37) and RMSE (1.24), producing a +5.97% error in the first picking and a -0.29% error in the second picking. The plant-based method overestimated yield by +73.60% in the first picking and underestimated by -31.20% in the second picking, reflecting selection bias and late-season boll attrition. Quadrat sampling showed persistent overestimation (+18.30% and +30.40%; s = 3.73). The findings support the 5 x 5 m crop-cut protocol as the most reliable approach among the methods evaluated.
Why it matches plant phenotyping methods綿花収量という植物形質の推定について、複数のサンプリング手法を比較し、収穫実測値を基準に精度・誤差・RMSEを検証しているため、手法検証が中心である。
abstractThis study evaluated the comparative accuracy, statistical efficiency and predictive reliability of three field sampling protocols for cotton yield estimation under actual farming conditions.
Accurate district-level wheat yield forecasting is critical for Kazakhstan, the world’s seventh-largest wheat exporter. Prior remote-sensing studies typically compute vegetation indices over entire administrative units without isolating cropland, diluting the crop-specific signal and biassing remote-sensing–climate comparisons. A 25-year (2000–2024) dataset was assembled for 149 Kazakh districts (n = 2378 district–year observations, ~390 features), integrating crop-masked Sentinel-2/Landsat-7 optical indices, Sentinel-1 SAR, TerraClimate, and station, soil, and terrain data, and a HistGradientBoosting model was evaluated under both spatial (GroupKFold) and temporal (expanding-window) cross-validation. Ten-metre cropland masking substantially improved index–yield correlations, especially early in the season, and SAVI consistently outperformed NDVI from June onward. The best configuration—crop-masked optical indices with TerraClimate—achieved R2 = 0.646 (RMSE = 0.349 t/ha) under spatial cross-validation, whereas adding SAR yielded no significant gain. Pre-season winter-climate data (January–March) reached about 91% of full-year accuracy, enabling forecasts months before sowing. Critically, temporal cross-validation produced a markedly lower mean R2 = 0.413, a predictability gap (ΔR2 = 0.233) that provides a more representative estimate of operational forecast accuracy. Residuals showed no significant spatial autocorrelation. These results indicate that cropland masking and joint reporting of spatial and temporal cross-validation are valuable for yield prediction in semi-arid continental environments.
Why it matches plant phenotyping methods作物マスク付き光学・SARリモートセンシング指標から小麦収量を推定し、交差検証、指標比較、時空間移転性を評価しており、植物形質取得・推定手法が研究の中心である。
abstractintegrating crop-masked Sentinel-2/Landsat-7 optical indices, Sentinel-1 SAR, TerraClimate, and station, soil, and terrain data, and a HistGradientBoosting model was evaluated under both spatial (GroupKFold) and temporal (expanding-window) cross-validation.
Tapioca is a vital root crop whose yield is influenced by multiple environmental, soil, and physiological factors.Traditional yield estimation methods depend upon statistical models and manual sampling, which often lack real-time accuracy and are time-consuming and labour-intensive.The combination of Internet of Things (IoT) sensor networks and Unmanned Aerial Vehicle (UAV)/satellite imagery, with deep learning (DL) models, gives a promising solution for accurate real-time yield prediction.In this study, sensor data (soil moisture, weather parameters, pH, NPK levels, temperature, and leaf chlorophyll content) are collected using devices like Davis Vantage Pro2, Decagon 5TE and SPAD-502, while image data are captured using DJI Phantom 4 Multispectral UAVs and Sentinel-2 satellite imagery.Pre-processing of sensor data involves missing value imputation, normalization, and feature selection using the Hybrid Frilled Lizard Osprey (HFLO) algorithm, while image data undergo resizing, augmentation, and filtering approach.Image based features are extracted by a position-attention DenseNet-201 model.Also, the features from image data and sensor data are fused using a concatenation mechanism.Finally, fully connected layers and improved support vector regression (ISVR) are used to identify the tapioca yield prediction.The integrated DL methods give higher accuracy than individual modalities for both modalities.The image-based model captures spatial and phenotypic variations, while the sensor-based model captures fine-grained environmental effects.The proposed approach obtained the MAE value of 0.0566, RMSE value of 0.654, and R 2 value of 99.5, demonstrating the potential of multimodal real-time data integration for precision agriculture in tapioca fields.
Why it matches plant phenotyping methodsUAV・衛星画像と環境センサーを統合し、深層学習でキャッサバの収量という植物形質を推定する手法の開発が中心である。
abstractThe combination of Internet of Things (IoT) sensor networks and Unmanned Aerial Vehicle (UAV)/satellite imagery, with deep learning (DL) models, gives a promising solution for accurate real-time yield prediction.
Abstract More than 20 years have passed since forest management inventories were first implemented using discrete-return linear-mode lidar (LML) and the area-based approach (ABA). Among recent sensor innovations, single-photon lidar (SPL) stands out as a particularly promising technology for improving the cost efficiency of ABA. The main objective of this study was to assess the cost efficiency of ABA when reducing SPL point density by increasing flight altitude, thereby enabling larger area coverage. Three SPL datasets (10.1, 24.2, and 59.3 first returns/m2) were compared with two LML datasets (2.6 and 136.9 first returns/m2) and digital aerial photogrammetry (DAP) (61.3 points/m2). The analysis used 249 systematically distributed ground plots across various boreal forest types, and nonlinear models were constructed for basal area, stem density, volume, Lorey’s mean height, and dominant height. Model predictions were further validated using 530 independent plots aggregated to 47 stands. The results showed that SPL achieved model accuracies comparable to LML and consistently better than DAP. When averaging relative root mean square error (RMSE) across all biophysical attributes and forest types, SPL low-density data yielded smaller errors than low-density LML data and DAP in both cross-validation and independent stand validation. For example, in mature, highly productive forest—where more than half of the validation stands were located—the RMSE values for volume were 9.3, 8.7, 15.6, 6.4, 6.8, and 6.2% for LML low density, LML high density, DAP, SPL low density, SPL medium density, and SPL high density, respectively. Furthermore, SPL data collected at multiple flight altitudes indicate that operating above commonly reported in the literature and manufacturer-recommended heights can allow for up to a 30% reduction in flight distance while maintaining comparable model accuracy, although such gains may not translate into proportional cost reductions due to technical and atmospheric constraints limiting suitable flight conditions.
Why it matches plant phenotyping methods森林プロットの生物物理形質を推定する複数のLiDAR・写真測量法を比較し、独立データで精度検証しているため、センサーに基づく植物形質計測法の検証が中心である。
titleA comparison of single-photon lidar, conventional lidar, and digital aerial photogrammetry for area-based forest inventory
A comprehensive intelligent system for corn yield prediction based on the synergy of a Spatio-Temporal Generative Adversarial Network (ST-cGAN) and a recurrent CNN-LSTM architecture has been developed and tested. A multimodal fusion of weather-independent Sentinel-1 radar data, ERA5-Land meteorological factors, and historical Sentinel-2 optical observations was applied. The problem of "biochemical blindness" in radar signals, where radar captures physical plant structure but fails to detect photosynthetic activity, and cloud cover limitations in optical remote sensing was successfully resolved. To achieve this, an early fusion strategy was implemented. The ST-cGAN simultaneously processes current SAR data for the structural macro-state, historical optical data for the last known biochemical baseline, and a 10-day history of meteorological priors to enforce physiological constraints. Consequently, if radar indicates high biomass but meteorological data reveals severe drought, the neural network mathematically recognizes biological stress and synthesizes proportionally depressed NDVI and NDRE indices, preventing the hallucination of falsely healthy crops. Dynamic synthesis of missing NDVI and NDRE vegetation indices was conducted under prolonged continuous cloud cover (up to 21 days), achieving a high structural similarity index (SSIM = 0.89). Temporal discriminators for frame sequence analysis were introduced into the architecture, improving the edge-preserving index by 18 % and minimizing spatial artifacts at field boundaries. Pixel-level regression was performed for a 15,000-hectare test area in the Western Forest-Steppe of Ukraine based on reconstructed time series covering 15 critical phenological stages. It was established that the proposed architecture reduces the root mean square error (RMSE) to 0.48 t/ha with a coefficient of determination (R2) of 0.90. Statistical analysis proved the significant superiority of the developed method over industry-standard gap-filling algorithms (e.g., STARFM). A scalable decision-support system for optimizing harvest logistics and financial planning under any atmospheric conditions was presented. Future research directions involving neural network knowledge distillation for IoT devices and UAV data integration were outlined.
Why it matches plant phenotyping methods雲下で欠測するNDVI・NDREなど植物状態指標を再構成する深層学習手法の開発と、SSIM・RMSE・R2および既存手法との比較検証が中心であり、単なる収量予測ではなく植物表現型推定手法に該当する。
abstractDynamic synthesis of missing NDVI and NDRE vegetation indices was conducted under prolonged continuous cloud cover (up to 21 days), achieving a high structural similarity index (SSIM = 0.89).
Accurate measurement of carbon is stored in plants is essential for evaluating strategies to reduce greenhouse gas emissions. The macauba palm (Acrocomia aculeata) is a native species of South America with high potential for oil production, ecological restoration, and carbon sequestration. Traditional methods to estimate carbon stocks, such as cutting down trees and performing laboratory analysis, are destructive, expensive, and impractical on a large scale. This study tested an alternative approach that combines UAV imagery, computer vision, and artificial intelligence to estimate carbon in macauba palms without damaging the plants. High-resolution aerial images were collected at four sites in Brazil, and a deep learning model (YOLOv8s-seg) was trained to automatically detect and measure palm crowns, achieving a mean Average Precision (mAP@50) of 0.956, precision of 0.946, and recall of 0.944. Plant height was estimated from canopy height models derived from photogrammetric processing of the UAV imagery. Crown diameter and height estimates showed strong correlations with field measurements (r = 0.81 and r = 0.82, respectively), with mean absolute errors of 0.26 m for diameter and 0.61 m for height. Both parameters were used in allometric equations to calculate carbon stock. Carbon estimates ranged from less than 1 ton per hectare in young plantations to more than 190 tonnes per hectare in older stands. These results demonstrate that artificial intelligence and UAV imagery provide a fast and scalable approach for estimating structural variables of macauba palms. However, carbon stock estimates remain sensitive to the allometric equations used and should be interpreted with caution, particularly at the individual level. Therefore, the proposed approach should be understood as a non-destructive monitoring framework rather than a fully generalized carbon prediction model, while still offering a valuable tool to support sustainable agriculture, carbon markets, and land-use policies.
Why it matches plant phenotyping methodsUAV画像、コンピュータビジョン、深層学習を用いてヤシの樹冠径・樹高を自動推定し、現地測定と比較検証している。植物の構造形質取得と炭素量推定の技術が研究の中心である。
abstractThis study tested an alternative approach that combines UAV imagery, computer vision, and artificial intelligence to estimate carbon in macauba palms without damaging the plants.
We evaluated a multi-output neural network framework for jointly analyzing maize grain yield (GY) and root lodging percentage (LP) using above-ground morphological traits measured under defined environmental conditions. To address model robustness, the multi-output neural network was compared with linear regression, elastic net, random forest, and XGBoost using repeated five-fold cross-validation, an 80/20 holdout split, and independent year-wise validation. Under repeated cross-validation, XGBoost provided the strongest average predictive performance for both traits, with R2 values of 0.57 for GY and 0.67 for LP. The multi-output neural network showed moderate performance, with R2 values of 0.49 for GY and 0.57 for LP. Final holdout performance for the neural network for GY and LP was R2 = 0.64 and R2 = 0.92, respectively. Year-wise validation showed weak temporal transferability because the two seasons differed not only in environmental conditions, but also in lodging mechanism. Repeated permutation importance identified ear width (EW), kernel row number (RNE), thousand kernel mass (KM1000), and kernel number per ear (KNE) as important predictors of GY, while LP prediction was most strongly associated with internode major diameter (IDmajor), ear length (EL), and the number of green leaves (NGL). Across both permutation importance and SHAP, only RNE and NGL were consistently shared between GY and LP. Supplementary ALE diagnostics indicated that RNE showed increasing model-estimated effects for both predicted GY and LP, whereas NGL showed a positive association with predicted GY but a decreasing or nonlinear association with predicted LP. These results show that joint modeling can support exploratory trait interpretation, but the predictive relationships remain environment-specific and should not be interpreted as causal or broadly transferable without further multi-environment validation.
Why it matches plant phenotyping methods穀粒収量と倒伏率という植物形質を推定する多出力ニューラルネットワーク等のモデルを開発・比較し、交差検証、ホールドアウト、年次外部検証で性能評価しており、計算的形質推定が中心である。
abstractWe evaluated a multi-output neural network framework for jointly analyzing maize grain yield (GY) and root lodging percentage (LP) using above-ground morphological traits measured under defined environmental conditions.
Accurate and wide-area estimation of seaweed biomass is essential for evaluating blue carbon. Conventional diver surveys and two-dimensional (2D) aerial imagery analysis face challenges such as intensive labor and biomass underestimation. While Unmanned Aerial Vehicle-based Light Detection and Ranging (UAV-LiDAR) provides dense 3D spatial data, classifying point clouds in extremely shallow coastal waters with dense kelp and artificial structures remains difficult. This study establishes a high-accuracy biomass estimation method using UAV-LiDAR and PointNet. A heuristic hybrid filtering approach combining physical constraints and local statistics was developed to automatically generate high-quality reference data. The trained PointNet successfully segmented complex point clouds into four classes with an overall accuracy of 94.2%. To calculate biomass, we introduced a volume correction model based on point cloud density (coverage) to mitigate overestimation caused by internal canopy gaps. This correction yielded estimated wet weights nearly identical to the in situ measurements (an approximate 3% difference), confirming highly accurate biomass reproduction. Furthermore, while the conventional 2D maximum likelihood method underestimated total biomass, our 3D point cloud analysis successfully quantified the dense, overlapping canopy. This framework significantly improves the efficiency and accuracy of blue carbon monitoring.
Why it matches plant phenotyping methodsUAV-LiDARとPointNetによる海藻の3D点群分割および biomass 推定手法を開発・検証しており、植物体のバイオマスという形質の取得が研究の中心である。
abstractThis study establishes a high-accuracy biomass estimation method using UAV-LiDAR and PointNet.
Plant phenotyping relevance match · UnverifiedOpenAlex · Crossref · Europe PMC · checked 5 Sept 2026
Quantitative phenotyping of pepper seedlings is important for greenhouse plug tray seedling cultivation, but it remains constrained by inefficient manual monitoring, complex greenhouse backgrounds, and growth-stage-dependent discrepancies between two-dimensional image traits and actual leaf biomass. In this study, a cascaded vision framework with stage-specific morphological correction was developed for nondestructive seedling phenotyping. The framework integrated Visual Dynamic Momentum YOLO (VDM-YOLO) for individual seedling localization and growth-stage recognition, Variance Guided Strip Ghost Gated UNet (VSG-UNet) for lightweight, high-resolution leaf segmentation, and a stage-aware correction model for leaf dry biomass estimation. In performance evaluation, VDM-YOLO achieved a mean average precision at an intersection over union threshold of 0.5 (mAP0.5) of 89.27%, improving mAP0.5 by 1.82 percentage points over YOLOv12. VSG-UNet achieved a mean intersection over union (mIoU) of 83.9% and a Dice coefficient of 81.8%, while reducing floating point operations (FLOPs) and parameters by 44.2% and 61.2%, respectively, compared with U-Net. After stage-aware calibration, the coefficient of determination (R2) between segmented area and leaf dry weight increased from 0.764 to 0.813, and the root mean square error (RMSE) decreased from 0.0210 g to 0.0190 g. These results demonstrated that the proposed framework provided a proof of concept approach based on RGB images for the nondestructive assessment of leaf area and leaf dry biomass in pepper seedlings under restricted experimental conditions.
Why it matches plant phenotyping methodsRGB画像による葉の検出・セグメンテーションと、葉面積から葉乾燥バイオマスを推定する手法を開発・評価しており、植物表現型取得が研究の中心である。
abstracta cascaded vision framework with stage-specific morphological correction was developed for nondestructive seedling phenotyping.
Background Accurate pre-harvest yield estimation of underground bulb crops such as onion and garlic is important for precision agriculture, harvest planning, and food-security-oriented decision-making. However, their harvestable organs develop below ground and cannot be directly observed using conventional remote sensing methods. This study aimed to develop a non-destructive yield estimation framework by integrating UAV-based hyperspectral imaging with hybrid machine learning models. Method Field experiments were conducted in Muan-gun, Korea, using onion and garlic as representative underground bulb crops. UAV-based hyperspectral images, crop growth traits, and destructive live bulb weight measurements were collected during the growing period. Hyperspectral images were processed through geometric correction, radiometric correction, and Savitzky-Golay spectral smoothing. Three dimensionality reduction methods, including genetic algorithm (GA), principal component analysis (PCA), and clustering, were used to reduce spectral redundancy. Five prediction models, including random forest (RF), XGBoost, partial least squares regression (PLSR), multilayer perceptron (MLP), and residual network (ResNet), were then evaluated for live bulb weight prediction. Result Significant spectral differences were observed in the 550-680 nm and 730-800 nm bands, which were closely associated with crop yield and below-ground bulb development. GA was the most effective feature selection method for extracting yield-related spectral bands. For onion yield prediction, the GA + RF model achieved the highest predictive accuracy, with an R 2 of 0.9656 and an NRMSE of 18.55%. For garlic yield prediction, PLSR showed the best performance, with an R 2 of 0.9260 and an NRMSE of 27.20%. Conclusion The proposed UAV-based hyperspectral framework enables accurate, real-time, and non-destructive yield estimation for underground bulb crops. This approach reduces reliance on labor-intensive destructive sampling and provides a practical tool for precision crop monitoring and data-driven agricultural management.
Why it matches plant phenotyping methodsUAVハイパースペクトル画像と機械学習による地下球根の収量（生体球重）推定フレームワークの開発・比較評価が研究の中心であり、植物形質の取得・推定手法に該当する。
abstractThis study aimed to develop a non-destructive yield estimation framework by integrating UAV-based hyperspectral imaging with hybrid machine learning models.
Predicting crop photosynthetic traits from UAV imagery requires frameworks that connect canopy-level spectral observations to leaf-level physiological processes. Existing approaches rely on empirical vegetation indices (VIs) and standard machine learning models, lacking physical interpretability and appropriate deep learning architectures for image data. We developed a physics-informed multi-output machine learning framework that combines PROSAIL radiative transfer model inversion-derived biophysical parameters with spectral VIs and texture features (TFs), applies two spatial deep learning architectures, a Vision Transformer (ViT) and a 2D convolutional neural network (CNN), to multispectral image patches, and introduces a hybrid architecture that fuses PROSAIL-derived features with ViT spatial embeddings. The framework was evaluated for predicting CO 2 assimilation rate ( A ), stomatal conductance ( g sw), Photosystem II efficiency ( F v’/ F m’), aboveground biomass (AGB), and grain yield in a subset of seven European winter wheat varieties selected from a larger 18-variety field experiment across two growing seasons (2022–2024). Model performance was evaluated using random hold-out tests and leave-one-variety-out (LOVO) validation with bootstrap confidence intervals. For grain yield, the best tabular models achieved R 2 = 0.92–0.96, and the ViT on image patches achieved a competitive R 2 = 0.92. ViT delivered the best performance in predicting g sw. BorutaSHAP selected PROSAIL-derived features alongside empirical VIs, confirming that physics-informed features provide complementary information. The hybrid ViT+PROSAIL model matched or outperformed ViT-only for most traits under LOVO validation, with the clearest gain observed for grain yield, indicating that physics-based features can help regularize spatial representations for improved cultivar-level transferability. This study demonstrates that integrating radiative transfer model physics with spatial deep learning advances UAV-based high-throughput phenotyping of photosynthetic traits in breeding programs.
Why it matches plant phenotyping methodsUAVマルチスペクトル画像から光合成形質、バイオマス、収量を推定する物理情報機械学習・画像解析フレームワークを開発し、複数の検証法で性能評価しており、植物表現型取得・推定法が中心である。
abstractWe developed a physics-informed multi-output machine learning framework that combines PROSAIL radiative transfer model inversion-derived biophysical parameters with spectral VIs and texture features (TFs), applies two spatial deep learning architectures, a Vision Transformer (ViT) and a 2D convolutional neural network (CNN), to multispectral image patches, and introduces a hybrid architecture that fuses PROSAIL-derived features with ViT spatial embeddings.
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.
Genome-wide association studies (GWAS) have advanced crop genetics by the detection of loci controlling complex traits; however, their power is often constrained by the quality and the throughput of phenotypic data. In this study, we integrated hyperspectral and genomics data to investigate the genetic architecture of spectral signatures associated with yield components in wheat. A diverse panel of 341 soft wheat lines was evaluated over three years, and hyperspectral data were collected using a UAV-mounted sensor. Among 273 spectral bands, those most strongly correlated with grain yield (GY), thousand-grain weight (TGW), and grains per unit area (GN) were selected. Principal component analysis was used for dimensionality reduction, and the first principal component (PC1), here defined as the hyperspectral phenome, accounted for 78.9%-97.1% of overall variance. The GWAS using both manual phenotypes and hyperspectral phenomes identified 31 significant marker-trait associations (MTAs), including several pleiotropic loci shared across traits and data types. A notable SNP on chromosome 1A, associated with all three hyperspectral phenomes, was located within a gene specifying a chlorophyll a-b binding protein, a key component of photosynthesis and stress response. Additional MTAs were linked to genes involved in cytochrome P450 metabolism and LRR proteins, highlighting their roles in yield and environmental response. Overall, this study shows that hyperspectral imaging serves as a valuable, high-throughput secondary correlated trait for uncovering novel loci and dissecting the genetic basis of complex yield traits in wheat.
Why it matches plant phenotyping methods小麦の収量関連形質を推定するUAV搭載ハイパースペクトル計測と、スペクトルデータからフェノームを抽出する解析が研究の中心であり、GWASへの実質的な応用として記述されている。
abstracthyperspectral data were collected using a UAV-mounted sensor
Abstract This study investigates the accuracy of Multiple Linear Regression (MLR) and Artificial Neural Networks (ANN), specifically a hybrid Genetic Algorithm-ANN (GA-ANN), for predicting wheat yield in plant breeding. This research, conducted using 782 wheat genotypes in Rafsanjan, Iran, compares MLR and ANN methodologies. MLR, using seven traits selected via stepwise regression, achieved an R² of 0.90, the root of mean square of error (RMSE) of 14, Average absolute percentage error (MAPE) of 13.3, and Average deviation of prediction from the actual value (MAE) of 10. Key traits identified were biological weight (weight of total plant per line, WPP) and harvest index (HI). Conversely, the GA-ANN model, employing six selected traits, demonstrated superior performance with R² values of 0.94, 0.96, and 0.94 for training, testing, and combined datasets respectively. Validation metrics for the ANN model were MSE of 144.3, RMSE of 12, and MAE of 5.7. GA-ANN selected height, peduncle length, days to flowering, spike length, biological weight, and harvest index as significant predictors. The results underscore that ANN models, particularly when combined with genetic algorithms for feature selection and optimization, can improve prediction accuracy by modeling complex, non-linear relationships in agricultural data, therefore providing more precise yield prediction tools for plant breeders. This study emphasizes the need for advanced predictive techniques in achieving more accurate assessments of crop yield for sustainable agriculture.
Why it matches plant phenotyping methods小麦遺伝子型レベルの収量という植物形質を対象に、MLRとGA-ANNの予測精度を比較・検証しており、計算による形質推定手法が研究の中心です。
abstractThis study investigates the accuracy of Multiple Linear Regression (MLR) and Artificial Neural Networks (ANN), specifically a hybrid Genetic Algorithm-ANN (GA-ANN), for predicting wheat yield in plant breeding.
Abstract Purpose Robotic harvesting systems are commonly evaluated in canopies treated as fixed operating environments, although kiwifruit canopy architecture is actively shaped by seasonal pruning, fruit thinning, tipping, and cane training. This study developed HarvestField, a decision-support framework for quantifying how robot-oriented canopy management affects harvesting feasibility before field operation. Methods HarvestField defines a spatial harvestability field \(\:\mathscr{H}\left(x\right)\in\:\left[\text{0,1}\right]\) as the product of reachability, visibility, clearance, and detachability sub-fields. A mass-weighted field average at fruit positions yields the Harvested Yield Index (HYI). The framework couples an L-system-based functional–structural plant model of Hayward kiwifruit with NSGA-III multi-objective optimisation over six management variables, jointly evaluating HYI, yield, and labour cost. Results Calibration against a published 12,000-fruit robotic kiwifruit harvesting benchmark produced HYI = 0.562, with an absolute deviation of 0.004 from the observed success rate of 0.558. HarvestField-optimised management increased mean HYI relative to standard management (0.642 versus 0.587). Under equal fruit counts, \(\:\mathscr{H}\)-guided thinning improved HYI by up to 0.301 compared with uniform thinning. Sobol analysis identified clearance neighbourhood radius as the dominant parameter (\(\:{S}_{T}=0.576\)). Conclusion HarvestField provides a spatially explicit and robot-specific framework for linking kiwifruit canopy management with harvesting feasibility. It supports management trade-off analysis while indicating the need for independent orchard-scale validation before deployment.
Why it matches plant phenotyping methodsキウイフルーツ樹冠の可視性・到達性・クリアランス・離脱性を統合して、果実位置ごとの収穫可能性を定量化する計算フレームワークが研究の中心であり、単なる収穫対象の検出を超えた植物構造由来の状態推定である。
abstractThis study developed HarvestField, a decision-support framework for quantifying how robot-oriented canopy management affects harvesting feasibility before field operation.
Plant phenotyping relevance match · UnverifiedOpenAlex · Europe PMC · Crossref · checked 6 Sept 2026
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
Plant phenotyping based on unmanned aerial vehicles still faces challenges regarding the direct correlation between spectral information with field-collected variables, due to the influence of environmental factors and the considerable variation among maize phenological stages. Therefore, the objectives of this research were: I) to evaluate the interaction of nitrogen doses and evaluation environments (phenological stages and growing seasons) and variance components for field variables and vegetation indices; II) to identify the most suitable indices according to the evaluation environments; and III) to predict field variables based on relevant vegetation indices identified through the proposed methodology. The study was conducted using a randomized complete block design with four repetitions, in which treatments consisted of six nitrogen (N) topdressing doses (0, 50, 100, 200, 300, and 400 kg ha−1) during the 2022/2023 and 2023/2024 growing seasons. Evaluations of agronomic variables and image acquisition were performed in five distinct phenological stages throughout the maize crop cycle. The data were analyzed using deviance analysis and variance components, principal component analysis (PCA), and multivariate linear modeling for the prediction of field variables. Our results demonstrated that all indices were affected by the interaction between N doses and evaluation environments (phenological stages and growing seasons). Additionally, the most reliable were EXGRaw, TGI, GNDVI, NDRE, CIRE, GVI, CVI, BNDVI, PanNDVI, SRNIRRe, SFDVI, RGBindex, NDVI, SAVI, MSAVI, and OSAVI, which showed clustering patterns according to growing season condition and phenological stage. Finally, the variables predicted using the proposed methodology achieved coefficients of determination above 0.80, except for shoot biomass and 100-grain weight. Therefore, it can be concluded that vegetation indices are influenced by the evaluated environment; however, the proposed framework based on the deduction of fixed and random effects enables the prediction of field variables with high accuracy using relatively simple models.
Why it matches plant phenotyping methodsUAVマルチスペクトル画像から植生指数を選定し、農業形質を予測する方法論の開発・評価が研究の中心であり、植物形質の取得・推定に直接関与している。
titleMethodology for Selecting Stable UAV-Based Vegetation Indices for Prediction of Agronomic Variables in Maize Using a Multispectral Sensor.
Reproduction assets foundThe paper's supplementary file contains the REML-BLUP adjusted values for all vegetation indices and field variables, which directly reproduce the paper's phenotyping measurements and underpin its computational analysis. The raw UAV imagery and field data are only available on request, and the EstimateBreed R package (Dataset · publicdual author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to people or property resulting from any ideas, methods, instructions or products referred to in the content.
Supplementary Materials
The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/plants15121782/s1 , Table_Supplementary_1. This table contains all vegetation indices and field variables with values adjusted using the RELM-BLUP methodology.
Author Contributions
C.d.S.L.: Conceptualization, methodology, validation, visualization, writing—original draft, writing—review and editing. A.J.T.S.: Data collection and iOpen asset ↗lines:76-146Plant phenotyping relevance match · UnverifiedEurope PMC · checked 5 Sept 2026
Abstract Accurate prediction of maize yield is crucial for improving field management and enabling timely yield estimation. To improve the accuracy and determine the optimal timing of field-scale spring maize yield estimation in the Junggar Basin, this study focuses on spring maize in this region. In 2023, UAV-based multispectral images were acquired at three key growth stages: jointing, filling, and milk stages. Eighteen spectral features significantly correlated with yield were selected. Spring maize yield prediction models were constructed using XGBoost, CatBoost, RF, DT, SVR, GP, LR, and a stacked ensemble learning model, respectively, revealing differences in prediction accuracy across growth stages. Finally, SHAP was used for model interpretability analysis. The results show that: (1) The milk stage achieved the highest prediction accuracy (R² = 0.761, MAE = 0.067 kg·m⁻², RMSE = 0.089 kg·m⁻², MAPE = 5.055%), outperforming the jointing and early grain-filling stages, thereby resolving the uncertainty regarding the optimal timing for UAV-based yield estimation of spring maize in the Junggar Basin. (2) Compared with traditional machine learning algorithms, the stacked ensemble model exhibited stronger robustness and generalization ability. This study provides a technical reference for timely yield estimation and field management of spring maize in irrigated areas of the Junggar Basin, supporting regional food production stability.
Why it matches plant phenotyping methodsUAVマルチスペクトル画像からトウモロコシ収量を推定し、複数生育段階・機械学習モデルの精度と頑健性を比較して最適推定時期を評価しており、表現型推定手法が研究の中心である。
abstractUAV-based multispectral images were acquired at three key growth stages: jointing, filling, and milk stages.
Advancing wheat breeding requires reliable digital traits that capture genotype × environment interactions and improve yield prediction across diverse growing conditions. Although vegetation indices such as the normalized difference vegetation index (NDVI) are widely used, their performance relative to yield variability and environmental stress remains underexplored in multi-environment trials. This study utilized unmanned aerial vehicle multispectral imagery to derive NDVI and assess its relationship with grain yield in 34 spring and winter wheat variety trials. These trials included data across seven Washington State locations in different precipitation zones, five years (2019 to 2023), and some irrigated trials. Environments were grouped into high-, moderate-, and low-stress clusters based primarily on precipitation and temperature. Variability was quantified using the coefficient of variation, and correlations between grain yield and NDVI were evaluated within and between varieties across environments based on market classes (hard and soft spring and winter wheat). Across all environments and varieties, NDVI strongly correlated with grain yield ( r = 0.79-0.82, p r = 0.72 in hard spring, r = 0.53 in soft spring). These conditions also improved discrimination between varieties. Although heritability patterns were not clearly differentiated by stress clusters, environments with higher genetic control of yield also tended to show stronger NDVI heritability. Overall, NDVI reliably captured wheat grain yield, which is governed by the genotype × environment driven variability, with its predictive value strongest in stress-prone conditions. These findings underline NDVI's usability as a practical digital trait for improving variety testing and guiding breeding decisions in challenging environments.
Why it matches plant phenotyping methodsUAVマルチスペクトル画像からNDVIを抽出し、複数環境・品種で収量との関係、予測性、遺伝率を評価しており、デジタル植物形質の測定・検証が中心である。
abstractThis study utilized unmanned aerial vehicle multispectral imagery to derive NDVI and assess its relationship with grain yield in 34 spring and winter wheat variety trials.
Reproduction assets found保存済みの本文根拠を更新済みルールで再検証し、公開資産1件を確認しました。Dataset · publicTrial data, including grain yield, variety, and market class information, were obtained from the Washington State University Extension Cereal Variety Selection and Testing Program ( https://smallgrains.wsu.edu/variety/ ).Open asset ↗lines:38-48Plant phenotyping relevance match · UnverifiedOpenAlex · Europe PMC · checked 15 Sept 2026
High-fidelity 3D reconstruction and precise phenotypic parameter extraction of banana plants are critical for crop growth monitoring and yield estimation in precision agriculture. However, traditional methods encounter significant bottlenecks: LiDAR systems are cost-prohibitive for widespread adoption, while traditional photogrammetry often fails to handle the complex canopy structures, severe occlusions, and weak texture features characteristic of banana leaves. To address these limitations, this article proposes a novel framework for 3D reconstruction and automatic phenotyping based on multi-view images captured by mobile phones. We introduce BN-NeRF, an enhanced Neural Radiance Field method built upon Instant-NGP. Specifically, we integrate three key technical improvements: (1) frame-level geometric calibration to correct camera pose drift caused by handheld motion; (2) sparse geometric anchoring to explicitly constrain depth and scale using sparse point clouds; and (3) thin-leaf prior regularization to suppress artifacts and improve the geometric accuracy of leaf surfaces. Building on this reconstruction, we establish a complete pipeline to recover explicit metric geometry from implicit radiance fields. By combining mesh topological analysis with geodesic algorithms, we achieve automated and precise extraction of key morphological parameters. Extensive experiments were conducted on a dataset of 90 banana plants in a real-world orchard. The results demonstrate that BN-NeRF achieves superior rendering quality (PSNR of 32.4 dB, SSIM of 0.951, and LPIPS of 0.152) while maintaining inference speeds comparable to Instant-NGP. Furthermore, the extracted phenotypic parameters showed strong agreement with manual ground truth across both leaf-level and structural traits. In addition to trait-specific regression performance, the evaluation also includes normalized completeness analysis, calibration-cube-based scale validation, and Bland-Altman agreement analysis, supporting the measurement reliability of BN-NeRF for field phenotyping. This study demonstrates that low-cost smartphone-based acquisition, combined with BN-NeRF, can support accurate field phenotyping of banana plants. In addition, an implemented mobile-cloud system was functionally validated through repeated end-to-end runs on an iPhone 13 client and a cloud workstation.
Why it matches plant phenotyping methodsスマートフォン画像からの3D再構成と植物形態形質抽出を中核とするBN-NeRF手法を開発し、圃場データで精度・再現性を検証しているため。
abstractthis article proposes a novel framework for 3D reconstruction and automatic phenotyping based on multi-view images captured by mobile phones
Accurate detection of tobacco plants in complex field environments is critical for precision agriculture, crop monitoring, and yield estimation. Traditional manual counting methods are time-consuming, labor-intensive, and susceptible to environmental and subjective factors. In this study, we propose an improved YOLO11-based framework for automated tobacco plant detection, specifically designed to address challenges such as scale variation, dense distribution, and background interference. The framework integrates four key modules: the Edge-Enhanced Feature Stem (EEFS) to strengthen low-level feature extraction, the Multi-Scale Kernel Interaction (MSKI) to capture multi-scale contextual information, the Adaptive Weighted Feature Fusion (AWFF) to optimize feature aggregation, and the Global–Local Synergistic Attention (GLSA) to enhance feature discrimination by jointly modeling local details and global context. A comprehensive UAV-based tobacco dataset was constructed, encompassing multiple lighting conditions, collection heights, and observation angles. Experimental results demonstrate that the proposed method significantly outperforms the YOLO11 baseline and achieves superior performance compared to mainstream YOLO variants. Ablation studies and heatmap visualizations confirm the effectiveness of each module. Furthermore, the model exhibits robust performance under multi-dimensional environmental perturbations, including varying illumination, scale, and camera angles. The proposed framework provides a practical and efficient solution for automated tobacco plant counting, offering potential applications in UAV-based precision agriculture and large-scale crop monitoring.
Why it matches plant phenotyping methodsUAV画像からタバコ個体を自動検出・計数する手法を開発し、専用データセット、比較実験、アブレーション、頑健性評価まで行っており、植物個体数の取得方法が中心です。
abstractwe propose an improved YOLO11-based framework for automated tobacco plant detection
Plant phenotyping relevance match · UnverifiedOpenAlex · Crossref · Europe PMC · checked 5 Sept 2026
Drought is the major abiotic stress limiting soybean growth and yield, yet accurately identifying genotypes that sustain yield under rainfed conditions remains a major bottleneck in soybean breeding. Canopy wilting scores are widely used as a proxy for evaluating plant responses to drought stress. However, most assessments rely on leaf-level visual observations that are inherently subjective and typically based on single time-point scores, providing only a snapshot of stress expression and failing to capture their relationship with yield retention under rainfed conditions. To address these limitations, this study used Unmanned Aerial Vehicle (UAV)-based high-throughput phenotyping at a single growth stage (R4/R5) as a more quantitative and objective alternative to visual scoring, with closer relevance to yield performance under drought conditions. From 2023 to 2025, a total of 85 soybean genotypes developed by soybean breeding programs in Arkansas, Missouri, Kansas, and North Carolina, along with commercial checks, were evaluated under irrigated and rainfed conditions in Stuttgart, Arkansas. Visual canopy wilting scores were recorded at R4/R5, along with vegetation indices captured using UAV-based multispectral imagery. UAV-derived indices showed significant correlations with yield ( r = 0.22 to 0.45, p<0.05) under rainfed conditions. In contrast, visual canopy wilting scores displayed weak and inconsistent associations with yield ( r = -0.28 to 0.35, p<0.05), suggesting limited ability to capture yield retention under rainfed conditions. Unsupervised k -means clustering ( n = 2) of UAV-derived vegetation indices separated genotypes into two distinct canopy response groups that were consistent across 2023 to 2025 rainfed seasons. Significant differences were observed among clusters for several vegetation indices (ARI, CIG, CIRE, GSAVI, GNDVI, GOSAVI, OSAVI, NDVI), indicating contrasting canopy stress responses. Under rainfed conditions, these UAV-defined clusters also differed for grain yield (2023: 1,925.6 vs 1,703.1 kg/ha; 2024: 1,849.9 vs 1,229.2 kg/ha; 2025: 2,056.7 vs 1,773.8 kg/ha), whereas visual wilting scores failed to distinguish yield-retaining genotypes. Overall, UAV-based high-throughput phenotyping offers a robust and yield-relevant alternative to visual wilting scores, supporting the development of drought-tolerant soybean germplasm and cultivars.
Why it matches plant phenotyping methodsUAVマルチスペクトル画像による植生指数抽出を、目視評価と比較・検証し、干ばつ応答および収量保持に関連する表現型測定法として中心的に評価している。
abstractthis study used Unmanned Aerial Vehicle (UAV)-based high-throughput phenotyping at a single growth stage (R4/R5) as a more quantitative and objective alternative to visual scoring
Yield estimation in sugarcane systems remains a major challenge in tropical regions due to the reliance on destructive, labor-intensive, and spatially limited field measurements. Although remote sensing has been widely used for crop monitoring, its predictive performance is often constrained when spectral information is used in isolation. This study proposes a data fusion framework integrating multitemporal Sentinel-2 spectral bands with meteorological variables to improve sugarcane biomass prediction under tropical conditions. A commercial field was monitored throughout the 2022–2023 growing season, and machine learning models, including random forest (RF), support vector machine (SVM), and multiple linear regression (MLR), were developed to estimate stem, foliage, and total biomass. To reduce potential spatial data leakage caused by spatial autocorrelation within the field, model performance was evaluated using Spatial Block Cross-Validation. Results showed that integrating spectral and meteorological data consistently improved predictive performance compared to spectral-only and weather-only scenarios. Spectral bands exhibited stronger relationships with biomass than derived vegetation indices, while maximum temperature and solar radiation were identified as key drivers of biomass variability. RF combined with spectral–weather fusion achieved the highest predictive performance, reaching R2 values up to 0.95, RMSE values as low as 5296.35, and rRMSE values close to 18% for stem biomass, consistently outperforming SVM and MLR. In contrast, spectral-only scenarios produced lower predictive accuracy and higher prediction errors across all biomass variables. This study provides one of the first field-scale implementations under humid tropical conditions in southeastern Mexico, where georeferenced yield data remain scarce.
Why it matches plant phenotyping methodsSentinel-2と気象データの融合および機械学習により、サトウキビの茎・葉・総バイオマスという植物形質を推定する手法を開発・比較検証しており、フェノタイピング手法が中心である。
abstractThis study proposes a data fusion framework integrating multitemporal Sentinel-2 spectral bands with meteorological variables to improve sugarcane biomass prediction under tropical conditions.
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.
Plant phenotyping relevance match · UnverifiedCrossref · Europe PMC · checked 5 Sept 2026
Abstract Deep learning, as a pivotal branch of machine learning, has demonstrated remarkable potential in advancing crop science by effectively integrating genomics and phenomics. This review systematically outlines the application of diverse deep learning architectures—such as convolutional neural networks, recurrent neural networks, and transformers—across key crop genomic tasks, including gene expression prediction, alternative splicing analysis, cis ‐regulatory element identification, epigenomic profiling, and genome‐based trait prediction. In phenomics, these models facilitate high‐throughput extraction of crop phenotypic traits from multispectral, unmanned aerial vehicle, and ground‐based imagery, supporting yield forecasting, disease diagnosis, and stress response monitoring. We critically evaluate the performance and limitations of each model type across tasks, considering trade‐offs between complexity, accuracy, and interpretability, to offer practical guidance for crop researchers. Additionally, the review addresses major challenges in deploying deep learning—such as data scarcity, model transparency, and computational demands—and proposes future pathways to enhance model generalizability, multimodal data integration, and applications in intelligent breeding and sustainable agriculture.
Why it matches plant phenotyping methods作物フェノミクスにおける深層学習による画像からの形質抽出を中心的にレビューしており、フェノタイピング手法の方法論的整理に該当する。
abstractIn phenomics, these models facilitate high‐throughput extraction of crop phenotypic traits from multispectral, unmanned aerial vehicle, and ground‐based imagery
Manual quantification of specialty crop traits, such as flowers and fruits, is often labor-intensive, time-consuming, and inconsistent, limiting scalability and precision. We present PhenoSnap, an artificial intelligence (AI)-powered web application that provides an intuitive and efficient interface for automated specialty crop trait extraction from images. PhenoSnap bridges the gap between advanced computer vision technologies and practical agricultural applications by eliminating the need for programming expertise. This ready-to-use solution can enable growers, breeders, and Extension faculty to accelerate field work and enhance decision-making related to strawberry and tomato yield estimation for breeding selections and strawberry runner management. Written by Santhi Daggubati, Xu Wang, Xue Zhou, Shubham Singh, and Jessica Chitwood-Brown, and published by the UF/IFAS Department of Agricultural and Biological Engineering, June 2026.
Why it matches plant phenotyping methods画像から花・果実などの植物形質を自動抽出するAIウェブアプリケーションの開発・提供が中心であり、植物フェノタイピング手法およびソフトウェアとして適格。
abstractWe present PhenoSnap, an artificial intelligence (AI)-powered web application that provides an intuitive and efficient interface for automated specialty crop trait extraction from images.
Reproduction assets foundThe article describes PhenoSnap, a publicly accessible AI web application for specialty crop trait extraction, and cites a publicly released Dryad imagery dataset (Zhou et al. 2025b) that is a subset of the training data for the Strawberry Runner model. Both are paper-specific, public, and actionable. No author code orDataset · publicDataset preparation
and the training process are detailed in Zhou et al. (2025a),
and a subset of the dataset has been publicly released on
Dryad (Zhou et al. 2025b).Open asset ↗Dryadpdf-raw-page:5 lines:1-55Code / dataset availability confirmedCrossref · Europe PMC · checked 6 Sept 2026
P henotyping remains a critical bottleneck in sorghum ( Sorghum bicolor L. Moench) breeding programs, limiting rates of genetic gain due to labor-intensive yield estimation methods. To address this concern, this study investigates the potential of integrating remote sensing data with machine learning (ML) and deep learning (DL) models to improve sorghum grain yield predictions. Unmanned aircraft systems (UAS)-based imagery was collected across multiple field trials, extracting standard vegetation indices, canopy height features, and panicle traits using a YOLOv11-based object detection model, "YOLO-SORG." Six ML models-including ridge regression (RR), elastic net (EN), LASSO regression (LR), support vector regression (SVR), random forest (RF), and XGBoost (XGB)-were trained to predict plot-level yield using three distinct feature sets: panicle traits, canopy traits, and a combination of both. Results indicate that models relying solely or partially on canopy-derived features provided the most consistent and accurate yield estimates (R 2 ≈ 0.74-0.76), whereas models relying solely on panicle traits performed poorly (R 2 ≈ 0.28-0.42), indicating nadir-derived panicle metrics were potentially being indirectly captured with the canopy traits. Traditional regression models outperformed tree-based ensemble methods in variance partitioning and repeatability ( R ≈ 0.59-0.60), making them more suitable for many breeding applications. These findings highlight the promise of UAS-driven ML pipelines for non-destructive yield prediction but underscore potential limitations of nadir imagery for capturing panicle morphology and use in a robust yield prediction model. Future research should explore the inclusion of multi-temporal imaging, refined feature extraction approaches, and use of oblique, non-nadir imagery to enhance predictive accuracy in sorghum breeding programs.
Why it matches plant phenotyping methodsUAS画像からキャノピー高、穂形質、植生指数を抽出し、機械学習でソルガムのプロット収量を推定するパイプラインが研究の中心であり、形質取得・推定手法の評価も行っている。
abstractthis study investigates the potential of integrating remote sensing data with machine learning (ML) and deep learning (DL) models to improve sorghum grain yield predictions.
