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.
Raman / spectroscopyLeafTissuePhysiological trait estimationLeaf traitsWater status / transpiration
Phenotyping extensive populations remains a major constraint in tree breeding programmes, particularly due to the time-consuming and labour-intensive nature of conventional methods. Near infrared (NIR) spectroscopy, which is a high-throughput phenotyping method, offers an alternative solution, providing a rapid and cost-effective approach for assessing growth- and function-based traits on large numbers of trees. This study aimed to evaluate the potential of NIR spectroscopy-based models for predicting such traits in Larch. Specifically, delta carbon-13 ( δ 13 C), carbon (C), nitrogen (N), specific leaf area (SLA), leaf dry matter content (LDM), and phenolics on needles; the branch hydraulic trait (P 50 ), and lignin and hydroxyphenyl/guaiacyl (H/G) ratio on wood cores from an experimental study on Larix species were predicted using multivariate modelling, specifically, partial least squares regression. Reliable models were obtained for N content (R 2 training = 0.95, r 2 testing = 0.94), lignin (R 2 training = 0.95, r 2 testing = 0.94), and H/G ratio (R 2 training = 0.88, r 2 testing = 0.89), while moderate predictive performance was observed for C content (R 2 training = 0.79, r 2 testing = 0.79) and δ 13 C (R 2 training = 0.76, r 2 testing = 0.69). This methodological approach and its results encourage the transition from traditional laboratory methods to efficient, large-scale-based trait evaluation techniques in forestry.
Why it matches plant phenotyping methodsNIR分光とPLS回帰を用いて樹木の複数形質を大規模推定する手法を評価しており、表現型取得・推定法が研究の中心である。
abstractNear infrared (NIR) spectroscopy, which is a high-throughput phenotyping method, offers an alternative solution, providing a rapid and cost-effective approach for assessing growth- and function-based traits on large numbers of trees.
Fruit quality is a critical determinant of economic returns in pear production, and maintaining an appropriate fruit load (FL) is essential for achieving high yield and quality. As a direct indicator of canopy photosynthetic capacity and assimilate supply, leaf number constitutes the key biological basis of reasonable FL determination under the leaf-to-fruit ratio concept. However, accurate and efficient estimation of leaf number in mature pear trees remains technically challenging, limiting its practical use in precision FL regulation. Here, we propose a data-driven framework for leaf number and reasonable FL estimation by integrating 3D point cloud-derived canopy structure with machine learning. A pipeline for extracting 3D architectural traits was developed and implemented in the software tool FTPCT, enabling rapid and standardized trait acquisition. Through correlation analysis, multicollinearity diagnosis, and variance inflation factor screening, five key traits strongly associated with leaf number were identified and incorporated into five machine learning models optimized using Bayesian optimization. Among them, the optimized random forest regression model achieved the highest and most stable performance, with R 2 of 0.85, RMSE of 239.74, and MAE of 149.26 for test dataset. SHAP analysis identified tree crown volume as the dominant contributor to leaf number estimation. Field validation demonstrated that FL regulation guided by the proposed framework significantly improved fruit weight and size without reducing yield compared with conventional practices. Notably, the proposed approach avoids explicit leaf-level reconstruction and relies on less canopy-scale traits, substantially reducing data requirements and computational cost, and thereby offering strong potential for rapid, field-deployable FL regulation in large-scale orchards.
Why it matches plant phenotyping methods3D点群から樹冠構造形質を抽出し、葉数と適正着果量を推定する手法およびソフトウェアを開発・検証しており、植物表現型取得が中心である。
abstractA pipeline for extracting 3D architectural traits was developed and implemented in the software tool FTPCT, enabling rapid and standardized trait acquisition.
Reproduction assets foundThe paper's phenotyping analysis assets are the authors' publicly released LeafNumPred source code and trained models, and the FTPCT software for 3D trait extraction from pear tree point clouds. Phenotype/point-cloud datasets are only available on request.Code · public. Supplementary data
The following is the Supplementary data to this article:
Multimedia component 1
mmc1.docx (1.6MB, docx)
Data availability
Data will be made available on request. Anyone who wants to obtain other public data can contact us at taost@njau.edu.cn. The source codes and models have been made publicly available at https://github.com/Zhang-Fanhang/LeafNumPred, and the FTPCT software has been released at https://github.com/Zhang-Fanhang/FTPCT/tree/Installation-package.
References
1.Tao S., Khanizadeh S., Zhang H., Zhang S. Anatomy, ultrastructure and lignin distribution of stone cells in two Pyrus species. Plant Sci. 2009;176:413–419. [Google Scholar]
2.Zhang F., Wang Q., Yuan K.Open asset ↗Zhang-Fanhang/LeafNumPredhtml-lines:284-315Code · publical variations [34,35]. The method for calculating these traits are shown in the Supplementary information 1.
2.5. Software implementation for 3D trait extraction (FTPCT)
To facilitate efficient and standardized extraction of canopy structural traits from point cloud data, we used a standalone software tool, FTPCT (available at: https://github.com/Zhang-Fanhang/FTPCT/tree/Installation-package), which integrates the trait extraction procedures applied in this study. The software provides a graphical user interface, enabling users to process tree-level point cloud data and extract key 3D structural traits without requiring advanced programming skills.
FTPCT implements a series of predefined proOpen asset ↗Zhang-Fanhang/FTPCThtml-lines:138-149Plant phenotyping relevance match · UnverifiedEurope PMC · checked 14 Sept 2026
Global trait axes reveal overarching dimensions of plant functional variation. However, how these dimensions are spatially organized within and across forest types remains unclear. We combined drone-based full-range imaging spectroscopy with crown-level measurements of 16 physiological, morphological and biochemical traits across temperate, subtropical and tropical forests in China to enable spatially-explicit trait mapping. Through site-training scenario, leaf-to-canopy scaling and spectral-domain modelling tests, we find that reliable canopy trait retrieval depends not only on trait and spectral coverage, but also on preserving trait-spectral relationships across sites and scales. Spectral predictions recovered observed multivariate covariation, summarizing crown variation into a leaf-economics dimension and two additional biochemical dimensions related to hydro-thermal regulation and defence/metabolism. Mapping these dimensions revealed distinct community-level trait organization alongside substantial species- and crown-level variation within forests. These findings link remotely sensed trait retrieval to environmental filtering and plant functional differentiation, providing a scalable framework for monitoring forest functional diversity.
Why it matches plant phenotyping methodsドローン分光画像と冠レベル形質測定を用いた植物形質の空間マッピング手法が中心で、スケーリングおよびスペクトルモデルの検証も行っている。
abstractWe combined drone-based full-range imaging spectroscopy with crown-level measurements of 16 physiological, morphological and biochemical traits across temperate, subtropical and tropical forests in China to enable spatially-explicit trait mapping.
Surface phenotyping underpins plant science, preclinical animal research and entomology, yet across all three the measurement is almost always a photograph, which records a projection and not the surface itself. Here we present the Gentschinator3000 , an open structured-light platform that brings high-end metric surface measurement within reach of laboratories with no optics expertise, combining documented open hardware, open reconstruction software and analysis workflows for under 4000 Euro in components. It resolves a planar reference to 45 µm local flatness, registers full rotations to a loop closure of 156 µm, and performs stably across acquisition ranges that we define. Applying one workflow to a leaf before and after desiccation, to murine anatomy and to a spread lepidopteran, we find that projection underestimates surface area by 11 to 41 %. That error grows with the condition under study, with the evaluation scale and with the direction of view, so it can confound phenotype comparisons dramatically. In murine limbs a 15-degree change of viewing direction shifts a projected inter-segment angle by up to 23.2 degrees, while the three-dimensional angle does not move. Projection geometry can therefore contribute as much to a measured phenotype as the biology it is meant to quantify.
Why it matches plant phenotyping methods植物表面の三次元形状を測定するオープンな構造化光プラットフォームと再構成・解析ワークフローを開発し、葉で投影バイアスを評価しており、表現型取得手法が中心である。
abstractHere we present the Gentschinator3000 , an open structured-light platform that brings high-end metric surface measurement within reach of laboratories with no optics expertise, combining documented open hardware, open reconstruction software and analysis workflows for under 4000 Euro in components.
Reproduction assets foundThe paper explicitly deposits three public Zenodo records: reconstructed 3D surfaces of all specimens (including the leaf and hop cone phenotyping measurements), the authors' analysis notebooks with derived and per-panel source data, and the reconstruction software with build documentation and working examples. All areDataset · publicData availability
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hereOpen asset ↗Zenodo · 10.5281/zenodo.22167598pdf-raw-page:35 lines:1-52Plant phenotyping relevance match · UnverifiedCrossref · checked 15 Sept 2026
Published31 Aug 2026International Scientific Journal of Engineering and ManagementCited by 0 · OpenAlex ↗
Abstract - Plant diseases can significantly affect plant growth, productivity, and overall health. This research presents a mobile-based plant analysis system designed to identify plants, assess their health condition, and analyze visible diseases from plant images. The proposed system allows users to capture an image using a mobile camera or upload an existing image. The image is processed and analyzed using machine learning and deep learning techniques. A Convolutional Neural Network (CNN) can be used to learn visual features such as leaf shape, color, spots, and disease symptoms for plant identification and disease analysis. The system also provides a health assessment and disease severity indication to support users in understanding the condition of a plant. A Flutter-based mobile application provides the user interface, while Python and Flask can be used for image-processing and model-serving tasks. The proposed approach aims to provide a simple and accessible tool for preliminary plant identification, health assessment, and disease analysis. Key Words: plant identification, plant health assessment, disease analysis, CNN, deep learning, Flutter.
Why it matches plant phenotyping methods植物画像から健康状態と病害症状・重症度を推定する機械学習システムの開発が中心であり、植物の病害状態という表現型を画像から取得・評価する方法を扱っている。
abstractThis research presents a mobile-based plant analysis system designed to identify plants, assess their health condition, and analyze visible diseases from plant images.
Plant phenotyping relevance match · UnverifiedOpenAlex · Europe PMC · Crossref · bioRxiv · checked 5 Sept 2026
Abstract Non-invasive, high-throughput phenotyping tools are needed that can identify environmental effects on plant structure and function to diagnose factors responsible for reduced growth in commercial and non-commercial settings. In this study, we explored whether the integration of 3D-multispectral (3D) and 2D-hyperspectral imaging (HSI), aided by machine learning (ML), could be used to identify environmental stress treatments imposed during plant growth. Controlled environment-grown Nicotiana Benthamiana plants were subjected to a range of abiotic treatments – including different growth irradiances, heat treatment and drought stress – with the treatments resulting in differences in shoot height, biomass, leaf area and spectral reflectance. ML models were trained to identify these treatments using morphological and spectral traits measured at 27, 29, 31, and 34 days after sowing (DAS). A 3D-multispectral scanner was used to obtain information on plant height, biomass, and leaf area. A visible and near-infrared (VNIR) HSI camera provided detailed spectral information for deriving spectral indices including the Normalised Difference Vegetation Index (NDVI), Photochemical Reflectance Index (PRI) and Normalized Difference Red Edge (NDRE). Manual measurements provided baseline comparative data. The 3D-multispectral scanner reliably estimated above-ground traits, with high correlations between manual and scanner-derived measurements. The ML models accurately differentiated among environmental stress treatments, with the fused 3D+HSI model achieving the best overall predictive performance across all evaluated metrics compared with models based on either imaging modality alone. Results demonstrated the effectiveness of combining 3D-multispectral and 2D-HSI data with ML analyses for non-destructive, high-throughput phenotyping. The integration of these techniques enabled non-destructive, high-throughput identification of environmental stress treatments imposed during plant growth.
Why it matches plant phenotyping methods3Dマルチスペクトル画像・ハイパースペクトル画像と機械学習を統合し、植物形態・スペクトル形質を非破壊かつ高スループットに取得・検証する方法が研究の中心である。
abstractNon-invasive, high-throughput phenotyping tools are needed that can identify environmental effects on plant structure and function
Introduction Leaf shape is a genetically determined crop phenotype, and its accurate classification underpins soybean germplasm assessment and genetic improvement. Manual classification is highly subjective and struggles to distinguish morphologically similar leaves, while mainstream supervised classification demands large labeled datasets and incurs high development costs. Efficient feature frameworks for soybean leaf categorization are still insufficient. Methods In this study, 581 biologically replicated terminal leaflets sampled from 194 soybean varieties were analyzed at the single-leaflet level using traditional morphological indices and novel leaf contour angular features. Unsupervised K-means clustering was used to classify soybean leaflet morphological phenotypes; t-SNE was applied exclusively for dimensional reduction visualization, while Welch's ANOVA combined with Games-Howell post-hoc tests was adopted to detect inter-cluster phenotypic differences. Clustering stability and external consistency against manual visual labeling were further quantified via Adjusted Rand Index to comprehensively verify the reliability of grouping outputs. Results The results revealed no significant difference in leaflet edge complexity (p = 0.41) between two manually divided leaf groups distinguished by overall leaf outline similarity; these two morphologically similar leaf clusters failed to be fully separated even though the first two principal components accounted for 90.2% of total variance. For K-means clustering, k = 3 achieved better overall performance with a Calinski–Harabasz (CH) index of 395.55, Davies–Bouldin (DB) index of 1.03, and silhouette coefficient (SC) of 0.38, compared with k = 4. Nevertheless, the angular feature attained an F-value of 951.62 in driving sample reallocation across clusters, serving as the core indicator for fine subdivision at k = 4. Under k = 4 clustering, all six morphological indices differed significantly among the four groups (p < 0.05). Additionally, the number of cross-clustered samples increased from 66 to 119 as k rose from 3 to 4, with 96.6% of cross-clustering attributed to the leaflet contour angular feature. Discussion This research provides a novel reference and technical support for the automated identification and fine classification of soybean leaf morphology.
Why it matches plant phenotyping methods大豆小葉の形態表現型を角度特徴量とクラスタリングで自動分類する手法が研究の中心であり、検証指標も明示されているため。
abstractLeaf shape is a genetically determined crop phenotype, and its accurate classification underpins soybean germplasm assessment and genetic improvement.
ABSTRACT Leaf shape is a fundamental trait of plant ecological strategies, influencing biotic interactions and ecosystem functioning. However, established quantitative metrics fail to capture subtle variations and irregularities, require user-based reference points or are challenging to compare among taxa with broadly different leaf shapes. In addition, established metrics typically conflate (aggregate) leaf edge complexity and macro-shape complexity, despite their independent functional significance and genetic foundations. Here, we introduce an entropy-based framework to quantify two new complexity metrics: edge complexity and macro-shape complexity. Based on three case studies, we show that these metrics outperform aggregate metrics in predicting Quercus robur chemical traits, provide more intuitive interspecific classifications, and strongly align with human perception. In addition, edge and macro-shape complexity show high complementarity, while aggregate metrics are highly redundant and typically strongly related to leaf area. Emerging as the strongest predictor of leaf chemistry and key visual cue for complexity as perceived by humans, the effects of edge complexity highlight the under-appreciated functional significance of leaf margins. Our framework and the proposed entropy-based complexity metrics thus promise to help unlock the potential of growing digital image archives of leaves, including images from herbaria and fossils, and are technically readily applicable to shapes of algae, bacteria, pollen, and beyond. The accompanying package ShapeComplexity enables the broad application of entropy-based metrics, providing a powerful tool to explore how the shape of organisms and biological structures influences ecological strategies, biotic interactions, and ecosystem functioning while tracking spatial and temporal variation.
Why it matches plant phenotyping methods葉の画像からエッジ複雑性とマクロ形状複雑性を定量化する新規指標とソフトウェアを開発しており、植物形質抽出法が研究の中心である。
abstractHere, we introduce an entropy-based framework to quantify two new complexity metrics: edge complexity and macro-shape complexity.
Reproduction assets foundThe paper's authors publicly release their ShapeComplexity analysis code (Rust) on GitHub, used to compute the paper's leaf edge- and macro-shape complexity metrics. Supplementary data/analysis code are on Dryad, but that URL is not in the allowed list. RMBG is a generic third-party background-removal model, not a phenCode · publicThe complete, open-source Rust-code (The Rust Team, 2025 ) is publicly available on GitHub ( https://github.com/Thornbach/ShapeComplexity ), ensuring transparency and reproducibilityOpen asset ↗Thornbach/ShapeComplexitylines:86-94Plant phenotyping relevance match · UnverifiedOpenAlex · checked 14 Sept 2026
Accurate estimation of the cotton seedling Leaf Area Index (LAI) is essential for yield prediction and precision crop management. Traditional manual methods are limited by low throughput, while two-dimensional remote sensing techniques often struggle with sparse canopy cover and soil background interference. Although three-dimensional LiDAR presents a promising alternative, existing deep learning approaches typically depend on costly fully supervised point-wise annotations. To address this challenge, this study proposes an end-to-end framework that integrates UAV-based LiDAR, weakly supervised segmentation, and physical parameter inversion. A weakly supervised network, termed CogNet, was developed—incorporating self-distillation and structure-aware label propagation—to achieve precise segmentation of cotton plants using only 10% sparse annotations. Following instance segmentation via Density-Based Spatial Clustering of Applications with Noise (DBSCAN), individual plant phenotypic traits were extracted. A nonlinear Extreme Gradient Boosting (XGBoost) model was then constructed to invert LAI by leveraging allometric relationships between 3D structural parameters and leaf area. Experimental results showed that CogNet achieved an Intersection over Union (IoU) of 85.34%, effectively mitigating overfitting to label noise and achieving performance competitive with the fully supervised RandLA-Net (82.13%). Notably, under the specific conditions of this cotton seedling dataset characterized by strong geometric priors, the weakly supervised model demonstrated enhanced robustness against annotation inconsistencies. The framework attained a plant detection rate of 96.2%, and the XGBoost model delivered high estimation accuracy (R² = 0.879, RMSE = 0.138). This study demonstrates that weakly supervised learning can substantially reduce annotation costs while maintaining model performance, providing an efficient and cost-effective solution for field-scale crop phenotyping.
Why it matches plant phenotyping methodsUAV-LiDAR、弱教師ありセグメンテーション、個体形質抽出、LAI推定を統合した作物フェノタイピング手法の開発・評価が研究の中心である。
abstractthis study proposes an end-to-end framework that integrates UAV-based LiDAR, weakly supervised segmentation, and physical parameter inversion.
Accurate quantification of plant disease severity is essential for evaluating host-pathogen interactions and assessing the effectiveness of disease management strategies. Traditional visual scoring methods and manual estimation of infected tissue are widely used but are often subjective and prone to observer bias. Digital image analysis offers an objective alternative by enabling automated identification and quantification of symptomatic plant tissues based on color and spatial characteristics. Here, we present a MATLAB-based image processing protocol for differentiating diseased and healthy plant tissue from digital leaf images. The workflow involves acquisition of standardized leaf images, conversion of RGB images into hue-saturation-value (HSV) color space, segmentation of diseased tissue using defined HSV thresholds, refinement of the segmented mask through morphological operations, and extraction of the whole leaf area. The protocol then calculates the diseased area and total leaf area in pixels and computes the percentage of infected tissue. The method uses MATLAB together with the Image Processing Toolbox and can be implemented using simple scripts. This protocol enables rapid and reproducible quantification of disease severity in plant leaves exhibiting visually distinct symptoms such as necrotic lesions or blight patches. By minimizing observer bias and providing quantitative measurements of infected area, the protocol offers a practical and reproducible approach for plant disease phenotyping and evaluation of disease management strategies across diverse plant-pathogen systems where diseased tissues can be clearly distinguished from healthy tissues under reasonably controlled imaging conditions. Key features • A reproducible MATLAB-based workflow for separating diseased and healthy plant tissue using color-space segmentation. • Applicable to plant diseases where symptomatic tissue contrasts clearly with healthy tissue (necrosis, blight lesions, rot patches). • Requires digital leaf images, MATLAB, and the MATLAB Image Processing Toolbox for image processing and disease quantification. • Enables rapid calculation of diseased leaf area and disease severity using automated pixel-based quantification.
Why it matches plant phenotyping methods植物病斑を画像から分割・定量し、感染面積と病害重症度を算出するMATLAB画像解析プロトコルが研究の中心であり、植物病害表現型の取得・抽出手法に該当する。
abstractHere, we present a MATLAB-based image processing protocol for differentiating diseased and healthy plant tissue from digital leaf images.
Reproduction assets foundThe protocol explicitly deposits its authors' MATLAB image-processing workflow (HSV segmentation, mask refinement, pixel-based disease quantification) in a public GitHub repository with README instructions and example images.Code · publicGitHub repository containing the MATLAB source code, README file with installation and execution instructions, and representative example image(s): https://github.com/pankajborahmajuli-source/Leaf-Disease-Detection-MATLAB-Code/blob/main/README.mdOpen asset ↗Leaf-Disease-Detection-MATLAB-Codehtml-lines:112-148Plant phenotyping relevance match · UnverifiedCrossref · checked 11 Sept 2026
Field / plotLiDAR / point cloudMultispectral / hyperspectralLeafMorphology / geometry measurementLeaf traits
Canopy Leaf Area Index (CLAI) is a stand attribute containing information on the real-time health and growth potential of managed pine plantations. Current remote sensing techniques for quantifying CLAI rely on simple linear models applied to satellite multispectral imagery, or on techniques based on light detection and ranging (LiDAR) data that are costly and less frequently collected. This study demonstrates a convolutional neural network (CNN) approach to retrieving CLAI from 10 m Sentinel-2 multispectral imagery with a model trained on gridded LiDAR-based CLAI estimates. We demonstrate large gains in accuracy with the CNN compared to traditional linear models based on vegetation indices (e.g., Simple Ratio), but also clear shortfalls in model skill when predicting “blind” in some spatial domains that were completely excluded during model training. Pixel-scale root mean squared error ranged from 0.34 to 0.64 by domain when exposed to CLAI training data from all available spatial domains, but rose to 0.58–1.74 when predicting without prior domain-specific training. Prediction accuracy was consistently lower when applied to completely unobserved USGS LiDAR-based CLAI estimates. Traditional linear models, in contrast, had the advantage of usually lower prediction error across unobserved spatial domains (0.43–1.98), but with lower maximum accuracy. These results demonstrate a potential route for deploying more complex models for LiDAR “mimicry”, e.g., between data acquisitions widely separated in time, but advocate for the development and use of more stable generalized approaches for use in unobserved managed pine stands.
Why it matches plant phenotyping methodsLiDARで得た林分の葉面積指数をSentinel-2画像とCNNから推定する手法を開発・比較検証しており、植物キャノピー形質の取得が研究の中心です。
abstractThis study demonstrates a convolutional neural network (CNN) approach to retrieving CLAI from 10 m Sentinel-2 multispectral imagery with a model trained on gridded LiDAR-based CLAI estimates.
Abstract Understanding the allometric relationships between leaf area and other plant traits is essential for non-destructive growth monitoring and efficient crop management. However, no comprehensive study has yet modeled leaf area in quinoa ( Chenopodium quinoa Willd.) using simple morphological traits across different sowing dates. This study aimed to quantify allometric relationships between leaf area and plant height, leaf dry weight, stem dry weight, panicle dry weight, and total dry matter, and to evaluate whether these relationships are modified by sowing date. A two-year field experiment was conducted with 12 sowing dates under a randomized complete block design with three replications. Leaf area index (LAI) dynamics were described using a logistic model, and allometric relationships were fitted using power-law equations. The results showed that LAI followed a logistic trend across all sowing dates, with maximum values ranging from 2.7 to 7.9. Plant height provided the most reliable prediction of leaf area (R² = 0.83, b = 1.2), followed by leaf dry weight (R² = 0.72, b = 0.97). The allometric coefficients for stem dry weight (b = 1.54, R² = 0.74) and panicle dry weight (b = 1.95, R² = 0.71) showed greater variability. A striking finding was the exceptionally high allometric coefficient (b = 4.95) recorded on May 6 of the second year, indicating a pronounced shift in resource allocation toward leaf area expansion. Total dry matter was a weak predictor (R² = 0.54), likely due to leaf fall during the growing season. The hypothesis that sowing date modifies allometric relationships was confirmed, as evidenced by considerable variation in allometric coefficients across sowing dates. This study provides, for the first time, a comprehensive set of allometric models for quinoa across multiple sowing dates. Plant height and leaf dry weight are recommended as simple, rapid, and non-destructive indicators for leaf area estimation, facilitating improved crop monitoring and management under diverse environmental conditions.
Why it matches plant phenotyping methods草丈や乾物重から葉面積を非破壊推定するアロメトリックモデルを中心に開発・評価しており、植物形質の取得手法が実質的な主題である。
abstractThis study aimed to quantify allometric relationships between leaf area and plant height, leaf dry weight, stem dry weight, panicle dry weight, and total dry matter, and to evaluate whether these relationships are modified by sowing date.
Abstract Purpose Long-term monitoring of crop biophysical and biochemical traits remains challenging in high-latitude regions due to short growing seasons, frequent cloud cover, and highly variable weather. In this context, unmanned aerial vehicles (UAVs) offer flexible, high-resolution observations, but their added value relative to low-cost proximal sensors and their effectiveness for radiative transfer model (RTM) inversion across diverse crop canopies remain insufficiently quantified. This study evaluated the potential of a two-band proximal spectral reflectance sensor (SRS) and a five-band multispectral UAV sensor for retrieving leaf area index (LAI), leaf chlorophyll content (LCC), and canopy chlorophyll content (CCC) using PROSAIL inversion across major crops in Northern Europe over two growing seasons (2023–2024). Methods and Results Two inversion approaches – look-up table (LUT) and artificial neural network (ANN) were applied to PROSAIL simulations. UAV–PROSAIL–ANN outperformed LUT-based inversion and SRS observations, achieving the highest accuracy for LAI (R 2 = 0.81–0.95; RMSE = 0.27–0.77 m 2 /m 2 ), followed by CCC (R 2 = 0.58–0.94; RMSE 2 ), while LCC remained less accurately estimated (R 2 = 0.26–0.78; RMSE 2 ). Across sensors and methods, retrieval accuracy decreased in the order of LAI, CCC, and LCC, reflecting the stronger spectral control of canopy structure compared to biochemical traits. Conclusions The UAV–PROSAIL–ANN framework effectively captured spatial and temporal variability in crop traits, producing canopy-scale maps consistent with field observations. These results demonstrate the robustness and scalability of hybrid PROSAIL–ANN inversion for high-latitude crop monitoring, while highlighting current limitations in biochemical trait retrieval using multispectral data.
Why it matches plant phenotyping methodsUAV・近接分光センサーとPROSAIL反転、ANNを用いてLAIや葉・群落クロロフィルを推定し、精度比較と圃場観測との整合性評価を行うことが研究の中心である。
abstractThis study evaluated the potential of a two-band proximal spectral reflectance sensor (SRS) and a five-band multispectral UAV sensor for retrieving leaf area index (LAI), leaf chlorophyll content (LCC), and canopy chlorophyll content (CCC) using PROSAIL inversion across major crops in Northern Europe over two growing seasons (2023–2024).
Reproduction assets foundThe paper's Data availability statement explicitly deposits the authors' UAV image processing code (irradiance normalization, vignetting, exposure compensation, radiometric calibration) in a public GitHub repository under GPL v3.0; other data are available only upon request.Code · publicData availability Code to perform irradiance normalization, vignetting, exposure compensation, and radio-
metric calibration is available at https://github.com/fieldSITES/scripts/tree/main/UAV under GNU General
Public License v3.0. Other data will be made available upon request.Open asset ↗UAVpdf-page:34 lines:1-40Plant phenotyping relevance match · UnverifiedCrossref · checked 14 Sept 2026
Published12 Aug 2026International Journal of Computer Information Systems and Industrial Management ApplicationsCited by 0 · OpenAlex ↗
Automated plant identification based on leaf morphology has gained significant attention in recent years due to its wide range of applications in precision agriculture, biodiversity conservation, environmental monitoring, and botanical informatics. Advances in digital image processing and machine learning have enabled the development of intelligent systems capable of identifying plant species from leaf characteristics with minimal human intervention. Despite these advancements, achieving reliable and accurate classification remains challenging because leaf images are often affected by variations in illumination, complex backgrounds, image noise, differences in orientation and scale, as well as natural leaf deformation. These factors can obscure important morphological features, reduce the effectiveness of feature extraction, and ultimately decrease the accuracy and robustness of automated plant classification systems. Consequently, there is a growing need for intelligent frameworks that can effectively handle these challenges while preserving critical leaf morphology and venation information for reliable plant identification. This study proposes an Intelligent Morphology-Driven Framework that integrates advanced digital image processing and machine learning for robust leaf venation analysis and plant classification. The proposed framework integrates multiple digital image processing and machine learning techniques to enable accurate and automated leaf venation analysis and plant classification. Initially, leaf images undergo preprocessing using grayscale conversion, histogram equalization, Contrast Limited Adaptive Histogram Equalization (CLAHE), Gaussian filtering, Laplacian sharpening, Gabor filtering, and homomorphic filtering to improve image quality and enhance venation and structural details. The enhanced images are then processed through threshold-based segmentation followed by morphological operations, including erosion, dilation, opening, closing, convex hull generation, and skeletonization, to accurately isolate leaf regions while preserving their geometric structure.To characterize leaf morphology, the framework extracts a comprehensive set of features, including geometric descriptors such as area, perimeter, circularity, aspect ratio, solidity, eccentricity, and vein density, together with Hu invariant moments that provide rotation-, translation-, and scale-invariant shape representation. In addition, the framework investigates the influence of image compression by comparing lossless PNG and lossy JPEG formats to evaluate their impact on preserving morphological features and venation details. The extracted feature vectors are subsequently classified using a Random Forest classifier to categorize leaf venation patterns into parallel, reticulate-pinnate, and reticulate-palmate classes.Experimental evaluation demonstrates that the proposed framework achieves an overall classification accuracy of 93.2%, while effectively preserving important morphological characteristics and maintaining computational efficiency. The combination of adaptive image enhancement, morphology-preserving segmentation, comprehensive feature extraction, and robust machine learning classification makes the proposed approach reliable, interpretable, and scalable. Consequently, the framework has significant potential for applications in digital herbarium systems, automated plant identification, biodiversity monitoring, botanical informatics, and precision agriculture.
Why it matches plant phenotyping methods葉画像から形態・葉脈形質を抽出し分類する画像処理・機械学習フレームワーク自体が研究の中心であり、植物表現型の取得・解析手法として適格。
abstractThis study proposes an Intelligent Morphology-Driven Framework that integrates advanced digital image processing and machine learning for robust leaf venation analysis and plant classification.
Accurate retrieval of crop structural and physiological traits from remote sensing data remains challenging due to limited field observations and poor cross-platform generalization of data-driven models. This study develops a physics-informed transfer learning framework to quantify the contributions of improving simulated data fidelity and increasing model complexity to retrieving winter wheat leaf area index (LAI) and canopy chlorophyll content (CCC) from hyperspectral observations. Two PROSAIL-D datasets with default and physically optimized leaf angle distributions were generated to represent different levels of simulation fidelity. Four dual-branch deep learning architectures (CNN, CNN–SE, CNN–Transformer, and CNN–SE–Transformer) integrating spectral bands and vegetation indices were pretrained on simulated datasets and transferred to real observations using progressive fine-tuning. Model performance was assessed using ground-based and unmanned aerial vehicle (UAV) hyperspectral datasets, and SHapley Additive exPlanations (SHAP) analysis was applied to interpret feature contributions. Results demonstrated that transfer learning substantially improved cross-domain generalization, while enhancing simulation fidelity provided greater performance gains than increasing network complexity. The CNN–Transformer model pretrained on physically optimized simulations achieved the highest accuracy and robustness for both LAI and CCC retrieval. At ground and UAV scales, it achieved LAI estimation accuracies of R2 = 0.55 (RMSE = 0.63) and R2 = 0.53 (RMSE = 0.62), respectively. For CCC estimation, the model obtained R2 = 0.59 at both scales, with RMSE values of 36.12 μg cm⁻2 and 37.56 μg cm⁻2 for ground and UAV observations, respectively. SHAP analysis indicated that physically optimized simulations shifted model attention toward physiologically relevant vegetation indices, whereas default simulations induced stronger dependence on unstable visible wavelengths. Physically informed simulation design combined with transfer learning effectively reduces simulation to reality discrepancies, whereas increasing deep model complexity alone provides limited improvement. The proposed framework offers an accurate, interpretable, and scalable solution for cross-platform crop trait retrieval from hyperspectral observations.
Why it matches plant phenotyping methodsハイパースペクトル観測から冬コムギのLAIと群落クロロフィル含量を推定する物理情報付き転移学習フレームワークを開発し、地上およびUAVデータで性能評価しており、植物形質取得・推定手法が中心である。
abstractThis study develops a physics-informed transfer learning framework to quantify the contributions of improving simulated data fidelity and increasing model complexity to retrieving winter wheat leaf area index (LAI) and canopy chlorophyll content (CCC) from hyperspectral observations.
TomatoLiDAR / point cloudLeafMorphology / geometry measurementSegmentationLeaf traits
Leaf parameters are crucial indicators reflecting the growing status of plants. Monitoring and analysis of leaf parameters significantly contributes to the improvement of crop yield and food quality. This study focused on three tomato plant varieties commonly grown in the Netherlands and proposed a fully automatic pipeline for leaf phenotyping. Three-dimensional (3D) point clouds of target plants were acquired with a specially designed imaging unit naming Maxi-Marvin. A semantic segmentation of plant organs was performed with PointNet++ model. To mitigate point cloud resolution decrement, the down-sampling operation in the baseline model was replaced with a distributed segmentation strategy. Leaf instances were further identified with Density-Based Spatial Clustering of Applications with Noise (DBSCAN), followed by a morphological phenotypic trait quantification based on 3D geometrical analysis. Target phenotypic traits including leaf length, leaf width, and leaf area. The evaluation results indicated that the distributed segmentation strategy achieved the best F 1 scores of 0.98 with block size set to 30,000. The Mean Average Errors (MAE) of leaf length, leaf width, and leaf area estimation were 2.09 cm, 1.78 cm and 8.98 cm 2 respectively. The estimation accuracies for leaf length, leaf width, and leaf area were 91.98%, 92.66%, and 89.67%, respectively.
Why it matches plant phenotyping methodsトマト葉の3D画像取得、器官セグメンテーション、葉インスタンス識別、形態形質推定を統合した自動フェノタイピング手法を開発・評価しており、方法が研究の中心です。
abstractproposed a fully automatic pipeline for leaf phenotyping
Reproduction assets foundThe paper's tomato point cloud dataset (with semantic and leaf instance annotations used for the phenotyping pipeline) is publicly available on Kaggle via a footnote. NPEC website is a facility page, and Open3D is a generic library, so neither qualifies.Dataset · public2. ^ The dataset used in this study is available at: https://www.kaggle.com/datasets/xinbolai/vtc-tomatoOpen asset ↗Kaggle · xinbolai/vtc-tomatolines:545-624Plant phenotyping relevance match · UnverifiedOpenAlex · Europe PMC · bioRxiv · checked 5 Sept 2026
Abstract Background Leaves maintain hydraulic homeostasis during photosynthesis through the coordinated action of stomata, which regulate gas exchange and transpiration, and veins, which supply water to the leaf lamina. While functional links between stomatal and vascular traits are known in dicots, their potential genetic coordination in C4 crops remains poorly understood. We investigated the genetic architecture of these traits in maize using a Multi-parent Advanced Generation Inter-Cross (MAGIC) population and a low-cost, high-throughput phenotyping platform integrating leaf clearing, digital microscopy, artificial intelligence, and image analysis Results We phenotyped 285 recombinant inbred lines and the MAGIC founder lines, generating 8,072 images from 2,026 leaf samples taken from seedlings grown in controlled conditions. A YOLOv8-based model automatically detected stomata, while a custom and efficient image-processing pipeline quantified vein traits and stomatal spatial distribution patterns along cell bundles. This enabled simultaneous characterization of stomatal density, size, and distribution together with vein density, thickness, and bundle-associated spatial patterning. Substantial phenotypic variation was observed among genotypes, with strong correlations between abaxial and adaxial traits but no significant correlations between stomatal and vein traits. QTL mapping identified 37 genomic regions associated with stomatal and vein traits, including loci containing known developmental regulators such as stomatal density and distribution1 and stomagen1 , as well as novel loci controlling stomatal spatial patterns, divergence between leaf surfaces and veins traits. Conclusions These results support independent genetic control of stomata and veins and decoupled contribution to water-use efficiency, providing a novel genetic framework to independently optimize leaf hydraulic capacity and gas exchange in target environments.
Why it matches plant phenotyping methods葉の気孔・葉脈形質を自動画像解析で同時定量する高スループット表現型解析プラットフォームが研究の中心であり、形質抽出手法も具体的に記述されている。
abstractusing a Multi-parent Advanced Generation Inter-Cross (MAGIC) population and a low-cost, high-throughput phenotyping platform integrating leaf clearing, digital microscopy, artificial intelligence, and image analysis
Reliable traits are needed for identification of tea ( Camellia sinensis ) cultivars, yet the stability of leaf morphology and color across leaf positions remains unclear. This study evaluated inter-cultivar variation and positional stability in leaf morphological, RGB color, and SPAD traits in six predominant cultivars. One-year-old shoots were sampled in a completely randomized design, and five fully expanded leaves below the apical bud were analyzed. SPAD values were measured with a chlorophyll meter, and scanned images were used to extract contour and RGB traits. Data were analyzed using ANOVA, correlation analysis, PCA, and discriminant analysis. Leaf morphology differed among cultivars and leaf positions, with significant cultivar-by-position interactions; however, the width-to-length ratio differed among cultivars but remained stable across positions in these cultivars. SPAD values increased with leaf position and were strongly associated with RGB components, being negatively correlated with R and G and positively correlated with B. Morphological traits explained 52.988% of total variance in PCA and yielded 64.6% overall classification accuracy, with LaoHan showing the highest accuracy (83.3%). Misclassification was concentrated among genetically similar cultivars. These findings suggest that stable leaf shape proportions and SPAD-RGB relationships provide useful descriptors, whereas genetic relatedness limits morphology-based cultivar identification under the present conditions.
Why it matches plant phenotyping methods茶品種識別のため、葉の形態・RGB・SPAD特性の取得と安定性、分類性能を中心に評価しており、画像由来形質抽出を含む実質的な表現型解析である。
abstractscanned images were used to extract contour and RGB traits
Reproduction assets found保存済みの本文根拠を更新済みルールで再検証し、公開資産1件を確認しました。Dataset · publicThe following supporting information can be downloaded at https://www.mdpi.com/article/10.3390/biology15151283/s1 , Table S1: Original data of leaf morphological traits, RGB values, and SPAD values from six tea cultivars in this study.Open asset ↗lines:368-409Plant phenotyping relevance match · UnverifiedCrossref · OpenAlex · checked 15 Sept 2026
Annotation scarcity, poor model generalization and lagged data processing remain key bottlenecks hindering the practical deployment of phenotyping robots. To address these issues, we developed a novel phenotyping robot capable of online 3D reconstruction and zero-shot segmentation directly on the edge. Diverging from conventional semantic SLAM, our core contribution is RT-ZSDR, a framework featuring two key methodological novelties. First, we introduce the ForeCut pipeline for target extraction, which innovatively fuses DINO features with 3D geometric spatial information, leveraging multi-view semantic-spatial consistency to achieve annotation-free, zero-shot dense segmentation and reconstruction. Second, we designed a hardware-coupled loop closure strategy utilizing the robotic arm's kinematic feedback as prior constraints to significantly improve loop closure recall. Supported by edge computing Jetson Orin NX, the tracking and segmentation process takes approximately 0.24 s per frame after an initialization period of 1.82 s. RT-ZSDR's phenotypic measurements demonstrated strong correlations with reference baseline in both laboratory settings (n=90, PlantEye measurements as reference baseline; R 2 =0.990, 0.939, 0.725, and 0.861 for plant height, projected leaf area, surface area, and volume) and practical greenhouse environments (n=48, manual measurements as reference baseline; R 2 =0.965, 0.862 for plant height and stem diameter). Additionally, evaluated against COLMAP benchmarks (n=24), the system achieved a mean 3D reconstruction F1-score of 0.816.
Why it matches plant phenotyping methods植物フェノタイピングロボット向けに、ゼロショット分割・3D再構成・エッジ処理を開発し、植物形質を基準測定およびベンチマークと比較検証しており、取得・抽出手法が研究の中心である。
abstractwe developed a novel phenotyping robot capable of online 3D reconstruction and zero-shot segmentation directly on the edge.
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
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.
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.
The ready-to-eat lettuce industry is rapidly expanding, increasing the need for reliable, scalable methods to assess seed germination and early growth under realistic soil conditions. This study presents an automated imaging-based approach for quantifying germination dynamics and seedling vigor using a low-cost multi-camera system under greenhouse conditions. Lettuce seeds were grown in soil either inoculated or non-inoculated with the soil-borne pathogen Rhizoctonia solani. Top-view images were acquired using commercial surveillance cameras and processed through a calibrated pipeline including geometric correction, color normalization, vegetation segmentation, clustering, and temporal tracking of emergence events. Seedling vigor was quantified through projected leaf area estimation. The proposed method enables accurate estimation of germination kinetics and growth dynamics under field-like conditions. Automated counts were validated against manual measurements at both intermediate and final time points, achieving high agreement in both cases. At the final assessment, the method reached R² = 0.98 and RMSE = 1.12, while at the midterm evaluation it achieved improved performance with R² = 0.998 and RMSE = 0.5, reflecting the lower complexity of plant structure at earlier growth stages. Results showed that pathogen inoculation significantly reduced both germination rate and seedling vigor, with up to 70% reduction in biomass accumulation. The proposed framework provides a robust, low-cost solution for high-throughput phenotyping of early plant development in soil-based systems, supporting scalable agricultural experimentation.
Why it matches plant phenotyping methods低コスト多カメラ画像システムと画像解析パイプラインを開発・検証し、発芽動態と幼植物活力を定量化しているため、植物フェノタイピング手法が中心です。
abstractThis study presents an automated imaging-based approach for quantifying germination dynamics and seedling vigor using a low-cost multi-camera system under greenhouse conditions.
Plants encounter multiple abiotic stresses. Among them, heat and drought stress play a substantial role in reducing the agricultural productivity of commercial plants. Hence, wild and underutilized plants can be a potential alternative as they are naturally tolerant to extreme climatic conditions and are a rich source of nutrition. Manual stress and disease detection is a laborious and expensive process, and hence automation in this field is required to reduce agricultural losses. This study evaluates the prediction and detection of abiotic stress in Acacia senegal bipinnate leaves, exploring various stress-induced changes using machine learning (ML) algorithms and biochemical analysis. A. senegal , an underutilized edible desert legume, was grown under controlled greenhouse conditions. After 2 months, these plants were segregated into groups and subjected to heat and drought treatments. Image acquisition was performed to obtain a dataset of 3,454 images of A. senegal leaves. Physiological parameters, such as fresh and dry leaf weight, shoot length, number of leaves, and biochemical assays like antioxidant assay (DPPH), total phenolic content (TPC), and total flavonoid content (TFC), were determined. LC-MS/MS analysis was conducted to identify over 50 phytochemical compounds. A hybrid model was developed consisting of a fine-tuned EfficientNet-based Convolutional Neural Network (CNN) followed by a Support Vector Machine (SVM) for the binary classification of A. senegal leaves. The model distinguishes between healthy and stress-affected unhealthy leaves and achieved an accuracy score of 86.6%. This report provides a significant lead toward stress phenotyping and prediction of a bipinnate leaf plant using ML algorithms. The overall study is useful to understand how the stress encountered by arid plants alters the nutritional quality.
Why it matches plant phenotyping methods画像データと機械学習モデルを用いて、アカシア葉の健全・ストレス状態を自動分類する手法を開発・評価しており、植物表現型取得が中心です。
abstractThis study evaluates the prediction and detection of abiotic stress in Acacia senegal bipinnate leaves
Reproduction assets foundThe paper's data availability statement explicitly makes the 3,454-image A. senegal leaf imaging dataset public on Zenodo and the ML implementation source code public on GitHub; both are paper-specific, public, and actionable.Dataset · publicThe plant leaf imaging data used in the work is publicly available at https://doi.org/10.5281/zenodo.16531486.Open asset ↗zenodo · 10.5281/zenodo.16531486html-lines:480-497Code · publicThe source code of the implementation is available at https://github.com/softwareinnovationslabBITS/CDRF_ASenegal_MLImagingOpen asset ↗github · softwareinnovationslabBITS/CDRF_ASenegal_MLImaginghtml-lines:480-497Plant phenotyping relevance match · UnverifiedCrossref · checked 14 Sept 2026
Field / plotLeafWhole plant / canopy / plot / fieldObject detectionPhysiological trait estimationGrowth / time-series analysisLeaf traitsWater status / transpiration
Abstract Understanding the vulnerability of plants to more severe and frequent drought events and developing adaptive management strategies requires robust methods for quantifying long‐term changes in plant water stress (PWS). Most data‐driven explorations of long‐term trends in PWS have focused on alterations in canopy structure (e.g., leaf area index) or canopy structure‐dependent variables (e.g., gross primary productivity and evapotranspiration). This is largely because long‐term trends in canopy structure are relatively easy to detect from satellite observations. However, a focus on structural responses limits our ability to detect physiological stress due to challenges in isolating it from the effects of structural greening. Consequently, this difficulty hampers a comprehensive examination of long‐term PWS in the context of global greening trends. To address this gap, we developed a new process‐based metric for PWS to isolate physiological responses from structural greening, which we then used to detect global PWS trends over the past four decades. Combining site‐level and satellite observations at the half‐degree resolution across the globe, we found that accounting for greening‐related changes substantially alters the sign of long‐term PWS trends inferred from traditional approaches. Specifically, our study reveals a significant increase in PWS that is only detectable when accounting for structural greening trends. When greening trends are not accounted for, global PWS appears to have decreased over time. Overall, our results highlight the need to integrate structural dynamics and greening into PWS detection. Such an integration of observations and land models will improve our understanding of plant‐water‐energy interactions.
Why it matches plant phenotyping methods植物の生理的な水ストレスを定量化する新しいプロセスベース指標を開発し、衛星・地上観測で検証・適用しており、表現型測定法が研究の中心である。
abstractTo address this gap, we developed a new process‐based metric for PWS to isolate physiological responses from structural greening, which we then used to detect global PWS trends over the past four decades.
Above ground crop traits provide an early indication of a plant's capacity to tolerate stress, and are important for breeding programs aimed at improving stress tolerance. In this work, we present a high-throughput methodology to study morphological and physiological traits of individual quinoa plants over time under control, drought, and saline conditions. We used daily sideview imaging of individual plants, followed by segmentation of the panicle, leaf and stem using the deep learning U-Net++ segmentation model. The resulting segmentations were used in regression models to estimate leaf area, fresh and dry biomass, and leaf dry weight. The regression models showed high predictive accuracy. Using these estimates, we could calculate specific leaf area and leaf weight ratio. In addition, radiation use efficiency for above-ground biomass production was calculated, providing an independent physiological check on the consistency of these predictions. Finally, using automated measurements of plant transpiration we were able to determine daily averages of whole plant stomatal conductance. The results show that image-derived morphological traits can be used to accurately estimate biomass-related traits and to derive physiologically meaningful indicators of plant performance over time. This method provides a framework for non-destructive monitoring of quinoa responses to drought and salinity.
Why it matches plant phenotyping methods画像取得、深層学習セグメンテーション、回帰による植物形質推定を中核とする高スループット表現型解析手法であり、ストレス実験での単なるルーチン測定ではない。
abstractwe present a high-throughput methodology to study morphological and physiological traits of individual quinoa plants over time
Premise Accurate species identification is crucial for ecological restoration and can be especially challenging for understudied non-model species. Quercus garryana is the only native oak species in the Pacific Northwest and is an important component of the endangered oak savanna ecosystem. Quercus robur is an imported ornamental species from Europe and has been found to be mistakenly planted as Q. garryana in habitat restoration projects. Methods We measured leaf morphological traits sampled from herbarium collections in their native ranges using the digital morphometric tools MorphoLeaf and Tomato Analyzer. We then used Lasso logistic analysis to generate a predictive model and tested it on leaves from Portland, Oregon. To streamline this species detection process, we developed Garryanalyzer, an ImageJ plug-in that automatically measures leaf traits and outputs species predictions. Results Garryanalyzer demonstrated 95% accuracy in predicting the species identity of herbarium specimens of oaks. Garryanalyzer correctly identified all Q. robur individuals sampled in Portland but showed lower accuracy for Q. garryana . Discussion Many existing morphometric software are not open source, which makes them unable to be customized to specific study systems. Garryanalyzer is built upon the widely used open-source ImageJ platform. This study also demonstrates a viable workflow for developing similar tools for other ecologically important non-model plant species.
Why it matches plant phenotyping methods葉の形態形質を自動測定し、種予測まで行うImageJプラグインとワークフローの開発・評価が中心であり、植物フェノタイピング手法として適格です。
abstractTo streamline this species detection process, we developed Garryanalyzer, an ImageJ plug-in that automatically measures leaf traits and outputs species predictions.
Reproduction assets foundThe paper's authors publicly released the Garryanalyzer ImageJ plug-in source code on GitHub, all original and modified leaf images used in the morphometric analyses on Zenodo, and the full leaf morphometric measurement dataset plus R Lasso analysis code in a second Zenodo repository. All are paper-specific, public,可直接Code · publicThe source code and installation instructions for Garryanalyzer can be accessed on GitHub at https://github.com/zxie8561/Garryanalyzer.Open asset ↗https://github.com/zxie8561/Garryanalyzer · zxie8561/Garryanalyzerhtml-lines:210-274Dataset · publicAll images used in the morphometric analyses, both original and modified, are available on Zenodo (https://doi.org/10.5281/zenodo.17462266).Open asset ↗https://doi.org/10.5281/zenodo.17462266 · 10.5281/zenodo.17462266html-lines:210-274Dataset · publicThe full dataset of leaf morphometric measurements of both GBIF and Portland samples, R code for Lasso analysis, and other miscellaneous files are available on a separate Zenodo repository (https://doi.org/10.5281/zenodo.17546152).Open asset ↗https://doi.org/10.5281/zenodo.17546152 · 10.5281/zenodo.17546152html-lines:210-274Plant phenotyping relevance match · UnverifiedEurope PMC · checked 15 Sept 2026
Seedling establishment represents a critical phase in early crop growth and development, directly influencing biomass accumulation and yield potential. To characterise early growth dynamics under field conditions, both growth rate and uniformity of emergence need to be assessed continuously; however, manual quantification of these dynamic traits in large-scale trials remains impractical. Here, we present LeafTip-RN, an open-source and deep learning (DL)-powered pipeline for dynamically measuring wheat (Triticum aestivum L.) early establishment in the field. To enable flexible and scalable data collection, ultralow-altitude drone phenotyping was employed, followed by the development of an optimised DL model to automate leaf-tip-related feature extraction from complex backgrounds. Notably, to address data sparsity arising from eight phenotyping timepoints, we integrated an image-to-video generative AI (GenAI) module into the pipeline to interpolate keyframes between early and late seedling stages (i.e. 18-40 days after sowing), resulting in a training library comprising 353,019 labelled leaf tips. Using the pipeline, we successfully quantified multiple agronomically important establishment-related traits (e.g. plot-level leaf tips and seedling spatial uniformity), followed by deriving their growth curves for 51 wheat varieties across two growing seasons (2024-2026). After validating these LeafTip-RN-derived traits, we further computed varietal relative growth rates and uniformity indices, based on which the 51 varieties were classified into high-, medium-, and low-performance groups, revealing discrepancies between LeafTip-RN-derived classification (18-40 DAS) and manual assessment at 40 DAS when dynamic early performance was considered. Finally, to facilitate broad adoption by the plant research community, we developed an openly accessible graphical user interface (GUI) for non-expert users to visualise and analyse rapid seedling developmental changes. Taken together, our study provides a scalable GenAI-powered solution for evaluating seedling establishment in wheat, offering valuable tools for breeders and researchers to identify varieties with enhanced early growth vigour and emergence dynamics that are extensible to other cereal crops.
Why it matches plant phenotyping methodsLeafTip-RNは、ドローン画像と深層学習・生成AIによって小麦の葉先や出芽均一性などの形質を自動抽出・連続推定する手法およびGUIを開発し、導出形質を検証しているため、植物フェノタイピング手法が研究の中心である。
abstractHere, we present LeafTip-RN, an open-source and deep learning (DL)-powered pipeline for dynamically measuring wheat (Triticum aestivum L.) early establishment in the field.
Plant phenotyping relevance match · UnverifiedOpenAlex · Europe PMC · bioRxiv · Crossref · checked 5 Sept 2026
Abstract Understanding the link between genetic variation and observable traits is key to crop breeding. Hyperspectral imaging captures physiological and biochemical profiles, but current supervised methods require costly trait annotations and treat each observation as a static snapshot, ignoring the temporal dynamics of plant development. We introduce SST-MAE, a self-supervised framework that learns genotype-discriminative representations from plant hyperspectral developmental trajectories, without requiring phenotypic labels. The model learns to reconstruct masked information, capturing multiple growth trajectories. Validated on 194 field-grown lettuce genotypes across eight time points, the frozen encoder serves as a feature extractor for downstream genotype classification. SST-MAE outperforms raw spectral and linear baselines, achieving AUROC > 0.89 for anthocyanin pigmentation SNPs and 0.77 for leaf serration. The learned features are highly label-efficient, attaining near-full performance with only 30–50% of labeled data, offering a scalable pathway toward high-throughput genetic screening from image-based phenotypes.
Why it matches plant phenotyping methods植物のハイパースペクトル時系列から表現型関連表現を抽出する自己教師あり手法を開発し、複数遺伝子型・時点で検証しているため、表現型取得・解析手法が中心です。
abstractWe introduce SST-MAE, a self-supervised framework that learns genotype-discriminative representations from plant hyperspectral developmental trajectories, without requiring phenotypic labels.
Accurate identification of crop varieties is essential for plant breeding programs and the protection of Plant Breeders' Rights (PBR), yet traditional morphological assessment methods remain subjective and time-consuming, particularly for species with complex morphological diversity such as Rubus crataegifolius . This study demonstrates that geometric morphometric techniques provide an objective, quantitative complementary approach for distinguishing Korean raspberry varieties, addressing the limitations of subjective visual assessment while remaining compatible with molecular marker analysis. We employed three complementary morphometric approaches: landmark-based analysis (19 anatomical points capturing vein junctions and leaf margins), Elliptic Fourier Descriptors (EFD) for outline contours, and a hybrid landmark-EFD dataset. Using these approaches, we analyzed primocane and floricane leaves from 10 accessions of R. crataegifolius comprising 8 varieties and 2 landraces and performed principal component analysis (PCA) and linear discriminant analysis (LDA) with leave-one-out cross-validation. As a result, among the three morphometric approaches applied to primocane and floricane leaves, landmark-based analysis of primocane leaves achieved the highest classification accuracy (87.2%), with an overall average accuracy of 72.0% (range: 51.1-87.2%) across all six analytical combinations. LDA visualization suggested the presence of four major morphological groups, and primocane leaves exhibited higher discriminatory power than floricane leaves, which may reflect greater morphological uniformity under normal growing conditions. Landmark analysis effectively detected subtle differences in leaf venation and leaflet architecture that are difficult to distinguish visually, highlighting the capacity of morphometrics for objective and multidimensional morphological analysis. These findings suggest that morphometric analysis provides a practical and cost-effective preliminary screening tool, complementary to molecular approaches, for supporting Distinctness, Uniformity, and Stability (DUS) examination in raspberry variety evaluation. This approach shows strong potential for offering a scalable solution for variety registration and protection and supporting sustainable horticultural development.
Why it matches plant phenotyping methods葉の形態を幾何学的モルフォメトリクスで定量化し、品種識別とDUS評価に応用した研究で、表現型の取得・解析手法が中心である。
abstractThis study demonstrates that geometric morphometric techniques provide an objective, quantitative complementary approach for distinguishing Korean raspberry varieties
Film mulching can promote maize canopy development by altering soil thermal conditions. However, commonly used air-temperature-based growing degree days (GDDs air ) may not adequately reflect mulch-induced soil warming or the effects of biodegradable film degradation on leaf area index (LAI) dynamics. To improve unified simulation of maize LAI under different film mulching conditions, field experiments were conducted in 2023 and 2024. Five treatments were established: 0.006, 0.008 and 0.010 mm biodegradable films (DM1, DM2 and DM3, respectively), a 0.010 mm conventional plastic film (PM), and a no-mulching control (CK). The compensation of increased soil temperature for air-temperature-based thermal accumulation during early maize growth was quantified. Modified Logistic LAI models were then developed using days after emergence (DAEs), GDDs air , soil-temperature-compensated growing degree days (GDDs stc ), and normalized GDDs stc (NGDDs stc ) as driving variables. The models were calibrated with observations from 2023 and independently validated with observations from 2024. The compensation effect acted through mulch-induced increases in 0-10 cm soil temperature during early maize growth and was stronger at the seedling stage than at the jointing stage. Compared with DM1 and DM2, daily compensation values were higher by 0.25-0.78 °C under DM3 and by 0.26-0.76 °C under PM. Independent validation showed that the GDDs stc -driven model had lower prediction error than the DAEs- and GDDs air -driven models. The NGDDs stc -driven model performed best; its RMSE values were 17.61%, 15.17% and 10.91% lower than those of the DAEs-, GDDs air - and GDDs stc -driven models, respectively. These results indicate that incorporating mulch-induced soil temperature compensation into the thermal time scale can more accurately represent maize canopy development under film mulching conditions.
Why it matches plant phenotyping methodsマルチ処理下のトウモロコシLAIという植物形質を推定するモデルを開発し、別年データで独立検証しており、形質推定手法が中心である。
abstractModified Logistic LAI models were then developed using days after emergence (DAEs), GDDs air , soil-temperature-compensated growing degree days (GDDs stc ), and normalized GDDs stc (NGDDs stc ) as driving variables.
The genetic identity of coffee cultivars is fundamental to the specialty coffee sector, where premium prices are paid under the assumption that the purchased planting material corresponds to the declared variety. However, many producing countries lack the certification infrastructure necessary to guarantee this identity in their informal seed systems, exposing producers to undetected varietal non-conformity. In this study, we examine a case from a specialty coffee ( Coffea arabica L.) farm in southern Ecuador where seeds labeled as Sidra (USD 100/kg) and Gesha (USD 500/kg) were purchased without genetic or phytosanitary certification. Using a combination of SSR-based DNA fingerprinting and quantitative morphological characterization, including plant architecture, leaf functional traits, and fruit characteristics, we documented varietal identity and assessed the discriminant capacity of morphological traits across the four resulting morphotypes. Using eleven microsatellite markers for SSR fingerprinting, we found that two of the four morphotypes did not match their declared commercial identity. One plant sold as Sidra was identified as compatible with Batian, a composite variety of Kenyan origin that is genetically unrelated to Ethiopian landraces. The plants acquired as Gesha corresponded to a pure Ethiopian landrace that is genetically similar to, but not identical to, the Panamanian Geisha reference accession T.02722. Only two morphotypes were confirmed as Sidra. Furthermore, the placement of Sidra within the Core Ethiopia genetic group is consistent with prior population-level analyses and with its likely status as a selected Ethiopian landrace rather than a variety of hybrid origin. Morphological linear discriminant analysis achieved 82.4% overall classification accuracy under leave-one-out cross-validation (LOOCV), with internode length dominating the first discriminant function (LD1 = 66.6%). These results demonstrate that varietal nonconformity in the specialty coffee seed sector can extend to the inadvertent introduction of genetically unrelated material and underscore the urgent need for accessible seed certification.
Why it matches plant phenotyping methodsコーヒー品種識別のための形態形質測定と判別分析が研究の中心であり、形態形質の識別性能をLOOCVで検証しているため、植物フェノタイピング手法の適用・検証に該当する。
abstractquantitative morphological characterization, including plant architecture, leaf functional traits, and fruit characteristics
Reproduction assets foundThe paper's morphological/functional trait dataset (used for the phenotyping and LDA analysis) is explicitly stated to be publicly available on Figshare (10.6084/m9.figshare.32841344). No author analysis code repository is stated; other URLs in the text are generic libraries or cited prior work.Dataset · publicThe morphological and functional trait dataset generated and analyzed in this study is publicly available in the Figshare repository at 10.6084/m9.figshare.32841344 .Open asset ↗Figshare · 10.6084/m9.figshare.32841344lines:526-568Plant phenotyping relevance match · UnverifiedCrossref · checked 14 Sept 2026
ABSTRACT The common bean is vital for food security, but its productivity is often limited by competition with weeds, requiring the use of herbicides. The response of genotypes to herbicides such as fomesafen and imazamox is variable, and the traditional evaluation of phytotoxicity through visual methods is subjective. Therefore, the present study aimed to: (i) propose a methodology based on image analysis for phenotyping herbicide‐induced phytotoxicity in common bean genotypes, aiming to reduce the subjectivity of traditional visual assessments; (ii) characterize common bean genotypes under the effects of different herbicides and their doses in progenies and parental lines, based on morphophysiological traits and indices derived from visible RGB (red, green, and blue) digital images. The experiment was conducted in a completely randomized design under a 3 × 3 × 6 factorial scheme (herbicide × dose × genotype) with three replications, evaluating fomesafen and imazamox at doses of 0%, 100%, and 200% of the recommended rates. Data were collected on visual phytotoxicity, plant height, stem diameter, number of leaves, and image indices (Green Index, Excess Green Index, Excess Red Index, and Color Index of Vegetation Extraction). Results indicated that the triple interaction was significant, revealing the complexity of plant responses to herbicides. Canonical discriminant analysis explained 78.66% of the total variation, with the first canonical discriminant function (29.42%) contrasting structural development and vitality with stress, the second canonical discriminant function (27.59%) reflecting overall plant vigor, and the third canonical discriminant function (21.65%) capturing stress and phytotoxicity negatively affecting growth. The analysis demonstrated that image‐based indices combined with multivariate techniques are effective for quantifying phytotoxicity and distinguishing genotypes (tolerant and sensitive to herbicide effects), overcoming the limitations of visual evaluations, and should be used as a complementary tool to traditional techniques. Therefore, the parental genotype IPR Campos Gerais and the progeny F1A were tolerant to herbicides at different doses, while the parental genotype BAF36 and the progeny F2B were sensitive. Hence, the proposed methodology is effective for identifying herbicide‐tolerant and sensitive genotypes.
Why it matches plant phenotyping methodsRGB画像解析と多変量解析による除草剤誘発 phytotoxicity の表現型評価法の提案が研究の中心であり、従来の主観的評価を改善する方法開発に該当する。
abstractthe present study aimed to: (i) propose a methodology based on image analysis for phenotyping herbicide‐induced phytotoxicity in common bean genotypes
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
Plant phenotyping relevance match · UnverifiedOpenAlex · Europe PMC · Crossref · checked 5 Sept 2026
Abstract Precision field management and high-throughput plant phenotyping increasingly rely on remote sensing to capture spatial and temporal variability in crop performance. Unmanned aerial vehicle (UAV) – based sensing offers unique advantages for field-scale data collection, including high spatial resolution, flexible deployment, and scalable throughput. However, the full potential of UAV platforms remains constrained by labor-intensive operations across flight execution, data transfer, and processing workflows. This study presents a systematic evaluation of an automatic UAV-based crop sensing platform through a season-long, multi-crop field experiment. Data acquisition was conducted over a maize irrigation trial and a soybean breeding experiment, resulting in 176 completed flights over 28 days during the growing season. High-frequency flights on selected days captured diurnal dynamics in key canopy traits, including maize leaf rolling under drought stress and genotype-dependent plot temperature variation in soybean. In the maize irrigation experiment, significant differences in diurnal canopy cover ratio (CCR) were observed among irrigation treatments. The predictive relationship between CCR and final grain yield strengthened throughout the day, with the coefficient of determination (R 2 ) increasing from 0.05 in the early morning (RMSE = 3.05 Mg ha − 1 ) to 0.65 at midday (RMSE = 1.87 Mg ha − 1 ), highlighting the importance of temporal optimization in UAV-based sensing. Temperature measurements from the onboard thermal infrared camera showed a strong overall linear correlation with ground truth measurements (R 2 = 0.85). In the soybean trial, the highest plot temperature was observed on the fast-wilting genotype. Additionally, regression models were developed to estimate key crop traits, including canopy height (CH) and leaf area index (LAI), demonstrating the platform’s quantitative sensing capability. Overall, this study demonstrates that automatic UAV systems enable high-temporal-resolution crop monitoring while substantially reducing operational cost. The results highlight their potential for precise crop management and scalable field phenotyping. Future work will focus on integrating automated data processing pipelines to support near-real-time analytics and decision-making.
Why it matches plant phenotyping methods自動UAVのRGB・熱画像センシング platform を圃場で系統的に評価し、温度・キャノピー被覆率・高さ・LAIなどの植物形質を定量化しているため、フェノタイピング手法が研究の中心である。
abstractThis study presents a systematic evaluation of an automatic UAV-based crop sensing platform through a season-long, multi-crop field experiment.
Purpose In recent years, there has been a growing use of unmanned aerial vehicle (UAV) based light detection and ranging (LiDAR) data for mapping plant area index (PAI) in orchards. However, using LiDAR time-series collected throughout the growing season to assess PAI variations in response to phenology, represents an understudied area of investigation. Furthermore, establishing the optimal spatial resolution for mapping biophysical variables of tree crops from LiDAR point cloud data remains poorly defined. Here, we assess the capability of a UAV-based LiDAR system to characterize cherry trees throughout the growing season, with a focus on monitoring PAI and the vertical structure of individual trees. Methods A time-series of 14 point cloud acquisitions with a density of 3300 points/m2 was collected between February and December 2022, covering all phenological stages of a cherry orchard in southern France. A voxel-based method was applied to create a three-dimensional grid within which PAI was estimated for each voxel. PAI was mapped by accumulating the individual voxel-based PAI values within each vertical voxel column. Results The results demonstrate that a voxel size of at least 0.7 m is required to retrieve reliable PAI estimates (RMSE = 0.58 m2.m−2, MAE = 0.48 m2.m−2, bias = 0.19 m2.m−2, rRMSE = 23%, and R2 = 0.51), while a voxel size of 1 m produced the most accurate PAI estimates (RMSE = 0.5 m2.m−2, MAE = 0.41 m2.m−2, bias = 0.07 m2.m−2, R2 = 0.59), when assessed against field-based PAI measurements obtained with a LAI-2200 Plant Canopy Analyzer. The temporal variation of canopy PAI illustrated the progression of key phenological stages, including flowering, leaf development, ripening and senescence, as well as the response of the canopy to drought stress (reduction in PAI due to leaf rolling) during the summer. The maps of PAI successfully described the variations in leaf canopy density for different cherry varieties and allowed assessment of the vertical PAI profile at the individual tree level, which provides valuable insight into tree condition. Conclusion This study confirms that seasonal UAV-LiDAR monitoring is a viable, informative approach for capturing orchard canopy dynamics at the individual tree and sub-canopy level, linking canopy structure to phenology, varietal differences, and stress responses across the growing season.
Why it matches plant phenotyping methodsUAV-LiDARとボクセル法による樹冠PAI・垂直構造の推定手法を開発・検証し、時系列および個体レベルで評価しているため、植物フェノタイピング手法が中心である。
abstractHere, we assess the capability of a UAV-based LiDAR system to characterize cherry trees throughout the growing season, with a focus on monitoring PAI and the vertical structure of individual trees.
Plant phenotyping relevance match · UnverifiedOpenAlex · Crossref · Europe PMC · checked 5 Sept 2026
Introduction: Plant phenotyping requires accurate and repeatable three-dimensional structural information, but practical acquisition conditions in greenhouses, seedling rooms, and indoor pot experiments often include complex backgrounds, handheld motion blur, and thin leaf structures. These factors reduce the robustness of conventional three-dimensional reconstruction methods and limit their use in low-cost and automated phenotyping. Methods: To address this problem, this paper proposes F2DMAS, an automated three-dimensional plant phenotyping workflow using consumer-grade smartphone videos. The workflow first converts multiview RGB videos into image sequences and removes motion-blurred frames through frequency-domain quality filtering. A frequency-spatial plant segmentation module, termed FSAM3, is then introduced to separate plant structures from complex backgrounds without task-specific annotated training data. The segmented image sequences are further reconstructed using 2D Gaussian Splatting, followed by TSDF-based meshing, scale recovery, and virtual measurement for extracting plant height, canopy width, leaf length, and leaf width. Results: Experiments were conducted on 15 plant species under two acquisition scenarios. The proposed workflow achieved stable plant reconstruction under non-ideal background conditions, with PSNR, SSIM, and LPIPS values of 31.09, 0.9711, and 0.0365, respectively. Compared with the baseline reconstruction workflow, F2DMAS substantially reduced the processing time for mesh extraction while improving reconstruction quality. The extracted phenotypic traits showed strong agreement with manual measurements, with R² values ranging from 0.90 to 0.99, RMSE values ranging from 0.64 to 1.21 cm, and MAPE values ranging from 4.50% to 9.73%. Discussion: These results indicate that F2DMAS can provide an end-to-end workflow from smartphone video acquisition and plant segmentation to three-dimensional reconstruction and phenotypic trait extraction. The proposed method offers a practical and deployable solution for greenhouse seedling cultivation, potted plant experiments, and low-cost three-dimensional plant phenotyping.
Why it matches plant phenotyping methodsスマートフォン動画から植物の3D構造を再構成し、複数の形態形質を抽出・検証するワークフロー自体が中心的な方法論的貢献である。
abstractThe extracted phenotypic traits showed strong agreement with manual measurements, with R² values ranging from 0.90 to 0.99
This study compared unsupervised and supervised machine learning, and deep learning (U-Net) classifiers on Unmanned Aerial Vehicle (UAV) multispectral imagery to identify nitrogen status in potato crops under nitrogen (N) fertilization treatments, irrigation (I), and their interaction (N × I). The U-Net model outperformed all other methods, achieving accuracies for crop nitrogen status of 65–99% in N, 84–100% in I, and 41–82% in N × I treatments, with variation due to different input data. Supervised machine learning also performed well, with Support Vector Machine achieving 53–87, 66–86, and 32–66% respectively, and Random Forest 61–96, 70–81, and 33–65%. Unsupervised K-means yielded the lowest accuracies (47–58, 9–65, and 8–34%), demonstrating necessity of substantial supervision to delineate crop nitrogen and water status. These findings were confirmed by repeated analyses of UAV imagery acquired later in the growing season with consistent results. Comparable classification performance was observed for crop water status and leaf area index at both time points. Despite being demonstrated in a single-field, single-crop framework, the results provide proof of concept for applying deep learning classifiers to detect subtle nitrogen and water stress under field conditions in precision agriculture. Future research could test diverse agroecosystems and growing seasons, alternative deep learning algorithms, and sensor data fusion to improve classification accuracies.
Why it matches plant phenotyping methodsUAVマルチスペクトル画像からジャガイモの窒素・水分状態およびLAIを推定する分類手法を比較・検証しており、植物状態の取得と手法性能評価が研究の中心である。
abstractThis study compared unsupervised and supervised machine learning, and deep learning (U-Net) classifiers on Unmanned Aerial Vehicle (UAV) multispectral imagery to identify nitrogen status in potato crops
Abstract has not been obtained from indexed metadata or an accessible article page.
Why it matches plant phenotyping methods圃場トウモロコシの葉面積を点群から抽出するセグメンテーション・幾何学的補完手法の開発が題名の中心であり、植物形質の取得方法に該当する。
titleLeaf area extraction framework: Transformer-based segmentation and geometric-based completion approaches for accurate extraction of field maize leaf area from point clouds
Published1 Jul 2026Microscopy and microanalysis : the official journal of Microscopy Society of America, Microbeam Analysis Society, Microscopical Society of CanadaCited by 0 · OpenAlex ↗
Fuzhou represents a critical center for tea genetic diversity, yet the micromorphological basis for differentiating its local landraces remains poorly understood. Scanning electron microscopy (SEM) was employed to investigate the foliar micromorphology of 28 tea landraces from Fuzhou and to characterize structural differences among them. Adaxial epidermal wax ornamentation, stomatal architecture, and nonglandular trichome patterns provided important taxonomic characters for germplasm classification. Our analysis reveals that stomata are consistently paracytic and randomly oriented on the abaxial surface. However, their dimensions exhibit high phenotypic plasticity, with mean areas ranging from 421.92 to 822.26 µm2. Leaf surface ornamentation showed high phenotypic variability, with three identifiable types: straight, wrinkled, and undulated. The length, width, and type of nonglandular trichomes varied among the landraces, with values of nonglandular trichome length ranging from 269.99 to 632.31 µm and diameter from 9.72 to 14.62 μm. The nonglandular trichome ornamentation was categorized as smooth, long-stripe, and short-stick. The study demonstrated that SEM-based analysis of foliar micromorphological traits provides a valuable tool for tea germplasm identification and cultivar improvement. Specifically, the combination of adaxial epidermal wax ornamentation and nonglandular trichome surface ornamentation provides stable and reliable diagnostic micromorphological markers for accurate differentiation and identification of Fuzhou tea landraces, filling a critical micromorphological gap in the systematic study of local tea germplasm.
Why it matches plant phenotyping methodsSEM画像に基づく葉の微細形態形質の取得・分類を中心に、茶遺伝資源の識別へ応用しており、単なる生物学的測定ではなく植物フェノタイピング手法として中心的です。
abstractScanning electron microscopy (SEM) was employed to investigate the foliar micromorphology of 28 tea landraces from Fuzhou and to characterize structural differences among them.
Abstract The leaf area index (LAI) is a key determinant of canopy architecture and yield potential in maize, primarily through its influence on photosynthetic efficiency. Although unmanned aerial vehicle (UAV) technology has greatly advanced field-based phenotyping, its potential for deciphering the genetic mechanisms underlying dynamic and complex trait development remains underexplored. In this study, multispectral UAV images were collected from a diverse maize panel across eight developmental stages in four environments over two consecutive years. Using multi-temporal data, a random forest model accurately predicted LAI (R² = 0.82–0.83), significantly outperforming models based on single time-point data. By integrating high-throughput phenotypic predictions with time-series genome-wide association studies (GWAS), 36 dynamic SNPs associated with LAI variation were identified. Principal component analysis (PCA) of temporal LAI data revealed two principal components that together explained 84.2–86.5% of the total phenotypic variance. GWAS based on these components identified an additional 51 SNPs, seven of which overlapped between the two analytical approaches. Among the 72 candidate genes identified, Zm00001d048615 exhibited significant variation in both phenotype and expression among different inbred lines. The heterologous overexpression of Zm00001d048615 in Arabidopsis induced leaf curling and a significant reduction in leaf size, indicating its potential role in regulating leaf development. Collectively, these findings establish a robust framework that integrates UAV-based phenomics with temporal GWAS to identify key genes regulating complex dynamic traits. This approach provides valuable insights and genetic targets for improving maize canopy architecture and yield potential through molecular breeding.
Why it matches plant phenotyping methodsUAVマルチスペクトル画像と時系列データからLAIを推定するモデルを開発・評価し、高スループット表現型解析に中核的に用いているため。
abstractmultispectral UAV images were collected from a diverse maize panel across eight developmental stages in four environments over two consecutive years.
Low-cost RGB imaging is accessible for phenotyping, but color varies with devices and illumination. We tested whether RGB-derived indices from a standardized smartphone setup can proxy cotton (Gossypium hirsutum L.) leaf traits at the early seedling stage. Leaves (n=80) from three growth-chamber experiments were imaged in a closed light-tent with an in-frame gray/white/black card, then corrected in Adobe Photoshop. Mean leaf RGB values (manual ROIs) were used to compute 15 RGB/CIELAB indices, which were screened against SPAD, specific leaf area (SLA), vein density, water content (WC), stomatal density, and stomatal size using Pearson r and second-order regression (adj. R², NRMSE). The strongest relationships were for SLA (h_ab; adj. R²=0.666), vein density (TGI; adj. R²=0.610), and SPAD (G; adj. R²=0.558). WC was moderately associated with c_ab (adj. R²=0.344), while stomatal traits were weakly explained, consistent with scale limits of top-down mean-color metrics. Standardized consumer RGB imaging can therefore support rapid first-pass screening of pigment- and structure-related leaf traits.
Why it matches plant phenotyping methods標準化スマートフォンRGB撮像と色補正・指数計算を用いて葉形質を推定し、SPAD、SLA、葉脈密度などとの関係を定量評価しているため、画像フェノタイピング手法の検証が中心である。
abstractWe tested whether RGB-derived indices from a standardized smartphone setup can proxy cotton (Gossypium hirsutum L.) leaf traits at the early seedling stage.
Accurate and rapid detection of maize seedling growth is critical in early breeding decisionmaking, smart management, and yield improvement. Traditional leaf age detection still relies heavily on labor-intensive and low-efficiency manual field surveys, underscoring the urgent need for high-throughput phenotyping. Integrating multisource sensor data from unmanned aerial vehicle (UAV) with measured information such as crop height can further enhance the estimation accuracy of crop phenotypic parameters. Accurate field plot segmentation is critical for field-scale phenotypic analysis. However, current approaches remain largely dependent on slow, manual segmentation. Automating this step would greatly reduce the workload of agronomists. This study used UAV RGB and multispectral imagery collected over maize inbred line population plots before the canopy closure stage to perform automatic plot segmentation on field orthophotos and combined measured plant height with relative flight dates to achieve high-throughput detection of leaf age during the maize seedling stage. First, this study proposed a maize plot automatic segmentation method based on orthophotos. Then, it extracted texture features, RGB, and multispectral vegetation indices of each plot. Combined with relative flight date and plant height, four datasets were constructed. Support vector regression (SVR), random forest regression (RFR), and automatic machine learning (AutoML) regression algorithms were used to build the leaf age detection model. The results showed that the orthomosaic from March 23 achieved the best plot-segmentation performance, with minimum intersection over union (IoU), mean IoU, and IoU standard deviation of 14.67%, 96.47%, and 8.65%, respectively. Incorporating relative flight dates and plant-height measurements improved model performance, and the AutoML demonstrated the greatest robustness, achieving a validation R2 of up to 0.862 and an RMSE as low as 0.715. This study proposed a leaf age estimation method that offers practical technical support for field-based maize seedling assessment and reduces manual labor demands.
Why it matches plant phenotyping methodsUAV RGB・マルチスペクトル画像、圃場区画 segmentation、特徴抽出、回帰モデルを統合し、トウモロコシの葉齢という植物形質を推定する方法を開発・評価しており、フェノタイピング手法が研究の中心である。
abstractThis study used UAV RGB and multispectral imagery collected over maize inbred line population plots before the canopy closure stage to perform automatic plot segmentation on field orthophotos and combined measured plant height with relative flight dates to achieve high-throughput detection of leaf age during the maize seedling stage.
Soybean leaf morphology is an important breeding trait that requires large-scale phenotyping in commercial breeding programs. Conventional leaf phenotyping still relies on manual destructive measurements, which are labor-intensive and inefficient. Low-altitude unmanned aerial vehicles (UAVs) have emerged as a high-throughput phenotyping platform, but the retrieval of leaf morphology in densely occluded canopies remains challenging due to complex canopy backgrounds, illumination heterogeneity, and leaf overlap under field conditions. To address this issue, this study developed an integrated UAV framework that couples a YOLOv10-based leaf detection module, a novel structure-adaptive segmentation network (DynamicU), and a regression-based trait prediction model for retrieving a set of leaf morphological parameters across 273 soybean genotypes under field conditions. The YOLOv10 detector reliably localized individual leaves under complex canopy conditions, achieving a mean average precision (mAP@50) of 0.84. Subsequently, the DynamicU network, whose architecture was automatically optimized via Emperor Penguin Optimization, achieved a segmentation accuracy of 97.2% and a mean Intersection over Union of 93.8%, substantially outperforming conventional models. Using random forest regression, the framework retrieved relative leaf shape traits, including length-to-width ratio and dissection index, with markedly higher accuracy (R 2 =0.97), compared to absolute morphological traits, including leaf length, width, perimeter, and area (R 2 : 0.76–0.84). Notably, relative leaf shape traits showed positive associations with oil yield per plant and protein yield per plant, supporting their potential as complementary indicators for screening soybean germplasm with differential industrial product output. This end-to-end framework establishes a reliable bridge between UAV remote sensing and leaf-level morphological quantification, advancing high-throughput phenotyping capabilities to support precision breeding in soybean.
Why it matches plant phenotyping methodsUAV画像、葉検出・セグメンテーション・回帰モデルを統合し、圃場でダイズ葉形態を自動定量するフレームワークの開発と性能評価が研究の中心であるため。
abstractthis study developed an integrated UAV framework that couples a YOLOv10-based leaf detection module, a novel structure-adaptive segmentation network (DynamicU), and a regression-based trait prediction model for retrieving a set of leaf morphological parameters across 273 soybean genotypes under field conditions.
Plants are geometrically and topologically complex objects, and methods and devices that produce plant point clouds often miss parts due to self occlusions, making further analysis, such as phenotypic trait extraction or 3D reconstruction, difficult. We introduce A-Occ-Plant , a novel method for point cloud completion. The first novelty of our algorithm is converting point clouds into a set of images, which are then completed using 2D amodal segmentation. The images are then converted into a complete point cloud by using view-consistent Gaussian splats. The second novelty is the use of a coarse-to-fine hierarchical Transformer with cross-scale attention. The completed soft masks are fused into a continuous 3D density field using Gaussian splatting, removing the need for external pose estimation or fixed-size inputs. We introduce a synthetic dataset using a procedural model and a real-world plant reconstruction benchmark with artificially generated occlusions. We further benchmark A-Occ-Plant against representative 3D point-cloud completion methods, demonstrate that it recovers downstream phenotypic traits (leaf count, leaf angle, plant height), and show that it generalizes to another crops (soybean). A-Occ-Plant achieves a 264.8% improvement in LPIPS and an 8.3% gain in SSIM compared to the current state of the art, while using only 2.3% of the parameters and running 39.4× faster. We release our code at https://github.com/JaeLee18/PlantPhenomics_Occlusion.
Why it matches plant phenotyping methods植物の遮蔽点群を補完し、葉数・葉角度・草丈という表現型形質を復元する手法を開発しており、データセット作成とベンチマーク検証も中心的に行っている。
abstractWe introduce A-Occ-Plant , a novel method for point cloud completion.
Reproduction assets foundThe paper explicitly releases authors' code and sample data (inference code, sample data for reproducing results) via a Google Drive project download and a GitHub repository, both with explicit availability statements and public URLs.Code · publicThe full code and data at https://github.com/JaeLee18/PlantPhenomics_Occlusion .Open asset ↗JaeLee18/PlantPhenomics_Occlusionlines:386-410Plant phenotyping relevance match · UnverifiedOpenAlex · checked 15 Sept 2026
Accurate retrieval of leaf area index (LAI) is vital for crop monitoring and genetic breeding. Although multi-modal unmanned aerial vehicle (UAV) remote sensing has advanced LAI estimation, conventional empirical models often overfit on small breeding populations and cannot disentangle the true causal effects of genetic backgrounds from confounding factors within a statistically rigorous framework. This study presents a robust framework for plot-scale maize LAI estimation across 800 breeding plots from four genetic subgroups: doubled haploid (DH), mixed, temperate (TEM), and tropical/subtropical (TST). From UAV RGB and multispectral imagery acquired at three phenological stages, we extracted 76 multi-modal features comprising point-cloud structural metrics, spectral vegetation indices, and texture features. Following a dual-criterion mutual information and multicollinearity filter, four algorithms, including traditional tree-ensembles and the Tabular Prior-data Fitted Network (TabPFN), were evaluated using nested validation. TabPFN achieved superior generalization performance, yielding a mean test R2 of 0.778 ± 0.031, an RMSE of 0.264 ± 0.024, and an MAE of 0.203 ± 0.022, significantly outperforming tree-ensemble models (p < 0.01). Across growth stages, retrieval accuracy peaked at the expanded bell-mouth stage (R2 = 0.802) and successfully captured the unimodal trajectory of canopy development. SHAP-based attribution showed that spectral indices contributed most to the predictions (55.9%), followed by canopy texture (26.3%), with the spatial heterogeneity metric Tex_Entropy being the most influential single feature (22.8%). When embedded as the nuisance estimator within a Double Machine Learning framework for causal inference, TabPFN confirmed that, relative to the TEM subgroup, only the DH genetic background exerted a consistent and significant negative causal effect on LAI (ATE = −0.070, p = 0.030). These results establish TabPFN as a reliable and extensible tool for non-invasive, high-throughput phenotyping in precision breeding.
Why it matches plant phenotyping methodsUAVマルチモーダル画像からトウモロコシLAIを推定する計算・画像解析ワークフローを開発・比較検証し、高スループット表現型解析への応用を示しているため、方法が中心的である。
abstractThis study presents a robust framework for plot-scale maize LAI estimation across 800 breeding plots from four genetic subgroups
LeafScans-Orchard is a curated, multi-year RGB image dataset of orchard plant leaves designed to support research in computer vision, machine learning, and plant phenotyping. The dataset comprises 9708 high-quality leaf scans acquired during collection campaigns conducted between 2015 and 2025, covering seven orchard crop species: apple, pear, sweet cherry, sour cherry, plum, peach, and apricot. In total, the dataset includes 67 cultivar labels. All samples were acquired using flatbed scanning under controlled conditions on a uniform background, ensuring high visual consistency and minimal background variability. The original scans were captured at 1200 dpi and subsequently converted into a public release format at 300 dpi, stored as lossless TIFF images to preserve morphological and textural details. Each image corresponds to a single leaf and is organized in a hierarchical directory structure by species, cultivar, and acquisition year, accompanied by image-level metadata and aggregated species–cultivar–year counts. LeafScans-Orchard is suitable for plant species classification, cultivar recognition, leaf morphology analysis, texture analysis, and general visual feature extraction. In addition to the main release, a representative subset of 300 original 1200 dpi scans is provided to support high-resolution analyses. The dataset is particularly suited for fine-grained classification, morphology-driven analysis, and methodological studies under controlled imaging conditions.
Why it matches plant phenotyping methods果樹葉のRGBスキャン画像を収録した公開データセットで、植物フェノタイピングおよび葉形態解析を目的とする。標準化された画像取得と再利用可能なデータ構成が中心であり、フェノタイピング用データセットとして適格。
abstractLeafScans-Orchard is a curated, multi-year RGB image dataset of orchard plant leaves designed to support research in computer vision, machine learning, and plant phenotyping.
Reproduction assets foundThe paper's core asset is the LeafScans-Orchard dataset itself (9708 RGB leaf scans, 300 dpi TIFF release plus 1200 dpi subset, image-level metadata and summary counts), openly deposited on Zenodo with an explicit DOI and CC BY 4.0 license. This is a paper-specific, public, actionable phenotyping image dataset. No codeDataset · publicthe published version of the manuscript.
Funding: This research received no external funding.
Institutional Review Board Statement: Not applicable.
Informed Consent Statement: Not applicable.
Data Availability Statement: The dataset described in this article is openly available in Zenodo
as LeafScans-Orchard Dataset (v1.0.0) at https://doi.org/10.5281/zenodo.20187966 (accessed on
10 May 2026). The repository includes the 300 dpi image release, the 1200 dpi high-resolution subset,
image-level metadata, aggregated species–cultivar–year counts, and supporting documentation. The
complete archive of original 1200 dpi scans is retained locally by the authors but is not included in
the current pubOpen asset ↗Zenodo · 10.5281/zenodo.20187966pdf-raw-page:12 lines:1-46Plant phenotyping relevance match · UnverifiedOpenAlex · checked 14 Sept 2026
Upland cotton (Gossypium hirsutum L.) is a critical economic crop, yet the efficiency of mechanized harvesting is heavily contingent upon effective pre-harvest defoliation. Traditional manual assessment of defoliation is labor-intensive and subjective, posing a significant bottleneck for large-scale genetic dissection of this dynamic trait. In this study, we established an integrated “high-throughput phenotyping-to-gene discovery” framework by utilizing UAV-based multispectral imaging to monitor 306 cotton cultivars across 4 environments. A Partial Least Squares Regression (PLSR) model was optimized to accurately estimate Leaf Area Index (LAI), and Gaussian curve fitting was employed to standardize LAI time series (ΔLAI) into a comparable dynamic phenotypic dataset. Genome-wide association studies (GWAS) based on these dynamic phenotypes identified 472 significant SNPs and 39 candidate genes. By integrating GWAS signals with transcriptome profiling of the petiole abscission zone and haplotype analysis, we identified 3 core regulatory genes: Ghi_A01G08401 (GhPIN3a), Ghi_D08G10716, and Ghi_D11G03091. Functional validation via virus-induced gene silencing (VIGS) and qRT-PCR demonstrated that Ghi_D08G10716 (encoding oxalyl-CoA synthetase) and Ghi_D11G03091 (encoding a VQ motif-containing protein) act as negative regulators in the defoliation process. These results provide a scalable technical paradigm and critical genetic resources for the precision breeding of cotton cultivars optimized for mechanized harvesting.
Why it matches plant phenotyping methodsUAVマルチスペクトル画像からLAIを推定し、時系列を動的表現型データへ変換する高スループット表現型解析手法が研究の中心であり、GWASへの実質的適用も行っている。
abstractwe established an integrated “high-throughput phenotyping-to-gene discovery” framework by utilizing UAV-based multispectral imaging to monitor 306 cotton cultivars across 4 environments.
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.
Plant phenotyping relevance match · UnverifiedCrossref · Europe PMC · checked 13 Sept 2026
Modern agriculture operates at an unprecedented crossroads, it must simultaneously accelerate crop yields to feed an expanding global population and adapt to the severe, fluctuating pressures of climate change, structural soil degradation, abiotic water deficits, and evolving biological threats. Historically, selecting resilient crop varieties and implementing field-scale management strategies relied extensively on destructive, labor-intensive, and fundamentally subjective visual metrics. This manual processing approach has long been recognized as the primary operational bottleneck in agricultural advancement.To bridge the gap between rapidly expanding genomic data and actual field performance, the systematic, non-destructive quantification of structural and functional plant traits, plant phenotyping, has emerged as a transformative frontier. By integrating high-throughput engineering, multi-scale remote sensing, deep learning, and advanced molecular biology, modern phenotyping transitions crop science away from qualitative estimation toward highly reproducible, multidimensional data frameworks. This Research Topic presents new advances in advanced 3D reconstruction and deep semantic segmentation at the seedling stage; amodal fruit segmentation, morphological extraction, and early water-stress diagnostics; high-throughput in-field seedling counting and dynamic density modeling; multimodal foundation models, network pruning, and intelligent phytoprotection; aerial and spaceborne remote sensing for canopy analysis and weed monitoring; plant physiology, functional spectroscopy, and functional genomics under abiotic stress; and automated diagnostics for real-time orchard scouting and vineyard management.Automating the characterization of complex spatial layouts under controlled or greenhouse environments is essential for early variety selection and early-stage structural evaluation. Several contributions within this volume provide key breakthroughs in navigating overlapping tissues, severe occlusions, and low-contrast edge regions. showcases how substituting standard convolutions with deformable convolutions enables deep neural networks to accurately isolate the main stem of mature, high-density crops like soybeans. This architecture overcomes the traditional challenges of color mimicry and severe occlusion by pods and leaves, achieving an outstanding mIoU of 90.58% and providing reliable indices for lodging resistance and structural yield modeling (R 2 = 0.9746).Accurately extracting fruit morphology under commercial greenhouse conditions remains heavily constrained by overlapping crop structures, foliage cover, and variable shadows. Simple semantic masks typically fail when a target fruit is partially blocked, leading to a loss of key volumetric data.To resolve the challenge of hidden boundaries, Li, Yin, et al. (2025) developed CGA-ASNet, a specialized RGB-D amodal segmentation network driven by a Contextual and Global Attention (CGA) module designed to restore occluded tomato regions. Trained on a high-fidelity synthetic greenhouse dataset (Tomato-sim) generated via NVIDIA Isaac Sim's Replicator Composer and optimized with a mean coordinate fusion algorithm for real-world validation, this architecture expands the network's receptive field to predict the complete, hidden circular forms of occluded tomatoes, achieving an F@0.75 score of 94.2 and an amodal mIoU of 82.4%. This proves that simulation-to-real (Sim2Real) domain pathways can successfully decode full physical volumes under dense commercial canopies.Complementing this structural restoration, Yang, Li, et al. (2025) designed an integrated diagnostic framework to identify early water stress dynamics in greenhouse tomatoes. Built upon an optimized YOLOv11n core, their system integrates adaptive kernel convolutions (AKConv) into the network backbone's C3k2 modules and implements a recalibration feature pyramid detection head based on the specialized P2 small-target layer. This combination achieved a 5.4% increase in mAP50-95 for identifying fine phenotypic parts. By applying automated geometric analysis to the extracted bounding boxes, the system extracts plant heights and petiole count with low relative errors, feeding these phenotypic parameters into a Random Forest classification routine that flags water-stressed plants with 98% accuracy to guide targeted, automated drip irrigation.Accurate plant stands during early vegetative stages represent the foundational metric required to establish true field emergence rates, validate seed vigor across diverse breeding blocks, and perform early yield predictions.To solve the challenges of small targets, extreme spatial density, and adjacent leaf overlap, Zang et al. (2025) designed DM_IOC_fpn, a wheat seedling counting framework that balances local and global contextual features. By structuring a point-annotated dataset and embedding a densityenhanced encoder module, their network balances micro-scale spatial limits with macro-scale canopy structures. Optimized through a combined loss function tracking counting, classification, and regression parameters, this architecture achieved low error scores (RMSE = 2.91; MAE = 2.23), outperforming standard object-detection benchmarks in complex field environments.At the same time, scaling up to real-time aerial monitoring required major reductions in model complexity to support resource-constrained edge computers on autonomous aerial platforms. Feng, Nie, and Li (2025) engineered an ultra-lightweight YOLOv8n variant tailored for real-time maize seedling counting from high-speed UAV RGB overflights. By reparametrizing RepConv with HGNetV2, they constructed a lean Rep_HGNetV2 backbone, integrated a Bidirectional Feature Pyramid Network (BiFPN) for multi-scale feature alignment, and implemented a Task Dynamically Aligned Detection Head (TDADH). This architecture compressed total model parameters by 47% and reduced weight sizes to 3.5 MB while maintaining a 96.5% detection accuracy and an ultra-fast processing speed of 146.3 FPS, paving the way for low-cost, real-time field scouting.Automated phytoprotection requires machine-vision architectures capable of generalizing across highly diverse species, complex field conditions, and varying computational boundaries. A significant subset of the published papers addresses these challenges through foundation model adaptation, multi-modal alignment, and efficient network compression.A major paradigm shift presented in this collection involves moving away from task-specific training and toward foundation model adaptation. Chen, Ruan, et al. (2026) introduce a novel architecture integrating the DinoV3 foundation model with a Unet framework to achieve robust leaf lesion segmentation across diverse species (such as coffee and black gram). By incorporating a Spatial Prior Module (SPM), their approach surpassed standard benchmark networks by over 10.5% in IoU while reducing inference times by approximately 93.6%, demonstrating that highparameter foundation models can be highly optimized for resource-constrained edge devices in real-time scouting.To solve the perennial problem of limited training data for rare or emerging crop diseases, Cooper et al. ( 2026) developed an ingenious synthetic data generation pipeline. Combining 3D procedural leaf modeling in Blender with diffusion-based disease synthesis (Stable Diffusion fine-tuned with LoRA and ControlNet), they synthesized highly accurate plant disease images with perfect groundtruth annotation masks. When deployed in low-resource data settings, combining these synthetic pipelines with restricted real-world datasets consistently drives significant improvements in downstream segmentation tasks. To tackle specific, complex pathologies, Xu, Chang, et al. (2025) developed the TSSC deep learning model, which embeds three-neighbor channel attention paired with a complementary squeeze-and-excitation mechanism. This specific architecture minimizes structural degradation risks while pushing classification accuracy to 99.61% for highly complex pea leaf pathologies. Similarly, Feng, Liu, et al. (2025) tackled overlapping leaf occlusions and small lesion footprints in citrus groves with YOLO-Citrus, an optimized framework integrating C3K2-STA, ADown modules, and a Wise-Inner-MPDIoU loss function to strike a balance between edge computational constraints and field deployment.UAVs and high-resolution satellite imagery have expanded the operational scale of phenotyping from individual pots to vast breeding blocks and commercial fields, allowing researchers to capture macro-dynamic parameters over time.In complex canopy systems that defy standard top-down aerial sensing, such as single-staked white Guinea yams, Iseki et al. (2026) demonstrated the distinct advantage of utilizing multi-angle (combined nadir and oblique) UAV imaging configurations. When coupled with support vector regression, this method captures complementary canopy-structure information to model shoot biomass trajectories (R 2 = 0.79) across multiple years and management zones. These nondestructive, time-series datasets enabled the fitting of genotype-specific Richard's growth curves using Bayesian inference, isolating valuable genetic variations in early growth allocation.To capture full-season vertical physiological changes over large scales, Li, Yue, and Luo (2025) developed a hybrid CNN-LSTM-Attention (CLA) model designed to estimate the full-period Leaf Area Index (LAI) in rice using multi-temporal UAV multispectral imagery. By using the CNN layer to extract instantaneous spatial features, the LSTM block to process seasonal time-series intervals, and a self-attention mechanism to weight critical growth transitions, their platform achieved a high coefficient of determination (R 2 = 0.92) and kept relative root mean square errors (RRMSE) below 9%. This network minimized soil background noise during early vegetative stages (LAI values 1-
Why it matches plant phenotyping methods植物フェノタイピングの技術動向を扱うEditorialであり、画像解析、UAVセンシング、深層学習、形質抽出などの方法が中心的に整理されている。
Magnetic field (MF) technologies have been applied in agriculture for decades. However, they have not achieved mainstream adoption, partly because no validated methodology exists for evaluating their effects under realistic field conditions. UAV-based multispectral sensing represents a potential pathway to address this limitation: by providing spatially explicit, non-destructive estimates of key canopy physiological variables at field scale, it could provide the monitoring infrastructure through which MF treatment responses are, for the first time, systematically evaluated and validated under open-field conditions. To exploit this complementarity, however, a common evidential ground must first be established, identifying which crop physiological variables are both consistently modulated by MF treatments and reliably detectable by UAV remote sensing. This study addressed this challenge through a dual-stream systematic review of 216 peer-reviewed publications, comprising 102 studies on MF treatments in agricultural crops and 114 studies on UAV-based multispectral monitoring. Evidence from both research domains was synthesised to identify physiological variables that are simultaneously responsive to MF treatments and detectable through UAV remote sensing. Five direct bridge variables were identified: chlorophyll content, nitrogen use efficiency/nitrogen assimilation, above-ground biomass, leaf area index, and yield. Chlorophyll content emerged as the strongest bridge variable, combining consistent MF responsiveness with UAV estimation accuracies of up to R² = 0.90. Based on these findings, a conceptual framework was developed linking MF treatments, UAV-derived vegetation indices, ground-truth measurements, and machine-learning approaches for field-scale validation. The results reveal a complete absence of integration between the two research domains despite their strong biological and methodological compatibility. The proposed framework provides the first operational pathway for evaluating MF technologies under realistic farming conditions and may support future research on sustainable and digitally enabled crop production systems.
Why it matches plant phenotyping methodsUAVマルチスペクトルセンシングによる作物生理形質の推定を体系的にレビューし、地上検証と機械学習を含むフィールドスケール評価フレームワークを提案しており、植物フェノタイピング手法が中心である。
abstractUAV-based multispectral sensing represents a potential pathway to address this limitation: by providing spatially explicit, non-destructive estimates of key canopy physiological variables at field scale
Lettuce (Lactuca sativa L.) is an important leafy vegetable with substantial diversity in leaf topology, geometry, color, and texture, which poses challenges for germplasm identification and new variety protection. However, current approaches to complex phenotypic analysis are often limited in their ability to explicitly represent and exploit semantic relationships among phenotypic traits. To address this limitation, a knowledge graph-enhanced graph learning framework for lettuce phenotypic traits was developed. Phenotypic traits were first extracted from leaf images of five lettuce types. Based on the trait description standards of the International Union for the Protection of New Varieties of Plants (UPOV), a Lettuce Leaf Phenotypic Trait Knowledge Graph (LLPT-KG) was constructed to represent semantic associations among traits. On this basis, a Dual-Channel Relational Graph Convolutional Network (DCR-GCN) was developed to jointly integrate node attribute features and graph structural information for lettuce type classification. To improve interpretability, node- and edge-level importance analyses were further performed to identify the phenotypic traits and semantic relations most relevant to type discrimination. The proposed framework achieved an accuracy of 0.94 and a Macro-F1 score of 0.94. Compared with the best-performing single-channel graph baseline, R-GCN (Relational Graph Convolutional Network), DCR-GCN improved accuracy by approximately 9% points and Macro-F1 by 10% points. These results demonstrate that combining knowledge graphs with graph neural networks can effectively capture complex phenotypic relationships in lettuce and improve classification performance. The proposed framework provides methodological support for precise lettuce germplasm identification, digital phenotypic evaluation for new variety protection, and digital-assisted pre-screening prior to field-based DUS (Distinctness, Uniformity, and Stability) testing.
Why it matches plant phenotyping methodsレタス葉画像から形態・色・テクスチャ等の表現型形質を抽出し、知識グラフとGNNによる分類手法を開発・評価しており、表現型取得・解析が研究の中心である。
abstractPhenotypic traits were first extracted from leaf images of five lettuce types.
Rooftop farms are urban green infrastructure integrating food production, ecological regulation, and public services, and their management increasingly relies on data-driven approaches. However, open built environments, microclimatic heterogeneity, and limited sensor deployment challenge continuous monitoring and short-term prediction of rooftop plant growth. This study proposes and validates a virtual sensor-driven digital twin system using a rooftop tomato case in Xiamen, China. The system adopts a five-layer architecture comprising data acquisition, transmission, modeling, processing, and application service layers. By coupling a Long Short-Term Memory (LSTM) weather prediction model with the Decision Support System for Agrotechnology Transfer (DSSAT) crop growth model, a predictive virtual sensor module was developed to forecast leaf area index (LAI), aboveground biomass, phenology, and yield for seven days. Results show that the system links environmental data acquisition, LSTM–DSSAT prediction, database storage, and three-dimensional visualization, transforming rooftop plant growth into an updatable, predictable, and visualized digital twin object. The coupled model showed high predictive accuracy, with R2 values of 0.9814 for LAI and 0.9966 for aboveground biomass, while supporting phenology and yield prediction. The system supports irrigation optimization, landscape management, and activity planning in sensor-constrained rooftop farms.
Why it matches plant phenotyping methods植物成長のLAI、地上部バイオマス、フェノロジー、収量を予測する仮想センサー・デジタルツインを開発し、精度検証しており、表現型推定手法が研究の中心である。
abstractThis study proposes and validates a virtual sensor-driven digital twin system using a rooftop tomato case in Xiamen, China.
BarleyCommon beanCowpeaGrowth chamberMesh / voxelLiDAR / point cloudMultispectral / hyperspectralLeafWhole plant / canopy / plot / fieldAnnotation / quality control
Abstract High-throughput 3D multispectral plant phenotyping platforms generate large volumes of point cloud files, but trait extraction is typically performed by sensor-bundled software whose internal algorithms are not publicly documented, which limits reproducibility and integration into custom research pipelines. Here we present PhytoScan3D, an open-source Python pipeline that extracts morphological and spectral phenotypic traits, spanning plant height, 3D leaf area, digital biomass, convex hull volume, leaf inclination, canopy geometry, NDVI, hue, and vegetation indices, from both PLY and PCD point cloud files generated by Phenospex PlantEye F500 and F600 sensors, and is portable to point clouds from any acquisition platform. PhytoScan3D was validated against HortControl (PhenoSpex) ground-truth measurements on 936 barley ( Hordeum vulgare ) pot-date observations from the growth chamber trial (20 Norwegian cultivars, 12 scan dates, Septemenr 2025 to January 2026), achieving Pearson r = 0.913 to 0.999 and ratio approximately 1.000 for Plant Height Max, 3D Leaf Area, and NDVI Average. A vectorised mesh face filtering implementation achieved a 120x speed improvement, increasing valid 3D Leaf Area coverage from 0.6% to 100% of files. Cross-format validation on 223 PlantEye F600 PCD files from the ICRISAT LeasyScan platform (four legume species: mungbean, cowpea, lima bean, and common bean; 1,523 plant observations) yielded r = 0.884 against independent cuboid annotation heights. The systematic positive bias (mean +27.2 mm, ratio = 1.44) is attributable to PhytoScan3D computing height from raw point cloud Z-range while cuboid annotations are fitted to segmented plant points only, with the offset consistent across all four species (per-species r = 0.880 to 0.888). Cross-dataset processing of 1,180 PLY files from the Crops3D benchmark (8 species, 3 acquisition methods) confirmed zero extraction errors. PhytoScan3D is available at “github.com/kovimallik/phytoscan3d” under the MIT licence and processes 1,651 files across three independent datasets in under 12 minutes on GPU hardware. Highlights PhytoScan3D is the first open-source Python pipeline for batch extraction of phenotypic traits, including plant height, 3D leaf area, digital biomass, convex hull volume, leaf inclination, NDVI, and excess green index, from both PLY and PCD point cloud files generated by Phenospex PlantEye sensors. Primary validation against HortControl ground-truth measurements on 936 barley pot-date observations achieved Pearson r = 0.913-0.999 for Plant Height Max, 3D Leaf Area, and NDVI Average. A 120x computational speedup in mesh face filtering (vectorised NumPy vs. set-based loop) increased the coverage of valid 3D Leaf Area extraction from 0.6% to 100% of files. Cross-format validation on 223 PlantEye F600 PCD files from ICRISAT LeasyScan (four legume species, 1,523 plants) achieved r = 0.884 against independent cuboid annotation heights. The systematic +27.2 mm bias reflects a methodological difference (raw Z-range vs. soil-segmented annotations), is consistent and predictable across all four species (per-species r = 0.880-0.888), and is correctable by a single linear factor. Cross-dataset processing of 1,180 PLY files from the Crops3D benchmark (8 species, 3 acquisition methods) confirmed zero extraction errors. Significant scan-unit variation was detected for Plant Height Max (F = 5.71, p < 0.001, η 2 = 0.138) and Canopy Width X (F = 6.32, p < 0.001, η 2 = 0.150), demonstrating the biological utility of extracted traits.