Reproduction assets foundThe authors explicitly state that the tabular data and code used in this sorghum yield prediction study are publicly available in their GitHub repository, which is a paper-specific asset containing the analysis code and phenotype data.Code · publicThe tabular data and code used in this study can be found in the following GitHub repository: https://github.com/AcePugh/Sorghum_Yield_Prediction_2025/Open asset ↗AcePugh/Sorghum_Yield_Prediction_2025lines:137-139Plant phenotyping relevance match · UnverifiedOpenAlex · Europe PMC · checked 14 Sept 2026
Predicting canopy traits non-destructively is important for understanding crop growth and improving phenotyping efficiency. Hyperspectral reflectance provides detailed spectral information, but the role of band selection in regression-based trait prediction at the canopy scale remains unclear. In this study, we evaluated the effects of different band-selection algorithms on the prediction accuracy of aboveground biomass (AGB), leaf area index (LAI), and canopy cover (CC) in soybeans across multiple sites, years, cultivars, and irrigation treatments. We compared a full-band partial least squares regression (PLS) model with three band-selection methods (PLS-Variable Importance in Projection (VIP), Bootstrapped least absolute shrinkage and selection operator (LASSO) (BoLASSO), and an ensemble approach), and model performance was assessed using independent validation datasets. The results showed that the effectiveness of band selection depended on the target trait. Full-band PLS provided the highest accuracy for AGB, whereas BoLASSO achieved comparable accuracy to PLS for LAI and CC using a reduced number of selected bands. The selected wavelengths were located mainly in the visible, red-edge, and near-infrared regions. These results indicate that band-selection strategies should be tailored to the target trait and provide a basis for efficient band design in crop phenotyping.
Why it matches plant phenotyping methodsハイパースペクトル反射を用いた作物形質推定について、バンド選択アルゴリズムと回帰モデルを比較・独立検証しており、フェノタイピング手法の技術評価が中心である。
abstractPredicting canopy traits non-destructively is important for understanding crop growth and improving phenotyping efficiency.
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.
Accurate aboveground biomass estimation with quantified uncertainty is essential for precision agriculture, enabling risk-aware decision-making and strategic model improvement. Existing approaches predominantly provide point estimates without uncertainty quantification, limiting their operational utility for trustworthy Artificial Intelligence (AI) deployment. This study presents a Multi-modal Attention-based Uncertainty Quantification Network (MA-UQNet), which achieves superior prediction accuracy (R 2 = 0.856) with well-calibrated uncertainty (97.18% coverage) for wheat aboveground biomass estimation through integrated multi-modal attention, growth stage-specific processing, and epistemic–aleatoric uncertainty decomposition. The framework integrates hyperspectral remote sensing with environmental variables via joint attention mechanisms that adapt to phenological variations. Model development employed a decade-spanning dataset (2012–2022, 1272 samples) collected under factorial combinations of nitrogen rates (0–270 kg/ha), irrigation levels (0–384 mm), and wheat cultivars across four growth stages. Temporal extrapolation validation using chronological partitioning (2012–2019 for training and 2020–2021 for testing) demonstrated robust generalization, substantially outperforming Random Forest (R 2 = 0.751, coverage = 76.61%) and nine representative baselines, including Bayesian Neural Networks (R 2 = 0.805, coverage = 38.31%). Uncertainty decomposition revealed epistemic uncertainty to be moderately dominant (53%) relative to aleatoric uncertainty (47%), indicating that strategic data collection offers greater potential for uncertainty reduction than improving measurement precision alone. These findings provide validated tools for uncertainty-aware biomass estimation in precision agriculture.
Why it matches plant phenotyping methods小麦の地上部バイオマスという植物形質を、ハイパースペクトルリモートセンシングと不確実性推定ネットワークで抽出する手法を開発し、時系列分割と既存手法との比較で検証しているため、植物フェノタイピング手法が中心である。
abstractThis study presents a Multi-modal Attention-based Uncertainty Quantification Network (MA-UQNet), which achieves superior prediction accuracy (R 2 = 0.856) with well-calibrated uncertainty (97.18% coverage) for wheat aboveground biomass estimation
Abstract Warmer temperatures, permafrost thaw, and increased wildfire activity are driving rapid ecological change across the Arctic, significantly altering plant productivity and aboveground biomass (AGB). These rapid changes highlight the urgent need to improve monitoring of vegetation dynamics in the Earth’s northern ecosystems, where high spatiotemporal heterogeneity occurs at scales finer than those captured by traditional satellite observations. The growing use of unoccupied aerial systems (UASs) presents an opportunity to overcome this limitation. Yet, the diversity of UAS platforms, sensors, and data collection and processing workflows presents challenges for developing standardized, generalizable approaches. To address this challenge, we compiled 672 AGB plots co-located with 183 UAS-based structure-from-motion (SfM) or light detection and ranging (LiDAR) surveys collected across the Arctic. Here, we: (1) evaluated the generalizability of UAS-derived canopy structure derived from high-resolution SfM and LiDAR for estimating AGB, (2) assessed scaling errors and their sources in two recent satellite-based AGB products derived from Landsat and moderate resolution imaging spectroradiometer, and (3) demonstrated the use of high-resolution AGB maps to quantify biomass variation across tundra plant functional types (PFTs) and to monitor post-fire recovery. Our results show that both SfM and LiDAR accurately captured AGB and its variability across tundra PFTs using a random forest model (overall root mean squared error: 0.332 kg m –2 ), with mapping performance varying slightly by region and data source. Using UAS-derived AGB maps as a benchmark, we identified systematic biases in satellite-derived AGB products, largely attributable to the magnitude of AGB and structural heterogeneity within coarse-resolution pixels. Applying our model to repeat UAS surveys following a tundra fire on Seward Peninsula, we observed rapid AGB recovery in non-shrub patches, with biomass recovering to pre-fire levels within two years. In contrast, shrub patches recovered more slowly, with AGB gains continuing over 2–4 years through both in-patch growth and lateral expansion (via dispersal) into remaining burned areas. Overall, these findings support the generalizability of UAS-based SfM and LiDAR data for estimating tundra AGB and highlight the need for broader collection and synthesis of such data to improve ecological monitoring and model benchmarking in the Arctic.
Why it matches plant phenotyping methodsUASのSfMおよびLiDARから植物群落の地上部 biomass (AGB) を推定する手法の一般化性能を評価し、衛星推定値のベンチマークにも用いており、植物形質取得が研究の中心である。
abstractevaluated the generalizability of UAS-derived canopy structure derived from high-resolution SfM and LiDAR for estimating AGB
Reproduction assets found保存済みの本文根拠を更新済みルールで再検証し、公開資産1件を確認しました。Code · publicThe codes and training data is available on GitHub: https://github.com/Daryl-Open asset ↗pdf-page:20 lines:1-30Plant phenotyping relevance match · UnverifiedOpenAlex · Crossref · checked 15 Sept 2026
Abstract Background Improving the nitrogen use efficiency (NUE) of pastures has the benefit of reducing costs of production and reducing nitrogen loss to the environment. Genetic variation has been shown to exist for NUE, and hence NUE is a trait for breeding programs. Methods In this study, we develop genomic selection methods for NUE in perennial ryegrass through developing high‐throughput sensor‐based phenotyping and genotyping by sequencing (GBS) technologies. NUE of an advanced perennial ryegrass breeding population was screened in a spaced plant field trial which contained 644 genotypes, 3 nitrogen treatment levels (0, 20, and 40 kg ha −1 per application), and 3 replicates. The trial was conducted for 2 years with a total of 6 nitrogen applications. An unmanned aerial system (UAS) equipped with multispectral sensors was deployed weekly over the trial. Approximately 4–5 weeks after nitrogen fertilizer application, 75–675 selected samples were cut for ground truthing. Prediction models for biomass were developed based on spectral and ground truth data and biomass for each plant was computed. Plants were genotyped by GBS transcriptomics. Results NUE, defined as biomass production per unit of N application, varied significantly with N application level, season and among genotypes. Moderate broad‐sense heritability (0.61–0.72) for NUE was observed. Genomic prediction accuracies were in the range of 0.3–0.5. Conclusions Our results demonstrated that genomic selection for NUE was possible. The genomic prediction developed in these advanced breeding lines may be tested in other genetic backgrounds. The technologies are ready to be extended into other perennial pasture grass species.
Why it matches plant phenotyping methodsUASマルチスペクトルセンシングと予測モデルによるバイオマス推定を開発し、NUE表現型の高スループット取得に用いており、フェノタイピング手法が中心的である。
abstractwe develop genomic selection methods for NUE in perennial ryegrass through developing high‐throughput sensor‐based phenotyping
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.
RSCM is an open-source, process-based crop simulation framework that integrates satellite-derived vegetation indices directly into parameter estimation via Bayesian Maximum A Posteriori (MAP) optimization. This approach automates estimation of leaf area index, aboveground dry matter, and grain yield without extensive ground-based calibration. The system couples a Python data interface with a high-performance C simulation engine, enabling efficient regional-scale processing. Validation using independent datasets for rice, wheat, and maize demonstrated robust performance: yield Model Efficiency reached 0.99, with a minimum ME of 0.67 for wheat. The Bayesian prior regularization constrained parameter estimates while maintaining predictive accuracy. Regional applications in South Korea, North Korea, and the U.S. Corn Belt captured spatial yield gradients and inter-annual variability across millions of pixels. RSCM provides a computationally efficient tool bridging process-based modeling and remote sensing for precision agriculture and food security monitoring.
Why it matches plant phenotyping methods衛星データと作物モデルを統合し、LAI・地上部乾物量・収量という植物形質を推定するソフトウェア手法を開発・検証しており、形質取得・推定法が研究の中心である。
abstractRSCM is an open-source, process-based crop simulation framework that integrates satellite-derived vegetation indices directly into parameter estimation via Bayesian Maximum A Posteriori (MAP) optimization.
Deficit irrigation (DI) is a crucial strategy for optimizing water use in arid and semi-arid agriculture, yet its success depends on accurately determining the crop yield response factor (K y ). This study introduces a novel, machine learning-assisted framework for large-scale estimation of sugarcane K y using satellite-derived water stress indicators. fused Landsat 7/8/9 and MODIS data within the Google Earth Engine platform to generate high-resolution daily Crop Water Stress Index (CWSI) maps for the 2023 season in southern Iran. The Random Forest (RF) algorithm was applied to correct biases in land surface temperature (LST), achieving high accuracy (RMSE < 1.0°C, nRMSE < 3%, rMBE ≈ 0%) before CWSI calculation. Ground measurements from 12 field points, including canopy temperature and yield, were used for calibration and validation. The satellite-based CWSI showed strong agreement with field data (RMSE = 0.05, nRMSE = 11%), with values ranging from 0.18 to 0.71 at dekadal scale. Using this CWSI, K y was computed at dekadal, monthly, and seasonal scales, revealing substantial spatiotemporal variability (0.2–1.63) and an average seasonal K y of 1.05. This value is lower than the FAO-66 default of 1.2, indicating that the standard coefficient may prompt over-irrigation without yield benefits. The analysis further identified early July as the period of peak water stress sensitivity, with K y values exceeding 1.82. This ML-enhanced, satellite-based approach provides a robust tool for deriving spatially explicit K y values, offering a significant advancement for precision irrigation planning and water resource management.
Why it matches plant phenotyping methods衛星データと機械学習で作物の水ストレス状態（CWSI）を推定し、地上測定で較正・検証する手法が中心であるため、植物生理状態のセンシング型フェノタイピングとして含める。
abstractThis study introduces a novel, machine learning-assisted framework for large-scale estimation of sugarcane K y using satellite-derived water stress indicators.
Urban forest carbon sequestration is vital for environmental health, climate change mitigation, and enhancing the quality of life in urban areas. This paper presents a framework for high density point clouds production by integrating point data from aerial photogrammetry, UAV-based LiDAR and terrestrial LiDAR for individual tree measurements and carbon storage estimation. The aerial photos, UAV-based LiDAR and terrestrial LiDAR were observed based on common ground control points and combined using Iterative Closest Point (ICP) algorithm. The combined point cloud was iltered to separate ground points and normalized based on Digital Terrain Model (DTM). The normalized point cloud was used for individual tree segmentation from which individual tree measurements such as, tree height, Diameter at Breast Height (DBH) and crown diameter were estimated. The estimated tree parameters were used for individual carbon estimation. The results show that the individual tree segmentation method signi icantly underestimated the number of trees. The estimation of DBH, tree height, and crown diameter achieved the Root Mean Square Error (RMSE) value of 0.107m, 1.385m and 2.650m respectively. However, in general the estimates experience underestimation as shown by Mean Bias Error (MBE) with 0.003m, -0.636m and 0.001m for DBH, tree height and crown diameter respectively. The estimated values for each individual tree were used for individual tree biomass and carbon storage recording the Root Mean Square Error (RMSE) at 1970.236 kg and 886.606 kgC respectively while attaining the Mean Bias Error (MBE) measure of 140.019 kg and 63.009 kgC each. The proposed framework showed promising results for individual tree carbon estimation. Nonetheless, further attention should be given on individual tree delineation process.
Why it matches plant phenotyping methods航空写真、UAV・地上LiDARを統合し、個体樹木の分離と樹高・DBH・樹冠径を推定して精度評価する手法が中心であり、植物形質計測の技術的検証に該当する。
abstractThis paper presents a framework for high density point clouds production by integrating point data from aerial photogrammetry, UAV-based LiDAR and terrestrial LiDAR for individual tree measurements and carbon storage estimation.
Spatially accurate estimates of forest above-ground biomass (AGB) are indispensable for carbon-stock accounting and sustainable silviculture. Existing mapping approaches face challenges in densely vegetated Coastal Plain forests because of seasonal optical variability, radar–optical saturation, and limited wall-to-wall structural information. We aimed to (i) develop and evaluate a multisensor, AI-enabled fusion framework for landscape-scale AGB mapping, (ii) quantify the added value of seasonal optical data and photogrammetric canopy-height profiles, and (iii) interpret model drivers using explainable artificial intelligence (AI) to relate predictors to forest structure and composition. We mapped AGB across ~ 10,500 km 2 in southeastern North Carolina using wall-to-wall predictors from optical, radar, and photogrammetric sources. Forest Inventory and Analysis plot data (n = 305) were used to train and evaluate an ensemble of gradient-boosted tree models (CatBoost, LightGBM, XGBoost) and a neural network (RealMLP) via cross-validation. Model behavior was interpreted using feature importance and partial dependence analysis. Expanding Sentinel-2 temporal coverage from summer-only to four-season composites improved normalized RMSE by 8.7%. Incorporating canopy-height profiles from NAIP produced the largest accuracy gain, lowering nRMSE by 15.9–18.0% relative to the multisensor baseline, which underscores the critical value of structural information for AGB prediction. Three key predictors illustrated complementary ecological dimensions: the 10th percentile canopy height captured canopy openness, L-band polarimetric alpha indicated volume-scattering regime, and spring red-edge reflectance captured vegetation biochemistry. These findings show that fusing structure, polarimetry, and spectral phenology yields robust AGB maps and improves generalizability across heterogeneous landscapes. This transferable, broadly accessible framework integrating structural, polarimetric, and spectral phenology data enables landscape-scale AGB monitoring and supports targeted conservation planning, restoration tracking, and adaptive management for carbon sequestration. The incorporation of high-resolution wall-to-wall structural data is particularly valuable for improving the accuracy and usability of forest AGB maps, thereby informing more responsive decision-making.
Why it matches plant phenotyping methods森林の地上部バイオマスという植物群落形質を対象に、光学・レーダー・写真測量データを融合した推定フレームワークを開発・評価しており、形質推定手法が研究の中心である。
abstractdevelop and evaluate a multisensor, AI-enabled fusion framework for landscape-scale AGB mapping
Reproduction assets foundThe authors explicitly state that the code reproducing all figures and analyses is archived in a GitHub repository and permanently preserved via Zenodo (doi 10.5281/zenodo.18688899). The GEDI-derived CHM25 product (Zenodo 11176727) is a cited prior-work dataset from Wang et al. (2025), not this paper's own asset, and FCode · publicGEDI data products are distributed by NASA’s Land Processes
Distributed Active Archive Center and are accessible through
Google Earth Engine. The code used to reproduce all figures
and analyses has been archived in a GitHub repository (https://
github.com/ChaoEcohydroRS/NC_SoutheastBiomass) and
permanently preserved via Zenodo (https://doi.org/10.5281/zenodo.18688899, submitted on 20 February 2026).
Declarations
Conflict of interest The authors declare no competing inter-
ests.
Disclaimer The findings and conclusions in this publication
are those of the author(s) and should not be construed to rep-
resent any official USDA or U.S. Government determination or
policy.
Open Access This articleOpen asset ↗Zenodo · 10.5281/zenodo.18688899pdf-raw-page:23 lines:1-89Plant phenotyping relevance match · UnverifiedEurope PMC · checked 5 Sept 2026
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.
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.
Plant phenotyping relevance match · UnverifiedOpenAlex · Europe PMC · checked 5 Sept 2026
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.
Abstract Accurate prediction of grain yield (GY) remains a major challenge in plant breeding due to complex interactions between genotype, environment, and management (G × E × M) factors. Remote sensing data from unmanned aerial vehicles (UAVs) equipped with multispectral sensors have emerged as a pivotal resource for high‐throughput phenotyping. In this study, we applied a deep transfer learning (DTL) approach to enhance GY prediction using UAV‐derived spectral and textural traits across multiple environments and developmental stages of winter wheat ( Triticum aestivum L.). The model's transferability and generalizability were evaluated across years, locations, nurseries, and stage‐specific scenarios. We employed fine‐tuning, which involves retraining a pretrained one‐dimensional convolutional neural network (1D‐CNN) model on scenario‐specific target data to enhance generalizability. Fine‐tuning was tested with 20%, 40%, 60%, and 80% of the target data to identify an optimal balance between model accuracy and adaptation, and compared with 1D‐CNN without DTL (baseline model). In cross‐year predictions, the baseline model (from 2022) performed poorly ( R 2 = −2.9 in 2023), while DTL improved prediction to an R 2 of 0.83 with 20% fine‐tuning, demonstrating strong temporal adaptability. Similarly, in cross‐location scenarios, baseline model performance was poor ( R 2 ranging from −15.3 to −0.4) but improved to 0.29–0.69 with 40% fine‐tuning. Stage‐specific predictions benefited most at Feekes stages 10.5 and 11, where DTL achieved an R 2 of 0.78 and 0.82, respectively, compared to baseline model R 2 values near 0. These results demonstrate that DTL improves model transferability and generalizability, increasing prediction accuracy and offering a resource‐efficient tool to accelerate selection for complex and labor‐intensive traits in modern breeding programs.
Why it matches plant phenotyping methodsUAVマルチスペクトル画像から抽出した植物形質を用い、深層転移学習による穀粒収量予測の汎化性・転移性を検証しており、表現型取得・推定ワークフローが中心である。
abstractRemote sensing data from unmanned aerial vehicles (UAVs) equipped with multispectral sensors have emerged as a pivotal resource for high‐throughput phenotyping.
To address the poor regression performance caused by strong spatiotemporal heterogeneity, inconsistent information scales and complex feature relationships in field-based multimodal data, this study proposes a hierarchical fusion framework embedded within an encoder – decoder network. The framework integrates multi-scale, interpretable, and cross-modal representations through coordinated modules that bridge feature discrepancy understanding and information flow regulation. A multi-scale parallel pathway structure is designed to enhance joint perception of local and global information by leveraging feature mappings with different receptive fields. An interpretable feature importance allocation strategy is further introduced to improve the backbone network’s ability to provide dynamic guidance on feature contributions. This enables the model to perform adaptive weighting and feature selection during multimodal fusion. In addition, a cross-modal dense interaction and gated fusion mechanism is constructed to regulate information flow and capture fine-grained associations across modalities. The improved feature-guided model is applied to yield regression using multimodal data collected over three consecutive years and multiple wheat varieties. Results show that, in the first year, the highest prediction accuracy reaches an R2 of 0.8112 with an rRMSE of 16.85%. Validation using data from the same planting region in the second and third years yields a highest R2 of 0.8107 and 0.7986, with corresponding rRMSE values of 17.92% and 17.27%, respectively. Compared with other deep learning models within the same year, the proposed approach improves R2 by up to 30.52%, 33.96% and 32.79% across the three years, while reducing rRMSE by up to 41.59%, 45.01% and 46.43%. The results demonstrate that the coordinated interaction among modules establishes an integrated optimization pathway that spans from feature discrepancy understanding to information flow regulation, while maintaining interpretability in the decision process. Under complex field conditions with multiple sources of uncertainty, the proposed framework achieves stable module contributions ranging from 5% to 10% based on cross-validation and t-test analyses. This effectively alleviates the difficulty of efficient multimodal feature fusion for robust yield prediction under stress conditions. The study provides a new methodological perspective for multimodal agricultural sensing and crop phenotyping. Proposes a multi-scale parallel-path architecture for joint perception of multimodal feature mappings.Develops a weight-guided method to enhance interpretability of multimodal features.Designs a cross-modal dense interaction and gated fusion mechanism.Establishes an encoder–decoder-based framework for coordination and fusion of heterogeneous multimodal features. Proposes a multi-scale parallel-path architecture for joint perception of multimodal feature mappings. Develops a weight-guided method to enhance interpretability of multimodal features. Designs a cross-modal dense interaction and gated fusion mechanism. Establishes an encoder–decoder-based framework for coordination and fusion of heterogeneous multimodal features.
Why it matches plant phenotyping methods小麦の収量という植物形質を対象に、マルチモーダルデータ融合と収量回帰のための新規エンコーダ・デコーダ手法を開発し、複数年・品種で検証している。フェノタイピング手法が中心である。
abstractthis study proposes a hierarchical fusion framework embedded within an encoder – decoder network
To address the poor regression performance caused by strong spatiotemporal heterogeneity, inconsistent information scales and complex feature relationships in field-based multimodal data, this study proposes a hierarchical fusion framework embedded within an encoder – decoder network. The framework integrates multi-scale, interpretable, and cross-modal representations through coordinated modules that bridge feature discrepancy understanding and information flow regulation. A multi-scale parallel pathway structure is designed to enhance joint perception of local and global information by leveraging feature mappings with different receptive fields. An interpretable feature importance allocation strategy is further introduced to improve the backbone network’s ability to provide dynamic guidance on feature contributions. This enables the model to perform adaptive weighting and feature selection during multimodal fusion. In addition, a cross-modal dense interaction and gated fusion mechanism is constructed to regulate information flow and capture fine-grained associations across modalities. The improved feature-guided model is applied to yield regression using multimodal data collected over three consecutive years and multiple wheat varieties. Results show that, in the first year, the highest prediction accuracy reaches an R2 of 0.8112 with an rRMSE of 16.85%. Validation using data from the same planting region in the second and third years yields a highest R2 of 0.8107 and 0.7986, with corresponding rRMSE values of 17.92% and 17.27%, respectively. Compared with other deep learning models within the same year, the proposed approach improves R2 by up to 30.52%, 33.96% and 32.79% across the three years, while reducing rRMSE by up to 41.59%, 45.01% and 46.43%. The results demonstrate that the coordinated interaction among modules establishes an integrated optimization pathway that spans from feature discrepancy understanding to information flow regulation, while maintaining interpretability in the decision process. Under complex field conditions with multiple sources of uncertainty, the proposed framework achieves stable module contributions ranging from 5% to 10% based on cross-validation and t-test analyses. This effectively alleviates the difficulty of efficient multimodal feature fusion for robust yield prediction under stress conditions. The study provides a new methodological perspective for multimodal agricultural sensing and crop phenotyping. Proposes a multi-scale parallel-path architecture for joint perception of multimodal feature mappings.Develops a weight-guided method to enhance interpretability of multimodal features.Designs a cross-modal dense interaction and gated fusion mechanism.Establishes an encoder–decoder-based framework for coordination and fusion of heterogeneous multimodal features. Proposes a multi-scale parallel-path architecture for joint perception of multimodal feature mappings. Develops a weight-guided method to enhance interpretability of multimodal features. Designs a cross-modal dense interaction and gated fusion mechanism. Establishes an encoder–decoder-based framework for coordination and fusion of heterogeneous multimodal features.
Why it matches plant phenotyping methodsマルチモーダル作物センシングから小麦収量を推定する encoder–decoder 手法を開発し、複数年・品種データで検証しており、表現型推定手法が研究の中心である。
abstractthis study proposes a hierarchical fusion framework embedded within an encoder – decoder network.
To address the poor regression performance caused by strong spatiotemporal heterogeneity, inconsistent information scales and complex feature relationships in field-based multimodal data, this study proposes a hierarchical fusion framework embedded within an encoder – decoder network. The framework integrates multi-scale, interpretable, and cross-modal representations through coordinated modules that bridge feature discrepancy understanding and information flow regulation. A multi-scale parallel pathway structure is designed to enhance joint perception of local and global information by leveraging feature mappings with different receptive fields. An interpretable feature importance allocation strategy is further introduced to improve the backbone network’s ability to provide dynamic guidance on feature contributions. This enables the model to perform adaptive weighting and feature selection during multimodal fusion. In addition, a cross-modal dense interaction and gated fusion mechanism is constructed to regulate information flow and capture fine-grained associations across modalities. The improved feature-guided model is applied to yield regression using multimodal data collected over three consecutive years and multiple wheat varieties. Results show that, in the first year, the highest prediction accuracy reaches an R2 of 0.8112 with an rRMSE of 16.85%. Validation using data from the same planting region in the second and third years yields a highest R2 of 0.8107 and 0.7986, with corresponding rRMSE values of 17.92% and 17.27%, respectively. Compared with other deep learning models within the same year, the proposed approach improves R2 by up to 30.52%, 33.96% and 32.79% across the three years, while reducing rRMSE by up to 41.59%, 45.01% and 46.43%. The results demonstrate that the coordinated interaction among modules establishes an integrated optimization pathway that spans from feature discrepancy understanding to information flow regulation, while maintaining interpretability in the decision process. Under complex field conditions with multiple sources of uncertainty, the proposed framework achieves stable module contributions ranging from 5% to 10% based on cross-validation and t-test analyses. This effectively alleviates the difficulty of efficient multimodal feature fusion for robust yield prediction under stress conditions. The study provides a new methodological perspective for multimodal agricultural sensing and crop phenotyping.
Why it matches plant phenotyping methodsマルチモーダル農業センシングから小麦収量という植物形質を推定するエンコーダ・デコーダ手法を開発し、複数年・品種データで検証しているため、フェノタイピング手法が中心的である。
abstractthis study proposes a hierarchical fusion framework embedded within an encoder – decoder network.
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
Abstract Crop mapping is one of the most frequent uses of yield monitor data in precision agriculture. Processing such data requires spatial interpolation to predict yields at unsampled locations. Ordinary kriging (OK) is the geostatistical interpolation method usually employed for mapping georeferenced data. In recent years, machine learning (ML) algorithms have gained attention for spatial interpolation tasks because of their ability to process large data volumes; however, their comparative performance for yield mapping at the field scale remains limited. This study compares the statistical behavior of ML methods, including quantile regression forest (QRF), generalized boosted regression models (GBM), extreme gradient boosting (XGB), and radial basis function neural networks (RBFNs) for processing yield monitor data. OK is applied as reference. To enhance the performance of ML algorithms for fine-scale yield mapping, covariates from the spatial neighborhood of sampled yield values were incorporated to predict yields at unsampled sites. Over 1,000 yield monitor datasets from multiple crop species were processed to assess algorithm performance. The ML methods—QRF, GBM, and XGB—demonstrated robust statistical performance, since they effectively handled large data volumes and improved spatial interpolation accuracy. The QRF method achieved the highest error reduction (on average, an 8.7% error reduction), was faster than OK, and generated high-quality uncertainty maps. GBM and XGB also performed better than OK. Coupled with spatial covariables, the studied ML algorithms are valuable alternatives to conventional kriging for yield mapping at the field scale.
Why it matches plant phenotyping methods作物収量という植物形質を対象に、収量モニターデータの空間補間手法を比較・評価し、未観測地点の収量推定性能を検証しているため、計算的フェノタイピング手法が中心である。
abstractThis study compares the statistical behavior of ML methods, including quantile regression forest (QRF), generalized boosted regression models (GBM), extreme gradient boosting (XGB), and radial basis function neural networks (RBFNs) for processing yield monitor data.
Forest digital twins play a crucial role in modern precision forestry by supporting biomass estimation and carbon cycle monitoring. However, existing 3D reconstruction methods struggle to simultaneously achieve metric-level structural accuracy and visual realism in complex understory environments. This study proposes a semantically constrained 3D Gaussian Splatting framework that fuses handheld LiDAR point clouds with unmanned aerial vehicle imagery. First, a multi-modal fusion mechanism is constructed to extract geometric anchors from registered LiDAR data for precise 3DGS spatial initialization, which mitigates rendering artifacts and geometric drift caused by poor initialization in purely visual methods. Second, a semantic regularization optimization strategy is proposed to realize differentiated modeling of tree trunks and canopies, effectively balancing the structural accuracy of rigid trunks and the photorealistic rendering of non-rigid canopies. Experiments conducted on three study plots demonstrate that the proposed approach achieves an average PSNR of 24.94 dB, SSIM of 0.773, and LPIPS of 0.231 across all plots, outperforming standard NeRF and baseline 3DGS, while enabling DBH estimation with R2 = 0.848 and RMSE = 2.705 cm. This method provides a solution for high-fidelity forest digital twin construction in open-canopy forest environments such as urban and campus forests.
Why it matches plant phenotyping methodsLiDAR・UAV画像を統合した3D再構成法を開発し、樹幹・樹冠の構造モデル化とDBH推定を評価しており、植物形質取得が中心的な技術貢献である。
abstractThis study proposes a semantically constrained 3D Gaussian Splatting framework that fuses handheld LiDAR point clouds with unmanned aerial vehicle imagery.
Understanding below-ground biomass dynamics is essential for improving crop performance in water-limited regions. Yet field-scale root monitoring remains constrained by destructive and labor-intensive sampling. This study presents explainable machine learning models to estimate root biomass of maize, millet, and sorghum using UAV multispectral imagery and key canopy phenotypic traits. Across 405 samples collected during the 2024 growing season, eight algorithms were evaluated, among which Random Forest and XGBoost achieved the highest predictive accuracy (R² = 0.763 for millet, 0.688 for maize, and 0.659 for sorghum). SHAP analysis revealed that leaf area was the dominant predictor across all crops, with 2-3 times greater influence than other traits, while leaf water content and chlorophyll-related parameters exhibited species-specific effects associated with drought adaptation. Under the conditions tested, these results suggest that UAV-based multispectral phenotyping, combined with interpretable machine learning, can enable non-destructive estimation of root biomass at the field scale. Within the limits of this single-site, single-season study, the approach demonstrates potential for large-scale root phenotyping and for supporting crop improvement in semi-arid regions. We quantify a 15-25% reduction in R² relative to above-ground trait prediction, which we term the 'cost of indirect inference'-highlighting the inherent challenge of estimating below-ground biomass from canopy-level data. These findings offer insights for precision agriculture, subject to broader validation.
Why it matches plant phenotyping methodsUAVマルチスペクトル画像と説明可能な機械学習を用いて根 biomass という植物形質を非破壊推定する手法が研究の中心であり、実証・比較評価も行っている。
abstractThis study presents explainable machine learning models to estimate root biomass of maize, millet, and sorghum using UAV multispectral imagery and key canopy phenotypic traits.
Accurate estimation of sorghum (Sorghum bicolor [L.] Moench) grain yield remains a major bottleneck in breeding programs across sub-Saharan West Africa, where traditional methods rely on manual counting and weighing of grains. These approaches are labor-intensive, time-consuming, and prone to-induced variability, limiting throughput and reproducibility. This study presents an end-to-end high-throughput phenotyping pipeline for automated grain detection and mass estimation using computer vision. The workflow integrates smartphone-based image acquisition, automated foreground extraction, and grain detection using YOLOv11 models, followed by count-to-mass calibration. Three YOLOv11 architectures, small, medium, and large, were evaluated under identical training conditions using transfer learning from COCO pre-trained weights. Among the tested models, the medium configuration provided the best trade-off between precision and detection performance, with precision values reaching up to 0.861. A preprocessing step based on automatic background masking was applied prior to detection, significantly improving robustness under heterogeneous field conditions. Grain count was converted to mass using a linear calibration model. For two locally relevant sorghum elite lines, Faourou and Payenne, strong linear relationships were observed between detected grain number and measured grain weight (R² > 0.998), with mass coefficients k ≈ 0.026 g/grain. To facilitate adoption, a user-friendly R Shiny application was developed, allowing users to upload images, perform automated grain detection, and estimate grain mass using user-defined calibration coefficients. This pipeline provides a scalable and reproducible approach for rapid grain phenotyping and offers strong potential to accelerate selection decisions in sorghum breeding programs under field conditions.
Why it matches plant phenotyping methodsソルガム粒の画像取得、検出、質量推定を統合した高スループット表現型解析パイプラインを開発・評価しており、方法が研究の中心である。
abstractThis study presents an end-to-end high-throughput phenotyping pipeline for automated grain detection and mass estimation using computer vision.
This article presents the development and experimental study of a compact, automated apple sorting machine based on computer vision, indirect fruit weight estimation, and color grading. It is designed for use in small and medium-sized farms, where the use of industrial lines is limited by high cost and complex maintenance. The proposed machine enables non-destructive assessing and sorting of apples in a continuous flow mode without the use of mechanical weighing, includes a fruit feeding and positioning module, a computer vision system, an image processing unit, and a sorting actuator synchronized with the conveyor movement. Fruit weight and color assessment is based on visual geometric parameters (diameter, fruit height, projected area, and the proportion of surface color), extracted from digital images, followed by classification by product category using regression models. As part of the experimental study, a correlation analysis was conducted between the actual weight of apples and their geometric parameters for five varieties typical of Kazakhstan. It was shown that the projected fruit area exhibits the most stable correlation with weight, justifying its use as the primary predictor in constructing a regression model for indirect weight estimation. An assessment of the accuracy of apple classification by product categories was carried out and the influence of conveyor speed on the stability and correctness of sorting was observed. The experimental results with a total 1250 apples of five varieties - Aport Alexander, Sinap Almaty, Kazakhski Yubileinyi, Ainur, and Nursat indicated that the optimal operating mode for the machine is an apple transport speed of 0.16 m/s. In this mode, sorting throughput is approximately 400 kg/hour, with an average accuracy of 92% for the automatic classification in accordance with GOST requirements. These results confirm that the proposed approach provides sufficient real-time sorting accuracy with a simple machine design. The machine can be used as a standalone sorting solution, as well as a base platform for further expansion of functionality by integrating surface defect assessment and grade identification modules.
Why it matches plant phenotyping methods果実の形態・色・重量を画像から推定し分類するコンピュータビジョン方式と装置の開発が中心であり、単なる品質測定ではなく、再利用可能な植物器官形質の取得・推定法を提示している。
abstractThis article presents the development and experimental study of a compact, automated apple sorting machine based on computer vision, indirect fruit weight estimation, and color grading.
The real-time quantitative estimation of herbaceous plant growth status holds significant potential for investigating fertilization effects, predicting growth curves, and enhancing crop yield. This study constructed a growth quantification model using an improved YOLOv5 architecture integrated with 3D point cloud processing, with pak choi as an exemplar crop. To improve the recognition accuracy while reducing the number of parameters, we employed a lightweight YOLOv5 model enhanced with Atrous Spatial Pyramid Pooling and Ghost convolution modules for individual pak choi plant localization and growth stage classification. We also developed a segmentation method based on the HSV color space to segment leaves. To estimate the total fresh weight of individual plants, we first calculated the leaf surface area by generating a triangular mesh from the corresponding leaf point clouds and predicted the chlorophyll content using a stacking ensemble model. Subsequently, to address the leaf occlusion issues, the leaf pixel ratio in the images, leaf surface area, and mean leaf chlorophyll content were collectively used as independent variables. Finally, a multiple linear regression model was developed to accurately estimate the total fresh weight of individual pak choi plants. Experimental results demonstrate that the modified YOLOv5 architecture achieves a 3.5% improvement in mAP@0.5 (reaching 96%) and a 4.66% increase in F1-score (attaining 90.26%), while significantly reducing the computational complexity compared to the baseline model. Statistical tests verified that the fitted equation could explain 79% of the variation in the total fresh weight, with an average relative error of 12.16%. This enables non-contact and accurate measurement of the pak choi growth status.
Why it matches plant phenotyping methodsYOLOv5、3D点群、葉面積・クロロフィル推定を統合し、個体の生体重という植物形質を非接触推定する手法が研究の中心である。
abstractThe real-time quantitative estimation of herbaceous plant growth status holds significant potential
Published20 May 20262026 7th International Conference on Intelligent Communication Technologies and Virtual Mobile Networks (ICICV)Cited by 0 · OpenAlex ↗
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
The accuracy of on-board yield monitoring for combine harvesters is limited by the difficulty of acquiring high-fidelity mass flow signals and achieving reliable cumulative integration under complex vibration and varying operating conditions. To address this challenge, this study developed a weighing-based on-board yield monitoring system (DW-ORMS), in which a flow-collecting weighing-type grain mass flow sensor (C-GMFS) served as the core sensing unit. The C-GMFS enables stable weighing observation in confined installation spaces through mechanical decoupling and a single force-transmission path. At the system level, a state-aware gating strategy and trusted update mechanism were introduced to improve the reliability of output and cumulative mass estimation during unsteady operating phases. Based on field-measured disturbance characteristics, a parameterized disturbance model was established and used to identify the valid operating window and fix the gating parameter range. Simulation results showed that the proposed method achieved band-limited interference suppression of A band ≥17.73 dB under strong disturbances while maintaining trend fidelity of PRR trend ≥41.73% and low processing delay. Field harvesting experiments were conducted at working speeds of 2–8 km·h − ¹. The cumulative strip mass showed excellent agreement with manual weighing references, with R ²=0.973 and RMSE = 0.84 kg, and the strip-level mass closure error remained within CE ≤ 5% (N = 35). No monotonic drift in error was observed across working-speed groups. These results demonstrate that the DW-ORMS provides a deployable and traceable solution for high-confidence on-board yield monitoring of combine harvesters under unsteady field conditions.
Why it matches plant phenotyping methods収量という植物由来の形質を対象に、動的秤量センサーと信号処理による圃場収量モニタリング手法を開発し、シミュレーションおよび実収穫データで検証しているため、方法が中心的である。
abstractthis study developed a weighing-based on-board yield monitoring system (DW-ORMS), in which a flow-collecting weighing-type grain mass flow sensor (C-GMFS) served as the core sensing unit.
Plant phenotyping relevance match · UnverifiedOpenAlex · Europe PMC · Crossref · checked 5 Sept 2026
Abstract Unmanned aerial vehicle (UAV)-based phenotyping has been applied to assess potato traits, however, its use to identify canopy traits associated with tuber yield across diverse genotypes remains limited. The objective of this study was to evaluate the use of UAV-based field phenotyping, integrating RGB and thermal imaging, to identify key canopy traits associated with tuber yield and it´s agronomic components in a set of eight potato genotypes grown across two environments and two growing seasons. Despite higher seasonal rainfall in Chiloé, tuber yields were consistently greater in Osorno, underscoring that total precipitation alone is less important than its temporal distribution and effective crop water availability; this makes it necessary to supplement with irrigation during the period of highest demand. RGB-derived vegetation indices and canopy temperature successfully differentiated genotypes, although their discriminatory power varied according to developmental stage and environmental conditions, with intermediate to late growth stages generally providing the strongest genotype separation. Canopy temperature supplied complementary physiological information related to canopy water status, whereas RGB traits captured broader variation in canopy structure and greenness. These findings highlight the importance of integrating phenological stage and environmental context when interpreting remote sensing data, and demonstrate the strong potential of UAV-based HTP to support breeding and agronomic strategies aimed at improving drought resilience, yield stability, and selection efficiency in potato.
Why it matches plant phenotyping methodsUAVによるRGB・熱画像を用いた圃場フェノタイピングが中心で、ジャガイモのキャノピー形質を抽出・評価し、遺伝子型間比較や収量関連性を検討している。
abstractevaluate the use of UAV-based field phenotyping, integrating RGB and thermal imaging, to identify key canopy traits associated with tuber yield
Genomic selection (GS) can accelerate crop breeding and enhance selection efficiency. However, accurately predicting genomic estimated breeding values (GEBVs) for complex traits and applying GS in diverse environments remains challenging. To address these issues, we developed a novel hybrid method capable of modelling gene-gene and gene-environment interactions. This method offers precise predictions of phenotypic performance for complex traits, identifies haplotypes associated with desirable phenotypes, and enables prediction of optimal haplotypes tailored to specific environments. We evaluated the approach using a dataset of 855 barley lines, with phenotypic data for grain yield and flowering time collected across multiple environments. The model incorporated 30,543 SNPs, nine soil parameters, and six daily environmental variables, achieving high prediction accuracies, with correlation coefficients of 0.93 for flowering time and 0.82 for grain yield. Our method identified 10 haplotype blocks significantly associated with flowering time and 13 blocks with grain yield, collectively accounting for over 90% of the total genetic variance. Additionally, we predicted the phenotypic effects of each haplotype and identified elite varieties carrying the most favourable haplotypes for crossing design and selection. The method also allows prediction of untested genotype × environment combinations, enabling selection of optimal genotypes for targeted environments. To facilitate its application, we developed a web-based interface (accessible at [https://penghaowang.shinyapps.io/shinygui/]), which enables breeders to identify optimal haplotypes and the varieties that carry them, streamlining the process of haplotype-based, environment-informed breeding. We note that the reverse prediction framework is currently applied on a single-trait basis and does not resolve multi-trait trade-offs such as between flowering time and yield, which remains a topic for future extensions.
Why it matches plant phenotyping methods複雑形質の表現型性能を遺伝子型・環境情報から予測する新規計算手法を開発し、オオムギの収量・開花期で評価している。ウェブインターフェースも提供され、形質推定ワークフローが中心である。
abstractwe developed a novel hybrid method capable of modelling gene-gene and gene-environment interactions.
Reproduction assets foundThe paper deposits its barley genotype, phenotype, and environmental datasets at three DOI repositories, and its analysis source code on GitHub, plus a public Shiny web tool.Dataset · publicDetailed information on all experimental lines, including their genotypes, phenotypic, and environmental data, is available at https://doi.org/10.60867/00000010 , https://doi.org/10.60867/00000003 , and https://doi.org/10.60867/00000011 , respectively.Open asset ↗10.60867 · 10.60867/00000010lines:31-42Dataset · publicDetailed information on all experimental lines, including their genotypes, phenotypic, and environmental data, is available at https://doi.org/10.60867/00000010 , https://doi.org/10.60867/00000003 , and https://doi.org/10.60867/00000011 , respectively.Open asset ↗10.60867 · 10.60867/00000003lines:31-42Dataset · publicDetailed information on all experimental lines, including their genotypes, phenotypic, and environmental data, is available at https://doi.org/10.60867/00000010 , https://doi.org/10.60867/00000003 , and https://doi.org/10.60867/00000011 , respectively.Open asset ↗10.60867 · 10.60867/00000011lines:31-42Code · publicAll the data and source codes have been uploaded to GitHub and can be accessed under the GNU Open License at: https://github.com/pwang2019/GxE_Model .Open asset ↗github.com/pwang2019/GxE_Modellines:196-205Plant phenotyping relevance match · UnverifiedEurope PMC · checked 5 Sept 2026
Abstract Background Faba bean is an important grain legume in temperate cropping systems because it provides protein-rich seed and contributes biological nitrogen fixation. However, its productivity is highly sensitive to drought, and breeding for improved drought performance is constrained by complex genotype by environment interactions and the difficulty of measuring relevant traits at scale. This study evaluated whether scanner-derived vegetation indices (VI), 3D canopy traits, and their combination can predict key agronomic and physiological traits in drought-stressed faba bean, and how predictive ability changes when information is used from single dates or cumulatively across the season. Results Predictive performance was strongly trait dependent and varied with predictor set and temporal strategy. Combined VI + 3D predictors generally produced the highest and most consistent predictive ability for major traits. Total grain yield reached 0.75 under cumulative VI + 3D prediction at 93 days after sowing (DAS 93), cumulative water uptake peaked at 0.80 at DAS 97, and total straw biomass reached 0.66 at DAS 104. In contrast, some component traits were predicted equally well or better by 3D information alone, including grain number with 0.70 and pod number with 0.55 under cumulative 3D prediction. Useful prediction windows also differed among traits, with broad late-season windows for major agronomic traits but narrower, more stage-specific windows for productive tillers, thousand kernel weight, and water-use efficiency. Conclusion Phenomic prediction under drought in faba bean was strongly shaped by trait type, predictor composition, and temporal design. Combined VI + 3D predictors were most effective for integrative traits, whereas several component traits were predicted equally well or better by 3D information alone. These findings highlight the potential of scanner-based multisensor phenotyping to support drought-related selection in faba bean breeding.