Why it matches plant phenotyping methods植物の3D点群・マルチスペクトルデータから形態・スペクトル形質を抽出するオープンソース手法を開発し、複数データセットで技術検証・ベンチマークしているため、植物フェノタイピング手法が中心である。
abstractHere we present PhytoScan3D, an open-source Python pipeline that extracts morphological and spectral phenotypic traits
Reproduction assets foundThe paper's own analysis code (PhytoScan3D pipeline) is publicly released on GitHub under the MIT licence, and the two external 3D point cloud datasets used for validation (Crops3D and ICRISAT LeasyScan) are publicly available on figshare. The primary barley PLY dataset is not yet public (to be deposited in NVA upon).Code · publicditing, Funding acquisition.
Declaration of Competing Interest
The authors declare that they have no known competing financial interests or personal
relationships that could have appeared to influence the work reported in this paper.
Data Availability
PhytoScan3D source code, documentation, and example datasets are available at
https://github.com/kovimallik/phytoscan3d under the MIT licence. The barley PLY dataset
will be deposited in the Norwegian Research Information Repository (NVA) upon acceptance.
The Crops3D benchmark dataset is publicly available at
https://doi.org/10.6084/m9.figshare.27313272 (Zhu et al. 2024). The ICRISAT LeasyScan
dataset is publicly available at https://doi.org/10Open asset ↗github.com/kovimallik/phytoscan3dpdf-raw-page:15 lines:1-36Dataset · publicData Availability
PhytoScan3D source code, documentation, and example datasets are available at
https://github.com/kovimallik/phytoscan3d under the MIT licence. The barley PLY dataset
will be deposited in the Norwegian Research Information Repository (NVA) upon acceptance.
The Crops3D benchmark dataset is publicly available at
https://doi.org/10.6084/m9.figshare.27313272 (Zhu et al. 2024). The ICRISAT LeasyScan
dataset is publicly available at https://doi.org/10.6084/m9.figshare.28270742 (Galba et al.
2025).
Acknowledgements
This work was supported by the PheNo, DLT-Farming and Soil2Milk from Research Council
of Norway and TWIN-NUE from Norwegian University of Life Sciences (NMBU). The
authoOpen asset ↗figshare · 10.6084/m9.figshare.27313272pdf-raw-page:15 lines:1-36Dataset · publicimallik/phytoscan3d under the MIT licence. The barley PLY dataset
will be deposited in the Norwegian Research Information Repository (NVA) upon acceptance.
The Crops3D benchmark dataset is publicly available at
https://doi.org/10.6084/m9.figshare.27313272 (Zhu et al. 2024). The ICRISAT LeasyScan
dataset is publicly available at https://doi.org/10.6084/m9.figshare.28270742 (Galba et al.
2025).
Acknowledgements
This work was supported by the PheNo, DLT-Farming and Soil2Milk from Research Council
of Norway and TWIN-NUE from Norwegian University of Life Sciences (NMBU). The
authors thank Sara Catarina Costa Laranjeira, Min Lin and other NMBU growth facility staff
for plant care and scanning operOpen asset ↗figshare · 10.6084/m9.figshare.28270742pdf-raw-page:15 lines:1-36Plant phenotyping relevance match · UnverifiedCrossref · checked 5 Sept 2026
Unmanned aerial vehicle (UAV) based remote sensing has emerged as a disruptive technology for detecting crop water stress (CWS) in real time, precisely and at low cost offering significant advancements over conventional approaches. The study examined the red green blue (RGB), multispectral (MSP), hyperspectral (HSP), thermal image sensors integrated with UAVs, which offers a high-spatial and temporal resolution of physiological indicators such as chlorophyll content and canopy cover, canopy temperature, stomatal conductance. The study highlights that in spring maize, random forest (RF) models using UAV-derived MSP and thermal indices with leaf area index (LAI) performed well (R² > 0.575, root mean square error (RMSE)
Why it matches plant phenotyping methodsUAV搭載センサーによる作物の水ストレスや生理形質のモニタリング技術をレビューしており、表現型取得法が中心である。
titleRecent trends in crop water stress monitoring using remote sensing technologies: A review
Plant 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
Plant 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.
Plant phenotyping relevance match · UnverifiedCrossref · OpenAlex · Europe PMC · checked 15 Sept 2026
Accurate acquisition of plant phenotypes is crucial for elucidating plant growth and development, underlying genetic mechanisms, and responses to environmental stimuli. Traditional three-dimensional (3D) phenotyping mainly captures geometric traits such as height, leaf area, and canopy volume, while overlooking physiological and biochemical information. Here, we present a hyperspectral point clouds generation method based on PlantGaussian (a 3D Gaussian Splatting technique) that integrates structural and spectral information, extending 3D phenotyping beyond geometry to include physiology. High-quality plant point clouds were first reconstructed using PlantGaussian, and hyperspectral images(HSI) were mapped onto them to produce hyperspectral point clouds. In potted soybean experiments, we built predictive models linking hyperspectral reflectance to SPAD (chlorophyll content) and EWT (equivalent water thickness), and visualized their 3D distributions. The hyperspectral point clouds achieved strong predictive performance for SPAD ( R 2 = 0.78, RMSE = 2.05) and EWT ( R 2 = 0.80, RMSE = 1.07), thereby validating the approach. It further revealed clear vertical stratification within the canopy, highlighting significant spatial heterogeneity of SPAD and EWT in individual plants. Temporal monitoring from August 6 to 21, 2025, captured a sharp increase in EWT after heavy rainfall on August 11. Overall, our results demonstrate that hyperspectral point clouds enable accurate, non-destructive trait estimation and provide a powerful tool for exploring plant function, monitoring stress responses, and advancing precision agriculture.
Why it matches plant phenotyping methods植物の3D形態とハイパースペクトル情報を統合してSPAD・EWTを推定する手法を開発し、予測性能を検証しているため、植物フェノタイピング手法が中心である。
abstractHere, we present a hyperspectral point clouds generation method based on PlantGaussian (a 3D Gaussian Splatting technique) that integrates structural and spectral information, extending 3D phenotyping beyond geometry to include physiology.
To overcome the limitations of single remote-sensing features in estimating maize canopy leaf area index (LAI), this study developed a UAV-based estimation approach by integrating multispectral vegetation indices (VIs) with digital surface model (DSM) features and stacking ensemble learning. Field experiments were conducted in Dehong, Yunnan Province, China, during 2023-2024, and UAV multispectral images and DSM products were acquired for maize grown under three planting-density treatments. Five vegetation indices and three DSM-derived texture/structural features were retained according to their correlation with measured LAI, statistical significance, and complementary spectral or structural information. The VI-based random forest (VI-RF) model achieved an R 2 of 0.835 and an NRMSE of 9.5%, whereas the DSM-based model showed lower performance (R 2 = 0.641; NRMSE = 14.2%). Under the same random-forest modeling framework, fusing VIs with DSM features improved the overall model performance to R 2 = 0.892 and NRMSE = 7.6%, indicating that DSM-derived structural information mainly enhanced the feature representation of maize LAI. Using the same VI-DSM feature set, the stacking model with support vector machine (SVM) as the meta-learner further improved the overall performance to R 2 = 0.930 and NRMSE = 6.3%. The additional gain from stacking was moderate but consistent, whereas feature fusion contributed the dominant improvement. The combined VI-DSM-Stacking workflow improved prediction stability across planting densities, especially under low- and high-density canopy conditions where soil background interference and spectral saturation were more evident. These results demonstrate that integrating spectral and DSM-derived structural information with stacking ensemble learning can improve the accuracy and robustness of UAV-based maize LAI estimation.
Why it matches plant phenotyping methodsUAV画像・DSM・アンサンブル学習を統合し、トウモロコシのLAI推定法を開発・比較検証しており、表現型取得・推定手法が研究の中心である。
abstractthis study developed a UAV-based estimation approach by integrating multispectral vegetation indices (VIs) with digital surface model (DSM) features and stacking ensemble learning
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.
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.
Abstract. Accurate monitoring of vegetation health and canopy structure is essential for optimizing agricultural productivity and managing natural resources. Remote sensing technologies, combined with artificial intelligence (AI) and advanced satellite data, have revolutionized the capacity to assess crop conditions at large scales with high temporal and spatial resolution. This study leverages Sentinel-2 multispectral imagery and a novel AI-driven model approach to estimate Leaf Area Index (LAI) across multiple fields for canola. By integrating spectral reflectance data with view and solar geometry parameters, the model effectively captures the complex interactions between canopy structure and environmental factors. The methodology employs a two-layer neural network calibrated with physically based normalization to translate Sentinel-2 spectral and angular inputs into accurate LAI estimates. Validation against observed field measurements demonstrates strong agreement, underscoring the model’s robustness and reliability. Spatial analysis reveals distinct LAI patterns among the crop types, highlighting differences in canopy density and growth dynamics. Temporal profiling further illustrates crop-specific development trends, with canola showing extended canopy expansion. The results confirm that the fusion of remote sensing data with AI modelling provides a powerful tool for precision agriculture, enabling detailed monitoring of crop growth and facilitating informed decision-making. This approach offers significant potential for enhancing yield prediction, resource management, and sustainable farming practices, ultimately supporting global food security efforts.
Why it matches plant phenotyping methodsSentinel-2画像とニューラルネットワークにより、作物のLAIという明示的な植物形質を推定し、実測値で検証する手法が研究の中心である。
abstractThis study leverages Sentinel-2 multispectral imagery and a novel AI-driven model approach to estimate Leaf Area Index (LAI) across multiple fields for canola.
Climate change poses increasing challenges to Chinese cabbage ( Brassica rapa L. ssp. pekinensis ) production through unpredictable weather patterns that induce premature bolting and physiological disorders. Traditional breeding programs rely on labor-intensive visual assessment that cannot capture continuous developmental dynamics or precisely quantify stress responses across variable environments. This study validated and applied an automated high-throughput phenotyping system for evaluating seasonal adaptation in 134 Chinese cabbage genotypes across contrasting autumn (favorable) and spring (stressful) seasons in Taiwan. The system, based on a FieldScan gantry platform equipped with multispectral 3D scanners, operated autonomously 2-3 times daily, continuously monitoring morphological parameters (3D leaf area, digital biomass, plant height) and spectral indices (NDVI, PSRI) throughout the growth cycle. The system’s automated components -continuous data acquisition and real-time parameter extraction – generated approximately 100,000 data points from 63 morphological, spectral, and structural parameters during 6-week pre-harvest period. Subsequent quality and statistical analysis enabled objective genotype classification and breeding decisions. Automated measurements showed season-dependent associations with visual assessment scores (R² = 0.37-0.56 in autumn; R² = 0.73-0.80 in spring), with spring models substantially outperforming autumn models due to enhanced physiological differentiation under stress. Spring cultivation induced severe stress responses, evidenced by 71% increase in PSRI (0.12 vs. 0.07) and 26% increase in plant height, with bolting resistance emerging as the critical determinant of adaptation. A quantile-based multi-dimensional classification framework integrating seasonal composite scores and Euclidean distances stratified germplasm into actionable breeding categories: stable genotypes (3.7%), spring-specific types (0.7%), poor performers (13.4%), and intermediate materials (82.1%). Continuous temporal monitoring enabled early stress detection, with binned PSRI measurements predicting subsequent morphological development one week in advance (R² = 0.62). This integrated phenotyping framework provides efficient tools for accelerating climate-resilient breeding through objective genotype classification, early stress detection, and data-driven decision support, with potential adaptation to other vegetable crops and integration with IoT-based collaborative breeding network.
Why it matches plant phenotyping methods高スループット3D・マルチスペクトル表現型計測プラットフォームの検証と応用が研究の中心であり、形態・スペクトル形質の自動取得、抽出、予測性能、遺伝子型分類を評価している。
abstractThis study validated and applied an automated high-throughput phenotyping system for evaluating seasonal adaptation in 134 Chinese cabbage genotypes
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.
Understanding diurnal canopy orientation in crops is important for interpreting plant responses to light and environmental conditions, yet field-based quantification remains limited. In this study, we present Heliocot, a field RGB imaging approach that converts time-resolved images into reference-area standardized projected leaf area (PLA) time series to quantify within-day canopy orientation dynamics in early-season cotton. Leaf instance segmentation was performed using YOLOv8m-seg and refined through a 144-combination post-processing optimization. On the held-out early-stage validation/tuning set, the selected workflow showed strong agreement with manual ground truth (R2 = 0.948; NRMSE = 0.082) and destructive leaf area measurements (R2 = 0.836). Derived diurnal metrics, including Daily Orientation Amplitude (DOA) and Peak Orientation Index (POI), consistently revealed a midday maximum (13:15) in canopy projection. Exploratory genotype-level analysis suggested negative associations between orientation indices and selected plant traits, including specific leaf area (SLA) versus DOA (r = −0.71, p = 0.021, R2 = 0.508), destructive leaf area (LA) versus DOA (r = −0.69, p = 0.028, R2 = 0.471), and stem dry weight (SDW) versus POI (r = −0.74, p = 0.014, R2 = 0.554), while plant height was not significantly associated with POI and DOA (p > 0.05). Although currently limited to early-season conditions and two field-imaging dates, this approach provides a practical workflow for field-based monitoring of canopy projection dynamics in cotton, while broader temporal and environmental validation remains necessary.
Why it matches plant phenotyping methods圃場RGB画像から葉面積と日周キャノピー配向動態を推定する手法を開発・検証しており、植物形質取得が研究の中心である。
abstractwe present Heliocot, a field RGB imaging approach that converts time-resolved images into reference-area standardized projected leaf area (PLA) time series to quantify within-day canopy orientation dynamics in early-season cotton.
Accurately estimating leaf area index (LAI) is vital for evaluating crop growth and predicting yields. Conventional approaches, however, often struggle due to the limited representativeness of available data and the complex structure of plant canopies, which reduce their reliability across diverse canopy architectures and observation conditions. To overcome these challenges, this work introduces an LAI retrieval framework that combines a three-dimensional radiative transfer model (3D RTM) with deep learning techniques. Representative 3D maize canopy scenarios were generated using the LESS model, producing synthetic LiDAR point clouds constrained by realistic structural parameters. A deep learning model based on PointNet++ was trained, and transfer learning (TL) was employed to facilitate knowledge transfer from simulated to actual measured data. The TL-enhanced model demonstrated significant improvement, with R2 rising from 0.537 to 0.842 and RMSE dropping from 0.541 to 0.288 m2·m−2. Moreover, retrieval performance was notably affected by scanning mode, angle, and stem diameter, achieving optimal results under TLS acquisition, moderate scanning angles, and intermediate stem widths. These findings suggest that integrating 3D RTM-generated synthetic point clouds with transfer learning is an effective strategy for enhancing the robustness and generalization of LiDAR-based LAI retrieval.
Why it matches plant phenotyping methodsLiDAR点群からトウモロコシのLAIを推定する手法を、3D放射伝達モデル、PointNet++、転移学習で開発・検証しており、植物形態形質の取得・推定が研究の中心です。
abstractthis work introduces an LAI retrieval framework that combines a three-dimensional radiative transfer model (3D RTM) with deep learning techniques.
Reproduction assets foundThe paper's field-measured LiDAR point cloud and LAI data (Yingke Oasis and Huazhaizi sites) come from a publicly accessible TPDC dataset with an explicit URL in the Data Availability Statement. No author analysis code, trained models, or synthetic dataset deposit is stated.Dataset · public2024WX06.
Data Availability Statement: The dataset used in this study was obtained from the National Tibetan
Plateau Data Center (TPDC, https://www.tpdc.ac.cn/ (accessed on 6 September 2025)), a publicly
accessible scientific data platform providing multi-source geoscientific datasets. The specific dataset
can be accessed via: https://www.tpdc.ac.cn/zh-hans/data/4d60d570-0aa9-417b-8a9d-c32b73b564
(accessed on 6 September 2025). The TPDC database integrates long-term observational and remote
sensing data with standardized quality control, ensuring the reliability and consistency of the datasets
for scientific research.
Acknowledgments: The authors would like to acknowledge the National TibetaOpen asset ↗4d60d570-0aa9-417b-8a9d-c32b73b564pdf-raw-page:19 lines:1-51Code / dataset availability confirmedCrossref · Europe PMC · checked 5 Sept 2026
Three-dimensional (3D) procedural plant architecture models have emerged as an important tool for simulation-based studies of plant structure and function, extracting plant architectural parameters from field measurements, and for generating realistic plants in computer graphics. However, measuring the architectural parameters for these models at the field and population scales remains prohibitively labor-intensive. We present a novel algorithm that generates the 3D plant architecture from an image, to create a functional structural plant model from an image that reflects organ-level geometric and topological parameters, providing a more comprehensive representation of the plant’s architecture. Instead of using 3D sensors or processing multi-view images with computer vision to obtain the 3D structure of plants, we propose a method that generates token sequences containing a procedural definition of the plant architecture. This work uses only synthetic images for training and testing, where “exact” architectural parameters were known, which allowed for testing of the hypothesis that organ-level architectural parameters could be extracted from imagery data using a vision language model (VLM). A synthetic dataset of cowpea plant images was generated using the Helios 3D plant simulator, with the detailed plant architecture encoded in XML files. We developed a plant architecture tokenizer for the XML file defining plant architecture, converting it into a token sequence that a language model can predict. Then, a VLM was trained to predict plant architecture token sequences from images. Our results demonstrate that the model can predict plant architecture tokens with an F1 score of 0.73 in a teacher-forcing method. Evaluation of the model was performed through autoregressive generation, achieving a BLEU-4 score of 94.00% and a ROUGE-L score of 0.5182. Our model achieves lower MAPE than feature regression-based methods in estimating bulk plant-level traits that require understanding of the occluded 3D structure of the plant, such as leaf count and leaf area. We conclude that generating plant architecture and parameter extraction from synthetic imagery are feasible using a VLM approach, supporting future extension to real imagery.
Why it matches plant phenotyping methods画像から器官レベルの植物構造と形態形質を抽出するVLM手法の開発・評価が中心であり、植物フェノタイピング手法に該当する。
abstractWe present a novel algorithm that generates the 3D plant architecture from an image, to create a functional structural plant model from an image that reflects organ-level geometric and topological parameters
Reproduction assets foundThe paper's footnotes explicitly state that the authors' code is available on GitHub and the synthetic cowpea image/XML dataset is available on Hugging Face, both paper-specific and publicly actionable. The Helios URL is a generic third-party simulator library, not a paper-specific asset.Code · public1. ^ Code is available at: https://github.com/GEMINI-Breeding/Image2PlantArchitecture .Open asset ↗GEMINI-Breeding/Image2PlantArchitecturelines:600-676Dataset · public2. ^ Dataset is available at: https://huggingface.co/datasets/heesup/Cowpea-Architecture-XML .Open asset ↗heesup/Cowpea-Architecture-XMLlines:600-676Plant phenotyping relevance match · UnverifiedCrossref · checked 15 Sept 2026
Published20 May 2026Journal of Advanced Computational Intelligence and Intelligent InformaticsCited by 0 · OpenAlex ↗
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
High-precision plant phenotyping requires efficient 3D reconstruction methods with high geometric quality. 3D Gaussian Splatting (3DGS) has recently emerged as a promising approach for real-time 3D reconstruction, achieving impressive visual quality. However, in crop environments dominated by monochromatic and low-texture regions, existing 3DGS methods often produce ambiguous geometries and fail to recover geometry-consistent 3D surfaces. To address these limitations, we propose LV-3DGS (Leafy Vegetables-3DGS), an optimized 3DGS-based framework tailored for the reconstruction of leafy vegetable scenes. First, a blurred reconstruction module is introduced to mitigate reconstruction artifacts caused by camera motion blur during multi-view image acquisition. Second, we propose a planar optimization strategy and design both local and global geometric consistency regularizations to optimize the model, thereby improving the surface reconstruction quality and geometric accuracy. Third, based on an analysis of individual Gaussian contributions, a contribution-based pruning strategy is developed to selectively remove inaccurate geometric components, achieving accurate scene geometry while reducing memory consumption and improving rendering efficiency. In addition, a quantitative geometric evaluation method is proposed for assessing reconstruction quality. Experimental results demonstrate that the proposed method achieves the highest accuracy among the tested baselines, with SSIM, PSNR, and LPIPS reaching 0.94, 34.53 dB, and 0.11, respectively. Moreover, the geometric consistency (GC) metric attains 0.317 cm. Finally, phenotypic parameters are measured from the reconstructed leafy vegetable point clouds. Compared with ground truth measurements, the proposed approach yields coefficients of determination (R2) of 0.9959, 0.9651, and 0.9895 for plant height, leaf number, and leaf area, respectively. These results are significantly outperform to some existing phenotyping methods, providing a new methodology and technical solution for high-precision, low-cost, and high-throughput crop phenotyping.
Why it matches plant phenotyping methods葉菜類の3D再構成とそこからの形質抽出を中心に、手法開発・幾何評価・実測値との検証を行っているため、植物フェノタイピング手法として中心的である。
abstractwe propose LV-3DGS (Leafy Vegetables-3DGS), an optimized 3DGS-based framework tailored for the reconstruction of leafy vegetable scenes.
To achieve high-precision and high-efficiency estimation of the Leaf Area Index (LAI) of jujube trees using drone remote sensing, and to overcome the limitations of traditional vegetation index methods, such as saturation in the later stages of crop growth, sensitivity to background noise, and difficulty in capturing temporal dynamics, this study proposes a parallel hybrid deep learning framework using CNN-GRU. The model adaptively extracts spatial-spectral local features from drone RGB images through a convolutional neural network (CNN) branch, while a gated recurrent unit (GRU) branch learns the sequential evolution of LAI during key phenological periods. Finally, a meta-learner integrates spatial-temporal information for decision-making. To verify the model's effectiveness and prediction performance, the study systematically collected multi-temporal ground-measured LAI data and synchronized drone remote sensing images during critical growth stages of jujube trees in two independent years: 2024 (Bachu, Xinjiang) and 2025 (Alaer, Xinjiang). A series of spectral and texture indices were extracted as model inputs. The experimental results show that the proposed CNN-GRU model exhibits excellent learning and fitting capabilities on the training set, with an R 2 value of 0.839. On the test set, after optimization with data augmentation strategies, the model's prediction accuracy is significantly improved, with prediction accuracy reaching its best level, with an R 2 of 0.83 and an RMSE of 0.150. All error metrics outperform mainstream comparative models such as Transformer, KNN, MLP, and CNN. This study demonstrates that the hybrid deep learning architecture, combining spatial feature extraction and time-series modeling, is an effective approach for accurate and robust remote sensing inversion of crop LAI in complex agricultural scenarios, providing a reliable technical tool for the digital management of smart orchards and precise agricultural decision-making.
Why it matches plant phenotyping methodsUAV RGB画像からナツメ樹のLAIを推定するCNN-GRU手法を開発し、複数年データと比較モデルで性能検証しており、植物形質取得が中心である。
abstractthis study proposes a parallel hybrid deep learning framework using CNN-GRU
Plant phenotyping relevance match · UnverifiedCrossref · Europe PMC · OpenAlex · checked 5 Sept 2026
Introduction With the continuous advancement of smart agriculture, multi-modal remote sensing based on unmanned aerial vehicles (UAVs) offers new technical approaches for monitoring and managing crop moisture in fields. However, significant challenges remain in developing high-precision field-scale crop Plant Moisture Content (PMC) prediction models and translating them into actionable irrigation strategies. Methods This study focuses on winter wheat, employing field experiments with PMC and water use efficiency (WUE) as indicators of crop water status. Vegetation indices (VIs) derived from UAV data were used to construct a leaf area index (LAI) inversion model. Crop Height was extracted from oblique photogrammetry point cloud data. By combining the Penman-Monteith equation with dual crop coefficients, an improved evapotranspiration (ET) model was developed, utilizing multispectral data from UAVs, thermal infrared data, point cloud-derived plant height, and LAI inversion results. Further utilizing VIs, temperature indices (TIs), and machine learning algorithms (Random Forest Regression (RFR), Back Propagation Neural Network (BPNN), Partial Least Squares Regression (PLSR), and Support Vector Regression (SVR), we established PMC prediction models for winter wheat at different growth stages. These models, integrated with WUE, form the basis for an irrigation scheduling optimization framework at the field scale. Results Results indicate that VIs, the difference between canopy temperature and air temperature (ΔT), Crop Water Stress Index (CWSI), and ET exhibit varying correlations with PMC during three critical growth stages of winter wheat, with ET showing the highest correlation during the jointing and heading stages (absolute correlation coefficient |r| ≥ 0.639). Compared to PMC prediction models constructed with different combinations of VIs, ET, VIs+ET, and VIs+TIs, the model employing the RFR algorithm with multimodal inputs (VIS+TIs+ET) demonstrated the best performance. The model’s predictive accuracy gradually improved across all growth stages, peaking during the grain-filling stage, with the coefficient of determination(R 2 ) of 0.900 and a normalized root mean square error (nRMSE) of 2.688%. Optimal WUE varied across growth stages under different irrigation treatments. The highest values were achieved at the jointing stage under treatment W3 (PMC = 81.8%), and at the heading and grain-filling stages under treatment W1 (PMC = 76.8% and 64.0%, respectively). Discussion The study suggests that stage-specific irrigation scheduling based on PMC thresholds can improve overall water use efficiency. This study shows that integrating multi-modal UAV data with machine learning and an improved ET model enables high-precision PMC monitoring, supporting data-driven irrigation scheduling in precision agriculture.
Why it matches plant phenotyping methodsUAVマルチモーダルデータと機械学習により、作物水分状態（PMC）、LAI、草高、蒸発散量を推定する手法を開発・評価しており、フェノタイピング手法が研究の中心である。
abstractCrop Height was extracted from oblique photogrammetry point cloud data.
Plant phenotyping relevance match · UnverifiedOpenAlex · Crossref · Europe PMC · checked 5 Sept 2026
Efficient phenotyping monitoring of cauliflower is crucial for its breeding and production. However, traditional manual measurement methods are time-consuming and labor-intensive, and existing deep learning (DL) methods mostly focus on the seedling stage, lacking systematic research covering the entire growth period. In this study, RGB images of cauliflower from seedling to harvest were collected. Through systematic screening and evaluation of instance segmentation models, accurate segmentation of plants and curds was achieved, and plant canopy width, leaf area, and curd traits were automatically extracted to track their dynamic changes. Evaluation results showed that YOLO12s-seg was the optimal model. It can achieved a segmentation mask mAP 50 of 99.4% for plants and curds in sparsely planted images and showed an advantage in identifying partially occluded early curds beneath inner leaves. Traits such as plant canopy width and curd diameter automatically extracted from segmentation results were highly consistent with manual measurements (R 2 > 0.90). Furthermore, the Richards model and Sine model were used to accurately fit the growth dynamics of leaf area and curd area, respectively. Based on growth kinetics, curds were classified into three types: mature and compact type, peak-burst type, and steady-increase type. Cluster analysis of 47 germplasms based on high-throughput phenotyping data revealed four groups and their growth characteristics: comprehensively coordinated type, mid-maturity compact type, large high-yield type, and curd-dominant type. Integrating the above functions, a platform for cauliflower growth monitoring and phenotypic analysis was developed. It provided full-process support from automatic image processing to growth dynamic analysis. This work provides an effective automated solution for high-throughput phenotyping analysis and growth dynamic monitoring of cauliflower, and offers a referable analytical framework for crop growth pattern research and intelligent breeding decision-making.
Why it matches plant phenotyping methods植物のインスタンスセグメンテーションから葉面積・草冠幅・花蕾形質を自動抽出し、手動測定との技術検証と成長動態解析、統合プラットフォーム開発を行っており、フェノタイピング手法が研究の中心である。
abstractThrough systematic screening and evaluation of instance segmentation models, accurate segmentation of plants and curds was achieved, and plant canopy width, leaf area, and curd traits were automatically extracted to track their dynamic changes.
Given the increasing frequency, severity, and socioecological impacts of wildfires, there is an urgent need for robust frameworks to better characterize fire behavior and flammability patterns across ecosystems to support early warning, mitigation, and management strategies. However, flammability remains difficult to quantify and scale, as it involves multiple interacting components that are typically measured at the bench scale. This study aimed to establish empirical links between spectral information, plant traits, and flammability metrics, and to scale these relationships to satellite imagery to translate these metrics into a spatial context. We combined laboratory spectroscopy, plant trait measurements including leaf mass per area, carbon, and cellulose, and combustion experiments using a simple and reproducible burning device. In total, 84 samples were collected and analysed, allowing us to characterise how spectral signatures relate to vegetation traits and fire behaviour. Spectral indices were developed to estimate plant traits, which were subsequently used as predictors in flammability models. These models were then transferred to Environmental Mapping and Analysis Program (EnMAP) hyperspectral imagery to derive spatial estimates across eucalypt forests and grasslands of the Australian Capital Territory (ACT). Spectral information distinguished fuel types and captured variability of the plant traits, while these traits showed associations with combustion behaviour. Based on these links, the best-performing model predicted the rate of temperature increase, a combustibility metric, in eucalypt forests (R2 = 0.70; Root Mean Square Error = 32.48 °C/s). In contrast, grassland models showed limited predictive performance, likely due to weaker relationships between plant traits and flammability metrics. Overall, this study demonstrates a practical and scalable approach for deriving flammability maps from hyperspectral and in situ data, highlighting the potential of plant-trait-based remote sensing. The resulting maps should not be interpreted as standalone fire risk products, but rather as a characterization of the structural and biochemical drivers of flammability. The main constraint of this work is the limited sample size. Future research should expand spatial and temporal coverage to better capture vegetation variability and enable the inclusion of independent validation datasets. Exploring alternative combustion protocols and testing more advanced spectral modelling approaches for trait estimation would provide additional insights.
Why it matches plant phenotyping methods植物形質を分光情報から推定し、ハイパースペクトル画像へ展開して可燃性関連の植物状態を評価する手法が研究の中心であり、モデル性能も検証しているため。
abstractSpectral indices were developed to estimate plant traits, which were subsequently used as predictors in flammability models.
Reproduction assets foundThe paper's supplementary materials (hosted publicly by MDPI) contain the paper-specific plant phenotype measurements: sampled species lists, fractional cover, and measured vegetation traits across dates and plots, plus combustion replicate variability and trait–flammability relationship data. The raw underlying data,谱Supplement · publicbroader environmental coverage, improved plant trait retrieval meth-
ods, and independent validation. Future work should also explore non-linear modelling
frameworks to better capture the complexity of vegetation flammability across ecosystems.
Supplementary Materials: The following supporting information can be downloaded at:
https://www.mdpi.com/article/10.3390/rs18101546/s1, Supplementary Table S1 provides the list of
sampled plant species and their percentage cover across sites, paddocks, plots, and fuel types; Table
S2 presents the fractional cover of each species and litter component; Figure S1 shows the study-site
vegetation map; Figures S2–S6 show the measured vegetation traits acrosOpen asset ↗pdf-raw-page:22 lines:1-49Plant phenotyping relevance match · UnverifiedCrossref · checked 13 Sept 2026
Leaf Area Index (LAI) is a key biophysical parameter for characterizing terrestrial vegetation dynamics and land surface processes. Time-series MODIS LAI products are widely used in ecological and land-related research, but cloud contamination and sensor noise lead to widespread spatio-temporal gaps, limiting their ability to support long-term, consistent vegetation monitoring over large areas. To address this issue, this study proposes a novel self-supervised LAI reconstruction framework (SSLAI) for generating gap-free and ecologically consistent LAI datasets across China. The framework integrates cross-modal environmental fusion, multi-scale spatio-temporal modeling, and adaptive phenological constraints to ensure the reconstructed LAI aligns with realistic vegetation growth rhythms. SSLAI outperforms seven traditional and state-of-the-art deep learning methods, maintaining a root mean square error (RMSE) below 0.20 even with 16 missing time windows. Field validation confirms its high accuracy, with a coefficient of determination (R2) of 0.885 and an RMSE of 0.477. Furthermore, SSLAI’s response to meteorological changes aligns with ecological principles, demonstrating favorable physical interpretability and ecological rationality. The reconstructed LAI exhibits superior spatial completeness and temporal consistency compared with MODIS, VIIRS, and GLASS products, and performs robustly under variable climatic conditions. This study provides an effective self-supervised solution for MODIS LAI gap-filling over large regions, and the generated high-quality LAI dataset can serve as a reliable data foundation for vegetation dynamics monitoring, land surface modeling, and global change research.
Why it matches plant phenotyping methods植物群落のLAIという明示的な植物形質を対象に、欠測補完の計算手法を開発し、既存手法との比較および野外検証を行っているため、方法開発・検証が中心である。
abstractthis study proposes a novel self-supervised LAI reconstruction framework (SSLAI) for generating gap-free and ecologically consistent LAI datasets across China.
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).
Plant phenotyping relevance match · UnverifiedOpenAlex · Europe PMC · Crossref · checked 5 Sept 2026
Eggplant (Solanum melongena L.) is a widely cultivated vegetable crop worldwide, occupying an important position in the agricultural industries of Asia, the Middle East, and Southern Europe. Its significance extends beyond agricultural economics to diverse dimensions such as dietary nutrition, rendering it of considerable research and application value. Traditional crop phenotyping methods suffer from low efficiency, substantial manual errors, and a tendency to damage tender seedlings, while existing three-dimensional phenotyping techniques face challenges including strong background interference and large data volumes. These dual constraints limit the accuracy and application feasibility of seedling phenotyping. To address these issues, this study proposes a non-destructive phenotyping method for eggplant seedlings, with the improvement of the PointNet++ architecture as its core and point cloud background purification as a key preprocessing step, aiming to enhance eggplant breeding efficiency and seedling screening accuracy. The raw point clouds first undergo background purification to actively remove seedling tray points, thereby improving point cloud purity and reducing data size. Concurrently, based on the PointNet++ model, we develop an improved point cloud segmentation model, EggplantPointNet++, by introducing multi-scale residual blocks, integrating channel attention mechanisms, incorporating a global context module, and refining the feature propagation layer. In conjunction with the DBSCAN clustering algorithm, this approach achieves semantic and instance segmentation of eggplant seedling point clouds, with certain improvements in segmentation accuracy and model efficiency under small-scale and occluded scenarios. To validate the technical effectiveness, multiple comparative experiments and ablation studies were conducted. The results demonstrate that EggplantPointNet++ outperforms the original model, background purification preprocessing provides positive gains, and each improved module contributes positively. The final model achieves improvements in core metrics including Recall and F1-score. Based on the segmented point cloud data, this study calculates core phenotypic parameters including plant height, stem diameter, cotyledon angle, and cotyledon area. Using the technical system established in this study, we completed the time-series measurement of three-dimensional morphological changes in eggplant seedlings during the cotyledon stage, providing quantitative references for seedling growth assessment and superior plant selection.
Why it matches plant phenotyping methodsナス幼苗の3D点群から形質を抽出する非破壊フェノタイピング手法を開発し、比較実験・アブレーションで技術性能を検証しているため、方法が中心的である。
abstractthis study proposes a non-destructive phenotyping method for eggplant seedlings
The leaf area index (LAI) is a key parameter for characterizing crop growth and water use efficiency. Therefore, efficient and accurate monitoring of LAI is essential for precision rice management. To overcome the limitations of traditional LAI measurement methods, which are time consuming, labor intensive, and difficult to scale, this study proposes an inversion framework that integrates multi-source UAV remote sensing features with machine learning models. The framework incorporates color indices (CIs) derived from RGB imagery, vegetation indices (VIs) derived from multispectral data, texture features (TIs), and texture feature indices (TFIs), and employs six machine learning algorithms to develop optimized LAI estimation models for the rice booting stage. The results indicate that at a flight altitude of 30 m, the CNN model integrating CIs and TIs achieved an accuracy of R 2 = 0.815. At 60 m, the RF model combining VIs and TFIs showed superior performance, with an R 2 of 0.866. Further integration of CIs, VIs, and TFIs at 30 m produced the best results, increasing R 2 to 0.901, reducing RMSE to 0.273, and raising RPD to above 3.0. These findings demonstrate that TFIs significantly enhance the spectral-spatial representation capability of multispectral data, thereby improving model accuracy. The combined use of CIs and VIs across different sensors compensates for the inherent limitations between spectral and spatial information, while the integration of multi-resolution TIs and TFIs effectively overcomes the constraints of single-source data. Overall, the proposed approach provides a robust and efficient solution for high-precision LAI estimation during critical growth stages of rice, offering strong support for precision agricultural management.
Why it matches plant phenotyping methodsUAV画像・マルチスペクトル特徴量と機械学習によるイネLAI推定フレームワークの開発・性能評価が研究の中心であり、植物形質の取得手法に該当する。
abstractthis study proposes an inversion framework that integrates multi-source UAV remote sensing features with machine learning models.
Multispectral / hyperspectralLeafRootMorphology / geometry measurementLeaf traitsRoot system architecture
Premise Selective breeding over thousands of years has prioritized aboveground yield, with little regard for changes belowground. Roots underpin plant growth and resilience, but our knowledge of these critical structures lags behind that of aboveground structures. Accurately phenotyping root traits is labor-intensive, expensive, and often destructive. High-throughput, nondestructive methods are required to advance understanding of the fundamental biology of root systems and to integrate hard-to-measure root traits into breeding programs. Methods We used American licorice (Glycyrrhiza lepidota Pursh.), a perennial legume with a rich ethnobotanical history, as a model to investigate root system phenotypes. We assessed root traits across multiple populations, analyzed relationships between above- and belowground phenotypes, and tested the use of multidimensional leaf traits, including spectral reflectance, in predicting root traits. Results Root traits of American licorice varied significantly across source populations. Root traits were strongly intercorrelated and each root trait correlated with an aboveground phenotype. Leaf spectral reflectance and elemental composition predicted belowground traits; however, interpretation of some trait-specific signals were complicated by isometric scaling between plant size and root traits. Conclusions These findings demonstrate the use of high-dimensional leaf traits as a proxy for root traits, with potential applications for understanding foundational questions in plant biology and in breeding programs targeting belowground structures of perennial herbaceous species. Further optimization and larger studies are needed to improve predictive models.
Why it matches plant phenotyping methods葉の高次元形質とスペクトル反射を用いて、測定困難な根形質を非破壊・高スループットに推定する方法が研究の中心である。
abstractHigh-throughput, nondestructive methods are required to advance understanding of the fundamental biology of root systems and to integrate hard-to-measure root traits into breeding programs.
Reproduction assets foundThe paper's data availability statement points to two public, paper-specific assets: raw root scans on Zenodo and a Figshare deposit containing RhizoVision Explorer output features, CropReporter data and metadata, spectral reflectance data, elemental composition data, and all R code needed to reproduce the analyses. NoDataset · publich Center Bioanalytical Chemistry Facility (RRID:SCR_001047). Finally, we thank the reviewers for their careful evaluation of our manuscript and constructive comments, which helped us clarify the conceptual framing and strengthen the overall quality of the work.
DATA AVAILABILITY STATEMENT
Raw root scans can be found on Zenodo ( https://zenodo.org/records/18852041 ). RhizoVision Explorer output features, CropReporter and associated metadata, spectral reflectance data, elemental composition data, and all R code needed to reproduce the analyses presented in this manuscript can be found on Figshare ( https://doi.org/10.6084/m9.figshare.28742870 ).
REFERENCES
Alahmad , S.
,
D.
Smith
,
C.
KatOpen asset ↗Zenodo · 18852041lines:173-419Dataset · publicILITY STATEMENT
Raw root scans can be found on Zenodo ( https://zenodo.org/records/18852041 ). RhizoVision Explorer output features, CropReporter and associated metadata, spectral reflectance data, elemental composition data, and all R code needed to reproduce the analyses presented in this manuscript can be found on Figshare ( https://doi.org/10.6084/m9.figshare.28742870 ).
REFERENCES
Alahmad , S.
,
D.
Smith
,
C.
Katsikis
,
Z.
Aldiss
,
S. M.
Brunner
,
S. V.
Meer
,
L.
Meijer
, et al. 2025 .
Phenotyping the hidden half: combining UAV phenotyping and machine learning to predict barley root traits in the field
. Journal of Experimental Botany
76 : 5161 ‐ 5178 .
40580084
10.1093/jxb/eraf268
PMC1Open asset ↗Figshare · 10.6084/m9.figshare.28742870lines:173-419Plant phenotyping relevance match · UnverifiedEurope PMC · OpenAlex · checked 6 Sept 2026
Abiotic stresses such as heat waves significantly reduce wheat productivity by altering leaf anatomy and physiology, leading to reduced photosynthetic carbon assimilation and crop yield. Despite the advancement in various imaging technologies at the field, canopy, plant, tissue, cellular, and subcellular levels, phenotyping of imaging-based leaf structural traits (e.g. vein density, stomatal density, and stomatal aperture) for abiotic stresses is still time-consuming and expensive without the aid of artificial intelligence (AI) and machine learning (ML). This review consolidates current knowledge of wheat leaf structural and functional adaptations to heat stress and highlights key advancements in imaging technologies for studying these important phenotypic traits. Recent high-resolution, non-destructive imaging technologies, including confocal laser scanning microscopy, X-ray computed tomography, and optical coherence tomography, have enabled in vivo visualization of plants. Integrating these imaging techniques with AI/ML facilitates high-throughput phenotyping and the modelling of stress responses. We emphasize the potential for future research to leverage these technological advancements in imaging and AI, combining imaging data with physiological and multi-omics studies to deepen the understanding of plant heat tolerance mechanisms. Such multidisciplinary integration in leaf structure phenotyping will accelerate the development of resilient wheat varieties, offering critical insights for crop improvement in the face of climate change.
Why it matches plant phenotyping methods植物の葉構造・機能形質を対象とする画像計測技術とAI/MLによる表現型解析を中心に整理したレビューであり、植物フェノタイピング手法レビューに該当する。
abstractThis review consolidates current knowledge of wheat leaf structural and functional adaptations to heat stress and highlights key advancements in imaging technologies for studying these important phenotypic traits.
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.
Abstract Verticillium wilt is one of the main factors hindering cotton yield increase, the more severe the disease, the more severe the yield loss. In order to achieve early detection and prevention of Verticillium wilt, this study investigated cotton plants naturally affected by Verticillium wilt in the field. We analyzed the cotton canopy multispectral data under the stress of Verticillium wilt and the leaf area index (LAI) data collected from the ground. Due to the low prediction accu-racy of traditional empirical models, this paper selected three different back propagation BP neural network models with 5, 10, and 15 hidden layer nodes (hln) and optimized them using four intelligent swarm algorithms: genetic algorithm (GA), particle swarm optimization (PSO), spotted hyena algorithm (SHO), and improved spotted hyena algorithm (ISHO) to estimate the cotton LAI under the stress of Verticillium wilt. Finally, BP algorithm with different node number of hidden layer was optimized by comparing four intelligent swarm optimization al-gorithms to estimate LAI of cotton under verticillium wilt stress. The findings indicated that GA-BP (hln15) was the best in the GA-BP algorithm; In the PSO-BP algorithm, PSO-BP (hln10) performed best; In the SHO-BP model, SHO-BP (hln5) had the highest model performance; In the ISHO-BP model, ISHO-BP (hln5) is the best, with a determination coefficient(R2), root mean square error(RMSE), and prediction accuracy(PA) of 0.952, 0.235, and 89.30%, respec-tively; The estimation results of ISHO-BP (hln5) model can better represent the distribution of Verticillium wilt plants than GA-BP (hln15), PSO-BP (hln10), and SHO-BP (hln5), and its estimation error range is (-0.8,0.5). Therefore, the application of ISHO-BP (hln5) model pro-vides a new method for estimating cotton LAI under pest and disease stress, and also provides technical support to meet the diversified needs of cotton farmers to increase their income and national economic development.
Why it matches plant phenotyping methodsUAVマルチスペクトルデータから綿のLAIを推定するモデルを比較・最適化しており、植物形質の取得・推定手法が研究の中心である。
abstractthis paper selected three different back propagation BP neural network models with 5, 10, and 15 hidden layer nodes (hln) and optimized them using four intelligent swarm algorithms
The article presents the developed algorithm and software for automated monitoring of strawberry plant growth using neural network technologies. The YOLO11x and YOLOx-seg models, pre-trained by transfer learning, are adapted to recognize and classify plants (plant class), leaves (leaf class), and a reference marker (ref_obj class) of a known size. Segmentation of strawberry leaves using the YOLO11x-seg model makes it possible to analyze the morphometric parameters of individual leaf plates (area, perimeter, roundness, aspect ratio). A set of RGB images (2000 pieces) obtained using a GoPro HERO11 camera under controlled laboratory conditions was formed and annotated, followed by augmentation to increase the model's resistance to variations in shooting conditions. The developed algorithm converts the coordinates of the bounding boxes and segmentation masks of recognized objects into metric units using calibration coefficients calculated from a marker of known size (100×100 mm). The software implemented using PyQt5, TensorFlow, Keras, and OpenCV libraries provides not only visualization of results but also data storage in a local SQLite database with the ability to export to JSON and Excel formats. Validation of the model showed high accuracy in detecting plant bounding boxes (mAP50 = 0.906) and leaf segmentation (mAP50 -mask = 0.625). The average processing speed was 20.3 ms/frame for detection and 34.5 ms/frame for segmentation. The measurement error was less than 3.5 % for the overall parameters of the plant and 5.2 % for the morphometric parameters of the leaves, confirming the effectiveness of the method for assessing the height, width and area of plants, as well as the analysis of the leaf apparatus. The research results show the promise of an approach for automating plant phenotyping in real time.
Why it matches plant phenotyping methods植物の成長・葉形態を画像から自動抽出するアルゴリズム、ソフトウェア、データセットを開発し、精度・処理速度・測定誤差を検証しているため、植物フェノタイピング手法が中心である。
abstractThe article presents the developed algorithm and software for automated monitoring of strawberry plant growth using neural network technologies.
Optimizing olive orchard management requires timely, per-tree data to enhance productivity and sustainability. Unoccupied aerial vehicle (UAV)-based red, green, and blue (RGB) imagery offers a low-cost solution for acquiring high-resolution spatiotemporal insights for orchard management, which are not yet common in Tunisia. This study monitored tree structural parameters, leaf area index (LAI), and leaf nitrogen content (%N DW) in two Tunisian olive orchards during 2022 and 2023. UAV-derived imagery was photogrammetrically processed into 3D point clouds and analyzed using an automated approach. Target variables of the automated approach included tree-wise estimates of height, projected crown area, and crown volume, as well as raster cell counts of the canopy cloud and spectral indices such as the normalized green-red difference index (NGRDI) and green leaf index (GLI). In addition, the estimated parameters per tree were used to model LAI and leaf nitrogen content. Analyses were conducted separately for trees represented by a high and a low number of points in the dense point cloud. Outcomes were compared to reference data collected in the field on dates close to the UAV flights. The findings showed strong relationships for the projected crown area (R2 = 0.82 and 0.91) and tree height (R2 = 0.89 and 0.88) when compared to reference values. Linear regression models for LAI (R2 = 0.73 and 0.68) and crown volume (R2 = 0.85 and 0.91) estimation also show strong relationships. However, leaf nitrogen estimation was not feasible from RGB spectral index values, as it showed a weak relationship (R2 = 0.34). A dataset with multispectral imagery could overcome this limitation but would increase costs, making it less suitable for the low-budget approach required in price-sensitive farming contexts, particularly in low-income regions.
Why it matches plant phenotyping methodsUAV画像から樹体形状・LAIなどの植物形質を自動推定し、圃場基準値との比較検証を行う手法が研究の中心である。
abstractUAV-derived imagery was photogrammetrically processed into 3D point clouds and analyzed using an automated approach.
Introduction Herbicide dose-response assays are routinely implemented to compare herbicide resistance among weed biotypes, which requires plant biomass to estimate the dose that reduces growth by 50% relative to untreated plants (GR 50 ). The Phenospex TraitFinder is a high-throughput, non-destructive, digital phenotyping system that collects data from 7 spectral parameters and 13 morphological parameters, including Digital Biomass (DB), which offers the opportunity for researchers to eliminate the time and labor associated with manual biomass collection. However, DB is the product of 3D Leaf Area and Plant Height (PH) Mean, making it a measurement of plant volume and an indirect indicator of biomass. While DB is highly correlated with true biomass, digitally collected plant volume data has not been implemented for dose-response assays or assessed for accuracy relative to true biomass data. Additionally, inaccurate PH measurements could impact the accuracy of DB measurements. Methods This study sought to assess the accuracy and utility of DB and the 19 remaining parameters in dose-response assays by comparing dose-response curves and GR 50 estimates generated from digital data and fresh biomass (FB) data. Accuracy of PH measurements were also assessed by comparing digital and manual measurements with the paired t-test. Pre-emergence dose-response assays using fomesafen and atrazine were implemented with common lambsquarters ( Chenopodium album L.). At 21 days after treatment, manual measurements of FB and PH were collected following digital data collection. Results Consistently strong correlations ( r = 0.97, P < 0.05) were observed between digitally collected data and their equivalent manual measurements. Comparisons of the dose-response curves indicated that only 3D Leaf Area, DB, Convex Hull Area, Projected Leaf Area, and Voxel Volume Total generated highly similar curves and GR 50 estimates relative to FB data, indicating that any one or all of these parameters could be utilized instead of FB. Small differences (approximately 1.06 to 1.77 mm) between manual and digital PH measurements were identified with the paired t-test, but since DB consistently produced similar dose-response curves and GR 50 estimates relative to FB, these differences did not impact the accuracy of DB measurements. Discussion Without requiring manual biomass collection, turnaround time for dose-response and other phenotyping assays decreases and allows faster sharing of research. Furthermore, herbicide-resistant plants can be preserved for phenotyping at later growth stages, tissue collection, and to produce progeny for future experiments.
Why it matches plant phenotyping methodsデジタル表現型システムで植物体積・草丈などを取得し、手作業の生体重測定との精度比較および除草剤用量反応曲線への有用性を検証しており、表現型取得法が中心です。
abstractThe Phenospex TraitFinder is a high-throughput, non-destructive, digital phenotyping system that collects data from 7 spectral parameters and 13 morphological parameters
Reproduction assets foundThe paper's digital phenotyping dose-response datasets are publicly deposited: the data availability statement names Ag Data Commons DOI 10.15482/USDA.ADC/29815082 and a figshare link, both paper-specific. No author analysis code repository is explicitly stated.Dataset · publicThe datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: 10.15482/USDA.ADC/29815082 or https://figshare.com/s/64d1bbac59a95c4721f1 .Open asset ↗figshare · 10.15482/USDA.ADC/29815082lines:548-573Plant phenotyping relevance match · UnverifiedOpenAlex · Crossref · checked 5 Sept 2026
Conventional approaches to measuring stomatal conductance (gs) and transpiration often rely on instruments that interfere with plant physiology. Porometers, for example, restrict natural leaf movement, apply pressure, and introduce dry airflow that can alter stomatal behaviour, thereby reducing the relevance of such measurements. Prior studies report discrepancies among devices attributable to such interferences (Toro et al. 2019). To minimise artefacts, transpiration should be estimated remotely without physical contact, which theoretically can be achieved via a thermal leaf energy-balance approach that infers gs from leaf temperature, radiative load, and boundary-layer terms. In this study, we combine 3D plant models, light interception models, and thermal imaging to solve the energy-balance equation of individual leaves, estimating transpiration entirely remotely. Approaches to estimate stomatal conductance based on the energy-balance equation were developed recently to aid phenotyping of plantss. Most methods either imposed rapid changes in air humidity to perturb transpiration and, consequently, leaf temperature (Driever et al. 2023), or relied on ‘dry’ and ‘wet’ reference surfaces (as in Leinonen et al. 2006) to compute stress indices (Vialet-Chabrand and Lawson 2020). These methods require reference materials to assess surface temperatures under maximum and zero transpiration, showing the effect of longwave radiation. However, reference-material methods were constrained by heterogeneity in light interception caused by variation in leaf angle and orientation, because reference surfaces could not reorient like real leaves (Zhang et al. 2025). In this study, we addressed this challenge by using thermal imaging and 3D photogrammetry to capture leaf temperature and geometry noninvasively, allowing parameter estimation for each leaf individually. Here, ρ is the density of air (kg m−3), cp is the specific heat capacity of air (J kg−1 K−1) and rHR is the parallel resistance to heat and radiative transfer on the leaf surface (s m−1), s is the slope of the curve relating saturating water vapour pressure to temperature (Pa °C−1). TL and TA are leaf and air temperatures (°C), respectively, δe is air vapour pressure deficit (Pa), γ is the psychrometric constant (Pa K−1) and rva is the boundary layer resistance to water vapour (s m−1) (Supporting Information S2: Equation S1). The net radiative energy Rn in the energy-balance term was obtained from the same 3D light interception model, which integrates measured direct and lateral scattered irradiance (W m−2) (Supplement Material and Methods, File S2). Stomatal conductance gs (m s−1) is the inverse of stomatal resistance rs (s m−1). To experimentally obtain a wide range of gs values, we grew eggplant (Solanum melongena L.) plants in hydroponic units in growth chambers under four sets of environmental conditions (Table 1). Thirty-day-old plants (4–5-leaf stage) were placed on balances (Supplementary Materials and Methods, File S2). Units were sealed with plastic film to minimise evaporation. Mass loss attributable to transpiration was logged automatically every 30 s. To induce short-term changes in stomatal conductance, we imposed an acute osmotic stress by delivering a saline NaCl solution with high electrical conductivity (60 mS cm−1) to the root zone, producing a steep drop in root osmotic potential. This created rapid physiological and morphological responses that altered incident irradiance at the leaves, leaf temperature, and consequently energy balance, stomatal conductance and transpiration. We chose this stressor for operational simplicity. Any perturbation that modifies transpiration dynamics and thus gas exchange could have served our purpose. The total transpiration of a leaf, Et (kg s−1), is the product of the total conductance to water vapour from the mesophyll to the atmosphere, gv (m s−1), calculated from the estimated stomatal resistance rs (s m−1) and the boundary layer conductance gva (m s−1), the difference between water vapour concentration inside the leaf Cvs (dimensionless), and in surrounding air Cva (dimensionless), the leaf area A (m2), and the density of water ρw (kg/m3) (Jones 1992). Estimated stomatal conductance was obtained from leaf energy balance calculation (Equation 1). Boundary-layer conductance was computed from measured wind speed and leaf dimensions (leaf area, length, width) extracted from structure-from-motion 3D reconstructions (Supporting Information S1: Equation S6; Grace et al. 1980). Transpiration was then calculated for each leaf at each thermal 3D imaging time point, and whole-plant transpiration for comparison with gravimetric logs was the sum of all per-leaf estimates. As a non-invasive approach, we evaluated the plausibility or our model derived stomatal conductance (Equation 2) indirectly by comparing calculated and measured whole plant transpiration. We emphasise that this is not a direct validation of gs. Rather, the close agreement between modelled and measured transpiration across the wide range of environmental treatments, both stressed and non-stressed, provides confidence that the inferred gs is realistic. RGB and thermal images acquired before, during, and after stress application enabled dynamic tracking of leaf position and temperature (Supplementary Material and Methods, File S2). As expected, osmotic stress application had immediate effects on morphology and physiology. While control leaves maintained an angle of around 110° throughout, osmotic shock induced immediate turgor loss and drooping in all environments except one (Figure 1A,B). Leaf angles recovered to pre-stress positions within 1 h, indicating adaptation to the osmotic shock and restoration of turgor. Only environment 4 (high light, low air temperature and low humidity) maintained turgor during stress. Angle shifts were most pronounced in older leaves, which drooped and reduced light interception; younger leaves better preserved structure and turgor (Supporting Information S1: Figure S2). These angle changes also altered incident irradiance at the leaf surface (Supporting Information S1: Figure S3). These morphological responses coincided with increases in leaf temperature, consistent with altered water fluxes and stomatal regulation after stress. Across environments, plants showed a uniform rise in leaf temperature following osmotic stress, regardless of initial temperature (Supporting Information S1: Figure S4). This response held across leaf ages, encompassing older (Figure 1C) and younger (Figure 1D) leaves. Stomatal conductance estimated with our method followed the same pattern, dropping rapidly after osmotic shock in both older (Figure 1E) and younger (Figure 1F) leaves (Supporting Information S1: Figure S5). We estimated no stomatal conductance recovery to pre-stress conditions over the time course of stress exposure. Model-estimated and gravimetrically measured transpiration showed identical time courses across all four environmental conditions (Figure 1G–J). Transpiration rates did not recover to the same extent as leaf turgor, indicating long-term effects of the osmotic shock. Across environments and time points, correlation between model estimated and measured whole-plant transpiration was high (Figure 1K). In this study, stomatal conductance (gs) is a model-derived quantity inferred from the same physically constrained framework and model (leaf temperature, boundary-layer conductance and vapour pressure deficit). Since we did not measure gs directly, we cannot validate gs directly. Instead, we used a non-invasive check via transpiration. Model predictions closely tracked measured transpiration across the four controlled environments. This agreement increases confidence that the inferred gs is realistic, while we acknowledge that transpiration agreement alone is not a rigorous validation and cannot fully rule out compensating errors. Our study demonstrated the potential of our approach to estimate transpiration accurately by combining 3D imaging and thermography with physiological modelling without the use of reference materials that imitate real leaves. This remote approach enables simultaneous assessment of morphological and physiological responses to stress, yielding a more integrated view on plant transpiration and gas exchange. In contrast to chamber and porometer measurements or IR methods requiring wet and dry references or calibration plates, our workflow is reference-free. Absorbed shortwave radiation is derived from measured irradiance and a 3D reconstruction of leaf geometry, with no external reference materials. Moreover, remote measurements avoid continuous pressure from clamp-on porometers, permitting long-term observation and capture of rapid stress responses without sustained damage or microclimate artifacts. Further, the approach is not limited by any clamp on sensors and as such enables multi-leaf tracking. Applied to crop canopies, this approach could improve understanding of canopy processes that influence productivity and enable remote estimation of canopy transpiration. Future research could further improve by replacing our strong saline solution stress by gradual soil drying to depict a more realistic and natural stress while testing the approach under long-term conditions. Recent studies indicate that, with rising atmospheric CO2 concentrations, breeding for reduced stomatal conductance could increases WUE without affecting photosynthetic capacity (Srivastava et al. 2024). As such, remote systems for high-throughput plant phenotyping (HTP) are required to scan vast quantities of plants. We see a potential use of our system for such purposes to quickly estimated whole plant and individual leaf transpiration, as initial image capturing is very fast. A large bottleneck in our work was 3D model generation speed and manual extraction of leaf parameters from these 3D models. Both could be streamlined with more automated software, possibly including neural network solutions. The authors have nothing to report. The authors declare no conflict of interest. The data that support the findings of this study are available from the corresponding author upon reasonable request. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Why it matches plant phenotyping methods3D画像、熱画像、光遮断モデル、エネルギーバランスモデルを統合し、葉ごとの蒸散と気孔コンダクタンスを非侵襲的に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。
abstractIn this study, we combine 3D plant models, light interception models, and thermal imaging to solve the energy-balance equation of individual leaves, estimating transpiration entirely remotely.
Wood apple (Feronia limonia L.) is an underutilized perennial fruit tree with substantial ecological, nutritional, and economic potential, yet its phenotypic diversity and trait organization remain poorly characterized. Here, we applied a mixed-scale multivariate framework to resolve phenotypic structure in 62 wood apple genotypes using 31 ordinal and categorical vegetative, leaf, floral, fruit, and seed descriptors. Trait interrelationships were examined through the complementary use of Spearman’s rank correlation and Cramér’s V association analyses, capturing both directional rank-based dependencies and scale-independent categorical linkages. Hierarchical clustering based on Gower distance separated the genotypes into three distinct phenotypic clusters, with inter-cluster dissimilarities (0.92–1.18) consistently exceeding intra-cluster variation (0.42–0.55), indicating well-supported phenotypic stratification based on cluster validation. Multiple Correspondence Analysis (MCA) explained 23.30% of total inertia across the first two dimensions, with tree growth habit, branch angle, tree shape, and fruit color emerging as the principal drivers of phenotypic differentiation. Vegetative and leaf traits formed a tightly integrated module, whereas fruit-related traits displayed weaker monotonic but persistent categorical associations, reflecting partial phenotypic independence. The strong concordance among association analyses, clustering, and MCA indicates structured patterns of coordinated and partially independent trait associations in wood apple. Overall, this study demonstrates the effectiveness of mixed-scale multivariate approaches for resolving complex trait architecture in underutilized perennial fruit crops and provides a quantitative phenotypic framework to support germplasm conservation, parent selection, and ideotype-oriented improvement of wood apple.
Why it matches plant phenotyping methods混合尺度の多変量解析を用いて植物遺伝資源の表現型構造を定量化する手法が研究の中心であり、単なる生物学的実験の routine 測定ではない。
abstractHere, we applied a mixed-scale multivariate framework to resolve phenotypic structure in 62 wood apple genotypes using 31 ordinal and categorical vegetative, leaf, floral, fruit, and seed descriptors.
Reproduction assets found保存済みの本文根拠を更新済みルールで再検証し、公開資産1件を確認しました。Supplement · publicAll data generated or analyzed during this study are available in the article and the accompanying Supplementary Table S1.Open asset ↗lines:137-161Plant phenotyping relevance match · UnverifiedCrossref · checked 14 Sept 2026
In this study, we addressed agricultural labor shortages by developing a smart farming sensor module that integrated low-cost environmental sensors with a multipoint soil moisture sensor to predict broccoli growth, plant height ( PH ), and leaf count (L n ). Multivariable regression confirmed that integrated solar radiation ( S ) was the most dominant factor, although broccoli growth involved a complex interplay of solar radiation, optimal temperature, humidity, and soil moisture. More importantly, the analysis revealed that the middle layer soil moisture (u m ) exhibited the strongest positive contribution to PH . This finding indicated that water availability in the main root zone was essential for vertical growth and highlighted the indispensability of multipoint sensing over conventional single-depth measurements to accurately model the intricate relationship between soil moisture and crop development. Moving forward, we aim to leverage the superiority of multipoint data to construct a sophisticated growth prediction model, thereby contributing to the optimization of irrigation and temperature management in smart farming systems.
Why it matches plant phenotyping methods環境・土壌水分センサーを統合した測定モジュールを開発し、植物高や葉数などの作物形質を予測する手法が研究の中心である。
abstractdeveloping a smart farming sensor module that integrated low-cost environmental sensors with a multipoint soil moisture sensor to predict broccoli growth, plant height ( PH ), and leaf count (L n ).
Plant diseases pose a significant threat to agricultural productivity and global food security, making accurate and timely diagnosis essential. Although deep learning has shown promising performance in plant disease recognition, most existing methods focus on single-task classification and lack interpretability and deployability. To address these limitations, this paper proposes a lightweight deep learning-based plant leaf disease assisted diagnosis system. The proposed framework integrates EfficientNet-B3 for disease classification and Small U-Net for leaf and lesion segmentation, enabling precise localization and quantitative analysis. Disease severity is further estimated based on the lesion-to-leaf area ratio, providing interpretable results for end users. Experimental results demonstrate that the proposed method achieves high accuracy and robust performance while maintaining low computational cost. The system also supports mobile-friendly deployment and generates practical recommendations, forming a complete closed-loop diagnostic pipeline suitable for real-world agricultural applications.
Why it matches plant phenotyping methods葉の病変セグメンテーションと病変面積比による病害重症度推定を開発しており、植物状態の画像ベース表現型取得が中心です。
abstractThe proposed framework integrates EfficientNet-B3 for disease classification and Small U-Net for leaf and lesion segmentation, enabling precise localization and quantitative analysis.
Automated quantification of plant-level development from multi-plant greenhouse scenes requires separating individual plants from shared scene-level reconstructions and quantifying organ-level development, a challenge that single-plant acquisition workflows do not directly address. This study presents an end-to-end phenotyping pipeline built on 3D Gaussian Splatting (3DGS) and a post-reconstruction extraction framework, LCR-GS, designed to isolate plant instances from full greenhouse scenes without scene-specific model retraining. LCR-GS integrates zero-shot 2D cues with multi-view lifting, geometric clustering, and chromatic refinement to convert large scene-level reconstructions (~2M Gaussians) into compact per-plant subsets (~16K Gaussians). Experiments on greenhouse-grown muskmelon at the early vegetative stage demonstrate high plant-extraction precision (0.933) and strong organ-level instance segmentation (mean AP50 = 0.924). Plant height and leaf count are validated against manual measurements (height R² = 0.98, RMSE = 1.88 cm; leaf count R² = 0.86), whereas additional morphological traits, including leaf area, leaf area index, mean internode length, and stem node count, are reported as pipeline-derived descriptors for within-cohort comparison. By decoupling semantic inference from reconstruction, the pipeline reduces scene-scale data by over 99% and provides a practical route to derive compact per-plant 3D representations from multi-plant greenhouse imagery for downstream organ-level analysis.
Why it matches plant phenotyping methods3DGS画像から個体・器官を抽出し、植物形質を定量化するフェノタイピング手法の開発と検証が中心である。
abstractThis study presents an end-to-end phenotyping pipeline built on 3D Gaussian Splatting (3DGS) and a post-reconstruction extraction framework, LCR-GS, designed to isolate plant instances from full greenhouse scenes without scene-specific model retraining.
Reproduction assets foundThe paper's Data Availability Statement points to a public GitHub repository containing the muskmelon 3DGS phenotyping dataset (scenes, Gaussian-level plant/background annotations, and point-level organ labels) used in this study.Dataset · publicThe datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: https://github.com/bblabNTU/3dgs-muskmelon-phenotyping-dataset.Open asset ↗bblabNTU/3dgs-muskmelon-phenotyping-datasethtml-lines:485-547Plant phenotyping relevance match · UnverifiedEurope PMC · bioRxiv · Crossref · checked 5 Sept 2026
Summary (1) Rationale Quantifying and predicting plant morphology is central to understanding development and evolution, yet many plant forms lack homologous features required for traditional morphometrics. We apply the Euler Characteristic Transform (ECT), an injective descriptor from topological data analysis, to encode 2D plant shapes. The ECT converts contours into image-like representations that preserve shape information while enabling deep learning. (2) Methods We computed ECTs for large datasets of leaf and pavement cell shapes and used convolutional neural networks (CNNs) for classification. We also trained CNNs to approximate the inverse mapping, predicting leaf shape masks from radial ECTs. (3) Key results ECT-based models achieved high classification accuracy, surpassing previous approaches on millions of herbarium-derived leaves. Notably, grapevine leaf venation was predicted from blade geometry alone, demonstrating that vascular structure is encoded in the outline. (4) Main conclusion The ECT provides a compact, information-preserving representation of biological shape that integrates naturally with deep learning. It enables both accurate classification and predictive reconstruction, revealing latent morphological information and offering new opportunities to study plant form across scales.
Why it matches plant phenotyping methods植物形状を定量化・分類し、葉形状や葉脈を推定するECTベースの計算手法を中心に開発・評価しているため、植物フェノタイピング手法研究に該当する。
abstractQuantifying and predicting plant morphology is central to understanding development and evolution
Sowing space and depth critically influence wheat canopy architecture, yet their layer-specific effects remain poorly understood. This two-year field study evaluated the effects of three sowing spaces (1.5, 3.0, 4.5 cm) and three sowing depths (2, 3, 6 cm) on canopy projection area, leaf inclination angle, leaf area distribution, and leaf area index (LAI) of dryland wheat (Triticum aestivum ‘Ningmai 13’) in Luhe, Nanjing, China, using image-based phenotyping with manual validation. Narrow spacing (1.5 cm) with intermediate depth (3 cm) produced the largest canopy projection area (0.239–0.245 m2) and an increase in leaf erectness in the middle canopy layer (+23% above average). The highest LAI values (4.23–4.28 m2 m−2) were achieved with narrow spacing (A1B1, A1B2), demonstrating that dense canopies can be established under dryland conditions. Grain yield (g/plant) was measured as a supporting agronomic indicator; the highest yield per plant (14.36 g/plant) was observed in A3B1. Image-based measurements showed excellent agreement with manual methods (R2 > 0.97 for all traits), validating the phenotyping pipeline. These findings contribute to a deeper understanding of how sowing parameters shape wheat canopies in dryland systems.
Why it matches plant phenotyping methods画像ベースの表現型測定パイプラインを用いてキャノピー形態・葉形質を抽出し、手動測定との一致性も検証しており、フェノタイピング手法が中心的です。
abstractusing image-based phenotyping with manual validation
Introduction To accurately segment point clouds and quickly calculate leaf length and stem diameter, thereby enabling phenotypic analysis and variety selection of greenhouse tomato plants, this paper proposes a voxel grid downsampling (VGDS)-PointNet++-based model for point cloud segmentation and trait calculation. Methods The point clouds of the tomato canopy were acquired using a depth camera. After labeling, point cloud augmentation was performed, and the tomato point cloud dataset (TPCD) containing 1,552 sets of data was rebuilt. Voxel grid downsampling was applied to replace the original sampling strategy of PointNet++. Models of PointNet, PointNet++, VGDS-PointNet++, and Point Transformer were trained with the TPCD and compared on segmentation quality with accuracy and mean Intersection over Union (mIoU). After segmentation, skeletal morphology was fitted for non-occluded leaves by applying a series of surface fitting techniques. The leaf lengths and stem diameters were automatically calculated and compared with the manually measured values. Results The validation results showed that the average runtime of voxel grid downsampling was 0.132 s, which was lower than under the same number of sampled points. Compared to the other three models, the proposed model had higher accuracy and mIoU, reaching up to 96.80% and 88.95%, respectively. The proposal's accuracy and mIoU increased by 3.9% and 4.45% over PointNet++, respectively. The determination coefficient R 2 between the automatic calculation and manual measurement values of leaf length and stem diameter was 0.93 and 0.87, respectively. Discussion This can help extract phenotypic traits of tomatoes using depth cameras.
Why it matches plant phenotyping methods深度カメラ点群のセグメンテーションと葉長・茎径の自動推定手法を開発し、手測定および複数モデルと比較検証しており、表現型取得が研究の中心である。
abstractthis paper proposes a voxel grid downsampling (VGDS)-PointNet++-based model for point cloud segmentation and trait calculation
LeafStem / branchPhysiological trait estimationLeaf traitsWater status / transpiration
Leaf and hydraulic traits are key determinants of growth rates, and hence potentially exhibit significant associations with wood density (WD) and its intraspecific variation (ITV). However, the extent to which functional traits could improve WD prediction accuracy, and how ITV in WD correlates with functional traits remain incompletely understood. We investigated WD and its ITV across 10,218 plant species, mapped the global distribution of WD, and analyzed the association of ITV in WD with niche breadth and functional traits. Plant species with an acquisitive resource-use strategy, characterized by higher specific leaf area (SLA), leaf nitrogen concentration (LN), and leaf maximum stomatal conductance (g max ), exhibited lower WD. Associations of WD with hydraulic traits indicated species with greater hydraulic safety exhibited higher WD. Moreover, the integration of leaf traits (i.e., SLA and LN) and hydraulic traits with environmental factors substantially enhanced WD prediction accuracy in a random forest model, raising the explained variance from 55% to 95%. Furthermore, resource-acquisitive species demonstrated higher ITV for WD. ITV was positively related to relative niche breadth concerning both climatic factors and soil properties. Overall, functional traits significantly improve WD prediction accuracy, and plant species with an acquisitive resource-use strategy exhibit lower WD but greater intraspecific variation.
Why it matches plant phenotyping methods木材密度という植物形質の予測モデルを構築し、機能形質・環境因子の統合による予測精度を検証しており、形質推定手法が中心的です。
abstractthe integration of leaf traits (i.e., SLA and LN) and hydraulic traits with environmental factors substantially enhanced WD prediction accuracy in a random forest model, raising the explained variance from 55% to 95%.
Reproduction assets foundThe paper's Data Availability Statement points to a public Zenodo deposit containing the authors' global wood density distribution data, which directly reproduces this paper's measurements. The TRY Plant Trait Database is a generic third-party database, not a paper-specific asset, and no author analysis code is stated.Dataset · publicData for the global distribution of wood density is available on Zenodo Repository https://sandbox.zenodo.org/records/425279.Open asset ↗Zenodo · 425279html-lines:405-429Plant phenotyping relevance match · UnverifiedOpenAlex · Crossref · Europe PMC · checked 5 Sept 2026
Introduction High-throughput field phenotyping (HTFP) holds great potential for elucidating the relationship between genomes and phenotypes. However, obtaining high-quality three-dimensional point cloud data of field populations and achieving single-plant phenotypic analysis remain challenging. Methods This study develops an integrated framework for field crop reconstruction based on 3D Gaussian splatting, incorporating a geometry-aware dynamic constraint algorithm to achieve instance segmentation and extract key phenotypic traits of individual plants. Using 3D Gaussian splatting technology, field-scale cotton population modeling is accomplished, generating dense 3D point clouds for regions of interest. Furthermore, the concept of a crop localization domain is proposed, establishing a longitudinal mapping that associates plant positional coordinates with long-term phenotypic attributes. Finally, through a dynamic spatial constraint mechanism, the accuracy and computational efficiency of instance segmentation for crop population point clouds are significantly improved, enabling rapid extraction of individual plant traits such as cotyledon node height, plant height, and leaf area. Results The results demonstrate that PhenotypeAI successfully reconstructed nine cotton populations with PSNR exceeding 30.0 dB. It successfully extracted regions of interest from 403 cotton plants, achieving an average F-score of 91.32% for instance segmentation and an average accuracy of 91.35%. The extracted traits—cotyledon node height, plant height, and leaf area—exhibited strong correlations with manual measurements, with coefficients of determination ( R 2 ) of 0.90, 0.91, and 0.91, respectively. Discussion The proposed method provides a low-cost solution for high-throughput field phenotypic analysis of field cotton and improves the efficiency of cotton breeding.
Why it matches plant phenotyping methods3D再構成と動的空間制約による個体セグメンテーションおよび形質抽出が研究の中心で、綿花の草丈・葉面積などを検証しているため。
abstractThis study develops an integrated framework for field crop reconstruction based on 3D Gaussian splatting, incorporating a geometry-aware dynamic constraint algorithm to achieve instance segmentation and extract key phenotypic traits of individual plants.
Abstract Maize（Zea mays L.） is an important crop, and improving its productivity is required even under challenging conditions such as labor shortages and uncertain climate fluctuations. One approach to enhancing yield is utilizing crop data for cultivation management and yield prediction. However, efficient acquisition of such data remains constrained by various limitations. In this study, we developed a non-contact and labor-efficient method for crop data acquisition by generating 3D models of maize at the ripening stage using Neural Radiance Fields (NeRF). Segmentation was performed on the obtained point clouds to estimate plant height, leaf area, and leaf angle. The coefficients of determination (R2) were 0.903, 0.954, and -0.521, respectively, demonstrating high accuracy for plant height and leaf area even at the ripening stage, while reducing the time required for data acquisition by 93% compared to manual measurements. Nevertheless, some manual operations−such as removing kernels and separating overlapping leaves−were still necessary, and full automation was not achieved. The main sources of error were identified as reconstruction errors in the base during scale adjustment, excessive removal of leaf sheaths, and the curvature of individual plants. Furthermore, we examined how measurement accuracy was influenced by factors such as the time of day and cultivar. The proposed method is expected to contribute to the practical implementation of a labor -saving 3D measurement technique that supports yield prediction and growth diagnosis in maize.
Why it matches plant phenotyping methodsNeRFによる3D再構成と点群セグメンテーションを開発し、トウモロコシの草丈・葉面積・葉角度を推定して精度と誤差要因を検証しており、表現型取得法が研究の中心である。
abstractwe developed a non-contact and labor-efficient method for crop data acquisition by generating 3D models of maize at the ripening stage using Neural Radiance Fields (NeRF).
Large-scale canopy-level plant trait quantification enhances crop yield and quality assessment, supports sustainable forestry economic development, and improves ecosystem monitoring globally. However, traditional methods relying on vegetation spectral libraries and machine learning models often face challenges in capturing the nonlinear and multivariate characteristics of canopy spectral responses. To overcome these challenges, we propose a novel deep learning framework, the Canopy-level Plant Functional Trait Retrieval Network (CTRN), which integrates Kolmogorov-Arnold Networks (KAN), Transformer, and Convolutional Neural Networks (CNN) to effectively extract informative representations from high-dimensional hyperspectral reflectance. The model is trained and evaluated using a comprehensive spectral-trait dataset, covering various plant species, different sensors, and multiple continents, and focuses on ten key canopy functional traits. Experimental results show that CTRN consistently outperforms other models, achieving R 2 values greater than 0.82 across all traits. Furthermore, even with just 44 spectral bands at a 40 nm resolution, CTRN demonstrates commendable accuracy in estimating LMA and C, with R 2 values approaching 0.80. These findings highlight the robust ability of the model to characterize complex associations between canopy spectra and plant functional traits, supporting accurate parameter retrieval in ecological and agricultural applications.
Why it matches plant phenotyping methodsキャノピーのハイパースペクトル反射から植物機能形質を推定する深層学習手法を開発・評価しており、形質取得法が研究の中心である。
abstractwe propose a novel deep learning framework, the Canopy-level Plant Functional Trait Retrieval Network (CTRN)
Currently operating commercial photovoltaics (PV) systems integrated with agricultural production (Agrivoltaics) offer immense potential for the dual harvest of renewable energy and agro-products. Within controlled-environment agriculture (CEA), the use of semi-transparent photovoltaics (ST-PV) and the ability to control the microclimate and shading are beneficial for the production of high-value crops such as cucumbers. The objective of this research was to commence the cultivation of cucumbers under evolving CEA-PV systems by combining greenhouse experiments with computer vision (CV) based driven phenotyping to create an analytical framework and system control framework for the cultivation of cucumbers in an evolving CEA-PV system. The method involved using the monitored plant vigor to control in real time the irrigation and shading of the cucumber plants. The control of irrigation and shading was based on the monitored plant vigor as determined by a U-Net++ implementation for canopy segmentation, an EfficientNet-B3 implementation for stress detection, and a CNN regressor for growth trait estimation. Within the greenhouse, uniform environmental and fertigation conditions were established to evaluate the effect of four shading regimes (0%, 20%, 40%, 60%) on the cucumbers. Simulated, yet representative results predicted cucumber yields to be stable (within ±4% of full yield) with a 20% shading and a 15-20% reduction in water use compared to full sun. Yield was also observed to drop by 10-14% under higher shading of 40 to 60% due to insufficient photosynthetic activity for fruiting. The CNN based models were robust, (segmentation IoU 0.91, stress-class F1 0.92, LAI regression R²≈0.93), allowing for precise and comprehensive monitoring in an annual non-invasive fashion. The greenhouse's annual photovoltaic (PV) output was estimated to be 1,550 to 1,750 kWh/kWp which is able to exceed the energy demand resulting to a net energy surplus. The outcome demonstrates that the cucumber crop can be successfully combined with controlled environment agrovoltaic systems with moderate shading for optimum cucumber yield. Moreover, informed supervision through Artificial Intelligence (AI) helps to navigate closed-loop systems and enhance the water-use efficiency and yield stability.
Why it matches plant phenotyping methodsCNNによるキャノピー分割、ストレス検出、成長形質推定を中核とする植物フェノタイピングおよび閉ループ制御フレームワークであり、性能指標も報告されているため。
abstractcombining greenhouse experiments with computer vision (CV) based driven phenotyping to create an analytical framework and system control framework for the cultivation of cucumbers
Abstract. Large-scale mapping of plant biophysical and biochemical traits is essential for ecological and environmental applications. Given their finer spectral resolution and unprecedented data availability, hyperspectral data, in concert with machine and particularly deep learning models, have emerged as a promising, non-destructive tool for accurately retrieving these traits. However, when deploying these methods on a large scale, reliably quantifying the associated uncertainty remains a critical challenge, especially when models encounter out-of-domain (OOD) data, i.e., samples that differ substantially from those of the training data, such as unseen geographical regions, species, biomes, data acquisition modalities, or scene components (e.g., clouds and water bodies). Traditional uncertainty quantification methods for deep learning models, including deep ensembles (deterministic and probabilistic) and Monte Carlo dropout, rely on the variance of predictions but often fail to capture uncertainty in OOD scenarios, leading to overly optimistic and possibly misleading uncertainty estimates. To address this limitation, we propose a distance-based uncertainty estimation method (Dis_UN) that quantifies prediction uncertainty by measuring the dissimilarity in the predictor space (spectral inputs) and embedding space (features learned by the deep model) between the training and test data. Dis_UN leverages residuals as a proxy for uncertainty and employs dissimilarity indices in data manifolds to estimate worst-case errors via 95-quantile regression. We evaluate Dis_UN using a pretrained deep learning model to predict multiple plant traits from hyperspectral images, analyzing its performance across OOD data, such as pixels containing spectral variations from urban surfaces, bare ground, water, clouds, or open surface waters. In this study, we target six leaf and canopy traits: leaf mass per area, chlorophylls, carotenoids, nitrogen content, equivalent water thickness, and leaf area index. Compared to scaled variance-based methods, Dis_UN provides (1) a superior estimation of uncertainty in OOD scenarios, achieving 36 % higher contrast (KS distances: 0.648 vs. 0.475) between non-vegetation pixels, particularly under mixed-pixel conditions at medium resolution (30 m); (2) uncertainty quantification without requiring normality or symmetry assumptions, accommodating asymmetric error patterns; (3) enhanced interpretability of uncertainty sources, as uncertainty is directly linked to sample dissimilarity from the training data; and (4) computational efficiency at inference (2.6–7.7× faster), requiring only a single forward pass compared to multiple passes for ensemble-based methods. Challenges remain for traits that are affected by spectral saturation. These findings highlight the advantages of distance-aware uncertainty quantification methods and underscore the necessity of diverse training datasets to minimize sampling biases and enhance model robustness. The proposed framework improves the reliability of uncertainty estimation in vegetation monitoring and offers a promising approach for broader applications.
Why it matches plant phenotyping methods植物形質をハイパースペクトル画像から推定する深層学習について、OOD条件での不確実性推定手法Dis_UNを開発・評価しており、表現型取得・推定手法が中心である。
abstractwe propose a distance-based uncertainty estimation method (Dis_UN) that quantifies prediction uncertainty
Reproduction assets foundThe paper's authors publicly released their uncertainty-analysis code (two GitHub repositories) and the study data (Hugging Face dataset) with explicit availability statements and URLs. The EnMAP and NEON hyperspectral scenes are third-party public data sources, not paper-specific deposits, and the supplement is not anCode · publicThe code for this study is available at: https://github.com/echerif18/Multi_trait_Uncertainty/ (last access: 8 March 2026).Open asset ↗echerif18/Multi_trait_Uncertaintylines:449-456Dataset · publicThe data used in this study are available on Hugging Face: https://doi.org/10.57967/hf/7838 (Cherif et al., 2026).Open asset ↗Hugging Face · 10.57967/hf/7838lines:457-483Plant phenotyping relevance match · UnverifiedOpenAlex · Europe PMC · checked 5 Sept 2026
Recent technological advancements employ imaging techniques to examine the morphological, physiological, and genetic differences among plant accessions, enhancing precision and productivity. High-throughput phenotyping serves as an essential method for selecting traits and reducing errors tied to manual data collection. However, the effects of camera-to-object distance in imaging acquisition for plant phenomics have received less attention. We analyzed the imaging parameters that define well the morphological characteristics of pepper and the effects of camera-to-object distance on the imaging of plant growth, leaf dimensions, fruit, and seed characteristics. Three camera-to-object distances (0.8, 1.0, and 1.2 m) were studied for the vegetative stage, and six camera-to-object distances (0.35-0.85 m) were used for the reproductive stages. The results demonstrated that imaging parameters such as Major (the longest line that can be drawn within the leaf) and Minor (the shortest line perpendicular to the major axis) are more effective for assessing canopy spread, while imaging Height provides a strong correlation (r = 0.9) for actual plant height measurement. An optimal camera-to-object distance of 0.8 m yielded better correlations for vegetative traits across all pepper genotypes, likely due to resolution factors at different growth stages. For fruit and seed traits, shorter distances of 0.55 m and 0.65 m were suitable. Additionally, the weights of fresh and dry fruit correlated highly with image area (r = 0.94 and 0.89, respectively, at 0.55 m). The studied pepper genotypes exhibited distinct seed characteristics, including variations in Roundness, Solidity, and Circularity. The imaging approach can accurately capture various plant characteristics and has the potential to replace traditional methods for assessing plants.
Why it matches plant phenotyping methodsRGB画像による植物形質取得を中心に、カメラ距離と撮像パラメータを最適化・検証しており、方法開発および技術検証に該当する。
titleDigitalised phenotyping of pepper (Capsicum spp.) using effective RGB imaging and optimised camera positioning.
Abstract A genome‐wide association study (GWAS) using digital images was conducted to delineate regions of the genome that govern the leaf flipping quantitative trait in soybean ( Glycine max (L.) Merr). However, converting the digital data to numerical scores for downstream analyses was challenging. We have developed an algorithm that operates in the hue, saturation, and value color space in a structured image processing pipeline that includes preprocessing, binary masking for leaf region isolation, contrast enhancement, grid‐based intensity analysis, and thresholding for detecting folded leaves, a response of soybean to drought. The outputs of this image analysis reached over 90% detection accuracy for images captured under different imaging conditions. GWAS using the processed images identified the same genetic loci underlying drought tolerance as were identified earlier by GWAS of the manually curated dataset from the same photos. This approach provides a robust, scalable, and cost‐effective tool for digital image‐based high‐throughput phenotyping.
Why it matches plant phenotyping methods大豆葉の反転表現型を画像から定量化する画像処理アルゴリズムを開発し、異なる撮像条件で精度検証しているため、植物フェノタイピング手法が中心である。
abstractWe have developed an algorithm that operates in the hue, saturation, and value color space in a structured image processing pipeline that includes preprocessing, binary masking for leaf region isolation, contrast enhancement, grid‐based intensity analysis, and thresholding for detecting folded leaves
Leaf Area Index (LAI) is a fundamental parameter for characterizing the growth of tea ( Camellia sinensis L.). However, in rugged mountainous regions, the combined effects of topographic relief and canopy structural heterogeneity severely constrain the accuracy of UAV-based multispectral LAI retrieval. This study develops an integrated framework combining topographic correction with interpretable machine learning to improve LAI estimation. We utilized a UAV multispectral dataset collected during the peak growing season from a typical tea-growing region in Fujian Province, China (altitude range: 58-186 m), comprising a total of 90 samples. Three topographic correction methods, including Sun-Canopy-Sensor (SCS), SCS with C correction (SCS+C), and Minnaert+SCS, were evaluated in combination with Linear Regression (LR), Decision Tree (DT), Random Forest (RF), and Extreme Gradient Boosting (XGBoost) models. Results indicated that the SCS+C algorithm outperformed other methods by effectively accounting for direct and diffuse radiation components, thereby reducing topographic dependence while maintaining radiometric consistency across heterogeneous surfaces. The XGBoost model combined with SCS+C correction achieved the highest performance (R 2 = 0.8930, RMSE = 0.6676, nRMSE = 7.93%, MAE = 0.4936, Bias = -0.0836). SHapley Additive exPlanations (SHAP) analysis revealed a structure-dominated retrieval mechanism, in which red-band textural features (Correlation_R) exhibited higher importance than conventional vegetation indices. Compared with previous studies that primarily focus on either topographic correction or model development, this study provides quantitative insights into the underlying retrieval mechanisms. This framework improves the precision of tea LAI retrieval in complex terrains and provides a robust methodological basis for digital management in mountainous agriculture.
Why it matches plant phenotyping methodsUAVマルチスペクトル画像と地形補正・機械学習を用いた茶園LAI推定手法の開発および比較検証が研究の中心であり、植物形態特性を直接推定している。
abstractThis study develops an integrated framework combining topographic correction with interpretable machine learning to improve LAI estimation.
PURPOSE: The leaf area index (LAI) is a crucial parameter for crop growth management. While UAV remote sensing has been utilized to estimate LAI at the plot scale, its application to complex farmland environments—characterized by heterogeneous backgrounds (e.g., soil, residue, and weeds)— has been less explored. METHOD: This study employed UAV-mounted hyperspectral and RGB sensors to gather data from both experimental plots and farmland environments. Data from diverse rapeseed cultivars and growth stages were used as the calibration dataset, while farmland-level data validated the models. The study compared three models: the PROSAIL model, an empirical model incorporating canopy spectral and morphological parameters without differentiating canopy cover types, and the proposed canopy morphological parameters (CMP) model. The CMP model estimated LAI using fractional vegetation cover (FVC) for sparse canopies and canopy height for closed canopies. RESULT: Despite challenges such as UAV image resolution and the limited availability of spatial data, the CMP model showed strong performance, with an R² of 0.779 and RMSE of 0.732. Although its R² was similar to that of the empirical spectral–morphological (ESM) model (R² = 0.780), the CMP approach achieved a notably lower RMSE (0.732 vs. 0.814). This improvement stems from its canopy-aware design, which adaptively uses fractional vegetation cover for sparse canopies and canopy height for closed canopies. Such differentiation enhances model stability and generalization in heterogeneous farmland scenes—conditions in which background interference and structural variability often degrade empirical models. In comparison, the PROSAIL model performed less accurately (R² = 0.618, RMSE = 1.094). CONCLUSION: These results highlight that the CMP model provides a robust and cost-effective solution for LAI estimation, supporting crop growth assessment and management in real farmland.
Why it matches plant phenotyping methodsUAV画像・センサーから rapeseed のLAIを推定するモデルを開発・比較し、異なる圃場条件で検証しているため、植物形質取得手法が研究の中心です。
abstractThe CMP model estimated LAI using fractional vegetation cover (FVC) for sparse canopies and canopy height for closed canopies.
Accurate and non-destructive estimation of rice Leaf Area Index (LAI) is vital for crop growth assessment and yield prediction. Close-range, non-contact optical methods are commonly used for LAI monitoring. However, their accuracy is often limited by the platform, and most rely on single-source data prone to saturation effects and background interference. To overcome these limitations, this study develops a phenotyping robot-based multi-source, high-resolution data fusion approach for field-scale LAI monitoring. A phenotyping robot equipped with multispectral and high-resolution RGB cameras was used to collect vegetation indices, color indices, texture features, and canopy coverage extracted from high-resolution RGB imagery. These features were further combined with meteorological variables to build machine learning models. The Random Forest model achieved the best performance (R² = 0.92, RMSE = 0.302). SHAP (Shapley Additive Explanations) was applied to interpret the model and quantify the importance of multispectral features, RGB-derived texture information, canopy coverage and meteorological factors. Canopy coverage, NDVI and Clgreen were identified as the key factors for improving model performance, and the complementary mechanism between canopy coverage and other features can alleviate the saturation effect in the high LAI stage. The results show that combining high-resolution remote sensing data from robots with meteorological data can effectively mitigate the saturation effect and soil background interference in LAI estimation, and significantly improve the accuracy of LAI estimation. This study provides a practical and scalable framework for field phenotyping and offers technical support for precise rice cultivation and smart agriculture.
Why it matches plant phenotyping methodsロボット搭載マルチセンサーと画像特徴量融合によるイネLAI推定手法を開発・評価しており、表現型取得・推定が研究の中心である。
abstractthis study develops a phenotyping robot-based multi-source, high-resolution data fusion approach for field-scale LAI monitoring.
Agrophotovoltaic (APV) systems provide a unique opportunity for improving agricultural land-use efficiency by combining solar energy capture via photovoltaic panels with crop production. However, in-depth information on plant growth patterns within the spatially heterogenous microclimate created by the intermittent shading of APVs is largely missing. In the present study, we implement a customized robot-mounted 3D-multispectral imaging system to closely monitor the growth and spectral reflectance patterns of a conventional soybean cultivar “Eiko” (EK) and a chlorophyll-deficient mutant variety MinnGold (MG) under an APV system. Weekly trends in canopy morphometric features revealed significant variations in plant height, 3D leaf area, light penetration, and canopy volume across the APV field depending on the proximity with the overhead solar panels for both EK and MG, with plants receiving adequate rainfall and intermittent shade performing the best. Furthermore, although spectral indices exhibited variations between EK and MG due to intrinsic differences in pigmentation, symptoms of stress could be detected for both genotypes within rain-shaded areas of the APV plot. Hence, the present investigation depicts the potential for complementary usage of robotics and machine vision for high-precision high-throughput crop monitoring under APVs, which would enable better crop management within such non-homogenous cultivation systems.
Why it matches plant phenotyping methodsロボット搭載の3D・マルチスペクトル画像システムを構築・適用し、作物の形態形質とストレス状態を高精度・高スループットに取得しており、表現型取得手法が研究の中心である。
abstractwe implement a customized robot-mounted 3D-multispectral imaging system to closely monitor the growth and spectral reflectance patterns
Cotton productivity plays a crucial role in the global agricultural economy; however, various leaf diseases significantly threaten crop yield and fiber quality. Early and accurate disease detection is essential for effective crop management, yet traditional inspection methods are time-consuming, labor-intensive, and dependent on expert knowledge, often leading to inconsistent results. Conventional machine learning approaches also face limitations in real-world agricultural environments due to variations in lighting conditions, complex backgrounds, and similarities between disease symptoms. To address these challenges, this research proposes an intelligent framework called Cotton Plant Disease Identification Using ResMobNet with Attention-Guided Localization and Severity Analysis (CPDI-RMN). The proposed system integrates advanced image preprocessing, hybrid feature extraction, deep learning classification, and attention-based localization to create a comprehensive disease detection framework. Initially, cotton leaf images are collected from a comprehensive dataset and preprocessed through image resizing, noise removal, contrast enhancement, and Min–Max normalization to improve visual quality and ensure stable model training. Data augmentation techniques such as rotation, flipping, zooming, and brightness adjustment are applied to enhance dataset diversity and improve model robustness against overfitting. For feature enhancement, contour visualization and geometric feature representation are combined with texture analysis using the Gray-Level Co-occurrence Matrix (GLCM) and Laplacian filtering. The core of the framework is the ResMobNet hybrid architecture, which integrates ResNet-50, EfficientNet-B3, and MobileNet-V2 to capture multi-scale spatial and texture features while maintaining computational efficiency. Gradient-Weighted Class Activation Mapping (Grad-CAM) is employed to generate attention maps for disease localization, followed by segmentation to isolate infected regions. Disease severity is then quantified by calculating the percentage of infected leaf area and classifying it into mild, moderate, and severe categories. Experimental results using five-fold cross-validation demonstrate that the CPDI-RMN model achieves 98.85% classification accuracy, outperforming CNN, ANN, ResNet, and MobileNetV2 models. Additionally, the attention-based localization achieves 96.8% Intersection over Union and 98.0% Dice Score, indicating highly accurate disease region detection. Overall, the proposed framework provides a reliable and scalable solution for intelligent cotton disease monitoring and supports precision agriculture through data-driven crop management.
Why it matches plant phenotyping methodsワタ葉画像から病変領域を抽出し、感染面積率に基づいて病害重症度を定量化する画像解析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。
abstractThe proposed system integrates advanced image preprocessing, hybrid feature extraction, deep learning classification, and attention-based localization to create a comprehensive disease detection framework.
Premise: Herbarium specimens are increasingly used to extract morphological traits for ecological and evolutionary studies, yet the effects of tissue desiccation on trait measurements remain poorly understood. Here, we tested whether higher tissue water content leads to greater measurement changes after herborization (H1) and whether fresh trait values can be reliably predicted from herbarium measurements (H2). Methods: We evaluated the reliability of herbarium-based measurements by comparing fresh and dried traits of leaves, flowers, fleshy fruits, and seeds across 262 individuals representing 133 Neotropical Myrtaceae species. Phylogenetic least square models and machine-learning regressions were used to test H1 and H2. Results: Leaves and flowers generally shrank after herborization, fruits size metrics tended to increase, and seeds were largely unaffected. Water content was significantly associated with the magnitude of herborization effects in flowers and some leaf and seed traits. Fresh trait values were accurately predicted from herbarium measurements. Prediction errors were lowest for leaf traits, followed by fruits, flowers, and seeds. Discussion: These results partially support H1 and support H2, indicating that herbarium specimens can be reliably used for trait analyses when organ-specific responses are considered, providing a practical framework to account for potential desiccation bias in functional trait research.
Why it matches plant phenotyping methodsハーバリウム標本による植物形態形質測定の信頼性評価と、生鮮形質の予測手法が研究の中心であり、植物フェノタイピング手法の検証に該当する。
abstractWe evaluated the reliability of herbarium-based measurements by comparing fresh and dried traits of leaves, flowers, fleshy fruits, and seeds across 262 individuals representing 133 Neotropical Myrtaceae species.
Reproduction assets foundThe authors explicitly state that the code used for the PGLS and machine-learning analyses is publicly available in a GitHub repository; raw phenotype data is promised only upon acceptance, so the code asset qualifies while the dataset is not yet actionable.Code · publicSupporting Information and the code used to perform the analyses are available at
https://github.com/ykilsztajn/fresh_dry_myrtaceae. All raw data will be made available in the
same repository upon acceptance for publication.Open asset ↗ykilsztajn/fresh_dry_myrtaceaepdf-page:9 lines:1-48Plant phenotyping relevance match · UnverifiedOpenAlex · checked 15 Sept 2026
Abstract Image processing techniques for plant phenotypes are rapidly evolving, allowing faster, non-destructive and objective evaluation of plant growth parameters than conventional methods for plant physiological studies. The aim of this study was to evaluate the green area rate (GAR) per plant through smartphone images of magnolia, and to predict the differences in the growth parameters including root length from the differences in green area rate of ordinary saplings and ones grown using cerium chloride (CeCl3). An image analysis program developed using fuzzy C-means clustering algorithm from digital images was used to estimate GAR of magnolia saplings, and the correlation between green area rate and growth parameters was determined and regression model was constructed. Correlation coefficient of GAR was the highest with leaf length of 0.98 and lowest with above ground total dry mass of 0.87. Accuracy between the predicted values and measured values was estimated, and then difference of GAR between control saplings and ones grown using cerium chloride was calculated. Based on the changes in green area percentage, we predicted difference in growth parameters. No significant difference existed between the predicted and the measured values. The results obtained in present paper will play a significant role in predicting the growth parameters of saplings without affecting the growth and in detecting effectiveness of various growth promoters.
Why it matches plant phenotyping methodsスマートフォン画像とファジーC-meansによる緑色面積率推定を開発し、植物の成長形質を予測・検証しており、表現型取得・抽出法が研究の中心である。
abstractAn image analysis program developed using fuzzy C-means clustering algorithm from digital images was used to estimate GAR of magnolia saplings
High-density planting is an effective strategy to increase maize yield but imposes greater demands on plant architectural adaptability. To elucidate the structural response mechanisms of maize under varying planting densities, we developed a high-throughput 3D phenotyping system tailored to complex field conditions. High-precision point clouds of field-sampled plants were obtained via multi-view 3D reconstruction. Using a deep learning network, stem and leaf organs were semantically segmented (95.6% accuracy), while leaves were individually separated via clustering (94.8% accuracy). From these data, 31 plant architectural traits and 14 ear-leaf traits were extracted, establishing a hierarchical trait characterization system. Results showed that increased planting density significantly influenced plant architecture reshaping and structural coordination, leading to more compact plant forms and ear height position centralization. Ear leaves exhibited heightened sensitivity to density variation, particularly in leaf area, vertical distribution, and leaf inclination angle, suggesting an early-response role. Principal component analysis and clustering further revealed patterns of structural differentiation and key traits driving these changes under density treatments. The integrated workflow-comprising data acquisition, modeling, segmentation, clustering, trait extraction, and analysis-offers a robust approach for structural phenotyping and intelligent breeding selection in maize and other tall crops. This pipeline provides valuable technical support and data resources for optimizing dense planting strategies and advancing digital agriculture.
Why it matches plant phenotyping methods高スループット3D表現型システムを開発し、点群再構成・器官分割・クラスタリングから多数の植物構造形質を抽出することが中心であるため。
abstractwe developed a high-throughput 3D phenotyping system tailored to complex field conditions
Reproduction assets foundThe paper's authors provide a public GitHub repository for the study's source code (segmentation/trait-extraction pipeline). The phenotype point-cloud dataset itself is only available on request from the corresponding author, so it is not a public asset.Code · publicThe code of this study will be made publicly available upon publication. The source code is available at https://github.com/CSC-csc426/3D-Point-Cloud-Driven-Organ-Semantic-Segmentation-to-Assess-Maize-Structural-Responses .Open asset ↗CSC-csc426/3D-Point-Cloud-Driven-Organ-Semantic-Segmentation-to-Assess-Maize-Structural-Responseslines:330-415Code / dataset availability confirmedEurope PMC · checked 14 Sept 2026
Recognizing lineages is a central challenge in plant systematics, making it essential to explore multiple analytical tools. In this context, this study investigates how frond shape can assist in discriminating against lineages within the Scaly clade of Microgramma (Polypodiaceae), and tests whether the integration of multiple lines of evidence enables a more consistent recognition of lineages than exclusively macromorphological approaches. We analyzed 271 specimens representing eight species, using Elliptical Fourier Analysis (EFA) to quantify frond shape, followed by multivariate statistical tests (PCA, MANOVA, LDA). Evolutionary relationships between spectral and morphometric data were assessed through phylogenetic generalized least squares (PGLS) regressions and phylogenetic partial least squares (Phylo-PLS) analyses. Dimorphic species exhibited higher discrimination capacity (average accuracy of 80–83%). Fertile and combined fronds yielded the highest accuracy values. Morphologically similar species, such as M. reptans and M. tobagensis, showed significant overlap, whereas M. percussa achieved the best performance (average accuracy of 80%). Morphometric-spectral integration showed a strong correlation (R² = 0.72; P = 0.003), and both the combined datasets (spectra and outline) and the individual datasets of spectral and shape features revealed a high phylogenetic signal (λ = 1–0.84), indicating partial coevolution between frond shape, chemical composition, and the evolutionary history of the group. Outline morphometry combined with infrared spectroscopy within a phylogenetic framework improves lineage discrimination, although overlap zones persist, reflecting complex evolutionary processes. Our study highlights the potential of integrative systematics to elucidate species boundaries in groups with high morphological disparity, as well as the need for broad sampling and multi-evidence approaches in future systematic reviews.
Why it matches plant phenotyping methodsフロンド形状をElliptical Fourier Analysisで定量化し、赤外分光との統合を用いて系統識別性能を評価しており、植物器官形質の取得・解析手法が研究の中心です。
abstractusing Elliptical Fourier Analysis (EFA) to quantify frond shape, followed by multivariate statistical tests (PCA, MANOVA, LDA).
Reproduction assets foundThe authors state that raw data, processed data, and R analysis code for the frond outline morphometrics are publicly available on GitHub (Microgramma-Outline), and the FT-NIR spectral data repository (Microgramma-FTNIR) is referenced in the methods. Both are paper-specific, public, and actionable.Code · publicSciELO Preprints - Este documento é um preprint e sua situação atual está disponível em: https://doi.org/10.1590/SciELOPreprints.15500
573 The raw data, processed data, and R analysis code are publicly available on GitHub:
574 https://github.com/labevofern/Microgramma-Outline.git.
575
576 REFERENCES
577 Ackerly D.D. (2004) Adaptation, Niche Conservatism, and Convergence: Comparative
578 Studies of Leaf Evolution in the California Chaparral. The American Naturalist, 163, 654–
579 671.