Why it matches plant phenotyping methodsスキャナー由来のスペクトル指標と3Dキャノピー形質を用いたマルチセンサー表現型解析・予測が研究の中心であり、乾燥ストレス下の収量、バイオマス、水利用などの植物形質を技術的に評価している。
abstractThis study evaluated whether scanner-derived vegetation indices (VI), 3D canopy traits, and their combination can predict key agronomic and physiological traits in drought-stressed faba bean
Abstract Background: The stink bug complex is one of the most damaging pests of soybean, reducing yield and seed quality. Genetic resistance remains the most sustainable and effective management strategy, but its quantitative inheritance and labor-intensive field phenotyping make its implementation in breeding programs challenging. Objective: This study explored high-throughput phenotyping (HTP) using unmanned aerial vehicles (UAVs) equipped with RGB cameras to evaluate a soybean population and the potential of phenotyping to stink bug resistance by correlating image-derived features and machine learning (ML) models. Methods: A population of 304 soybean lines was evaluated in alpha-lattice design trials across two seasons under natural infestations. Five resistance-related traits, grain yield (GY), healthy seed weight (HSW), number of days to maturity (NDM), tolerance (TOL), and leaf retention (LR), were manually scored and linked to UAV-derived vegetation indices (VIs) and texture indices (TIs). Three ML models (AdaBoost, SVM, MLP) were tested to predict these traits from aerial features. Results: Results showed that VIs, particularly Visible Atmospherically Resistant Index at the 25th percentile (VARI_P25), were consistently associated with resistance-related traits, while decision tree analysis highlighted TIs at 45° and 135° as complementary sources of structural information. Prediction ability was highest for GY, HSW, and NDM, especially in flights near flowering and maturity, but remained low for TOL and LR. Integrating multiple flights modestly improved accuracy, whereas cross-season predictions were unreliable. Nonetheless, indices such as VARI_P25 provided useful cross-season correlations for HSW and TOL, enabling early screening of less promising lines. Conclusion: This pioneering study demonstrates that UAV–ML pipelines can capture genetic signals of stink bug resistance in soybean, despite environmental complexity. These findings open new avenues for resistance phenotyping, supporting more efficient breeding strategies and accelerating genetic gains in soybean improvement.
Why it matches plant phenotyping methodsUAV画像と機械学習を用いて、ダイズの抵抗性関連形質や収量を推定するHTPパイプラインを技術的に評価しており、表現型取得・推定法が研究の中心である。
abstractThis study explored high-throughput phenotyping (HTP) using unmanned aerial vehicles (UAVs) equipped with RGB cameras to evaluate a soybean population and the potential of phenotyping to stink bug resistance by correlating image-derived features and machine learning (ML) models.
Accurate quantification of forest coverage and combustible biomass (fuel load) is critical for wildfire risk assessment and ecosystem management. However, traditional methods relying on airborne LiDAR or field surveys are cost-prohibitive and time-intensive, while satellite imagery often lacks the vertical resolution required for canopy volume analysis. This paper proposes a novel, automated pipeline for rapid forest inventory using virtual remote sensing data derived from Google Earth Studio (GES). Our approach first generates low-altitude orbital imagery and camera poses for a target region. For dense 3D reconstruction, we employ Pi-Long, developed within the VGGT-Long framework. This model serves as a scalable extension of the Pi-3 feed-forward Transformer architecture. To address the inherent scale ambiguity in monocular reconstruction, we introduce a metric recovery module that aligns the reconstructed trajectory with GES ground truth poses via Sim(3) Umeyama optimization. The metric-scale point cloud is then orthogonally projected into Bird's-Eye-View (BEV) height and density maps. Finally, we employ a watershed-based segmentation algorithm combined with height variance analysis to classify tree species (conifer vs. broadleaf), calculate Leaf Area Index (LAI), and estimate total fuel load. Experimental results demonstrate that this pipeline offers a scalable, cost-effective alternative to physical scanning, enabling near-real-time estimation of forest biomass with high geometric consistency.
Why it matches plant phenotyping methods森林の3D再構成、BEVマップ、分割・高さ分散解析を組み合わせ、LAIと燃料量という植物・群落形質を推定するパイプライン自体が中心的な技術貢献であるため。
abstractThis paper proposes a novel, automated pipeline for rapid forest inventory using virtual remote sensing data derived from Google Earth Studio (GES).
Autumn-winter forage scarcity limits subtropical livestock systems. This study aimed to: (1) develop a segregating F 1 population from parents contrasting in autumn-winter biomass yield (WBY) in tetraploid Paspalum notatum ; (2) estimate phenotypic and genetic variability for WBY across environments; and (3) evaluate the relationship between WBY and spring-summer biomass yield (SBY), and the feasibility of unmanned aerial vehicle (UAV)-derived vegetation indices as non-destructive estimators of WBY. A population of 182 tetraploid F 1 hybrids was evaluated at two sites in Corrientes Province, Argentina (2022-2024). WBY exhibited wide genotypic variability across locations and years ( p H 2 ) ranged from 0.41 to 0.64, reflecting sensitivity to the thermal and moisture conditions of each environment. WBY showed a positive, moderate association with SBY ( R 2 = 0.20-0.26), indicating that selection for cool-season yield does not compromise summer productivity. The Normalized Difference Red Edge Index (NDRE) was the most robust WBY predictor ( R 2 up to 0.67 at MES-2022 vs. 0.58-0.59 for ARVI, GNDVI and NDVI at the same site-year), though predictive accuracy varied with environmental conditions. The results demonstrate substantial and exploitable genetic variation for cool-season forage yield in P. notatum .
Why it matches plant phenotyping methodsUAV由来の植生指数を用いた非破壊的な飼料収量推定を評価し、複数指数の予測性能を比較しているため、植物形質取得法の実質的な適用・検証を含む。
abstractevaluate the relationship between WBY and spring-summer biomass yield (SBY), and the feasibility of unmanned aerial vehicle (UAV)-derived vegetation indices as non-destructive estimators of WBY.
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).
This study evaluates the performance of LiDAR sensing and UAV photogrammetry for three-dimensional canopy reconstruction and structural parameter estimation in precision agriculture. Experiments were conducted in Sicily (Italy) on Moringa oleifera Lam. and Ficus macrophylla subsp. columnaris, representing contrasting canopy architectures. LiDAR and UAV data were used to generate canopy models and estimate canopy height, volume, and vegetation density. A voxel-based approach was applied to LiDAR point clouds to analyze internal canopy structure. LiDAR significantly outperformed UAV photogrammetry, achieving lower errors in canopy height estimation (RMSE = 0.19–0.21 m vs. 0.52–0.60 m) and canopy volume (3.5–4.2% vs. 13.7–16.1%). UAV photogrammetry provided reliable estimates of canopy surface but underestimated structural parameters in dense vegetation due to occlusion effects. Differences were more pronounced in Ficus macrophylla than in Moringa oleifera, highlighting the influence of canopy complexity. These findings demonstrate that LiDAR-derived structural metrics can improve canopy characterization and support precision agriculture applications such as biomass estimation, irrigation planning, and canopy management in Mediterranean cropping systems.
Why it matches plant phenotyping methodsLiDARとUAVフォトグラメトリによる樹冠の3次元再構成と、樹冠高・体積・密度推定を比較検証しており、植物形質取得手法が研究の中心です。
abstractThis study evaluates the performance of LiDAR sensing and UAV photogrammetry for three-dimensional canopy reconstruction and structural parameter estimation in precision agriculture.
Wheat is one of the most widely cultivated crops worldwide and provides essential nutrition for millions of people. Accurate and timely wheat yield mapping is critical for strategic planning and decision making to ensure global food security, particularly through early prediction at the field scale to support precision agriculture. Recently, hyperspectral imaging (HSI) integrated with machine learning (ML) techniques has emerged as a robust and reliable approach for assessing crop characteristics and predicting yield. This study combines Visible Near Infrared (VNIR) HSI data (400-1000 nm) with explainable ML models to enhance early and accurate wheat yield prediction and enable comprehensive image based agricultural analysis. The performance of Partial Least Squares Regression (PLSR), Random Forest (RF), and Convolutional Neural Networks (CNN) was compared. Hyperparameters of the CNN model were optimized using Bayesian optimization, resulting in superior performance with R 2 of 0.76, RMSE of 1022.24 gm/plot, and RPD of 2.03 compared with optimized PLSR and RF models. Three distinct explainable artificial intelligence (XAI) methods (Kernel-SHAP, Tree-SHAP and DeepExplainer) were further employed to analyze the predictions of the PLSR, RF, and CNN models and to determine the relative importance of key wavelengths. The CNN model developed using important wavelengths was further employed to visualize the spatial distribution of leaf regions most influential for yield prediction. These findings demonstrate the effectiveness of integrating HSI with explainable ML for advanced agricultural analysis and reliable early yield prediction.
Why it matches plant phenotyping methodsハイパースペクトル画像と機械学習による小麦収量の早期推定を中心に、複数モデルの比較・性能評価・重要波長解析を行っており、植物形質取得手法が主要な貢献です。
abstractThis study combines Visible Near Infrared (VNIR) HSI data (400-1000 nm) with explainable ML models to enhance early and accurate wheat yield 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.
Plant phenotyping relevance match · UnverifiedCrossref · Europe PMC · checked 5 Sept 2026
Accurate seed-yield prediction is essential for optimizing nitrogen (N) management in buffalograss seed production. However, current UAV-based approaches often rely directly on vegetation indices (VIs), which provide limited physiological insight and not transfer well across growing seasons. To address this limitation, we developed a trait-based yield prediction methold that integrates UAV-derived plant height (PH) and canopy nitrogen concentration (CNC), representing crop structural and physiological status, respectively. Field experiments were conducted from 2022 to 2024 under seven N application rates. Using data from 2022 and 2023, we calibrated a quadratic PH-CNC model and then evaluated its predictive performance with an independent 2024 dataset. We also compared this framework with a conventional direct VI-based model. The trait-based model explained 89% of the variation in seed yield during calibration and showed better cross-year predictive performance than the VI-based model (R 2 = 0.70, NRMSE = 17% versus R 2 = 0.52, NRMSE = 22%). In addition, the model captured the decline in seed yield under excessive N input, indicating that it reflected biologically meaningful crop responses. These results demonstrated that combining structural and physiological traits can provide a more robust and interpretable alternative to conventional VI-based methods for UAV-based yield prediction. This framework has practical potential for improving precise and sustainable N management in buffalograss seed production.
Why it matches plant phenotyping methodsUAV由来の草高と群落窒素濃度を統合した形質ベース予測法を開発し、独立年データで検証・従来法と比較しており、表現型取得と解析手法が中心である。
abstractwe developed a trait-based yield prediction methold that integrates UAV-derived plant height (PH) and canopy nitrogen concentration (CNC)
Hyperspectral imaging (HSI) systems offer rich spectral information for precision agriculture applications such as yield forecasting, but their high cost and complexity limit widespread adoption. The relationship spectral data complexity and prediction accuracy in non-destructive crop monitoring remains unclear, challenging the assumption that more complex spectral data inherently yields better predictions. We developed a workflow integrating UAV-based HSI (150 bands) with deep learning to non-destructively estimate fresh weight of cabbage heads (n = 680). A two-dimensional convolutional neural network (2D-CNN) was deployed to identify the single most predictive wavelength through systematic feature extraction. Performance was benchmarked against 20 conventional multi-band vegetation indices (VIs). The CNN identified a single spectral band at 565.63 nm as the optimal predictor. A predictive model using only this single-band input achieved a coefficient of determination (R²) of 0.49 on an independent test set, with a root mean square error (RMSE) of 0.99 kg and a mean absolute error (MAE) of 0.84 kg. This performance substantially surpassed the best-performing conventional multi-band VI (MCARI2, R² = 0.34), representing a 44% improvement in explained variance using single-band data input. This AI-driven approach autonomously distill HSI complexity into a single optimal wavelength that outperforms established multi-band indices. The findings provide a methodological framework for designing simplified, cost-effective spectral sensors for precision agriculture, potentially improving accessibility and scalability of crop monitoring technologies.
Why it matches plant phenotyping methodsキャベツ結球の生体重という植物形質を、UAVハイパースペクトル画像とCNNで非破壊推定するワークフローを開発し、独立テストと既存指標との比較で検証しており、形質取得手法が中心である。
abstractWe developed a workflow integrating UAV-based HSI (150 bands) with deep learning to non-destructively estimate fresh weight of cabbage heads (n = 680).
Accurate rapeseed yield and biomass estimation at the meter scale prior to harvest is crucial for precision harvesting. However, there is a scarcity of structured research on the estimation of rapeseed biomass yield. This study aims to address this gap by focusing on rapeseed in Jiangsu Province. Multispectral and RGB images captured by unmanned aerial vehicles (UAVs) were taken during key growth stages (budding, flowering, and podding stages). Using the extracted multidimensional features, we developed biomass-yield estimation models using four machine learning techniques. Subsequently, we employed ensemble learning with multidimensional, multi-stage data and used Shapley additive explanation (SHAP) for feature contribution analysis, thereby constructing a framework for predicting rapeseed harvest characteristics with high estimation accuracy and interpretability. Our analysis indicates that spectral‒texture is the most effective feature combination for biomass estimation, whereas the optimal combination for yield estimation includes three-dimensional (3D) spectral‒textural‒structural features. The synergy of these features, coupled with an ensemble learning model, significantly enhanced the accuracy of rapeseed biomass-yield estimation (biomass: coefficient of determination ( R 2 )=0.72, relative root mean square error (rRMSE)=14.35%; yield: R 2 =0.68, rRMSE=13.67%). The proposed model also achieved stable prediction results across the variety‒density interaction. Overall, this study presents an accurate and generalizable approach for estimating rapeseed biomass yield across various planting patterns, offering new insights for precision harvesting.
Why it matches plant phenotyping methodsUAV画像から抽出した多次元特徴とアンサンブル学習により、ナタネのバイオマス・収量を推定する方法が研究の中心であり、精度評価も実施しているため、植物フェノタイピング手法として適格です。
abstractUsing the extracted multidimensional features, we developed biomass-yield estimation models using four machine learning techniques.
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
Sugarcane is a high-value industrial crop vital for sugar and biofuel production, yet increasingly constrained by climate variability, biotic and abiotic stresses, soil degradation, and inefficient input use. Traditional breeding and crop management approaches are often slow, labour-intensive, and less precise, emphasizing the need for digital transformation in sugarcane agriculture. AI now offers powerful tools to accelerate genetic improvement, enhance stress resilience, and optimize resource-use efficiency. This review synthesizes recent advances in AI applications across the sugarcane improvement pipeline, including high-throughput phenotyping, genomic prediction, digital crop monitoring, and AI-driven decision-support systems. ML and DL models enable automated, accurate prediction of key traits such as biomass, canopy temperature, nitrogen status, and sugar recovery using UAV, satellite, and proximal sensing data. AI-powered genomic selection approaches leveraging convolutional networks, transformers, and attention mechanisms improve prediction accuracy for yield, ratooning ability, and stress tolerance by integrating SNPs, pedigree, and multi-environment datasets. Emerging innovations such as digital twins, multimodal data fusion, reinforcement learning-based irrigation scheduling, and climate-smart advisory models further strengthen real-time crop intelligence. The integration of blockchain-enabled breeding databases, FAIR data standards, and interoperable analytics pipelines supports scalable and collaborative research. Literature analysis reveals 15-30% gains in selection efficiency, >90% accuracy in disease detection, and phenotyping cost reductions of up to 70%. Key challenges remain, including scarce annotated datasets, genotype × environment complexity, model interpretability, and adoption barriers for smallholders. A future roadmap is proposed featuring multimodal foundation models, edge-AI deployment, and explainable breeder dashboards. AI is redefining sugarcane research from reactive to predictive, enabling climate-resilient, sustainable, and profitable production systems.
Why it matches plant phenotyping methodsサトウキビ育種におけるAI応用の総説であり、高スループット表現型解析、UAV・衛星・近接センシングによる形質推定を主要な対象として扱っているため、フェノタイピング手法レビューとして適格。
abstractThis review synthesizes recent advances in AI applications across the sugarcane improvement pipeline, including high-throughput phenotyping, genomic prediction, digital crop monitoring, and AI-driven decision-support systems.
This paper proposes a method based on UAV low-altitude photogrammetry and deep learning algorithms for corn crop growth monitoring. During the shooting process, a unified UAV photogrammetry strategy is set to ensure that the obtained images have high spatial resolution, and after pre-processing the original images, a convolutional neural network (CNN) model is utilized to extract features from the images and improve the accuracy of the CNN with the help of the idea of transfer learning. In addition, multi-scale feature fusion and attention mechanism are introduced to allow the model to focus on important location information, and weighted multi-task loss function is used to jointly optimize the multi-objective values such as plant height, leaf area index, and biomass. Experiments show that the method has good real-time performance and scalability while maintaining high prediction accuracy, providing an effective solution for crop monitoring in precision agriculture.
Why it matches plant phenotyping methodsUAV画像と深層学習を用いてトウモロコシの草丈、葉面積指数、バイオマスを推定する手法自体が研究の中心であり、植物形質推定の方法開発・応用に該当する。
abstractThis paper proposes a method based on UAV low-altitude photogrammetry and deep learning algorithms for corn crop growth monitoring.
Water stress is a global challenge that severely impacts crop production by hindering essential physiological processes. To address this issue, proximal sensing has emerged as a promising technique for the early identification of stress in vegetables, enabling timely management interventions and optimizing yield. This study aimed to use RGB image indices and an artificial neural network (ANN) model to quantify the responses of various plant traits, such as fresh biomass (FB) weight, dry biomass (DB) weight, canopy water content (CWC), relative chlorophyll content (SPAD), soil moisture content (SMC), and tomato yield across different irrigation levels. Field experiments were conducted during the 2022 and 2023 growing seasons, capturing digital RGB images and measuring plant traits at the flowering and fruit-ripening stages. The results revealed that a reduced irrigation level led to a decrease in various plant traits. The study also revealed significant differences in RGB image indices between different irrigation levels, with strong positive relationships identified for the majority of RGB image indices incorporating green components (G) and R2 reaching 0.99 for various plant traits. However, the red-blue simple ratio (RB) index, which does not consider the G, did not significantly correlate with any of the plant traits. The ANN models achieved high prediction accuracy, with high R2 values reaching 0.99 for various plant traits and yields. These findings underscore the practicality and reliability of employing RGB imaging indices in conjunction with ANN models for effectively managing tomato crop growth and production, particularly under limited water conditions.
Why it matches plant phenotyping methodsRGB画像指標とANNによる植物形質・収量の定量推定が研究の中心であり、予測精度も評価しているため、画像ベース形質推定の方法適用・検証に該当する。
abstractThis study aimed to use RGB image indices and an artificial neural network (ANN) model to quantify the responses of various plant traits
Abstract Data from high‐throughput phenotyping (HTP) could be used for phenotype imputation to enhance genomic selection (GS) or gene discovery, but this has not been explored in crop species. Three machine learning models: multiple linear regression (MLR), missForest, and k ‐nearest neighbors, were evaluated for grain yield (GY) phenotype imputation in wheat ( Triticum aestivum L.), using 2414 lines across six environments. Three multispectral vegetation indices (VIs) collected over time from aerial imagery were used as predictors for imputation of simulated missing data ranging from 10% to 70%. Statistical analyses examined the accuracy of imputed GY (IGY) as well as its reliability, heritability, and genetic correlation with GY. Imputation accuracies were highest for MLR, but accuracy differences between methods were small. Accuracies only decreased slightly as percent missing data increased. Genetic correlations between IGYs and observed GY within the environment ranged from −0.01 to 0.51, consistently greater than the corresponding genetic correlations between VIs and GY. Respectively, the reliabilities and heritabilities of IGY were 24% and 45% lower than those of GY, and like those of the VIs. Altogether, this study found that HTP data can be used to impute GY phenotypes suitable for use in further analyses; however, imputed and observed GY should be modeled as separate traits. Further research is needed to improve the heritability of IGY and to evaluate the utility of IGY in GS models.
Why it matches plant phenotyping methodsHTP由来の航空画像データを用いて小麦収量表現型を機械学習で補完し、複数手法の精度・信頼性・遺伝率を評価しており、表現型推定手法が研究の中心である。
abstractThree machine learning models: multiple linear regression (MLR), missForest, and k ‐nearest neighbors, were evaluated for grain yield (GY) phenotype imputation in wheat
Introduction. The projected growth of the global population poses a significant challenge in ensuring sufficient food production. Crop genetic improvement, essential to meet this demand, relies on advanced technologies to accelerate field phenotyping processes. Objective. To predict plant height and biomass yield in sorghum using photogrammetry and multispectral data acquired through small unmanned aircraft system (sUAS) flights. Materials and methods. Six sorghum genotypes were evaluated in Cañas, Guanacaste, Costa Rica, using a completely randomized design with eight replications per genotype. Multispectral sensor flights were conducted at selected phenological stages to generate vegetation indices, digital terrain models (DTMs), and digital surface models (DSMs). Manual plant height measurements were used for correlation and simple linear regression analyses, while biomass was predicted using random forest regression. Results. The DTMs and DSMs enabled reliable estimation of plant height during early growth stage (R² = 0.53) and achieved higher accuracy at later stages (R²= 0.76; RMSE = 0.13 m). Biomass prediction was most accurate at the booting stage (r= 0.72; RMSE = 1.40 t·ha-¹), with NDRE (Normalized Difference Red-Edge Index) and IKAW (Kawashima Index) identified as the most relevant spectral indices. Conclusions. The DTMs and DSMs derived from multispectral imagery accurately predicted plant height during later growth stages but were less accurate in early stages. Incorporating plant height alongside spectral indices into predictive models enhanced biomass yield prediction. The findings demonstrate that sUAS-mounted sensors and multispectral indices are valuable tools for phenotyping in sorghum breeding programs in Costa Rica.
Why it matches plant phenotyping methodssUASマルチスペクトル画像とフォトグラメトリから草丈・バイオマスを推定し、実測値との相関・回帰および予測精度を評価する手法中心の研究である。
abstractObjective. To predict plant height and biomass yield in sorghum using photogrammetry and multispectral data acquired through small unmanned aircraft system (sUAS) flights.
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。
Abstract Purpose The primary objective of this study was to evaluate the potential of high spatial resolution Jilin-1 satellite imagery for plot-level prediction of sugarcane yield, millable stalk population, and Brix, and to assess whether integrating spectral, texture, soil, and fertilization information could improve prediction performance for precision sugarcane management. Methods Jilin-1 satellite imagery acquired at four growth stages, from seedling to maturity, was used to derive vegetation indices (VIs) and texture indices (TIs), including the normalized difference texture index (NDTI), enhanced vegetation texture index (EVTI), and double-difference ratio texture index (DDRTI). Soil chemical properties (SCPs) and fertilization information (FI) were further incorporated with the remotely sensed variables. Machine learning models were developed for plot-level prediction of sugarcane traits across plant cane and first ratoon cane, and texture window size was optimized to improve TI extraction and model performance. Results For yield, the combination of VIs and TIs outperformed VIs alone at the tillering stage (R 2 CV = 0.65, RMSECV = 15.06 t/ha, RPDCV = 1.68). Adding SCPs and FI further improved yield prediction across plant cane and first ratoon cane (R 2 CV = 0.70, RMSECV = 13.84 t/ha, RPDCV = 1.83). Millable stalk population was best predicted at the maturation stage by VIs and Tis, achieving the best performance (R 2 CV = 0.63, RMSECV = 6602 stalks/ha, RPDCV = 1.66). The best Brix model integrated VIs, TIs, SCPs, and FI at the maturation stage (R 2 CV = 0.44, RMSECV = 0.53 °Bx, RPDCV = 1.33). SHAP analysis identified VIs as the dominant features for sugarcane traits prediction. And, DDRTI contributed more than NDTI and EVTI in yield and Brix prediction. Conclusion It is concluded that integrating spectral, texture, soil, and fertilization information from high spatial resolution Jilin-1 imagery is a promising approach for improving plot-level prediction of key sugarcane traits.
Why it matches plant phenotyping methods衛星画像からサトウキビの収量、可販茎数、Brixを plot レベルで推定し、テクスチャ特徴抽出の最適化と機械学習性能評価を行っており、表現型取得・推定手法が中心である。
abstractThe primary objective of this study was to evaluate the potential of high spatial resolution Jilin-1 satellite imagery for plot-level prediction of sugarcane yield, millable stalk population, and Brix
Reproduction assets foundThe paper's data availability statement explicitly links a public GitHub repository containing part of the authors' model-training code and test data for the sugarcane trait prediction analysis. No public phenotype dataset or imagery deposit is stated; additional data are only available on request.Code · publicPart of the code and test data for model training are available at https://github.com/guangtaoxu08-dev/SPT_JL .Open asset ↗guangtaoxu08-dev/SPT_JLlines:228-248Code / dataset availability confirmedCrossref · checked 15 Sept 2026
Phenotyping plant traits using UAV-based multispectral imaging offers a robust and unbiased approach to assessing crop status. With approximately 70% of smallholder farmers in East and Southern Africa cultivating common beans as a key source of food and income, there is a critical need for accurate and timely measurements of crop health and yield to support data-driven management decisions and disease mitigation. Traditional phenotyping methods are labor-intensive, and existing remote sensing and machine learning approaches remain limited. This study presents a comprehensive framework for plot-level assessment of common bean health and yield using time-series RGB and multispectral imagery. Data collected over three growing seasons (2022–2024) were used to extract canopy variables and vegetation indices (VIs) across phenological stages. For yield prediction, traditional machine learning models achieved a root mean squared error (RMSE) of 242.33 kg ha⁻¹ and an R² of 0.66 using an Extra Trees Regressor. A novel BY-GRU architecture improved performance, achieving an RMSE of 242.40 kg ha⁻¹ and an R² of 0.79. The analysis also identified 45–60 days after sowing as the optimal window for prediction. To address limitations in conventional plant health assessments, this study introduces a novel Health Index. Comparative analysis demonstrated its robustness across genotypes and stronger correlation with yield. Machine learning and deep learning models, including MaxViT, were applied to estimate the Health Index, achieving improved predictive performance. Overall, this work integrates UAV sensing and modelling to provide scalable tools for phenomics, crop management, and breeding.
Why it matches plant phenotyping methodsUAVのRGB・マルチスペクトル画像から作物の健康状態、収量、キャノピー形質を推定するセンシング・機械学習フレームワークが研究の中心であり、植物フェノタイピング手法として適格です。
abstractThis study presents a comprehensive framework for plot-level assessment of common bean health and yield using time-series RGB and multispectral imagery.
Reproduction assets foundThe preprint's DATA AVAILABILITY section states that all processed data required to reproduce the results are publicly available in a Google Drive repository, which qualifies as a paper-specific public phenotype dataset asset. No author analysis code or trained model checkpoints are explicitly deposited.Dataset · publicCommon Bean Breeding Program for
facilitating field trials. We also thank the Phenomics team for their valuable assistance with UAV-based
data collection.
CONFLICT OF INTEREST
The authors declare no conflict of interest.
DATA AVAILABILITY
The datasets generated and/or analyzed during the current study are publicly available at:
https://drive.google.com/drive/folders/1fN3Q9n3bK_YoXFK8VFKZ3uEb13y9iRWj?usp=sharing. This
repository includes all processed data required to reproduce the results presented in this study.
SUPPLEMENTAL MATERIAL
Supp. Figure 1. Drone-based field view of the bean trial site at CIAT Palmira Research Station: A) RGB
image and B) NDVI image.
Supp. Figure 2. Drone Features Open asset ↗pdf-raw-page:40 lines:1-46Plant phenotyping relevance match · UnverifiedbioRxiv · checked 15 Sept 2026
Accurate estimation of forest growing stock volume (GSV) at fine spatial scales is essential for sustainable forest management, carbon accounting, and local decision-making. However, traditional forest inventories often lack sufficient sampling density to provide reliable estimates for small areas. This study evaluates the performance of two small area estimation approaches: the Empirical Best Predictor (EBP) based on a nested-error linear regression model, and the Mixed-Effects Random Forest (MERF) for estimating GSV at the forest stand level using multi-source remote sensing data. The analysis was conducted in the Vallombrosa Nature Reserve (Italy), integrating field measurements from 101 plots with auxiliary variables derived from Sentinel-2 imagery and airborne LiDAR. Both methods were applied to estimate the mean and total GSV across 658 forest stands, many of which lacked direct observations. Model performance was assessed using spatial cross-validation, and uncertainty was quantified using root-mean-square error (RMSE). Results show that MERF outperformed EBP in predictive accuracy, achieving higher R2 (0.67 vs. 0.37) and lower RMSE (151 vs. 202 m3 ha{square}1). MERF also produced more stable and precise uncertainty estimates, with improved coverage of observed values. While both methods yielded comparable total GSV estimates, EBP exhibited greater variability and sensitivity to model assumptions. In contrast, MERF effectively captured non-linear relationships and handled multicollinearity among predictors, though at the cost of reduced interpretability and higher computational demand. Overall, findings highlight the advantages of integrating machine learning with mixed-effects modeling for SAE in forestry, particularly under conditions of sparse sampling and complex ecological variability.
Why it matches plant phenotyping methods森林スタンドの生長蓄積量（GSV）という明示的な植物群落形質を、衛星・LiDARデータと統計／機械学習手法で推定し、空間交差検証とRMSEで性能比較しているため、方法の適用・検証が中心である。
abstractThis study evaluates the performance of two small area estimation approaches: the Empirical Best Predictor (EBP) based on a nested-error linear regression model, and the Mixed-Effects Random Forest (MERF) for estimating GSV at the forest stand level using multi-source remote sensing data.
Plant phenotyping relevance match · UnverifiedOpenAlex · Europe PMC · checked 15 Sept 2026
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.
Effective high-throughput phenotyping is crucial for modern plant breeding, yet the optimal image acquisition parameters for UAV-based systems in forage crops remain poorly defined. We optimized UAV-based phenotyping methods for a Megathyrsus maximus biparental population, examining how ground sampling distance (GSD), environment, and harvest date affect the accuracy of RGB-derived digital traits in predicting yield and canopy height. Machine learning algorithms and mixed model analyses were applied to evaluate predictive power and heritability. Pixel count and Haralick's entropy showed strong correlations with conventional yield measurements, particularly in Environment 2, while most vegetative indices were poor predictors. Integrating machine learning substantially enhanced predictive power for green and dry matter yield (r > 0.80). For canopy height, machine learning models achieved correlations of 0.71 with ground truth measurements despite weak pairwise correlations. Mixed model analysis revealed high broad-sense heritability (0.7 < H 2 < 0.87) for yield traits, pixel count, and entropy, while vegetative indices and canopy height showed greater environmental susceptibility. Moderate GSD resolutions (0.5–1.0 cm) consistently outperformed both very high (0.27 cm) and very low (1.5 cm) resolutions. Coincidence index analysis demonstrated 80% correspondence between top genotypes ranked by pixel count and conventionally measured dry matter yield. This study provides an optimized framework for UAV-based phenotyping in M. maximus , demonstrating that combining advanced digital traits with machine learning accurately predicts key agronomic traits and significantly enhances genotype selection efficiency in forage breeding programs.
Why it matches plant phenotyping methodsUAV画像取得条件、RGBデジタル形質、機械学習による収量・草高推定を最適化・検証する研究であり、植物表現型取得法が中心的です。
abstractWe optimized UAV-based phenotyping methods for a Megathyrsus maximus biparental population, examining how ground sampling distance (GSD), environment, and harvest date affect the accuracy of RGB-derived digital traits in predicting yield and canopy height.
Reproduction assets foundThe paper's data availability statement points to a public Mendeley Data repository containing the study's UAV-derived digital phenotyping and conventional trait datasets. No author analysis code repository is explicitly deposited.Dataset · publicThe datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: https://data.mendeley.com/datasets/jrrb76x82h/1 .Open asset ↗jrrb76x82h/1lines:435-487Plant phenotyping relevance match · UnverifiedCrossref · checked 15 Sept 2026
Published21 Apr 2026International Scientific Journal of Engineering and ManagementCited by 0 · OpenAlex ↗
Abstract— Sugarcane cultivation faces significant challenges due to biotic stresses such as fungal and viral diseases, as well as abiotic factors including climate variability and soil nutrient imbalance. Accurate disease diagnosis and yield estimation are critical for improving productivity and ensuring sustainable agricultural practices. This study proposes an integrated machine learning framework for automated sugarcane disease classification and yield prediction.A Convolutional Neural Network (CNN)-based deep learning model is implemented for image-based disease detection, enabling automatic feature extraction and high-accuracy classification of major sugarcane diseases. For yield prediction, supervised regression algorithms including Random Forest Regressor and Gradient Boosting are employed to model the relationship between environmental parameters, soil properties, and historical yield data.Experimental evaluation demonstrates improved predictive performance in both classification and regression tasks. The proposed system provides a data-driven decision support tool for farmers, enhancing crop management efficiency and reducing agricultural losses. Keywords: Sugarcane, Disease Prediction, Yield Prediction, Machine Learning, Convolutional Neural Network (CNN), Random Forest, Support Vector Machine (SVM), Artificial Neural Network (ANN), Precision Agriculture, Crop Monitoring.
Why it matches plant phenotyping methodsCNNによるサトウキビ病害の画像ベース分類は、植物の病徴・状態を観測から推定する中心的手法であり、方法適用として収録対象です。収量予測も含まれますが、環境・土壌・履歴データに基づく農業予測で、病害画像分類部分が主な適格要素です。
abstractThis study proposes an integrated machine learning framework for automated sugarcane disease classification and yield prediction.
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.
Reliable Aboveground Biomass (AGB) estimates for woody crops are essential for carbon accounting and for Measurement, Reporting and Verification (MRV) frameworks. However, it remains unclear how LiDAR modality and sampling geometry influence plot-scale and tree-scale AGB predictions in intensively managed Mediterranean orchards. In this study, we benchmarked four LiDAR modalities, namely open national airborne laser scanning from the Spanish National Aerial Orthophotography Plan (PNOA/ALS), a dedicated Riegl airborne laser scanner (ALS), unmanned laser scanning (ULS) and mobile laser scanning (MLS), across three woody-crop sites in Córdoba (southern Spain): IFAPA, Doña María, and Villaseca. Plot-level LiDAR metrics (mean height, 95th height percentile, maximum height, and canopy cover proxies) were extracted from normalised point clouds and related to field AGB using Random Forest and XGBoost regression models, together with an ensemble predictor, under an 80/20 train–test split. In parallel, TreeQSM-based Quantitative Structure Models (QSMs) were evaluated as an independent tree-level three-dimensional reconstruction approach. XGBoost achieved the lowest errors at IFAPA (RMSE = 0.400 Mg ha⁻¹; R² = 0.994) and Villaseca (RMSE = 0.872 Mg ha⁻¹; R² = 0.995), whereas PNOA/ALS was competitive at Doña María (RMSE = 0.725 Mg ha⁻¹; R² = 0.994). TreeQSM closely matched field inventory at the low-biomass IFAPA site but tended to overestimate biomass at Doña María and Villaseca, and only 28% of scanned trees yielded usable reconstructions. The results support the use of cross-platform LiDAR for orchard AGB and carbon mapping and identify the conditions under which open national LiDAR can enable scalable MRV of Mediterranean woody crops.
Why it matches plant phenotyping methods複数LiDARプラットフォームと3次元再構成・機械学習を比較検証し、樹木・圃場レベルの地上部バイオマスという植物形質を推定する手法が研究の中心である。
abstractwe benchmarked four LiDAR modalities, namely open national airborne laser scanning from the Spanish National Aerial Orthophotography Plan (PNOA/ALS), a dedicated Riegl airborne laser scanner (ALS), unmanned laser scanning (ULS) and mobile laser scanning (MLS)
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
Abstract Improving selection for multiple disease resistance (MDR) and yield in maize ( Zea mays L.) requires high‐throughput, objective phenotyping tools, particularly under field conditions where several foliar diseases co‐occur. We evaluated drone‐based multispectral vegetation indices (VIs) for predicting resistance to northern leaf blight (NLB; inoculated), northern leaf spot (NLS; natural), anthracnose top dieback (ATD; natural), and for predicting grain yield across 2 years in near‐isogenic inbreds, near‐isogenic hybrids, and a diverse hybrid panel. VIs showed lower coefficients of variation but broad‐sense heritability ranging from 0.09 to 0.95, compared with 0.30 to 0.99 for visual disease scores and 0.21 to 0.97 for yield. Correlations between VIs and ground traits were strongest in near‐isogenic hybrids, particularly for early‐season yield prediction ( r = 0.98–0.99 in 2018; r = 0.87–0.90 in 2019), and moderate for total disease severity (e.g., r = −0.61 to −0.68 in 2018). Associations were weaker and less consistent in the diverse hybrid panel (yield r = 0.11–0.28). Disease‐specific signals were temporally structured: NLS correlated most strongly with early‐season VIs ( r = −0.59 to −0.75), whereas ATD was best detected mid‐season ( r = −0.63 to −0.66) along with NLB ( r = −0.66 to −0.75). Overall, multispectral VIs captured meaningful canopy variation related to MDR and yield, with predictive performance depending on germplasm structure and flight timing. These findings highlight the potential of drone‐based temporal phenotyping to complement visual assessments and improve selection efficiency in maize breeding programs.
Why it matches plant phenotyping methodsドローン multispectral による作物キャノピー形質の取得・予測性能を検証し、病害抵抗性と収量予測への適用を評価しており、フェノタイピング手法が中心である。
abstractWe evaluated drone‐based multispectral vegetation indices (VIs) for predicting resistance to northern leaf blight (NLB; inoculated), northern leaf spot (NLS; natural), anthracnose top dieback (ATD; natural), and for predicting grain yield across 2 years
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.
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.
To improve crop genetics, high-throughput, effective and comprehensive phenotyping is a critical prerequisite. While such tasks were traditionally performed manually, recent advances in multimodal foundation models, especially in vision-language models (VLMs), have enabled more automated and robust phenotypic analysis. However, plant science remains a particularly challenging domain for foundation models because it requires domain-specific knowledge, fine-grained visual interpretation, and complex biological and agronomic reasoning. To address this gap, we develop PlantXpert, an evidence-grounded multimodal reasoning benchmark for soybean and cotton phenotyping. Our benchmark provides a structured and reproducible framework for agronomic adaptation of VLMs, and enables controlled comparison between base models and their domain-adapted counterparts. We constructed a dataset comprising 385 digital images and more than 3,000 benchmark samples spanning key plant science domains including disease, pest control, weed management, and yield. The benchmark can assess diverse capabilities including visual expertise, quantitative reasoning, and multi-step agronomic reasoning. A total of 11 state-of-the-art VLMs were evaluated. The results indicate that task-specific fine-tuning leads to substantial improvement in accuracy, with models such as Qwen3-VL-4B and Qwen3-VL-30B achieving up to 78%. At the same time, gains from model scaling diminish beyond a certain capacity, generalization across soybean and cotton remains uneven, and quantitative as well as biologically grounded reasoning continue to pose substantial challenges. These findings suggest that PlantXpert can serve as a foundation for assessing evidence-grounded agronomic reasoning and for advancing multimodal model development in plant science.
Why it matches plant phenotyping methodsPlantXpertは作物フェノタイピング向けの画像ベンチマークとVLM評価基盤を構築しており、表現型解析手法・データセットの開発が研究の中心である。
abstractwe develop PlantXpert, an evidence-grounded multimodal reasoning benchmark for soybean and cotton phenotyping.
Abstract Accurate estimation of individual tree above‐ground biomass (AGB) and its component‐wise allocation is crucial for advancing ecological research and forest management. However, current biomass estimation methods, such as destructive sampling and allometric equation–based approaches, face limitations in both operational efficiency and cost‐effectiveness, and only destructive sampling can provide component‐wise biomass measurements, which is impractical for large‐scale studies or repeated measurements. In this study, we present a terrestrial laser scanning (TLS)‐based workflow integrating wood–leaf separation, voxel‐based foliage estimation and detailed 3D reconstruction of tree architecture to achieve accurate estimation of individual tree AGB and its component‐wise allocation. A total of 68 trees were scanned to obtain high‐resolution TLS data and subsequently destructively harvested to acquire field reference measurements for validation. The results demonstrate that the workflow achieved high accuracy in predicting AGB at the individual tree level (coefficient of determination/ R 2 = 0.88, root mean squared error/RMSE = 16.83 kg, mean absolute error/MAE = 12.18 kg), significantly outperforming estimates derived from locally calibrated allometric equations ( R 2 = 0.61, RMSE = 29.86 kg, MAE = 24.52 kg). Furthermore, this study provides evidence of the strong capability of TLS in estimating branch‐level biomass, with high accuracy achieved across branch orders ( R 2 ranging from 0.66 to 0.91, RMSE from 3.55 to 380 g and MAE from 2.97 to 290 g). By providing precise, non‐destructive estimates of biomass distribution across branches and leaves, this workflow demonstrates strong potential for improving the accuracy of tree biomass quantification, supporting investigations of resource allocation strategies, and enhancing forest carbon monitoring.
Why it matches plant phenotyping methodsTLSによる樹木の地上部・器官別バイオマスを推定するワークフローを開発し、破壊的実測で精度検証しており、植物形質取得法が研究の中心である。
abstractwe present a terrestrial laser scanning (TLS)‐based workflow integrating wood–leaf separation, voxel‐based foliage estimation and detailed 3D reconstruction of tree architecture to achieve accurate estimation of individual tree AGB and its component‐wise allocation.
Abstract Modern agriculture faces the dual challenge of sustainably increasing food production while mitigating the environmental impact of intensive monocultures. Mixed cropping, which is the cultivation of multiple species or varieties, may provide ecological benefits that address productivity and environmental sustainability challenges. However, evaluating its multifunctionality in conventional agricultural field experiments is costly and labour-intensive, and small sample sizes and high spatial variability often make it difficult to detect the statistical significance of mixed cropping effects. This study aims to introduce and validate a high-throughput field phenotyping (HTP) framework that integrates aerial imagery obtained from unmanned aerial vehicles (UAVs) to efficiently assess the multifunctionality of mixed cropping systems. We conducted a field experiment comparing monocultures of oat, rye, and barley; intraspecific mixed cropping combining three oat varieties; and interspecific mixed cropping combining oat, rye, and barley. Using UAV-derived data across the entire field, including vegetation cover, plant height, and the normalised difference vegetation index, we evaluated five multifunctionalities (biomass production, spatial variability in biomass production, early canopy closure, lodging resistance, and lodging resilience). This framework reveals that mixed cropping outperforms monocropping in several key ecological functions. The proposed UAV-based HTP approach enables cost-effective, robust, and scalable evaluation of mixed cropping systems, facilitating their optimisation for multifunctionality and contributing to the advancement of sustainable agriculture.
Why it matches plant phenotyping methodsUAV画像を用いた高スループット圃場フェノタイピング枠組みを導入・検証し、植生被覆、草丈、NDVIから複数の植物形質・状態を抽出しており、フェノタイピング手法が中心的です。
abstractThis study aims to introduce and validate a high-throughput field phenotyping (HTP) framework that integrates aerial imagery obtained from unmanned aerial vehicles (UAVs)
Reproduction assets foundThe paper's Data availability statement explicitly deposits the datasets generated and analysed (UAV-derived phenotyping measurements) in a public Zenodo repository with a DOI matching an allowed URL.Dataset · publicThe datasets generated and analysed during the current study are available in the Zenodo repository, https://doi.org/10.5281/zenodo.17042273.Open asset ↗Zenodo · 10.5281/zenodo.17042273lines:197-235Plant phenotyping relevance match · UnverifiedEurope PMC · checked 14 Sept 2026
Accurate estimation of crop yield from remote sensing remains challenging due to the crop-specific nature of yield drivers and the difficulty of interpreting spectral indicators across agronomic systems. While many studies prioritise predictive accuracy through complex models, fewer explicitly examine the stability and physiological relevance of in-dividual spectral and phenological indicators under controlled analytical conditions. This study investigates yield–spectral relationships in wheat and cotton using a harmonised Sentinel-2 indicator framework applied across multiple growing seasons in a Mediterra-nean agricultural environment. A consistent set of spectral and thermal indicators was derived from two phenologically targeted Sentinel-2 acquisitions per season and analysed using correlation analysis, univariate regression, constrained multivariate modelling, and recurrence analysis within an identical workflow for both crops. Distinct crop-specific patterns were observed. Wheat yield was most strongly associated with water-sensitive and canopy-related indicators, with NDWI-based metrics reaching Pearson correlations up to r = 0.85 and multivariate models explaining a substantial proportion of yield varia-bility (up to R² ≈ 0.82) under controlled analytical conditions. In contrast, cotton yield var-iability was dominated by thermal accumulation, with growing degree day indicators showing correlations up to |r| = 0.59 and multivariate performance reaching R² = 0.76. Recurrence analysis confirmed the stability of these indicator families across analytical stages. Overall, the results indicate that parsimonious, physiologically interpretable indi-cator combinations can account for a substantial proportion of yield variability without reliance on black-box modelling, supporting crop-aware indicator selection for precision agriculture applications.
Why it matches plant phenotyping methodsSentinel-2のスペクトル・熱指標から作物収量を推定する統一ワークフローを構築・比較し、指標の安定性と予測性能を検証しており、収量フェノタイピング手法が中心です。
abstractThis study investigates yield–spectral relationships in wheat and cotton using a harmonised Sentinel-2 indicator framework
The contemporary challenge of sustainable agriculture necessitates the deployment of robust, data-driven decision support systems. This review paper details the architecture and efficacy of an integrated AI-based system, termed 'Sarv Sampoorna Kisan Mitra,' for comprehensive crop disease identification and management. The system is predicated on two core technological pillars: the use of advanced Deep Learning (DL) models, specifically Convolutional Neural Networks (CNNs), for rapid, visual diagnosis of crop diseases; and the implementation of a Knowledge Graph (KG) for prescriptive management recommendations. The paper explores the full lifecycle, from data acquisition via remote sensing and IoT, through predictive modeling for yield forecasting, and culminating in the generation of actionable, customized advice for fertilizer application and pest control. By transforming raw diagnostic data into contextualized, actionable knowledge, this integrated AI-KG framework offers a scalable solution to enhance precision farming efficiency and minimize resource wastage.
Why it matches plant phenotyping methods植物病害を画像から診断する手法と統合システムの構成・有効性が中心であり、病害状態の画像ベース推定を扱うレビューとして収録対象。
abstractThis review paper details the architecture and efficacy of an integrated AI-based system, termed 'Sarv Sampoorna Kisan Mitra,' for comprehensive crop disease identification and management.
Accurate, species-specific estimation of aboveground biomass (AGB) at the individual plant level is essential for characterizing forest structure, supporting ecological and wildfire modelling, and enabling fine-scale carbon accounting. This study presents a methodological framework for estimating species-specific AGB at individual plant level in Mediterranean ecosystems using UAV-based digital aerial photogrammetry (UAV-DAP). High-resolution point clouds were processed through a multi-step workflow including object-based segmentation, thirteen species classification and AGB regression modeling. The overall accuracy of species classification across six study areas was 81.6%, with a maximum of 89.9%. The regression models for AGB estimation yielded an average R 2 of 0.69 across all species, highlighting species such as Anthyllis cytisoides (R 2 = 0.83, RMSE = 0.07 kg, n = 47), Juniperus oxycedrus (R 2 = 0.83, RMSE = 3.17 kg, n = 32); or Pinus halepensis (R 2 = 0.77, RMSE = 11.79 kg, n = 20). These findings demonstrate the potential of UAV-DAP for practical estimates of AGB. The study underscores UAV-DAP as a cost-effective tool for forest management, ecological monitoring, and biomass assessments, paving the way for broader applications in environmental science and resource management.
Why it matches plant phenotyping methodsUAV-DAP点群から個体レベルの樹種別地上部バイオマスを推定する画像・計算ワークフローが中心で、セグメンテーション、分類、回帰と精度評価を含むため、植物形質計測手法として適格。
abstractThis study presents a methodological framework for estimating species-specific AGB at individual plant level in Mediterranean ecosystems using UAV-based digital aerial photogrammetry (UAV-DAP).
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.
Aeroponic vertical tower farming is a cost-effective, sustainable method for optimizing the food crop-Lactuca Sativa (lettuce-a greeny leaf vegetable); yet accurate biomass prediction of the lettuce crop remains challenging due to the non-linear relationship between the climatic conditions and the variable lettuce growth parameters. To address this challenge, a robust machine learning model called UniTriRob regression model has been developed. This model primarily focuses on mitigating the effects of outliers and heteroskedastic errors across key growth-related parameters, including pH, total dissolved solids (TDS), temperature, electrical conductivity (EC), turbidity, humidity, light intensity and growth. The experimental validation highlights the model's capability with high R-squared value of 97.8386% and the minimized error rate of 0.46, that outperforms the conventional forecasting methods. Hence, the model presents a viable alternative for maximizing aeroponic lettuce production efficiency and increasing yield forecast accuracy, contributing to sustainable agricultural practices.
Why it matches plant phenotyping methodsレタスのバイオマス・収量という植物形質を予測する機械学習回帰モデルの開発と実験的検証が研究の中心であり、単なる農業実験のルーチン測定ではない。
abstractTo address this challenge, a robust machine learning model called UniTriRob regression model has been developed.
Background: This review study examines the transformative potential of machine learning (ML) methods for real-time and continuous evaluation of legume crop development. It provides a structured and comprehensive synthesis of current ML applications, highlighting their potential to improve legume crop management in terms of accuracy, efficiency, scalability and sustainability. Unlike existing reviews, this study specifically emphasizes real-time monitoring frameworks that integrate multi-source data (satellite, UAV, IoT and sensors) for legume crops. Methods: Various machine learning methods, including supervised, unsupervised and deep learning paradigms, are reviewed with respect to their applications in crop health prediction, disease detection and yield estimation. The review further analyzes the integration of ML models with Internet of Things (IoT), edge computing and sensor-based systems to address challenges related to data quality, model interpretability, computational efficiency and real-time decision-making. Result: While challenges remain, such as data heterogeneity, limited model generalization and the integration of ML with traditional agronomic practices, recent technological advancements demonstrate promising solutions. Key trends include the development of robust and transferable models, improved human–machine interfaces and decision-support tools for farmers. These advances have the potential to enhance precision, resilience and sustainability in legume crop monitoring, thereby contributing to global food security and climate-smart agriculture.
Why it matches plant phenotyping methodsマメ科作物の生育・健康・病害・収量を対象に、機械学習と衛星・UAV・IoT・センサーを統合したモニタリング手法をレビューしており、植物形質・状態の取得および推定方法が中心である。
abstractThis review study examines the transformative potential of machine learning (ML) methods for real-time and continuous evaluation of legume crop development.
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
PURPOSE: Above-ground biomass (AGB) is a critical indicator for assessing the growth status of winter wheat. Since the range of extracted color indices (CIs) tends to remain constant after flowering and UAV RGB images cannot capture the lower and middle structures of the canopy under dense planting conditions, the efficiency of AGB estimation models is limited. Therefore, this study aimed to improve the accuracy of winter wheat AGB estimation by incorporating canopy volume information with RGB-based CIs. METHODS: RGB images were acquired to generate Digital Orthophoto Maps (DOM) and Digital Surface Models (DSM) at Feekes 10, Feekes 10.5.2, Feekes 10.5.4, and Feekes 11.3 growth stages. Eight biomass-related CIs were extracted from the DOM, and canopy volume (V) was calculated from the DSM for corresponding regions. The RReliefF algorithm was applied to rank feature importance and select optimal features. Eight statistical and machine learning regression algorithms, including Gaussian process regression (GPR), were used to construct AGB estimation models with different feature combinations. RESULTS: The results showed that the GPR algorithm outperformed other regression methods, achieving the highest estimation accuracy with R² values of 0.775, 0.741, 0.702, and 0.568 at the four growth stages, respectively. Compared with models using CIs alone, integrating canopy volume with CIs improved AGB estimation accuracy from Feekes 10.5.2 to Feekes 11.3, with R² increases of 7.31%, 6.55%, and 22.98%, respectively. CONCLUSION: Overall, combining canopy volume features derived from UAV-based RGB imagery with CIs and applying effective machine learning algorithms enables rapid and accurate estimation of winter wheat AGB.
Why it matches plant phenotyping methodsUAV画像から色指数とキャノピー体積を抽出し、冬コムギの地上部バイオマスを推定する取得・解析手法が研究の中心であるため。
titleWheat biomass estimation by fusing color index and canopy volume based on UAV RGB images
In precision agriculture, the assessment and estimation of key crop parameters are crucial aspects for the optimisation of input usage and, as an ultimate goal, for the improvement of yield quality and quantity. In this context, a reliable prediction of yield by remotely sensed imagery is an enabling technology for optimisation. In this work, an innovative method for estimating yield in maize cultivation is presented, which exploits multi-temporal and multispectral Sentinel-2 satellite imagery with supervised Machine Learning (ML) techniques. For model training and validation, yield ground truth experimental data from combine harvesters was used, enabling the yield estimation at sub-field scale. The investigation, which was conducted on five case study plots, involved a preliminary comparison of four ML-based algorithms, trained with raw spectral bands. An assessment of the effect of the training dataset on the yield prediction accuracy was then performed. A set of Vegetation Indices (VIs) and Two Band Indices (TBIs) was also considered for this purpose. Finally, a multi-temporal analysis was conducted, in which the temporal evolution of crop spectral data over the maize growing season was exploited using imageries acquired in different epochs. The obtained results proved that an accurate estimation of maize yield can be reached using a Gaussian process regression model, exploiting multi-temporal features directly provided by the raw spectral bands. The model showed a high accuracy in the estimation of maize yield, even when fed with data acquired during only the maize vegetative phase, thus proving its capacity as a prediction tool.
Why it matches plant phenotyping methodsSentinel-2画像と機械学習を用いてトウモロコシ収量という植物形質を推定する手法を開発・比較・検証しており、フェノタイピング手法が研究の中心である。
abstractan innovative method for estimating yield in maize cultivation is presented, which exploits multi-temporal and multispectral Sentinel-2 satellite imagery with supervised Machine Learning (ML) techniques.
Plant phenotyping relevance match · UnverifiedCrossref · Europe PMC · checked 5 Sept 2026
Accurate prediction of grain yield is essential for enhancing food security, particularly in the context of climate change. Although remote sensing indices have been extensively utilized to monitor vegetation growth and estimate crop yields, there has been limited research comparing their effectiveness for predicting grain yield, especially across different growth stages. This study examined the performance of multi-source indices, such as normalized difference vegetation index (NDVI), near-infrared reflectance of vegetation (NIR V ), and solar-induced chlorophyll fluorescence (SIF), in predicting grain yield at various growth stages at Shangshan Rice Research Station in Zhejiang Province, China. The results indicated that SIF exhibited the strongest and most consistent correlation with grain yield ( R 2 = 0.34 to 0.75), followed by NIR V ( R 2 = 0.34 to 0.71). SIF also demonstrated advantages in capturing the dynamic changes of GPP during the reproductive period. During both the vegetative and reproductive stages, leaf area index (LAI) showed significant correlations with NDVI, NIR V , and SIF, whereas leaf chlorophyll concentration exhibited comparatively weaker associations with these indicators. These findings provide valuable insights for improving crop yield forecasts using remote sensing, thereby contributing to enhanced agricultural management and food security strategies under climate change.
Why it matches plant phenotyping methods作物収量を推定するマルチソースリモートセンシング指標の成長段階別性能比較・検証が研究の中心であり、植物の収量やLAIなどの形質推定手法を評価している。
abstractThis study examined the performance of multi-source indices, such as normalized difference vegetation index (NDVI), near-infrared reflectance of vegetation (NIR V ), and solar-induced chlorophyll fluorescence (SIF), in predicting grain yield at various growth stages
Accurate fresh weight (FW) estimation is essential for growth monitoring and yield prediction in greenhouse fruit vegetables, but remains challenging due to the dynamic allocation between vegetative and reproductive organs. This study aimed to systematically evaluate modeling strategies for FW estimation in sweet pepper and identify which approach is most suitable under conditions of dynamic biomass partitioning. Non-destructive morphological measurements were collected under greenhouse cultivation, and allometric models based on geometric equations were established as baselines. Their performance was compared with machine learning (ML) models and ensemble learning frameworks. To address limited data availability, numerical data augmentation with Gaussian noise and a variational autoencoder was applied. Among the allometric models, the stick model combined with a sigmoid function showed the highest performance, with an R2 of 0.80 for shoot FW and 0.54 for fruit FW. All ML models outperformed the allometric models, and the ensemble model achieved the highest predictive accuracy, with an R2 of 0.96 for shoot FW and 0.89 for fruit FW. Data augmentation further improved predictive performance across all ML models, particularly for fruit FW prediction. Feature contribution analysis revealed that temporal progression was the dominant predictor of fruit FW, while structural traits played the primary role in shoot FW estimation. Ensemble-based ML, combined with data augmentation, provides a methodological framework for non-destructive FW estimation of sweet pepper in controlled environments such as greenhouses and smart farming systems.
Why it matches plant phenotyping methods非破壊形態計測からピーマンの地上部・果実の生重を推定するアロメトリック／機械学習／アンサンブル手法を比較・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 aimed to systematically evaluate modeling strategies for FW estimation in sweet pepper
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.
Abstract Pea ( Pisum sativum L.) is a strategic crop in the development of sustainable agriculture. However, the genetic gain remains limited despite advances in breeding. Genomic selection holds promise to accelerate varietal improvement, but its high implementation cost restricts its use in crops. Phenomic selection, based on near‐infrared spectroscopy data, is a cost‐effective alternative demonstrated in various crops, but not yet undertaken in pea. This study aims to assess the predictive ability of phenomic selection, alone and combined with genomic selection, for yield‐related traits in a panel of elite spring pea lines evaluated across 12 environments. Three cross‐validation scenarios were implemented to simulate predictions across different years and locations. Our results show that phenomic selection is as effective as genomic selection at predicting yield. The integrative model, combining spectral and molecular data, consistently achieved the highest accuracy for most traits, particularly for complex traits such as seed yield and seed protein yield. In temporal prediction scenarios, the most accurate predictions were obtained using the spectra data from the same year as phenotyping. In spatial prediction scenarios, predictive accuracy varied by site and year, nevertheless, integrative phenomic‐genomic models consistently outperformed univariate approaches. These findings confirm the potential of phenomic selection in pea and underscore the added value of combining near‐infrared spectroscopy and genotyping data to improve the prediction of complex traits in breeding programs. In the face of increasing environmental variability, the integrative approach offers a valuable tool for accelerating genetic gain.
Why it matches plant phenotyping methods近赤外分光データを用いるフェノミック選抜と予測モデルの性能評価が研究の中心であり、収量関連形質の推定・検証を行っているため。
abstractPhenomic selection, based on near‐infrared spectroscopy data, is a cost‐effective alternative demonstrated in various crops, but not yet undertaken in pea.
Accurate and spatially resolved yield estimation is a critical requirement for precision agriculture and orchard management. This paper presents a geometrically consistent, orchard-scale apple yield estimation framework that integrates GNSS–visual-inertial odometry (VIO) fusion, deep learning-based object detection, multi-frame tracking, three-dimensional triangulation, and incremental factor-graph optimization. Camera poses are obtained using ZED GNSS–VIO fusion and subsequently refined using an iSAM2-based nonlinear smoothing approach that incorporates strong relative-motion constraints and soft global ENU (East-North-Up) translation priors. Apples are detected using a YOLO-based model and associated across frames via CoTracker3, enabling robust multi-view landmark reconstruction. Reprojection factors and landmark priors are incorporated into a unified nonlinear factor graph to jointly optimize camera trajectories and 3D apple positions. The reconstructed apples are spatially aggregated into a grid-based mass map, where individual fruit volumes are estimated assuming spherical geometry and converted to mass using density models. The resulting ENU-referenced yield plot provides a structured representation of orchard production variability. Experimental results demonstrate significant reductions in reprojection error after optimization and improved global consistency of the trajectory, leading to stable and spatially coherent 3D reconstructions. The proposed pipeline bridges perception, geometry, and optimization, providing a scalable solution for orchard-scale yield mapping and decision support in precision agriculture.
Why it matches plant phenotyping methods果実の三次元再構成から体積・質量・収量を推定する画像・計算パイプラインが研究の中心であり、植物器官の形態および収量形質を技術的に抽出している。
abstractThis paper presents a geometrically consistent, orchard-scale apple yield estimation framework that integrates GNSS–visual-inertial odometry (VIO) fusion, deep learning-based object detection, multi-frame tracking, three-dimensional triangulation, and incremental factor-graph optimization.
The existing fruit tree yield prediction methods mainly rely on fruit period images or long-term meteorological and soil data, which make it difficult to meet the needs of early yield prediction. In addition, the flowering period images contain complex spatial distribution and severe overlap between flowers, which makes it challenging to directly extract stable structural indicators related to yield. Most existing research has focused on simple statistical indicators such as the number of flowers, while the spatial clustering structure of flowers and their relationship with yield have not been fully explored. Therefore, this article proposes an early apple yield prediction based on flowering stage image thinning simulation characteristics. In this study, blossom images and fruit maturity yield data from 100 apple trees were collected, with flower mask images extracted through standardized image processing. First, the traditional DBSCAN clustering algorithm was enhanced by integrating a KDTree acceleration structure and an adaptive multi-scale mechanism, forming the adaptive multi-scale clustering algorithm (AMS-DBSCAN) to achieve efficient identification of flower clusters and individual flowers. Based on this, two flower thinning simulation strategies based on density and spatial uniformity were designed to model artificial thinning rules and construct multi-dimensional, interpretable phenotypic features. Then, the original statistical features were fused with strategy-generated features and optimized using Lasso. We compared multiple models including XGBoost, BPNN, and SVR for yield prediction. The experimental results showed that XGBoost achieved good predictive performance under the hybrid feature set (R 2 = 0.856, RMSE = 3.098), which was further improved to R 2 = 0.900 after feature optimization with Lasso. The results demonstrate that the proposed method enables reliable early yield estimation, providing a new reference for precision management and early decision-making in fruit tree cultivation.
Why it matches plant phenotyping methods花画像から花群・個体を抽出し、間引きシミュレーション由来の解釈可能な表現型特徴を構築する画像解析手法が研究の中心であり、収量推定に技術的に応用・評価されている。
abstractflower mask images extracted through standardized image processing
Abstract Accurate estimation of aboveground biomass (AGB) is essential for forest monitoring and carbon stock assessment. Airborne laser scanning (ALS) is widely used for large-scale AGB estimation, yet acquiring reference biomass from field measurements for training biomass regression models remains time-consuming and labour-intensive. Here we explore the potential of synthetic ALS data to enhance forest biomass estimation. Two virtual forest plots were generated using a voxel-based forest reconstruction approach to simulate ALS data. We compared the model performances under varying amount and proportion of simulated and real samples in the training set. We find that models trained exclusively on simulated samples underperform models trained solely on real samples. When real samples are scare, incorporation of synthetic samples substantially improves the model performance, with coefficient of determination (R²) increased by 0.001–0.73 and the root mean square error (RMSE) decreased by 0.07–2.26 Mg ha–1. When sufficient real samples are available, adding a small number of simulated samples further improves model performance, with RMSE decreased by 0.12–1.46 Mg ha–1. The optimal performance (R² = 0.852, RMSE = 33.47 Mg ha–1) is obtained when real samples comprise about 83% of the training samples. These findings demonstrate that synthetic ALS data can effectively complement real datasets in AGB modelling, improving accuracy under diverse data availability conditions.
Why it matches plant phenotyping methods森林プロットの地上部バイオマスという植物形質を、合成ALSデータとボクセル再構成で推定する手法を開発・比較評価しており、形質取得・推定法が研究の中心である。
abstractTwo virtual forest plots were generated using a voxel-based forest reconstruction approach to simulate ALS data.
Abstract Purpose Crop growth models (CGM) are valuable tools for agricultural monitoring. However, the need for many input parameters, the uncertainties related to model parametrization and structure, and the lack of spatial information motivate the application of techniques such as data assimilation (DA). This paper proposes a DA framework to improve maize biomass estimation. Methods A particle filter (PF) was used to assimilate remotely sensed reflectance and soil moisture (SM) data, both independently and simultaneously, into the Agricultural Production Systems sIMulator (APSIM) model. Reflectance observations from Sentinel-2 were assimilated through coupling APSIM with the radiative transfer model (RTM) PROSAIL, while SMAP L-band SM products were directly assimilated into APSIM. Results The synthetic experiment, designed to evaluate the reliability of the proposed procedure, highlighted the strength of assimilating reflectance to constrain crop traits and of SM to reduce ensemble spread and improve robustness. Real-case results confirmed these findings. DA assimilation of SM especially contributed to improving overall biomass accuracy, particularly under data gaps and drought conditions. Although it did not consistently surpass single-source assimilation, the joint assimilation yielded consistent results. In 2022, it achieved a root-mean-square error (RMSE) of 2275.20 kg/ha, a normalized RMSE (nRMSE) of 44.99%, and a bias of 1081.90 kg/ha. In 2023, RMSE, nRMSE and bias were 1120.29 kg/ha, 14.79%, and 284.05 kg/ha, respectively. Furthermore, the joint assimilation led to a tighter ensemble spread than single source-assimilation. Conclusion The proposed framework demonstrates the potential of multi-source DA to enhance biomass estimation and support robust, spatially explicit crop monitoring.
Why it matches plant phenotyping methodsSentinel-2反射率とSMAP土壌水分をAPSIMへ同化し、トウモロコシのバイオマスを推定するデータ同化フレームワークが研究の中心であり、植物形質の取得・推定手法を提案・評価している。
abstractThis paper proposes a DA framework to improve maize biomass estimation.
Unmanned aerial systems (UAS) equipped with multispectral sensors enable within-season crop phenotyping; however, conventional vegetation index–based approaches often lack accuracy in predicting crop growth and yield. This study evaluated the performance of three machine learning (ML) algorithms, support vector machine (SVM), random forest (RF), and extreme gradient boosting (XGBoost), for predicting maize leaf area index (LAI), relative chlorophyll content (SPAD), aboveground biomass (AGB), plant height, nitrogen (N) uptake, and grain yield, and compared their performance with stepwise multiple linear regression (SMLR). Multispectral imagery (five spectral bands) was collected across multiple growth stages during the 2021 and 2022 growing seasons near College Station, Texas, under varying split N-fertilizer applications. Band reflectance and eight vegetation indices were used as model inputs. All ML models outperformed SMLR in predicting LAI, SPAD, AGB, N uptake, and plant height. SVM, RF, and XGBoost showed comparable performance for LAI (R² = 0.82–0.83), AGB (R² = 0.86–0.92), and plant height (R² = 0.95–0.97). However, XGBoost exhibited overfitting, resulting in lower validation accuracy for SPAD (R² = 0.54) and N uptake (R² = 0.68) compared with SVM (R² = 0.73 and 0.80, respectively). Grain yield prediction accuracy increased with crop maturity, with reproductive-stage imagery producing the highest accuracy across models (R² = 0.88–0.98), where all ML models outperformed SMLR. However, at the V6 growth stage, SVM and RF did not perform as well as SMLR. Overall, integrating ML with UAS-based multispectral imagery improved prediction accuracy across key maize phenotypic and nutrient traits, providing a robust framework for non-destructive, high-throughput phenotyping and precision N management.
Why it matches plant phenotyping methodsUASマルチスペクトル画像と機械学習により、作物の形態・生理・収量関連形質を推定する方法を比較評価しており、フェノタイピング手法が研究の中心である。
abstractThis study evaluated the performance of three machine learning (ML) algorithms, support vector machine (SVM), random forest (RF), and extreme gradient boosting (XGBoost), for predicting maize leaf area index (LAI), relative chlorophyll content (SPAD), aboveground biomass (AGB), plant height, nitrogen (N) uptake, and grain yield
Plant phenotyping relevance match · UnverifiedOpenAlex · Europe PMC · checked 5 Sept 2026
Abstract High-throughput phenotyping using unmanned aerial vehicle (UAV) multispectral imagery offers a promising approach for predicting wheat yields under variable sowing conditions. This study evaluated the effectiveness of UAV-based vegetation indices compared to the GreenSeeker handheld sensor in estimating yield-related traits in 13 bread wheat genotypes. UAV-based multispectral indices— Normalized Difference Vegetation Index (NDVI), Green Normalized Difference Vegetation Index (GNDVI), Red-edge Normalized Difference Vegetation Index (RNDVI and simple ratio (SR) were captured using a MicaSense sensor at two growth stages [52 and 79 days after sowing (DAS) for timely sown; 16 and 43 DAS for late sown]. Simultaneously, NDVI was recorded using a GreenSeeker handheld sensor for direct comparison with UAV-derived NDVI. UAV-derived indices showed consistently stronger correlations with biological yield (BY), grain yield (GY), and thousand grain weight (TGW), particularly during the anthesis stage. GNDVI and SR emerged as the most predictive indices for BY and GY, while TGW showed stronger associations with early-stage indices. GreenSeeker NDVI correlations were weaker and less consistent across growth stages and sowing conditions. Genotypes such as Phule Samadhan, MACS 2496, and GS 4042 exhibited superior adaptability under late-sown heat stress, maintaining higher vegetation index values throughout. UAV-based multispectral imaging outperformed the handheld sensor in predicting key yield traits and detecting inter-genotypic variation under stress. Statistical and multivariate analyses (ANOVA, PCA, and heatmap visualization) revealed distinct inter-genotypic variability in vegetation indices, effectively distinguishing high-vigor and stress-susceptible wheat genotypes under varying sowing environments. These findings highlight UAV-based multispectral imaging as a robust, efficient, and scalable phenotyping tool for identifying stress-tolerant and high-yielding genotypes, underscoring the importance of phenological timing and optimal index selection in breeding and precision agriculture.
Why it matches plant phenotyping methodsUAVマルチスペクトル画像と地上センサーによる植生指数の取得・比較を中核とし、収量関連形質と遺伝子型差の推定に用いる実質的な植物フェノタイピング研究である。
abstractHigh-throughput phenotyping using unmanned aerial vehicle (UAV) multispectral imagery offers a promising approach for predicting wheat yields under variable sowing conditions.
Severe foliage occlusion and dynamically changing lighting conditions in complex orchard environments pose significant challenges for visual perception systems in automated apple harvesting, including low detection accuracy, poor robustness, and insufficient real-time performance. To address these issues, this study proposes an improved lightweight detection network based on YOLOv11, named YOLO-WBL, along with a precise yield estimation algorithm based on 3D point clouds, termed CLV. The YOLO-WBL network is optimized in three aspects: (1) A C3K2_WT module integrating wavelet transform is introduced into the backbone network to enhance multi-scale feature extraction capability; (2) A weighted bidirectional feature pyramid network (BiFPN) is adopted in the neck network to improve the efficiency of multi-scale feature fusion; (3) A lightweight shared convolution separated batch normalization detection head (Detect-SCGN) is designed to significantly reduce the parameter count while maintaining accuracy. Based on this detection model, the CLV algorithm deeply integrates depth camera point cloud information through 3D coordinate mapping, irregular point cloud reconstruction, and convex hull volume calculation to achieve accurate estimation of individual fruit volume and total yield. Experimental results demonstrate that: (1) The YOLO-WBL model achieves a precision of 93.8%, recall of 79.3%, and mean average precision (mAP@0.5) of 87.2% on the apple test set; (2) The model size is only 3.72 MB, a reduction of 28.87% compared to the baseline model; (3) When deployed on an NVIDIA Jetson Xavier NX edge device, its inference speed reaches 8.7 FPS, meeting real-time requirements; (4) In scenarios with an occlusion rate below 40%, the mean absolute percentage error (MAPE) of yield estimation can be controlled within 8%. Experimental validation was conducted using apple images selected from the dataset under varying lighting intensities and fruit occlusion conditions. The results demonstrate that the CLV algorithm significantly outperforms traditional average-weight-based estimation methods. This study provides an efficient, accurate, and deployable visual solution for intelligent apple harvesting and yield estimation in complex orchard environments, offering practical reference value for advancing smart orchard production.
Why it matches plant phenotyping methodsリンゴ果実の検出と3D点群による個別果実体積・総収量推定を開発し、精度・速度・遮蔽条件下で検証しており、植物形質取得が中心的な方法論的貢献である。
abstractthis study proposes an improved lightweight detection network based on YOLOv11, named YOLO-WBL, along with a precise yield estimation algorithm based on 3D point clouds, termed CLV.
Sugar beet is a major sugar crop in temperate regions and rapid, high-throughput, and accurate estimation of field phenotypes is essential for variety selection and production optimization. In this paper, ten commercial sugar beet varieties adapted to high latitudes are investigated using unmanned aerial vehicle (UAV) based red-green-blue (RGB), multispectral, and thermal infrared imaging across multiple growth stages. Canopy structural, texture, spectral, and temperature features are extracted, and three machine learning algorithms, random forest (RF), partial least squares (PLS), and support vector machine (SVM), are used to predict sugar content, root fresh weight, and yield. The results show that all three methods estimate sugar content well, with relative root mean square error (rRMSE) values below 11.0%, while RF and PLS outperform SVM. Multispectral features provide higher accuracy than RGB features, and multi-sensor feature combinations generally improve sugar content prediction compared with single-sensor inputs. For root fresh weight, SVM slightly outperforms RF and PLS, and RGB features are more informative than multispectral features. The integration of thermal infrared features does not notably improve RF or PLS models, but the combination of multispectral and thermal infrared features achieves the best SVM performance ( R2=0.58, RMSE = 75.3 g, and rRMSE = 23.7%). For yield estimation, RF achieves the highest accuracy, with rRMSE values ranging from 15.4% to 18.8%. Yield prediction accuracy increases as the time of image acquisition approaches harvest, and combining multi-temporal data from periods close to harvest further improves model performance. Overall, multi-sensor UAV data can effectively estimate sugar content, root fresh weight, and yield in sugar beet, providing a useful approach for phenotypic analysis, precision management, and variety selection.
Why it matches plant phenotyping methodsUAVマルチセンサー画像から糖含量、根 fresh weight、収量という植物形質を抽出・推定し、センサー特徴量と機械学習モデルの性能を比較しているため、表現型取得・推定手法が中心である。
abstractrapid, high-throughput, and accurate estimation of field phenotypes is essential for variety selection and production optimization.
Abstract Soil salinization constrains agricultural productivity across approximately 950 million hectares worldwide. In the Yellow River irrigation district of Ningxia, secondary salinization severely depresses maize yields. Existing crop–water–salt models lack day-by-day bidirectional coupling between salt transport and crop growth, over-simplify salt stress representation, and amplify stress through multiplicative integration. To address these gaps, we developed a fully coupled WOFOST–HYDRUS-1D model linking the Richards equation and convection–dispersion equation with crop photosynthesis, transpiration, and assimilate partitioning through a modified Maas–Hoffman function. Salt stress is transmitted via three physiological pathways, and the combined stress factor is computed using Liebig’s law of the minimum. The model was calibrated with 43 sampling points spanning low-to-high salinity gradients (1.49–6.79 g kg⁻¹) in Huinong District during 2024, and independently validated with 30 points (1.29–7.75 g kg⁻¹) in 2025. Calibration yielded R² = 0.883, RMSE = 0.744 t ha⁻¹, NRMSE = 10.96%, and NSE = 0.795; validation gave R² = 0.824, RMSE = 0.753 t ha⁻¹, NRMSE = 11.13%, and NSE = 0.810, confirming strong inter-annual parameter stability. Under high salinity (> 4 g kg⁻¹), simulated mean yield declined to 3.75 t ha⁻¹, a 53% reduction compared with low-salinity conditions. Compared with the standard WOFOST model (R² = 0.450, RMSE = 1.399 t ha⁻¹), the coupled model substantially improved accuracy.These results show that the coupled model can improve yield prediction under salinity stress and provide a useful tool for irrigation scheduling and water–salt management in salinized farmland.
Why it matches plant phenotyping methodsWOFOST–HYDRUS-1Dの結合モデルを開発し、トウモロコシの生育・塩ストレス・収量を推定する手法として独立検証しており、植物状態の推定手法が中心である。
abstractwe developed a fully coupled WOFOST–HYDRUS-1D model linking the Richards equation and convection–dispersion equation with crop photosynthesis, transpiration, and assimilate partitioning through a modified Maas–Hoffman function.
Plant phenotyping relevance match · UnverifiedCrossref · Europe PMC · checked 5 Sept 2026
Advancements in agricultural technologies have increasingly emphasized technical innovations aimed at improving the predictability and reliability of agricultural outputs. These aspects encompass developments in agricultural machinery, automation technologies, biotechnology, and controlled environment farming systems. This article focuses on Remote Sensing (RS)-based approaches applied to agricultural yield estimation for both crops and plants. RS technologies offer enhanced precision and scalability, making them particularly effective for large-scale agricultural monitoring and analysis. A systematic classification of RS-based methodologies employed for crop yield estimation is presented in this study. These methodologies are categorized into: (i) Sensor-Based approaches, (ii) Platform-Based approaches, (iii) Analytical and Modeling-based methods, and (iv) Machine Learning (ML)-driven models. Based on findings reported across multiple studies, it is observed that Deep Learning (DL)-based architectures consistently achieve superior performance across key evaluation metrics, including accuracy, precision, recall, and F1-score. This performance advantage stems from their capacity to learn hierarchical representations, capture complex non-linear relationships, scale efficiently with large datasets, and reduce reliance on manual feature engineering. Following this classification, our article presents a comprehensive discussion of the limitations associated with these methodologies. These challenges are organized into four major categories: (i) Environmental, (ii) Algorithmic, (iii) Hardware and Operational, and (iv) Wireless Sensor Networks (WSNs) related limitations. The adopted classification framework helps readers identify and address the key challenges associated with effective yield estimation in crops and plants. Moreover, the article concludes by outlining several future research directions intended to support and guide both early-career and experienced researchers in this domain.
Why it matches plant phenotyping methods作物収量という植物形質のリモートセンシング推定法を体系的に分類・比較し、環境・アルゴリズム・ハードウェア上の限界を論じる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。
titleA review of remote sensing-based crop yield estimation: machine learning techniques and environmental, algorithmic, and hardware limitations
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
Plant phenotyping relevance match · UnverifiedOpenAlex · Europe PMC · bioRxiv · checked 5 Sept 2026
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
BACKGROUND: Root biomass serves as a critical indicator of plant eco-physiological status and crop productivity, yet its non-destructive monitoring remains challenging because of its underground location. The use of transparent nutrient film technique (NFT) systems enables direct observation of entire root systems, rendering image-based phenotyping feasible. In this study, we investigated and compared the performance of RGB and hyperspectral imaging for predicting root dry weight in hydroponically grown spinach (Spinacia oleracea L.). RESULTS: Using 430 root segments divided from 60 plants, three models were developed: (1) an area-based regression based on root coverage, (2) a convolutional neural network (CNN) using RGB images, and (3) a partial least squares regression (PLSR) model using hyperspectral data (450-950 nm). The area-based regression exhibited limited accuracy (R² = 0.446) because of saturation at high root coverage. The CNN model improved predictive performance (R² = 0.739) but tended to overestimate sparse roots as a result of resolution constraints. The PLSR model achieved the highest accuracy (R² = 0.822, RMSE = 0.019 g/segment), with significantly lower error than RGB-based approaches (P < 0.01). Variable importance in projection analysis indicated that PLSR effectively exploited spectral signatures at 450 nm (background contrast) and 750 nm (tissue scattering), thereby maintaining stable accuracy across the full biomass range. When validated using 104 independent plants, the PLSR model achieved high predictive accuracy. Furthermore, as a proof of concept, this model successfully visualized the spatiotemporal dynamics of root biomass accumulation over 50 days, with only a 7.70% relative error at harvest. CONCLUSIONS: To our knowledge, this study is among the first to demonstrate the non-destructive monitoring of biomass distribution within entire root systems under production conditions. Hyperspectral imaging combined with PLSR outperforms RGB-based approaches by capturing spectral signatures that reflect internal tissue properties of roots, thereby overcoming limitations caused by morphological occlusion. This approach provides a robust tool for precision agriculture and high-throughput phenotyping, enabling continuous assessment of root growth through simple modifications to the existing hydroponic systems.
Why it matches plant phenotyping methodsRGB・ハイパースペクトル画像と機械学習／PLSRを用いて根乾物重を非破壊推定・検証する方法研究であり、植物表現型の取得と定量化が中心である。
abstractThe use of transparent nutrient film technique (NFT) systems enables direct observation of entire root systems, rendering image-based phenotyping feasible.
Reproduction assets foundThe paper's Data availability statement deposits the paper-specific phenotyping assets (raw hyperspectral images, RGB images, and root dry weight measurements) in a Zenodo record. The provided URL includes a token and 'preview=1', suggesting the record may not yet be fully open, but it is the authors' stated public URLDataset · publicThe datasets generated and analyzed during the model construction of the current study are available in the Zenodo repository: [https://zenodo.org/records/18072801?preview=1&token=eyJhbGciOiJIUzUxMiJ9.eyJpZCI6ImFiYTkzMzY2LTIzZjktNDlkMy1iZTBjLTk3M2E5YTUyOTFmZCIsImRhdGEiOnt9LCJyYW5kb20iOiIzNGE1ZjMxNDZhYjhiYjlhZWRiOWFjNzBkNzcwY2I3NyJ9.uR4HfosoSaVWhtSblMOS1v9bJFA5MvHwXvcW9uoNbcTWRDU4RNxZpVHjXTC3ulBM1JTlBbeHp_4T5EcILawxdg].The dataset includes:
- Raw hyperspectral images and data- RGB images
- Root dry weight measurementsOpen asset ↗Zenodo · 18072801lines:176-248Plant phenotyping relevance match · UnverifiedCrossref · checked 8 Sept 2026
Agriculture currently faces the dual pressures of ensuring global food security and adapting to rapid climate change. To cope with these challenges, researchers have introduced several modern mechanization technologies, including advanced farm machinery, autonomous navigation systems, artificial intelligence, sensing technologies, and communication tools, to enhance productivity and sustainability (Syed et al., 2025a). These technologies enable data-driven decision-making by allowing continuous, large-scale acquisition and analysis of crop and environmental information. Consequently, accurately predicting crop yields and monitoring plant health in real time have become critical prerequisites for precision agricultural management (Syed et al., 2025). Traditional measurement methods-often labor-intensive, destructive, and spatially limited-are increasingly unable to meet the demands of modern large-scale farming. In this context, the integration of Remote Together, these ten contributions illustrate the maturation of agricultural remote sensing, moving towards models that are not only more accurate but also lighter, more interpretable, and more resilient to environmental noise. By combining satellite and UAV data with advanced computational models, these innovative approaches are paving the way for a more resilient and productive global food system. Future research will increasingly focus on improving the precision of crop yield estimation models through multi-dimensional analyses. As agricultural environments grow more complex, integrating AI-powered models with multi-sensor fusion technologies will be essential. Innovations such as lightweight neural networks and multimodal cross-attention frameworks will enable the detection of small, occluded, and densely packed targets with greater accuracy, thereby refining crop-specific metrics such as photosynthetically active radiation (FPAR) and nitrogen content. This, in turn, will enhance crop health monitoring and yield predictions.Additionally, UAV-based remote sensing, combined with multitier feature selection, will improve nitrogen content analysis in crops such as cotton, while image dehazing models and light-use efficiency frameworks will bolster biomass estimation.Emerging technologies such as the Ta-YOLO framework will further optimize small fruit detection in dense canopies, advancing overall crop detection accuracy.A key challenge lies in adapting these models to handle real-world complexities, such as variable environmental conditions. Future work will focus on improving the robustness of these models through dynamic coding networks and performance optimization, ensuring they can operate in heterogeneous agricultural environments.Interdisciplinary collaboration between agriculture, AI, and remote sensing experts will accelerate the development and deployment of these approaches, paving the way for more efficient crop yield estimation systems that are critical for ensuring food security and sustainable agricultural practices.
Why it matches plant phenotyping methods作物収量・健康・バイオマス・窒素含量などの植物形質を、衛星・UAVリモートセンシングと計算モデルで推定する手法群を中心に扱う編集レビューであり、方法論的役割が明確。
titleInnovative approaches in remote sensing for precise crop yield estimation: advancements, applications, and future directions
Field / plotLiDAR / point cloudWhole plant / canopy / plot / fieldYield / biomass estimationBiomass / plant weight
Introduction Accurate estimation of individual tree aboveground biomass (AGB) is essential for tree species selection, carbon accounting, and precision forestry. Unmanned aerial vehicle (UAV) LiDAR provides rapid access to detailed tree structural information, offering a promising tool for high-frequency biomass assessment. Methods In this study, a nonlinear mixed-effects (NLME) model integrating UAV LiDAR and field measurements was developed to quantify the influence of genetic heterogeneity and environmental factors on AGB estimation of Catalpa bungei . Data from 2,941 trees across 79 genotypes were collected in Henan Province, including LiDAR-derived tree height ( L H ), LiDAR-derived crown diameter ( L CD ), and AGB. By incorporating genotype as a random effect and planting density as a dummy variable, the NLME model significantly outperformed traditional dummy-variable models. Results Genotype effects explained significant AGB variation, achieving high accuracy (R²=0.7916, RMSE = 3.7095) and reducing TRE by 23.29% compared to the basic power function model. Leave-one-genotype-out cross-validation confirmed robustness. Calibration with the four largest trees yielded the best performance (TRE = 13.09%), while a simplified scheme using only two trees per genotype maintained high accuracy (TRE = 13.24%), markedly reducing field effort. Discussion These results highlight the superiority of NLME AGB models over linear approaches and demonstrate that accounting for genotype effects is critical for reliable biomass estimation. The proposed framework provides an efficient and cost-effective solution for biomass monitoring, tree breeding, carbon sink assessment, and precision forestry.
Why it matches plant phenotyping methodsUAV LiDARと非線形混合効果モデルを統合し、個体樹木の地上部バイオマスという植物形質を推定する方法を開発・検証しており、フェノタイピング手法が中心である。
abstracta nonlinear mixed-effects (NLME) model integrating UAV LiDAR and field measurements was developed to quantify the influence of genetic heterogeneity and environmental factors on AGB estimation of Catalpa bungei
Service crops are grown to provide ecosystem services in viticulture, but their adoption remains limited due to their competition with grapevine for soil resources. To identify trade-offs between services, the effect of service crops management strategies on grapevine performances still need further research. This dataset presents data from two experiments conducted to study the effect of service crops management on soil resources and grapevine performances. The inter-row vegetation was sampled in two Mediterranean vineyards using quadrats for biomass estimation. In addition, an unmanned aerial vehicle (UAV) was regularly flown over the vineyards for a period spanning more than four years in total over the two vineyards. The dataset presented here includes both raw data acquired during fieldwork and processed data derived from this raw inputs. The raw data consists of image series captured by two UAVs during each flight campaign, including RGB and multispectral imagery. Images were acquired between 2021-06-10 and 2022-07-29 for the first vineyard, and between 2023-06-08 and 2025-03-12 for the second vineyard. Based on these raw data, the processed data comprises spatial vectors, raster layers, and dense point clouds generated from UAV images using a Structure from Motion (SfM) photogrammetry workflow, at a 5 cm spatial resolution. The raster layers and dense point clouds provide specific information on vineyard characteristics for each UAV flight date, including elevation, vegetation indices, visible and near-infrared reflectance, and canopy height. In addition, the processed data include measurements of vegetation dry biomass, as well as separate measurements of dry biomass and leaf area measured for selected service crops species. This dataset can be reused for the calibration and/or evaluation of classification algorithms aimed at discriminating vines from the inter-row vegetation, or as part of a larger dataset to explore relationships between remotely-sensed vegetation indices and field-measured vegetation biomass or surface.
Why it matches plant phenotyping methodsUAV画像とSfM処理により、植生指数・樹冠高・バイオマス等の植物形質を取得した再利用可能なデータセットで、分類アルゴリズムの校正・評価用途も明示されており、植物フェノタイピング手法・データ基盤が中心です。
abstractThe dataset presented here includes both raw data acquired during fieldwork and processed data derived from this raw inputs.
Reproduction assets foundThe paper is a Data in Brief article describing a public dataset on Research Data Gouv (doi: 10.57745/MXM55R) containing UAV RGB/multispectral imagery, SfM-derived rasters and point clouds, and field-measured vegetation biomass/leaf-area data from two Mediterranean vineyards — directly the paper's phenotyping inputs. ADataset · publicollected in vineyards located in southern France near Montpellier (43°32.5243′N, 3°50.8240′E). Data are stored on Research Data Gouv, a remote storage solution curated by the French Department of Research.
Data accessibility
Repository name: Research Data Gouv
Data identification number: doi: 10.57745/MXM55R
Direct URL to data: https://doi.org/10.57745/MXM55R
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The fine scale imaging of vineyards (i.e., 5 cm resolution) allows for classification of the vegetation in the vineyard inter-rows, and subsequent exploration of its respective dynamics.
•Open asset ↗Research Data Gouv · 10.57745/MXM55Rlines:1-47Plant phenotyping relevance match · UnverifiedCrossref · checked 15 Sept 2026
Precision agriculture is an essential approach to improving productivity, sustainability, and resilience in modern farming systems amid global changes. Drone-based monitoring represents a significant part of this agricultural transition because it can collect data across extensive regions and across multiple crop growth stages. Perennial cash crops are associated with farmers’ livelihoods and with links to global supply chains. Yield estimates for crops like cocoa and cashew are challenging because of the difficulty of measuring yields under very high canopy cover, erratic fruiting, and inefficient conventional in-field methodologies that involve excessive human error, labour, and time constraints. This paper proposes a hybrid deep learning model, GradTabViTNet, for multi-stage crop condition and yield estimation. The architecture integrates Vision Transformers (ViT) for geospatial attribute extraction, TabNet for attention-based tabular data analysis, CSRNet for accurate object counting in dense canopy environments, and Grad-CAM to enable interpretability by marking key regions in drone images. Classification and counting features are then combined using LightGBM regression to accurately estimate yield. Experimental evaluation using the cashew and cocoa datasets demonstrates that the proposed GradTabViTNet model outperforms existing methods, achieving 99.25% accuracy of 99.10%, precision 98.40%, recall, and 99.27% an F1-score of. The fusion of aerial monitoring with interpretable deep learning methods creates an extensible, stable approach for crop yield prediction, enabling sustainable agriculture, enhanced decision-making for farmers, and stronger food security through data-driven management of high-value perennial crops.
Why it matches plant phenotyping methodsドローン画像から樹冠下の作物状態と収量を推定する深層学習手法を提案し、カシューナッツ・カカオデータセットで既存手法と比較評価しているため、植物形質取得・推定法が中心である。
abstractThis paper proposes a hybrid deep learning model, GradTabViTNet, for multi-stage crop condition and yield estimation.