580 Adams D.C., Collyer M.L. (2018) Multivariate Phylogenetic Comparative Methods:
581 Evaluations, Comparisons, and RecoOpen asset ↗labevofern/Microgramma-Outline · Microgramma-Outlinepdf-layout-page:25 lines:1-48Dataset · publicbiting the highest
157 perpendicular distance from the line connecting the first and last bands in the R² × ranking
158 plot (Fig. S2). Following the methods described in Mendonça et al. (2026), spectral data were
159 acquired using a PerkinElmer Frontier™ near-infrared Fourier transform spectrometer (FT-
160 NIR) available at (https://github.com/labevofern/Microgramma-FTNIR).
161 Phylogenetic comparative analyses
162 To provide a phylogenetic framework for comparative morphometric and spectral analyses,
163 we used the pruned version of the Microgramma chloroplast phylogenetic inference from
164 Mendonça et al. (2026). This tree was based on the Bayesian phylogenetic tree published by
165 AOpen asset ↗labevofern/Microgramma-FTNIR · Microgramma-FTNIRpdf-layout-page:8 lines:1-55Plant phenotyping relevance match · UnverifiedEurope PMC · checked 5 Sept 2026
Introduction Accurate and stable diagnosis of cotton nitrogen status across growth stages is essential for precision fertilization in drip-irrigated systems. However, the instability of conventional nitrogen-related indicators across different phenological stages often reduces diagnostic performance and limits their broader application. Methods A field experiment was conducted in Xinjiang, China, under four irrigation levels (60%, 80%, 100%, and 120% ET c ) and four nitrogen application rates (0, 245, 300, and 350 kg N ha -1 ). UAV multispectral imagery was acquired at the squaring, flowering, boll-setting, and boll-opening stages. Based on ground-measured leaf area index (LAI) and upper-canopy leaf nitrogen weight (LNWupper), an Integrated Nitrogen Diagnosis Index (INDI) was developed. Random Forest (RF), Gradient Boosting Decision Tree (GBDT), and Extreme Gradient Boosting (XGBoost) models were used to evaluate the inversion performance of INDI. In addition, the nitrogen nutrition index (NNI), derived from the critical nitrogen dilution curve, was used to validate the diagnostic stability of INDI. Results Multispectral vegetation indices were strongly correlated with LAI, LNWupper, and INDI, with red-edge- and near-infrared-based indices showing the highest sensitivity. Among the three models, XGBoost achieved the best inversion accuracy for INDI (R 2 = 0.85, RMSE = 0.61). INDI was significantly correlated with NNI across growth stages, with R 2 values of 0.58, 0.77, 0.81, and 0.70 at the squaring, flowering, boll-setting, and boll-opening stages, respectively, and the highest accuracy observed at the boll-setting stage. Moreover, the spatial distribution maps of INDI effectively distinguished nitrogen differences under different water-nitrogen treatments and were consistent with NNI-based classifications. Discussion INDI accurately captured nitrogen dynamics throughout cotton growth, and the INDI-XGBoost framework provided a robust approach for high-precision spatial nitrogen diagnosis. These results support precision fertilization management in drip-irrigated cotton fields in Xinjiang.
Why it matches plant phenotyping methodsUAVマルチスペクトル画像からワタの窒素状態を推定する指標とXGBoost反転手法を開発・検証しており、植物生理状態の取得・推定が研究の中心である。
abstractBased on ground-measured leaf area index (LAI) and upper-canopy leaf nitrogen weight (LNWupper), an Integrated Nitrogen Diagnosis Index (INDI) was developed.
Leaf morphology in tea plants (Camellia sinensis L.) profoundly influences tea quality and agronomic value, yet its genetic basis remains elusive due to labor-intensive phenotyping, foliage architecture, and ecological sensitivity of traits. Moreover, traditional methods forfeit quantitative color gradients and population-level morphological complexity. To address this challenge, we developed coleaf, an open-source image recognition-based software that demonstrated 97.6% accuracy over conventional ImageJ measurements, while offering higher efficiency and color hues quantification. We then estimated 7 key morphological traits focusing on leaves from a collection of ~ 4,200 mature leaves and ~ 5,000 bud-leaf samples across 167 genetically diverse tea accessions by coleaf. While classical understanding suggests leaf shape differentiation between two varieties in genus sinensis assamica (CSA) and sinensis (CSS), our phenotypic clustering revealed incomplete congruence with phylogenetic relationships, suggesting the presence of additional genetic or environmental modulators beyond population divergence. Furthermore, we integrated phenotypic data with whole-genome resequencing for multi-model genome-wide association studies (GWAS). Candidate genes associated with leaf architecture were involved in plant development (e.g., CsFAS2), cell division and elongation (e.g., CsFIP1), and cellular morphogenesis (e.g., CsRLK), whereas those associated with leaf color, regulated pigment accumulation (e.g., ABC transporters, CsMYB113). In conclusion, this study establishes a standardized computational framework validating automated image recognition for plant leaf phenomics. The end-to-end framework from high-throughput phenotyping to gene discovery provides critical genetic targets for tea breeding, demonstrating transformative potential in accelerating the genetic improvement of tea plants.
Why it matches plant phenotyping methods茶葉形態の画像認識ソフトウェアを開発・検証し、高スループットな形質抽出フレームワークとして適用しており、植物フェノタイピング手法が研究の中心である。
abstractwe developed coleaf, an open-source image recognition-based software that demonstrated 97.6% accuracy over conventional ImageJ measurements
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 · publicAll codes and tools used in this study are described in Methods, coleaf is available on github (https://github.com/mengmeng-jiang/coleaf).Open asset ↗mengmeng-jiang/coleafhtml-lines:390-460Plant phenotyping relevance match · UnverifiedCrossref · checked 15 Sept 2026
Monitoring crop conditions is crucial for effective crop management and provides valuable insights into soil-plant-atmosphere interactions. While some studies have used unmanned aerial vehicle (UAV)-based light detection and ranging (LiDAR) data for mapping plant area index (PAI) in orchards, LiDAR-based time-series analysis to assess PAI variations with phenology throughout the growing season represents a significant gap in knowledge. Tracking PAI dynamics across phenological stages reflects canopy development and leaf expansion, which are directly linked to yield formation. Furthermore, the optimal spatial resolution for mapping biophysical variables of tree crops from LiDAR point clouds is yet to be determined. This study aimed to demonstrate the potential of UAV-derived LiDAR time-series to monitor the PAI and tree vertical profiles at high spatial resolution throughout the growing season of a cherry orchard located in southeastern France. A time series of 14 point cloud acquisitions with a density of 3300 points/m² was collected between February and December 2022, with at least one acquisition per month, covering all phenological stages of the cherry orchard. Field measurements were collected on May 30, and October 6, to measure the PAI at twilight using an LAI-2200C Plant Canopy Analyzer (LI-COR Biosciences, Lincoln, NE, USA), with 248 trees sampled. A voxel-based method was applied on the LiDAR point cloud data to create a three-dimensional grid within which PAI was estimated for each voxel. The results showed that a voxel size of at least 70 cm is required to retrieve reliable PAI estimates, while a voxel size of 100 cm produced the most accurate PAI estimates (RMSE = 0.5 m2.m-2, bias = 0.07, R2 = 0.59), when assessed against in-situ PAI measurements. The temporal variation of canopy PAI illustrated the progression of the phenological stages, including flowering, leaf development, ripening and senescence, and the response of the canopy to drought stress (reduction in PAI due to leaf rolling) during the summer. The maps of PAI successfully described the variations in leaf canopy density for different cherry varieties and allowed assessment of the vertical PAI profile at the individual tree level. The LiDAR-derived PAI maps and vertical profiles were able to detect trees exhibiting poor leaf development, which is an important health indicator for effective crop management in orchard settings. Future work should focus on applying UAV-derived observations to optimize crop models to enhancing decision-making tools for effective orchard management.
Why it matches plant phenotyping methodsUAV LiDARとボクセル解析により、樹木レベルのPAIおよび垂直プロファイルを推定し、実測値で精度検証しているため、植物表現型取得手法が研究の中心である。
abstractA voxel-based method was applied on the LiDAR point cloud data to create a three-dimensional grid within which PAI was estimated for each voxel.
Global plant maps of plant traits, such as leaf nitrogen or plant height, are essential for understanding ecosystem processes, including the carbon and energy cycles of the Earth system. However, existing trait maps remain limited by the high cost and sparse geographic coverage of field-based measurements. Citizen science initiatives offer a largely untapped resource to overcome these limitations, with over 50 million geotagged plant photographs worldwide capturing valuable visual information on plant morphology and physiology. In this study, we introduce PlantTraitNet, a multi-modal, multi-task uncertainty-aware deep learning framework that predicts four key plant traits (plant height, leaf area, specific leaf area, and nitrogen content) from citizen science photos using weak supervision. By aggregating individual trait predictions across space, we generate global maps of trait distributions. We validate these maps against independent vegetation survey data (sPlotOpen) and benchmark them against leading global trait products. Our results show that PlantTraitNet consistently outperforms existing trait maps across all evaluated traits, demonstrating that citizen science imagery, when integrated with computer vision and geospatial AI, enables not only scalable but also more accurate global trait mapping. This approach offers a powerful new pathway for ecological research and Earth system modeling.
Why it matches plant phenotyping methods植物画像から複数の形態・生理形質を推定する深層学習フレームワークを開発し、独立データで検証・既存手法と比較しており、表現型取得・推定手法が研究の中心である。
abstractwe introduce PlantTraitNet, a multi-modal, multi-task uncertainty-aware deep learning framework that predicts four key plant traits (plant height, leaf area, specific leaf area, and nitrogen content) from citizen science photos using weak supervision.
Mountain ecosystems play a critical role in global biodiversity conservation, water regulation, and climate change adaptation. However, their pronounced topographic complexity poses major challenges for the large-scale estimation of plant functional traits using remote sensing, limiting our ability to characterize ecosystem functioning and vegetation responses to global warming. Variations in slope, aspect, and elevation strongly affect illumination conditions, viewing geometry, and canopy structure, introducing biases that are often overlooked in trait–reflectance relationships. Vegetation indices and empirical models are widely used to estimate plant traits from optical remote sensing data, yet their performance degrades in complex terrain due to topographic artifacts and limited field calibration data. Alternatively, radiative transfer models (RTMs) provide a physics-based framework for linking spectral reflectance to vegetation biophysical and biochemical properties. Despite their theoretical advantages, most commonly used RTMs assume flat or gently sloping terrain and are therefore poorly suited for mountainous landscapes, potentially compromising trait retrievals in these environments.In this study, we quantify the influence of terrain complexity on the performance of both empirical and physically based models applied to hyperspectral data for estimating functional leaf traits in Andean forest ecosystems. Field data were collected in more than 120 plots distributed according to a fractal sampling design across strong gradients in elevation, slope, and aspect in the Mapocho River basin (central Chile). For each plot, we measured species abundance, leaf-level functional traits, and topographic variables, and linked these data with airborne hyperspectral reflectance. Our results show that model performance is highly sensitive to terrain conditions. Across traits and modelling approaches, explained variance ranged from near zero to approximately 50%, substantially lower than values typically reported in studies conducted in low-relief landscapes. Trait-specific responses were evident: some functional traits were better explained by spectral reflectance, while others were more strongly associated with topographic variables alone. Residual analyses further revealed systematic terrain-driven biases, indicating that both empirical models and RTMs struggle to disentangle spectral signals related to plant traits from those induced by complex topography.These findings highlight a strong methodological and geographical bias in current remote sensing approaches for trait estimation, driven by the predominance of studies conducted in flat or gently undulating terrain. Because mountainous regions are essential for biodiversity, ecosystem services, and climate sensitivity, excluding or oversimplifying topographic effects limits the transferability and scalability of trait-based remote sensing models. Our study underscores the urgent need to develop terrain-aware modelling frameworks that explicitly integrate topography into hyperspectral trait estimation to improve ecological inference and support monitoring efforts in complex mountain systems.
Why it matches plant phenotyping methodsハイパースペクトルデータと経験モデル・放射伝達モデルを用いて植物の機能的葉形質を推定し、地形による推定性能のバイアスを定量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応用・検証に該当する。
abstractquantify the influence of terrain complexity on the performance of both empirical and physically based models applied to hyperspectral data for estimating functional leaf traits
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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Value of the Data
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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:1-47Code / dataset availability confirmedEurope PMC · checked 5 Sept 2026
Rapid and accurate identification of DUS (Distinctness, Uniformity, and Stability) test traits in lettuce leaves is essential for advancing multi-omics-driven intelligent breeding. It also plays a critical role in germplasm protection and enhancing agricultural competitiveness. However, the phenotypic traits of lettuce leaves are highly diverse and complex due to both genotypic variation and environmental influences, posing significant challenges for precise DUS trait quantification. To address these challenges, we propose a high-precision phenotypic trait extraction pipeline and introduce an interpretable phenotypic fingerprinting framework for lettuce subgroup identification. First, a lightweight semantic segmentation network guided by group attention is developed to extract leaf components. Then, shape, color, and texture traits are comprehensively quantified. Following UPOV (International Union for the Protection of New Varieties of Plants) guidelines, we establish quantitative methods for seven DUS test traits: leaf shape, leaf tip shape, leaf margin shape, leaf vein shape, color hue, brightness, and anthocyanin coloration. Finally, PCA (Principal component analysis) was used to select 13 key traits, capturing over 95.82% of the total variance, for constructing "phenotypic ID" of lettuce varieties. Experiments conducted on 709 lettuce leaf image datasets showed that the accuracy of subgroup identification based on phenotypic fingerprints reached 98.59%. This study offers a scalable approach for automated DUS test trait evaluation and intelligent crop variety identification, providing a novel paradigm with strong potential for application in precision breeding and germplasm resource management.
Why it matches plant phenotyping methodsレタス葉画像からDUS形質を抽出・定量化する画像解析パイプラインを開発し、709画像で評価しており、植物フェノタイピング手法が研究の中心である。
abstractwe propose a high-precision phenotypic trait extraction pipeline and introduce an interpretable phenotypic fingerprinting framework for lettuce subgroup identification.
Reproduction assets foundThe article provides a public GitHub repository containing the authors' source code for the lettuce phenotypic fingerprint pipeline. The 709-image dataset and annotations are only available upon request, so they do not qualify as public assets.Code · publicThe data used to support the findings of this study are available upon request from the corresponding author, and the source code is accessible at https://github.com/qiuguangjie87/PP_Phenotypic_Fingerprint .Open asset ↗PP_Phenotypic_Fingerprintlines:263-278Plant phenotyping relevance match · UnverifiedOpenAlex · arXiv · checked 5 Sept 2026
Intelligent forest tree breeding has advanced plant phenotyping, yet existing research largely focuses on large-leaf agricultural crops, with limited attention to fine-grained leaf analysis of sapling trees in open-field environments. Natural scenes introduce challenges including scale variation, illumination changes, and irregular leaf morphology. To address these issues, we collected UAV RGB imagery of field-grown saplings and constructed the Poplar-leaf dataset, containing 1,202 branches and 19,876 pixel-level annotated leaf instances. To our knowledge, this is the first instance segmentation dataset specifically designed for forestry leaves in open-field conditions. We propose LeafInst, a novel segmentation framework tailored for irregular and multi-scale leaf structures. The model integrates an Asymptotic Feature Pyramid Network (AFPN) for multi-scale perception, a Dynamic Asymmetric Spatial Perception (DASP) module for irregular shape modeling, and a dual-residual Dynamic Anomalous Regression Head (DARH) with Top-down Concatenation decoder Feature Fusion (TCFU) to improve detection and segmentation performance. On Poplar-leaf, LeafInst achieves 68.4 mAP, outperforming YOLOv11 by 7.1 percent and MaskDINO by 6.5 percent. On the public PhenoBench benchmark, it reaches 52.7 box mAP, exceeding MaskDINO by 3.4 percent. Additional experiments demonstrate strong generalization and practical utility for large-scale leaf phenotyping.
Why it matches plant phenotyping methods森林葉の個体分割と表現型解析のためのUAV画像データセットおよび新規セグメンテーション手法を開発・評価しており、植物表現型取得が中心である。
abstractwe collected UAV RGB imagery of field-grown saplings and constructed the Poplar-leaf dataset, containing 1,202 branches and 19,876 pixel-level annotated leaf instances.
Modeling plant growth dynamics plays a central role in modern agricultural research. However, learning robust predictors from multi-view plant imagery remains challenging due to strong viewpoint redundancy and viewpoint-dependent appearance changes. We propose a level-aware vision language framework that jointly predicts plant age and leaf count using a single multi-task model built on CLIP embeddings. Our method aggregates rotational views into angle-invariant representations and conditions visual features on lightweight text priors encoding viewpoint level for stable prediction under incomplete or unordered inputs. On the GroMo25 benchmark, our approach reduces mean age MAE from 7.74 to 3.91 and mean leaf-count MAE from 5.52 to 3.08 compared to the GroMo baseline, corresponding to improvements of 49.5% and 44.2%, respectively. The unified formulation simplifies the pipeline by replacing the conventional dual-model setup while improving robustness to missing views. The models and code is available at: https://github.com/SimonWarmers/CLIP-MVP
Why it matches plant phenotyping methods植物画像から葉数・植物齢を推定するマルチビュー表現学習手法を開発し、ベンチマークで性能評価しており、表現型取得・推定が研究の中心である。
abstractWe propose a level-aware vision language framework that jointly predicts plant age and leaf count using a single multi-task model built on CLIP embeddings.
Reproduction assets foundThe paper explicitly states that the model and code are publicly available at the authors' GitHub repository, which qualifies as a paper-specific public code asset.Code · publicm 7.74 to 3.91 and mean leaf-count MAE from 5.52 to 3.08 compared to the GroMo baseline, corresponding to improvements of 49.5% and 44.2%, respectively. The unified formulation simplifies the pipeline by replacing the conventional dual-model setup while improving robustness to missing views. The modela and code is available at: https://github.com/SimonWarmers/CLIP-MVP
Index Terms:
Plant phenotyping, Multi-view learning, Multi-task regression, Precision agriculture
† † address: † Computer Vision Lab, CAIDAS, IFI, University of Würzburg, Germany
‡ Technological University Dublin, Ireland
1 Introduction
Plant phenotyping from multiview imagery is crucial for precision agriculture, enabling non-Open asset ↗SimonWarmers/CLIP-MVPlines:1-53Code / dataset availability confirmedEurope PMC · checked 15 Sept 2026
This article describes a multi-sensor dataset collected during the TIRAMISU (Thermal InfraRed Anisotropy Measurements in India and Southern eUrope) campaign at the Nawagam research site in Gujarat, India, during the 2023 monsoon season. The objective was to acquire continuous ground-based optical and thermal measurements over a homogeneous rice canopy across different crop growth stages. The dataset integrates several complementary components. Thermal data were acquired with an Optris longwave infrared camera (8-14 µm) at high temporal resolution, capturing canopy temperature dynamics throughout the diurnal cycle. Optical data were obtained with a Micasense RedEdge-M multispectral sensor, providing imagery in Blue, Green, Red, RedEdge, and Near-Infrared bands with radiometric corrections. An Apogee radiometer supplied reference radiometric temperature. Meteorological measurements included air temperature, humidity, wind speed and direction, and net radiation. Ancillary field measurements comprised Leaf Area Index (LAI), plant height, emissivity sampling, hyperspectral observations, and crop stage information. The datasets are provided with metadata and processing workflows, including calibration procedures for optical reflectance and thermal radiance. Together, these components form a comprehensive record of canopy-atmosphere interactions over a homogeneous rice field. The datasets can support research on optical and thermal directional anisotropy, canopy radiative transfer, emissivity characterization, and crop biophysical parameter estimation. In addition, they are relevant for applications in vegetation monitoring, agricultural water stress assessment, and surface energy balance studies. By combining optical, thermal, and meteorological observations, the resource is suited for multidisciplinary investigations in remote sensing, agronomy, and environmental sciences.
Why it matches plant phenotyping methods光学・熱画像、校正手順、処理ワークフロー、LAIや草丈などの植物形質を含む再利用可能な作物キャノピーデータセットが研究の中心であり、植物表現型取得基盤として適格。
abstractThe dataset integrates several complementary components.
Reproduction assets foundThe paper is a Data in Brief describing the TIRAMISU rice-canopy dataset (thermal/multispectral images, meteorological, ancillary LAI/height, hyperspectral, emissivity) publicly deposited at doi.org/10.6096/1028, including processing scripts (Thermal_CSV_to_Image.py, MicaSense notebook) for reproducibility.Dataset · publicRepository name: Optical, Thermal Infrared, and Meteorological Dataset from the Thermal InfraRed Anisotropy Measurements in India and Southern eUrope (TIRAMISU) Rice Canopy Experiment
Data identification number: doi.org/10.6096/1028
Direct URL to data: https://doi.org/10.6096/1028
Instructions for access: Publicly accessible repository; representative subsets provided with metadata and processing scripts.
Related research article
Pinnepalli, C., Roujean, J.-L., Irvine, M., et al. [ 1 ]. Measuring and modelling directional effects in the frame of TIRAMISU. ISPRS Annals, X–3–2024 , 325–330. https://doi.orgOpen asset ↗doi.org · 10.6096/1028lines:49-77Plant phenotyping relevance match · UnverifiedCrossref · OpenAlex · checked 14 Sept 2026
Maize phenotyping remains a major bottleneck in genetic analysis and breeding. Despite advances in drones, field robots, and gantry phenotyping systems, ultra-affordable, high-throughput, field-based maize phenotyping at single-plant resolution is still lacking, largely due to the high cost, complex deployment, and limited flexibility of existing platforms under heterogeneous field conditions. To address these challenges, we propose a novel paradigm that integrates DIY imaging devices with customized computer vision–based analytics, and present GLiMPSe ( G iraffe + Li zard M aize P henotyping S yst e m), including two end-to-end phenotyping modules for maize plant architecture (the Giraffe module) and leaf traits (the Lizard module). The imaging device in the Giraffe module are built from modular electronics and 3D-printed parts from local retailers to achieve high-quality image acquisition. The Giraffe and the Lizard modules operate at speeds of 15 seconds and 8 seconds per sample, with costs of $379.1 and $241.1, respectively. Both modules feature fine-tuned YOLOv11x segmentation models for reliable and robust target segmentation, followed by customized Python-based analytical pipelines that enable precise extraction and quantification of phenotypic traits. This methodology achieves high accuracies ( R² ) for five key traits, including plant height (0.928), heights of above-ear leaves (0.87∼0.958), ear height (0.925), above-ear leaf number (0.837), and leaf width (0.937). To enhance accessibility, we developed user-friendly graphical interfaces and publicly released manually annotated datasets and source code to support broader adoption and further innovation. This work provides a practical and accessible solution for high-throughput field phenotyping and offers new opportunities for democratizing crop phenomics through affordable, open-source technologies.
Why it matches plant phenotyping methods低コストな撮像装置、コンピュータビジョン解析、形質抽出パイプライン、GUI、データセットとコードを統合したトウモロコシ表現型測定システムの開発・検証が研究の中心である。
abstractwe propose a novel paradigm that integrates DIY imaging devices with customized computer vision–based analytics, and present GLiMPSe
Maize leaf morphology is poorly investigated because quantifying maize leaf geometry is still an open question due to the complexity of the 3D curved shape. By utilization of geometric curves, maize leaf morphology can be effectively described parametrically and quantitatively. We divided maize leaf into three components: midrib, cross-section and blade contour. Each component is represented by parametric curves and controlled by a group of parameters. A 3D maize leaf model is generated by translation, rotation and scaling of the three components. We demonstrated the parametric maize leaf model allows the applications of leaf geometry analysis, leaf-level radiation capture simulation and dataset synthesis for phenotyping pipeline. The parametric maize leaf model is configurable, extensible and scalable, allowing it to be used in agricultural digital-twin and high-accuracy phenotyping. It also has potential to serve as a platform for maize biophysical and biomechanical studies. The code for 3D maize leaf model generation is available at https://github.com/xzcppm/parametric_maize_leaf.
Why it matches plant phenotyping methodsトウモロコシ葉の3D形態・幾何をパラメトリックにモデル化し、表現型解析用データ合成にも利用できる手法を開発しているため、植物表現型取得・解析手法が中心である。
abstractA 3D maize leaf model is generated by translation, rotation and scaling of the three components.
Reconstruction of crop three-dimensional (3D) point clouds is essential for monitoring phenotypic parameters, like plant height and leaf area index (LAI), which is a critical phenotype predictor for smart crop breeding. The main 3D reconstruction technologies include image-based approaches, laser scanning, and depth camera methods. Among these methods, image-based structure-from-motion (SfM) is widely used due to its low cost and high accuracy. However, field crop canopy image data for high-resolution point cloud construction are often large-scale, unordered, and uncalibrated. Conventional SfM methods struggle with 3D reconstruction due to high computational costs and long processing times, delaying phenotypic analysis. To address this issue, we developed an improved global SfM algorithm, which increases the point cloud reconstruction speed by an average of 1.39 times compared to traditional incremental SfM methods and by more than 10 % on average compared to two mainstream global SfM algorithms. In addition, we integrated three types of predictors, point cloud features, color indices and texture features, through multi-feature data fusion and machine learning. A random forest algorithm for the prediction of LAI for a combined data set of four different crops, and using all three categories of predictors, achieved higher monitoring accuracy compared to using a single feature category (R²=0.78 vs R²=0.71–0.74). This new method, which includes an improved global SfM algorithm and a three-predictor fusion-based LAI monitoring approach, offers an efficient and reliable solution for precise crop phenotyping and continuous growth monitoring in complex field environments, enabling accurate assessment of crop morphology and developmental dynamics.
Why it matches plant phenotyping methods改良型SfMによる3D再構成と、特徴量融合・機械学習によるLAI推定を開発しており、植物表現型取得手法が研究の中心である。
abstractwe developed an improved global SfM algorithm
Reliable and intelligent retrieval of leaf traits from hyperspectral reflectance is crucial for assessing ecosystem functions, yet conventional approaches struggle with spectral complexity and nonlinearities. To address these challenges, we developed the Leaf Trait Retrieval Network (LTRN), a novel deep learning framework that integrates Kolmogorov–Arnold Network (KAN), Transformer, and Temporal Convolutional Networks (TCN) for end-to-end trait estimation. Model validation was carried out using a large spectral–trait database covering hundreds of plant species and four functional traits. Experimental results demonstrated that LTRN model outperforms state-of-the-art deep learning models, achieving R² values greater than 0.78 for estimating chlorophyll content (Chlₐ₊b), equivalent water thickness (EWT), carotenoid content (Ccₐᵣ), and leaf mass per area (LMA). Further analyses indicated that the LTRN model delivers stable estimation performance across spectral resolutions of 10–25 nm. Moreover, the model demonstrates strong stability across varying proportions of training samples. These findings underscore the robustness and stability of LTRN for large-scale vegetation trait retrieval, offering a valuable framework for advancing the intelligent estimation of other ecological parameters.
Why it matches plant phenotyping methods植物のハイパースペクトル反射から葉形質を推定する深層学習手法を開発し、複数形質・種を含むデータベースで性能と頑健性を検証しており、表現型取得・抽出法が中心である。
abstractwe developed the Leaf Trait Retrieval Network (LTRN), a novel deep learning framework that integrates Kolmogorov–Arnold Network (KAN), Transformer, and Temporal Convolutional Networks (TCN) for end-to-end trait estimation.
Timely, field-scale retrieval of crop biophysical variables is widely regarded as central to data-driven agronomy. In this study, a practical workflow was evaluated in which high-resolution unmanned aerial system (UAS) multispectral imagery was coupled with PROSAIL inversion to map rice canopy traits across three phenological stages. Multispectral and RGB acquisitions were processed, and indices sensitive to chlorophyll, water, and pigment dynamics (e.g., Normalized Difference Red-Edge Index (NDRE), Leaf Chlorophyll Index (LCI), Modified Chlorophyll Absorption Ratio Index (MCARI), Normalized Difference Vegetation Index (NDVI), Normalized Difference Water Index (NDWI), Structure-Insensitive Pigment Index 2 (SIPI2), Triangular Greenness Index (TGI), and Visible Atmospherically Resistant Index (VARI)) were derived. Leaf and canopy parameters, leaf chlorophyll content (Cab), carotenoids (Car), leaf water content (Cw), dry matter (Cm), mesophyll structure (N), and leaf area index (LAI)—were retrieved via lookup-table (LUT) inversion of PROSAIL. Independent ground measurements were used for validation, and a same-date Sentinel-2 benchmark was performed (subject to cloud constraints). Consistent phenological trajectories were observed: NDRE/LCI and Cab/LAI were found to peak at maximum greenness, while SIPI2 was observed to rise during senescence alongside declining Cab and Cw. Stage-dependent errors were identified in PROSAIL RMSE maps, with the lowest and most homogeneous errors detected at peak canopy. Strong agreement with field data was obtained (R² > 0.98 for most variables at the first date). For Cab, R²/RMSE values of 0.996/1.555, 0.978/2.104, and 0.972/0.2 were recorded across the three dates, respectively. Lower accuracy was produced by Sentinel-2 at field scale (e.g., LAI R²/RMSE ≈ 0.81/0.7; Cab ≈ 0.78/6.5), although useful cross-sensor complementarity was indicated. An operational pathway to within-field mapping of rice biophysics is thereby offered by the “UAS multispectral + PROSAIL” pipeline. The results demonstrate high accuracy at field scale, with phenology-dependent retrievals outperforming Sentinel-2-based estimates, highlighting the potential of UAV-based approaches for precise crop monitoring. Enhanced robustness to phenological change and cloud-related gaps is achieved when red-edge and pigment-ratio indices are fused with physical inversion, and straightforward extensibility to other cereals and management contexts is suggested.
Why it matches plant phenotyping methodsUAVマルチスペクトル画像とPROSAIL逆解析を統合し、イネの生理・構造形質を推定して地上測定で検証するワークフローが研究の中心であり、実質的な植物フェノタイピング手法の適用・評価である。
abstracta practical workflow was evaluated in which high-resolution unmanned aerial system (UAS) multispectral imagery was coupled with PROSAIL inversion to map rice canopy traits across three phenological stages.
MaizeLiDAR / point cloudLeafStem / branchMorphology / geometry measurementSegmentationLeaf traits
Maize leaf phenotypic parameters effectively reflect the photosynthesis and growth information of maize plants, which is crucial for breeding superior maize varieties. Current challenges include separating stems and leaves from a single maize plant and accurately measuring the phenotypic parameters of maize leaves. This study proposes a stem-leaf segmentation method based on region growing, incorporating adaptive cuboid region growing and slice region growing, alongside techniques for measuring phenotypic parameters of maize leaves. First, terrestrial laser scanning (TLS) was employed to obtain three-dimensional (3D) point cloud data of maize at the five-leaf (V5) and six-leaf (V6) stages. The point cloud data were then preprocessed to isolate single plant point clouds. Next, the maize point clouds were pre-segmented into three categories-central point clouds, partially expanded leaf point clouds, and unexpanded leaf point clouds-using center-edge segmentation, statistical filtering, and leaf classification. Adaptive cuboid region growing was applied to segment the unexpanded leaf point clouds, while slice region growing was used for partially expanded leaves, with Euclidean clustering optimizing the leaf point clouds, completing the segmentation process. Finally, various methods-including clustering counting, point-to-point distance accumulation, point-to-line distance, vector angle, point cloud triangulation, and triangle area accumulation-were utilized to automatically measure the number of maize leaves, leaf length, leaf width, leaf inclination angle, and leaf area. Compared with other point cloud stem-leaf segmentation methods based on geometric features and common 3D point cloud deep learning models (PointNet++, PointTransformer), the method proposed in this paper performs better. The segmentation results indicated that the Precision (P), Recall (R) and F₁-Score (F₁) for stem-leaf segmentation of all maize plants at the V5 stage exceeded 92.00%, with average values of 96.87%, 97.08%, and 96.97%, respectively. At the V6 stage, P, R, and F₁ exceeded 95.00%, with averages of 97.73%, 97.01%, and 97.67%, respectively. The algorithm accurately measured the number of leaves at the V5 stage, while a small error was noted at the V6 stage, yielding a percentage error (PE) of 0.93%. Measurement accuracy for leaf length, width, and area at both growth stages was greater than 93.80%, 92.80%, and 89.50%, respectively. Measurement accuracy for leaf inclination angle was lower, at 82.00% and 88.02% for the V5 and V6 stages, respectively. The proposed methods for stem-leaf segmentation and measurement of leaf phenotypic parameters are fast and accurate, providing technical support for high-quality breeding and intelligent management of maize. Our point cloud data of maize and source code is available from https://github.com/lmj-cau/stem-leaf-segmentation.git.
Why it matches plant phenotyping methodsトウモロコシの3D点群から茎葉を分割し、葉数・長さ・幅・面積・傾斜角を自動推定する手法を開発・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 study proposes a stem-leaf segmentation method based on region growing, incorporating adaptive cuboid region growing and slice region growing, alongside techniques for measuring phenotypic parameters of maize leaves.
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).
ABSTRACT Early detection of herbicide‐induced stress is essential for optimising weed control, improving crop safety and advancing precision agriculture practices. While non‐destructive imaging technologies offer great potential for rapid stress diagnosis, direct comparisons of their performance across species, herbicides and application rates remain scarce. This study systematically compared three high‐throughput imaging methods: chlorophyll fluorescence imaging, multispectral imaging and 3D multispectral scanning, for their ability to detect and classify early physiological and morphological responses to bentazone (HRAC 6) and glyphosate (HRAC 9) in a weed (velvetleaf, Abutilon theophrasti ) and a crop species (common bean, Phaseolus vulgaris ). Plants were imaged daily, immediately before treatment and for five consecutive days after herbicide application. Chlorophyll fluorescence parameters, particularly NPQ, q P and F s ′, emerged as the earliest and most sensitive indicators, detecting stress within 24 h of treatment. Stepwise discriminant analysis revealed that intermediate time points (48–72 h after application) achieved the highest classification accuracies, reaching up to 100%, with chlorophyll fluorescence as the dominant trait for selection. Multispectral traits, such as reflection in red and far red, and saturation, together with morphological traits like total leaf area and leaf inclination, provided complementary information and enhanced discrimination accuracy among herbicides. These findings highlight the superiority of chlorophyll fluorescence imaging for detecting early herbicide stress, while demonstrating the added value of integrating spectral and morphological traits. The results support the development of multi‐sensor phenotyping pipelines for rapid, accurate and field‐adaptable diagnostics in both weed and crop management.
Why it matches plant phenotyping methods複数の高スループット画像計測法を比較・評価し、植物の生理・形態応答を用いた早期ストレス検出性能を検証しているため、フェノタイピング手法が中心です。
abstractThese findings highlight the superiority of chlorophyll fluorescence imaging for detecting early herbicide stress, while demonstrating the added value of integrating spectral and morphological traits.
TomatoLiDAR / point cloudLeafStem / branchMorphology / geometry measurementSegmentationLeaf traits
Tomatoes are a globally important horticultural crop, and their high-yield, high-quality breeding relies on high-throughput, precise phenotyping. While 3D point cloud technology offers a new avenue for non-destructive plant phenotyping, the inherent complexity of tomato plant organ morphology and growth dynamics poses a significant challenge to existing segmentation methods. To address this, this study employed multi-view RGB image reconstruction to cost-effectively acquire high-quality point cloud data from four growth cycles. Based on the characteristics of our data, we adapted and proposed a hybrid dual-path downsampling method (HDPD) for dataset augmentation, and constructed a dynamic reference point propagation network (DRP-Net) for semantic segmentation. The DRP-Net architecture addresses geometric feature mismatches between organs through a dynamic kernel edge convolution module (DKEC). Furthermore, it utilizes a global–local semantic feature fusion upsampling module (GL-SFFU) to overcome boundary blurring caused by plant growth and enhance detail discrimination. Based on the semantic segmentation results, a clustering algorithm was used to achieve leaf instance segmentation and extract key phenotypic parameters. Experimental results demonstrate that DRP-Net achieves significant performance in the tomato stem and leaf segmentation task, with mean precision, recall, F1 score, and mIoU reaching 94.97%, 93.93%, 94.43%, and 89.34%, respectively. The extracted phenotypic parameters, such as leaf length, leaf width, and leaf area, exhibit strong correlations with manual measurements (R² greater than 0.92 and 0.88, respectively). This study provides an effective technical solution for the precise segmentation of complex plant organs and high-throughput phenotyping analysis for breeding.
Why it matches plant phenotyping methodsトマトの3D点群から茎葉をセグメンテーションし、葉形質を抽出する手法を開発・検証しており、植物フェノタイピングが研究の中心である。
abstractconstructed a dynamic reference point propagation network (DRP-Net) for semantic segmentation
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
Plant phenotyping relevance match · UnverifiedCrossref · OpenAlex · Europe PMC · checked 15 Sept 2026
Reconstruction of crop three-dimensional (3D) point clouds is essential for monitoring phenotypic parameters, like plant height and leaf area index (LAI), which is a critical phenotype predictor for smart crop breeding. The main 3D reconstruction technologies include image-based approaches, laser scanning, and depth camera methods. Among these methods, image-based structure-from-motion (SfM) is widely used due to its low cost and high accuracy. However, field crop canopy image data for high-resolution point cloud construction are often large-scale, unordered, and uncalibrated. Conventional SfM methods struggle with 3D reconstruction due to high computational costs and long processing times, delaying phenotypic analysis. To address this issue, we developed an improved global SfM algorithm, which increases the point cloud reconstruction speed by an average of 1.39 times compared to traditional incremental SfM methods and by more than 10 % on average compared to two mainstream global SfM algorithms. In addition, we integrated three types of predictors, point cloud features, color indices and texture features, through multi-feature data fusion and machine learning. A random forest algorithm for the prediction of LAI for a combined data set of four different crops, and using all three categories of predictors, achieved higher monitoring accuracy compared to using a single feature category (R²=0.78 vs R²=0.71–0.74). This new method, which includes an improved global SfM algorithm and a three-predictor fusion-based LAI monitoring approach, offers an efficient and reliable solution for precise crop phenotyping and continuous growth monitoring in complex field environments, enabling accurate assessment of crop morphology and developmental dynamics.
Why it matches plant phenotyping methods改良したSfMによる3D再構成と、特徴量融合・機械学習によるLAI推定を開発・評価しており、植物表現型取得手法が研究の中心である。
abstractwe developed an improved global SfM algorithm
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.
Accurate retrieval of plant functional traits is critical for monitoring crop growth and improving agronomic management. Canopy structural parameters, such as leaf area index (LAI) and leaf inclination distribution function (LIDFa), strongly influence inversion accuracy. Quantifying canopy structural uncertainties and developing strategies to improve retrieval accuracy are crucial. In this study, we developed an inversion framework based on the Soil Canopy Observation of Photosynthesis and Energy fluxes (SCOPE) model, integrating reflectance and solar-induced fluorescence (SIF) data. Using both simulation modelling and field measurements in NEON STER crop field, we introduced multi-level prior noise and evaluated how uncertainties in LAI and LIDFa propagate into the retrieval of chlorophyll content (Cab), maximum carboxylation rate (Vcmax), and fluorescence quantum efficiency (fqe). To assess the influence of canopy structure and improve retrieval accuracy, three inversion strategies—Prior-Matched (PM), Regularized (RI), and No-Prior (NP)—were designed and tested for their accuracy and robustness. The results showed that second-order Sobol’ indices (S2) captured interactions among canopy structural parameters and functional traits, particularly between Cab-LAI, Cab-LIDFa and fqe-LAI, with sensitive spectral ranges at 680–740 nm (fluorescence) and 600–720 nm (reflectance). Error amplification analysis under six noise levels showed that structural uncertainties significant amplified reflectance and fluorescence variations, with red-edge shifts (ΔRE) and 740 nm fluorescence changes (ΔF740) being most sensitive. Incorporating prior canopy structure information improved inversion accuracy by up to 7.93 % in R² and reduced RMSE by 21.25 %, although this advantage diminished under high noise levels. LAI uncertainty had a greater impact than LIDFa, and additive noise introduced more uncertainty than multiplicative noise. Comparison of the inversion strategies revealed that the RI strategy achieved higher accuracy (simulated data: R²=0.954; measured data: R²=0.799) and greater robustness to noise than the PM strategy. These findings demonstrate the value of integrating canopy structure into computational inversion models to enhance the reliability of remote sensing trait retrieval, supporting precision agriculture and sustainable crop production.
Why it matches plant phenotyping methods植物機能形質のリモートセンシング推定を対象に、SCOPEモデルに基づく反演フレームワークと複数の反演戦略を開発・比較し、ノイズへの頑健性と精度を検証している。形質取得・推定手法が研究の中心である。
abstractwe developed an inversion framework based on the Soil Canopy Observation of Photosynthesis and Energy fluxes (SCOPE) model, integrating reflectance and solar-induced fluorescence (SIF) data.
Accurate estimation of the Leaf Area Index (LAI) is essential for assessing vegetation health and managing agricultural productivity. This study examines the application of Unmanned Aerial Vehicle (UAV)-based hyperspectral imaging and convolved EnMAP spectral data for estimating corn LAI, utilizing machine learning (ML) models to improve prediction accuracy. Various ML models, including k-nearest Neighbors (KNN), Support Vector Machines (SVM), Partial Least Squares Regression (PLS), and Random Forests (RF), were assessed to predict LAI from hyperspectral, EnMAP, and vegetation index features. Results demonstrate that PLS models consistently outperformed other ML approaches, achieving coefficients of determination (R²) ranging from 0.79 to 0.82. Notably, for the top two performing models (PLS and SVM) spectral indices such as NDRE, GNDVI, and NDVI proved more effective for LAI prediction than individual spectral bands. Interestingly, no matter the incorporation of hyperspectral wavelengths or EnMAP bands, the models predicting LAI were comparable. Feature importance analysis reinforced the dominance of vegetation indices as key predictors. The findings emphasize the benefits of high-resolution UAV hyperspectral imaging, convolved satellite spectral data, and machine learning, particularly PLS, for scalable and accurate LAI estimation in agroecosystems.
Why it matches plant phenotyping methodsUAVハイパースペクトル画像と機械学習を用いてトウモロコシのLAIという植物形質を推定し、複数モデルと特徴量の性能を比較・評価しているため、形質取得手法が中心である。
abstractThis study examines the application of Unmanned Aerial Vehicle (UAV)-based hyperspectral imaging and convolved EnMAP spectral data for estimating corn LAI, utilizing machine learning (ML) models to improve prediction accuracy.
Accurate canopy photosynthesis modeling is essential for understanding and optimizing crop growth and yield in greenhouse agriculture. Current models have limited predictive capability due to inadequate responsiveness to dynamic environments and delays in parameter acquisition, making accurate predictions challenging under the complex conditions of solar greenhouses. This study aimed to develop a dynamic canopy photosynthesis model for greenhouse tomatoes, leveraging an IoT sensor network for real-time biological feedback and parameterization. By integrating real-time monitoring with dynamic feedback, the model facilitates precision management of greenhouse tomato cultivation, thereby optimizing plant growth, resource use efficiency, and yield predictability. To achieve this, a non-destructive inversion method based on a dual weighing system was developed, enabling accurate dynamic monitoring of tomato canopy leaf area index (LAI, R² ≥ 0.94) and the photosynthetic leaf area index (LAIₚ, R² ≥ 0.91), continuously providing parameters for updating modelling (validated against destructive sampling and actual measurements for trait specifics). Based on accurate parameter acquisition, a dynamic canopy photosynthesis model was developed using LAIₚ as the core variable, integrating above-canopy radiation. A newly developed parameter, which integrates the radiation component of transpiration, serves as a key factor for estimating photosynthesis. This innovative approach allows for accurate daily prediction and assessment of assimilated biomass. Experimental results from 2022 and 2023 showed that the LAIₚ model performed better than the comparison model, showing higher accuracy and adaptability (R² = 0.87 and 0.89, NRMSE = 0.17 and 0.12 vs. R² = 0.70 and 0.80, NRMSE = 0.26 and 0.15). These results confirmed the reliability of the integrated modeling framework, which forms a closed-loop system connecting real-time plant monitoring, statistical parameter inversion, online model adaptation, and biomass feedback verification. This modeling approach provides a solid foundation for precise growth simulation, sustainably improving yield and quality in solar greenhouse tomatoes, and advancing digital twin-enabled intelligent production.
Why it matches plant phenotyping methods植物キャノピーのLAIおよび光合成LAIを非破壊・連続推定するセンサー／逆解析法を開発し、破壊サンプリング等で検証している。植物形質取得とモデル連携が研究の中心である。
abstracta non-destructive inversion method based on a dual weighing system was developed, enabling accurate dynamic monitoring of tomato canopy leaf area index (LAI, R² ≥ 0.94) and the photosynthetic leaf area index (LAIₚ, R² ≥ 0.91)
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
Field / plotNeRF / 3D Gaussian SplattingPhotogrammetry / SfM / MVSLiDAR / point cloudLeafStem / branchWhole plant / canopy / plot / fieldMorphology / geometry measurement2D/3D reconstructionSkeletonization / topology
Saplings are key indicators of forest regeneration and overall forest health. However, their fine-scale architectural traits are difficult to capture with existing 3D sensing methods, which make quantitative evaluation difficult. Terrestrial Laser Scanners (TLS), Mobile Laser Scanners (MLS), or traditional photogrammetry approaches poorly reconstruct thin branches, dense foliage, and lack the scale consistency needed for long-term monitoring. Implicit 3D reconstruction methods such as Neural Radiance Fields (NeRF) and 3D Gaussian Splatting (3DGS) are promising alternatives, but cannot recover the true scale of a scene and lack any means to be accurately geo-localised. In this paper, we present a pipeline which fuses NeRF, LiDAR SLAM, and GNSS to enable repeatable, geo-localised ecological monitoring of saplings. Our system proposes a three-level representation: (i) coarse Earth-frame localisation using GNSS, (ii) LiDAR-based SLAM for centimetre-accurate localisation and reconstruction, and (iii) NeRF-derived object-centric dense reconstruction of individual saplings. This approach enables repeatable quantitative evaluation and long-term monitoring of sapling traits. Our experiments in forest plots in Wytham Woods (Oxford, UK) and Evo (Finland) show that stem height, branching patterns, and leaf-to-wood ratios can be captured with increased accuracy as compared to TLS. We demonstrate that accurate stem skeletons and leaf distributions can be measured for saplings with heights between 0.5m and 2m in situ, giving ecologists access to richer structural and quantitative data for analysing forest dynamics.
Why it matches plant phenotyping methodsNeRF・LiDAR SLAM・GNSSを融合した幼木の3D再構成・定位パイプラインを開発し、樹高、分枝、葉対木質比などの植物形質をTLSと比較検証しており、表現型取得手法が中心である。
abstractIn this paper, we present a pipeline which fuses NeRF, LiDAR SLAM, and GNSS to enable repeatable, geo-localised ecological monitoring of saplings.
Plant phenotyping relevance match · UnverifiedOpenAlex · Crossref · Europe PMC · checked 15 Sept 2026
Heat stress damage leads to yield penalties in many wheat-growing areas. Climate change models predict warmer scenarios and more frequent heat shocks. Consequently, wheat breeders need to develop more productive varieties for warm conditions, and therefore, the identification of heat-tolerance traits is needed. Albedo is an integrative trait of the optical properties of the canopy defined as the ratio of reflected light to total light received. High albedos in warm conditions may help reduce damaging radiation. Despite its potential relevance for heat avoidance, albedo has been little explored in wheat breeding. In this work, a selection of 30 wheat ( Triticum aestivum L.) genotypes of diverse origin were sown at two sowing dates in Australia (NSW) in 2018 and 2019. A high-throughput phenotyping method based on spectroradiometer measurements [Analytical Spectral Devices (ASD)] to measure canopy albedo was developed to explore its relationship with temperature and other heat tolerance-related traits. ASD albedo was validated via continuous albedometer measurements on a subset of genotypes. Data were captured at flowering (one of the most critical periods for heat-related damage). Genotypic differences for albedo were found in most environments. However, genotypic effects were most noticeable at noon in optimally sown materials (H 2 0.71–0.86). Albedo was directly related to canopy architecture and light interception (r = 0.74) and varied depending on genotype and genotype by environment interaction. Air temperature in the canopy profile and canopy temperature (CT) were also monitored continuously in a subset of genotypes to explore the relationship between albedo and canopy micrometeorology. Canopies with higher albedos had larger air temperature differences across the canopy profile at the flowering stage (r = 0.48). However, canopy temperature was not related to albedo, even though it was strongly correlated (r = 0.99) with air temperature around the spike. Overall, these results indicate that canopy architecture is the primary influence on albedo under warm conditions. Although higher albedo was not associated with lower canopy temperature, its influence on canopy micrometeorology suggests that albedo may contribute to heat avoidance and could therefore be considered an additive trait for phenotyping and breeding for environments under high temperatures.
Why it matches plant phenotyping methods小麦群落アルベドを分光放射計で測定するハイスループット表現型計測法を開発し、連続アルベドメーターで検証しているため、方法が研究の中心である。
abstractA high-throughput phenotyping method based on spectroradiometer measurements [Analytical Spectral Devices (ASD)] to measure canopy albedo was developed
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:531-564Code / dataset availability confirmedEurope PMC · checked 15 Sept 2026
Grapevines ( Vitis vinifera L.) undergo structural and physiological changes throughout the growing season, progressing through distinct phenological stages that require regular monitoring. This dataset consists of high-resolution point cloud data acquired with a stationary terrestrial laser scanner (TLS) to document grapevine development from early leaf development to dormancy. Georeferenced point clouds were generated from 15 TLS scans along two vineyard rows at nine phenological stages. The dataset also includes multispectral and RGB photogrammetric point clouds and orthorectified raster products from an unmanned aerial vehicle survey conducted before harvest. Ground-truth measurements leaf area index, grape production, and pruning wood biomass were collected for each monitored grapevine. As a result, the dataset provides multi-temporal TLS observations that support grapevine structural analysis and development, phenological monitoring, and can be used for the development of AI-based models for precision viticulture.
Why it matches plant phenotyping methodsブドウの生育・構造・フェノロジーを対象とするTLS点群および関連画像データセットであり、植物フェノタイピング用の再利用可能なデータ基盤として中心的です。
titleTLS-grapevine2024: A terrestrial laser scanner point cloud dataset of grapevines at different phenological stages.
Reproduction assets foundThe paper is a Data in Brief article describing the TLS-grapevine2024 dataset itself, publicly deposited on Zenodo with DOI 10.5281/zenodo.16751663. This is a paper-specific, openly available asset containing the TLS point clouds, UAV imagery/rasters, and ground-truth agronomic measurements (LAI, grape production, prunDataset · publicditions: clear sky.
Data source location
Institution: University of Trás-os-Montes e Alto Douro
City/Town/Region: Arroios, Vila Real, Norte
Country: Portugal
Coordinates: 41°17′28.83″N 7°43′17.90″W,
Altitude: 435 m
Data accessibility
Repository name: Zenodo
Data identification number: 10.5281/zenodo.16751663
Direct URL to data: https://doi.org/10.5281/zenodo.16751663
Related research article
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Value of the Data
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This dataset covers nine phenological stages of grapevine growth from April 2024 to January 2025, providing multi-temporal terrestrial laser scanner (TLS) observations for structural and phenological analysis.
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It includes TLS point clouds collected at multiple stages and muOpen asset ↗Zenodo · 10.5281/zenodo.16751663lines:1-50Code / dataset availability confirmedOpenAlex · Europe PMC · bioRxiv · checked 5 Sept 2026
1 Abstract Accurate quantification of plant disease is essential for resistance breeding, variety testing, and precision agriculture, yet visual ratings are limited by subjectivity, low precision, and restricted throughput. Image-based phenotyping can address these limitations, but field applications face substantial challenges due to spatial heterogeneity, symptom-level diagnostic requirements, and the need for very high-resolution imagery with limited spatial coverage. This introduces a fundamental trade-off: high-resolution images provide precise local measurements of disease, but spot-level estimates can be highly variable within experimental units. We analyzed a large image data set of wheat foliar diseases to characterize the distribution, spatial dependence, and aggregation behavior of spot-level severity estimates in plots. We combined high-resolution macro-scale imaging with focus bracketing to increase the sampled leaf area. Our results highlight focus bracketing as a promising approach for simultaneous diagnosis and quantification of disease in field plots. Autocorrelation in severity estimates both within focal image stacks and across plot positions was comparable, with 10 focal stack images or 10 positions per plot contributing approximately 2.5 independent observations each. Modeling plot-level severity as a latent Beta-distributed variable enabled robust estimation of mean severity and associated uncertainty. This supports both hypothesis testing and efficient sampling across the full range of disease severity associated with genotypic diversity and seasonality of developing epidemics. The proposed imaging approach is non-invasive and, in principle, transferrable to autonomous ground-based phenotyping platforms, offering the potential to shift the dominant source of uncertainty in estimating disease severity from measurement-related limitations toward biologically and environmentally driven variability in disease expression.
Why it matches plant phenotyping methods高解像度画像とフォーカスブラケティングを用いて植物病害の重症度を定量化し、圃場プロット単位の推定精度と不確実性を評価する手法が研究の中心であるため。
abstractWe combined high-resolution macro-scale imaging with focus bracketing to increase the sampled leaf area.