Breeding rice varieties that are both salt-tolerant and high-yielding is essential for utilizing saline-alkaline lands and ensuring food security. However, However, high-throughput and accurate phenotyping at early growth stages remains a major bottleneck in breeding programs. In this study, unmanned aerial vehicle (UAV) imaging was employed to screen salt-tolerant and high-yielding varieties among 60 rice varieties under saline-alkaline field conditions. Red-green-blue (RGB), multispectral, and thermal canopy images were acquired throughout the growing season by UAV, from which 41 phenotypic traits were extracted at each growth stage. These traits were categorized into early-stage (tillering and jointing), late-stage (booting, flowering, and maturity), and whole-growth-stage (from tillering to maturity) and subsequently used to screen salt-tolerant and high-yielding rice varieties. Results showed that: (1) An early high-throughput screening method for salt-tolerant rice varieties was developed based on the membership function and UAV phenotypes (MFuav), achieving high performance (Precision >0.8, OA > 0.7). MFuav demonstrated the highest accuracy at the early-stage, with Precision increasing by 0.29 and 0.43 compared to the late- and whole-stage models, respectively. (2) A machine learning based UAV phenotypes framework (MLuav) was developed to further improve salt-tolerance screening performance. Within this framework, the partial least squares regression (PLSR) was employed for early-stage salt-tolerance screening, which achieved a Precision of 0.97 and an OA of 0.78, outperforming the MFuav by 0.11 and 0.08, respectively. In addition, within the same MLuav framework, early-stage UAV phenotypes were further used for actual yield prediction using a Random Forest (RF) model. The model achieved a high Recall for high-yielding varieties (Recall = 1.00), ensuring that no potentially high-yielding germplasm was missed, although this was accompanied by a moderate Precision (0.51) and an overall accuracy of 0.70. (3) The MLuav consistently outperformed the MFuav in screening salt-tolerant and high-yielding varieties across all 60 rice varieties. Among the five referenced salt-tolerant and high-yielding rice varieties, the MLuav correctly screened four using early-stage phenotypes, whereas the MFuav only screened three. Overall, the proposed method enables early screening of salt-tolerant and high-yielding rice varieties, offering an efficient tool for the screening and utilization of elite stress-resilient germplasm.
Why it matches plant phenotyping methodsUAV画像から多数のイネ表現型形質を抽出し、塩耐性・収量性を早期スクリーニングする方法と機械学習フレームワークを開発・評価しており、表現型取得・解析手法が研究の中心である。
abstracthigh-throughput and accurate phenotyping at early growth stages remains a major bottleneck in breeding programs
Reliable aboveground biomass (AGB) estimates for woody crops are required for carbon accounting and MRV; however, it remains unclear how LiDAR modality and sampling geometry influence plot-scale and tree-scale AGB predictions in intensively managed orchards. We benchmarked four LiDAR modalities across three Mediterranean woody-crop sites in Córdoba (Spain), IFAPA, Doña María, and Villaseca using open national airborne laser scanning (PNOA/ALS), Riegl ALS, unmanned laser scanning (ULS), and mobile laser scanning (MLS). The field inventory used 58 fixed-area plots (20×50 m; 0.1 ha) collected in December 2024-January 2025 (1,867 trees) and species-specific allometries based on D2r to derive tree and plot AGB; carbon was computed using wood carbon fractions (0.445 olive; 0.457 almond) and CO2e via IPCC conversion. Plot-level LiDAR metrics (e.g., mean height, p95, maximum height, and cover proxies) were extracted from normalized point clouds and modeled with Random Forest, XGBoost, and an ensemble under an 80/20 train-test split. Mean field AGB differed among sites (33.89, 30.94 and 12.76 Mg ha−1 for Villaseca, Doña María, and IFAPA). In the provided summaries, XGBoost achieved the lowest errors at IFAPA (RMSE = 0.400 Mg ha−1; R2 = 0.994) and Villaseca (RMSE = 0.872 Mg ha−1; R2 = 0.995), whereas PNOA was competitive at Doña María (RMSE = 0.725 Mg ha−1; R2 = 0.994). The results support cross-platform LiDAR for orchard AGB mapping and identify conditions under which open national LiDAR can enable scalable MRV. In addition, we evaluated TreeQSM-based quantitative structure models (QSMs) as an independent tree-level 3D reconstruction approach and examined their site-dependent agreement with field inventory estimates.
Why it matches plant phenotyping methods複数のLiDARモダリティと解析手法を比較・ベンチマークし、樹木およびプロットの地上部バイオマスを推定する技術評価が研究の中心であるため。
abstractWe benchmarked four LiDAR modalities across three Mediterranean woody-crop sites
Unmanned aerial vehicle (UAV) remote sensing has evolved from experimental imaging into an operational diagnostic infrastructure supporting climate-smart agriculture through high-resolution, flexible, and timely crop observation. This review synthesizes advances in UAV platforms, multisensor payloads, artificial intelligence (AI) analytics, and multisource data fusion to evaluate their combined potential for monitoring heterogeneous smallholder systems. A PRISMA-guided analysis of 59 studies (2013–2024) classified sensing architectures, analytical approaches, and application domains across diverse agroecological contexts. Integrated UAV–AI frameworks improve detection of crop stress, yield variability, biomass distribution, and phenological dynamics compared with conventional monitoring, particularly when multimodal sensor data are fused with satellite and ground observations. Predictive performance and diagnostic reliability increase when spectral, thermal, and structural datasets are analyzed jointly using machine-learning or deep-learning models. However, scalability remains constrained by operational, infra-structural, and regulatory factors, especially in resource-limited systems. These findings demonstrate that integrated sensing–analytics systems form a critical foundation for scalable climate-smart agricultural transformation and data-driven decision support across farm, landscape, and institutional scales.
Why it matches plant phenotyping methodsUAVセンシングとAIによる作物ストレス、収量変動、バイオマス、フェノロジーの観測・推定技術を体系的にレビューしており、植物形質・状態の取得方法が中心である。
abstractThis review synthesizes advances in UAV platforms, multisensor payloads, artificial intelligence (AI) analytics, and multisource data fusion
Grassland canopy height is one of the most important traits for determining plant diversity and community structure, directly affecting the resource use efficiency of livestock in grassland ecosystems. However, broad-scale changes in grassland canopy height are seldom reported due to the complex effects of species aggregation on both interspecific and intraspecific structures. Here, we decouple grassland aboveground biomass into vertical and horizontal allocations, thereby offering a pathway to mirror changes in grassland canopy height. Grassland aboveground biomass is estimated using a machine learning algorithm by fusing climatic factors, satellite-driving metrics, and 8-year consecutive ground-truth surveys; the horizontal allocation of grassland aboveground biomass is derived from optimized linear spectral mixture analysis. We find that changes in horizontal biomass allocation primarily accounted for increases in Chinese grassland aboveground biomass from 2001 to 2022, resulting in a significant decline in grassland canopy height. The decline in grassland canopy height is shaped by reduced radiation and, more importantly, by the combined effects of warming and grazing, while also being related to variations in plant diversity. The dwarfing grassland community with declining canopy height may increase the impact of livestock disturbances, thus diminishing the resistance of grassland ecosystems to climate fluctuations.
abstractHere, we decouple grassland aboveground biomass into vertical and horizontal allocations, thereby offering a pathway to mirror changes in grassland canopy height.
Developing climate-resilient wheat varieties requires combining high yield with stability across diverse environments, especially under increasingly variable precipitation and rising temperatures. This study evaluated 64 post-Green Revolution durum wheat cultivars under irrigated and rainfed conditions at two contrasting Mediterranean sites in Spain. A classification framework was developed to support genotype selection based on yield and yield stability, estimated using linear mixed models and yield slopes across environments. Genotypes were classified by interquartile thresholds, and those showing either low yield or low stability were considered undesirable for selection. High-throughput phenotyping was conducted throughout the season using ground-sensor Red-Green-Blue (RGB) and multispectral (MS) vegetation indices (VIs), along with UAV-derived RGB, MS, and thermal-infrared (TIR) data. VIs and TIR at anthesis and grain filling, and their differences (senescence proxies), were used to train Random Forests for yield and stability estimation including sequential feature selection. Environmental covariates (water input, reference evapotranspiration) were integrated in yield models, with strong outcomes (R 2 > 0.74; MAPE <23.6%). Stability predictions were based on VI stability and, though moderate (R 2 up to 0.56; MAPE <17.75%), outperformed previous studies. Selected features were used to evaluate seasonal reflectance phenotypes: “keep” genotypes (intermediate/high yield or/and stability) exhibited early-vigor but lower green retention by the end of grain filling, while “discard” genotypes (low yield or/and stability) showed reduced early vigor and “stay-green” behavior. This study highlights early-vigor and earlier senescence over “stay-green” for wheat selection, offering a cost-effective approach shifting the breeding focus from yield maximization to joint yield-stability evaluation, promoting sustainability.
Why it matches plant phenotyping methods高スループットの地上・UAVセンサーによる表現型取得と、機械学習による収量・安定性推定が研究の中心であり、育種選抜に用いる手法を実質的に評価・適用している。
abstractHigh-throughput phenotyping was conducted throughout the season using ground-sensor Red-Green-Blue (RGB) and multispectral (MS) vegetation indices (VIs), along with UAV-derived RGB, MS, and thermal-infrared (TIR) data.
Reproduction assets foundThe authors explicitly state that the datasets and analysis scripts for all analyses (yield/stability modeling, VI extraction, Random Forest workflows) are publicly available in their Zenodo repository (DOI 10.5281/zenodo.17435708), referenced both in the statistical analysis section and the Data Availability statementCode · publicThe datasets and scripts for all the analyses conducted are available in our repository ( https://doi.org/10.5281/zenodo.17435708 ).Open asset ↗zenodo · 10.5281/zenodo.17435708lines:222-237Code / dataset availability confirmedCrossref · Europe PMC · OpenAlex · checked 5 Sept 2026
Quantitative characterization of complete canopy architecture is essential for accurate evaluation of crop photosynthesis and yield potential, thereby supporting crop ideotype design. Although various sensing technologies enable three-dimensional (3D) reconstruction of individual plants and canopies, they often fail to describe canopy architecture accurately because of severe occlusion in dense populations. To address this limitation, we developed an effective framework for the 3D reconstruction of complex and dynamic population-scale canopy architecture in rapeseed using unmanned aerial vehicle multi-view imagery combined with a novel point cloud completion model. A complete point cloud generation pipeline was first established to enable automated training data annotation, allowing discrimination between surface points and occluded points within the canopy. The proposed crop population point cloud completion network (CP-PCN) integrates a multi-resolution dynamic graph convolutional encoder, a point pyramid decoder, a dynamic graph convolutional feature extractor, and a generative adversarial network-based loss function to predict occluded canopy points. CP-PCN achieved chamfer distance values of 3.35 to 4.51 cm across four growth stages, outperforming the state-of-the-art transformer-based method PoinTr. Ablation analyses confirmed that each of the four modules contributes to overall model accuracy. In addition, validation experiments showed that the improved architectural completeness achieved by CP-PCN resulted in more accurate yield estimation compared with incomplete and PoinTr-completed point clouds. CP-PCN also demonstrated strong cross-crop generalizability by successfully reconstructing mature rice canopies. Overall, this framework provides a scalable approach for quantitative analysis of complex canopy architectures in field-grown crops.
Why it matches plant phenotyping methodsUAVマルチビュー画像から遮蔽点を補完し、作物群落の3Dキャノピー構造を再構成する手法を開発・検証しており、植物表現型取得が研究の中心です。
abstractwe developed an effective framework for the 3D reconstruction of complex and dynamic population-scale canopy architecture in rapeseed using unmanned aerial vehicle multi-view imagery combined with a novel point cloud completion model
Reproduction assets foundThe paper's Data and code availability statement explicitly deposits all source code and test data for the CP-PCN phenotyping pipeline on a public GitHub repository, matching an allowed URL.Code · publicAll source code and test data used in this study are publicly available on GitHub ( https://github.com/Ziyue-Guo/CP-PCN.git ).Open asset ↗https://github.com/Ziyue-Guo/CP-PCN.git · CP-PCNlines:133-158Plant phenotyping relevance match · UnverifiedEurope PMC · checked 15 Sept 2026
Published1 Mar 2026Computers and Electronics in Agriculture.
Accurate yield forecasting is crucial in optimizing resource management and decision-making processes in agriculture, particularly in crops such as strawberries, which require precise predictions due to their rapid and continuous ripening cycles. This study introduces PheMuT, a novel phenology-informed, multi-modal time-series model that integrates visual and meteorological data streams to enhance strawberry yield forecasting. The proposed method employs advanced computer vision techniques, including two YOLOv11 detectors, an optimized ByteTrack tracker, Segment Anything (SAM), and Depth Anything v2 (DAv2), for precise fruit detection, canopy, and volume estimation. Concurrently, high-frequency weather data are processed using a self-supervised autoregressive Temporal Convolutional Network (TCN), resulting in concise and informative weather embeddings. These visual and weather features are fused within an LSTM-based model to produce weekly yield forecasts. PheMuT was validated using two strawberry cultivars at a Florida research facility over two consecutive seasons. Results indicated that PheMuT improved forecasting accuracy, reducing mean absolute error (MAE) by 10.7%, root mean squared error (RMSE) by 12.5%, and mean absolute percentage error (MAPE) by 18.6% compared to baseline manual methods. Additionally, the model exhibited a notable improvement of 17.2% in the coefficient of determination (R²). PheMuT offers an efficient, automated framework for yield forecasting. Code and data are available athttps://github.com/Sycamorers/PheMuT. The full datasets used in this study are available from the authors upon request.
Why it matches plant phenotyping methods果実検出、キャノピー・体積推定などの画像ベース表現型取得と時系列モデルを統合した収量予測手法を開発・検証しており、表現型取得ワークフローが中心的である。
abstractThis study introduces PheMuT, a novel phenology-informed, multi-modal time-series model that integrates visual and meteorological data streams to enhance strawberry yield forecasting.
Improving sugar beet yield under variable environmental conditions requires a detailed understanding of the physiological mechanisms that drive yield formation. In sugar beet, canopy development determines resource capture, while radiation use efficiency (RUE) regulates the transformation efficiency of primary resources, and assimilate partitioning regulates the allocation of dry matter to the storage root. High-throughput phenotyping offers opportunities to quantify these physiological processes across diverse environments and genetic backgrounds, thereby identifying key traits for yield improvement. A scalable drone-based pipeline was established and validated to estimate physiological yield components – leaf area index (LAI), radiation interception efficiency (RIE), RUE, and harvest index (HI). Unmanned Aerial Vehicle (UAV)-derived multispectral imagery, combined with environmental records and harvest measurements, was used across more than 1300 field plots in Germany and Italy (2023–2024), covering three contrasting environments, two irrigation managements, and up to 171 genotypes. LAI estimation was calibrated and validated under different water regimes in northern Germany (mean absolute error, MAE = 0.30 m² m⁻²). Dynamic UAV-based LAI enabled continuous estimation of radiation interception and biomass accumulation. Total dry matter correlated strongly with cumulative effective (temperature-dependent) radiation interception (R² = 0.81), indicating a comparatively stable RUE across diverse conditions. Genotypic variation in yield formation was mainly driven by canopy-level processes: RIE accounted for 65 % of variation under water-limited conditions, while RUE accounted for 46 % under irrigation. Partitioning traits (HI and Sugar HI) contributed minimally in both irrigation managements. The results highlight the dominant role of canopy development and radiation use in sugar beet yield formation under contrasting environmental conditions. The proposed UAV-based framework provides a transferable, high-throughput approach to quantify physiological yield drivers in field settings. This enables targeted trait selection for breeding and facilitates integration of functional yield components into crop improvement strategies.
Why it matches plant phenotyping methodsUAVマルチスペクトル画像によるLAI等の生理的形質推定パイプラインを構築・検証しており、フェノタイピング手法が研究の中心である。
abstractA scalable drone-based pipeline was established and validated to estimate physiological yield components – leaf area index (LAI), radiation interception efficiency (RIE), RUE, and harvest index (HI).
Accurate acquisition of phenotypic characteristics in protected crops is a crucial prerequisite for intelligent control and digital breeding in greenhouses. To accurately assess the phenotypic traits of protected lettuce, a specialized in situ phenotypic detection method has been developed. The Multimodal Features and Attention Mechanism for Phenotype Detection Model (MFAMNet) was developed for protected lettuce, employing a segmented multi-source image dataset for synchronous regression testing. The results revealed that the predicted values generated by MFAMNet exhibited a strong correlation with the measured values, achieving coefficients of determination of 0.96, 0.92, 0.95, 0.94, and 0.95 for plant height, crown width, leaf area, fresh weight, and dry weight, respectively. Ablation tests demonstrated that the deep learning detection framework based on multi-modal feature fusion significantly outperformed single-feature detection models, highlighting the advantages of integrating diverse data modalities. In addition, the multi-modal feature attention mechanism (MMF) facilitates both inter-modality and intra-modality interactions by capturing the global correlations between modalities and employing dynamic sparse spatial attention. The effectiveness of MMF has been validated through comparative experiments, demonstrating its suitability for the phenotypic detection of artificially cultivated lettuce. In summary, the method proposed in this study facilitates real-time monitoring of facility crops, enabling precise control of environmental parameters in protected agriculture and optimizing resource allocation. This approach contributes to the development of a comprehensive intelligent agriculture system and establishes a foundation for unmanned farms.
Why it matches plant phenotyping methodsレタスの草丈、株幅、葉面積、 fresh weight、dry weightを推定するマルチモーダル画像ベース手法を開発し、実測値との比較およびアブレーション・比較実験で検証しており、フェノタイピング手法が研究の中心である。
abstracta specialized in situ phenotypic detection method has been developed
Automated phenotyping of wheat growth stages from 3D point clouds is still limited. The study presents a concise framework that reconstructs multi-view UAS imagery into 3D point clouds (jointing to maturity) and performs plot-level phenotyping. A novel 3D wheat plot detection network—integrating spatial–channel coordinated attention and area attention modules—improves depth-direction feature recognition, and a point-cloud-density-based row segmentation algorithm enables planting-row-scale plot delineation. A supporting software system facilitates 3D visualization and automated extraction of phenotypic parameters. We introduce a dynamic phenotypic index of five temporal metrics (growth stage, slow growth stage, height/area reduction stage, maximum height/area difference stage, and height/area change rate) for growth-stage classification and yield prediction using static and time-series models. Experiments show strong agreement between predicted and measured plot heights (R 2 = 0.937); the detection net achieved AP 3D = 94.15 % and AP BEV = 95.35 % in “easy” mode; and a Bi-LSTM incorporating dynamic traits reached 82.37 % prediction accuracy for leaf area and yield, a 6.14 % improvement over static-trait models. This workflow supports high-throughput 3D phenotyping and reliable yield estimation for precision agriculture. • Developed a novel 3D wheat plot detection net with spatial–channel coordinated attention and area-attention modules, reaching 94.15% AP 3D and 95.35% AP BEV in high-precision mode, outperforming traditional methods. The CFPT 3D module boosts depth-direction feature extraction for dense planting. • Introduced 5 temporal phenotypic metrics (e.g., growth stage transitions, height/area change rates) to capture dynamic growth patterns. • Bi-LSTM models using these traits predicted yield with 82.37% accuracy, 6.14% higher than static-trait models. • Released a PyQt5-based 3D phenotype extraction tool for automated parameter calculation (height, canopy area, LAI) and visualization. • Proposed a density-based row segmentation algorithm enabling accurate row-level phenotyping, validated in single- and multi-row systems.
Why it matches plant phenotyping methods3D画像・点群から小麦区画の形態形質を抽出する手法、検出・行分割アルゴリズム、動的形質指標、ソフトウェアを中心的に開発・検証しているため。
abstractThe study presents a concise framework that reconstructs multi-view UAS imagery into 3D point clouds (jointing to maturity) and performs plot-level phenotyping.
Improving yield is one of the core goals of crop breeding. By predicting the potential yield of different breeding materials, breeders can screen these materials at different growth stages to select the best-performing breeding materials. However, existing yield prediction methods struggle to balance accuracy, interpretability, and robustness, often facing trade-offs between model complexity, data requirements, and generalizability. To address the above challenges, this study proposed a new hybrid method integrating remote sensing data assimilation and deep learning. The leaf area index was assimilated into the calibrated and validated WOFOST crop model using a newly designed data assimilation algorithm. The dataset, including partial outputs from the WOFOST model, development day, and vegetation indexes (VIs), was used to train the Temporal Fusion Transformer model for wheat yield prediction. The results showed that the new hybrid method achieved the highest performance in wheat yield prediction for different breeding materials in different study areas (R² of 0.831 and RMSE of 372.8 kg/ha in Yuhang experiment; R² of 0.704 and RMSE of 605.3 kg/ha in Zijingang experiment), which was better than other process-based model-driven methods and data-driven methods. This showed that the hybrid method had superior applicability in accurate yield prediction. Other results showed that increasing the number of data collections during the growth stage could significantly improve the performance of yield prediction and reduce error. Data from the middle and late growth stages contributed more to prediction performance than data from the early stages. Physiological variables and some VIs were the most important factors for yield prediction, while morphological characteristics contributed less. The importance and impact of each feature varied at different growth stages, highlighting the complex nonlinear relationship between characteristics and yield. In addition, since existing methods are difficult to fully utilize multi-source heterogeneous data related to yield in the breeding process, and the usability and user-friendliness of yield prediction software are also insufficient, an interactive yield prediction website has been developed based on a new hybrid method, a large language model (Llama), and related technologies to assist breeding decisions. This study aims to improve the efficiency of breeding material screening, provide an accurate, user-friendly, and well-interpretable yield prediction tool for wheat breeding, and facilitate smart breeding and decision making.
Why it matches plant phenotyping methodsコムギの収量という植物形質を、リモートセンシング・データ同化・深層学習で予測する手法を開発・比較検証し、育種向けソフトウェアも開発しているため、フェノタイピング手法が中心的である。
abstractThe results showed that the new hybrid method achieved the highest performance in wheat yield prediction for different breeding materials in different study areas
Accurate crop yield estimation is crucial for decision-making and planning in modern agriculture with increasing challenges with food security. Yield predictions provide farmers with insights into expected production, facilitating optimized resource allocation, improved agricultural management strategies, and enhanced profitability. This study investigates the application of machine learning (ML) techniques, including Feedforward Neural Networks (FNN), Long Short-Term Memory (LSTM), and Random Forest (RF) models, for predicting crop yields using multi-sensory time-series data that has been collected on two fields over a four-year timeframe. The focus is on corn (Zea mays) and cotton (Gossypium hirsutum) yield, two of the top critical crops in Mississippi region. A multi-sensory dataset was collected using multispectral cameras and LiDAR sensors mounted on unmanned aircraft systems (UAS), along with soil moisture and temperature data from volumetric probes and environmental data from a nearby weather station. Over four years, more than 30 features were extracted weekly from five major categories, with 235 ground truth yield records from plots in the field. The study outlines the methodology for feature selection and examines its impact on yield prediction accuracy. Using percentile root mean square error (RRMSE) and mean absolute percentage error (MAPE) as performance metrics, the study found that the proposed LSTM model produced lower field-wise errors (9 − 21 % MAPE) compared to other models and validation, indicating superior performance in predicting yields across selected weeks. The proposed ML-based approach, validated through year-based and field-wise cross-validation methods, demonstrates the effectiveness of using UAS-collected multi-sensor data for accurate yield estimation in corn and cotton.
Why it matches plant phenotyping methodsUASのマルチセンサー画像・LiDARデータから圃場プロットの収量を推定する計算ワークフローを開発・評価し、交差検証で性能を検証しているため、植物表現型取得が中心である。
abstractThis study investigates the application of machine learning (ML) techniques, including Feedforward Neural Networks (FNN), Long Short-Term Memory (LSTM), and Random Forest (RF) models, for predicting crop yields using multi-sensory time-series data
Robust quantification of crop status in real-time is essential for agile decision-making. While use of unmanned aerial vehicle data (UAV) appears promising in this vein, the contribution and transferability of various features (e.g. vegetation indices, plant height and texture features) in crop above-ground biomass (AGB) prediction remain poorly understood. Here, our objectives were to (1) evaluate the performance of various machine learning (ML) algorithms in the synthesis of multiple features, (2) elicit the contribution of various UAV features, (3) assess the transferability of features across growth stages and sites. Four field experiments, incorporating several water and nitrogen treatments across two sites, were assembled for use in AGB prognostics. We invoked four ML algorithms—Random forest (RF), Lasso regression (LR), K-nearest neighbors (KNN) and a stacked ensemble integrating the three methods (SML)—to predict wheat AGB using multiple UAV data and phenological information. Additionally, interpretable ML techniques were employed to elucidate the influence of UAV features on AGB prediction across growth stages. Our results showed that all algorithms exhibited robust performance in predicting wheat biomass, with RMSE values of 1.64, 1.71, 1.71, and 1.57 Mg ha −1 for RF, LR, KNN, and SML, respectively. RF predominantly relied on plant height features, LR leveraged vegetation indices, and KNN prioritized texture features, while SML synthesized the advantages of multiple ML algorithms. Fusion of multiple datasets amplified model prognostic capacity and scalability, with R 2 and rRMSE of 0.92 and 22 % when using data from external sites. Features pertaining to vegetation indices and plant height during vegetative growth and around flowering had seminal contributions of model predictions. Texture features significantly reduced the saturation effect during the reproductive stage but diminished the model’s transferability during the vegetative stage. Complementarity among data types enhanced effectiveness of ensemble machine learning, which leverages strengths of diverse data to improve the accuracy and robustness of AGB predictions. Future studies could combine multiple sources of remote sensing, such as LiDAR and thermal infrared alongside system modeling, to improve ML accuracy and generalization capability.
Why it matches plant phenotyping methodsUAV由来の植物高・植生指数・テクスチャ等から小麦バイオマスを推定する機械学習手法を比較・検証し、異なる生育段階や圃場への転移性も評価しており、表現型推定法が中心である。
abstractevaluate the performance of various machine learning (ML) algorithms in the synthesis of multiple features
Efficient irrigation of horticultural crops under increasing water scarcity requires crop models that exploit high–resolution remote–sensing (RS) data. This study evaluated how unmanned aerial vehicle (UAV) multispectral and thermal observations improved AquaCrop-OSPy simulations of canopy cover (CC), actual evapotranspiration (ETₐ) and yield for irrigated broccoli under Mediterranean conditions. Broccoli was grown for two seasons in a 0.2 ha field in eastern Spain under two irrigation strategies: decision–support Irrigation Advisor (IA) versus farmer practice. A global sensitivity analysis (GSA) and two–stage calibration against Season 1 CC and yield identified canopy growth (CGC), harvest index (HIₒ) and transpiration phenology (GDDᵤₚ) as dominant controls; the calibrated model was validated in Season 2. UAV imagery provided CC via supervised classification and ETₐ via a two–source energy balance model (pyTSEB), which were assimilated into AquaCrop-OSPy on three dates using a hybrid observed–simulated scheme. Compared with lysimeter measurements, pyTSEB reproduced ETₐ with root–mean–square error (RMSE) 0.39 mm d⁻¹ and Nash–Sutcliffe efficiency (NSE) 0.93, whereas baseline AquaCrop-OSPy showed RMSE 1.24 mm d⁻¹ and NSE 0.27. Without assimilation, AquaCrop-OSPy reproduced mean yield but not subplot variability (RMSE 1.67 t ha⁻¹). Assimilating CC reduced yield RMSE by 8.9 %, ETₐ alone gave smaller gains, and joint CC + ETₐ assimilation achieved the lowest RMSE (1.47 t ha⁻¹, 11.9 % reduction). Across seasons, IA applied 20.6 % more water than farmer practice with no consistent yield or water–productivity benefits. These results, obtained within the limitations of this study, indicate that UAV-derived CC, complemented by ETₐ, modestly improves AquaCrop-OSPy yield predictions. Nevertheless, they should be interpreted as indicative rather than definitive and motivate further evaluations.
Why it matches plant phenotyping methodsUAV画像からブロッコリーの canopy cover と実蒸発散量を推定し、作物モデルへの同化性能を検証することが研究の中心であり、植物形質・状態の取得と技術評価に該当する。
abstractUAV imagery provided CC via supervised classification and ETₐ via a two–source energy balance model (pyTSEB), which were assimilated into AquaCrop-OSPy on three dates using a hybrid observed–simulated scheme.
Rapid and accurate acquisition of field crop yield is of great significance for agriculture management optimization, food security and crop productivity. By the non-destructive and high-throughput data acquisition, the unmanned aerial vehicle (UAV) remote sensing has become a key tool for crop growth monitoring. However, the scarcity of in-situ samples poses technical barriers and efficiency challenges to yield model training. This study has developed a new yield estimation framework that integrates process models, optical remote sensing, and transfer learning to improve the stability and accuracy of crop yield estimation under small sample conditions. The DSSAT was calibrated with hyperspectral UAV derived crop growth variables, to describe the spatial-temporal variation of small-scale field winter canola leaf nitrogen content during growing season. Firstly, a process-interpretative crop yield estimation framework, TrSC2Y, was pre-trained using the PROSAIL radiative transfer model and the DSSAT crop growth model. Secondly, TrSC2Y was fine-tuned using field observations and UAV hyper-spectra images from three-years canola experiment. Finally, the actual performance and application potential of fine-tuned TrSC2Y in canola yield estimation were evaluated with machine learning as a benchmark test. The results show that: (1) Pre-trained by the crop spectra dataset (from PROSAIL) and yield dataset (from DSSAT), TrSC2Y can accurately extract crop phenotype parameters from theoretical canopy spectra. The joint use of phenotype parameters from multiple growth stages can achieve the best yield estimation (R²= 0.98;RMSE= 33.07 kg/ha;MAE= 1.26 %);(2) Fine-tuned TrSC2Y can be transferred to the field winter canola yield estimation task and shows stable performance (R²= 0.86;RMSE=224.42 kg/ha;MAE=6.5 %). Compared with the machine learning benchmark test, the demand of modeling samples for TrSC2Y is reduced by 50 %; (3) TrSC2Y supports the visualization of field-scale winter canola yield and captures the spatial variability of winter canola yield caused by irrigation-fertilizer treatments.The above results provide a lightweight, cost-effective, and innovative method for field crop yield estimation, promoting the development of precision agriculture management and intelligent applications.
Why it matches plant phenotyping methodsUAVハイパースペクトル画像と作物モデル・転移学習を統合し、収量などの植物表現型を抽出・推定する枠組みを開発・評価しており、取得・推定手法が研究の中心である。
abstractThis study has developed a new yield estimation framework that integrates process models, optical remote sensing, and transfer learning to improve the stability and accuracy of crop yield estimation under small sample conditions.
This study addresses the challenge of forecasting maize yield in southeastern Quebec by comparing weekly Unmanned Aerial Vehicle (UAV) and PlanetScope satellite imagery throughout the cropping season and across diverse growing conditions. Using five nitrogen treatments over three years with two sowing windows each year to generate variability within the dataset, eleven vegetation indices were evaluated to identify the best-performing indices and the optimal forecasting window. Indices were interpolated using curve fitting to enable evaluation at any stage of the growing season. Cross-validation simulated real-world application by excluding entire sowing events during model testing. Using a linear regression approach, results demonstrate that indices combining green and near-infrared bands (Green Normalized Difference Vegetation Index [GNDVI] and Chlorophyll Index Green [CIG]) exhibit superior forecasting potential compared to red-near-infrared (like NDVI) and RGB-based indices (like NGRDI). The optimal forecast window occurs during early grain filling (R2-R3 stages, around 2300 Crop Heat Units [CHU]), achieving Root Mean Square Coefficient of Variation (RMSCV) values of 12.51 % for UAVs and 15.28 % for PlanetScope. While PlanetScope maximum performance approached UAV capabilities, results showed a CHU range between 200 and 400 in the effective forecasting period (RMSCV < 20 %) compared to 850 to 1450 for UAV. For PlanetScope, adding multiple indices marginally improved precision, slightly reduced forecasting window and reduced model transferability. The analysis revealed weak correlations between indices and yield during early vegetative and senescence phases, indicating limited potential for enabling timely in-season management interventions. This study established UAV-based models as a reference point for assessing the limitations of satellite-derived forecasts.
Why it matches plant phenotyping methodsUAV・衛星画像と植生指数によるトウモロコシ収量推定を比較・交差検証しており、植物収量という形質の取得・予測手法が中心である。
abstractcomparing weekly Unmanned Aerial Vehicle (UAV) and PlanetScope satellite imagery throughout the cropping season
Wildfires are the leading cause of forest degradation and reduce the carbon sequestration capacity of forest ecosystems. As climate change intensifies fire regimes, accurately mapping burn severity and biomass loss remains difficult, particularly in complex mountainous terrain. Traditional remote sensing approaches based on optical data often fail to capture sub-canopy and structural variations, while field-based methods are constrained by scale, access, and logistical complexity. To address these limitations, this study utilises NASA’s Global Ecosystem Dynamics Investigation (GEDI) LiDAR data to capture three-dimensional forest structure and monitor changes in aboveground biomass. Focusing on the Indian Himalayan Region (IHR), we utilised GEDI structural metrics for fire severity classifications derived from NASA’s Fire Information for Resource Management System (FIRMS) data. Spatial fire density mapping revealed that Evergreen Needleleaf (ENL), Evergreen Broadleaf (EBL), and Deciduous Broadleaf (DBL) plant functional types (PFTs) are particularly vulnerable to recurring fires. The GEDI Level 4 A AGBD product, when tested in the IHR, showed a tendency to underestimate biomass relative to regional field studies, indicating the need for localised calibration in rugged terrain. We found that the pre-monsoon fire season resulted in a biomass loss of 14.33 Mg/ha for the ENL PFT, while the EBL PFT showed a biomass gain of 3.15 Mg/ha. A Random Forest model utilising GEDI structural inputs for fire severity classification achieved an overall accuracy of 85 %. We found that vegetation structural complexity, rather than canopy height, is a more important predictor of high fire severity. We also evaluated the Waveform Structural Complexity Index (WSCI), a novel GEDI metric that effectively characterised fire severity across the under-storey vegetation. These findings underscore the importance of incorporating 3D vegetation structure into fire impact assessments, moving beyond the limitations of conventional two-dimensional optical datasets.
Why it matches plant phenotyping methodsGEDI LiDARによる森林構造・バイオマス損失・火災重症度の推定を中心に、既存AGBD製品の地域較正と新規指標WSCIの評価を行っており、植物状態の取得・推定手法が中核である。
abstractwe utilised GEDI structural metrics for fire severity classifications
Cotton (Gossypium hirsutum L.) is a vital fiber crop that thrives with proper management. Accurate decision-making also improves cotton productivity. However, many field experiments assume uniform conditions and ignore within-field variability caused by nitrogen doses and cultivar differences. Therefore, this field experiment was conducted to develop UAV-based yield-prediction models for cotton under varying nitrogen doses. Five nitrogen treatments were applied as urea fertilizer rates: T0 (0 kg/ha), T1 (100 kg/ha), T2 (120 kg/ha), T3 (140 kg/ha), and T4 (160 kg/ha), with other fertilizer doses kept constant across two cotton varieties, CB Hybrid-1 and CB HYV-15. The findings revealed that increasing nitrogen fertilizer doses boosted vegetative growth and height, but yield decreased at the highest fertilizer rate for both varieties. The most efficient urea fertilizer treatments were T2 (120 kg/ha) for the high-yielding variety and T3 (140 kg/ha) for the hybrid variety. Stepwise Multiple Linear Regression (MLR) and Least Absolute Shrinkage and Selection Operator (LASSO) models were used to predict cotton yield during early growth stages using UAV-based vegetation indices. The Normalized Difference Red Edge (NDRE) was identified as the most effective predictor in the Stepwise MLR model, which performed well at 72 days after sowing (DAS) (R2 = 0.89). The LASSO model also showed strong performance at 79 DAS (R² = 0.75), with the Normalized Difference Vegetation Index (NDVI) as a key predictor. Overall, this study demonstrates that UAV-derived vegetation indices can effectively predict cotton yield and highlight the impact of nitrogen fertilizer on yield.
Why it matches plant phenotyping methodsUAVマルチスペクトル画像から植生指数を抽出し、綿花収量を予測する手法の開発・評価が研究の中心であり、単なる窒素処理実験における routine 測定ではない。
abstractthis field experiment was conducted to develop UAV-based yield-prediction models for cotton under varying nitrogen doses.
Efficient nitrogen (N) management is critical for maximising yield while minimising environmental impacts in oilseed rape production. While Unmanned Aerial Vehicle (UAV)-based monitoring of N status has advanced rapidly, translating estimated N status into actionable fertilization strategies remains limited. This study proposes a multistage N topdressing recommendation framework for winter oilseed rape that integrates UAV multispectral data with prior agronomic knowledge using machine learning algorithms. The framework accurately estimated the nitrogen nutrition index (NNI), with the random forest model performing best (r² =0.73 and RMSE = 0.11) for the validation dataset. By integrating estimated NNI, critical NNI thresholds, and optimal N uptake levels, dynamic, stage-specific N fertilizer topdressing rates were computed. A field experiment with varying basal N fertilizer rates was conducted to validate the framework, with UAV-guided topdressing performed after each monitoring event. Compared with the local conventional fertilization practice, the UAV-guided treatment with 90 kg N/ha basal fertilizer rates significantly improved yield by 20.2 % and N use efficiency by 80.1 %. This study bridges the gap between remote sensing-based diagnostics and in-field N fertilization, offering a feasible data-driven approach for real-time N management to enhance productivity and sustainability in oilseed rape cultivation.
Why it matches plant phenotyping methodsUAVマルチスペクトル画像から植物の窒素栄養指数（NNI）を推定する手法を機械学習で構築・検証し、その推定に基づく施肥フレームワークを評価しており、植物状態の取得・抽出が中心的です。
abstractThis study proposes a multistage N topdressing recommendation framework for winter oilseed rape that integrates UAV multispectral data with prior agronomic knowledge using machine learning algorithms.
Forecasting crop performance through non-destructive tools is crucial for enabling timely, data-driven decisions for sustainable cotton production. This study evaluated physiological, PIs [chlorophyll index (CI), nitrogen balance index (NBI)], vegetation, VIs [normalized difference vegetation index (NDVI), normalized difference red edge (NDRE)], and biochemical, BIs [leaf nitrogen, petiole nitrate-N] indicators to forecast aboveground biomass accumulation (AGB), nitrogen (N) uptake, and lint yield in cotton. We hypothesized that the predictive strength of each indicator would vary by type and growth stage. Field experiments were conducted across five site-years in West and North Florida, USA, using six N rates (0–252 kg N/ha) in four replications. Quadratic regression (QR) model identified PIs at peak flowering and VIs at first flower and cutout growth stages as the most robust predictors of AGB. A random forest regression (RF) model also showed similar results, with PIs at peak flowering and VIs at peak flowering and first flower as the best indicators for AGB prediction. A strong relationship of BIs with N uptake at bloom and post-bloom growth stages evaluated through QR and RF supports their use for early reproductive assessment. Lint yield predicted using QR and RF was best forecasted by VIs at peak flowering, and cutout. Principal component analysis confirmed mid-to-late season VIs as major drivers of AGB and lint yield variability, while as early reproductive BIs as major indicators of N uptake. This research establishes a robust framework for real-time indicator and growth stage-based biomass, N uptake, and yield forecasting in cotton.
Why it matches plant phenotyping methods綿花の非破壊的な生理・植生指標を用いて、バイオマス、窒素吸収、収量という植物形質を予測し、複数地点年および回帰モデルで指標の予測性能を評価しているため、測定・予測手法が中心である。
abstractForecasting crop performance through non-destructive tools is crucial for enabling timely, data-driven decisions for sustainable cotton production.
Accurate and timely crop-yield prediction is essential for ensuring food security, managing agricultural risk, and supporting policy formulation. To address the respective limitations of traditional crop growth models and deep learning methods under complex environmental conditions, a hybrid modeling framework is proposed that integrates remote-sensing data assimilation, a process-based crop growth model, and deep learning techniques. Using spring maize in Jilin Province, China (2015–2020) as the case study, leaf area index (LAI) retrieval accuracy is first improved by coupling the PROSAIL model with machine-learning algorithms. A complete meteorological sequence for the target year is then constructed using a dynamic time warping (DTW) algorithm to overcome early-season prediction challenges caused by missing real-time weather data. Retrieved LAI is assimilated into the WOFOST crop growth model through an ensemble Kalman filter (ENKF) to calibrate state variables and enable dynamic yield prediction across growth stages. Finally, a deep learning model (Convolutional Neural Network–Attention Long Short-Term Memory with Multi-Task Learning, CNN-ALSTM-MTL) is developed to fuse assimilation outputs with multi-source heterogeneous data, leveraging multi-task learning to enhance adaptability to regional heterogeneity and improve yield prediction performance at the regional scale. Assimilation is found to substantially improve maize-yield estimation, increasing R² by 0.2 and reducing RMSE by 276 kg ha⁻¹. Compared with the assimilated crop growth model alone, the hybrid framework further increases R² by 35 % and decreases RMSE by 23 % by hierarchically capturing feature information relevant to maize-yield estimation. The best performance is achieved during the key growth stage (jointing to tasseling stage), with an R² of 0.75 and an RMSE of 592 kg ha⁻¹, enabling reliable yield prediction approximately two months before harvest. This framework demonstrates potential for cross-crop and cross-regional applications and provides robust methodological support for regional-scale yield forecasting and food-security early warning.
Why it matches plant phenotyping methodsLAIという植物形質の推定・同化と収量推定を中核とする統合的な計算フェノタイピング／予測フレームワークを開発・検証しており、単なる農業実験での routine 測定ではない。
abstracta hybrid modeling framework is proposed that integrates remote-sensing data assimilation, a process-based crop growth model, and deep learning techniques
본 연구는 UAV 기반 다중분광 영상을 활용하여 양파 및 마늘 재배지에서 작물 분할 기법이 식생지수 기반 생산량 예측 성능에 미치는 영향을 분석하는 것을 목적으로 한다. 기존 연구에서는 처리구(plot)별 ROI 평균을 이용한 식생지수 산출이 주로 활용되었으나, 작물 분할 전략 자체가 예측 성능에 미치는 영향은 충분히 검토되지 않았다. 이에 본 연구에서는 비지도 학습 기반작물 분할(none, otsu-NDVI, k-means, GMM)을 적용하고, 분할 방법에 따른 처리구 단위 식생지수 특성과 예측 성능 차이를 비교하였다. 6개 생육 시점의 UAV 다중분광 영상으로부터 분할된 식생 영역 대상으로 9개 식생지수를 산출하고, PLS 기반으로 차원 축소하고 머신러닝 모델을 이용해 생산량을 예측하였다. 모델 성능은 처리구 단위 Leave-one-out 교차검증으로 평가하였다. 분석결과, 작물 분할 적용 시 식생지수 분포가 유의하게 변화하였으며, 반복측정 분산분석을 통해 분할 방법과 생육 시점 간 상호작용 효과가 확인되었다. 이러한 입력 변수 특성의 개선은 생산량 예측 성능 향상으로 이어졌고, 특히 군집 기반 분할에서 RMSE 및 MAPE가 가장 크게 감소하였다.
Why it matches plant phenotyping methodsUAV多波長画像における作物分割手法を比較し、植生指数から収量を推定する方法と性能を評価しており、表現型取得・抽出が研究の中心である。
Abstract Context The amount and ratio of data required for training spectral grain yield (GY) prediction models remain critical for sampling reference data, but have been rarely addressed so far. Given the high cost for collecting ground truth data, common data splitting ratios which use the majority of the data for training and the rest for testing the models, should be reduced, which in turn may affect prediction accuracy. Methods Therefore, this study evaluated 11 different train-test data splitting ratios (TSR), ranging from using 5% to 95% of the data for training, and the remaining portion as test set. Models with six different machine learning algorithms were compared in winter wheat breeding trials conducted with each several thousand plots in two locations in Germany over a period of four years. The input data consisted of the UAV-based NDRE index data from individual measurements dates as well as incremental date combinations. Results The results indicate that GY prediction was relatively stable when decreasing TSR to about 0.30. Conversely, multi-date models tended to profit more from higher TSR than single-date models. Support vector machine and random forest algorithms showed relative advantage for higher TSR and multi-date models, whereas partial least squares and ridge regression were the best algorithms for lowest TSR-values. Prediction results from repeated data splitting indicates minimum R²-variability at TSR-values of 0.30 but substantially increasing R²-variation for high TSR-values. Conclusions It is concluded that decreasing TSR while considering algorithm selection can reduce costs without compromising prediction accuracy, therefore making spectral phenotyping methods more accessible and ready-to-use.
Why it matches plant phenotyping methodsUAV multispectral画像と機械学習による収量推定について、データ分割比・アルゴリズム・予測安定性を体系的に評価しており、スペクトル表現型計測ワークフローの技術的検証が中心である。
abstractTherefore, this study evaluated 11 different train-test data splitting ratios (TSR), ranging from using 5% to 95% of the data for training, and the remaining portion as test set.