Reproduction assets foundThe paper states that R code to reproduce the full analysis (Beta-distribution modeling, autocorrelation/AR(1) mixed models, effective sample size estimation for wheat disease severity phenotyping) is publicly available on the authors' GitHub repository. The repository name appears truncated in the supplied text ('plotCode · publicR-code to reproduce the full analysis is available at https://github.com/and-jonas/plot-spot-Open asset ↗and-jonas/plot-spot-pdf-page:9 lines:1-61Plant phenotyping relevance match · UnverifiedEurope PMC · checked 5 Sept 2026
Sorghum is a globally important crop. Under the breeding goals of high yield and stress resistance, the precise selection of elite germplasm is crucial. Phenotypic parameters such as plant height and leaf area at the seedling stage are core indicators for evaluating growth vitality. However, traditional manual measurement is inefficient and error-prone, making it difficult to meet the needs of high-throughput research. To address this, this study proposes an improved model (PTV2-Fr) based on Point Transformer V2 (PTV2), which combines 3D point cloud technology to realize the automatic extraction of sorghum seedling phenotypic parameters and explores the regulatory effects of different gibberellin (GA 3 ) concentrations. In this study, videos of sorghum seedlings were collected using the relevant system of Nanjing Agricultural University, and reconstructed into.ply format 3D point cloud files via the open-source software Colmap. The core optimizations of the PTV2-Fr model are as follows: Firstly, it proposes a Multi-Radius Dual-Coordinate Attention (MRDCA) mechanism to address the problems of leaf overlap and uneven point cloud density, thereby enhancing feature discrimination ability; Secondly, it introduces a Point-Graph Invariant Feature Refinement (PG-InvFR) module to improve the sensitivity of the segmentation head to local geometric details; Thirdly, it constructs a composite loss function (EL Loss) combining class-weighted cross-entropy loss and Lovász loss to alleviate class imbalance and boost segmentation accuracy. We selected 50 valid datasets from 112 video groups, annotated into three categories: Stem, Leaf, and Pot. The results show that PTV2-Fr outperforms PTV2 by 2.5% in accuracy, with significant improvements in Recall and mean F1-score (mF1). Ablation experiments confirm the positive effects of MRDCA, PG-InvFR, and EL Loss. Furthermore, PTV2-Fr demonstrates good robustness in analyzing GA concentrations, revealing that 50-100 mg/L GA concentrations promote seedling growth, while concentrations exceeding 200 mg/L inhibit growth. The PTV2-Fr model provides an efficient solution for the automatic determination of sorghum seedling phenotypes, and the revealed GA 3 regulatory mechanism can offer theoretical references for high-quality seedling cultivation and hormone management.
Why it matches plant phenotyping methods3D点群分割ネットワークを開発・検証し、ソルガム幼苗の草丈や葉面積などの表現型形質を自動抽出する方法が研究の中心である。ジベレリン処理の解析は付加的な応用であり、方法論的貢献が明確。
abstractthis study proposes an improved model (PTV2-Fr) based on Point Transformer V2 (PTV2), which combines 3D point cloud technology to realize the automatic extraction of sorghum seedling phenotypic parameters
Abstract has not been obtained from indexed metadata or an accessible article page.
Why it matches plant phenotyping methodsロボット統合型マルチセンサーと機械学習によるイネ葉面積指数（LAI）の推定精度向上が主題であり、植物形質の取得・推定手法が中心である。
titleImproving rice leaf area index monitoring accuracy via robot-integrated multi-sensors and meteorological data fusion with explainable machine learning
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.
Abstract PlantCV is an open‐source Python project aimed at developing tools to address a range of image‐based, plant phenotyping questions. PlantCV has been used for more than 10 years to automate trait collection from image data, and the newest release, PlantCV version 4, continues to lower the barrier to entry for users without substantial coding experience through extensive example use‐case tutorials and simplified installation. In addition to usability, we document added functionality since the release of PlantCV v2, including support for more image types such as fluorescence, thermal, and hyperspectral data. Finally, we describe the development of a new subpackage focused on morphological trait measurements like leaf angle, and demonstrate its utility as compared to more manual methods of data collection.
Why it matches plant phenotyping methodsPlantCV v4は、画像から植物形質を自動抽出するオープンソースソフトウェアの開発・機能拡張・比較評価を主題としており、植物フェノタイピング手法が中心である。
abstractPlantCV is an open‐source Python project aimed at developing tools to address a range of image‐based, plant phenotyping questions.
Reproduction assets foundThe paper's Data Availability Statement explicitly deposits the authors' analysis scripts on GitHub (danforthcenter/plantcv-4-paper), which directly reproduces this paper's phenotyping analyses.Code · publicerest.
DATA AVA I L A B I L I T Y S TAT E M E N T
Links to code, tutorials, documentation, and other resources
are available on the PlantCV homepage at https://plantcv.org. PlantCV source code is available on GitHub at https://
github.com/danforthcenter/plantcv. Scripts used for analyses
in this paper are available on GitHub at https://github.com/danforthcenter/plantcv-4-paper.O RC I D
HaleySchuhl https://orcid.org/0000-0002-8825-8297
KeelyE. Brown https://orcid.org/0000-0002-5371-5830
ParagK. Bhatt https://orcid.org/0000-0002-0396-6412
DominikSchneider https://orcid.org/0000-0002-5846-5033
Anna L. Casto https://orcid.org/0000-0002-9597-0514
Lucia Acosta-Gamboa https://orcid.org/0000-0001-77Open asset ↗danforthcenter/plantcv-4-paperpdf-raw-page:15 lines:1-97Code / dataset availability confirmedEurope PMC · OpenAlex · checked 5 Sept 2026
Estimating canopy structure - leaf inclination distribution (LIDFa), leaf area index (LAI), and fractional vegetation cover (FCover) - is vital for breeding, yet the added value of multi-angular UAV sensing over nadir-only baselines remains insufficiently quantified. This study developed a UAV-based multi-angular inversion framework that derived high-resolution bidirectional reflectance factors (BRF) from oblique photogrammetry and fitted a kernel-driven BRDF model to characterize reflectance anisotropy. Using transfer learning across cultivars and dates, we compared the retrieval performance of multi-angle versus nadir-only baselines for LIDFa, LAI, and FCover. BRDF model simulations agreed well with airborne BRF (optimal R 2 > 0.80, RRMSE R 2 = 0.59 vs. 0.38 for the best MA and NAD models, respectively) and LIDFa ( R 2 = 0.46 vs. 0.37). For FCover, both configurations achieved high accuracy ( R 2 ≥ 0.73), with MA models providing marginal gains ( R 2 = 0.75). Methodologically, CNN-based transfer learning proved most effective for LAI and FCover, while a Random Forest model using raw multi-angle spectra yielded the best results for LIDFa. Optimal viewing configurations were trait-dependent, generally favoring forward scattering directions with zenith angles between 15° and 45°. These results indicate that kernel-driven BRDF modeling effectively captures spectral anisotropy in dense wheat canopies, and that multi-angular observations provide a distinct advantage for retrieving structural parameters with complex scattering behaviors, such as LAI and LIDFa.
Why it matches plant phenotyping methods小麦育種材料のキャノピー構造形質を対象に、UAVマルチアングルセンシング、BRDFモデル、CNN/RFによる推定フレームワークを開発・比較しており、形質取得手法が研究の中心である。
abstractThis study developed a UAV-based multi-angular inversion framework that derived high-resolution bidirectional reflectance factors (BRF) from oblique photogrammetry and fitted a kernel-driven BRDF model to characterize reflectance anisotropy.
Reproduction assets foundThe paper's data availability statement explicitly deposits the complete source code for BRDF modeling and the transfer learning pipeline, plus a subset of preprocessed field data, in a public GitHub repository matching an allowed URL. Additional data are available only on request.Code · publicThe complete source code for BRDF modeling and the transfer learning pipeline, along with a subset of the preprocessed field data used in this study, are openly available in the GitHub repository at https://github.com/ZWM-RS/UAV-multi-angle-inversion-of-canopy-structure-parameters-in-wheat-breeding-materials.git . Any additional data supporting the findings of this study are available from the corresponding author upon reasonable request.Open asset ↗ZWM-RS/UAV-multi-angle-inversion-of-canopy-structure-parameters-in-wheat-breeding-materialslines:451-474Plant phenotyping relevance match · UnverifiedOpenAlex · Crossref · checked 5 Sept 2026
Abstract Aims This study evaluated the suitability of root electrical capacitance measurements for nondestructive plant phenotyping in a free-air CO 2 enrichment (FACE) experiment. Methods A two-year FACE study was conducted with maize grown under ambient and elevated [CO 2 ], and low and high nitrogen supply in three replicate plots. The saturation root electrical capacitance (C R *) was monitored during the plant growth cycle. Aboveground plant parameters were measured in situ at flowering. Results Capacitance measurements revealed a seasonal pattern in root development with a peak at flowering, and the positive effect of higher nitrogen dose and [CO 2 ] enrichment on plant growth. At anthesis, C R * was significantly ( p < 0.001) and linearly correlated with stem basal area (R 2 : 0.51–0.68), aboveground biomass index (basal area × plant height; R 2 : 0.47–0.62) and leaf chlorophyll concentration (R 2 : 0.40–0.56). However, the best correlation (R 2 : 0.73 and 0.74) was found for plant leaf area, which is closely related to root water uptake, suggesting that the applied current signal penetrated the roots, and that the capacitance method directly measured root status in the field. In addition, C R * at flowering was a reasonable early predictor of maize grain yield (R 2 : 0.58 and 0.64) under our experimental conditions. Conclusions The electrical capacitance method proved to be a practical high-throughput tool for phenotyping not only the root but the whole plant in the field. Being noninvasive, it is particularly beneficial in FACE systems, where destructive sampling and soil disturbance should be minimized. It would also provide cost-effective support for breeding stress-tolerant and climate-resilient crops. Graphical Abstract
Why it matches plant phenotyping methods根の電気容量測定を非破壊・高スループットな植物フェノタイピング手法として評価し、圃場での相関および予測性能を検証しているため、方法が研究の中心である。
abstractThis study evaluated the suitability of root electrical capacitance measurements for nondestructive plant phenotyping in a free-air CO 2 enrichment (FACE) experiment.
Analyzing three-dimensional (3D) phenotypic parameters of maize seedlings is of significant importance for maize cultivation and selection. However, existing methods often struggle to balance cost, efficiency, and accuracy, particularly when capturing the complex morphology of seedlings characterized by slender stems. To address these issues, this study proposes a novel end-to-end automated framework for extracting phenotypes using only consumer-grade RGB cameras. The pipeline initiates with Instant-NGP to rapidly reconstruct dense point clouds, establishing the 3D data foundation for phenotypic extraction. Subsequently, we formulate a directed topological graph-based mechanism. By mathematically defining bifurcation constraints via vector analysis, this mechanism guides a depth-first traversal strategy to explicitly disentangle stem and leaf skeletons. Building upon these decoupled skeletons, organ-level point cloud segmentation is achieved through constraint-based expansion, followed by density-based spatial clustering (DBSCAN) to detect individual leaves. Algorithms combining point cloud geometry with 3D Euclidean distance are also implemented to calculate key phenotypes including plant height and stem width. Finally, single-leaf skeleton fitting is used to estimate leaf length, and principal component analysis (PCA) is adopted to determine the stem–leaf angle, realizing the comprehensive automatic extraction of maize seedling phenotypes. Experiments show that the proposed method achieves high accuracy in extracting key phenotypic parameters. The mean relative errors for plant height, stem width, leaf length, stem-leaf angle, and leaf area are 0.76%, 2.93%, 1.26%, 2.13%, and 3.33%, respectively. Compared with existing methods as far as we know, the proposed method significantly improves extraction efficiency by reducing the processing time per plant to within 5 min while maintaining such high accuracy.
Why it matches plant phenotyping methodsRGBカメラとNeRF・点群処理・骨格解析を統合し、トウモロコシ幼苗の形質を自動抽出する手法を開発・精度評価した研究であり、フェノタイピング手法が中心である。
abstractthis study proposes a novel end-to-end automated framework for extracting phenotypes using only consumer-grade RGB cameras.
Plant phenotyping relevance match · UnverifiedOpenAlex · Europe PMC · checked 5 Sept 2026
BACKGROUND: Precise, non-destructive phenotyping of saffron during vegetative growth is critical for optimizing corm yield and accelerating breeding programs, yet systematic 3D measurements have remained elusive due to extreme morphological challenges: ultra-narrow leaves, severe mutual occlusion, and prostrate growth architecture. Traditional single-view imaging systems fail to resolve individual leaves under such conditions, limiting phenotypic analysis to whole-canopy descriptors. Here, we developed a specialized organ-level 3D phenotyping workflow specifically designed for narrow, overlapping leaves using a low-cost dual-camera rotary acquisition system integrated with open-source Structure-from-Motion Multi-View Stereo (SfM-MVS) reconstruction. RESULTS: > 0.94, MAPE < 6%), achieving accuracy benchmarks established for broad-leaved crops using commercial-grade hardware at 100 × lower cost. Systematic voxel sensitivity analysis across nine scales identified optimal preprocessing parameters (2 cm voxel size) balancing measurement precision with computational efficiency, addressing a critical reproducibility gap in plant phenotyping. Exploratory longitudinal tracking revealed that above-ground biomass was correlated with final corm yield (r = 0.68, P < 0.001), with mid-vegetative canopy volume also showing strong correlation (r = 0.52, P < 0.01), suggesting potential resource allocation trade-offs between vegetative expansion and storage organ development. CONCLUSIONS: This work demonstrates that organ-level 3D phenotyping of narrow, overlapping leaves is achievable using low-cost imaging hardware and transparent methodological workflows. Complete documentation of algorithmic parameters and hardware specifications enables direct replication and adaptation to other narrow-leaved crops (wheat, rice, onion, leek), democratizing access to high-throughput phenotyping in resource-limited settings. The workflow advances plant phenomics by demonstrating that methodological transparency and cost-effectiveness need not compromise measurement precision, opening new avenues for phenotype-to-genotype mapping and predictive breeding in underutilized crops.
Why it matches plant phenotyping methods低コストの双眼カメラとSfM-MVSによるサフラン葉の器官レベル3D形質取得ワークフローを開発し、精度検証、再現性、パラメータ最適化まで扱っており、植物フェノタイピング手法が研究の中心である。
abstractHere, we developed a specialized organ-level 3D phenotyping workflow specifically designed for narrow, overlapping leaves using a low-cost dual-camera rotary acquisition system integrated with open-source Structure-from-Motion Multi-View Stereo (SfM-MVS) reconstruction.
This data descriptor presents a dataset comprising crop and soil parameters measured in winter wheat fields near the town of Knezha, Bulgaria. The data were collected as part of a project evaluating the potential of vegetation indices derived from Sentinel-2 satellite imagery to predict biophysical and biochemical crop parameters. The core dataset consists of measurements obtained from 20 m × 20 m field plots and includes a broad range of parameters: leaf area index, fraction of absorbed photosynthetically active radiation, vegetation cover fraction, chlorophyll content, above-ground biomass, plant nitrogen content, biological yield, surface soil moisture, spectral reflectance, plant density, crop height, visual assessments of disease or pest damage, and data on weed occurrence. The dataset is complemented by unmanned aerial vehicle imagery, crop calendars, and field management information. The main soil types in the study area were characterized through soil profiles, while meteorological data were obtained from an automated weather station. The data were collected during the 2016–2017 and 2017–2018 agricultural seasons. The dataset is freely available for download and serves as a valuable resource for researchers in remote sensing—particularly for validating satellite-derived products—as well as for specialists involved in winter wheat monitoring, modeling, and agronomic studies.
Why it matches plant phenotyping methods冬小麦の複数の植物形質を含む再利用可能なデータセットを提示し、UAV画像や衛星由来指標の検証を主目的としているため、植物フェノタイピング用データセットとして採用。
abstractThis data descriptor presents a dataset comprising crop and soil parameters measured in winter wheat fields near the town of Knezha, Bulgaria.
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 · publicDataset: In situ and UAV dataset with crop and soil parameters obtained from winter
wheat fields. https://doi.org/10.5281/zenodo.17475742.Open asset ↗zenodo · 10.5281/zenodo.17475742pdf-page:1 lines:1-56Plant phenotyping relevance match · UnverifiedOpenAlex · Crossref · Europe PMC · checked 5 Sept 2026
3D phenotyping refers to the quantitative characterization of a plant's structural and morphological traits in three-dimensional space, allowing for a detailed analysis of plant architecture and growth patterns. In recent years, rapid advancements in non-destructive, high-throughput 3D imaging technologies have enabled the precise measurement of these traits. Initially focused on single-plant traits under controlled conditions, the field has now expanded towards robust applications in real-world field environments, enabling large-scale analyses of plant canopies and complex structures. This study focuses on the recent advancements in 3D crop phenotyping using point cloud technologies. It compares sensor technology and its application in controlled environments (Chamber-Crop Phenotyping, CCP) and field conditions (Field-Crop Phenotyping, FCP). Technologies such as Multiview stereo (MVS) reconstruction, LiDAR, and laser triangulation have enhanced plant phenomics by enabling high-throughput, non-destructive measurements of key traits such as canopy structure, leaf area, and stem diameter. This review highlights the strengths of the CCP, where environmental variables and flexibility are tightly controlled, facilitating precise trait measurement, and contrasts it with the challenges of the FCP, where unpredictable factors, such as occlusion, wind, light variability, and terrain complexity, complicate data acquisition. Various sensor platforms, including ground-based robotic systems and unmanned aerial vehicles (UAVs), have been discussed regarding their ability to overcome occlusion and limited sensor range in real-world conditions. The need to transition these technologies from laboratory environments to real-world agricultural applications is emphasized, highlighting their potential to improve crop management and plant breeding through accurate phenotypic trait extraction. Finally, current research gaps and future directions for integrating advanced sensor platforms and analytical techniques in both CCP and FCP settings are identified, emphasizing the need to enhance the scalability and robustness of 3D phenotyping for field applications.
Why it matches plant phenotyping methods3D作物フェノタイピングのセンサー技術、点群処理、対象形質、検証上の課題を中心に扱う方法論レビューであり、植物形質の取得手法が明確に中心である。
abstractThis study focuses on the recent advancements in 3D crop phenotyping using point cloud technologies.
Sugarcane is an important economic crop, and key phenotypic traits such as plant height and leaf area play a crucial role in yield potential assessment and breeding selection. However, the quantification of these traits currently relies mainly on inefficient and destructive manual measurements, making it difficult to achieve continuous monitoring of plant growth. To address this limitation, this study integrates a YOLOv8x-seg instance segmentation model with 3D Gaussian Splatting (3DGS) and proposes a non-contact, high-precision 3D phenotyping method based on low-cost data acquisition using a smartphone. Multi-view RGB images are first processed using YOLOv8x-seg to extract plant foreground masks, which are then used as inputs for 3DGS-based reconstruction to generate 3D models. Plant height is automatically measured from the reconstructed models, while leaf area extraction involves a semi-automatic workflow combining image processing and manual steps. Experimental results demonstrate that the proposed approach enables accurate trait estimation, achieving a coefficient of determination (R2) of 0.9644 for plant height estimation (evaluated on a subset of 15 plants, with a mean absolute percentage error of approximately 1.5%) and an R2 of 0.8551 for leaf area estimation (validated on 10 plants). Ground-truth plant height was measured using a telescopic measuring rod, and leaf area was determined through destructive measurement with a leaf area meter (LI-COR Model LI-3000A). Ground-truth plant height values were obtained using a telescopic measuring rod, and leaf area was determined through destructive measurement with a leaf area meter (LI-COR Model LI-3000A). This method demonstrates the feasibility of using consumer-grade devices for high-fidelity 3D phenotyping and offers an effective approach for high-throughput sugarcane breeding applications.
Why it matches plant phenotyping methodsスマートフォン画像、インスタンスセグメンテーション、3D再構成を統合し、サトウキビの草高・葉面積を自動／半自動推定するフェノタイピング手法を開発・検証しており、方法が研究の中心である。
abstractproposes a non-contact, high-precision 3D phenotyping method based on low-cost data acquisition using a smartphone
Leaf area index (LAI) is a key indicator of crop growth and development and is widely used in both agricultural research and precision farming applications. PlanetScope imagery is generally used for monitoring crop growth due to its high revisit frequency, broad spatial coverage, and cost-effective access to consistent high-resolution multispectral data. Therefore, we developed regression models to estimate peanut LAI, combining PlanetScope spectral bands and vegetation indices (VIs). Specifically, we compared the performance of random forest (RF), eXtreme Gradient Boosting (XGBoost), and Partial Least Squares Regression (PLSR) regression algorithms for peanut LAI estimation. Our results showed that most of the VIs exhibited strong relationships with LAI. Thirteen VIs were individually evaluated for estimating LAI using the aforementioned algorithms, and our results showed that the best single predictors of LAI are: TSAVI (RF: R 2 = 0.87, RMSE = 0.83 m 2 /m 2 , RRMSE = 24.20%; XGBoost: R 2 = 0.77, RMSE = 0.95 m 2 /m 2 , RRMSE = 27.96%); and RTVIcore (PLSR: R 2 = 0.68, RMSE = 1.12 m 2 /m 2 , RRMSE = 32.88%). The top six ranked VIs were used to calibrate the RF, XGBoost, and PLSR algorithms. Model validation indicated that RF achieved the highest accuracy (R 2 = 0.844, RMSE = 0.858 m 2 /m 2 , RRMSE = 25.17%), followed by XGBoost (R 2 = 0.808, RMSE = 0.92 m 2 /m 2 , RRMSE = 26.99%), whereas PLSR showed comparatively lower performance (R 2 = 0.76, RMSE = 0.983 m 2 /m 2 , RRMSE = 28.85%). Further results showed that PlanetScope VIs provided superior model accuracy in estimating peanut LAI compared to the use of spectral bands alone. Additionally, integrating spectral bands with VIs reduced LAI estimation accuracy, underscoring the importance of selecting predictor variables in ensuring optimal model performance. Overall, the presented results are significant for future crop monitoring using RF to reduce overreliance on multiple models for peanut LAI estimation.
Why it matches plant phenotyping methodsPlanetScopeスペクトルデータと複数の回帰手法により、ピーナッツのLAIという植物形質を推定し、モデル性能を比較・検証している。形質取得・推定手法が研究の中心である。
abstractwe developed regression models to estimate peanut LAI, combining PlanetScope spectral bands and vegetation indices (VIs).
Plant phenotyping relevance match · UnverifiedCrossref · Europe PMC · OpenAlex · checked 15 Sept 2026
Hyperspectral imaging (HSI) has emerged as a powerful tool for precision agriculture, enabling the non-destructive monitoring of crop biochemical and physiological traits. However, HSI alone lacks structural context, which limits its ability to accurately capture complex canopy architectures and organ-level traits. Integrating HSI with depth-sensing modalities such as Light Detection and Ranging (LiDAR), Red, Green, Blue, and Depth (RGB-D) cameras, and computational reconstruction technique such as photogrammetry enables the generation of three-dimensional hyperspectral point clouds, combining spectral richness with geometric fidelity. This multi-modal fusion enhances crop trait estimation, including biomass, leaf chlorophyll content, canopy height, leaf area, and stress indicators, while improving the robustness of phenotyping under occlusions, shadows, and varying illumination. Dimensionality reduction, feature selection, and machine learning approaches, including deep learning and explainable AI, are useful for handling high-dimensional hyperspectral data and extracting actionable agronomic insights. Moreover, the integration of thermal, radar, and Global Navigation Satellite System (GNSS) data further expands the capabilities of multi-modal sensing, enabling continuous, all-weather crop monitoring and accurate spatial referencing. Despite these advances, most studies to date focus on controlled environments, highlighting the need for field-based validation to ensure the reliability and scalability of HSI-depth fusion techniques. This review consolidates current knowledge on multi-modal hyperspectral and 3D crop reconstruction, highlighting methods, applications, and challenges, and outlines future directions for implementing high-throughput, real-time phenotyping and precision agriculture solutions.
Why it matches plant phenotyping methods植物形質推定のためのハイパースペクトル・深度センシング融合と3D再構成を中心に扱うレビューであり、フェノタイピング手法の方法論的整理が主題。
abstractThis review consolidates current knowledge on multi-modal hyperspectral and 3D crop reconstruction, highlighting methods, applications, and challenges
Timely and precise harvest scheduling is critical for maintaining tea quality and improving labor efficiency. This study aimed to develop an integrated Internet of Things (IoT) and artificial intelligence (AI) framework for automated monitoring and growth modeling of tea shoots, enabling data-driven plantation management. Solar-powered Plantation Monitoring Systems (PMS) were deployed to continuously capture canopy images and environmental data, reducing reliance on manual inspections. An enhanced YOLOv11 segmentation model, incorporating HSI color space conversion, monocular depth estimation, and shape-based temporal tracking, was used to detect pluckable tea shoots with high accuracy. The computed Tea Shoot Density Index (TSDI) showed strong agreement with ground truth measurements (RMSE = 2.542, R² = 0.931). Three sigmoid growth models − 3PL, 4PL, and Gompertz − were evaluated using growing degree days (GDD) as the time scale. The 4PL model achieved the best performance (RMSE = 0.698, R² = 0.897) and predicted optimal harvest timing with a mean absolute error (MAE) of 2.7 days, while offering interpretable parameters that reflect shoot retention, growth rate, and maturation dynamics. These parameters provided actionable insights for optimizing irrigation, fertilization, and harvest scheduling across different growth stages. The proposed system delivers a scalable and automated solution for precision tea agriculture, enhancing productivity, improving tea quality, and supporting the transition from experience-based to data-driven management.
Why it matches plant phenotyping methods茶園画像から摘採可能な新芽を検出し、密度指標と生育・成熟状態を推定するIoT・AI計測手法の開発と精度検証が研究の中心であるため。
abstractThis study aimed to develop an integrated Internet of Things (IoT) and artificial intelligence (AI) framework for automated monitoring and growth modeling of tea shoots
Plant phenotyping relevance match · UnverifiedCrossref · Europe PMC · OpenAlex · checked 14 Sept 2026
Why it matches plant phenotyping methodsSBR耐性品種のスクリーニングを目的に、ハイパースペクトル画像、2D画像、構造化光3Dスキャン、機械学習を用いた植物形態・スペクトル形質の取得と評価が研究の中心である。
abstractDigital plant phenotyping can support the screening process for tolerant varieties by characterizing traits of interest and quantifying tolerance.
PURPOSE: Multispectral remote sensing plays an increasingly vital role in precision agriculture, with the green area index (GAI) being a key parameter due to its relevance for yield formation. However, sensor-specific GAI calibration is labor-intensive and time-consuming, contrasting with the rapid advancement of UAV-based spectral sensors and their short market life spans. Therefore, this study investigated exemplarily the feasibility of transferring GAI calibrations between two UAV-based sensors. METHODS: A multi-year, multi-crop dataset was used to evaluate three strategies for cross-calibrating MicaSense RedEdge-MX data to GAI produced by published Sequoia models rather than by destructive sampling: (1) band-to-band, (2) ratio-to-ratio, and (3) ratio-to-GAI. Each approach was tested using crop-specific and universal models. To assess the impact of prediction errors, GAI time series were generated for two crops over two years to compute radiation interception and radiation use efficiency (RUE), emphasizing that plausible RUE values provide an indirect verification. RESULTS: All methods showed high predictive accuracy (R² = 0.83–0.97), but only the ratio-to-GAI approach provided stable GAI dynamics and reliable RUE estimates, especially at low canopy densities. This approach benefited from the combined use of multiple spectral ratios and the inclusion of an additional band not provided by the Sequoia sensor. It also leveraged the RedEdge-MX’s superior wavelength positions for universal GAI calibration, resulting in minimal differences between crop-specific (R² = 0.88–0.99) and universal models (R² = 0.87–0.99). The extensive dataset revealed date-specific and phenology-driven changes in sensor correlations, emphasizing that concise, ratio-based GAI calibrations may be more robust than complex models. CONCLUSION: These findings underline the importance of efficient cross-calibration strategies in a fast-evolving UAV sensor landscape.
Why it matches plant phenotyping methodsUAVマルチスペクトルセンサー間の交差校正を開発・評価し、GAIという植物キャノピー形質を推定する方法が研究の中心である。複数戦略の精度比較と時系列・RUEによる検証も行っている。
abstractTherefore, this study investigated exemplarily the feasibility of transferring GAI calibrations between two UAV-based sensors.
Hyperspectral imaging (HSI) has emerged as a powerful tool for precision agriculture, enabling the non-destructive monitoring of crop biochemical and physiological traits. However, HSI alone lacks structural context, which limits its ability to accurately capture complex canopy architectures and organ-level traits. Integrating HSI with depth-sensing modalities such as Light Detection and Ranging (LiDAR), Red, Green, Blue, and Depth (RGB-D) cameras, and computational reconstruction technique such as photogrammetry enables the generation of three-dimensional hyperspectral point clouds, combining spectral richness with geometric fidelity. This multi-modal fusion enhances crop trait estimation, including biomass, leaf chlorophyll content, canopy height, leaf area, and stress indicators, while improving the robustness of phenotyping under occlusions, shadows, and varying illumination. Dimensionality reduction, feature selection, and machine learning approaches, including deep learning and explainable AI, are useful for handling high-dimensional hyperspectral data and extracting actionable agronomic insights. Moreover, the integration of thermal, radar, and Global Navigation Satellite System (GNSS) data further expands the capabilities of multi-modal sensing, enabling continuous, all-weather crop monitoring and accurate spatial referencing. Despite these advances, most studies to date focus on controlled environments, highlighting the need for field-based validation to ensure the reliability and scalability of HSI-depth fusion techniques. This review consolidates current knowledge on multi-modal hyperspectral and 3D crop reconstruction, highlighting methods, applications, and challenges, and outlines future directions for implementing high-throughput, real-time phenotyping and precision agriculture solutions.
Why it matches plant phenotyping methods植物形質推定のためのハイパースペクトル・深度センシング・3D再構成手法を中心に扱うレビューであり、フェノタイピング手法レビューに該当する。
abstractThis review consolidates current knowledge on multi-modal hyperspectral and 3D crop reconstruction, highlighting methods, applications, and challenges
Vertical farming offers a promising solution to global food security and urbanization challenges, yet its widespread adoption is hindered by high costs, particularly for lighting. Addressing this requires enhancing light use efficiency (LUE) through intelligent control strategies. While numerous studies have investigated the effects of light intensity on lettuce growth, relatively few have explored the potential benefits of stage-specific light regulation. In this study, we first developed an automated 3D phenotyping pipeline based on multi-view reconstruction to quantify canopy morphology and light interception. Utilizing this quantitative framework, we conducted a dynamic light experiment with lettuce in a commercial plant factory to evaluate four dynamic light-intensity strategies. The proposed 3D phenotyping pipeline demonstrated promising performance for canopy information extraction, with RMSEs for plant height, canopy diameter, and projected leaf area of 0.79 cm, 1.05 cm, and 44.3 cm², respectively. The “high-low-high” dynamic lighting strategy, applying higher light intensity during the early and late growth stages and lower intensity during the mid-growth stage, successfully optimized canopy morphology for better light capture. This treatment significantly increased shoot fresh and dry weights by 28 % and 65 %, respectively, compared to constant lighting. Furthermore, it enhanced LUE based on incident and intercepted light integrals by 67 % and 19 %, while reducing electricity consumption per unit of fresh weight by 24 %. Nutritional quality analysis showed the treatment increased soluble sugars and starch contents. By integrating advanced 3D phenotyping with dynamic light intensity control, this study demonstrates a prototype for intelligent decision-making to enhance yield and energy use efficiency in practical vertical farming.
Why it matches plant phenotyping methods自動3Dフェノタイピングパイプラインを開発し、マルチビュー再構成で植物体形態と光遮断を定量化、精度評価も実施しており、フェノタイピング手法が研究の中心である。
abstractwe first developed an automated 3D phenotyping pipeline based on multi-view reconstruction to quantify canopy morphology and light interception.
Accurate and efficient estimations of leaf area index (LAI) are crucial for crop management, including intelligent crop breeding, nutrient management, and yield prediction. Unmanned aerial vehicle (UAV)-based multispectral sensors with machine learning models provide high-precision solutions for LAI estimation but are hindered by the challenge of acquiring adequate ground truth data. Transfer learning, one type of deep learning framework, offers a solution by leveraging prior knowledge learned through models that have been pre-trained, thus ensuring robust performance despite limited data availability. This study evaluates the efficacy of the fine-tuning PROSAIL-Informed Deep Neural Network model (PROSAIL-DNN) for estimating LAI of different oat varieties and growth periods using UAV multispectral images. We compared this model with several widely used machine learning algorithms, including partial least squares (PLS), least absolute shrinkage and selection operator (Lasso), support vector regression (SVR), and extreme gradient boosting (XGBoost)), and a DNN, using training datasets consisting of 70 %, 60 %, and 50 % of the field data to assess the impact of data volume on model performance. Our results demonstrated that the PROSAIL-DNN model outperformed other algorithms across different growth periods and all growth periods. Specifically, with only 50 % of the training data used, the average R² of the PROSAIL-DNN model was 5.44 %, 28.76 %, 12.98 %, 12.72 %, and 22.90 % higher than those of DNN, Lasso, PLS, SVR, and XGBoost, respectively. The PROSAIL-DNN model also demonstrated higher accuracy in monitoring LAI during different growth periods, especially at early jointing period (P1) (R² = 0.838, RMSE = 0.376, and RPD = 2.483) and at post-heading period (P3) (R² = 0.881, RMSE = 0.298, and RPD = 2.896). Our findings underscore the potential of combining PROSAIL with deep transfer learning to accurately and robustly estimate oat LAI at various growth periods using UAV multispectral images with limited field data. This approach provides a solid foundation for applying transfer learning in crop monitoring and can be adapted for other crop variables in future studies.
Why it matches plant phenotyping methodsUAVマルチスペクトル画像とPROSAIL-DNNを用いて、オート麦の葉面積指数（LAI）を推定する画像解析・機械学習手法が研究の中心であり、複数モデルとの技術比較とデータ量による性能評価も実施している。
abstractThis study evaluates the efficacy of the fine-tuning PROSAIL-Informed Deep Neural Network model (PROSAIL-DNN) for estimating LAI of different oat varieties and growth periods using UAV multispectral images.
Field / plotLeafRootWhole plant / canopy / plot / fieldMorphology / geometry measurementLeaf traitsPlant / canopy heightRoot system architecture
To explore the distinctness, uniformity, and stability(DUS) testing technology for Angelica dahurica and develop its DUS testing guidelines, this study conducted systematic research on the morphological and growth characteristics of A. dahurica throughout its whole growth period. The research was based on 428 A. dahurica lines from 48 sampling sites across China, with unified standardized field planting, regular and fixed-point observation, classified statistics of phenotypic characteristics, and comprehensive data analysis. Ultimately, 49 test characteristics were identified, including 36 basic characteristics and 13 optional characteristics. Classified by attribute, they consisted of 4 qualitative characteristics, 3 pseudo-qualitative characteristics, and 42 quantitative characteristics. Classified by organ and growth stage, the characteristics covered 2 cotyledon characteristics, 19 leaf characteristics(including basal leaves and cauline leaves), 2 plant characteristics, 3 saccate leaf sheath characteristics, 5 fruit characteristics, 9 root characteristics, 5 stem characteristics, 3 flower characteristics, and 1 growth period characteristic. Through the evaluation of characteristic discriminability and stability, five grouping characteristics were screened out, namely "basal leaf: anthocyanin coloration on the back of the leaf sheath" "basal leaf: anthocyanin coloration at the attachment site of the petiolule" "flowering period" "plant: height" "main root: arrangement pattern of lenticel-like protuberances". These can serve as important bases for the preliminary screening and classification of A. dahurica varieties. Meanwhile, 20 standard varieties with typical phenotypes were identified to provide a unified reference for characteristic observation. In addition, the guidelines also specify the scope of application, requirements for propagation materials, growth stages, observation periods, observation methods, DUS judgment criteria, and other content. This study fills the gap in the field of DUS testing technology for A. dahurica, and provides a scientific basis and technical support for DUS testing, resource identification and description, variety breeding of A. dahurica varieties, as well as management and protection of new A. dahurica arieties.
Why it matches plant phenotyping methodsアンジェリカ・ダフリカ品種のDUS試験に向け、標準化された形質観察法、判定基準、識別性・安定性評価を開発しており、植物表現型取得手法が研究の中心である。
abstractTo explore the distinctness, uniformity, and stability(DUS) testing technology for Angelica dahurica and develop its DUS testing guidelines
Abstract Most computer vision‐ and machine learning‐based plant phenotyping systems compute traits such as shape and size rather than the color distribution of the plant surface, even though color can provide important insights into plant physiology. Therefore, we developed Speedy Measurement of Arabidopsis Rosette Traits (SMART), an open‐source plant phenotyping pipeline that analyzes a red–green–blue (RGB) top‐view image captured by any imaging device to compute color traits as well as shape and size. SMART combines a pretrained U2‐Net machine learning model and a color clustering method to segment plants from their background and compute basic morphological traits. SMART showed a good average accuracy of 95% for morphological traits using a public benchmark dataset. Uniquely, SMART also analyzes the color of plant surfaces by calculating a normalized color difference index and comparing plant surface colors with reference colors in the L*a*b* color space, which are converted from the RGB color space. The color difference index also showed good correlation with independent measurements of the chlorophyll fluorescence parameter F v / F m (maximum quantum yield of photosystem II) ( R 2 > 0.71), chlorophyll content ( R 2 > 0.73), and leaf temperature ( R 2 > 0.76) in our experimental conditions. Therefore, we show that SMART is not only an affordable, open‐source tool for calculating morphological traits such as shape and size but also it is also useful for exploring relationships between color traits and physiological traits. SMART represents a promising new approach to low‐cost, high‐throughput phenotyping, thus benefiting the entire plant science community.
Why it matches plant phenotyping methodsSMARTはRGB画像から植物の形態・色彩・生理関連形質を抽出するオープンソース表現型解析パイプラインであり、開発とベンチマーク検証が研究の中心です。
abstractTherefore, we developed Speedy Measurement of Arabidopsis Rosette Traits (SMART), an open‐source plant phenotyping pipeline that analyzes a red–green–blue (RGB) top‐view image captured by any imaging device to compute color traits as well as shape and size.
Early blight, caused by Alternaria alternata, poses a critical challenge to tomato (Solanum lycopersicum L.) production, causing significant yield losses worldwide. Accurate quantification of plant disease severity is essential for the development of intelligent, site-specific crop protection systems. This study investigates the morphological responses of tomato plants following incidence of early blight disease across different stages of disease progression, with the objective of establishing biologically meaningful indicators for imaging-based disease severity classification. Key plant morphological parameters, including plant height, total leaf area, and diseased leaf area, were monitored over time and compared with healthy plants. Analysis of variance revealed a statistically significant difference in plant height between healthy and diseased plants after inoculation of disease, with average plant height after 90 days of growth were 94.86 and 81.81 cm respectively, indicating the impact of disease on overall plant growth. Temporal analysis of leaf area and diseased area exhibited distinct disease progression patterns, comprising an initial latent phase, a rapid symptom expansion phase, and a terminal phase characterized by tissue degradation. Disease severity was quantified using an area-based severity percentage derived from the ratio of diseased area to total leaf area, providing a normalized and scalable metric of infection intensity. The observed morphological and spatial disease characteristics closely correspond to features that can be extracted using machine vision techniques, such as changes in canopy geometry and lesion extent. The findings highlight the potential and the importance of severity based assessment of disease for variable-rate site-specific spraying systems, demonstrating clear advantages over conventional target-specific approaches in reducing chemical application, improving disease control efficiency, and supporting sustainable crop protection practices.
Why it matches plant phenotyping methods植物病害の重症度を、葉面積・病斑面積などの形態指標から画像ベースで定量化する方法の開発が中心であり、単なる病害実験のルーチン測定ではない。
abstractwith the objective of establishing biologically meaningful indicators for imaging-based disease severity classification
Background Rice plant architecture underpins yield and grain quality, yet two obstacles impede accurate field characterization in dense paddies. First, single-plant reconstruction is constrained by severe inter-plant occlusion, cluttered backgrounds, and limited viewpoints. These factors obscure culms, leaves, basal tillers, and the true physical scale of the plant. Active ranging devices are cumbersome in outdoor plots and can lose accuracy, whereas conventional passive photogrammetry performs poorly under such conditions. Second, delineating panicles within a 3D rice model is intrinsically difficult. Panicles are slender, highly branched, and visually similar to surrounding foliage, often interwoven and partially hidden. These factors result in fragmented boundaries and missing details. Direct point-cloud segmentation struggles with such discontinuous geometry and requires costly 3D annotation, whereas generic image segmentation models trained on natural scenes transfer poorly to paddy imagery. These challenges motivate a field-ready workflow that both reconstructs whole plants at high resolution in dense plantings and reliably segments panicles to enable trait extraction. Results A low-cost, in-field, multi-view pipeline for whole-plant three-dimensional reconstruction, termed One Stop 3D Target Reconstruction And segmentation (OSTRA), operates on color images with a reference-board setup. The pipeline builds detailed three-dimensional models of individual rice plants and automatically segments key organs (in this case, panicles), despite dense surrounding vegetation. When applied to 231 diverse rice landraces grown in a crowded field setting, the method produced high-fidelity plant models with clearly delineated panicle structures. From these reconstructions, three architectural traits were derived: plant height, leaf area, and panicle length. Genome-wide association analysis of the measured traits identified strong genotype-phenotype associations tagging known candidate genes. Natural variants at D2 and RFL/APO2 were associated with plant height variation, variants at FLW7 were linked to differences in leaf area, and allelic variation at AAI1 corresponded to panicle length variation. These loci are established regulators of plant growth and morphology, indicating that this three-dimensional phenotyping pipeline attains accuracy sufficient to rediscover meaningful genetic signals. Conclusions This study provides a practical tool for precise rice phenotyping even under dense field planting conditions, overcoming occlusion and structural complexity. By enabling non-destructive, field-based measurement of complete plant architecture and linking these phenotypes to specific genes, the pipeline bridges field phenomics and genomics. The integrated reconstruction and analysis framework advances the study of rice architecture and offers a general route to connect complex traits with their genetic determinants.
Why it matches plant phenotyping methods密植圃場でのイネ全体3D再構築、器官分割、形質抽出を中核とする画像ベース表現型解析手法の開発・実証であり、明確に収載対象。
abstractA low-cost, in-field, multi-view pipeline for whole-plant three-dimensional reconstruction, termed One Stop 3D Target Reconstruction And segmentation (OSTRA), operates on color images with a reference-board setup.
Reproduction assets foundThe paper explicitly states that the 3D rice plant models (231 landraces) are deposited on Zenodo and the OSTRA source code is publicly available on GitHub. Both are paper-specific, public, and actionable.Code · publicThe source code of OSTRA is available on GitHub at [http://github.com/ganlab/ostra] (http:/github.com/ganlab/ostra).Open asset ↗github · ganlab/ostralines:217-246Plant phenotyping relevance match · UnverifiedOpenAlex · checked 14 Sept 2026
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).
Sustainable agriculture in arid regions faces critical challenges due to water scarcity, high temperatures, and inefficient traditional farming practices. This study presents an AI-enabled smart farming framework for optimizing date palm (Phoenix dactylifera) cultivation through the integration of Machine Learning (ML) and Internet of Things (IoT) technologies. A structured multimodal dataset comprising biometric features palm height, trunk diameter, and leaf number, environmental parameters soil moisture, temperature, and humidity, and categorical attributes variety and health status was analyzed to classify palm health and support data-driven irrigation management. Four ML algorithms Random Forest (RF), Gradient Boosting Machine (GBM), Artificial Neural Network (ANN), and Support Vector Machine (SVM) were developed and optimized using grid search with five-fold cross-validation. Among them, the Random Forest model achieved the highest classification accuracy of 95.3%, demonstrating strong robustness for heterogeneous agricultural data. Feature importance analysis highlighted soil moisture, humidity, trunk diameter, and leaf number as key contributors to palm health prediction. The proposed AI-IoT framework enables real-time monitoring, predictive diagnostics, and automated decision support for sustainable water use and crop management, aligning with Saudi Vision 2030 objectives for technology-driven and resource-efficient agriculture.
Why it matches plant phenotyping methodsヤシの生体特徴から健康状態を分類する機械学習手法を開発・比較し、分類性能を評価しているため、植物状態推定が中心的な方法的貢献である。
abstractThis study presents an AI-enabled smart farming framework for optimizing date palm (Phoenix dactylifera) cultivation through the integration of Machine Learning (ML) and Internet of Things (IoT) technologies.
Field / plotMultispectral / hyperspectralLeafVisualization / data managementLeaf traitsPhotosynthesis / fluorescence
Abstract. Accurate assessment of leaf functional traits is crucial for a diverse range of applications from crop phenotyping to parameterizing global climate models. Leaf reflectance spectroscopy offers a promising avenue to advance ecological and agricultural research by complementing traditional, time-consuming gas exchange measurements. However, the development of robust hyperspectral models for predicting leaf photosynthetic capacity and associated traits from reflectance data has been hindered by limited data availability across species and environments. Here we introduce the Global Spectra-Trait Initiative (GSTI), a collaborative repository of paired leaf hyperspectral and gas exchange measurements from diverse ecosystems. The GSTI repository currently encompasses over 7500 observations from 397 species and 41 sites gathered from 36 published and unpublished studies, thereby offering a key resource for developing and validating hyperspectral models of leaf photosynthetic capacity. The GSTI database is developed on GitHub (https://github.com/plantphys/gsti, last access: 4 January 2026) and published to ESS-DIVE https://doi.org/10.15485/2530733, Lamour et al., 2025). It includes gas exchange data, derived photosynthetic parameters, and key leaf traits often associated with traditional gas exchange measurements such as leaf mass per area and leaf elemental composition. By providing a standardized repository for data sharing and analysis, we present a critical step towards creating hyperspectral models for predicting photosynthetic traits and associated leaf traits for terrestrial plants.
Why it matches plant phenotyping methods葉のハイパースペクトルとガス交換・光合成形質を標準化して収録するデータベースを構築し、植物フェノタイピングモデルの開発・検証に供することが中心である。
abstractHere we introduce the Global Spectra-Trait Initiative (GSTI), a collaborative repository of paired leaf hyperspectral and gas exchange measurements from diverse ecosystems.
Reproduction assets foundThe paper describes the GSTI database of paired leaf hyperspectral and gas-exchange measurements, with both the data and R processing/model-fitting code publicly available on GitHub and archived releases on ESS-DIVE.Code · publicThe GSTI data and code are available in the public GitHub repository at https://github.com/plantphys/gsti (last access: 4 January 2026)Open asset ↗https://github.com/plantphys/gstilines:537-549Code / dataset availability confirmedCrossref · Europe PMC · checked 5 Sept 2026
Abstract Phenotyping is crucial for understanding crop trait variation and advancing research, but is currently limited by expensive, labor-intensive monitoring. New phenotypic trait monitoring methods are being proposed to reduce this so-called phenotyping bottleneck via automation. These methods are often data-driven, requiring a dataset recorded with a specific sensor and corresponding reference values for developing novel methods. To this end, we present the MuST-C (Multi-Sensor, multi-Temporal, multiple Crops) dataset, which contains field data from various sensors collected over a growing season, covering six crop species. All data was georeferenced for alignment across sensors and dates. To collect our dataset, we deployed aerial and ground robotic platforms equipped with RGB cameras, LiDARs, and multispectral cameras, aiming to capture a wide variety of modalities and observations from different viewpoints. In addition to sensor data, we also provide manually collected leaf area index and biomass reference measurements. Our dataset enables the development of novel automatic phenotypic trait estimation methods, allows comparisons across different sensors, and generalizability across crop species.
Why it matches plant phenotyping methods複数センサー・ロボットプラットフォームによる圃場フェノタイピング用データセットを構築・提供し、形質推定法の開発、センサー比較、汎化評価を可能にすることが中心的な貢献である。
abstractwe present the MuST-C (Multi-Sensor, multi-Temporal, multiple Crops) dataset
Reproduction assets foundThe paper's MuST-C multi-sensor, multi-temporal crop phenotyping dataset (RGB/multispectral images, LiDAR point clouds, LAI and biomass reference measurements) is publicly available via the authors' project webpage, and the authors' custom Python processing/loading code is publicly available on GitHub.Dataset · publicThe MuST-C dataset is available via our project webpage https://www.ipb.uni-bonn.de/data/MuST-C/or directly via the bonndata public access repository 10.60507/FK2/OX9XTM34Open asset ↗html-lines:421-440Plant phenotyping relevance match · UnverifiedOpenAlex · checked 13 Sept 2026
This study develops a voxel-based leaf area estimation framework and validates it using a three-year multi-temporal dataset (2022–2024) of pergola-trained grapevines. The workflow integrates 2D image analysis, ExGR-based leaf segmentation, and 3D reconstruction using Structure-from-Motion (SfM). Multi-angle canopy images were collected repeatedly during the growing seasons, and destructive leaf sampling was conducted to quantify true leaf area across multiple vines and years. After removing non-leaf structures with ExGR filtering, the point clouds were voxelized at a 1 cm3 resolution to derive structural occupancy metrics. Voxel-based leaf area showed strong within-vine correlations with destructively measured values (R2 = 0.77–0.95), while cross-vine variability was influenced by canopy complexity, illumination, and point-cloud density. In contrast, optical LAI tools (DHP and LAI–2000) exhibited negligible correspondence with true leaf area due to multilayer occlusion and lateral light contamination typical of pergola systems. This expanded, multi-year analysis demonstrates that voxel occupancy provides a robust and scalable indicator of canopy structural density and leaf area, offering a practical foundation for remote-sensing-based phenotyping, yield estimation, and data-driven management in perennial fruit crops.
Why it matches plant phenotyping methodsブドウ樹の葉面積・樹冠構造を推定する画像解析、SfM、ボクセル化ワークフローを開発し、破壊測定および既存LAI手法と比較検証しており、植物表現型取得法が研究の中心である。
abstractThis study develops a voxel-based leaf area estimation framework and validates it using a three-year multi-temporal dataset (2022–2024) of pergola-trained grapevines.
Estimating olive (Olea europaea L.) leaf area is an important aspect of monitoring plant health and evaluating growth processes in agriculture. Accurate estimation of leaf area allows for a better understanding of processes such as water and nutrient utilization, photosynthesis efficiency, respiration, and yield potential. This study aims to determine the most accurate, easy, and reliable leaf area estimation model using the geometric properties (length and width) of olive leaves. Additionally, the predictive performances of multiple linear regression (MLR) and artificial neural network (ANN) were compared. A total of 1320 leaf samples collected from 22 olive cultivars were used in the study. Leaf length and width were taken as input parameters, and both MLR and ANN models were developed for each cultivar. Both multiple linear regression (MLR) and artificial neural network (ANN) models demonstrated high predictive accuracy for olive leaf area estimation across 22 cultivars. The MLR models explained up to 96% of the variation in leaf area using leaf length (LL) and leaf width (LW), with low root mean square errors, indicating strong reliability. When cultivar identity was modeled as a categorical factor through dummy encoding, the model captured significant cultivar-specific effects without altering the overall predictive performance. The ANN models achieved slightly higher accuracy, with determination coefficients exceeding 0.99 and minimal prediction errors, confirming their superior ability to model nonlinear relationships. Across both approaches, leaf width contributed more strongly to leaf area than leaf length. Cultivar-specific differences were statistically significant for only a few genotypes, while most cultivars exhibited comparable patterns after adjustment for multiple testing. In conclusion, both MLR and ANN models demonstrated high accuracy in predicting olive leaf area, with ANN models showing slightly superior performance. However, MLR models also yielded highly reliable results, indicating that both approaches are viable for practical applications in olive cultivation. These predictive models can be effectively used for rapid, non-destructive phenotyping, growth monitoring, and precision management in olive breeding and production systems.
Why it matches plant phenotyping methodsオリーブ葉面積という植物形質を対象に、葉長・葉幅からMLRとANNで推定モデルを開発・比較しており、非破壊フェノタイピング手法が中心です。
abstractThis study aims to determine the most accurate, easy, and reliable leaf area estimation model using the geometric properties (length and width) of olive leaves.
ABSTRACT Three‐dimensional measurement technology based on point clouds can effectively solve the problem of plant occlusion and is a hot research direction for plant phenotyping methods. Rapid and low‐cost 3D reconstruction and accurate 3D point cloud segmentation are two major challenges in 3D phenotyping technology. Taking watermelon seedlings as an example, we proposed a new phenotyping method that uses the Instant‐NGP for 3D reconstruction and the improved PointNet++ for 3D point cloud segmentation. We performed dynamic downsampling and filtering based on the point cloud scale and designed different phenotypic measurement methods for hypocotyl and leaf point clouds. To overcome the difficulty of measuring the hypocotyl caused by slenderness, curvature and inclination, we proposed a segmented stem 3D point cloud skeleton extraction algorithm. The experimental results show that our method achieved satisfactory measurement results for the seedling phenotypes of four growth stages. The detection accuracy of the number of cotyledon leaves and the number of true leaves both exceed 95% and the coefficient of determination ( R 2 ) of leaf area, hypocotyl length and stem diameter phenotypes are all beyond 0.8. The proposed method provides a novel, efficient and precise 3D plant phenotyping solution, with good application and promotion value.