With the increasing cost of labor, smart agriculture has emerged as a key trend for the future of agricultural development. This paper presents an integrated approach for tomato maturity clas-sification and yield estimation using both RGB and multispectral images. The proposed approach consists of three main components: tomato detection, tomato tracking and counting, and maturity classification of tomatoes. YOLOv8 combined with OSNet is first employed to detect tomatoes, while StrongSORT is then adopted to track consistent identities across image sequences. For maturity classification, multiple vegetation indices, including NDVI, GNDVI, and GRRI, are first transformed using principal component analysis, followed by classification using support vector machines, k-nearest neighbors, and neural networks. Tomatoes are categorized into three ma-turity levels: immature, almost mature, and mature. Results demonstrate that the proposed ap-proach can effectively estimate yield of tomatoes at each maturity stage. This capability provides practical support for harvest planning and labor allocation in precision agriculture.
Why it matches plant phenotyping methodsRGB・マルチスペクトル画像からトマトの成熟度と収量を推定する画像解析ワークフローが中心で、果実状態および収量という植物形質を直接評価している。
abstractThe proposed approach consists of three main components: tomato detection, tomato tracking and counting, and maturity classification of tomatoes.
Introduction. The projected growth of the global population poses a significant challenge in ensuring sufficient food production. Crop genetic breeding, essential to meet this demand, relies on advanced technologies to accelerate field phenotyping processes. Objective. To predict plant height and biomass yield in sorghum using photogrammetry and multispectral data acquired through small unmanned aircraft system (sUAS) flights. Materials and methods. Six sorghum genotypes were evaluated in Cañas, Guanacaste, Costa Rica, using a completely randomized design with eight replications per genotype. Multispectral sensor flights were conducted at selected phenological stages to generate vegetation indices, DTMs (digital terrain models), and DSMs (digital surface models). Manual plant height measurements were used for correlation and simple linear regression analysis, while biomass was predicted using random forest regression. Results. DTMs and DSMs enabled reliable estimation of plant height during early growth stage (R² = 0.53) and achieved higher accuracy at later stages (R²= 0.76; RMSE= 0.13 m). Biomass prediction was most accurate at the booting stage (r= 0.72; RMSE= 1.40 t·ha-¹), with NDRE (Normalized Difference Red-Edge Index) and IKAW (Kawashima Index) identified as the most relevant spectral indices. Conclusions. DTMs and DSMs derived from multispectral imagery predicted plant height accurately in later growth stages but were less accurate in early stages. Incorporating plant height alongside spectral indices into models enhanced biomass prediction. The findings showed that sUAS-mounted sensors and multispectral indices are promising tools for phenotyping in sorghum breeding programs in Costa Rica.
Why it matches plant phenotyping methodssUASマルチスペクトル画像と写真測量からソルガムの草丈・バイオマスを推定し、手測定との相関、回帰、精度評価を行う方法中心の研究である。
abstractTo predict plant height and biomass yield in sorghum using photogrammetry and multispectral data acquired through small unmanned aircraft system (sUAS) flights.
Accurate in-season prediction of seed yield and seed composition traits such as oil and protein are useful for gaining accuracy and efficiency in soybean breeding. These predictions can also inform farmers, enabling them to improve their field management practices, and guide their market decisions. We report a Transformer-based deep learning framework built on 30 years of multi-environment performance data from the Northern and Southern Uniform Soybean Tests (UST) across North America. Unlike earlier studies on seed yield, oil and protein prediction that focus on limited years, regions, single modalities, we utilized a comprehensive dataset that includes weather, genotype, and management factors, ensuring a more holistic approach to soybean yield, oil, and protein prediction. Our model integrates multivariate time-series weather data with genotypic relationship information, maturity group, and geographic location, to predict variety performance in diverse environments. Our model captures complex temporal patterns associated with trait variability; showing high predictive accuracy (R2) of 77.6 ± 0.2%, 63.9 ± 4.7%, and 79.3 ± 2.3% for seed yield, oil, and protein, respectively. Additionally, for seed yield, we also evaluated multiple interpretability methods to assess feature importance for predictor variables and critical growing timepoints, and solar radiation and temperature were noted as the key predictors. Overall, these results demonstrate the usefulness of a Transformer-based model in trait predictions, and the utility of large cooperative datasets from breeding programs.
Why it matches plant phenotyping methodsTransformerによるダイズ収量・油・タンパク質形質の予測フレームワークが研究の中心であり、植物形質の計算的推定手法を開発・評価している。
abstractWe report a Transformer-based deep learning framework built on 30 years of multi-environment performance data
To address the inefficiency and high cost of manual counting of tobacco leaves, this study proposes a UAV-based method for automatic leaf counting in field-grown tobacco using 3D point clouds and an improved PointNext network. Although UAV imagery has been applied to crop phenotyping, most existing UAV-based leaf-counting methods still rely on 2D images or hand-crafted features and rarely exploit 3D point clouds with dedicated leaf-level segmentation, which limits accuracy and robustness under leaf overlap, variable viewing angles, and complex field backgrounds. In this work, oblique UAV photogrammetry is used to reconstruct individual plants into 3D point clouds, and a segmentation network, SRW-PointNext, is developed by integrating an SCSA attention mechanism and a Residual-SegHead to enhance feature extraction and segmentation performance, while a re-weighted loss alleviates class imbalance. Leaf point clouds are then clustered using MeanShift to obtain leaf counts. Experiments on field-grown tobacco demonstrate that the proposed method achieves a point-cloud segmentation precision of 92.09%, a MIoU of 76.13%. Compared with the original PointNext baseline, SRW-PointNext increased MIoU and overall precision by 3.34% and 2.42% respectively. The final accuracy rate of leaf counting was 92.61%, effectively achieving accurate and stable leaf counting under actual field conditions, and providing technical support for digital management, yield estimation and seedling breeding in tobacco production.
Why it matches plant phenotyping methodsUAV三次元画像と改良セグメンテーション手法により圃場タバコの葉数を推定する方法を開発・検証しており、表現型取得が研究の中心である。
abstractthis study proposes a UAV-based method for automatic leaf counting in field-grown tobacco using 3D point clouds and an improved PointNext
Reproduction assets foundThe paper reports a UAV-based tobacco leaf counting method with an annotated 1000-plant point cloud dataset and SRW-PointNext code, both explicitly declared publicly available at author-provided Zenodo and GitHub URLs matching the allowed list.Dataset · publicData supporting the reported results can be found at: https://zenodo.org/records/15130271 .Open asset ↗zenodo · 15130271lines:531-564Code · publicThe code used in this study is available at: https://github.com/Nan20377/SRW-Pointnext.git .Open asset ↗github · Nan20377/SRW-Pointnextlines:531-564Plant phenotyping relevance match · UnverifiedEurope PMC · checked 15 Sept 2026
Published25 Feb 2026TAG. Theoretical and applied genetics. Theoretische und angewandte GenetikCited by 1 · OpenAlex ↗
Key message A genetic algorithm-optimized deep neural network was developed using proximal sensing data to accurately predict wheat yield at field scale, outperforming traditional machine learning models under diverse conditions. Hand held or vehicle-mounted active proximal sensing technologies offer a rapid, non-destructive method for real-time crop monitoring through spectral vegetation indices. This study integrates such proximal sensing data into a deep learning framework for field-scale wheat yield prediction. Specifically, wheat yield is predicted using normalized difference vegetation index (NDVI), canopy temperature (CT), and plant height (PH) through a deep neural network (DNN) optimized using a genetic algorithm (GA). The model is trained on data from 3,350 diverse wheat germplasm grown under irrigated and rainfed conditions at two locations during the 2020-2021 winter season. Comparative analysis demonstrates that the GA-optimized DNN outperforms traditional machine learning models such as Random Forest Regression (RFR), Least Absolute Shrinkage and Selection Operator (LASSO), and Support Vector Regression (SVR). Among individual feature groups, NDVI measured at five wheat growth stages showing strong predictive capability, with R 2 values ≥ 60% under irrigated and ≥ 50% under rainfed conditions. Additionally, RFR is employed to identify the most influential features for predicting grain yield. This pioneering study introduces the first-ever application of a GA-optimized deep neural network, leveraging handheld or vehicle-mounted proximal sensing data for predicting crop yield, in the context of Indian agriculture. The proposed approach offers a robust and scalable solution for pre-harvest yield estimation, supporting breeders and researchers in efficient genotype selection and contributing to the achievement of sustainable development goals.
Why it matches plant phenotyping methods近接センシングによるNDVI・群落温度・草丈からの収量推定と、遺伝的アルゴリズム最適化DNNの開発・比較検証が研究の中心であり、植物表現型（収量）を推定する方法論的研究である。
abstractA genetic algorithm-optimized deep neural network was developed using proximal sensing data to accurately predict wheat yield at field scale, outperforming traditional machine learning models under diverse conditions.
Precise and timely prediction of wheat yield is pivotal for ensuring global food security and optimizing agricultural management practices, particularly through advanced remote sensing and machine learning techniques. In this study, wheat yield was accurately estimated by leveraging remote sensing-derived soil and vegetation indices. Yield data from 189 study points were collected, and Sentinel-2 (10-meter resolution) imagery from the Tillering and Anthesis growth stages was used. The models incorporated 25 variables, including 16 optical indices (e.g., NDVI, SAVI, MSAVI2) and three topographic factors. The key novelty of this research is the rigorous comparison of the predictive value and synergistic contribution of Sentinel-1 Synthetic Aperture Radar (SAR) data when integrated with Sentinel-2 optical indices within machine learning frameworks. Three machine learning approaches (Multiple Linear Regression (MLR), Support Vector Machine (SVM), and Random Forest (RF)) were employed and evaluated using 70% training and 30% testing subsets. Results revealed that the RF model, leveraging data from the Anthesis phenological stage, exhibited superior performance in wheat yield estimation, achieving an R² of 0.92 and an RMSE of 0.14 ton ha -1 for the training set, and an R² of 0.90 and an RMSE of 0.29 ton ha -1 for the testing set. To enhance model accuracy, Sentinel-1 radar data were integrated into the RF framework. This addition reduced the training set RMSE to 0.13 ton ha -1 but increased the testing set RMSE to 0.33 ton ha -1 , with R² values remaining stable at 0.92 and 0.90 for the training and testing sets, respectively. Variable importance analysis indicated that optical soil and vegetation indices were the dominant predictors. Although the inclusion of Sentinel-1 SAR data offered additional insights, it did not outperform the predictive capacity of optical indices. These findings validate the efficacy of the combined Sentinel-2 remote sensing approach for generating reliable wheat yield forecasts approximately 50 days prior to harvest.
Why it matches plant phenotyping methodsSentinel-1/2リモートセンシングと機械学習による小麦収量という植物形質の推定が中心で、モデル比較・評価と予測精度検証を実施している。
abstractwheat yield was accurately estimated by leveraging remote sensing-derived soil and vegetation indices.
Confronted with the severe imperatives to food security posed by a growing population and the urgent need for sustainable development amid climate change, traditional agricultural models face significant resource-intensive efficiency bottlenecks. Deep learning-based image recognition is driving a future-oriented intelligent agricultural revolution by enabling high-throughput phenotyping and autonomous decision-making across the production chain. This paper systematically reviews key advancements in image recognition within modern agriculture, mapping the fundamental paradigm shift from traditional hand-crafted feature engineering to adaptive deep feature learning. We critically analyze technological implementation and performance across five core application scenarios: high-precision pest and disease diagnosis, spatio-temporal growth monitoring and yield prediction through multi-source image fusion, agricultural robots for automated harvesting, non-destructive quality inspection of products, and intelligent precision management of farmland. The review further identifies critical challenges hindering large-scale technology adoption, primarily centered on the high costs of constructing high-quality agricultural datasets and model robustness in complex field environments. Consequently, this study provides a comprehensive and forward-looking reference for advancing the deep integration of vision technology, thereby offering a strategic path toward achieving more intelligent, efficient, and sustainable global agricultural production systems in the digital era.
Why it matches plant phenotyping methods画像認識による高スループット表現型解析を含む農業画像技術を、実装・性能・課題の観点から体系的にレビューしており、植物フェノタイピング手法のレビューが中心です。
abstractThis paper systematically reviews key advancements in image recognition within modern agriculture
Maize productivity is increasingly constrained by water deficit stress (WDS), particularly under erratic rainfall conditions. Efficient early-stage phenotyping coupled with field validation is critical for breeding WDS-tolerant genotypes. In this study, we developed a two-tier screening strategy integrating hydroponics-based root trait evaluation at pre-reproductive stage with subsequent field validation of maize inbreds under managed WDS at CIMMYT, Hyderabad. A set of 50 diverse maize inbreds were evaluated for root architectural traits and plant growth stages including grain yield components. Hydroponic screening applied PEG6000-induced osmotic stress to assess root length, tips, forks, segments and diameter, whereas field trials imposed pre-reproductive WDS through cumulative growing degree day-based irrigation withdrawal. Significant genotypic variation and genotype × trait interactions were observed across both environments, reflecting trait and environment-specific responses. Key root traits, including root tips, total length, forks and segments, showed strong positive correlations (r ≥ 0.70) with yield components and Normalized difference vegetation index (NDVI), underscoring their importance in WDS resilience. Multivariate analysis further confirmed the alignment of root vigor with kernel traits and canopy health as critical determinants of yield stability. Among the evaluated lines, introgressed ILM23 and ILM24 emerged as the principal donor lines, while PML1249, PML1275, and PML1285 were identified as promising donor sources, all exhibiting robust root systems, stable anthesis-silking interval (ASI) and superior stress tolerance indices. Spearman's rank correlation (ρ = 0.988) between hydroponics and field rankings highlighted the predictive reliability of controlled root phenotyping for field performance under WDS. This integrated hydroponics-to-field approach provides a rapid, efficient and cost-effective framework for the early identification of WDS-tolerant or high water-use-efficiency (WUE) maize hybrids, facilitating the accelerated breeding of resilient cultivars.
Why it matches plant phenotyping methods水耕栽培による根系形態フェノタイピングを開発し、圃場条件で予測信頼性を検証する二段階スクリーニング手法が研究の中心である。
abstractwe developed a two-tier screening strategy integrating hydroponics-based root trait evaluation at pre-reproductive stage with subsequent field validation
Drone-based phenotyping using unmanned aerial vehicles (UAVs) has emerged as a revolutionary approach for high-throughput, precise, and scalable measurement of plant traits critical to crop improvement. This technology integrates advanced imaging sensors—including RGB, multispectral, hyperspectral, and thermal cameras—with sophisticated image processing and artificial intelligence algorithms to non-destructively capture key phenotypic data such as plant height, biomass, canopy temperature, maturity timing, and disease symptoms under natural field conditions. Compared with traditional manual phenotyping and satellite-based remote sensing, UAV phenotyping offers superior spatial and temporal resolution, enabling dynamic monitoring of complex traits such as drought tolerance and disease resistance. Applications span early stress detection, quantitative trait assessment, yield prediction, and accelerating breeding cycles by facilitating objective, rapid selection of superior genotypes across multiple crop species. Despite its transformative potential, challenges remain in standardizing protocols, managing large-scale complex datasets, integrating phenotypic with genomic and environmental data, and providing training resources for widespread adoption. Ongoing advancements in sensor technology, data analytics, open-source tools, and capacity building are poised to cement drone-based phenotyping as a cornerstone technology for sustainable, climate-resilient crop breeding and global food security.
Why it matches plant phenotyping methodsUAV画像・センサーによる植物形質計測を中心に扱う明示的なフェノタイピングレビューであり、手法の応用、技術、課題を総合的に論じている。
abstractDrone-based phenotyping using unmanned aerial vehicles (UAVs) has emerged as a revolutionary approach for high-throughput, precise, and scalable measurement of plant traits critical to crop improvement.
Abstract Agricultural research increasingly relies on data-driven approaches for crop yield prediction that complement more established crop growth models, including machine learning techniques. However, these approaches rely on large training datasets. Here, we present the Crop Yields, Climate, Soils, and Satellites (CYCleSS) dataset, a large-scale crop yield dataset derived from precision yield data for 934 fields across England on which a variety of crops are grown. In addition, the data also contains satellite-derived remote sensing data, weather data, and data on soil type, all aligned at a grid resolution of 10 km. Weather data is available at a daily temporal resolution, satellite data at 5-day resolution, while crop yield data is available at yearly resolution. This effort has been made possible through careful anonymisation of the yield data while preserving the alignment with remote sensing, weather, and soil data. This data will be useful both to train machine learning models of yield prediction as well as to parameterize mechanistic crop growth models. Furthermore, the anonymisation procedure itself will be of interest to the research community, as it represents a solution to a common problem on the interface of agricultural research and farming practice.
Why it matches plant phenotyping methods圃場単位の作物収量という植物形質を、衛星・気象・土壌情報と整合した再利用可能な大規模データセットとして構築しており、収量予測モデルの訓練・評価用データ基盤が中心です。
abstractHere, we present the Crop Yields, Climate, Soils, and Satellites (CYCleSS) dataset, a large-scale crop yield dataset derived from precision yield data for 934 fields across England
Reproduction assets foundThe paper's authors provide public R code for merging/aligning climate, soil, and Sentinel-1 data and anonymising yield data in a GitHub repository. The CYCLeSS dataset itself is on figshare, but that URL is not in the allowed list, so only the code asset is reported.Code · publicnts of this repository. Researchers who are further interested in the underlying data should contact the authors affiliated with UKCEH.
Code availability
R code used to merge and align available UK climate, soil, and Sentinel-1 synthetic aperture radar data to the same 1 km 2 grid is provided in the following GitHub repository: https://github.com/alan-turing-institute/CYCLeSS-dataset-code . Dummy data and code needed to replicate the final process of merging climate, soil, and satellite data with UKCEH precision yield data and anonymisation of field locations is contained within the ‘CLYCESS_anonymisation.zip’ folder shared as part of this repository. R version 4.2.3 was used for the creatioOpen asset ↗https://github.com/alan-turing-institute/CYCLeSS-dataset-codelines:200-271Plant phenotyping relevance match · UnverifiedEurope PMC · checked 5 Sept 2026
Single-boll weight (SBW) is difficult to estimate after defoliant application because canopy spectra include numerous mixed pixels from lint, soil, and senescent leaves, leading to strong background interference. Here we propose a UAV multispectral workflow that combines object-based boll extraction, spectral feature selection, and machine-learning regression to improve SBW mapping. Data were collected from a two-year drip-irrigated cotton experiment in Xinjiang, China involving four varieties evaluated under five planting densities treatments. Boll extraction was treated as a supervised object-based classification problem, and maximum likelihood, mahalanobis distance, and parallelepiped classifiers were compared. Fifteen vegetation indices were computed from the extracted boll pixels; informative features were identified using Pearson correlation and SHapley Additive exPlanations importance ranking. SBW was then estimated with ridge regression, random forest regression, and neural network regression using an independent validation dataset. Maximum likelihood consistently achieved overall accuracy above 97% with Kappa values above 0.93, outperforming the other classifiers. Indices derived from the red, red-edge, and near-infrared bands, particularly those designed to reduce soil background effects, showed the strongest relationships with SBW and ranked highest in SHAP. The best-performing model, which integrated maximum likelihood-based boll extraction with neural network regression, achieved a coefficient of determination of 0.80 and a root mean square error of 0.31 g on the validation set. Relative errors remained below 15% across different years, varieties, and planting densities. This workflow reduces background interference and enables transferable SBW spatial estimation for breeding evaluation and density and harvest management.
Why it matches plant phenotyping methodsUAVマルチスペクトル画像から綿花の単一ボール重量を抽出・推定する方法を開発し、分類器と回帰モデルを比較検証しており、植物形質取得が研究の中心である。
abstractHere we propose a UAV multispectral workflow that combines object-based boll extraction, spectral feature selection, and machine-learning regression to improve SBW mapping.
Plant phenotyping relevance match · UnverifiedCrossref · Europe PMC · OpenAlex · checked 15 Sept 2026
Abstract To address challenges in food security, a better understanding of crop performance under varying and changing environmental conditions is required. Plant time warping (PTW) is a deep learning model that integrates high-throughput field phenotyping data with genomic and environmental information to predict wheat yield. PTW leverages image time series, genetic markers, and environmental covariates to learn genotype-specific physiological responses to temperature and vapour pressure deficit. Compared with mere genomic prediction models, PTW demonstrates superior performance when predicting yield in unseen environments across 48 year–locations in Europe. The PTW model captures non-linear growth responses varying with phenological stages and identifies distinct patterns associated with yield performance and stability. Specifically, varieties with higher yield stability exhibit reduced sensitivity to vapour pressure deficit around 1.5 kPa and distinctive temperature responses during emergence and senescence. The learned response pattern enables retrospective and prospective yield predictions, providing a foundation for location-specific variety recommendations and targeted breeding strategies. The integration of phenomic, genomic, and enviromic data has the potential to substantially advance research in climate adaptation strategies for crop production by addressing generalization challenges of predictions to novel environmental conditions.
Why it matches plant phenotyping methods画像時系列を含む高スループット圃場フェノタイピングデータから小麦収量を予測する深層学習モデルを開発・評価しており、フェノタイピング解析が研究の中心である。
abstractPlant time warping (PTW) is a deep learning model that integrates high-throughput field phenotyping data with genomic and environmental information to predict wheat yield.
Plant phenotyping relevance match · UnverifiedOpenAlex · Crossref · Europe PMC · checked 15 Sept 2026
BACKGROUND: Kale (Brassica oleracea var. acephala) is a high value leafy vegetable with an extensive domestication history and germplasm diversity, making it an ideal target for genetic improvement. To meet growing food security needs particularly with controlled environment agriculture (CEA) systems, specialized breeding strategies are required. The goal of this study was to survey the phenotypic architecture of a global kale germplasm collection under commercial CEA conditions. This study establishes a phenotypic baseline and serves as a hypothesis generating resource for future genetic and physiological studies in kale and other leafy vegetables grown under CEA. RESULTS: A total of 203 kale accessions were phenotyped for 113 quantitative traits using high-throughput phenotyping methods. Significant differentiation was observed across all traits, with coefficient of variation ranging from 2.5% to 180.7%, confirming broad genetic variability among accessions. Trait correlation networks and hierarchical clustering grouped phenotypes into seven biologically corresponding modules including leaf, stem and root morphology, plant architecture, hyperspectral indices, and seedling growth. These modules highlight coordinated phenotypic patterns among traits. Integrative yield analyses combining partial least squares variable importance in projection with differential trait analysis identified 28 phenotypes most strongly associated with total aboveground fresh weight, a robust proxy for CEA vegetative yield. Principal component analysis further distilled these traits into three orthogonal components explaining 87.1% of total yield variation. These components represented modules related to plant organ size, canopy structure, and density, emphasizing their biological contribution to harvestable biomass. CONCLUSIONS: This study generates a foundational phenomics resource and comprehensive dissection of kale’s yield architecture under CEA conditions. The composition of traits identified constitutes a targeted set of breeding traits to be further validated for improved leafy vegetable yield. By integrating large-scale germplasm resources with phenomics, this work establishes the utility of a high-throughput phenotypic analysis for further leafy crop research and improvement.
Why it matches plant phenotyping methods大規模なハイスループット植物表現型解析を中核とし、113形質の取得、統合解析、再利用可能なフェノミクス資源の構築を行っているため。
abstractA total of 203 kale accessions were phenotyped for 113 quantitative traits using high-throughput phenotyping methods.
Optimizing biomass partitioning is essential for achieving sustainable yield improvement in wheat, particularly under increasing environmental stress. Traits such as spike partitioning index (SPI), harvest index (HI), and fruiting efficiency (FE) are central to understanding how assimilates are allocated between vegetative and reproductive organs. However, their complex physiology and the difficulty of manual phenotyping have limited their routine use in breeding programs. This study assessed the potential of unmanned aerial vehicle (UAV)-based hyperspectral reflectance data to predict biomass partitioning traits and related yield components in wheat. Three trials of facultative soft wheat lines (2022-2024) and an independent validation set of advanced breeding lines were used to develop genomic prediction (GP), phenomic prediction (PP), and integrated multi-omic models combining genomic, phenomic, and environmental covariates (ECs). Kernel-based best linear unbiased prediction (BLUP), and machine-learning based, random forest regression and partial least squares regression were implemented to estimate predictive ability (PA). Phenomics-driven models markedly outperformed GP across most traits, achieving PA up to 0.61 for SPI, 0.56 for FE, 0.71 for grains/m 2 (GN), and 0.66 for grain yield (GY). Hyperspectral data provided higher accuracy than vegetation indices, and multi-omic integration slightly improved prediction (PA up to 0.73 for GN). These results demonstrate that UAV-based hyperspectral phenotyping can effectively capture canopy-level physiological signals associated with biomass partitioning, offering a scalable and data-driven approach for in-season selections. This can help wheat breeding programs to optimize biomass partitioning in modern wheat cultivars for long-term yield resilience and genetic gain.
Why it matches plant phenotyping methodsUAVハイパースペクトルデータによる作物形質推定と予測モデルの開発・検証が研究の中心であり、単なる生物学的実験の測定ではない。
abstractThis study assessed the potential of unmanned aerial vehicle (UAV)-based hyperspectral reflectance data to predict biomass partitioning traits and related yield components in wheat.
Green canopy cover dynamics extracted from high-throughput RGB imagery via automated labeled segmentation enabled nonlinear modeling that accounted for short-term weather variation, explaining up to 56% of protein yield variation in 150 soybean genotypes across ten seasons and enabling prediction in new environments as well as identification of tolerant genotypes.
Why it matches plant phenotyping methods高スループットRGB画像から自動セグメンテーションでキャノピー被覆率を抽出する手法が研究の中心であり、気象変動を考慮したモデル化と新環境での予測まで行っているため、植物表現型手法として採用。
abstractGreen canopy cover dynamics extracted from high-throughput RGB imagery via automated labeled segmentation
Aboveground biomass (AGB) is a critical indicator for assessing crop growth status and productivity, yet accurately linking fine-scale ground measurements with coarse-resolution satellite imagery remains challenging. Here, we propose an integrated ground-UAV-satellite framework that combines high-resolution UAV observations with an optimized systematic sampling-Global Moran's I (SS-GMI) procedure and a simple allometric growth model. Multi-variety sugar beet cultivated across heterogeneous habitats was used as a case study. Results indicate that a power-law model effectively captures the allometric relationships between AGB, plant height, and the Dreg vegetation index in sugar beet, achieving high accuracy and strong transferability. Incorporating phenological information from Biologische Bundesanstalt, Bundessortenamt und CHemische Industrie (BBCH) codes and a thermal index further enhanced model robustness across independent habitat trials, yielding coefficients of determination ( R 2 ) of 0.80 and 0.83. The SS-GMI sampling procedure integrates systematic sampling with Global Moran's I to reduce spatial autocorrelation while ensuring uniform spatial coverage, thereby enabling the acquisition of representative and spatially independent samples from UAV-derived AGB maps. These samples were used to develop satellite-based AGB estimation models for PlanetScope and Sentinel-2A imagery, achieving R 2 values of 0.83 and 0.73, respectively. This study provides a practical and scalable framework for field-to-satellite AGB upscaling, offering new insights for the scale conversion of multi-source data in agricultural remote sensing.
Why it matches plant phenotyping methodsUAV・衛星観測とSS-GMIサンプリング、モデル化を組み合わせ、サトウダイコンの地上部バイオマスという植物形質を推定する統合手法が研究の中心である。
abstractHere, we propose an integrated ground-UAV-satellite framework that combines high-resolution UAV observations with an optimized systematic sampling-Global Moran's I (SS-GMI) procedure and a simple allometric growth model.
In the new age of greenhouse management, smart space adaptive systems are required to allow environmental control and crop analytics. This study presents an end-to-end deep learning architecture for spatiotemporal prediction and control in agriculture, which enables seamless integration between the different components of a decision loop. A ConvLSTM model predicts zone-specific microclimate variations, and a Dueling DQN agent selects the optimal actions for irrigation, ventilation, and fertilization according to energy demand, emission prediction, and soil moisture balance. The proposed EMMYP-Net (Enhanced Multimodal Multitask Yield Prediction Network) involves a CNN-BiLSTM-attention architecture that combines visual canopy data with multi-sensor sequences to co-classify growth stages and estimate yield. Experimental tests in a 1,200 m² four-zone greenhouse showed remarkable improvements, as ConvLSTM decreased RMSE by 45±2.3% compared to ARIMA and by 31±1.8% compared to LSTM. EMMYP-Net achieved an accuracy of 96.0% for classification, as well as an R² of 0.912±0.007 in predicting yields. This process-integrated approach enhanced resource sustainability by achieving savings of 19.3% in energy, 16.5% in water, and 15.2% in fertilizers relative to a conventional system. Combining predictive control and crop intelligence offers a scalable basis for sustainable data-driven greenhouse management. The key novelty of this work lies in the seamless integration of ConvLSTM-based spatiotemporal forecasting with the EMMYP-Net multimodal crop analytics within a unified reinforcement-learning-driven decision loop, enabling both predictive control and biological feedback in real time.
Why it matches plant phenotyping methods視覚的キャノピー情報とマルチセンサー系列から生育段階と収量を推定するEMMYP-Netが技術的中核であり、植物の状態・形質の計測手法として評価されている。温室制御全体を扱うが、フェノタイピング部分も実質的に記述・検証されている。
abstractThe proposed EMMYP-Net (Enhanced Multimodal Multitask Yield Prediction Network) involves a CNN-BiLSTM-attention architecture that combines visual canopy data with multi-sensor sequences to co-classify growth stages and estimate yield.
Plant phenotyping relevance match · UnverifiedbioRxiv · OpenAlex · Europe PMC · Crossref · checked 6 Sept 2026
To address challenges in food security, a better understanding of crop performance under varying and changing environmental conditions is required. Plant Time Warping (PTW) is a deep learning model that integrates high-throughput field phenotyping data with genomic and environmental information to predict wheat yield. PTW leverages image time series, genetic markers, and environmental covariates to learn genotype-specific physiological responses to temperature and vapor pressure deficit. Compared to mere genomic prediction models, PTW demonstrates superior performance when predicting yield in unseen environments across 48 year-locations in Europe. The PTW model captures non-linear growth responses varying with phenological stages and identifies distinct patterns associated with yield performance and stability. Specifically, varieties with higher yield stability exhibit reduced sensitivity to vapor pressure deficit around 1.5 kPa and distinctive temperature responses during emergence and senescence. The learned response pattern enable retrospective and prospective yield predictions, providing a foundation for location-specific variety recommendations and targeted breeding strategies. The integration of phenomic, genomic, and enviromic data has the potential to substantially advance research in climate adaptation strategies for crop production by addressing generalization challenges of predictions to novel environmental conditions. HighlightWe present a novel deep learning model that seamlessly combines high-throughput image data, genomic data, and weather data, enabling better crop predictions for future climates.
Why it matches plant phenotyping methods画像時系列を用いた高スループット圃場フェノタイピングを、ゲノム・環境情報と統合して収量を推定する深層学習手法PTWが研究の中心であり、手法開発・評価に該当する。
abstractPlant Time Warping (PTW) is a deep learning model that integrates high-throughput field phenotyping data with genomic and environmental information to predict wheat yield.
Fine-grained 3D phenotypic analysis of rice plays a vital role in rice breeding and yield estimation. However, a comprehensive rice data acquisition and segmentation pipeline is still lacking. While Neural Radiance Fields (NeRF) have shown impressive results in crop-level 3D reconstruction, their high sensitivity to data volume and camera viewpoints often leads to reconstruction failures for rice. In addition, the large-scale rice point clouds, coupled with heavy occlusion and visual similarity among grains, pose significant challenges for fine-grained trait extraction. To address the challenge of reconstructing rice point clouds under low-quality data conditions, we propose a novel method named Multi-Scale NeRF(MSNeRF). This method incorporates a structure-detail collaborative reconstruction mechanism and a dynamic initialization density scheduling strategy. Furthermore, we introduce a multimodal and multitask rice dataset (MMR) as a benchmark resource for future research. For rice point cloud segmentation, we develop Vision Rice Knowledge Graph Network(VRKGNet), which comprises an image segmentation module, a projection module, and a point cloud segmentation module enhanced with a Transformer to enlarge the receptive field. VRKGNet performs standalone point cloud segmentation and integrates image segmentation results from multiple viewpoints as prior knowledge to enhance semantic and instance-level segmentation. Extensive experiments demonstrate that MSNeRF achieves high-fidelity point cloud reconstruction with as few as 10 viewpoints. VRKGNet achieves superior rice plant segmentation with a semantic segmentation mIoU of 88.79% and an instance segmentation AP 25 of 84.55%, outperforming mainstream algorithms.
Why it matches plant phenotyping methods米の3D形質取得・再構成・分割を中核とする手法開発であり、データセット／ベンチマークも提供しているため、植物フェノタイピング手法文献に該当する。
abstractwe propose a novel method named Multi-Scale NeRF(MSNeRF)
Reproduction assets foundThe paper's authors explicitly state that the source code for MSNeRF and VRKGNet is publicly available on GitHub with testing scripts and test cases to reproduce the main results. The MMR dataset itself is only available upon request from the corresponding author, so it does not qualify as a public asset.Code · publicof Hefei Artificial Intelligence Breeding Accelerator Co. Ltd. ( NB2024005-02 ).
Data availability
The source code for the proposed methods, MSNeRF and VRKGNet, is publicly available on GitHub. The released repositories contain testing scripts and test cases used to reproduce the main results presented in this paper:
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MSNeRF : https://github.com/qfwysw/MSNeRF.git
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VRKGNet : https://github.com/qfwysw/VRKGNet.git
The datasets used in the experiments are available from the corresponding author upon reasonable request. For access or further inquiries, please contact the corresponding author.
Declaration of competing interest
The authors declare that they have no known competing financial iOpen asset ↗https://github.com/qfwysw/MSNeRF.gitlines:620-663Code · publicator Co. Ltd. ( NB2024005-02 ).
Data availability
The source code for the proposed methods, MSNeRF and VRKGNet, is publicly available on GitHub. The released repositories contain testing scripts and test cases used to reproduce the main results presented in this paper:
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MSNeRF : https://github.com/qfwysw/MSNeRF.git
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VRKGNet : https://github.com/qfwysw/VRKGNet.git
The datasets used in the experiments are available from the corresponding author upon reasonable request. For access or further inquiries, please contact the corresponding author.
Declaration of competing interest
The authors declare that they have no known competing financial interests or personal relationships that could haveOpen asset ↗https://github.com/qfwysw/VRKGNet.gitlines:620-663Plant phenotyping relevance match · UnverifiedEurope PMC · checked 5 Sept 2026
The integration of unmanned aerial vehicle (UAV)-assisted remote sensing with the Internet of Things (IoT) and Internet of Everything (IoE) offers a robust platform for optimizing precision agriculture by capturing spatiotemporal variability in crop growth. In this context, the present study aimed to predict the bulb yield of rainy-season onion crops across four staggered planting dates using UAV-based multispectral imagery. Canopy reflectance mosaics acquired at key growth stages, along with vegetation indices (VIs), viz. NDVI, NDRE, SAVI, LAI, NORM2, and GNDVI, were extracted for yield modeling. Yield prediction models at three onion growth stages were developed and assessed using five machine learning algorithms: linear regression (lm), random forest (rf), support vector machine with radial kernel (svmRadial), gradient boosting (gbm), and elastic net regression (glmnet), with model training and evaluation performed using 10-fold cross-validation. Among these, random forest consistently outperformed the other models at all growth stages, showing promising results at the bulb development stage, with a training R 2 = 0.944, RMSE = 1.919 t ha -1 , MAE = 1.523 t ha -1 , and a validation R² = 0.755, RMSE = 3.824 t ha -1 , and MAE = 3.11 t ha -1 . The support vector machine also demonstrated strong generalization (training R² = 0.787; validation R 2 = 0.716), highlighting its predictive capability. Year-wise evaluation revealed notable interannual variability in model performance, with models trained on data from 2024 outperforming those from 2023. Overall, these results demonstrate the efficacy of UAV-derived multispectral sensing, combined with machine learning, as an effective, scalable, and timely approach for reliable onion yield prediction and decision support in rainy-season onion crops under varying agronomic conditions.
Why it matches plant phenotyping methodsUAVマルチスペクトル画像からタマネギの収量を推定する取得・解析ワークフローと機械学習モデルを開発・評価しており、植物表現型の測定が中心である。
abstractthe present study aimed to predict the bulb yield of rainy-season onion crops across four staggered planting dates using UAV-based multispectral imagery.
AI-driven imaging is becoming central to crop monitoring, with proximal and unmanned aerial vehicle (UAV) platforms now routinely used for disease and stress detection, yield estimation, canopy structure, and fruit counting. Yet, as these models move from plots to farms, the main bottleneck is no longer raw accuracy but robustness under distribution shift. Systems trained in one field, season, cultivar, or sensor often fail when the scene, sensor, protocol, or timing changes in realistic ways. This review synthesizes recent advances on robustness and transferability in proximal and UAV imaging, drawing on a corpus of 42 core studies across field crops, orchards, greenhouse environments, and multi-platform phenotyping. Shift types are organized into four axes, namely scene, sensor, protocol, and time. The article also maps the empirical evidence on when RGB imaging alone is sufficient and when multispectral, hyperspectral, or thermal modalities can potentially improve robustness. This serves as a basis to synthesize acquisition and evaluation practices that often matter more than architectural tweaks, which include phenology-aware flight planning, radiometric standardization, metadata logging, and leave-one-field/season-out splits. Adaptation options are consolidated into a practical symptom/remedy roadmap, ranging from lightweight normalization and small target-set fine-tuning to feature alignment, unsupervised domain adaptation, style translation, and test-time updates. Finally, a benchmark and dataset agenda are outlined with emphasis on object-oriented splits, cross-sensor and cross-scale collections, and longitudinal datasets where the same fields are followed across seasons under different management regimes. The goal is to outline practices and evaluation protocols that support progress toward deployable and auditable systems, noting that such claims require standardized out-of-distribution testing and transparent reporting as emphasized in the benchmark specification and experiment suite proposed here.
Why it matches plant phenotyping methods植物の近接・UAV画像による病害・ストレス・収量・キャノピー構造・果実数の推定について、頑健性、転移性、取得・評価プロトコル、ベンチマークを体系化する方法論レビューであり、フェノタイピング手法が中心です。
abstractThis review synthesizes recent advances on robustness and transferability in proximal and UAV imaging, drawing on a corpus of 42 core studies across field crops, orchards, greenhouse environments, and multi-platform phenotyping.
Deep learning has achieved promising performance for fruit and vegetable image analysis, by possessing strong representation power, and providing resilient generalization and broad transferability on large-scale data for classification, detection, and segmentation tasks, which is indispensable role in optimizing agricultural practices. This comprehensive survey reviews over 270 recent studies, offering a deep exploration of the key techniques and strategies, fundamental properties, and advancements and future directions according to different categories of deep learning methods for fruit and vegetable image analysis. Furthermore, this paper outlines the novelty and concept of fruit and vegetable image analysis, summarizes publicly available datasets, evaluation metrics, and discusses successful applications in disease detection, quality grading, yield estimation, localization, and multiple application integration. The survey emphasizes the need for processing large-scale datasets and exploring the potential of efficient deep learning for enhancing real-time applications and specific tasks. By comprehensively comparing and analyzing the fundamental attributes of the fruit and vegetable image analysis methods from a fresh perspective, this survey reveals the commonalities and disparities of divert techniques and guides researchers and practitioners toward developing more efficient and accurate solutions.
Why it matches plant phenotyping methods果実・野菜画像解析の深層学習手法を包括的にレビューし、疾患検出や収量推定など植物の状態・形質推定、データセット、評価指標を扱うため、フェノタイピング手法レビューとして中心的です。
abstractThis comprehensive survey reviews over 270 recent studies
High-throughput field phenotyping bridges genotype, environment, and phenotypic performance. Conventional plot-level approaches relying on manual surveys are labor-intensive, and error-prone and fail to capture variability among individual plants, limiting seed cotton yield estimation and genotype screening under natural conditions. To address these limitations, a complex framework was developed, integrating single-plant instance segmentation, multi-trait inversion, plot-level stability characterization, and yield estimation. The enhanced vision-model framework, TopoRefineSAM, combines YOLOv12 detection with SAM2 segmentation and incorporates adaptive enhancement and topological refinement modules, enabling efficient, robust, and cost-effective single-plant identification under weak annotation. Based on this segmentation, multi-source UAV imagery (RGB, multispectral, thermal infrared, and DSM) was used to build ensemble learning models for inversion of physiological and biomass traits. A Stability Index Group (SIG) translates inter-plant variability into plot-level stability features, improving interpretability and consistency in yield estimation and cultivar screening. Results demonstrated that TopoRefineSAM achieved high segmentation accuracy for single-plant extraction under complex field conditions. In multi-trait inversion, Gradient Boosting Decision Trees (GBDT) achieved the highest performance. Our results demonstrated strong consistency between multimodal features and measured traits. In yield estimation, incorporating the SIG substantially improved predictive performance across growth stages. In cultivar screening, the method achieved high agreement with field measurements, showing robust identification of top-performing cultivars. Collectively, the findings establish a scalable, cost-effective, and high-accuracy framework for field-based phenotypic analysis and yield estimation, providing both methodological innovations and practical support for precision breeding and large-scale crop improvement.
Why it matches plant phenotyping methods単一植物のセグメンテーション、マルチモーダル画像による形質推定、安定性指標、収量推定を統合した圃場フェノタイピング手法の開発が中心である。
abstractTo address these limitations, a complex framework was developed, integrating single-plant instance segmentation, multi-trait inversion, plot-level stability characterization, and yield estimation.
Aiming at the hysteresis problem of traditional contact-type mechanical throughput detection method during combine harvester operation, this study proposes a multimodal data-driven online throughput prediction method. By building a multimodal sensor system that integrates vehicle-mounted cameras, GPS, grain moisture content, and feeding auger power sensors, a throughput prediction framework based on wheat ear biomass characteristics was established: Firstly, the WEC-MVFF wheat ear online counting density map estimation model is designed, and MobileViT is used to build a feature extraction backbone network. The multi-scale fusion module and the centralized conversion module are combined to realize the collaborative extraction of shallow texture features and deep semantic features of dense wheat ears in the field. Secondly, divide the image into regions of interest and establish a throughput prediction model based on multimodal information of wheat ear number (image) − moisture content (sensor) − travel speed. At the same time, a detection model based on feeding auger power is constructed as a comparison benchmark. Field tests show that the WEC-MVFF model maintains an average counting accuracy of more than 90 % under different wheat ear density, travel speed and light intensity conditions. The model’s online counting advantage is verified through ablation study and comparative tests with other counting models. The throughput prediction method achieved an MAE of 0.70 kg/s and 0.77 kg/s in test area 1 and 2 respectively, the first-order difference fluctuation was stable in the range of ±0.50 kg/s, and the prediction frame rate of 10-13fps met the real-time requirements. Compared with the single-modal image prediction method, the accuracy of the multimodal method considering moisture content was improved by 0.80 kg/s and 0.75 kg/s in the two test areas, respectively. Compared with traditional mechanical quantity detection methods, it has higher accuracy and stability while achieving early prediction, providing reliable feedforward information support for the intelligent control of harvesters.
Why it matches plant phenotyping methods小麦穂の画像計数とマルチモーダルセンサを用いて、穂密度・バイオマス特性および収量流量を推定する手法を開発・検証しており、植物形質の取得・推定が研究の中心である。
Accurate and timely forage yield prediction in alfalfa-grass mixtures (AGM) is essential for supporting precision agriculture management decisions. This study aimed to develop and evaluate UAV-borne remote sensing models to predict total dry matter yield (DMY) and legume dry matter yield (LY) across multiple harvests and field sites. UAV-borne high-resolution true-colour images were used to derive canopy height models via structure-from-motion. At the same time, multispectral imagery enabled the calculation of reflectance-based vegetation indices. Biomass was destructively sampled, and DMY and LY were determined through drying and botanical fractioning. A total of 276 biomass samples were collected over four harvests, including samples from three AGM fields. To predict DMY and LY, two machine learning regression models (random forest and extreme gradient boosting) were trained and validated using leave-spatial-temporal-group-out cross-validation to ensure robustness across locations and time. Random forest models using fused spectral and height data achieved the best performance, with median prediction errors of 0.51 t ha⁻¹ for DMY (median R² = 0.49) and 0.40 t ha⁻¹ for LY (median R² = 0.65), demonstrating good generalizability under varying agronomic conditions. The study highlights the potential of combining UAV-borne height and spectral data for high-resolution yield mapping in complex forage systems. Predictive maps of DMY and LY provide spatial insights that can inform management and support sustainable nitrogen cycling in crop rotations.
Why it matches plant phenotyping methodsUAV画像から樹冠高・スペクトル情報を抽出し、機械学習で乾物収量とマメ科収量を推定する手法の開発・検証が研究の中心であるため。
abstractThis study aimed to develop and evaluate UAV-borne remote sensing models to predict total dry matter yield (DMY) and legume dry matter yield (LY) across multiple harvests and field sites.