Why it matches plant phenotyping methods3D再構成、点群セグメンテーション、骨格抽出、形質測定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、精度評価も実施している。
abstractwe proposed a new phenotyping method that uses the Instant‐NGP for 3D reconstruction and the improved PointNet++ for 3D point cloud segmentation.
Three-dimensional (3D) plant modeling is fundamental for precise phenotyping analysis. In this study, a high-throughput, multi-stage 3D reconstruction pipeline is proposed to efficiently generate point clouds with real-world physical scales. The pipeline comprises five core components: data acquisition, semantic segmentation, sparse reconstruction, dense reconstruction, and phenotypic trait extraction. To enhance the accuracy of plant structure identification, the SegFormer semantic segmentation model is employed for pixel-level segmentation, thereby guiding the subsequent reconstruction stages to focus specifically on plant regions. In feature-based sparse reconstruction, the scarcity of texture information often results in an insufficient number of matching point pairs, leading to failures in camera parameter estimation. Furthermore, the reconstructed point clouds frequently lack consistency with real-world scale. To address these challenges, a calibration-constrained sparse reconstruction method, Sparse Reconstruction from Calibrated Images (SRCI) was proposed. By integrating precise calibration results computed in a custom world coordinate system, SRCI circumvents the limitations of traditional feature matching in scenarios with scarce features, thereby resolving camera pose estimation failures caused by insufficient matching pairs and generating sparse point clouds with true physical scale. Subsequently, CL-MVSNet was employed to generate dense point clouds. The validation experiments are conducted from three perspectives: visual comparison, phenotypic accuracy assessment, and reconstruction accuracy evaluation. First, five groups of rapeseed plants are selected to perform visual comparisons between the proposed reconstruction pipeline and other advanced reconstruction software. The results demonstrate that the proposed reconstruction pipeline achieves superior performance in terms of visual quality. Additionally, three phenotypic parameters of rapeseed plants—plant height, leaf width, and chord length are manually measured and compared with the corresponding phenotypic parameters extracted from the reconstructed point clouds. The analysis revealed mean absolute errors of 4.93 mm, 3.16 mm, and 6.02 mm; root mean square errors of 6.38 mm, 4.56 mm, and 8.35 mm; and coefficients of determination of 0.98, 0.94, and 0.93, respectively. To further validate the generalization performance and accuracy of the proposed method, four additional plant categories with progressively increasing complexity were selected for accuracy evaluation. For the first three plant categories, the Chamfer distances between the reconstructed point clouds and ground truth point clouds were all within 2.4 mm. In the most complex rice reconstruction experiments, the Chamfer distances between the reconstructed point clouds and ground truth point clouds were all within 9 mm, while other methods failed to achieve effective reconstruction. The proposed high-throughput, automated, and high-quality 3D reconstruction framework provides reliable technical support and data resources for genetic research applications, including gene localization, quantitative trait locus analysis, and genome-wide association studies. • We propose a Plant-to-Camera system for high-quality 3D plant reconstruction within 6 minutes, showing strong generalizability. • Our Sparse Reconstruction from Calibrated Images (SRCI) method prevents failures in feature-scarce scenes. • We develop SFNet, a feature descriptor module that fuses multi-frequency to enhance plant feature representation.
Why it matches plant phenotyping methods植物の3D再構成と形質抽出パイプラインを開発し、植物形質および再構成精度を検証しており、フェノタイピング手法が中心である。
abstracta high-throughput, multi-stage 3D reconstruction pipeline is proposed to efficiently generate point clouds with real-world physical scales
Abstract Plant phenomics is an emerging discipline that uses image analysis to extract quantitative phenotypic data to understand plant growth and development. However, phenomics tools often require a precise format of image acquisition that is set during software development or that is part of a proprietary software environment. To remove these barriers and align with NASA's Transform to Open Science initiative, we have created a web-based application to measure plant aerial phenotypes called Simple Online Automated Plant Phenomics (SOAPP). SOAPP uses two open-source Python packages, PlantCV and OpenCV, and is available either online as a web application or can be run locally from a Docker image. Users simply upload their images, select sample-specific color spaces, and specify regions of interest. Foliage size, shape characteristics, and color values are then automatically extracted. SOAPP has been successfully used to characterize plant growth in hydroponic systems, pots, and Petri plates. ArUco machine-recognizable tags further allow automated scale-finding, image plane correction, and color standardization and correction. These adjustments for variations in the distance and axis at which the images were taken greatly enhance the quantitative accuracy of data extracted from hand-held crew photography, enhancing science return from both current and future spaceflight settings.
Why it matches plant phenotyping methods植物画像から葉面積・形状・色を抽出するウェブ型フェノタイピング手法SOAPPの開発と精度向上が中心であり、明確な方法開発・プラットフォーム研究である。
abstractwe have created a web-based application to measure plant aerial phenotypes called Simple Online Automated Plant Phenomics (SOAPP).
Accurate monitoring of crop phenology, biophysical attributes and agroclimatic variability is essential for optimizing agricultural practices, particularly in smallholder farming systems. In this study, we evaluated how field camera-derived Green Chromatic Coordinate (GCC) reflected variations in agroclimatic factors (rainfall and soil moisture) and biophysical attributes (leaf area index, crop height, chlorophyll content, and stomatal conductance) across agroecological zones (AEZs) in Kenya. Next, we utilized GCC time series to detect six key phenological stages of maize (Zea mays L.) - emergence, stem elongation, tasseling, kernel development, ripening, and senescence - using an amplitude-based relative threshold method. This approach was cross-validated against field observed phenology. Our analysis revealed positive correlations between GCC and plant height, chlorophyll content, and leaf area index (LAI). Daily-scale Pearson lag correlation between GCC and agroclimatic factors revealed that crops in drier ecosystems exhibited shorter response times to agroclimatic fluctuations (32 days to rainfall and 14 days to soil moisture), highlighting site-specific differences in vegetation dynamics captured by field cameras. Furthermore, results indicate that GCC effectively captured phenological stages with high accuracy (R² = 0.9, RMSE = 7.1–7.7 days), though variability was observed across sites and growth stages. Comparisons between within-site and inter-site validation suggest that localized calibration can improve accuracy. Nevertheless, the method remains robust across varying conditions, which is supported by comparison against established curve-fitting methods. Our findings highlight the potential of field cameras as a cost-effective tool for crop monitoring at a high spatial and temporal scale, with applications in crop phenology detection, biophysical monitoring, and validation of remote sensing products. Integrating this approach into regenerative agriculture frameworks could enhance decision-making and management interventions in smallholder farms.
Why it matches plant phenotyping methods圃場カメラ画像からGCCを抽出し、トウモロコシの生育ステージと生物物理形質を推定する手法を開発・検証しており、フェノタイピング手法が研究の中心である。
abstractwe utilized GCC time series to detect six key phenological stages of maize
[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).
To accurately invert the canopy parameters (Total photosynthetic area index, TPAI) of oilseed rape, a microwave characteristic layered measurement experiment was designed, and a multilayer microwave scattering semiempirical model (MLMSSM) was constructed based on the radar response changes induced by the differences in the vertical structure and canopy components at different phenological stages. This model was then applied to the main oilseed rape production areas to conduct regional TPAI inversion. Microwave characteristic layered measurement experiments were performed at six-leaf, flowering, beginning ripening and fully ripening stages of oilseed rape in the laboratory of target microwave properties (LAMP). The MLMSSM was constructed based on the LAMP-measured data, corresponding to different plant structures containing two- and three-layer submodels, and the TPAI inversion model was derived based on the correlation between the MLMSSM parameters and the crop biophysical variables. Finally, regional TPAI inversion and validation were carried out in the main oilseed rape production area (Hengyang), using Sentinel-1 SAR data. Visualization results, MLMSSM parameters and TPAI inversion results based on LAMP data all revealed the occurrence of multiple scattering interactions among distinct oilseed rape structural layers and verified the effectiveness of the measurement scheme and the model. The regional validation results showed high TPAI inversion accuracy throughout entire oilseed rape growth stages, with R² = 0.78, RMSE = 1.03, and MAE = 0.74 under VV polarization, and R² = 0.84, RMSE = 0.75, and MAE = 0.52 under VH polarization. The MLMSSM was found to significantly outperform the modified water cloud model (MWCM), increasing R² by 0.05 and 0.18 under VV and VH polarization respectively, while reducing the RMSE and MAE by 0.49–0.72. These results prove the accuracy and applicability of the MLMSSM for regional TPAI inversion of oilseed rape.
Why it matches plant phenotyping methods油糧ナタネの群落光合成面積指数を推定するマイクロ波計測・散乱モデルを開発し、Sentinel-1 SARで地域検証しており、植物形質取得法が中心である。
abstracta multilayer microwave scattering semiempirical model (MLMSSM) was constructed
The accurate three-dimensional (3D) distribution of plant area density (PAD) within forests is crucial for understanding canopy structure and provides essential scene inputs for 3D Radiative Transfer Models (RTMs) to facilitate remote sensing interpretation. However, current lidar-based voxelization methods that estimate detailed PAD distributions often cover limited areas, constraining their applications in conducting broad forest studies and interpreting Earth Observation Satellite (EOS) data of various scales and resolutions. To address this, we developed the Large-Scale Path Volume Leaf Area Density (LS-PVlad), a novel forest 3D reconstruction workflow capable of producing extensive high-resolution 3D voxelized forest scenes (up to 100 km² with ≤2 m voxel size) from worldwide open-access airborne lidar scanning (ALS) data. By applying LS-PVlad to the ALS data acquired during the extensive NASA Goddard's LiDAR, Hyperspectral & Thermal Imager (G-LiHT) campaigns, we developed the first release of FoScenes—a high-fidelity PAD product comprising 40 seamless scenes from 28 diverse forest sites, with individual area ranging from ∼50 to ∼11,000 ha. The leaf area estimates of LS-PVlad have been validated by two-year field-measured leaf area index (LAI) from litter collection (best RMSE = 0.35 m²/m²) and digital hemispherical photography (DHP) images (RMSE = 0.46 m²/m²) across multiple plots at a deciduous forest site. Additionally, a broad comparison between FoScenes and MODIS plant/leaf area index product demonstrates high consistency (R² = 0.70, RMSE = 0.86 m²/m²). By providing multi-dimensional forest characterizations, FoScenes enables temporal insights into structure dynamics. Its integration with the discrete anisotropic radiative transfer (DART) model underscores the potential of FoScenes for extensive 3D RTM applications at various scales.
Why it matches plant phenotyping methods森林の植物面積密度を推定する3D再構成ワークフローを開発し、実測LAI等で検証した大規模フェノタイピング製品・データセットであり、植物形質取得が中心である。
abstractwe developed the Large-Scale Path Volume Leaf Area Density (LS-PVlad), a novel forest 3D reconstruction workflow
Field / plotLeafMorphology / geometry measurementLeaf traits
AIMS: Specific leaf area (SLA), the ratio of leaf surface area to dry mass, is a key functional trait widely used to characterize resource allocation to light interception in plants. However, inconsistencies in SLA measurement-particularly whether petiolar tissues (such as petioles and rachises) are included-could lead to discrepancies in SLA estimates, especially in woody plants with compound leaves. This study investigates how two SLA measurement protocols (including vs. excluding the petiolar component) affect SLA estimates in both simple and compound leaves, with the goal of clarifying their implications for ecological studies. LOCATION: Tropical forests of the Peruvian Amazon. METHODS: Leaf area and dry mass were measured in 2758 individuals representing 1054 woody plant species from three sampling areas. We evaluated differences in the relationship between leaf area and dry mass across leaf types and measurement protocols while controlling for species‐level variation and phylogenetic structure. Additionally, a literature review was conducted to evaluate prevailing SLA measurement practices. RESULTS: Compound leaves exhibited consistently higher SLA than simple leaves of similar size, regardless of the protocol, with differences increasing with leaf size. Excluding the petiolar component amplified the disparity between leaf types, while SLA estimates for simple leaves remained relatively consistent across protocols. SLA declined with increasing leaf area in all cases. The literature review revealed that 46.8% of studies did not specify SLA measurement protocols, and among those that did, 76.2% included the petiolar component. CONCLUSIONS: SLA measurement protocol substantially influences trait estimates, particularly for compound leaves. While the protocol choice should be guided by the specific goals of each study, we argue that a default approach incorporating both laminar and petiolar components is optimal, as it is cost‐effective and easy to implement. Clear methodological reporting is essential for ensuring comparability across studies and advancing the use of SLA in plant ecological research.
Why it matches plant phenotyping methodsSLAという植物形質の測定プロトコルを比較・評価し、プロトコル差が推定値に与える影響と標準的手順を検討しており、形質取得法が研究の中心である。
abstractThis study investigates how two SLA measurement protocols (including vs. excluding the petiolar component) affect SLA estimates in both simple and compound leaves
Field / plotRGB / grayscaleLeafMorphology / geometry measurementLeaf traits
Abstract Despite similar universal primary physiological functions, plant leaves exhibit myriad shapes and sizes. Understanding this morphological variation is invaluable in plant taxonomy, ecology, evolution, and biomimetics. Achieving a comprehensive understanding of eco-evo-devo research requires diverse leaf-image datasets collected across regions and over time. While many datasets support morphometric studies using advanced imaging and machine learning, few provide standardised leaf images that enable uniform interspecific comparisons. We present a dataset of 161 high-quality RGB images of leaves of wild and cultivated tree species from Kerala, India, collected between 2020 and 2023. All leaves, including their petioles, were scanned using a digital scanner (Epson L360), centrally framed on a white background, and uniformly scaled to 1024 × 1024 pixels. In addition, the dataset comprises codes to compute the leaf morphometry using two novel objective morphometric measures: Segmental fractal complexity ( D ΣS ) and Geometric entropy ( S L ). These metrics were validated against the leaf dataset, showing strong correlations between D ΣS and leaf dissection index ( LDI ) ( ρ = 0.94) and between S L and D ΣS ( ρ = 0.94), confirming the relationship between leaf patterns and leaf lobiness, pinnation, and serration. D ΣS surpasses LDI by incorporating spatial positioning of leaflets, lobes and fine serration features. Both D ΣS and S L outperform geometric morphometric techniques, which are limited to intraspecific comparisons. Their objectivity, ease of use, and lack of statistical preprocessing make D ΣS and S L reliable metrics for interspecific leaf comparisons. We encourage researchers to expand or replicate our analysis using codes and leaf datasets from diverse locations. This dataset supports the development and validation of future leaf morphometric techniques. Despite limitations in high-resolution imaging and intraspecific variability, it remains valuable for advancing research and fostering collaboration across taxonomy, ecology, and computer vision.
Why it matches plant phenotyping methods葉画像データセットの提供に加え、葉形態を定量化する新規指標とコードを提示・検証しており、植物表現型の取得・抽出手法が中心である。
abstractWe present a dataset of 161 high-quality RGB images of leaves of wild and cultivated tree species from Kerala, India, collected between 2020 and 2023.
Near-real-time (NRT) daily crop monitoring at the field scale is crucial for precision agriculture, yet remains challenging due to limitations in the spatial or temporal resolution of existing remote sensing methods. While Sentinel-2 provides adequate spatial resolution for field-level applications, its temporal resolution is insufficient for capturing rapid crop dynamics, especially in cloudy regions. Existing spatiotemporal fusion techniques require multiple clear-sky images and lack true NRT capability, while ground-based sensors offer continuous monitoring but with limited spatial coverage. To address these limitations, this study develops the Near-Real-Time Ground-Satellite Fusion (NRT-GSF) algorithm, a novel approach based on a Bayesian dynamic linear model and Kalman filtering. The algorithm uniquely integrates Sentinel-2 imagery with continuous measurements from Internet of Things for Agriculture (IoTA) systems to generate daily 10-m Green Area Index (GAI) products. Its recursive framework supports both forward prediction in NRT mode following satellite overpasses and backward updating to refine historical profiles. Implemented over French wheat fields using 34 IoTA systems and Sentinel-2 time series from 2019, the algorithm effectively enhanced spatiotemporal completeness and accuracy (R = 0.75–0.98, RMSE = 0.1–0.49). A comprehensive leave-one-out Sentinel-2 evaluation demonstrated its superiority over the current Consistent Adjustment of the Climatology to Actual Observations (CACAO) algorithm. Ground validation using handheld RGB cameras further confirmed the accuracy of the GAI products from the new algorithm (RMSE = 0.5). The NRT-GSF framework offers a robust and operationally solution for daily, high-resolution crop GAI mapping in NRT mode, and it can be extended to other traits or applications in the near-real-time context.
Why it matches plant phenotyping methods圃場規模の日次Green Area Index（GAI）という植物形態形質を、衛星画像と地上センサーから推定する融合アルゴリズムを開発し、比較評価と地上検証を行っているため、植物フェノタイピング手法が中心である。
abstractthis study develops the Near-Real-Time Ground-Satellite Fusion (NRT-GSF) algorithm
The tea plant (Camellia sinensis) is economically and nutritionally important because of its bioactive compounds. Photosynthesis directly affects tea's growth and productivity, requiring a detailed study of its relationship with cultivation outcomes. We developed a novel computational pipeline for constructing three-dimensional (3D) canopy photosynthesis models of tea plant, leveraging multi-view stereo 3D reconstruction. The ISBNet architecture was optimized for precise leaf–stem segmentation from point cloud data, achieving 0.897 average precision (AP) for leaves and 0.793 AP for stems. We then created a plant leaf morphology-adapted meshing algorithm optimized for plant leaf morphology, achieving an average mesh reduction of approximately 96% while maintaining morphological fidelity compared with conventional meshing methods. We generated multiple tea plant canopies representing distinct planting patterns, and used a ray tracing algorithm to simulate the spatiotemporal distribution of light within these structures. Canopy photosynthesis simulation revealed significant cultivar-specific differences, with 'Yuehuang 1' exhibiting the highest photosynthetic activity. Dense planting (10 cm spacing) significantly enhanced canopy photosynthetic rates compared with wider spacing (20 cm), and a strong linear correlation (r = 0.99) was identified between total leaf area and daily canopy photosynthetic rate across cultivars. This work establishes a methodological foundation for precision agriculture optimization in perennial crops, providing quantitative guidance for maximizing tea plantations' productivity through optimal cultivar selection and spatial configuration.
Why it matches plant phenotyping methods茶樹キャノピーの3D再構築、葉・茎セグメンテーション、形態適応メッシュ化、光線追跡による光合成推定を統合した方法開発が中心であり、植物形態・光合成状態の定量化に直接つながる。
abstractWe developed a novel computational pipeline for constructing three-dimensional (3D) canopy photosynthesis models of tea plant, leveraging multi-view stereo 3D reconstruction.
Leaf area index (LAI) is a key indicator for measuring crop photosynthesis and growth status. In the monitoring of winter wheat LAI at the scale of large unmanned farms, satellite imagery is stable but lacks spatial resolution for precise monitoring, while UAV imagery is spatially detailed but prone to weather interference, resulting in poor spectral data consistency. To address this, this study took winter wheat in a large unmanned farm in Zouping City, Shandong Province as the research object and proposed a "coarse-fine fusion" two-step fusion method for UAV and Sentinel-2 imagery. Based on the fusion results, a feature set for winter wheat LAI inversion was constructed, and the SHAP model was used to evaluate feature contributions and screen the optimal combination. Machine learning models such as XGBoost and Random Forest were employed to invert LAI at key growth stages of winter wheat under different data fusion modes. Model hyperparameters were optimized through grid search to analyze the impact of data fusion methods on LAI inversion across growth stages. Experiments showed that the two-step fusion method significantly improved spectral consistency and accuracy, with the correlation coefficient between fusion results and Sentinel-2 NDVI values reaching 0.82. Nine key features were selected for model construction, among which the near-infrared band and plant height showed high positive contributions to LAI inversion. Under the two-step fusion data mode, the Random Forest algorithm performed best, achieving an overall R² of 0.895, MAE of 0.216 m²/m², and RMSE of 0.295 m²/m². Inversion accuracy varied across growth stages, with R² of 0.86 during the jointing stage, accurately reflecting dynamic LAI changes. This study provides an efficient and feasible solution for precision monitoring of large-area winter wheat, supporting precision agriculture and food security.
Why it matches plant phenotyping methodsUAV・衛星画像の融合、特徴選択、機械学習による冬小麦LAI推定手法を中心に開発・評価しており、植物形質の取得・推定が研究の主要目的である。
abstractproposed a "coarse-fine fusion" two-step fusion method for UAV and Sentinel-2 imagery
The characterization of wheat genetic resources constitutes a fundamental prerequisite for their effective use in breeding programs aimed at preventing future food shortages. Continued technological developments in plant phenotyping for remote and proximal sensing have enabled multidimensional data acquisition and analysis, making the screening of large numbers of genotypes more accessible and costeffective. Within this framework, 36 bread wheat landraces collected from different localities across Serbia were grown under rainfed conditions during the 2024/25 growing season at Rimski Šančevi, near Novi Sad (45.20° N, 19.51° E) and analyzed using several proximal non-destructive phenotyping devices. In the field trials, genotypes were evaluated at two growth stages for seven traits associated with plant productivity: green cover, leaf area index, maximum plant height, normalized difference vegetation index (Literal sensor, Hiphen), chlorophyll content, and nitrogen balance index (DUALEX optical leaf clip meter, Metos). After harvest, the landraces were assessed for thousand grain weight and grain size fractions (length, width, area) using the MARViN system (MARViTECH), and basic technological parameters (protein, moisture, carbohydrates, oil contents) using the GrainSense Analyzer (Oulu). Principal Component Analysis revealed a clear separation among the analyzed genotypes, reflecting their substantial genetic diversity with respect to the evaluated traits, and highlighting their potential as a valuable source of novel alleles for enhancing breeding value and developing high-yielding varieties with improved technological quality.
Why it matches plant phenotyping methods複数の近位非破壊センシング機器を用いて、遺伝資源の生育・形態・生理・収量関連形質を体系的に取得することが研究の中心であり、実質的なフェノタイピング手法の適用に該当する。
abstractanalyzed using several proximal non-destructive phenotyping devices
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
The study focuses on utilizing plant leaf characteristics for plant identification and disease detection. Leaves are pivotal for gathering information about plants. The proposed model uses computer vision and smart agricultural technologies to discern venation and texture features in various plant leaves. This research utilized a modified dataset derived from the Flavia leaf image dataset, comprising images of 32 plant species. The dataset was divided into two subsets (one with 1907 images and another with 1000 images) to differentiate between tuned and untuned image processing. Techniques such as GLCM, LBP, Gabor filters, Fractal Dimension, and box-counting were employed to extract leaf texture features, including venation patterns. The study conducted four experiments with training and testing splits of 70/30 and 80/20. A novel method combining SVM with fractal dimension analysis was benchmarked against six classifiers (Random Forest, KNN, DNN, Naïve Bayes, Decision Tree, andSVM), achieving an impressive accuracy of 88% and a Fractal Dimension of 1.8709. This research holds significant potential for advancing digital and modern agriculture, particularly in the early detection of plant diseases and accurate plant identification.
Why it matches plant phenotyping methods葉の輪郭・葉脈・テクスチャ特徴を画像から抽出する手法の開発と分類器比較が研究の中心であり、植物器官の観測可能な形態特徴を定量化しているため含める。
abstractThe proposed model uses computer vision and smart agricultural technologies to discern venation and texture features in various plant leaves.
Accurate and efficient leaf trait measurement is essential for plant phenotyping, agronomy, and ecological studies. In this work, we introduce Leaf Analyzer, a novel open-source, fully automated computer vision-based tool for high-throughput leaf morphological trait measurement such as leaf area, dimensions, perimeter, count, and percent damage. Unlike existing methods that rely on strong foreground-background contrast or controlled imaging conditions, Leaf Analyzer employs an unsupervised clustering approach based on the K-means++ clustering algorithm and a novel Leaf Background Separation (LBS) feature, which combines the L∗ and b∗ channels from CIEL∗a∗b∗ color space and the saturation channel from HSV color space. The proposed method and the LBS feature can effectively distinguish leaves from the background across varying lighting conditions, leaf colors, and camera orientations. To evaluate the performance of the new software, we conducted comprehensive quantitative and qualitative comparison experiments with two widely used software tools - Petiole Pro and LeafByte, demonstrating that Leaf Analyzer achieves superior accuracy and consistency, particularly under challenging imaging conditions. Additionally, we explore methods to further enhance measurement precision, including leaf flattening and the integration of supplementary leaf features such as texture features and color specific features. Beyond leaf trait measurement, we showcase the versatility of Leaf Analyzer in a range of applications, including nondestructive plant phenotyping, seed counting, root trait analysis, leaf area measurement for petri dish-grown plants, plant projected silhouette area or crown projection area estimation, leaf damage assessment, and broader plant science applications, making it a valuable tool for researchers working in laboratory and field environments.
Why it matches plant phenotyping methods葉形態形質を自動抽出するオープンソース画像解析ツールの開発と、既存ツールとの定量比較検証が研究の中心であるため。
abstractIn this work, we introduce Leaf Analyzer, a novel open-source, fully automated computer vision-based tool for high-throughput leaf morphological trait measurement such as leaf area, dimensions, perimeter, count, and percent damage.
Reproduction assets foundThe authors state that the Leaf Analyzer source code, installer files, and all data (including evaluation images) used in this study are publicly available on their GitHub repository.Code · publicThe Leaf Analyzer source code, platform-specific installer files, and all data used in this study are publicly available on our GitHub repository at https://github.com/squashking/Leaf-Analyzer .Open asset ↗squashking/Leaf-Analyzerlines:239-277Dataset · publicAll the images used in the evaluation have been published on our Github repository ( https://github.com/squashking/Leaf-Analyzer ).Open asset ↗squashking/Leaf-Analyzerlines:134-155Plant phenotyping relevance match · UnverifiedOpenAlex · Europe PMC · checked 5 Sept 2026
High-throughput phenotyping using unmanned aerial vehicle (UAV)-based imagery offers substantial potential for improving sugarcane breeding efficiency. This study utilized UAVs-equipped multispectral sensors to capture high-resolution imagery of 652 sugarcane varieties under high-density planting condition, enabling the development of predictive models for key phenotypic traits including plant height, leaf length, leaf width, and relative chlorophyll content (SPAD value). A comprehensive feature extraction process yielded 100 vegetation indices, 7 texture indices, and canopy height parameters derived from the UAV imagery. To develop robust predictive models, we implemented three feature processing strategies—correlation-based filtering (COR), stepwise regression selection (SWR), and principal component analysis (PCA)—in conjunction with five machine learning algorithms: Lasso Regression (LASSO), Ridge Regression (Ridge), Support Vector Machine Regression (SVM), Random Forest (RF), and Gradient Boosting Regression Trees (GBR). Two ensemble methods, Bayesian Model Averaging (BMA) and Stacked Generalization, were also employed. Results demonstrated that LASSO performed best among traditional machine learning models, whereas the Stacking ensemble method, which integrated predictions from all individual algorithms, achieved the highest prediction accuracy (the coefficient of determination ( R 2 ) = 0.77; root mean squared error ( RMSE ) = 12.99 cm for plant height). Additionally, K-means clustering partitioned the sugarcane varieties into two distinct clusters (A and B; p ≤ 0.001). Notably, cluster-specific models trained on PCA-processed features demonstrated exceptional predictive accuracy during validation, achieving R 2 values of 0.94, 0.91, 0.87, and 0.90 for plant height, leaf length, leaf width, and SPAD value, respectively. This research presents an integrated framework combining optimized feature processing, population clustering, and ensemble learning to enhance trait prediction in large-scale UAV-based phenotyping for sugarcane breeding.
Why it matches plant phenotyping methodsUAVマルチスペクトル画像からサトウキビの複数形質を推定する予測モデルと統合的な表現型解析フレームワークを開発・検証しており、表現型取得・抽出手法が研究の中心である。
abstractHigh-throughput phenotyping using unmanned aerial vehicle (UAV)-based imagery offers substantial potential for improving sugarcane breeding efficiency.
WheatAerial / UAVMultispectral / hyperspectralGrowth / development / phenologyLeaf traits
Wheat growth monitoring plays a vital role in agricultural decision-making and food security. This study aims to develop an accurate and efficient monitoring method for wheat growth by integrating satellite remote sensing and machine learning techniques. Based on preprocessed Sentinel-2 satellite images and measured wheat leaf area index (LAI) data, a set of 11 vegetation indices-such as NDVI, NDRE, and RVI-were selected and ranked through Pearson correlation analysis. A comprehensive index system was then constructed by selecting the top eight indices using a stepwise optimization approach. Three machine learning models-Linear Regression (LR), Backpropagation Neural Network (BPNN), and XGBoost-were applied to evaluate the performance of the index system, with the Particle Swarm Optimization (PSO) algorithm employed to optimize each model. The results demonstrate that the PSO-optimized XGBoost model achieved the highest accuracy (R² = 0.94, MSE = 0.075), exhibiting strong stability and robustness to data fluctuations. These findings suggest that the proposed approach provides a reliable solution for wheat growth monitoring.
Why it matches plant phenotyping methods衛星リモートセンシングと機械学習により小麦のLAIを推定する監視手法の開発・評価が研究の中心であり、植物キャノピー形質の取得方法を扱っている。
abstractThis study aims to develop an accurate and efficient monitoring method for wheat growth by integrating satellite remote sensing and machine learning techniques.
Leaf area is a key indicator of plant health and development. However, manual measurement is time-consuming and labor-intensive, especially when monitoring aeroponic-grown potato plants with multiple leaves over extended periods. This study applied a computer vision-based system to automate leaf growth monitoring using the YOLO (You Only Look Once) v8 framework. A dataset was collected from a controlled aeroponic system: 25 images of young leaves (4,869 individual leaf segments) and 35 of mature leaves (12,368 segments). Based on evaluation of various YOLOv8 model configurations, the best model achieved a mask mAP@50 of 0.396 and 0.250 for young leaves and mature leaves, respectively. The challenge to track the mature canopy was due to severe leaf occlusion and self-similarity in dense foliage. Despite the challenge, this study demonstrates proof of concept for tracking early leaf growth and highlights the significant computer vision challenges posed by dense, mature canopies in aeroponic systems.
Why it matches plant phenotyping methods植物の葉面積・葉成長をコンピュータビジョンで自動追跡する手法の開発と評価が中心であり、植物表現型の取得方法を直接扱っている。
abstractThis study applied a computer vision-based system to automate leaf growth monitoring using the YOLO (You Only Look Once) v8 framework.
Field / plotLeafMorphology / geometry measurementLeaf traits
Quantifying inequality in the leaf area distribution within a single module is critical for elucidating plant resource allocation strategies, but the accuracy of theoretical Gini coefficients derived from statistical distributions remains poorly validated against observed values. To resolve this gap, we analyzed 9,242 leaves from 121 culms of the bamboo Semiarundinaria densiflora , a model system with minimal ontogenetic noise and moderate leaf counts (36-187 leaves per culm) that enables robust Lorenz curve construction. Four candidate distributions were tested: the normal, log-normal, two-parameter Gamma, and two-parameter Weibull distributions. The parameters of the normal and log-normal distributions were estimated directly from sample statistics, whereas the parameters of the Gamma and Weibull distributions were estimated using the maximum likelihood method. Goodness of fit was assessed using the Kolmogorov-Smirnov (K-S) test for distributional validity, and the Akaike's information criterion (AIC) for model selection. Although the Gamma distribution passed the K-S test for a slightly higher percentage of culms (99%) than the Weibull distribution (97.5%), the Weibull distribution was selected as the superior model because it yielded significantly lower AIC values. Crucially, the theoretical Gini coefficients of the Gamma and Weibull distributions (denoted as G G and G W , respectively) were tested against the observed Gini coefficients ( G P ) calculated nonparametrically using the polygon method. Linear regression demonstrated that G W predicted G P with near isometric accuracy: the intercept's 95% confidence interval included zero (-0.006 to 0.017) and the slope's 95% confidence interval included unity (0.929 to 1.039). In contrast, G G exhibited significant bias. Notably, pooling leaves across culms violated all distributions due to microhabitat driven multimodality, confirming that intra-culm inequality assessments require organism level analysis. This work provides an empirical validation that the Weibull shape parameter reliably quantifies intra-culm leaf area inequality. By bridging theoretical distribution models with field-derived inequality metrics, our approach provides insights into canopy efficiency, photosynthetic optimization, and hydraulic trade-offs. Future work should test this approach in other grass species and assess its generalizability in plants with contrasting canopy architectures.
Why it matches plant phenotyping methods竹の葉面積不均一性を定量化する統計的フェノタイピング手法を、観測Gini係数との比較で検証しており、方法論が研究の中心です。
abstractThis work provides an empirical validation that the Weibull shape parameter reliably quantifies intra-culm leaf area inequality.
Successful establishment and growth of constructed saltmarshes can be evaluated through consistent monitoring of plant biophysical parameters, such as aboveground biomass and leaf area index. Monitoring during the early establishment stage is vital for ensuring the long-term effectiveness of constructed saltmarshes in delivering anticipated ecosystem services, including wave energy dissipation, which strongly depends on vegetation biophysical characteristics. Efficient, low-disturbance methods are needed for the successful adoption of such monitoring plans. This study combines laboratory measurements and remote sensing observations to evaluate the performance of vegetation indices in capturing changes in aboveground biomass, leaf area index, and wave energy dissipation in a constructed saltmarsh. Allometric equations were also investigated to predict aboveground biomass from non-destructive plant traits. Results showed acceptable correlations between vegetation indices, measured biophysical parameters and wave energy dissipation characteristics. All species performed better with NIR-R-based indices for leaf area index, while aboveground biomass predictions varied, with both NIR-R- and G-R-based indices performing best depending on species. Wave energy dissipation also correlated with vegetation indices, aligning closely with the best predictors of aboveground biomass, particularly when vegetation was submerged. These findings indicate that remote sensing combined with allometric equations offers a promising method for monitoring newly established marshes and estimating their biophysical parameters, which serve as key indicators of successful establishment and initial wave energy dissipation.
Why it matches plant phenotyping methodsリモートセンシング指標とアロメトリック式によって植物のバイオマスや葉面積指数を推定し、その性能を評価することが研究の中心であるため、植物フェノタイピング手法として適格。
abstractThis study combines laboratory measurements and remote sensing observations to evaluate the performance of vegetation indices in capturing changes in aboveground biomass, leaf area index, and wave energy dissipation in a constructed saltmarsh.
The Distributed System for Scientific Collections (DiSSCo) is a research infrastructure to integrate European natural science collections (NSCs) digitally. The aim is to facilitate and enhance the access, management and analysis of collection assets in one unified digital collection. The Machine Annotation Services (MAS) are essential components of DiSSCo’s Digital Specimen Architecture (DSArch). These services automate the annotation of digital objects to enable labelling and categorisation of NSC's digital assets. To further advance this, a Machine Learning as a Service (MLaaS) approach was developed which provides researchers with the access to pre-trained machine-learning models for complex tasks, such as instance segmentation and morphological analysis of datasets. MLaaS enhances the DiSSCo’s scalability and flexibility and allows the integration of machine-learning tools in close alignment with the FAIR (Findable, Accessible, Interoperable, Reusable) principles. This study employs DiSSCO's MLaaS framework for the quantitative analysis of herbarium specimens. Machine-learning models, such as Mask R-CNN and YOLO11, are comparatively applied to detect and generate the pixel-level masks of plant organs in herbarium sheets. Subsequently, these models are used to reconstruct the scale in the herbarium sheet and to calculate the surface area of identified plant organs. The determination of quantitative characteristics of plant specimens, such as measuring leaf area or the timestamp of the floral transition, opens up herbarium data for reuse in the large prognosis platforms currently developed in the framework of the Common European Data Spaces. In this way, plant trait data mobilised from natural science collections can improve the predictive capability of the vegetation model components of climate-related data spaces.
Why it matches plant phenotyping methodsハーバリウム画像から植物器官を検出・セグメンテーションし、葉面積などの形質を定量化する機械学習手法と基盤の応用が研究の中心である。
abstractThis study employs DiSSCO's MLaaS framework for the quantitative analysis of herbarium specimens.
Accurate and efficient plant phenotyping is essential for modern precision agriculture. as it provides reliable information for seedling quality evaluation, early detection of plant stress, and data support for crop breeding and yield prediction. Traditional three-dimensional (3D) reconstruction and analysis methods are often costly and time-consuming, because they usually depend on expensive laser scanning devices or require many input images. Even with these resources, they often fail to capture fine plant structures such as leaves and branches, which limits their application in seedling monitoring. To address these challenges, we propose an integrated framework that combines neural radiance fields (NeRFs) for high-fidelity 3D reconstruction, PointNet++ for robust semantic segmentation, and a customized algorithm for extracting key morphological parameters of tomato seedlings. The proposed framework can be used to reconstruct detailed 3D models at a low computational cost using only ordinary cameras and a limited number of 2D images. We validate the framework on the basis of a tomato seedling dataset and show that our approach outperforms traditional multiview stereo scanners and simple commercial 3D scanners in terms of both detail and efficiency. The accuracy of plant part segmentation reaches 90 %, and the extracted parameters (e.g., leaf area, stem height, branch angle, and internode distance) are highly correlated with the manual measurements (e.g., R 2 = 0.875 for the leaf area). This study provides a low-cost and scalable solution for 3D plant analysis, with direct benefits for automated monitoring of seedling quality in nursery production. Moreover, the proposed framework can be extended to other crops with complex structures, thus supporting wider applications in smart agriculture.
Why it matches plant phenotyping methodsトマト苗の3D再構成、植物部位分割、形態形質抽出を統合した低コスト画像ベース手法を開発・検証しており、植物フェノタイピングが研究の中心である。
abstractwe propose an integrated framework that combines neural radiance fields (NeRFs) for high-fidelity 3D reconstruction, PointNet++ for robust semantic segmentation, and a customized algorithm for extracting key morphological parameters of tomato seedlings.
Leaf vein segmentation is a critical task in plant phenotyping and species classification, yet it remains challenging due to the hierarchical, curvilinear nature of veins and interference from complex backgrounds. Existing methods face three key limitations. First, they lack directional context modeling, leading to blurred vein boundaries and the omission of fine venation. Second, they fail to effectively capture global dependencies, limiting semantic coherence across spatial regions. Third, they do not incorporate explicit mechanisms for detecting vein discontinuities, which is essential for complete topological understanding. To address these challenges, we propose MultiTaskVenationNet (MTV-Net), a multi-task deep segmentation framework that integrates four complementary modules. The Strip Pooling Module (SPM) captures orientation-specific long-range context by performing directional pooling along horizontal and vertical axes, enhancing the visibility of delicate vein structures. The Global Context Block (GCBlock) aggregates long-range dependencies through channel attention at the bottleneck stage, improving the semantic consistency of encoded features. A dual-branch decoder explicitly separates the learning objectives for vein segmentation and breakpoint detection. At the same time, a hybrid upsampling strategy combines bilinear interpolation and transposed convolution to accurately reconstruct vein boundaries without introducing artifacts. Extensive experiments on the LVD2021 benchmark dataset demonstrate that MTV-Net outperforms state-of-the-art models such as U-Net, GCNet, CE-Net, and HRNet, achieving an IoU of 76.46 ± 0.27 and a Dice coefficient of 86.61 ± 0.18. The model also exhibits strong generalization across diverse leaf morphologies, vein densities, and lighting conditions, validating its effectiveness and robustness for high-precision leaf vein analysis.
Why it matches plant phenotyping methods葉脈という植物形態を画像から抽出する深層学習セグメンテーション手法を開発し、ベンチマークで性能・頑健性を検証しており、植物フェノタイピング手法が中心である。
abstractLeaf vein segmentation is a critical task in plant phenotyping and species classification
This Research paper develops an automated Plant Health Monitoring system that leverages Convolutional Neural Networks (CNNs) to perform simultaneous leaf- level disease classification and leaf counting from plant images. The proposed pipeline uses a CNN-based feature extractor feeding two task-specific branches: a classification head that identifies healthy versus diseased leaves (and the disease type) and a counting head that estimates leaf number via a regression/segmentation approach. Input images are preprocessed with augmentation and normalization to improve robustness to lighting, occlusion, and background variation. The model is trained on a curated set of annotated plant images and adapted for efficient inference using transfer learning and lightweight architectures suitable for edge deployment. Results show the approach provides reliable disease detection and accurate leaf counts, enabling timely alerts and actionable insights for precision agriculture. The system aims to reduce manual inspection effort, speed up diagnosis, and support better crop-management decisions.
Why it matches plant phenotyping methods植物画像から病害状態と葉数を推定するCNNベースの取得・解析パイプラインが研究の中心であり、植物表現型の計測手法として明示的に開発・評価されている。
abstractdevelops an automated Plant Health Monitoring system that leverages Convolutional Neural Networks (CNNs) to perform simultaneous leaf- level disease classification and leaf counting from plant images.
Early-stage, accurate and high-throughput phenotyping through leaf area estimation is critical for future rapeseed breeding, but faces two key constraints: expensive data annotation and persistent challenge of leaf occlusion. To address these issues, we present a data-efficient deep learning framework using smartphone-captured top-down RGB images for rapeseed leaf area quantification. Our approach utilizes a two-stage strategy where a Vision Transformer (ViT) backbone is first pre-trained on a large, aggregated dataset of diverse, non-rapeseed public plant datasets using the DINOv2 self-supervised learning method. This pre-trained model is then fine-tuned on a custom rapeseed dataset using a novel Canopy-Mix data augmentation technique to handle fragmented views analogous to occlusion, and a hybrid loss function combining Smooth L1 and Log-Cosh for robust convergence. Through rigorous 5-fold cross-validation, our proposed model achieved strong predictive performance (Coefficient of Determination, R[Formula: see text]=0.805). Moreover, the predicted leaf area demonstrated a remarkably strong correlation with both fresh weight (r=0.900) and dry weight (r=0.885). The model significantly outperformed a range of baselines, including models trained from scratch, those pre-trained on ImageNet, and a heuristic method based on manually annotated bounding boxes. Ablation studies confirmed the essential contribution of each component, while qualitative analysis of attention maps demonstrated the model's ability to precisely localize the leaf canopy and ignore background distractors. This study demonstrates that domain-specific self-supervised pre-training offers a powerful solution to overcome data limitations in agricultural vision, providing a robust and scalable tool for non-destructive phenotyping that can potentially accelerate the rapeseed breeding cycle.
Why it matches plant phenotyping methods葉面積という植物形質をRGB画像から推定する深層学習法を開発し、交差検証・ベースライン比較・アブレーションで技術検証しているため、方法が中心である。
abstractwe present a data-efficient deep learning framework using smartphone-captured top-down RGB images for rapeseed leaf area quantification.
Leaf Area Index (LAI) is a key biophysical descriptor of crop canopies and is essential for growth monitoring and yield estimation. We present a physics-driven machine-learning framework for operational LAI retrieval and end-to-end uncertainty quantification that couples the PROSAIL radiative transfer model with a genetic-algorithm-optimised multilayer perceptron (NN–GA). PROSAIL is sampled across plausible parameter priors and spectra are convolved with Sentinel-2B spectral response functions to build a 30,000-sample training library; a GA is used to globally optimise network weights and biases. Total retrieval uncertainty is decomposed into a simulation component (PROSAIL parameter variability) and a training component (variability across repeated NN–GA trainings) and combined via the law of propagation of uncertainty. The model was developed in Minqin (modelling/testing area; entirely maize) and transferred to Zhangye (transfer/validation area; predominantly maize, with one sunflower plot). Sentinel-2B validation results were RMSE/R2 = 0.44/0.73 (Minqin) and 0.40/0.56 (Zhangye), indicating reasonable cross-site generalisation. The uncertainty split indicates physical-driven contributions of 11.42% and 11.48% and machine-learning contributions of 18.06% and 12.96%, respectively. The framework improves 10 m LAI retrieval accuracy and supplies a reproducible, per-pixel uncertainty budget to guide product use and refinement.
Why it matches plant phenotyping methods作物キャノピーのLAIという明示的な植物形質を、放射伝達モデルと機械学習で衛星データから推定し、不確実性定量化とサイト間検証まで行う手法中心の研究。
abstractWe present a physics-driven machine-learning framework for operational LAI retrieval and end-to-end uncertainty quantification
The accurate estimation of grapevine biophysical parameters is important for decision support in precision viticulture. This study addresses the use of unmanned aerial vehicle (UAV) multispectral data and machine learning (ML) techniques to estimate leaf area index (LAI), pruning wood biomass, and yield, across mixed-variety vineyards in the Douro Region of Portugal. Data were collected at three phenological stages, from veraison to maturation and two modeling approaches were tested: one using only spectral features, and another combining spectral and geometric features derived from photogrammetric elevation data. Multiple linear regression (MLR) and five ML algorithms were applied, with feature selection performed using both forward and backward selection procedures. Logarithmic transformations were used to mitigate data skewness. Overall, ML algorithms provided better predictive performance than MLR, particularly when geometric features were included. At harvest-ready, Random Forest achieved the highest accuracy for LAI (R2 = 0.83) and yield (R2 = 0.75), while MLR produced the most accurate estimates for pruning wood biomass (R2 = 0.83). Among geometric variables, canopy area was the most informative. For spectral data, the Modified Soil-Adjusted Vegetation Index (MSAVI) and the Soil-Adjusted Vegetation Index (SAVI) were the most relevant. The models performed well across grapevine varieties, indicating that UAV-based monitoring can serve as a practical, non-invasive, and scalable approach for vineyard management in heterogeneous vineyards.
Why it matches plant phenotyping methodsUAVマルチスペクトル画像と機械学習により、ブドウのLAI、バイオマス、収量を推定する手法を開発・比較しており、表現型取得と推定が研究の中心である。
abstractThis study addresses the use of unmanned aerial vehicle (UAV) multispectral data and machine learning (ML) techniques to estimate leaf area index (LAI), pruning wood biomass, and yield
The lamina joint is a critical determinant of leaf angle and crop architecture. While epidermal cells play a fundamental role in organ morphogenesis, influencing the overall shape and function of plants, their impact on lamina joint morphology has been largely overlooked. A live-imaging system for the rice lamina joint epidermis is established in this study, enabling precise tracking of cellular dynamics during leaf angle formation. It is found that asymmetric elongation between the lateral and medial edges, determined by spatial differences in the longitudinal elongation and number of epidermal cells, is a key factor in leaf angle formation. Mutations in the homeobox genes OsZHD1 and OsZHD2 disrupt the growth patterns of lamina joint epidermal cells, resulting in a decreased leaf angle. Epidermis-specific restoration of OsZHD1 expression rescues the reduced leaf angle phenotype of oszhd1 oszhd2, confirming the pivotal role of epidermal development in lamina joint morphogenesis. Transcriptomic analysis indicates that OsZHD1 and OsZHD2 regulate auxin activity, which modulates leaf angle by restricting lamina joint epidermal growth. This study underscores the significance of epidermal cells in shaping the lamina joint and elucidates the critical role of OsZHD1 and OsZHD2 in regulating epidermal cell behavior and leaf angle formation.
Why it matches plant phenotyping methodsイネ葉舌関節表皮の細胞動態を追跡するライブイメージング系を確立し、葉角形成に関わる形態・成長を定量的に解析しており、表現型取得法が研究の中核に含まれる。
abstractA live-imaging system for the rice lamina joint epidermis is established in this study, enabling precise tracking of cellular dynamics during leaf angle formation.
Abstract Leaf appearance is a crucial plant phenotype. However, traditional methods for extracting this information are inefficient, limiting its full utilization. Deep learning based on convolutional neural networks (CNNs) enables us to capture previously inaccessible information from images. In this study, we made the surprising discovery that the leaf appearance of each individual plant is unique. Using deep learning, leaves from one plant could be efficiently distinguished from those of another plant of the same species and cultivar. We term this phenomenon the “ Plant Face ” and suggest the potential to develop a “plant face recognition system,” analogous to human facial recognition. We also applied similar methods to study the relationship between leaflet appearance and their position on compound leaves, leaf bilateral symmetry, and differences in leaves from twining stems with different chirality. These results collectively indicate that plant genetic characteristics, growth conditions, and developmental features can be stored within their appearance. With appropriate decoding, leaf appearance is poised to play an increasingly important role in phenomics. Significance The saying “no two leaves in the world are identical” holds philosophical significance, as such variation encompasses considerable contingency and randomness. Here, we assert that no two trees have identical leaves ; meaning that even for plants of the same species and cultivar, the leaf morphology of each individual plant is distinct at the population level, even though single leaves may overlap in appearance. Genetic, environmental, and developmental information is recorded in some manner within the phenotypic appearance of leaves. With advancements in computational technologies like artificial intelligence, this information can now be decoded. Highlights The leaves of each individual plant are statistically unique. The relationship between leaflet appearances in compound leaves hints at their developmental patterns. Leaves are not necessarily bilaterally symmetric in a statistical sense. Leaves from stems with different chirality (twining direction) exhibit distinct appearances.
Why it matches plant phenotyping methods葉画像から植物の個体差や形態情報を深層学習で抽出・識別する手法が研究の中心であり、植物フェノタイピングへの応用を明示している。
abstractLeaf appearance is a crucial plant phenotype. However, traditional methods for extracting this information are inefficient
Reproduction assets found保存済みの本文根拠を更新済みルールで再検証し、公開資産1件を確認しました。Code · publicCodes are available at git-hub.Open asset ↗pdf-page:13 lines:1-54Code / dataset availability confirmedEurope PMC · checked 15 Sept 2026
Field / plotLeafStem / branchMorphology / geometry measurementLeaf traitsStress response / toleranceWater status / transpiration
Background Plant functional traits provide key information about species' ecological strategies and their responses to environmental disturbances such as fire. This dataset documents 14 morpho-functional traits of leaves (specific leaf area, leaf water content and leaf dry matter content), stems (maximum height, bark thickness, diameter at 40 cm, wood density, stem water content and stem dry matter content), one regenerative trait (resprouting capacity), as well as fire-related traits (ignition time, flaming time and flammability) and growth form in 50 woody plant species (27 trees, 22 shrubs and one liana) inhabiting a pine-oak forest in the "Barranca del Cupatitzio" National Park (BCNP), located in Uruapan, Michoacán, Mexico. This dataset is formatted according to the Darwin Core Archive standard and is publicly available for use. New information This dataset is standardised under the Darwin Core framework. It includes 14 morpho-functional and fire-related traits. The data were obtained from 50 woody species with a diameter at breast height (DBH) > 2.5 cm (27 trees, 22 shrubs and one liana), in a pine-oak forest located in the western Trans-Mexican Volcanic Belt, in the Municipality of Uruapan, Michoacán, Mexico. Here, we report flammability-related traits for these species for the first time. The collection of biological material and the measurement of functional traits followed internationally recognised protocols, ensuring methodological consistency and facilitating integration with other global datasets. The dataset includes values for flammability, ignition time, flaming time, specific leaf area, wood density, stem water and dry matter content, bark thickness, leaf water and dry matter content, maximum height, stem diameter at 40 cm above the ground, plant growth form and resprouting capacity. This information is particularly valuable for studies in functional ecology, ecological restoration, the dynamics of woody plant communities and fire management in temperate, fire-prone ecosystems.
Why it matches plant phenotyping methods植物の形態・機能・火災関連形質を体系的に収集し、Darwin Coreで標準化した再利用可能なデータセットであり、形質測定とデータ提供が中心である。
abstractThis dataset documents 14 morpho-functional traits of leaves
Reproduction assets foundThe paper is a data paper whose own trait/flammability dataset is deposited publicly on GBIF via DOI 10.15468/46f8xe, explicitly linked as the data package for this study's measurements.Dataset · publiche Creative Commons Attribution 4.0 International License (CC-BY 4.0), which permits use, distribution and reproduction in any medium, provided the original authors are properly credited.
Data resources
Data package title
Functional traits related to fire in woody species from Barranca del Cupatitzio National Park
Resource link
https://doi.org/10.15468/46f8xe
Number of data sets
2
Data set 1.
Data set name
occurrence.txt
Data format
Darwin Core
Data set 1.
Column label
Column description
id
Unique identifier for each occurrence.
institutionID
The identifier for the institution having custody of the specimens.
institutionCode
Full name of the institution having custody of the specimeOpen asset ↗10.15468/46f8xelines:87-297Plant phenotyping relevance match · UnverifiedEurope PMC · checked 15 Sept 2026
Published1 Dec 2025Computers and Electronics in Agriculture.