Purpose: Coffee farming plays an essential role in the global economy, making accurate productivity prediction methods indispensable for strategic decision-making in the sector. This study aimed to develop models for early prediction of coffee production per plant based on morphological indices.Methods:Two models were proposed using the following attributes: plant height, canopy width, and the number of fruits on the productive internodes of plagiotropic branches. In Model 1, fruit counts were manually conducted at the 4th and 5th productive nodes of the branches, while in Model 2, the average fruit count from the 1st to the 5th productive nodes was obtained automatically through branch image analysis using Detectron2, an open-source object detection library. Both models were developed using data collected at two distinct periods before harvest—the first five months prior and the second three months prior. The research was conducted in three coffee plots in Viçosa, Minas Gerais, Brazil, where 60 plants were selected to evaluate the production prediction model. During harvest, the production of each plant was individually recorded, enabling validation of the predictions. Results: The results revealed a strong correlation between the models and the field-observed production data, especially for the model based on data collected three months before harvest. Model 1 demonstrated a better fit (R² = 0.889; RMSE = 0.923 L/plant; MAE = 0.635 L/plant), while Model 2 had a lower absolute error (R² = 0.747; RMSE = 0.374 L/plant; MAE = 0.460 L/plant). Additionally, productivity maps were generated for each plot, showing good agreement with field-observed productivity data.Conclusions: It was concluded that the proposed models are promising for application in coffee farming, contributing to early production prediction.
Why it matches plant phenotyping methodsコーヒー果実数を枝画像から自動抽出し、個体あたり生産量を早期予測する手法を開発・検証しており、表現型取得と予測ワークフローが研究の中心である。
abstractBoth models were developed using data collected at two distinct periods before harvest—the first five months prior and the second three months prior.
BACKGROUND: Digital image analysis combined with deep learning offers powerful tools for detecting plant nutrient deficiency (ND), a critical challenge in precision agriculture. AIMS: This study aims to develop an ensemble transfer learning approach for ND detection in black pepper (BP) and evaluate its effectiveness for classification and yield‐loss (YL) prediction. METHODS: An ensemble of MobileNetV2 and a custom‐made shallow convolutional neural network was implemented, with U2Net‐based background removal to improve feature extraction. The model was validated on the BP Dataset (DS)—BPNutriDef03 (4469 images)—and tested on a rice DS (4399 images). The framework included (1) ND classification using leaf imagery analysis and (2) YL forecasting based on nutrient deficiency severity (NDS). RESULTS: The ensemble achieved classification accuracies of 99.22% for BP and 95.14% for rice. The yield prediction based on the NDS model estimated the YL of 27.83% for BP and 33.42% for rice. CONCLUSIONS: The proposed approach demonstrates robust performance and generalizability, offering a scalable, automated decision‐support system for ND monitoring and yield prediction in precision crop management.
Why it matches plant phenotyping methods植物の葉画像から栄養欠乏状態を推定する画像解析・深層学習手法を開発し、複数データセットで検証しているため、植物フェノタイピング手法が中心である。
abstractDigital image analysis combined with deep learning offers powerful tools for detecting plant nutrient deficiency (ND)
Improving crop yield prediction accuracy is crucial for precision agriculture, particularly for irrigation management. Unmanned aerial vehicle (UAV)-based multispectral imaging has become a key tool for crop phenotyping due to its high spatiotemporal resolution and cost-effectiveness. In this study, field experiments were conducted in northwestern China over two consecutive growing seasons (2021–2022), incorporating different mulching practices and supplemental irrigation treatments, to systematically analyze the sensitivity of soybean seed yield to various physiological and growth indices measured at different phenological stages. The results indicated that the full pod stage (R4) was the most sensitive window for yield prediction. At this stage, canopy cover (CC) and chlorophyll content reached their peak values. Most vegetation indices (VIs), texture features (TFs), and texture indices (TIs) extracted from the UAV imagery showed significant correlations (P < 0.05) with final seed yield. Among these, the ratio texture index (RTI, defined as DIS1/HOM3) exhibited the strongest correlation with yield (R = 0.69). A three-source data fusion framework combining VIs, TFs, and TIs was constructed, and an extreme gradient boosting (XGBoost) algorithm was applied to optimize feature weighting. This integrated model achieved optimal performance at the R4 stage, with coefficient of determination R² = 0.83 on the validation set, root mean square error (RMSE) = 280.80 kg ha⁻¹ , and mean relative error (MRE) = 6.32 %. Compared to a model based solely on spectral VIs (R² = 0.63), the multi-source XGBoost model improved R² by 31.7 % and reduced the error metrics (RMSE) by up to 17.5 %. These findings provides a theoretical basis for precise field management in arid areas and a technical framework for remote sensing monitoring of crop yield.
Why it matches plant phenotyping methodsUAVマルチスペクトル画像からキャノピー形態・生理指標を抽出し、特徴量融合とXGBoostで大豆収量を推定する手法が中心であり、検証性能も報告している。
abstractUnmanned aerial vehicle (UAV)-based multispectral imaging has become a key tool for crop phenotyping due to its high spatiotemporal resolution and cost-effectiveness.
Cultivation of dedicated bioenergy crops on marginal lands is critical for sustainable development, yet breeding climate-resilient genotypes remains a major bottleneck. This study introduces a powerful, integrated framework for accelerating the selection of high-performance Miscanthus hybrids adapted to saline-alkaline soils. The framework uniquely combines phenotypic classification (scatter vs. cespitose plant types) with explainable machine learning (ML). An Extra Trees Regressor (ETR) model, optimized through hyperparameter tuning, achieved high predictive accuracy for biomass (R² = 0.916) in a diverse hybrid population. Crucially, SHapley Additive exPlanations (SHAP) analysis revealed two distinct, data-driven ideotypes: the optimal cespitose type maximizes tiller number, whereas the optimal scatter type prioritizes individual tiller biomass and stem diameter. SHAP also uncovered critical physiological trade-offs, identifying potential thresholds for key traits beyond which biomass gains diminish. Applying this framework, we screened 216 genotypes and identified five superior lines. Subsequent two-year field trials on both farmland and saline-alkaline soil validated our approach, with genotype S88 demonstrating superior yield and stability under stress. This study not only establishes a scalable strategy for industrial crop breeding but also offers novel insights into the architectural determinants of yield under marginal conditions.
Why it matches plant phenotyping methods植物形態形質と機械学習を統合した選抜フレームワークが研究の中心で、バイオマス予測、形態型分類、SHAPによる形質解釈、圃場検証まで実施しているため、単なる生物学的実験のルーチン測定ではない。
abstractThis study introduces a powerful, integrated framework for accelerating the selection of high-performance Miscanthus hybrids adapted to saline-alkaline soils.
Improving nitrogen use efficiency (NUE) in commercial maize production remains a persistent challenge. A major barrier is the lack of simple, remote sensing–based decision-support frameworks that enable broad adoption of in-season, site-specific nitrogen (N) management. This study developed and evaluated a practical framework that contextualizes the Holland–Schepers sensor algorithm using PlanetScope (PS) satellite imagery to guide multiple in-season, variable-rate fertigation delivered through a flow-proportional injection system integrated with a center pivot system equipped with variable-rate irrigation. Field implementation was carried out during the 2023 and 2024 seasons across four N rates (0-N, Low-N, Fertigation, Full-N) and three irrigation treatments: full (BMP), deficit (50 %BMP), and rainfed. Normalized Difference Red Edge (NDRE)-derived sufficiency index (SI) values informed the amount, timing, and spatial distribution of N applications. In 2024, PS-guided fertigation achieved yields statistically comparable to Full-N while reducing total N input by 23 %. Significant improvements in NUE were observed, with Fertigation outperforming Full-N by 12 % in agronomic efficiency (AE) and 26 % in partial factor productivity of N (PFPN). Satellite-derived SI values were strongly correlated with UAV benchmarks from the MicaSense Altum and RedEdge-3 sensors (ρ = 0.82–0.95). However, PS consistently overestimated NDRE relative to UAV data, particularly under N-deficient conditions, underscoring the need for local calibration and bias correction. To improve diagnostic specificity, a biologically informed, rule-based stress-classification framework was developed to differentiate nitrogen stress from water stress using NDRE and soil water depletion (SWD) as diagnostic variables. Retrospective yield and management data were used to establish physiologically meaningful NDRE–SWD thresholds for stress diagnosis during the critical in-season fertigation window (V10–R2). Full-Yield plots achieved approximately 12,000 kg/ha at NDRE = 0.78 and SWD = 64 mm. The resulting NDRE–SWD–yield patterns highlight the feasibility of disentangling stress types under commercial field conditions. However, further validation across seasons and environments, along with integration of canopy water or temperature indices, is needed to improve water-stress detection and enable real-time decision-making. Overall, these results offer actionable guidance for implementing satellite-guided fertigation at commercial scale. The developed framework delivers scalable, data-driven N recommendations that enhance profitability and support environmentally responsible maize production. It also provides a reference for future research and extension programs aiming to turn satellite remote sensing into practical tools for site-specific N management.
Why it matches plant phenotyping methods衛星・UAVリモートセンシングによるNDRE指標を用いて植物の窒素・水ストレスを診断し、センサー間の検証とルールベース分類法の開発を行っているため、植物状態の取得・推定手法が中心的である。
abstractThis study developed and evaluated a practical framework that contextualizes the Holland–Schepers sensor algorithm using PlanetScope (PS) satellite imagery to guide multiple in-season, variable-rate fertigation
Crop yield prediction (CYP) along with crop growth parameter estimation (CGPE) recently gained prominence as essential means for optimizing agricultural resource use and addressing global food security challenges, particularly in regions with vulnerable climates and diverse agricultural systems, such as the Mediterranean one. Artificial intelligence (AI) and remote sensing (RS) play an important role in achieving such objectives. To identify present methodologies and frameworks, emerging trends, research gaps and future directions in the integrated use of AI and RS in the Mediterranean area for CYP and CGPE. We systematically reviewed the published scientific literature on the topic (106 studies) by means of the PRISMA methodology. We found that integration of AI, particularly machine learning methods such as Random Forest, Support Vector Machine, and Artificial Neural Networks, along with satellite-based RS platforms such as Sentinel-2, Sentinel-1, MODIS, and Landsat-8, demonstrated strong potential to enhance monitoring and support adaptive agricultural decision-making. Deep learning models, such as Convolutional Neural Networks and Long Short Term Memories, are emerging tools for spatio-temporal modelling, although their use is limited, likely due to data and computational constraints. Wheat is the most frequently analyzed crop, alongside high-value perennial crops like olives and vineyards. Data acquisition relies predominantly on satellite imagery, though hybrid approaches incorporating unmanned aerial vehicle and ground-based data are promising in improving prediction accuracy. Despite these advancements, significant challenges persist, including uneven geographical research coverage, limited model transferability, and insufficient consideration of crop phenology. A critical lack of standardized validation datasets and the underrepresentation of North African and Middle Eastern countries further constrain progress. To fully harness AI-RS integration for sustainable agriculture and food security in the Mediterranean area, and similar agroecosystems, future efforts should aim at i) prioritizing cross-regional collaboration, ii) focusing on hybrid AI-RS methods, iii) developing phenology-aware models, and iv) widening access to data.
Why it matches plant phenotyping methodsAI・リモートセンシングによる作物生育パラメータ推定を中心に、手法群・データ取得・検証課題を体系的にレビューしており、植物形質推定手法の方法論的レビューに該当する。
titleIntegration of artificial intelligence and remote sensing for crop yield prediction and crop growth parameter estimation in Mediterranean agroecosystems: Methodologies, emerging technologies, research gaps, and future directions
Plant phenotyping relevance match · UnverifiedOpenAlex · Crossref · Europe PMC · checked 5 Sept 2026
With the development of artificial intelligence (AI) in complicated imaging and remote sensing technologies, plant research is transitioning from manual measurements to automated data collecting. High-throughput image-based phenotyping enables the precise and automated acquisition of traits across various spatial and temporal scales, ranging from controlled laboratory settings to intricate field. Furthermore, AI facilitates the combination of satellite observations, unmanned aerial vehicle (UAV) imaging, soil and climate data, and spatiotemporal information to enhance the precision of trait monitoring and yield prediction. These advances enhance the ability to evaluate and predict crop performance under variable environmental conditions. This paper offers a cross-disciplinary paradigm for accurate and sustainable modern agriculture by merging AI methodologies with plant phenotyping and yield forecasting.
Why it matches plant phenotyping methods画像ベース・リモートセンシングによる植物形質取得とAI解析を中心に扱う方法論的レビューであり、植物フェノタイピング手法が中心的である。
abstractThis paper offers a cross-disciplinary paradigm for accurate and sustainable modern agriculture by merging AI methodologies with plant phenotyping and yield forecasting.
Accurate prediction of sunflower oil yield is essential for crop management and breeding decisions, particularly under water-limited environments. In this study, 100 pure oilseed sunflower lines were evaluated under normal and drought stress conditions across two consecutive growing seasons (2014–2016), and all morphological and physiological variables were measured directly in the field. Input variables were selected based on their previously demonstrated influence on grain yield and oil-related traits, while the complete two-year dataset was used for model training, validation, and testing following data augmentation, standardization, and 7-fold cross-validation. The predictive performance of multiple linear regression (MLR) and deep learning regression (DLR) models was compared using different combinations of input variables. The DLR model consistently demonstrated superior performance, achieving higher accuracy and lower prediction errors across all scenarios. The best results were obtained under drought stress with 11 input variables, where the DLR model achieved (R2 = 0.98, RMSE = 0.4, MSE = 0.16, MAE = 0.20 (train), R2 = 0.96, RMSE = 0.55, MSE = 0.31, MAE = 0.34 (test)), along with markedly lower RMSE and MAE values than MLR. Even when fewer variables were used, the DLR model maintained strong predictive ability, highlighting its capacity to learn complex nonlinear relationships and generalize from limited data. Overall, the findings underscore the potential of DLR as a robust predictive tool for estimating oil yield under contrasting environmental conditions and provide practical implications for genotype selection, harvest planning, and sunflower breeding strategies.
Why it matches plant phenotyping methods深層学習回帰によるヒマワリ油収量という植物形質の推定手法を開発し、複数モデルの性能比較と交差検証を行っており、予測・検証が研究の中心である。
abstractThe predictive performance of multiple linear regression (MLR) and deep learning regression (DLR) models was compared using different combinations of input variables.
Forecasting vulnerability of cultivated and wild species to climate changes is highly challenging. Evolutionary genomic models enable the prediction of mal-adaptation (genomic offset - GO) across environments and future climates under the assumption that populations are currently locally adapted but do not predict but the resulting phenotypic changes. To do so, we developed a new genomic prediction model (GP) integrating both genomic offset (GO) and within-population gene diversity (Hs) to capture genotype by environment interaction and inbreeding effects, respectively (GP-HO-Hs). As proof of concept, we applied this GP-GO-Hs model to a collection of 397 maize populations (landraces) evaluated across 25 environments in Europe using high-throughput DNA pool genotyping. GP-GO-Hs model accurately predicted yield, plant height and flowering time. It increased by 13% the predictive abilities of GP model for predicting yield of new landraces in new environments. GP-GO-Hs model also predicted that the more diverse the landrace, the more stable its agronomic performance across environments. GP-GO-Hs model generated phenotypic adaptive landscapes for each landrace in future climatic scenarios, enabling the identification of landraces with enhanced potential to adapt to future or emerging cultivation conditions. This GP-GO-Hs model could be easily applied to other wild and cultivated species. Teaser Identify promising landrace adapted to new and future environments by combining genomic selection and offset
Why it matches plant phenotyping methodsゲノム情報と環境適応指標を統合した新規予測モデルを開発し、収量・草丈・開花期という植物形質を予測することが研究の中心であるため、計算的フェノタイピング手法として収録する。
abstractwe developed a new genomic prediction model (GP) integrating both genomic offset (GO) and within-population gene diversity (Hs)
Sahelian ecosystems play a crucial role in climate regulation, particularly through their capacity to store atmospheric carbon. However, their carbon sequestration potential remains poorly quantified due to the high cost and logistical constraints of conventional field-based methods. This study investigates the use of low-cost unmanned aerial vehicles (UAVs) to assess dendrometric parameters and estimate the carbon storage capacity of woody vegetation within a 10-hectare Sahelian plot in Senegal. High-resolution aerial imagery was acquired using a DJI Phantom 4 Pro+ drone and processed with photogrammetric software. Tree height and crown diameter were extracted and validated using field measurements, showing a strong correlation for tree height (R² = 0.94) and a moderate correlation for crown diameter (R² = 0.74). Spectral index analysis enabled the identification of dominant woody species, including Balanites aegyptiaca, Sclerocarya birrea, Acacia raddiana, and Acacia senegal.The results indicate that Balanites aegyptiaca contributes the highest amount of carbon storage per hectare (1520.76 ± 185.5 kg ha⁻¹), mainly due to its high stem density (23.3 individuals ha⁻¹), whereas Sclerocarya birrea exhibits the highest average carbon stock per individual tree (206.8 ± 107.8 kg). These findings highlight the significant role of these species in climate change mitigation strategies. By demonstrating the effectiveness of low-cost UAVs for rapid and non-destructive assessment of Sahelian ecosystems, this study provides a promising approach for large-scale ecological monitoring and sustainable natural resource management. It also identifies methodological improvements required to enhance crown dimension estimates. Overall, this UAVbased approach represents a reliable alternative to destructive methods and is well suited to the ecological and operational challenges of Sahelian environments, with strong potential for application in similar regions.
Why it matches plant phenotyping methodsUAV画像から樹高・樹冠径という植物形態形質を抽出し、地上測定で検証する手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含める。
abstractTree height and crown diameter were extracted and validated using field measurements, showing a strong correlation for tree height (R² = 0.94) and a moderate correlation for crown diameter (R² = 0.74).
Accurate estimation of tree biomass and volume is essential for sustainable forest management, climate change mitigation, and ecosystem service assessment. Recent advances in unmanned aerial vehicle (UAV) technology enable the acquisition of ultra-high-resolution optical and three-dimensional data, providing a resource-efficient alternative to traditional field-based inventories. This review synthesizes 181 peer-reviewed studies on UAV-based estimation of tree biomass and volume across forestry, agricultural, and urban ecosystems, integrating bibliometric analysis with qualitative literature review. The results reveal a clear methodological shift from early structure-from-motion photogrammetry toward integrated frameworks combining three-dimensional canopy metrics, multispectral or LiDAR data, and machine learning or deep learning models. Across applications, tree height, crown geometry, and canopy volume consistently emerge as the most robust predictors of biomass and volume, enabling accurate individual-tree and plot-level estimates while substantially reducing field effort and ecological disturbance. UAV-based approaches demonstrate particularly strong performance in orchards, plantation forests, and urban environments, and increasing applicability in complex systems such as mangroves and mixed forests. Despite significant progress, key challenges remain, including limited methodological standardization, insufficient uncertainty quantification, scaling constraints beyond local extents, and the underrepresentation of biodiversity-rich and structurally complex ecosystems. Addressing these gaps is critical for the operational integration of UAV-derived biomass and volume estimates into sustainable land management, carbon accounting, and climate-resilient monitoring frameworks.
Why it matches plant phenotyping methodsUAV画像・3Dデータによる樹木のバイオマス、体積、樹高、樹冠形状などの植物形質推定手法を181研究から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す。
abstractThis review synthesizes 181 peer-reviewed studies on UAV-based estimation of tree biomass and volume across forestry, agricultural, and urban ecosystems, integrating bibliometric analysis with qualitative literature review.
Abstract Reliable forest biomass assessments are becoming increasingly important, as Parties to the Climate Convention are required to report changes in multiple carbon pools, including both above- and belowground biomass. In some regions, use of remote sensing is the only viable option for obtaining such estimates, whereas in other regions it bears potential to improve the accuracy of ground inventory-based biomass estimates. However, statistically rigorous estimation through remote sensing poses several challenges. This study systematically and comprehensively reviews the methodological quality of large-area biomass assessment studies from 1992 to 2022, based on core survey elements for successful biomass surveying assisted by remote sensing. For each element, we reviewed the studies in relation to “ideal standards” derived from the literature, which served as evaluation criteria. Our review revealed an increasing trend in use of remote sensing for biomass surveys, coupled with gradual improvements in methodological quality for all survey elements evaluated. For example, advances in remote sensing techniques, particularly the increased use of Light Detection and Ranging, Radio Detection and Ranging, and digital aerial photogrammetry, all technologies able to capture information on forest structure, have enhanced the reliability of biomass estimates. However, several problems remain, such as field data scarcity for model calibration, signal saturation in high-biomass regions, and misconceptions about the use of statistical methods. We identified five remaining key challenges for improving remote sensing assisted large-area biomass assessments. These include (i) obtaining sensor data that correlate stronger with biomass, (ii) acquiring larger sets of harmonized field data at the level of trees and plots for calibrating models, (iii) adequate use of statistical principles, (iv) developing methods for domain estimation, and (v) improved quality assurance and quality control. While upcoming new airborne technologies and satellite missions may mitigate some challenges, continued methodological innovation and further enhancement of the rigor of statistical and other procedures will remain essential for advancing remote sensing-based biomass assessments.
Why it matches plant phenotyping methods森林の植物バイオマスという明示的な形質を対象に、リモートセンシングによる推定手法の方法論的品質、校正、統計、精度向上を体系的に評価しており、単なるバイオマス測定の報告ではない。
abstractThis study systematically and comprehensively reviews the methodological quality of large-area biomass assessment studies from 1992 to 2022, based on core survey elements for successful biomass surveying assisted by remote sensing.
While essential for precision agriculture, the accurate and dynamic monitoring of crop phenotypic parameters faces challenges, including the constraints of single-data sources and insufficient model generalization across growth stages. This research introduced an integrated framework that leverages multi-source data fusion and the XGBoost algorithm to estimate key soybean parameters, including Leaf Area Index (LAI) and Above-Ground Biomass (AGB). Field experiments incorporated different irrigation methods (drip/micro-sprinkler) and planting densities (210,000/270,000 plants ha −1 ), multispectral images and corresponding ground truth data were acquired across five critical growth stages.We extracted 11 vegetation indices (V) and 8 texture features (T) and constructed inversion models using Support Vector Regression (SVR), Random Forest (RF), and eXtreme Gradient Boosting (XGBoost) based on single and multi-source (V+T) features. The results indicated that: the multi-source feature fusion model outperformed single-feature models. The XGBoost algorithm outperformed all other models, achieving average R 2 values of 0.673, and 0.671, and RMSE values of 0.117, and 79.751 kg ha −1 for LAI, and AGB inversion, respectively. The full pod stage (R4) was identified as the optimal remote sensing observation window, where the best models achieved R 2 values of 0.846 (LAI) and 0.731 (AGB), with RMSE values of 0.131 and 81.01 kg ha −1 , respectively. Drip irrigation combined with high planting density significantly ( P < 0.05) increased soybean LAI and AGB. This study provides a robust, high-throughput technical solution for dynamic crop phenotyping, it highlights the value of fusing multi-source UAV features with machine learning for advancing data-driven smart agriculture. • Achieved dynamic soybean phenotyping by fusing unmanned aerial vehicle (UAV) multi-source features with machine learning. • Multi-source feature fusion outperformed single-feature models in accuracy and robustness. • Full pod stage identified as the optimal UAV remote sensing observation window. • Drip irrigation with high planting density significantly enhanced soybean Leaf Area Index and Above-Ground Biomass.
Why it matches plant phenotyping methodsUAVマルチソース画像と機械学習により、LAIおよび地上部バイオマスを推定する方法を開発・比較検証しており、植物表現型取得が研究の中心である。
abstractThis research introduced an integrated framework that leverages multi-source data fusion and the XGBoost algorithm to estimate key soybean parameters, including Leaf Area Index (LAI) and Above-Ground Biomass (AGB).
Plant phenotyping relevance match · UnverifiedOpenAlex · Europe PMC · bioRxiv · Crossref · checked 15 Sept 2026
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 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 breeding trials, maintaining an uptime of over 85% while capturing frequent RGB and NoIR 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.
Why it matches plant phenotyping methodsAGIcamは圃場での植物表現型取得を目的とするIoTカメラ基盤であり、画像取得、時系列形質抽出、収量予測を技術的に評価しているため、方法・プラットフォームが中心である。
abstractThis study introduces AGIcam, an open-source IoT camera system for automated and continuous in-field plant phenotyping and yield prediction.
The purpose of Precision Agriculture is to incorporate technology into various agricultural processes to increase efficiency and productivity. In fact, Precision Agriculture uses advanced technologies such as sensors and data analytics to improve crop yields. However, a significant challenge in this area is effectively integrating multiple data sources to accurately predict crop health and yield using all available information. This problem arises because traditional models typically use spectral analysis or deep learning techniques independently. Due to this separation, neither method generates the desired results. Researchers propose a solution to this issue by combining spectral analysis and deep learning for multimodal data fusion in precision agriculture. Our integrated approach begins with the collection of multispectral data from drone- or satellite-based sensors to characterise crop types. Spectral analysis will determine each crop type's chlorophyll and water content, which affect plant health. Deep learning will be used to analyse the intricate interconnections between crop yields and derived attributes to understand their relationships better. Integrated use of these two technologies will give us a broader range of data and knowledge about crop variety health and yield than single-use or standalone applications.
Why it matches plant phenotyping methodsマルチスペクトルセンサーと深層学習を統合し、作物のクロロフィル・水分量、健康状態、収量を推定する方法が研究の中心である。
titleIntegrating Deep Learning and Spectral Analysis for Multi-Modal Data Fusion in Precision Agriculture for Enhancing Crop Health Monitoring and Yield Prediction
High-dimensional time series phenotypic data is becoming increasingly common within plant breeding programmes. However, analysing and integrating such data for genetic analysis and genomic prediction remains difficult. Here we show how factor analysis with Procrustes rotation on the genetic correlation matrix of hyperspectral secondary phenotype data can help in extracting relevant features for within-trial prediction. We use a subset of Centro Internacional de Mejoramiento de Maíz y Trigo (CIMMYT) elite yield wheat trial of 2014-2015, consisting of 1,033 genotypes. These were measured across three irrigation treatments at several timepoints during the season, using manned airplane flights with hyperspectral sensors capturing 62 bands in the spectrum of 385-850 nm. We perform multivariate genomic prediction using latent variables to improve within-trial genomic predictive ability (PA) of wheat grain yield within three distinct watering treatments. By integrating latent variables of the hyperspectral data in a multivariate genomic prediction model, we are able to achieve an absolute gain of .1 to .3 (on the correlation scale) in PA compared to univariate genomic prediction. Furthermore, we show which timepoints within a trial are important and how these relate to plant growth stages. This paper showcases how domain knowledge and data-driven approaches can be combined to increase PA and gain new insights from sensor data of high-throughput phenotyping platforms.
Why it matches plant phenotyping methods航空機搭載ハイパースペクトルセンサーによる植物表現型時系列データから潜在特徴を抽出し、収量予測に統合する解析手法が研究の中心であるため。
abstractfactor analysis with Procrustes rotation on the genetic correlation matrix of hyperspectral secondary phenotype data can help in extracting relevant features for within-trial prediction
Reproduction assets foundThe paper's Data and code statement provides public GitHub repositories containing the authors' analysis scripts for the hyperspectral latent-factor/Procrustes workflow and the glfBLUP R package implementing the genomic prediction methodology. The hyperspectral phenotype dataset itself is only available upon request, iCode · publicy of secondary trait data and successful integration in multivariate genomic prediction.
As such, this method can contribute to a greater understanding of high-dimensional data in plant breeding trials.
Data and code
Scripts to generate the hyperspectral datasets, as well as the results presented in this paper, are available at https://github.com/KunstJF/glfBLUP-Procrustes . The glfBLUP methodology is implemented in an R-package available at https://github.com/KillianMelsen/glfBLUP . The hyperspectral dataset is available upon reasonable request from J. Crossa
References
Antonio et al. (2022)
O. Antonio, M. López, A. Montesinos López, and J. Crossa
Multivariate statistical machine learning mOpen asset ↗KunstJF/glfBLUP-Procrusteslines:388-492Code · publicntribute to a greater understanding of high-dimensional data in plant breeding trials.
Data and code
Scripts to generate the hyperspectral datasets, as well as the results presented in this paper, are available at https://github.com/KunstJF/glfBLUP-Procrustes . The glfBLUP methodology is implemented in an R-package available at https://github.com/KillianMelsen/glfBLUP . The hyperspectral dataset is available upon reasonable request from J. Crossa
References
Antonio et al. (2022)
O. Antonio, M. López, A. Montesinos López, and J. Crossa
Multivariate statistical machine learning methods for genomic prediction .
Springer , Cham, Switzerland .
External Links: ISBN 978-3-030-89009-4 978-3-030-8901Open asset ↗KillianMelsen/glfBLUPlines:388-492Plant phenotyping relevance match · UnverifiedEurope PMC · checked 5 Sept 2026
Aiming at the problem that the current traditional apple yield estimation methods rely on manual investigation and do not make full use of multi-source information, this paper proposes an apple orchard yield prediction framework combining multispectral remote sensing features and ground features. The framework is oriented to the demand of yield prediction at different scales. It can not only realize the prediction of apple yield at the district and county scales, but also modify the prediction results of small-scale orchards based on the acquisition of orchard features. The framework consists of three parts, namely, apple orchard planting area extraction, district and county large-scale yield prediction and small-scale orchard yield prediction correction. (1) During apple orchard planting area extraction, the samples of some apple planting areas in the study area were obtained through field investigation, and the orchard and non-orchard areas were classified and discriminated, providing a spatial basis for the collection of subsequent yield prediction-related data. (2) In the large-scale yield prediction of districts and counties, based on the obtained orchard-planting areas, the corresponding multispectral remote sensing features and environmental features were obtained using Google Earth engine platform. In order to avoid the noise interference caused by local pixel differences, the obtained data were median synthesized, and the feature set was constructed by combining the yield and other information. On this basis, the feature set was divided and sent to Apple Orchard Yield Prediction Network (APYieldNet) for training and testing, and the district and county large-scale yield prediction model was obtained. (3) During the part of small-scale orchard yield prediction correction, the optimal model for large-scale yield prediction at the district and county levels is utilized to forecast the yield of the entire planting area and the internal local sampling areas of the small-scale orchard. Within the local sampling areas, the number of fruits is identified through the YOLO-A model, and the actual yield is estimated based on the empirical single fruit weight as a ground feature, which is used to calculate the correction factor. Finally, the proportional correction method is employed to correct the error in the prediction results of the entire small-scale orchard area, thus obtaining a more accurate yield prediction for the small-scale orchard. The experiment showed that (1) the yield prediction model APYieldNet (MAE = 152.68 kg/mu, RMSE = 203.92 kg/mu) proposed in this paper achieved better results than other methods; (2) the proposed YOLO-A model achieves superior detection performance for apple fruits and flowers in complex orchard environments compared to existing methods; (3) in this paper, through the method of proportional correction, the prediction results of APYieldNet for small-scale orchard are closer to the real yield.
Why it matches plant phenotyping methodsマルチスペクトル情報、地上特徴、果実検出を統合してリンゴ収量を推定する技術的フレームワークが研究の中心であり、単なる農業実験のルーチン測定ではない。
abstractthis paper proposes an apple orchard yield prediction framework combining multispectral remote sensing features and ground features
Abstract Plant breeders and weed scientists address weed management collaboratively by selecting for herbicide tolerance in breeding programs. Metribuzin, a Group 5 PSII‐inhibiting herbicide, is labeled for use in wheat ( Triticum aestivum L.). However, application to currently available lines results in frequent, variable, and unpredictable crop injury. Breeding for enhanced metribuzin tolerance would allow growers to utilize this herbicide effectively while minimizing the risk of crop injury. Incorporating an additional herbicide mode of action in winter wheat production would enhance rotational flexibility and weed resistance management. Selection for improved herbicide tolerance in crops has traditionally relied on visual estimation, yet assessments can be variable. The objective of this study was to improve the accuracy and efficiency of selecting for herbicide tolerance in a breeding program by utilizing a drone‐mounted multispectral sensor. Multispectral data were collected on paired rows of an diversity panel and advanced generation lines grown in paired plot yield trials. Vegetation indices calculated include normalized difference vegetation index (NDVI), normalized difference red edge (NDRE), transformed chlorophyll absorption reflectance index, normalized water index, and modified triangular vegetation index. Visual assessments of injury, plant height, and grain yield were also recorded. Correlations between reflectance indices and grain yield were stronger than those between visual injury assessments and grain yield. The top 10 lines overlapped 45%–53% when selected by highest yield and highest NDVI or NDRE, respectively, in treated plots. The relationship between yield and index differences in treated and nontreated plots showed that the difference in indices (multiple R 2 = 0.0802–0.5434) explained more yield variation than visual assessments (multiple R 2 = 0.0003–0.1915). These results suggest that multispectral analysis at the plot level is a more accurate and efficient indicator of herbicide injury in winter wheat than traditional visual assessments.
Why it matches plant phenotyping methodsドローン搭載マルチスペクトルセンサーと植生指数を用いて、冬コムギの除草剤傷害・耐性を従来の目視評価より高精度かつ効率的に推定する方法を実証しており、表現型取得法が研究の中心である。
abstractThe objective of this study was to improve the accuracy and efficiency of selecting for herbicide tolerance in a breeding program by utilizing a drone‐mounted multispectral sensor.
Reproduction assets foundThe article's Data Availability Statement explicitly deposits the datasets generated and analyzed (phenotype/trait and vegetation index data from the metribuzin tolerance phenotyping experiments) in the Washington State University Research Exchange repository with a public DOI. No author analysis code repository is URLDataset · public20-
67037-30671, 2022-67013-36426, and 2022-68013-36439.
C O N F L I C T O F I N T E R E S T S TAT E M E N T
The authors declare no conflicts of interest.
DATA AVA I L I B I L I T Y S TAT E M E N T
The datasets generated and analyzed for this study are avail-
able in the Washington State University Research Exchange
repository (https://doi.org/10.7273/000007507).O RC I D
Melinda Zubrod https://orcid.org/0000-0001-7024-8421
AndrewW. Herr https://orcid.org/0000-0001-5111-2342
ArronH. Carter https://orcid.org/0000-0002-8019-6554
R E F E R E N C E S
Ahmadi, Z., Mehrabadi, M., Fazli, M., Khalesro, S., Abedi, R., &
Mokhtassi-Bidgoli, A. (2025). Enhancing tolerance of wheat culti-
vars to meOpen asset ↗Washington State University Research Exchange · 10.7273/000007507pdf-raw-page:12 lines:1-81Plant phenotyping relevance match · UnverifiedEurope PMC · checked 5 Sept 2026
Timely and accurate prediction of crop traits is critical for precision breeding and regional agricultural production. Previous studies have primarily focused on single crop yield traits, neglecting other crop traits and variety-specific analyses. To address this issue, we employed a Meta-Hybrid Regression Ensemble (MHRE) approach by using multiple machine learning (ML) approaches as base learners, integrating regional multi-year, multi-variety crop field trials with satellite remote sensing indices, meteorological and phenological data to predict major crop traits. Results demonstrated MHRE's optimal performance for rice and cotton, significantly outperforming individual models (RF, XGBoost, CatBoost, and LightGBM). Specifically, for rice crop, MHRE achieved highest accuracy for yield trait (R 2 = 0.78, RMSE = 0.59 t ha -1 ) compared to the best individual model (XGBoost: R 2 = 0.76, RMSE = 0.61 t ha -1 ); traits like effective spike also showed strong predictability (R 2 = 0.64, RMSE = 27.81 10,000·spike ha -1 ). Similarly, for cotton, MHRE substantially improved yield trait prediction (R 2 = 0.82, RMSE = 0.33 t ha -1 ) compared to the best individual model (RF: R 2 = 0.77, RMSE = 0.36 t ha -1 ); bolls per plant accuracy was highest (R 2 = 0.93, RMSE = 2.27 bolls plant -1 ). Moreover, rigorous validation confirmed that crop-specific MHRE models are robust across five rice and three cotton varietal groups and are applicable across six distinct regions in China. Furthermore, we applied the SHAP (SHapley Additive exPlanations) method to analyze the growth stages and key environmental factors affecting major traits. Our study illustrates a practical framework for regional-scale crop traits prediction by fusing multi-source data and ensemble machine learning, offering new insights for precision agriculture and crop management.
Why it matches plant phenotyping methods複数ソースデータとメタ・ハイブリッド回帰アンサンブルにより、イネ・ワタの収量や形態関連形質を推定し、モデル比較と品種群・地域横断検証を行っているため、植物形質推定手法が中心である。
abstractwe employed a Meta-Hybrid Regression Ensemble (MHRE) approach by using multiple machine learning (ML) approaches as base learners, integrating regional multi-year, multi-variety crop field trials with satellite remote sensing indices, meteorological and phenological data to predict major crop traits.
Accurate estimation of above-ground biomass (AGB) and plant height is essential for precision crop management. However, traditional methods like synthetic aperture radar (SAR) data and optical vegetation indices (VIs) often face signal saturation at medium to high AGB levels. To address this, we proposed two polarization texture indices, i.e., Ratio SAR Texture Index (RSTI) and Normalized Difference SAR Texture Index (NDSTI), derived from Sentinel-1 (S-1) data to estimate crop AGB and height. We further investigated their integration with S-1 polarizations and Sentinel-2 (S-2) VIs using four machine learning algorithms to enhance retrieval performance. Results revealed that both RSTI and NDSTI outperformed individual polarizations, polarization texture features, and most of VIs in estimating crop AGB and height. Furthermore, the combination of these indices with S-2 VIs significantly improved the retrieval accuracy. The optimal models achieved R2 values up to 0.75 and 0.80 for maize and soybean AGB, 0.89 and 0.94 for maize and soybean height, respectively. Validation with an independent dataset confirmed the robustness and transferability of the proposed models for estimating maize AGB and height. Overall, RSTI and NDSTI, along with their integration with optical VIs, provide an effective approach for improving crop AGB and height estimation for agricultural monitoring.
Why it matches plant phenotyping methodsSentinel-1/2リモートセンシングから作物バイオマスと草丈を推定する新規テクスチャ指数を開発し、独立データで検証しており、植物形質取得手法が中心である。
abstractwe proposed two polarization texture indices, i.e., Ratio SAR Texture Index (RSTI) and Normalized Difference SAR Texture Index (NDSTI), derived from Sentinel-1 (S-1) data to estimate crop AGB and height.
Mangrove biomass is a key indicator for quantifying carbon cycling in blue-carbon ecosystems, yet conventional approaches face significant challenges. To improve large-scale mangrove biomass assessment and provide a baseline for targeted conservation, present study proposes a Single-tree-Plot-Community-Region (AGB T/F~U~S ) upscaling method that integrates UAV-SfM, SAR, MSI, and field surveys, and applies it to Chonburi, Thailand. In 2023, total mangrove aboveground biomass in Chonburi Province was 145.24 kt, with a mean AGB density of 101.61 Mg/ha, slightly below the global mangrove average. Long-term records reveal an initial decline followed by post-2015 recovery to about 85% of the 1996 level. Relative to the conventional plot-satellite model, the AGB T/F~U~S framework substantially improves estimation performance and reduces prediction error (ΔR²≈0.47; ΔRMSE ≈ 66.03 Mg/ha), and remains robust under limited training data, with accuracy gains saturating once plot numbers exceed a moderate threshold. These results demonstrate that multi-scale upscaling provides a transferable pathway for mangrove biomass mapping in data-scarce regions and offers a practical baseline for blue-carbon accounting and targeted restoration planning.
Why it matches plant phenotyping methodsUAV-SfM、SAR、MSIと現地調査を統合し、マングローブの地上部バイオマスを推定するマルチスケール手法を開発・比較評価しており、植物形質の取得・推定が研究の中心です。
abstractpresent study proposes a Single-tree-Plot-Community-Region (AGB T/F~U~S ) upscaling method that integrates UAV-SfM, SAR, MSI, and field surveys
[Objective]Maize leaf dry biomass is a key trait that reflects plant morphology, growth vigor, and physiological processes including photosynthetic production. Its dynamic changes can effectively characterize the growth status of maize. Accurate estimation of maize leaf dry biomass is crucial for accurately predicting maize yield and informing production management decisions. Extensive research on crop dry biomass estimation indicates that 3D point cloud data characterizing crop morphological structure, along with features derived therefrom, exhibit an extremely high correlation with crop dry biomass. However, traditional dry biomass prediction studies focus primarily on the population canopy scale, and lack effective prediction methods for dry biomass at the plant and organ scales. Research on non-destructive measurement methods for maize leaf dry biomass, based on 3D point clouds and machine learning, the demand is conducted to address for rapid acquisition of organ-level dry biomass information in maize cultivation and management research.[Methods]Maize leaf point cloud data were acquired using three techniques: Multi-view stereo (MVS), LiDAR scanning, and 3D digitalization (DT). The leaf point clouds underwent preprocessing steps that included plant segmentation, denoising, mesh refinement, and uniform subsampling. Subsequently, morphological traits were extracted from the processed data, including leaf length, leaf area, bounding box dimensions, and the number of points contained within the leaf point clouds. Three machine learning methods: random forest (RF), gradient boosting regression tree (GBRT), and support vector regression (SVR), as well as two deep learning methods: convolutional neural network (CNN) and fully connected neural network (FCNN), were employed for predicting maize leaf dry weight. A point cloud-based maize leaf dry biomass prediction model was subsequently developed. This study utilized the mean squared error reduction method inherent to RF and the cumulative improvement method based on decision tree splits in GBRT to rank and visualize feature importance for optimal models. The resulting rankings were then visualized. Simultaneously, Pearson correlation analysis was used to analyze the correlations of the features from the fused dataset (integrating data from the three devices) as well as those from the DT data with maize leaf dry biomass.[Results and Discussions]The results demonstrated that, among the dry biomass prediction models developed in this study, the model based on Laser point cloud data and the FCNN method achieved the highest accuracy, with a mean absolute error (MAE) of 0.08 g, a mean absolute percentage error (MAPE) of 4.60%, a root mean square error (RMSE) of 0.10 g, and a coefficient of determination (R2) of 0.98. In the correlation analysis, the leaf area exhibited the strongest correlation with dry biomass (r = 0.92), followed by the number of points (r = 0.88), leaf width (r = 0.86), and leaf length (r = 0.77). In the feature importance ranking, the leaf area trait consistently ranked within the top two positions, whereas the number of points ranked among the top three in most cases. However, features such as the height of the leaf base above the ground, the horizontal distances from the leaf tip and apex to the stem, and the azimuth angle demonstrated low correlations with dry biomass and low feature importance.[Conclusions]Among all the maize leaf features investigated in this study, size-related traits (such as leaf area, point count, leaf length, and leaf width) had the greatest impact on the accuracy of dry biomass estimation. The utilization of high-resolution 3D point clouds of maize leaves, combined with machine learning methods, enabled a high-accuracy estimation of leaf dry weight and provided a novel approach for the non-destructive measurement of dry biomass in crop organs.
Why it matches plant phenotyping methods3D点群取得・前処理・形態形質抽出と機械学習を組み合わせ、トウモロコシ葉の器官レベル乾物重を非破壊推定する手法を開発・評価しており、表現型取得と推定が研究の中心である。
abstractMaize leaf point cloud data were acquired using three techniques: Multi-view stereo (MVS), LiDAR scanning, and 3D digitalization (DT).
Precision horticulture demands intelligent monitoring systems for automated crop management. While traditional biomass estimation relies on destructive sampling, modern ICT-driven approaches offer transformative solutions. This study presents an AI-powered methodology integrating YOLOv11 for autonomous biomass estimation and stress monitoring in tomato crops. High-resolution RGB imagery was captured across multiple phenological stages under two irrigation regimes. YOLOv11’s computer vision capabilities enabled automated canopy detection, segmentation, and digital biomass quantification, eliminating destructive sampling. Novel AI-driven metrics were introduced: convex hull area for stress-induced canopy alterations and compactness (digital biomass to convex hull ratio) for automated canopy assessment. This integrated approach achieved robust accuracy in stress detection and biomass estimation (R² =0.821), enabling real-time monitoring for precision horticulture. The model demonstrated exceptional performance with segmentation precision of 0.950, recall of 0.979, and mean average precision of 0.975 at IoU 0.5, with mAP50-95 of 0.826. The rapid inference time of 2.3ms per image enables high-throughput phenotyping and decision support for site-specific management. YOLOv11-derived digital biomass correlated strongly with fresh biomass (R² = 0.821). Image-derived features effectively differentiated control and stress conditions. Genotype analysis revealed variation in biomass accumulation: Arka Abhed and Arka Rakshak performed better under optimal irrigation, while Arka Vikas showed greater stress resilience. These results validate YOLOv11 as a scalable solution for intelligent crop monitoring and precision input application in next-generation digital horticulture.
Why it matches plant phenotyping methods植物の画像からバイオマスと水ストレスを推定するコンピュータビジョン手法を開発・検証しており、表現型取得が研究の中心である。
abstractThis study presents an AI-powered methodology integrating YOLOv11 for autonomous biomass estimation and stress monitoring in tomato crops.
Accurate estimation of biomass in energy cane is essential for cultivar selection in breeding programs and biomass supply forecasting in bioenergy production. This study evaluated the integration of Uncrewed Aircraft System (UAS) based Light Detection and Ranging (lidar) and Red-Green-Blue Structure-from-Motion (RGB-SfM) photogrammetry to enhance biomass prediction for high-throughput phenotyping (HTP). Seven cultivars were monitored between December 2023 and July 2024 at an experimental field in Weslaco, Texas. Structural metrics such as percentile-based heights, canopy volume, and interaction variables were extracted and used to train four machine learning models: Random Forest (RF), Extreme Gradient Boosting (XGBoost), Light Gradient Boosting Machine (LightGBM), and a one-dimensional Convolutional Neural Network (1D-CNN). Ensemble tree algorithms consistently outperformed CNN, with XGBoost and LightGBM providing the most stable and interpretable predictions. For single sensor inputs, lidar models (R² = 0.70–0.78; RMSE = 1.36–1.60 kg/m²) generally outperformed RGB-SfM (R² = 0.69–0.73; RMSE = 1.52–1.63 kg/m²), though RGB-SfM performed competitively with XGBoost. Fused models combining lidar and RGB-SfM features achieved the highest accuracies (XGBoost: R² = 0.80, RMSE = 1.31 kg/m²; LightGBM: R² = 0.79, RMSE = 1.36 kg/m²), mitigating the underestimation of high-biomass plots in RGB-SfM and the slight overestimation of lidar at the upper tail. Cultivar specific analysis confirmed TH16–22 as the top performer, followed closely by Ho02–113 and TCP10–4928, demonstrating the capacity of UAS HTP to support breeding decisions. These findings confirm the biological relevance of percentile-based height metrics (particularly the 75th percentile), canopy volume, and their interactions for biomass accumulation and underscore the value of sensor fusion in reducing systematic bias. This study provides systematic demonstration of lidar and RGB-SfM fusion for biomass estimation in energy cane, establishing a scalable and non-destructive approach that advances high-throughput phenotyping and supports the development of sustainable bioenergy cropping systems.
Why it matches plant phenotyping methodsUAS搭載LiDAR・RGB-SfMによる植物構造特徴の取得と機械学習によるバイオマス推定を開発・比較評価しており、表現型取得・抽出手法が研究の中心である。
abstractThis study evaluated the integration of Uncrewed Aircraft System (UAS) based Light Detection and Ranging (lidar) and Red-Green-Blue Structure-from-Motion (RGB-SfM) photogrammetry to enhance biomass prediction for high-throughput phenotyping (HTP).
High-throughput field phenotyping (HTFP) has become an important approach for improving the efficiency and objectivity of phenotypic evaluation in modern plant breeding. Within the PHENO_MaizE project the practical application of UAV-based RGB phenotyping in temperate maize breeding under field conditions is investigated. The project integrates repeated drone imaging, extraction of image-derived traits, and predictive modeling in order to evaluate the potential of digital phenotyping for the selection of superior maize genotypes. Experimental material includes maize inbred lines and their corresponding testcrosses evaluated across multiple environments in Serbia. UAV surveys conducted during the growing season will enable monitoring of temporal crop development and extraction of traits such as plant height, canopy cover, vegetation indices, and growth dynamics. The research within the project will also assess the potential of phenomic prediction models for estimating important agronomic traits, including grain yield, flowering time, and grain moisture at harvest. Special emphasis is placed on developing a practical, cost-effective, and scalable HTFP framework adapted to medium-sized breeding programs. The expected outcomes may support wider implementation of digital phenotyping and data-driven selection strategies in maize breeding.
Why it matches plant phenotyping methodsUAV画像、画像由来形質抽出、予測モデルを統合した圃場フェノタイピング枠組みの開発・実装が中心であり、単なる育種試験のルーチン測定ではない。
abstractThe project integrates repeated drone imaging, extraction of image-derived traits, and predictive modeling
Accurate estimation of the harvest index (HI), the ratio of grain yield to total aboveground biomass (AGB), is crucial for evaluating crop productivity and resource-use efficiency in wheat breeding programs. While traditional HI measurement methods use destructive field sampling, which is labour-intensive and impractical for large-scale breeding trials, recent advances in UAV-based remote sensing now offer non-destructive alternatives capable of delivering high-throughput, plot-level HI estimation. In this study, we present a high-throughput phenotyping framework that combines UAV-based multispectral imaging and ensemble machine learning to estimate HI under field environments. Multispectral data were collected at two key growth stages, anthesis and maturity, using a DJI M300 RTK drone equipped with a RedEdge-P sensor. Vegetation indices (VIs), including the normalized difference vegetation index (NDVI), normalized difference red edge index (NDRE), and green NDVI (G-NDVI), were extracted using data from sensors and ground truth monitoring and used as predictors to estimate grain yield and AGB for calculating HI. An ensemble learning model, based on a stacking architecture comprising five regressors and a ridge regression meta-learner, was employed to enhance prediction accuracy. Results showed strong correlations between UAV-derived and ground-truth VIs ( R 2 > 0 . 94 , RMSE < 0 . 023). The ensemble model demonstrated high accuracy and strong generalization for HI estimation across both experimental sites and growing seasons. At the anthesis stage, the NDVI-based ensemble model achieved the best performance. For the Indian Head site, it yielded a testing R 2 of 0.87, RMSE of 4.18 g/p, and NRMSE of 2.73%, based on a training R 2 of 0.83. At the Swift Current site, the model produced a testing R 2 of 0.84, RMSE of 8.67 g/p, and NRMSE of 5.67%. Similarly, at the maturity stage, the NDRE-based ensemble model was the top performer. It recorded a testing R 2 of 0.86, RMSE of 7.10 g/p, and NRMSE of 4.64% at Indian Head, and a testing R 2 of 0.83 with an RMSE of 8.06 g/p, and NRMSE of 5.27% at Swift Current. Across all indices and stages, the ensemble model consistently outperformed individual models, achieving high testing R 2 values and low RMSE, which confirms its robustness and predictive power on unseen data. The proposed UAV machine learning framework demonstrates a reliable and non-destructive approach for field-level HI estimation, thereby improving germplasm selection efficiency for yield improvement. It offers a valuable tool for accelerating trait-based wheat breeding and precision agriculture applications.
Why it matches plant phenotyping methodsUAVマルチスペクトル画像と機械学習により、小麦の収穫指数を非破壊・高スループット推定する手法が研究の中心であり、検証結果も提示している。
abstractIn this study, we present a high-throughput phenotyping framework that combines UAV-based multispectral imaging and ensemble machine learning to estimate HI under field environments.
Monitoring plant weight during its development cycle is crucial for effective growth monitoring; it provides valuable information on plant’s health and development. Weight data are essential to determine the optimal harvest time and ensure that plants are harvested when they are at their best. This work aimed to design and implement a workflow that allows the study of growth and development variables in a spinach crop cycle using high spatial resolution multispectral images acquired with an Unmanned Aerial Vehicle (UAV). We based this workflow on applying a multitask attention U-Net model for plant segmentation and advanced statistical analysis, including regression methods and hierarchical analysis, to build and evaluate a Random Forest (RF) model and a Generalized Linear Model (GLM) for spinach fresh weight estimation. The segmentation model achieved a mean Intersection over Union (mIoU) of 0.90 and an F-score of 0.93 against manually drawn labels. Experimental validation of the estimation of the fresh weight of spinach plants from geometric and spectral characteristics with an R2 of 0.90 and RMSE = 23.48 g for the RF model constructed from explanatory variables found with hierarchical analysis. Results demonstrate the utility of a novel hybrid approach for analysis of multispectral imagery from UAVs in crop monitoring.
Why it matches plant phenotyping methodsUAVマルチスペクトル画像から植物セグメンテーションと幾何・スペクトル特徴を抽出し、ホウレンソウの生体重を推定するワークフローを開発・検証しており、表現型取得・推定手法が中心である。
abstractThis work aimed to design and implement a workflow that allows the study of growth and development variables in a spinach crop cycle using high spatial resolution multispectral images acquired with an Unmanned Aerial Vehicle (UAV).
Accurate prediction of complex agronomic traits such as grain yield and yield components remains a central challenge in winter wheat breeding because these traits are controlled by many genes and are strongly influenced by environmental variation. The integration of high-throughput phenotyping (HTP), genomics, and advanced machine learning approaches offers new opportunities to improve predictive accuracy and accelerate genetic gain in plant breeding. This study evaluates the use of an unmanned aerial vehicle (UAV)-based multispectral phenomics combined with genomic information, and deep learning approaches to enhance the prediction of grain yield (GY), test weight (TW), grain protein content (GPC), and tiller density (TD) in a winter wheat breeding program. The research was conducted during the 2022 to 2024 growing seasons at three locations in South Dakota: Brookings, Dakota Lakes, and Winner, across multiple breeding nurseries, including the Elite, Advanced, and Preliminary yield trials. UAV-derived spectral indices collected across multiple developmental stages were first integrated into deep neural network (DNN)-based phenomic prediction models and multi-trait genomic selection (MT-GS) frameworks. Significant associations were observed between UAV-based spectral indices and key agronomic traits. Phenomic prediction using DNN achieved strong accuracy for single-location trials (R² = 0.71, 0.62, and 0.49 for GY, TW, and GPC, respectively), with further improvement when models were trained on multi-location datasets (R² = 0.76, 0.64, and 0.75). Prediction accuracy for GY was highest at the Feekes 11 stage. Forward prediction of preliminary breeding lines using models trained on multi-location advanced lines improved accuracy by 32% relative to single-location training. Incorporating UAV-derived spectral indices as covariates in MT-GS models further improved predictive ability for GY (0.40) compared to single-trait genomic selection models (0.23), demonstrating the value of integrating phenomic information into genomic prediction frameworks. To address challenges associated with model transferability across environments, a deep transfer learning (DTL) strategy based on a one-dimensional convolutional neural network (1D-CNN) was implemented. Baseline cross-year and cross-location predictions showed poor performance (R² as low as -15.3); however, partial fine-tuning with 20-40% of target data substantially improved accuracy, achieving R² values up to 0.83 in cross-year and 0.29-0.69 in cross-location scenarios. Growth stage-specific modeling further revealed predictive performance highest at Feekes 10.5 and 11 (R² = 0.78-0.82), highlighting the importance of developmental timing in UAVbased trait prediction. Beyond predicting primary agronomic traits, UAV-based phenomics also provides opportunities to estimate important yield components that are difficult to measure at scale in breeding programs. Finally, UAV multispectral imagery was used to estimate early-season tiller density (TD). Among evaluated models, an attention-based convolutional neural network achieved the highest predictive performance (R² = 0.82; RMSE% = 15.20), outperforming conventional machine learning and standard deep learning approaches. Collectively, these findings demonstrate that integrating UAVbased HTP, genomic information, and deep learning approaches substantially improves the accuracy, generalizability, and scalability of complex trait prediction in winter wheat breeding. By enabling earlier and more reliable estimation of key agronomic traits across environments, these data-driven phenomic and genomic prediction frameworks accelerate breeding decisions and support the development of high-yielding and climate-resilient wheat cultivars.
Why it matches plant phenotyping methodsUAVマルチスペクトル画像による作物形質推定と、深層学習・転移学習モデルの開発および検証が研究の中心であり、再利用可能なHTPワークフローとして実質的な方法論的貢献がある。
abstractThis study evaluates the use of an unmanned aerial vehicle (UAV)-based multispectral phenomics combined with genomic information, and deep learning approaches to enhance the prediction of grain yield (GY), test weight (TW), grain protein content (GPC), and tiller density (TD)
Accurate estimation of aboveground biomass (AGB) helps to monitor maize growth and yield prediction, and unmanned aerial vehicles (UAVs) have become one of the most significant technological tools in precision agriculture. However, previous studies have mainly focused on utilizing spectral indices, texture metrics and structural features derived from UAV multispectral imagery. These methods often involve significant uncertainties and ignore overall maize morphological characteristics. In this study, an innovative partial pixel integration (PPI) parameter is introduced to characterize both horizontal and vertical structural features of maize (Zea mays L.) at the plot scale. Field experiments were conducted in Dafeng District, Yancheng City, Jiangsu Province, China. Multispectral UAV imagery was captured at five flight altitudes (10 m, 20 m, 30 m, 50 m, and 80 m). Five structural features—fractional vegetation cover (FVC), plant height (PH), FVC × PH, pixel integration (PI), and PPI—were extracted to develop Fresh and Dry AGB estimation models based on linear, exponential, and power functions. The models were verified with the method of five-fold cross-validation to evaluate the predictive performance of different parameters. The results revealed that: (1) The models with PPI parameter outperformed that with all other metrics (FVC, PH, FVC×PH, PI), achieving the highest R² values of 0.968 for Fresh AGB (at 20 m flight altitude) and 0.948 for Dry AGB (at 10 m flight altitude); (2) Fresh AGB estimation models were generally more accurate than Dry AGB estimation models; (3) Contrary to expectations, increasing UAV flight altitude did not necessarily reduce AGB prediction accuracy. These findings demonstrate that the PPI parameter delivers high accuracy and robustness, presenting a novel and reliable approach for in-field maize AGB estimation.
Why it matches plant phenotyping methodsUAV画像からトウモロコシの形態特徴を抽出し、PPIという新規パラメータで地上部バイオマスを推定・検証することが研究の中心であり、植物表現型取得手法として適格。
abstractan innovative partial pixel integration (PPI) parameter is introduced to characterize both horizontal and vertical structural features of maize
Abstract has not been obtained from indexed metadata or an accessible article page.
Why it matches plant phenotyping methodsアブラナの莢を対象に、マルチビューUAV画像からのセグメンテーションと遮蔽補償によって収量を推定する手法開発が中心であり、植物形質推定に該当する。
titleA structure-aware deep learning combining fine-grained silique segmentation with occlusion compensation for rapeseed yield estimation from multi-view UAV imagery
Timely and accurate crop yield estimation is important for sustainable agricultural planning and resource optimization. This study is motivated by the need for a scalable, non-destructive, phenology-aware yield estimation pipeline that can outperform spectral index-based methods. A novel in-season crop yield estimation framework is presented that uses high-resolution UAV-based multispectral imagery and deep neural networks. The pipeline integrates automated phenological stage mapping using a custom Spatial Phenology Attention and Feature Cross (SPARC) Network, canopy structure modeling, and wheat head segmentation via a U-Net model fine-tuned on masks generated with SAM 2. UAV imagery is collected across 18 timestamps, processed to produce reflectance maps, vegetation indices (VIs), canopy height models (CHMs), and fractional cover maps. Plot-level phenological and morphological features are extracted to train multiple regression models for in-season yield estimation. Results show that combining temporal phenological features with structural head metrics significantly improve estimation accuracy, with Gradient Boosting Regression achieving an R2 of 0.89. The proposed approach not only improves the granularity and timeliness of in-season yield estimations but also enables scalable, non-destructive crop monitoring solutions, providing practical information for both farmers and breeders alike.
Why it matches plant phenotyping methodsUAV画像と深層学習を用いて、作物のフェノロジー、形態特徴、穂形状を抽出し、圃場区画レベルの収量を推定する技術パイプラインが研究の中心である。
abstractA novel in-season crop yield estimation framework is presented that uses high-resolution UAV-based multispectral imagery and deep neural networks.
Abstract has not been obtained from indexed metadata or an accessible article page.
Why it matches plant phenotyping methodsUAV-SfMによる植物高の評価が中心で、植物形質の取得法を検証し、収量推定・個体選抜へ応用している。
titleEvaluation of Unmanned Aerial Vehicle-Based Structure-from-Motion (UAV-SfM)-Derived Plant Height for Yield Estimation and Individual Selection in Cool-Season Grass Breeding
Aboveground biomass (AGB) of forests is a crucial metric for assessing ecosystem carbon storage and cycling. The geographical complexity of offshore islands, especially their perennial cloud cover, poses a challenge to traditional AGB remote sensing, so unmanned aerial vehicle (UAV) based remote sensing technology is particularly important. However, UAV approaches face limitations from ground interference, structural parameter errors, and allometric equation discrepancies. This study develops a framework integrating UAV photogrammetry and the Mask R-CNN to identify tree species, quantify forest structure, and estimate AGB in a representative offshore island to infer the impact of tree species differences, dominated by allometric equations and structural parameter errors, dominated by canopy occlusion on the estimated AGB of island forests. Compared to the AGB results calculated by species identification of individual trees, multispectral sensors effectively identified four dominant tree species and land cover, as general allometric equations resulted in significant errors ranging from − 68 % to + 36 %. The optimized canopy height model (CHM) approach revealed a 5.6 % underestimation of tree height and 10.0 % error in diameter at breast height (DBH) due to canopy occlusion. This study provides new insights into AGB estimation and forest species identification methodologies, which are important for studying carbon management activities in similar ecosystem types.
Why it matches plant phenotyping methodsUAVマルチスペクトル写真測量とMask R-CNNを用いて樹種、樹木構造、樹高・DBH・地上部バイオマスを推定する手法を開発し、誤差も評価しており、植物表現型取得が中心である。
abstractThis study develops a framework integrating UAV photogrammetry and the Mask R-CNN to identify tree species, quantify forest structure, and estimate AGB
Accurate crop yield mapping is essential for assessing climate change impacts on agriculture and identifying yield gaps. While high spatiotemporal resolution satellite products such as Planet Fusion (PF) with daily 3 m resolution imagery, offer new opportunities for detailed crop monitoring, the impact of the spatiotemporal resolution of satellite data on crop yield estimation remains underexplored. In this study, we create a benchmark dataset consisting of a 3 m resolution rice yield map for a heterogeneous paddy landscape with different cultivars, using PF-based accumulated near-infrared radiation from vegetation (NIRvPₐccᵤₘ) between heading and harvest stages. Comparisons against plot-level rice yield measurements yield an R² of 0.76. We cross-compare yield estimates from other satellite products—MODIS, Sentinel-2, Landsat 8, and a spatial-temporal Savitzky-Golay product—against the PF-based benchmark yield data resampled to relevant coarser spatiotemporal scales. We find that, compared to PF-based yield estimation, lower spatiotemporal resolution leads to higher yield underestimation. Additionally, the downsampled PF data exhibit patterns similar to those observed in the coarser-resolution products. High-spatiotemporal resolution PF data captures peak growth stages more accurately, alleviating the mixed-pixel problem and mitigating nonlinear effects where reflectance-yield relationships deviate from linear scaling. In contrast, coarser-spatiotemporal resolution products, such as Landsat 8 has longer revisit intervals, often miss critical phenological phase transitions (e.g., peak growing season), resulting in substantial yield underestimations compared to PF. Notably, we find that yield underestimations caused by lower spatiotemporal resolutions can surpass inter-annual yield variations. These findings underscore the importance of using satellite imagery with both high spatial resolution and frequent revisits to achieve sufficiently accurate yield estimates in smallholder-dominated, heterogeneous landscapes. By highlighting the trade-offs associated with different satellite-based spatiotemporal resolutions, the study underscores the importance of considering resolution impacts on yield estimation, offering insights for optimizing Earth observation-based agricultural management, particularly in smallholder farming settings.
Why it matches plant phenotyping methods衛星データによるイネ収量推定を中心に、ベンチマークデータセットの作成、異なる衛星時空間解像度の比較、圃場収量との検証を行っており、植物形質取得法が中核である。
abstractwe create a benchmark dataset consisting of a 3 m resolution rice yield map
To address challenges in food security, a better understanding of crop performance under varying and changing environmental conditions is required. Plant time warping (PTW) is a deep learning model that integrates high-throughput field phenotyping data with genomic and environmental information to predict wheat yield. PTW leverages image time series, genetic markers, and environmental covariates to learn genotype-specific physiological responses to temperature and vapour pressure deficit. Compared with mere genomic prediction models, PTW demonstrates superior performance when predicting yield in unseen environments across 48 year-locations in Europe. The PTW model captures non-linear growth responses varying with phenological stages and identifies distinct patterns associated with yield performance and stability. Specifically, varieties with higher yield stability exhibit reduced sensitivity to vapour pressure deficit around 1.5 kPa and distinctive temperature responses during emergence and senescence. The learned response pattern enables retrospective and prospective yield predictions, providing a foundation for location-specific variety recommendations and targeted breeding strategies. The integration of phenomic, genomic, and enviromic data has the potential to substantially advance research in climate adaptation strategies for crop production by addressing generalization challenges of predictions to novel environmental conditions.
Why it matches plant phenotyping methods画像時系列を含む高スループット圃場フェノタイピングデータから、深層学習モデルで小麦の収量と生理応答を推定する手法が研究の中心であり、技術的検証も行っている。
abstractPlant time warping (PTW) is a deep learning model that integrates high-throughput field phenotyping data with genomic and environmental information to predict wheat yield.
The grain flow sensor is a core component for achieving precise online yield measurement in combine harvesters. However, the accuracy and stability of sensor monitoring are affected by factors such as the harvester structure, operational vibrations, dust, and electromagnetic interference. Improving sensor performance under these constraints has long been a key research focus in the industry. To enhance the monitoring accuracy and stability of grain mass flow rate in combine harvesters, this study proposes a flow-guided and weighing-based grain mass flow sensor (GMFS), which incorporates flow-guiding, buffering, and flow-stabilising functions. Based on dynamic analysis, a multivariable dynamic monitoring model for the grain mass flow rate was developed, integrating key parameters such as screw conveyor speed and grain weight. Dedicated circuits for weak signal amplification, noise filtering, and signal acquisition were developed, and an improved Kalman filter (KF) was employed to enhance monitoring precision. Building on this foundation, a GMFS prototype was integrated into combine harvesters and tested, and its buffering and deceleration performance was validated through simulations. The simulation results indicated that the average particle velocity magnitude at the GMFS outlet was lower and more stable than at the inlet, confirming the sensor’s effectiveness in buffering and decelerating grain flow. Bench test results showed that, under varying mass flow conditions, the GMFS achieved a signed mean relative error (MRE) of 0.64 % and a root mean square error (RMSE) of 0.041 kg·s⁻¹ for the steady-segment (Δt₁) flow rate, with 95 % confidence intervals (CIs) reported for the MRE. Dynamic tests on a combine harvester demonstrated comparable monitoring accuracy, with an MRE of 0.97 % (95 % CI: 0.31–1.63 %) and an RMSE of 0.107 kg·s⁻¹ for the steady-segment flow rate, and an MRE in full-interval total mass of –0.28 % (mean absolute error: 1.10 %). This study provides an accurate and stable sensor design for real-time monitoring of grain mass flow in combine harvesters and provides robust support for yield monitoring technology.
Why it matches plant phenotyping methodsコンバイン収穫時の穀粒質量流量（収量）をリアルタイム計測するセンサーを設計・実装し、シミュレーション、ベンチ試験、実機試験で精度を検証しており、植物の収量形質取得法が中心的である。
abstractTo enhance the monitoring accuracy and stability of grain mass flow rate in combine harvesters, this study proposes a flow-guided and weighing-based grain mass flow sensor (GMFS)
Accurate yield estimation is crucial for ensuring national food security and balancing supply and demand. Remote sensing (RS) process models are commonly used for regional-scale crop yield estimation, with the maximum carboxylation rate at 25° C (Vm25) being a key parameter influenced by genetic varieties, environmental conditions, and spatio-temporal variations. However, most remote sensing process models use a fixed Vm25value to simulate maize yield at regional scales. These models ignore variations in Vm25across time, space, and environmental conditions, leading to uncertainties in simulation. To address this issue, we developed a convolutional neural network (CNN) model combined with Vm25-related variables to estimate dynamic Vm25values for maize in Ningxia (NX), a typical semi-arid region of China. By integrating the Normalized Difference Vegetation Index (NDVI), Enhanced Vegetation Index (EVI), and Leaf Area Index (LAI) with three drought-related hydrometeorological factors—Evapotranspiration (ET), Vapor Pressure Deficit (VPD), and Soil Water Content (SWC)—the model's prediction accuracy of Vm25was significantly improved, achieving an R2of 0.88 and an RMSE of 2.21 μmol m-2s-1on the test set. These dynamic Vm25values were then integrated into the RS process model (PRYM-Maize-Dr) to improve maize yield simulations under drought conditions in NX. Validation using data from 2010 to 2021 showed that, at the city level, the R2increased from 0.67 to 0.78 and RMSE decreased from 0.57 t ha-1to 0.43 t ha-1, while at the county level, the R2increased from 0.59 to 0.71 and RMSE decreased from 0.60 t ha-1to 0.53 t ha-1. These results highlight the potential of integrating RS process models with optimized Vm25for accurate spatio-temporal crop yield estimation at the regional scale.
Why it matches plant phenotyping methodsCNNとリモートセンシング変数により、トウモロコシの生理形質Vm25を動的推定する手法を開発・検証しており、単なる収量測定ではなく植物形質の取得・抽出が中心である。
abstractwe developed a convolutional neural network (CNN) model combined with Vm25-related variables to estimate dynamic Vm25values for maize
In a time of shifting disturbance regimes and anthropogenic pressures, effective management of forest and woodland ecosystems depends on continuous, landscape-level monitoring of canopy structure. While remote sensing can help meet this need, its broad operational implementation is often impeded by a myriad of data constraints, necessitating careful tailoring of monitoring programs to specific management objectives across heterogeneous environments. For example, certain regions, such as African savannas, are heavily data-limited and present unique challenges for detecting subtle structural variations within sparse, low-stature vegetation. Conversely, data-rich regions introduce complexities in reconciling disparate reference datasets created with varied methodologies. Furthermore, widely available 3D remote sensing resources like digital aerial photogrammetry (DAP) remain vastly underutilized, despite directly measuring fundamental attributes like canopy height. A final, critical gap is that remote sensing maps are rarely evaluated for one of their primary intended applications, which is aiding in the estimation of population means or totals for vegetation attributes over distinct management areas. To address these gaps, this dissertation investigates the strategic integration of multi-sensor remote sensing and diverse reference datasets across forest and savanna ecosystems. Crucially, each investigation moves beyond map development to evaluate how these products improve population estimates of vegetation structure using post-stratified and small area estimators. This hybrid approach empowers land managers and forest inventory programs by pairing time-series maps that visualize continuous landscape dynamics with rigorous statistical estimates that deliver defensible, population-level metrics for adaptive decision-making. The first chapter evaluates combining remote sensing predictors from multiple sources for extending canopy measurements from spaceborne waveform lidar (GEDI) across data-limited African savannas. By combining optical time series, synthetic aperture radar, and environmental covariates, parsimonious models successfully quantified annual structural changes from herbivory and woody encroachment, though the estimated magnitude of change was muted. The second chapter examines how the selection of canopy cover reference data for building Landsat-based canopy cover maps ultimately influences the precision of population estimates of forest area and aboveground biomass in the Rocky Mountains. Comparing diverse field, aerial, and lidar-based canopy cover sources revealed that the efficiency of post-stratified estimators for aboveground biomass is driven primarily by the plot-level correlation between the reference data and the target variable, rather than marginal improvements in mapping accuracy. Finally, the third chapter demonstrates the operational viability of multi-temporal DAP for statewide forest structure estimation and post-fire canopy change assessment. While DAP struggled to capture residual standing dead stems and sparse woodlands at high resolutions, spatial aggregated canopy height models closely matched airborne lidar benchmarks and achieved nearly identical precision in statewide aboveground biomass estimation. These investigations together advance broad-scale operational use of remote sensing in diverse and complex environments to support forest inventories and effective land management.
Why it matches plant phenotyping methods森林・サバンナの個体群／プロットレベルで樹冠高・樹冠被覆・構造をリモートセンシングにより推定し、異なるセンサーや参照データとの比較、精度評価、航空レーザーとのベンチマークを行っている。植物構造形質の取得・検証が中心であり、単なる生態学的ルーチン測定ではない。
abstractthis dissertation investigates the strategic integration of multi-sensor remote sensing and diverse reference datasets across forest and savanna ecosystems
Accurate and timely crop yield prediction is crucial for global food security and modern agricultural management. Traditional methods often lack the scalability and granularity required for precision farming. This paper introduces FARM (Fine-tuning Agricultural Regression Models), a deep learning framework designed for high-resolution, intra-field canola yield prediction. FARM leverages a pre-trained, large-scale geospatial foundation model (Prithvi-EO-2.0-600M) and adapts it for a continuous regression task, transforming multi-temporal satellite imagery into dense, pixel-level (30 m) yield maps. Evaluated on a comprehensive dataset from the Canadian Prairies, FARM achieves a Root Mean Squared Error (RMSE) of 0.44 and an R2 of 0.81. Using an independent high-resolution yield monitor dataset, we further show that fine-tuning FARM on limited ground-truth labels outperforms training the same architecture from scratch, confirming the benefit of pre-training on large, upsampled county-level data for data-scarce precision agriculture. These results represent improvement over baseline architectures like 3D-CNN and DeepYield, which highlight the effectiveness of fine-tuning foundation models for specialized agricultural applications. By providing a continuous, high-resolution output, FARM offers a more actionable tool for precision agriculture than conventional classification or county-level aggregation methods. This work validates a novel approach that bridges the gap between large-scale Earth observation and on-farm decision-making, offering a scalable solution for detailed agricultural monitoring.
Why it matches plant phenotyping methods衛星画像から圃場内の作物収量を推定する回帰手法を開発し、独立データで検証しており、植物の収量形質の取得・推定が中心である。
abstractThis paper introduces FARM (Fine-tuning Agricultural Regression Models), a deep learning framework designed for high-resolution, intra-field canola yield prediction.
Agricultural systems are entering an era defined not just by mechanization but by real-time, spatially aware, data driven production practices. This shift which has rapidly evolved from novelty to necessity in precision agriculture. At the center of this shift Unoccupied Aerial Vehicles (UAV) or drones have operationalized high-resolution aerial data into sustainable agricultural outcomes. This chapter provides an application-focused roadmap for integrating UAV into modern agronomic workflows as pre, during, and post flight operations for agronomic flight planning. It bridges the engineering of flight platforms and sensors with the applications in crop stress detection, variable-rate input application, and predictive yield modeling. We explore UAV architecture and their implications for data resolution, field scale, and operational complexity. Sensor systems use the portions of electromagnetic spectrum (RGB, multispectral, hyperspectral, thermal, LiDAR) and are examined through their applications for plant physiology and soil interactions. Ground sampling distance, spectral calibration, geospatial accuracy and photogrammetry are not treated as ancillary steps, but as critical determinants of agronomic utility. We describe the full data pipeline from FAA (Federal Aviation Administration) regulations to machine learning-driven analytics, acquisition, orthomosaic generation, digital surface modeling, vegetation index extraction, and the development of actionable prescription maps. In the context of AI evolution, we emphasize how AI-ML methods classification, regression, clustering, and dimensionality reduction help with integrating complex patterns in time-series UAV imagery, enabling early and precise management of nutrients, water, weeds, and disease. By synthesizing global regulatory frameworks and field-based use cases, the chapter concludes UAV as tools that transforms data into agronomic decisions.
Why it matches plant phenotyping methodsUAVセンサー、校正、フォトグラメトリ、オルソモザイク、植生指数抽出、機械学習解析を含む一連の植物状態・ストレス推定ワークフローをレビューしており、単なる生物学的実験の測定ではなく、取得・解析手法とプラットフォームが中心です。
abstractThis chapter provides an application-focused roadmap for integrating UAV into modern agronomic workflows as pre, during, and post flight operations for agronomic flight planning.
Accurate simulation of the crop growth process was the foundation for the development of smart agriculture. However, the uncertainty of crop growth models limits their practical application. This study integrates the Soil Water Atmosphere Plant (SWAP) model with the Iterative Ensemble Smoother (IES) algorithm to develop the SWAP-IES optimization approach and explores various uncertainty factors of the system, including the ensemble size, observational errors setting, combination of observation variables and their corresponding observation stages, and uncertain parameters selection. The results suggested that, under water stress conditions, an ensemble size of 50 was recommended. It was advisable to choose leaf area index (LAI) and soil moisture content (SW) as observation variables, focusing on monitoring data from the flowering to the milk stage. The suitable observational error settings for LAI and SW were 0.3-0.5 m² m⁻² and 0.03-0.05 cm³ cm⁻³, respectively. For uncertain parameters, it was recommended to select the five crop parameters (RGRLAI, SPAN, CVO, EFF, and CVL) and three soil parameters (θₛ, Kₛ, and n) for simulation. The SWAP‐IES, validated with 2020 and 2021 spring wheat (Triticum aestivum L.) experiments, demonstrated high accuracy in simulating yields, with root mean square error values of 0.56 and 0.61 t ha⁻¹, respectively. The SWAP-IES optimization approach could significantly reduce the uncertainty in the simulation process and improve simulation accuracy by optimizing the system settings strategy.
Why it matches plant phenotyping methodsSWAP-IESという計算的な作物成長・収量推定手法を開発し、観測変数や不確実性設定を検討したうえで春コムギ実験により検証しており、植物形質（収量・LAI）の推定手法が中心である。
abstractThis study integrates the Soil Water Atmosphere Plant (SWAP) model with the Iterative Ensemble Smoother (IES) algorithm to develop the SWAP-IES optimization approach
Potato yield is a key indicator for optimizing cultivation practices in agriculture. Potato yield can be estimated on harvesters using RGB-D cameras, which capture three-dimensional (3D) information of individual tubers moving along the conveyor belt. However, point clouds reconstructed from RGB-D images are incomplete due to self-occlusion, leading to systematic underestimation of tuber weight. To address this, we introduce PointRAFT, a high-throughput point cloud regression network that directly predicts continuous 3D shape properties, such as tuber weight, from partial point clouds. Rather than reconstructing full 3D geometry, PointRAFT infers target values directly from raw 3D data. Its key architectural novelty is an object height embedding that incorporates tuber height as an additional geometric cue, improving weight prediction under practical harvesting conditions. PointRAFT was trained and evaluated on 26,688 partial point clouds collected from 859 potato tubers across four cultivars and three growing seasons on an operational harvester in Japan. On a test set of 5,254 point clouds from 172 tubers, PointRAFT achieved a mean absolute error of 12.0 g and a root mean squared error of 17.2 g, substantially outperforming a linear regression baseline and a standard PointNet++ regression network. With an average inference time of 6.3 ms per point cloud, PointRAFT supports processing rates of up to 150 tubers per second, meeting the high-throughput requirements of commercial potato harvesters. Beyond potato weight estimation, PointRAFT provides a versatile regression network applicable to a wide range of 3D phenotyping and robotic perception tasks. The code, network weights, and a subset of the dataset are publicly available at https://github.com/pieterblok/pointraft.git.
Why it matches plant phenotyping methods部分点群からジャガイモ塊茎重量を推定する3D深層学習手法を開発・評価しており、植物形質取得が研究の中心である。
abstractwe introduce PointRAFT, a high-throughput point cloud regression network that directly predicts continuous 3D shape properties, such as tuber weight, from partial point clouds.
Reproduction assets foundThe paper publicly releases its authors' analysis code and trained network weights on GitHub, and a subset of its potato tuber partial point cloud dataset (with ground truth weights) on Hugging Face. Both are paper-specific, public, and actionable.Code · publicThe code, network weights, and a subset of the dataset are publicly available at https://github.com/pieterblok/pointraft.git .Open asset ↗pieterblok/pointraftlines:1-93Dataset · publicA subset of the datasets generated and/or analyzed during this study is publicly available at: https://huggingface.co/datasets/UTokyo-FieldPhenomics-Lab/3DPotatoTwinOpen asset ↗UTokyo-FieldPhenomics-Lab/3DPotatoTwinlines:447-463Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Timely and accurate in-season estimation of aboveground biomass (AGB) and yield in winter wheat is crucial for optimizing resources and ensuring food security. Light use efficiency (LUE) models have proven effective in estimating crop gross primary productivity and yield across sites and years due to their strong physiological and ecological mechanisms. However, existing studies are limited to satellite applications and have not utilized unmanned aerial vehicle (UAV) imagery. This study proposed a practical framework for accurate in-season estimation of AGB and yield in winter wheat from UAV imagery by combining a LUE model and machine learning (LUE-ML) across five plot experiments. Subsequently, the scalability of the LUE-ML yield prediction approach was assessed in farmer's fields from five counties of Jiangsu Province, China. The results demonstrated that while the AGB for the heading stage was estimated by combining the retrieved LAI and 20-day accumulated meteorological features, the AGB during the post-heading period could be estimated accurately using the stage-skipping or stage-progressive strategy, with the latter ( R val 2 = 0.93) outperforming the former ( R val 2 = 0.84). The combination of one spectral index, LUE-derived AGB, and three 20-day accumulated relative meteorological features (Comb. #6) performed the best ( R cal 2 = 0.89; R val 2 ≥ 0.79) for yield prediction among all combinations. When extended to farmer-field yield prediction across the province, Comb. #6 also achieved acceptable performance. This study suggests the use of LUE-ML models represents a significant step forward towards mechanistic estimation of AGB and yield for cereal crops from UAV imagery.
Why it matches plant phenotyping methodsUAV画像から冬コムギの地上部バイオマスと収量を推定するLUE-ML手法を開発・評価し、圃場で性能検証しているため、植物形質取得・推定が研究の中心である。
abstractThis study proposed a practical framework for accurate in-season estimation of AGB and yield in winter wheat from UAV imagery by combining a LUE model and machine learning (LUE-ML) across five plot experiments.
Reproduction assets foundThe paper's Data Availability statement explicitly hosts the core code for the two UAV-LUE AGB estimation strategies and related test data in a public GitHub repository; other data are only available upon request.Code · publicThe core code for the two strategies and related test data in the UAV-LUE method for estimating wheat AGB are hosted in a public repository: https://github.com/qtaocheng/agb-estimation-uav-lue-two-strategies . Other data that support the findings of this study are available from the corresponding author (T.C.) upon reasonable request.Open asset ↗qtaocheng/agb-estimation-uav-lue-two-strategieslines:507-519Plant phenotyping relevance match · UnverifiedOpenAlex · Europe PMC · Crossref · checked 5 Sept 2026
Abstract Conventional plant phenotyping relies on visual scoring and manual measurements, which are labor-intensive, time-consuming, and prone to human error. To address these limitations, Unmanned Aircraft Systems (UASs) are increasingly being applied in breeding trials to capture various phenotypic traits. High Throughput Phenotyping (HTP) offers enhanced speed, accuracy, and efficiency, while potentially reducing costs in plant breeding programs. This study explores UAS-based phenotyping in wheat breeding trials with the aim to integrate HTP platforms across breeding pipelines. UAS images were acquired using a Parrot Bluegrass drone equipped with a sequoia multispectral sensor, processed via Agisoft Metashape (open-source) and Pix4D mapper (licensed), and analyzed using PlotPhenix (licensed) for Vegetation Indices (VIs) and plot segmentation. Comparisons between UAS-based and ground-based measurements revealed that grain yield is significantly negatively correlated (r = -0.74) with yellow rust disease severity. Multispectral-derived indices, particularly **Red, Red Edge, and NIR bands, showed positive correlations with grain yield (ranging from 0.22 to 0.23), though RGB-generated indices exhibited stronger correlations. The findings confirm that UAS-generated indices effectively assess yellow rust disease severity and predict grain yield. UAS-based phenotyping enhances efficiency and accuracy in trait collection and disease assessment, facilitating the development of improved wheat varieties and promoting the integration of UAS technologies into breeding programs.
Why it matches plant phenotyping methodsUAS・マルチスペクトル画像を用いた作物形質取得、区画分割、疾病重症度評価、収量予測を中心に扱う高スループット表現型解析研究であり、方法の適用とプラットフォーム統合が中心です。
titleApplication of Unmanned Aircraft Systems (UASs) for Disease Assessment and High Throughput Field Phenotyping of Plant Breeding Trials
Abstract Accurate and timely forage yield prediction in alfalfa-grass mixtures (AGM) is essential for supporting precision agriculture management decisions. This study aimed to develop and evaluate UAV-borne remote sensing models to predict total dry matter yield (DMY) and legume dry matter yield (LY) across multiple harvests and field sites. UAV-borne high-resolution true-colour images were used to derive canopy height models via structure-from-motion. At the same time, multispectral imagery enabled the calculation of reflectance-based vegetation indices. Biomass was destructively sampled, and DMY and LY were determined through drying and botanical fractioning. A total of 276 biomass samples were collected over four harvests, including samples from three AGM fields. To predict DMY and LY, two machine learning regression models (random forest and extreme gradient boosting) were trained and validated using leave-spatial-temporal-group-out cross-validation to ensure robustness across locations and time. Random forest models using fused spectral and height data achieved the best performance, with median prediction errors of 0.51 t ha⁻¹ for DMY (median R² = 0.49) and 0.40 t ha⁻¹ for LY (median R² = 0.65), demonstrating good generalizability under varying agronomic conditions. The study highlights the potential of combining UAV-borne height and spectral data for high-resolution yield mapping in complex forage systems. Predictive maps of DMY and LY provide spatial insights that can inform management and support sustainable nitrogen cycling in crop rotations.
Why it matches plant phenotyping methodsUAV画像から草冠高・スペクトル情報を抽出し、乾物収量とマメ科収量を予測する手法の開発・検証が研究の中心であり、植物の収量形質を直接推定している。
abstractThis study aimed to develop and evaluate UAV-borne remote sensing models to predict total dry matter yield (DMY) and legume dry matter yield (LY) across multiple harvests and field sites.
Accurate and timely forage yield prediction in alfalfa-grass mixtures (AGM) is essential for supporting precision agriculture management decisions. This study aimed to develop and evaluate UAV-borne remote sensing models to predict total dry matter yield (DMY) and legume dry matter yield (LY) across multiple harvests and field sites. UAV-borne high-resolution true-colour images were used to derive canopy height models via structure-from-motion. At the same time, multispectral imagery enabled the calculation of reflectance-based vegetation indices. Biomass was destructively sampled, and DMY and LY were determined through drying and botanical fractioning. A total of 276 biomass samples were collected over four harvests, including samples from three AGM fields. To predict DMY and LY, two machine learning regression models (random forest and extreme gradient boosting) were trained and validated using leave-spatial-temporal-group-out cross-validation to ensure robustness across locations and time. Random forest models using fused spectral and height data achieved the best performance, with median prediction errors of 0.51 t ha⁻¹ for DMY (median R² = 0.49) and 0.40 t ha⁻¹ for LY (median R² = 0.65), demonstrating good generalizability under varying agronomic conditions. The study highlights the potential of combining UAV-borne height and spectral data for high-resolution yield mapping in complex forage systems. Predictive maps of DMY and LY provide spatial insights that can inform management and support sustainable nitrogen cycling in crop rotations.
Why it matches plant phenotyping methodsUAV画像から草冠高・スペクトル情報を抽出し、乾物収量という植物形質を予測する手法の開発・検証が中心です。
abstractThis study aimed to develop and evaluate UAV-borne remote sensing models to predict total dry matter yield (DMY) and legume dry matter yield (LY) across multiple harvests and field sites.
The non-destructive estimation of grain yield could increase the efficiency of soybean breeding through early genotype testing, allowing for more precise selection of superior varieties. High-throughput phenotyping (HTPP) data can be combined with machine learning (ML) to develop accurate prediction models. In this study, an unmanned aerial vehicle (UAV) equipped with a multispectral camera was utilized to collect data on plant density (PD), plant height (PH), canopy cover (CC), biomass (BM), and various vegetation indices (VIs) from different stages of soybean development. These traits were used within random forest (RF) and partial least squares regression (PLSR) algorithms to develop models for soybean yield estimation. The initial RF model produced more accurate results, as it had a smaller error between actual and predicted yield compared with the PLSR model. To increase the efficiency of the RF model and optimize the data collection process, the number of predictors was gradually decreased by eliminating highly correlated VIs and selecting the most important variables. The final prediction was based only on several VIs calculated from a few mid-soybean stages. Although the reduction in the number of predictors increased the yield estimation error to some extent, the R2 in the final model remained high (R2 = 0.79). Therefore, the proposed ML model based on specific HTPP variables represents an optimal balance between efficiency and prediction accuracy for in-season soybean yield estimation.
Why it matches plant phenotyping methodsUAVマルチスペクトル画像から植物形質を取得し、機械学習でダイズ収量を推定するワークフローが研究の中心であり、形質抽出・予測モデルの開発と効率化を扱っている。
abstractHigh-throughput phenotyping (HTPP) data can be combined with machine learning (ML) to develop accurate prediction models.
Alfalfa (Medicago sativa) is a globally important forage crop; however, improvements in its biomass yield have stagnated due to its complex genetic architecture and the costly, labor-intensive phenotyping. This study evaluated the potential of the normalized difference vegetation index (NDVI) to predict biomass yield and enhance selection efficiency in alfalfa breeding programs. Specifically, nineteen alfalfa experimental populations (AEXP 1–19) and one control cultivar (OS 66) were evaluated over two growing seasons in Croatia. NDVI was measured at four development stages using a GreenSeeker sensor and compared with forage yield, dry matter yield, and plant height. NDVI values varied significantly among genotypes, years, and growth stages, ranging from 0.23 to 0.87, and increased consistently from early to late vegetative phases. Strong positive correlations were observed between NDVI and forage yield (r = 0.543–0.843) and plant height (r = 0.537–0.738) at early vegetative, late vegetative, and early bud stages. Conversely, NDVI at the mid-vegetative stage correlated negatively with yield and height (r = –0.622 to –0.794). High-performing populations (AEXP 2, AEXP 15, AEXP 18) also exhibited the highest NDVI values. NDVI is a reliable, non-destructive indicator for early selection of high-yielding alfalfa genotypes, although multi-location validation is advised to confirm its broader applicability.
Why it matches plant phenotyping methodsNDVIセンサーによる非破壊的な生育・収量形質推定を育種選抜へ適用し、収量や草丈との相関で妥当性を評価しており、フェノタイピング手法が中心である。
abstractThis study evaluated the potential of the normalized difference vegetation index (NDVI) to predict biomass yield and enhance selection efficiency in alfalfa breeding programs.