Three-dimensional phenotyping technology is paramount in the field of peanut breeding and cultivation. The intricate topological structure of plants substantially complicates the development of effective peanut phenotyping technologies. In this study, we present the development of a point-cloud-based pipeline for three-dimensional phenotypic analysis of peanut plants. An efficient multi-view image acquisition system and three-dimensional reconstruction techniques were employed to generate point clouds of peanut plants. A dataset comprising 188 labelled samples of peanut point clouds was constructed for the development of semantic and leaf-instance segmentation models based on the transformer architecture. The segmentation accuracy of these models surpassed that of the conventional general segmentation techniques for plant point clouds. Based on the results of the segmentation, 11 three-dimensional phenotypic traits were automatically calculated at both the plant and leaf scales. Among these, five phenotypic traits, including plant height and leaf length, exhibited a mean absolute percentage error (MAPE) of less than 0.12 compared to the measured values. In addition, the Jensen-Shannon divergence (JS divergence) between the probability distributions of the three leaf phenotypic traits and their corresponding measured values was below 0.1. The three-dimensional phenotypic analysis pipeline developed in this study exhibited satisfactory generalisation capabilities, thereby offering an efficacious and expeditious high-throughput phenotyping analysis instrument for the intelligent breeding and cultivation of peanuts.
Why it matches plant phenotyping methodsピーナッツの3D画像取得、点群再構成、分割、形質自動算出を統合したフェノタイピングパイプラインの開発と精度検証が中心である。
abstractwe present the development of a point-cloud-based pipeline for three-dimensional phenotypic analysis of peanut plants
Abstract High‐throughput and noninvasive phenotyping methods are promising technology for improving efficiency in plant research and breeding. In this study, we evaluated the performance of a digital phenotyping system (DPS) based on three‐dimensional (3D) model reconstruction for quantifying key growth traits in rice ( Oryza sativa ). The DPS was used to estimate plant height, biomass, color, leaf morphology, and tiller angle in four rice varieties (Koshihikari, Nipponbare, PL9, and Tachiaoba). The results show high accuracy and correlation between manually measured and DPS‐derived traits. Notably, the 3D volume analysis can quantify biomass accumulation and growth dynamics and revealed distinct differences among varieties. The strong correlation between the green‐red normalized difference index (a red‐green‐blue‐based index) and soil plant analysis development also demonstrated the viability of the system in monitoring leaf color without using a multispectral instrument. The analysis also captured growth patterns over time, including canopy development and senescence, which are often challenging to quantify through manual measurements alone. Furthermore, the tiller angle estimation derived from DPS provided an alternative method to plant architecture evaluation, demonstrating its potential for use in breeding programs aimed to optimize canopy structure. These findings establish DPS as a reliable and scalable tool for a digital phenotyping platform that enables comprehensive trait analysis with reduced labor and increased precision and the capability to continuously monitor plant growth and biomass accumulation. This study shows the potential of this novel digital tool for automating manual measurements, which can increase efficiency and expedite research and breeding in rice and other crops.
Why it matches plant phenotyping methods3Dモデル再構築に基づくデジタル表現型解析システムを開発・評価し、イネの複数形質を手測定と比較検証しているため、方法が研究の中心です。
abstractwe evaluated the performance of a digital phenotyping system (DPS) based on three‐dimensional (3D) model reconstruction for quantifying key growth traits in rice
Reproduction assets foundThe paper's data availability statement explicitly says the analysis code is openly available on GitHub at the authors' repository Rice_VTGa.O, which contains the digital phenotyping/leaf-tracing analysis code for this study. No phenotype dataset or image deposit is stated.Code · publicGrant Number 39 [2023] and 38 [2024]),
and Microbiome and Metabolome Control Project, University
of Miyazaki, Japan.
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 A B I L I T Y S TAT E M E N T
Codes used for analysis in this study are openly available on
GitHub at https://github.com/sandysan42/Rice_VTGa.O RC I D
SorawichPongpiyapaiboon https://orcid.org/0000-0002-9314-8375
Kenji Aoki https://orcid.org/0000-0001-7003-1994
MasatsuguHashiguchi https://orcid.org/0000-0003-0637-2780
RyoAkashi https://orcid.org/0000-0002-5651-8285
Yuji Kishima https://orcid.org/0000-0002-0942-3371
Hidenori Tanaka https://orcid.org/0000-0002-4237-8154Open asset ↗https://github.com/sandysan42/Rice_VTGa.O · Rice_VTGa.Opdf-raw-page:13 lines:1-84Code / dataset availability confirmedCrossref · OpenAlex · Europe PMC · checked 6 Sept 2026
RiceWheatField / plotMesh / voxelNeRF / 3D Gaussian SplattingLiDAR / point cloudPanicle / ear / spikeLeafRootSeed / grain
Advanced plant phenotyping technologies are vital for trait improvement and accelerating intelligent breeding. Due to the species diversity of plants, existing methods heavily rely on large-scale high-precision manually annotated data. For self-occluded objects at the grain level, unsupervised methods often prove ineffective. This study proposes IPENS, an interactive unsupervised multi-target point cloud extraction method. It utilizes radiance field information to lift 2D masks, segmented by SAM2 (Segment Anything Model 2), into 3D space for target point cloud extraction. A multi-target collaborative optimization strategy addresses the challenge of segmenting multiple targets from a single interaction. On a rice dataset, IPENS achieves a grain-level segmentation mean Intersection over Union (mIoU) of 63.72%. For phenotypic trait estimation, it achieves a grain voxel volume coefficient of determination R 2 = 0.7697 (Root Mean Square Error, RMSE = 0.0025), leaf surface area R 2 = 0.84 (RMSE = 18.93), and leaf length and width prediction accuracies of R 2 = 0.97 and R 2 = 0.87 (RMSE = 1.49 and 0.21). On a wheat dataset, IPENS further improves segmentation performance to a mIoU of 89.68%, with exceptional phenotypic estimation results: panicle voxel volume R 2 = 0.9956 (RMSE = 0.0055), leaf surface area R 2 = 1.00 (RMSE = 0.67), and leaf length and width predictions reaching R 2 = 0.99 and R 2 = 0.92 (RMSE = 0.23 and 0.15). Without requiring annotated data, IPENS rapidly extracts grain-level point clouds for multiple targets within three minutes using single-round image interactions. These features make IPENS a high-quality, non-invasive phenotypic extraction solution for rice and wheat, offering significant potential to enhance intelligent breeding.
Why it matches plant phenotyping methods植物形質抽出のためのNeRF-SAM2融合手法を開発し、作物データセットで分割性能と形質推定精度を検証しているため、方法開発・検証が中心である。
abstractThis study proposes IPENS, an interactive unsupervised multi-target point cloud extraction method.
Reproduction assets foundThe paper's analysis code is publicly available on GitHub. The rice/wheat MMR/MMW phenotype datasets (multi-view images, point clouds, annotations) are only available upon reasonable request, so they are not public.Code · publicCode is available at https://github.com/Vincent-Songwentao/IPENS-Code.git .Open asset ↗https://github.com/Vincent-Songwentao/IPENS-Code.gitlines:472-496Plant phenotyping relevance match · UnverifiedEurope PMC · checked 15 Sept 2026
Published1 Dec 2025Computers and Electronics in Agriculture.
Three-dimensional high-throughput plant phenotyping technology offers an opportunity for simultaneous acquisition of plant organ traits at the scale of plant breeders. Wheat, as a multi-tiller crop with narrow leaves and diverse spikes, poses challenges for organ segmentation and measurement due to issues such as occlusion and adhesion. Therefore, building on previous research, this paper establishes a phenotyping pipeline and develops a 3D phenotypic automated analysis system for individual wheat plants at different growth stages. This system enables automated and precise three-dimensional phenotypic acquisition and analysis of wheat plant architecture, spike morphology, and flag leaf traits. To address the challenges posed by the significant structural differences among wheat spikes, leaves, and stems, as well as their compact spatial distribution, we propose a point cloud segmentation model based on deep learning called ICFMNet. ICFMNet relies on an instance center feature matching module, which extracts features from each instance’s central region and matches them with global point-wise features by computing feature similarity. This approach enables precise instance mask generation independent of the spatial structure of the point cloud. In the analysis of wheat phenotypes, we introduce a contour-based method to accurately extract the barren segment from 3D-scale wheat spikes. Furthermore, we perform the analysis of a total of 19 phenotypes, including flag leaf phenotypes and whole-plant phenotypes. In the organ point cloud segmentation tests for wheat spikes, stems, and leaves, the semantic segmentation achieves mPrec, mRec, and mIoU values of 95.9 %, 96.0 %, and 92.3 %, respectively. The instance segmentation attains mAP and mAR scores of 81.7 % and 83.0 %, respectively. Moreover, in comparison to five other segmentation network models, ICFMNet demonstrates superior segmentation performance. To better assess barren segment localization accuracy, additional evaluations are conducted using two metrics: interval overlap and interval error, achieving values of 92.33 % and 0.1123 cm, respectively. Experimental results indicate that our method excels in terms of accuracy, efficiency, and robustness, providing a reliable systematic platform for precise identification and breeding research of wheat plant types. The source code and trained models for ICFMNet are available at https://github.com/xiao-pl/ICFMNet.
Why it matches plant phenotyping methods小麦個体・器官の3D形質を自動取得・抽出するセグメンテーションおよび解析パイプラインの開発と技術評価が研究の中心である。
abstractthis paper establishes a phenotyping pipeline and develops a 3D phenotypic automated analysis system for individual wheat plants at different growth stages.
Cost-effective remote sensing solutions are critically needed to democratize precision agriculture technologies. While hyperspectral and LiDAR systems deliver high accuracy, their prohibitive costs limit widespread adoption. This study demonstrates that systematic multi-modal feature integration transforms standard UAV-based RGB imagery into a powerful phenotyping instrument, achieving crop trait prediction accuracy comparable to systems costing 10–50 times more. We developed a comprehensive framework integrating spectral indices, geometric parameters, and texture metrics from commodity RGB sensors to predict five critical cotton traits: leaf area index (LAI), intercepted photosynthetically active radiation (IPAR), above-ground biomass, lint yield, and seed cotton yield. The progressive integration approach employed Random Forest regression with four feature configurations: baseline color indices (CIbₐₛₑ), refined color indices (CIᵣₑf), geometric parameters (CIᵣₑf + GP), and texture metrics (CIᵣₑf + GP + T). Field experiments across three trials over two growing seasons (2022–2023) with varying genotypes, planting densities, and sowing dates provided 2,126 ground truth measurements for model development and validation. The optimal multi-modal model achieved R² = 0.97 for IPAR (rRMSE = 6 %), R² = 0.91 for LAI (rRMSE = 15 %), and R² = 0.85 for biomass (rRMSE = 32 %), with lint yield and seed cotton yield demonstrating R² values of 0.92 and 0.77, respectively. Variance partitioning analysis revealed texture features as the dominant contributor (16.2 % ± 7.1 %), followed by spectral indices (9.1 % ± 4.2 %) and geometric parameters (8.0 % ± 2.8 %), with substantial shared variance (45–65 %) indicating strong feature complementarity. Phenological analysis demonstrated that flowering-stage imagery outperformed boll opening stage measurements, while stage-general models showed superior robustness. Cross-temporal validation confirmed model generalizability, with trial-general models achieving R² values of 0.91–0.97 for IPAR across diverse environmental conditions. The framework enables sub-meter spatial resolution trait mapping while maintaining operational simplicity and cost-effectiveness, demonstrating that systematic feature engineering can democratize high-precision phenotyping technologies for broader agricultural applications.
Why it matches plant phenotyping methodsUAV-RGB画像から複数の綿形質を推定する特徴統合フレームワークを開発・検証しており、形質取得・抽出手法が研究の中心である。
abstractThis study demonstrates that systematic multi-modal feature integration transforms standard UAV-based RGB imagery into a powerful phenotyping instrument
Cotton is a significant broadacre crop globally, and monitoring its growth is crucial for improving agricultural productivity. With the development of unmanned aerial vehicle (UAV) remote sensing technology, the inversion of cotton growth parameters (including plant height (PH), and leaf chlorophyll content (LCC), leaf area index (LAI), above-ground biomass (AGB)) from remote sensing data has emerged as a prominent research area. To address the issue of limited accuracy in traditional stacking algorithm for remote sensing inversion, this study proposes an enhanced stacking algorithm (ESA). First, multi-source remote sensing data is acquired using UAV equipment equipped with an integrated payload of a LiDAR sensor and a visual RGB camera and raw features are extracted from the data. Then, principal component analysis (PCA) is used to reduce the dimensionality of these features. The model construction is optimized through the following steps: first, explore all feature combinations and train each using multi-class learners to construct the entire set of base models; second, remove over- or under-fitting models to build a candidate pool; third, introduce iterative screening to the pool—each round incorporates the algorithm with the greatest performance gain and removes those with negative contributions, iterating to construct an efficient subset of base models; finally, RidgeCV is used to fuse base-model outputs. The experimental results show that ESA outperforms other traditional methods in terms of prediction performance for the four growth parameters. Specifically, on the test set, the R2 values for PH, LCC, LAI, and AGB are 0.9320, 0.8015, 0.8638, and 0.8272 , respectively. Compared with the second-best model, the relative improvement is approximately 4.6% (PH), 3.6% (LCC), 7.5% (LAI), and 11.2% (AGB) . ESA offers an effective approach for high-precision inversion of cotton growth parameters, providing new insights for the precision management of other crops.
Why it matches plant phenotyping methodsUAVのLiDAR・RGBデータから綿花の複数生育形質を推定するスタッキングアルゴリズムを開発し、他手法と性能比較しており、表現型取得・推定法が中心です。
abstractthis study proposes an enhanced stacking algorithm (ESA)
Accurate estimation of canopy geometric and structural characteristics, such as leaf area (LA), is essential for improving resource efficiency in fruit tree crop management. LA is a key biophysical parameter, influencing physiological processes like carbon fixation, evapotranspiration, and light interception, as well as fruit quality and yield. However, its measurement is complex due to the substantial number of leaves and the three-dimensional nature of tree canopies.An alternative approach, the Projected Tree Row Surface (PTRS), has shown a strong correlation with LA and has been recognized by the scientific community. Despite its robustness, the original PTRS method requires time-consuming manual data collection, which limits its practical application in the field.This study introduces a novel automated methodology for calculating the PTRS, validated using high-resolution ground-truth data providing LA values at 0.1-m intervals along the tree rows. When evaluated on almond, pear, and apple trees as well as vineyards, the method achieved remarkably high correlations between PTRS and LA, with coefficients up to r = 0.97 and r = 0.99 at optimal resolutions (0.1 –0.2 m PTRS per 1 m row section). These results demonstrate that the approach delivers consistent and reliable measurements of LA under diverse field conditions, enabling real-time, high-resolution assessment of tree-row canopies.The automated PTRSₙ approach enables fast and efficient LA estimation and can be adapted to any point cloud dataset. It supports flexible resolution to balance accuracy and processing time and can be applied to full rows, individual trees, or canopy segments. This methodology represents a step forward in automating LA assessment and supports the development of real-time applications in precision agriculture.
Why it matches plant phenotyping methods果樹・ブドウ樹冠の葉面積を推定するLiDARベースの自動PTRS手法を開発し、実測LAで検証しており、植物形質取得法が研究の中心である。
abstractThis study introduces a novel automated methodology for calculating the PTRS, validated using high-resolution ground-truth data providing LA values at 0.1-m intervals along the tree rows.
Accurately estimating individual plant evapotranspiration is essential for precise management and sustainable resource use in greenhouse cultivation. Integrating evapotranspiration models with crop-monitoring devices capable of acquiring images and solar radiation data may enable plant-level estimation of crop evapotranspiration. In this study, a plant-specific crop evapotranspiration estimation system was developed for hydroponic tomato cultivation in greenhouses during the harvest season. The evapotranspiration was estimated using a simplified Penman–Monteith model based on the leaf area index (LAI), solar radiation, air temperature, and relative humidity. The model was subsequently generalized through z-score normalization. To acquire side-view RGB images of individual tomato plants and measure the solar radiation distribution, a rail-based crop-monitoring device was employed. A ResNet-based convolutional neural network model was developed to estimate the LAI from the acquired images. The images were augmented via permutations with repetition to enhance the model’s accuracy. An image-merging method and a You Only Look Once version 8 Nano-based object detection model were used for rapid and automated image acquisition. The system calculated the crop evapotranspiration for each plant, and its performance was evaluated in a tomato cultivation greenhouse. Validation tests revealed strong correlations between the estimated and measured LAI (R² = 0.89, RMSE = 0.06) and between the predicted and actual evapotranspiration values (R² = 0.88, RMSE = 26.43 g h⁻¹ plant⁻¹). Distribution maps for the LAI and evapotranspiration were generated using the developed system. The system can accurately assess plant-specific evapotranspiration, thereby supporting precision crop management and helping improve productivity in greenhouse cultivation.
Why it matches plant phenotyping methods個体別のLAI画像推定と蒸発散量推定を中核とする監視システムを開発し、実測値との相関で検証しているため、植物表現型取得・推定手法として対象に含める。
abstracta plant-specific crop evapotranspiration estimation system was developed for hydroponic tomato cultivation in greenhouses
Plant density is an important variable for management and phenotyping of small-grain cereal crops such as wheat and barley. While many image-based estimation methods exist to replace laborious manual counting, most of them rely on empirical relationships that may not generalize well to different sites, growth stages, species and varieties. In this study, we propose a novel small-grain cereal plant density estimation method that uses leaf tip density dynamics derived from submillimeter-scale images acquired at 45° view zenith angle. This method contained two steps. In the first step, a P2PNet deep learning detection model was trained to estimate leaf tip count in a surface of known area to get the leaf tip density. An occlusion correction method was then applied on this density, leading to an estimation error of about 20% at critical growth stages. In the second step, a wheat leaf dynamic model was used to simulate the evolution of leaf tip density over thermal time as functions of several variables, including mean time of plant emergence, phyllochron and plant density. This model was then inverted using a lookup table approach to estimate plant density from leaf tip density dynamics. The results obtained on three test datasets indicated that two observations performed before the appearance of the second and third leaves could be sufficient to attain a relative plant density estimation error of about 10%. We also discussed that this method should be able to work on other datasets without recalibration, and estimate other variables such as phyllochron at early growth stages. The code will be available at: https://github.com/wdwzytc/WheatPlantDensity.
Why it matches plant phenotyping methodsRGB画像から葉先密度を抽出し、植物密度を推定する画像ベースの表現型計測法を開発・評価しており、方法が研究の中心である。
abstractwe propose a novel small-grain cereal plant density estimation method that uses leaf tip density dynamics derived from submillimeter-scale images
Under the dual pressures of food security and sustainable agricultural development, rapid and simultaneous detection of multiple crop growth parameters has become a core technological requirement for optimizing field management and improving resource utilization efficiency. UAVs carrying one or more sensors to collect of different crop growth parameters have achieved remarkable results in the field of single morphological or physiological parameter analysis. However, existing low-cost devices often failed to collect 3D geometric data and high-resolution spectral information simultaneously in field conditions, while the different nature and data structure of point cloud and spectral data brought special challenges to data fusion, restricting the ability of simultaneous multi-parameter resolution. Facing such challenges, in this paper, we design and develop a system that can take into account the simultaneous acquisition of 3D geometric data and high-resolution spectral information in field conditions through multi-sensor fusion and deep learning algorithm innovation. Based on a mature color point cloud data structure, we combine RGB cameras and laser radar sensors to fuse RGB images and point cloud data. We improved a spectral reconstruction network, construct a dedicated chlorophyll response sensitive band dataset for training, and reconstructed hyperspectral images with 36 channels in the 500–850 nm band range from RGB images, which greatly reduces the cost of the spectral information acquisition device. Experiments show that the SAM (Spectral Angle Mapper) value between the reconstructed hyperspectral data and the original hyperspectral data is less than 0.03. Finally, the growth parameters of crops are estimated using spectral and point cloud data. The developed equipment was calibrated and tested, and experimental data were collected under real field conditions for plant height (PH), leaf area index (LAI), and chlorophyll content estimation. The experimental results showed that the system could accurately analyze maize PH and LAI with Rt2 of 0.98 and 0.97, respectively, and that the chlorophyll content analysis capability was at the same level as that of other studies that have used UAV-mounted hyperspectral cameras for leaf chlorophyll content (LCC) detection, and the established estimation model Rt2 reached 0.66. The canopy chlorophyll content (CCC) of maize could be accurately estimated by fusing the data, and the Rt2 reached 0.95.
Why it matches plant phenotyping methodsRGB画像・LiDAR融合と深層学習による3D形状およびハイパースペクトル情報の再構成システムを開発し、圃場で植物形質推定を校正・検証しており、フェノタイピング手法が中心である。
abstractin this paper, we design and develop a system that can take into account the simultaneous acquisition of 3D geometric data and high-resolution spectral information in field conditions through multi-sensor fusion and deep learning algorithm innovation.
As an economically important crop, tobacco requires the precise extraction of phenotypic characterization data, which is crucial for breeding, cultivation practices, physiological research, and industrial applications. However, there is currently a lack of automated algorithms for extracting key basic phenotypic traits such as plant height, leaf number, leaf area, and stem-leaf angle. In this study, we developed a set of computational methods for fully automated extraction of these phenotypic features from 3D tobacco point cloud data. Specifically, our pipeline includes: (1) preprocessing the 3D point cloud data, involving operations such as downsampling, denoising, normal vector estimation, and coordinate transformation; (2) integrating a graph neural network with a region-growing algorithm to segment leaves, stems, and other organs, and refining the segmentation results to address the challenge of overlapping leaves; and (3) calculating fundamental phenotypic attributes including plant height, leaf count, leaf area, and stem-leaf angle based on the segmentation output. Additionally, to address potential gaps in the scanned point cloud, we implemented perforation detection and repair operations. The effectiveness and accuracy of the proposed algorithm were validated through mathematical model simulations. Distinct from traditional statistical discriminative methods, this approach provides a novel framework for the precise extraction of tobacco phenotypic data.
Why it matches plant phenotyping methods3D点群から植物器官を分割し、草丈・葉数・葉面積・茎葉角を自動抽出する計算手法の開発と検証が中心である。
abstractwe developed a set of computational methods for fully automated extraction of these phenotypic features from 3D tobacco point cloud data.
Accurate crop monitoring is essential for agricultural planning and food security. This study developed a coupling framework of unmanned aerial vehicle (UAV) multimodal data and crop models based on a sequential data assimilation method, offering technical support for crop growth simulation and precision management under drip irrigation modes in the Hexi Corridor of Northwest China. Multispectral and thermal infrared image data of spring maize at different growth stages were acquired via UAVs. The UAV-derived leaf area index (LAI) and soil moisture (SM) were assimilated into the WOFOST model using the ensemble Kalman filter (EnKF). Three assimilation schemes including (a) LAI, (b) SM, and (c) LAI+SM were compared to explore the effects of different mulching treatments (mulched vs. non-mulched) and irrigation gradients on assimilation performance under drip irrigation modes. Our results showed that the fusion of UAV-based multispectral and thermal infrared multimodal data enabled accurate retrieval of LAI and SM, with a maximum R² of 0.85. The three assimilation schemes exhibited significant differences, and the joint assimilation of LAI and SM outperformed the others. This may be since LAI and SM, as key indicators of crop growth and development, undergo dynamic changes throughout the growth period, and their joint assimilation fully captures the temporal variability of crops and soil. In addition, the proposed framework demonstrated marked variations in simulation accuracy across different drip irrigation modes. Overall, the performance for shallow buried drip irrigation (SBDI) was superior to that for surface drip irrigation (SDI) and film-mulched drip irrigation (FDI). This may be attributed to the direct influence on soil evaporation and evapotranspiration under the latter two modes, which in turn modifies crop growth and development processes and ultimately affects the model's simulation accuracy.
Why it matches plant phenotyping methodsUAVマルチスペクトル・熱赤外データからLAIを推定し、作物モデルへ同化する手法の開発と性能比較が研究の中心であり、植物形質取得の技術的評価を含む。
abstractThis study developed a coupling framework of unmanned aerial vehicle (UAV) multimodal data and crop models based on a sequential data assimilation method
Crop models are an integral component in greenhouse control systems, enabling the simulation of plant responses to environmental conditions and facilitating optimal operational decisions for high productivity with low energy use. However, existing crop models often lack transferability beyond their original development conditions. Additionally, cultivar-specific parameterization remains challenging, as some parameters can be empirically determined while others require complex calibration. This study adapted the reduced TOMGRO model to simulate growth and yield for four local tomato cultivars under Shanghai greenhouse conditions. Through Sobol’s global sensitivity analysis and Bayesian optimization, four highly influential parameters were identified and optimized, including growth efficiency (E), maintenance respiration coefficient (rₘ), extinction light coefficient (K), and leaf quantum efficiency (Qₑ). This combined approach provides an effective framework for model calibration, with the calibrated model achieving an average R² > 0.94 for node number, plant dry weight, fruit dry weight, and leaf area index predictions in all cultivars. Model validation using 2023–2024 greenhouse data confirmed model effectiveness for the target variables (average R² > 0.92 for cultivar QX and > 0.88 for LZ), whereas the model showed limitations in simulating mature fruit growth. This calibrated model offers reliable predictions of key growth variables, informing both plant breeding and greenhouse management.
Why it matches plant phenotyping methods作物モデルの感度分析・ベイズ最適化によるパラメータ校正と、植物成長形質予測の検証が研究の中心であり、再利用可能な計算フェノタイピング手法に該当する。
abstractThrough Sobol’s global sensitivity analysis and Bayesian optimization, four highly influential parameters were identified and optimized
We constructed a computational methodology to assess health of plant-microbiome system through microbiome structure modelling combined with plant remote sensing. As a test dataset, we selected soil mycobiome and morphometry of Tilia cordata in nursery and forest sites. Our method is also applicable on forest or regional scale. Microbiome part called GiaC ( G u i lds a nd o C currences) combines taxonomic and trophic composition as well as species co-occurrence modelled with advanced graph methods. We complemented state-of-the-art approaches with novel ones for visualisations, species filtering (Flexible99) and graph transformation modelling species clusters (ClusterCollapse). Flexible99 is a method that adjusts the species abundance cut-off to each sample set and removes rare species. ClusterCollapse generalises co-occurrence networks to species clusters by edge contraction and serves as an implicit homogeneity test. To assess biomass of the seedlings we used low-cost and field-adopted morphometric and manual measurements. Top and side tree images, acquired with handheld RGB camera, were analysed using colour segmentation and pixel count based methods. Parameters, such as crown size, shape, area and pigment content, number of leaves, branch length and foliage density, allowed the seedlings to be classified into three different vitality groups. Presented multimodal approach was capable to differentiate and characterize distinct best, suboptimal or critical states of microbiome-host system, both on microbial and plant side. Our results show that more stable fungal co-occurrence patterns should be attributed to the plant set of the best growth. In contrast, more chaotic patterns can be considered non-optimal for plant-mycobiome cooperation.
Why it matches plant phenotyping methods植物の健康・活力状態を推定するマルチモーダル手法の一部として、RGB画像の色分割・画素計数から樹冠形状、葉数、枝長、葉密度などの形質を抽出しており、フェノタイピング手法の適用が実質的に含まれる。
abstractWe constructed a computational methodology to assess health of plant-microbiome system through microbiome structure modelling combined with plant remote sensing.
Crop status forecasting by crop model simulations can benefit from assimilating remote sensing observations. When conducting data assimilation (DA) using a common procedure – the Ensemble Kalman Filter (EnKF), arbitrary inflation factors are normally adopted to account for unspecified uncertainties, so as to alleviate filter divergence. Here, we developed a more effective Bayesian methodology, in which the uncertainties were systematically quantified by combining multiple methods in one framework. Its applicability and performance in the EnKF were tested using the crop model GECROS (Genotype-by-Environment interaction on CROp growth Simulator) and the data collected from two years of field experiments for rice. Aboveground biomass (Wₐbₒᵥₑ), grain weight (Wgᵣₐᵢₙₛ), aboveground nitrogen (N) content (Nₐbₒᵥₑ), grain N content (Ngᵣₐᵢₙₛ) and leaf traits like leaf dry weight, leaf N content and leaf area index were measured in the experiments. Using only the observations from the first year, the uncertain parameters in GECROS were calibrated by a Markov Chain Monte Carlo approach, while the parameters in the uncertainty model that describes the errors of crop model simulations were estimated simultaneously. The calibrated model parameters performed well in the validation year, except for the simulated leaf traits (Normalized Root Mean Squared Error (NRMSE) > 0.38). Remotely sensed leaf traits predicted by a Gaussian Process Regression (GPR) model were more accurate (NRMSE < 0.32), with uncertainties of the remote sensing observations estimated from the GPR model itself. Assimilating simulated and predicted leaf traits with their estimated uncertainties into EnKF prevented filter divergence, and the forecast accuracy of crop model improved in the validation year. Compared with simulation without assimilating in-season remote sensing observations, the assimilation procedure led the NRMSE to decrease from 0.37 to 0.20 for whole-season Wₐbₒᵥₑ and Nₐbₒᵥₑ and from 0.39 to 0.20 for the end-season Wgᵣₐᵢₙₛ and Ngᵣₐᵢₙₛ. The updated crop traits of our method also agreed better with the measurements than those of common EnKF with arbitrarily assumed uncertainties and with adjusted inflation factors. The developed method contributes to systematic uncertainty analysis in DA and accurate forecasting of crop growth and yield for smart farming.
Why it matches plant phenotyping methodsリモートセンシングから葉形質を推定し、その不確実性を定量化してデータ同化する計算手法が研究の中心であり、植物形質推定・予測ワークフローとして評価されている。
abstractRemotely sensed leaf traits predicted by a Gaussian Process Regression (GPR) model were more accurate (NRMSE < 0.32), with uncertainties of the remote sensing observations estimated from the GPR model itself.
PURPOSE: Climate change, increasing aridity, water scarcity and population growth, enhancing food demand and irrigated land expansion, are expected to increase the extent of salinity-affected areas. This study aims to combine the crop-energy-water balance model FEST-EWB-SAFY with Leaf Area Index (LAI) and Land Surface Temperature (LST) data from remote sensing to monitor maize development in a field with a shallow water table and highly affected by salinity. METHODS: The FEST-EWB-SAFY model couples the distributed energy-water balance FEST-EWB model, which computes time-continuous soil moisture and evapotranspiration, and the SAFY crop model for yield prediction. The model was employed in synergy with satellite observations of LST and LAI. LST was used for the calibration/validation of the water and energy balances, whereas LAI was used both for the calibration of crop parameters and a data assimilation scheme. RESULTS: The data assimilation scheme was able to reproduce the observed spatial heterogeneity in crop development, associated to the uneven water table depth and salinity distribution, as these effects were picked up from satellite. A good correspondence was also found between modelled yield and the distributed samplings from a combined harvester equipped with a yield monitor. CONCLUSION: The results, comparable to those obtained with the a posteriori calibration, show that data assimilation of remote sensing observations allow to improve the model as the agricultural season progresses, including information which is difficult to monitor continuously in-situ.
Why it matches plant phenotyping methods衛星リモートセンシングによるLAI・LST観測を作物モデルに同化し、圃場内のトウモロコシの発達と空間的不均一性を推定する技術的ワークフローが中心である。
abstractThe model was employed in synergy with satellite observations of LST and LAI.
The purpose of this study is to develop and evaluate a multi-modal fusion model that integrates image and environmental data collected from a vertical farm to accurately predict crop growth stages and growth rates. RGB images and key environmental parameters, including CO₂ concentration, temperature, relative humidity, and light intensity, were synchronously collected over a defined period at a vertical farm test site, and a multi-modal training dataset was constructed through preprocessing and feature extraction. Leaf area, greenness, shape indices, and proxy VI were extracted from the image data, while the temporal variations of the environmental sensor data were modeled using a long short-term memory (LSTM) network. These were then merged with convolutional neural network (CNN)–based image features to perform simultaneous growth stage classification and growth rate prediction.
Why it matches plant phenotyping methods画像特徴量と環境センサーデータを融合し、葉面積・緑色度・形状指標などの植物形質から生育段階と生育速度を推定する手法の開発・評価が中心である。
abstractThe purpose of this study is to develop and evaluate a multi-modal fusion model that integrates image and environmental data collected from a vertical farm to accurately predict crop growth stages and growth rates.
This study analyzes the evolution of phenological (start-of-season, end-of-season, length-of-season, day of maximum-of-season) and productivity (small and large seasonal integrals) parameters for six major crop types in Czechia (winter cereals, spring cereals, winter rapeseed, fodder crops, sugar beetroot, and corn), using a 35-year Landsat time series (1986–2020). The leaf area index (LAI) was retrieved using an artificial neural network regression model trained on PROSAIL radiative transfer simulations and validated with extensive in situ measurements collected in 2017 and 2018 in the lowlands of Central Bohemia. The supervised classification of Landsat quarterly composites enabled the identification of crop spatial patterns for each growing season. Phenological and productivity indicators were then derived from LAI time series aggregated at the level of ten agro-climatic regions using the threshold approach. Changes in phenological and productivity parameters over the examined period were assessed through the linear least squares regression analysis and the significance of trends was tested. Results revealed significant negative trends in the end-ofseason and day of maximum-of-season for winter and spring cereals, winter rapeseed (up to –0.7 days/year), and fodder crops (up to –1.6 days/year), indicating an earlier maturation and harvest. Significant differences in trends in phenological and productivity parameters were observed between agro-climatic regions in more than 40% of cases, and the response was observed to be highly crop-specific. While the shift in harvest dates and the shortening of the season for corn and fodder crops were more pronounced in warmer regions, the shift in winter rapeseed phenology occurred more rapidly in colder regions. The findings underscore the relevance of crop type and regional climate in shaping phenological responses, offering a basis for future research and planning of agricultural adaptation strategies.
Why it matches plant phenotyping methodsLandsatからLAIを推定し、作物のフェノロジー・生産性形質を抽出するリモートセンシング手法を、PROSAIL/ANNモデルと現地測定で検証しており、形質取得ワークフローが主要な役割を担う。
abstractThe leaf area index (LAI) was retrieved using an artificial neural network regression model trained on PROSAIL radiative transfer simulations and validated with extensive in situ measurements collected in 2017 and 2018 in the lowlands of Central Bohemia.
Introduction: Leaf morphology is vital for plant identification, but traditional methods are subjective and inconsistent. Methods: This pilot study presents an image analysis pipeline for Pithecellobium dulce leaves using ImageJ and MATLAB. Steps included grayscale conversion, Sobel/Canny edge detection, GLCM texture analysis, and SSIM comparison. Results: Canny edge detection showed higher edge density than Sobel. Texture metrics were consistent, and SSIM scores (0.6700–0.699) indicated high structural similarity among leaves. Discussion: Canny edge detection captured finer venation than Sobel, while GLCM and SSIM confirmed strong structural similarity among leaves. The pipeline demonstrated reproducible, objective, and scalable quantification of leaf morphology, reducing observer bias and enabling automated phenotyping. Conclusion: The pipeline offers reproducible, objective leaf analysis, reducing bias and supporting applications in taxonomy and digital phenotyping.
Why it matches plant phenotyping methods葉形態を画像解析で自動・再現可能に定量化するパイプラインの開発が中心であり、植物フェノタイピング手法に該当する。
abstractThis pilot study presents an image analysis pipeline for Pithecellobium dulce leaves using ImageJ and MATLAB.
Accurate plant organ segmentation and efficient phenotypic parameter acquisition remain major challenges in plant phenomics. This study develops an automated phenotyping framework for maize that integrates deep learning with 3D point cloud analysis to overcome the inefficiency and subjectivity of traditional manual methods. A high-quality 3D maize point cloud dataset was constructed, and a segmentation model named PSCSO was proposed based on the PointNet++ architecture. The model incorporates an SCConv module to reduce feature redundancy and uses the Sophia optimizer to improve convergence efficiency. Experimental results show the model achieved segmentation accuracies of 0.926 on the training set and 0.861 on the testing set, with a MIoU of 0.843, while significantly reducing training time. Based on the segmentation results, the model automatically estimates seven key phenotypic parameters: plant height, crown diameter, stem height, stem diameter, leaf length, leaf width, and leaf area. This is achieved by integrating point cloud algorithms including linear regression, PCA, and Delaunay triangulation. The predictions showed excellent agreement with manual measurements, with all parameters achieving R2 values exceeding 0.91. Overall, this automated framework provides a reliable and high-throughput solution for plant phenotypic analysis.
Why it matches plant phenotyping methods3D点群と深層学習によるトウモロコシ器官セグメンテーションおよび7種類の表現型形質推定を開発・検証した研究であり、フェノタイピング手法が中心である。
abstractThis study develops an automated phenotyping framework for maize that integrates deep learning with 3D point cloud analysis
Drought stress poses a significant threat to rice production, particularly in indica cultivars that form the staple diet for a large portion of the world's population. Efficient and reliable screening methods are essential to accelerate the development of drought-tolerant rice varieties. The objective of the study was to assess and validate the efficacy of the Drought Tolerance Degree (DTD) method for early-stage drought tolerance screening in a diverse population of 118 doubled haploid (DH) indica rice lines and their parents. Plants were subjected to controlled severe drought stress under pot culture in a net house environment, and drought responses were assessed using DTD method alongside key physiological traits including relative water content (RWC), chlorophyll content index, leaf rolling and drying scores, leaf canopy temperature, leaf area, tiller and leaf numbers, and plant height. The DTD values exhibited strong positive correlations with RWC (r = 0.771) and chlorophyll content (r = 0.526), and strong negative correlations with leaf rolling (r = -0.850), leaf drying scores (r = -0.778), canopy temperature, and tiller number. Principal component and hierarchical clustering analyses further confirmed the association of DTD with drought tolerance-related traits and effectively discriminated tolerant and susceptible genotypes. In comparison with traditional methods, the DTD assay is cost-effective, rapid, and requires minimal technical expertise, making it practical for high-throughput screening in breeding programs. However, its applicability is limited to early growth stages due to the confounding effects of natural leaf senescence at maturity. Overall, this work demonstrates the reliability and efficiency of the DTD method in assessing drought tolerance in indica rice, offering a valuable phenotyping tool to facilitate the selection of drought-resilient cultivars in breeding pipelines.
Why it matches plant phenotyping methodsDTD法をイネの乾燥耐性表現型スクリーニングに用い、その有効性・信頼性を検証した研究であり、表現型取得法が中心です。
abstractThe objective of the study was to assess and validate the efficacy of the Drought Tolerance Degree (DTD) method for early-stage drought tolerance screening
The accurate three-dimensional (3D) distribution of plant area density (PAD) within forests is crucial for understanding canopy structure and provides essential scene inputs for 3D Radiative Transfer Models (RTMs) to facilitate remote sensing interpretation. However, current lidar-based voxelization methods that estimate detailed PAD distributions often cover limited areas, constraining their applications in conducting broad forest studies and interpreting Earth Observation Satellite (EOS) data of various scales and resolutions. To address this, we developed the Large-Scale Path Volume Leaf Area Density (LS-PVlad), a novel forest 3D reconstruction workflow capable of producing extensive high-resolution 3D voxelized forest scenes (up to 100 km 2 with ≤2 m voxel size) from worldwide open-access airborne lidar scanning (ALS) data. By applying LS-PVlad to the ALS data acquired during the extensive NASA Goddard's LiDAR, Hyperspectral & Thermal Imager (G-LiHT) campaigns, we developed the first release of FoScenes—a high-fidelity PAD product comprising 40 seamless scenes from 28 diverse forest sites, with individual area ranging from ∼50 to ∼11,000 ha. The leaf area estimates of LS-PVlad have been validated by two-year field-measured leaf area index (LAI) from litter collection (best RMSE = 0.35 m 2 /m 2 ) and digital hemispherical photography (DHP) images (RMSE = 0.46 m 2 /m 2 ) across multiple plots at a deciduous forest site. Additionally, a broad comparison between FoScenes and MODIS plant/leaf area index product demonstrates high consistency (R 2 = 0.70, RMSE = 0.86 m 2 /m 2 ). By providing multi-dimensional forest characterizations, FoScenes enables temporal insights into structure dynamics. Its integration with the discrete anisotropic radiative transfer (DART) model underscores the potential of FoScenes for extensive 3D RTM applications at various scales. • We developed a large-scale ALS-data-driven 3D forest reconstruction workflow. • FoScenes product consists of 40 various forest scenes derived from NASA G-LiHT data. • The estimated leaf/plant area index strongly aligns with field data and EOS products. • FoScenes captures temporal structure variation by multi-dimensional characterization. • FoScenes can be integrated into DART for realistic simulations at varied scales.
Why it matches plant phenotyping methods森林の植物面積密度・葉面積指数を推定するALSベースの3D再構成ワークフローを開発し、実測LAI等で検証した方法・データセット研究であり、植物形態の取得が中心です。
abstractwe developed the Large-Scale Path Volume Leaf Area Density (LS-PVlad), a novel forest 3D reconstruction workflow
Introduction The Leaf Area Index (LAI) is a critical biophysical parameter for assessing crop canopy structure and health. Unmanned Aerial Vehicles (UAVs) equipped with multispectral sensors offer a high-throughput solution for LAI estimation, but flight altitude compromises between efficiency and image resolution, ultimately impacting accuracy. This study investigates the integration of super-resolution (SR) image reconstruction with multi-sensor data to enhance LAI estimation for soybeans across varying UAV flight altitudes. Methods RGB and multispectral images were captured at four flight altitudes: 15 m, 30 m, 45 m, and 60 m. The acquired images were processed using several SR algorithms (SwinIR, Real-ESRGAN, SRCNN, and EDSR). Texture features were extracted from the RGB images, and LAI estimation models were developed using the XGBoost algorithm, testing data fusion strategies that included RGB-only, multispectral-only, and a combined RGB-multispectral approach. Results (1) SR performance declined with increasing altitude, with SwinIR achieving superior image reconstruction quality (PSNR and SSIM) over other methods. (2) Texture features from RGB images showed strong sensitivity to LAI. The XGBoost model leveraging fused RGB and multispectral data achieved the highest accuracy (relative error: 4.16%), outperforming models using only RGB (5.25%) or only multispectral data (9.17%). (3) The application of SR techniques significantly improved model accuracy at 30 m and 45 m altitudes. At 30 m, models incorporating Real-ESRGAN and SwinIR achieved an average R 2 of 0.86, while at 45 m, these methods yielded models with an average R 2 of 0.77. Discussion The results demonstrate that the fusion of SR-reconstructed imagery with multi-sensor data can effectively mitigate the negative impact of higher flight altitudes on LAI estimation accuracy. This approach provides a robust and efficient framework for UAV-based crop monitoring, enhancing data-driven decision-making in precision agriculture.
Why it matches plant phenotyping methodsUAV画像の超解像・マルチセンサー融合・機械学習を用いて、植物キャノピー形質であるダイズLAIの推定手法を開発・評価しており、フェノタイピング手法が中心です。
abstractThis study investigates the integration of super-resolution (SR) image reconstruction with multi-sensor data to enhance LAI estimation for soybeans across varying UAV flight altitudes.
Leaf area index (LAI) is a critical indicator of canopy architecture and physiological performance, serving as a key parameter for crop growth monitoring and management. Although UAV multispectral imagery provides rich spectral and spatial information, the limitations of single texture features for LAI estimation still require further exploration. To address this issue, this study developed a multi-source feature fusion framework that integrates vegetation indices (VIs), texture features (TFs), and texture indices (TIs) within a stacked ensemble approach combining Partial Least Squares Regression (PLSR) with Support Vector Machine (SVM), Random Forest (RF), and Gradient Boosting Decision Tree (GBDT) algorithms to estimate maize LAI.A field experiment was conducted under three planting densities (42,000, 63,000, and 84,000 plants ha -1 ) and four nitrogen rates (0, 80, 160, 240 kg N ha -1 ) to assess the potential of UAV-based multispectral imagery for maize LAI estimation. The results show that when using partial least squares regression (PLSR) combined with RF, SVM and GBDT to estimate maize LAI, the R 2 values are 0.653, 0.697 and 0.634, and the RMSE is 0.650, 0.608 and 0.668, respectively, when only vegetation indices (VIs) is used as input. After texture features (TFs) incorporation, the R 2 increases to 0.717, 0.794, and 0.801, and the RMSE decreases to 0.587, 0.500, and 0.492. Further inclusion of the texture indices (TIs) raises the R 2 to 0.789, 0.804, and 0.844, with RMSE of 0.506, 0.489, and 0.436, respectively. Independent test set validation under contrasting conditions confirmed that our multi-model fusion framework (PLSR+GBDT) with multi-source feature fusion (VIs+TFs+TIs) effectively estimated LAI, achieving an R 2 of 0.859 and 0.794. These results demonstrate that multi-source feature integration via machine learning enables robust and accurate estimation of maize LAI, providing a valuable tool for precision agriculture and crop growth monitoring.
Why it matches plant phenotyping methodsUAVマルチスペクトル画像と機械学習によるトウモロコシLAI推定手法を開発・検証しており、植物形態・生理状態の定量的推定が研究の中心である。
abstractthis study developed a multi-source feature fusion framework that integrates vegetation indices (VIs), texture features (TFs), and texture indices (TIs) within a stacked ensemble approach
Plant phenotyping relevance match · UnverifiedCrossref · Europe PMC · checked 6 Sept 2026
Growth chamberLeafClassificationCountingObject detectionGrowth / development / phenologyLeaf traits
Climate change, shrinking arable land, urbanization, and labor shortages increasingly threaten stable crop production, attracting growing attention toward AI-based indoor farming technologies. Accurate growth stage classification is essential for nutrient management, harvest scheduling, and quality improvement; however, conventional studies rely on time-based criteria, which do not adequately capture physiological changes and lack reproducibility. This study proposes a phenotyping-based and physiologically grounded growth stage classification pipeline for basil. Among various morphological traits, the number of leaf pairs emerging from the shoot apex was identified as a robust indicator, as it can be consistently observed regardless of environmental variations or leaf overlap. This trait enables non-destructive, real-time monitoring using only low-cost fixed cameras. The research employed top-view images captured under various artificial lighting conditions across seven growth chambers. YOLO automatically detected multiple plants, followed by K-means clustering to align positions and generate an individual dataset of crop images–leaf pairs. A regression model was then trained to predict leaf pair counts, which were subsequently converted into growth stages. Experimental results demonstrated that the YOLO model achieved high detection accuracy with mAP@0.5 = 0.995, while the A convolutional neural network regression model reached MAE of 0.13 and R² of 0.96 for leaf pair prediction. Final growth stage classification accuracy exceeded 98%, maintaining consistent performance in cross-validation. In conclusion, the proposed pipeline enables automated and precise growth monitoring in multi-plant environments such as plant factories. By relying on low-cost equipment, the pipeline provides a technological foundation for precision environmental control, labor reduction, and sustainable smart agriculture.
Why it matches plant phenotyping methodsバジルの葉対数という植物形質を低コストカメラ画像から自動推定し、生育段階へ分類する画像解析パイプラインを開発・評価しており、フェノタイピング手法が中心である。
abstractThis study proposes a phenotyping-based and physiologically grounded growth stage classification pipeline for basil.
The possibility of using the phytoindication method to study the stability of plant development is considered. The study is carried out on plants of Alchemilla baltica, in which morphological (length of veins) and optical (transmission coefficients in the visible range) signs of leaf surface areas are measured. The indices of fluctuating asymmetry are determined based on morphological and optical features. A fluctuometer is developed that allows non-contact method to obtain information about the fluctuating asymmetry of the light transmission coefficient by leaf tissues as a bilateral feature. The fluctuometer measurement scheme is based on the alternate determination of illumination created by a light stream falling from above passing through sections of a plant leaf located symmetrically to the left and right of its central vein. A strong linear relationship is revealed between the data obtained for the two types of features (Pearson correlation coefficient 0.86), which is confirmed by the value of the coefficient of determination of the linear model is 0.74; the value of the coefficient of concordance is 0.7. Thus, the proposed method and device make it possible to implement an express method of phytoindication of the environment.
Why it matches plant phenotyping methods葉の形態・光学的特徴から植物発生の安定性を評価する非接触測定装置（フルクチュオメータ）を開発し、既存特徴との相関で検証しており、植物フェノタイピング手法が中心である。
abstractA fluctuometer is developed that allows non-contact method to obtain information about the fluctuating asymmetry of the light transmission coefficient by leaf tissues as a bilateral feature.
Leaf counting has numerous applications in plant phenotyping, such as plant growth analysis, yield prediction, and disease detection. However, manual counting is labor-intensive and time-consuming, posing a significant limitation. To address this issue, deep learning-based object detection models are implemented for automated leaf counting. Existing works that explore automated leaf counting are limited due to the inherent structure of plants, e.g., plants are small and occur in overlapping clusters, causing the models to perform sub-optimally. Furthermore, the numerous amount of object detection models introduces a problem of choosing the proper model. Currently, there is limited understanding in determining which object detection architectures perform well for automated leaf counting, particularly when dealing with complex plant anatomy. To address the gap in the literature, three foundational object detection models with different characteristics are compared: YOLOv8, YOLOv12, and Faster R-CNN. The three models chosen display key distinctions such as one-stage vs. two-stage detections and convolution-based vs. attention-based. To provide comprehensive results, multiple optimization techniques were applied to each model. Our experimental results showed that YOLOv8 had the best performance on all performance metrics (mAP50, mAP5095, IOU, MAE, and MAPE). Specifically, YOLOv8 achieved an IOU of 0.6412, while YOLOv12 and Faster R-CNN only achieved an IOU of 0.567 and 0.606, respectively.
Why it matches plant phenotyping methods植物の葉数という形態形質を対象に、重なり葉条件下での自動計数手法として複数の物体検出モデルを比較・最適化し、性能評価しているため、方法比較・検証が中心です。
abstractdeep learning-based object detection models are implemented for automated leaf counting
The study was conducted in the month of August, 2023 at the College of Forestry, Kerala Agricultural University, Kerala, India to identify the peak drought stress period and optimize phenotyping techniques for drought tolerance screening in teak seedlings under tropical humid conditions. The experiment subjected eight-month-old vegetatively propagated teak seedlings to controlled drought conditions over 20 days. Morpho-physiological parameters such as number of leaves, relative water content (RWC), photosynthetic rate, stomatal conductance, transpiration rate, and chlorophyll fluorescence were monitored bi-daily. The results revealed that the 9th and 10th days after withholding irrigation marked the maximum drought stress period, with significant reductions in photosynthesis (0.372 mole CO2 m-2 s-1), stomatal conductance, and RWC (51.14%). Biochemical analysis showed increased levels of proline, glycine betaine, and total soluble sugars, confirming stress adaptation. Upon rewatering, partial recovery was observed in physiological traits, while biochemical markers indicated ongoing stress response adjustments. Correlation and regression analyses highlighted strong interrelations between photosynthesis and traits such as stomatal conductance, RWC, and chlorophyll fluorescence. The findings were revalidated through repeated trials, confirming the 10th day as the optimal time for drought phenotyping in teak seedlings in given condition. This study enhances our understanding of teak’s drought response and offers critical insights for breeding programs and sustainable plantation management strategies.
Why it matches plant phenotyping methods乾燥ストレス評価におけるフェノタイピング時期・手法の最適化を主題とし、反復試験で再検証しているため、単なる生理測定ではなく方法開発・検証に該当する。
abstractidentify the peak drought stress period and optimize phenotyping techniques for drought tolerance screening in teak seedlings
In modern agricultural production, accurate monitoring of maize growth and leaf counting is crucial for precision management and crop breeding optimization. Current UAV-based methods for detecting maize seedlings and leaves often face challenges in achieving high accuracy due to issues such as low spatial-resolution, complex field environments, variations in plant scale and orientation. To address these challenges, this study develops an integrated detection and visualization software, DP-MaizeTrack, which incorporates the DP-YOLOv8 model based on YOLOv8. The DP-YOLOv8 model integrates three key improvements. The Multi-Scale Feature Enhancement (MSFE) module improves detection accuracy across different scales. The Optimized Spatial Pyramid Pooling-Fast (OSPPF) module enhances feature extraction in diverse field conditions. Experimental results in single-plant detection show that the DP-YOLOv8 model outperforms the baseline YOLOv8 with improvements of 3.9% in Precision (95.1%), 4.1% in Recall (91.5%), and 4.0% in mAP50 (94.9%). The software also demonstrates good accuracy in the visualization results for single-plant and leaf detection tasks. Furthermore, DP-MaizeTrack not only automates the detection process but also integrates agricultural analysis tools, including region segmentation and data statistics, to support precision agricultural management and leaf-age analysis. The source code and models are available at https://github.com/clhclhc/project.
Why it matches plant phenotyping methodsUAV画像からトウモロコシ個体数と葉数を抽出するソフトウェアを開発しており、植物形質取得が研究の中心です。
abstractthis study develops an integrated detection and visualization software, DP-MaizeTrack
Reproduction assets foundThe paper explicitly states that the authors' source code and trained models for DP-MaizeTrack/DP-YOLOv8 are publicly available on GitHub. No public dataset deposit is stated; the UAV image dataset is described but not declared publicly available.Code · publicThe source code and models are available at https://github.com/clhclhc/project .Open asset ↗https://github.com/clhclhc/projectlines:224-300Plant phenotyping relevance match · UnverifiedEurope PMC · checked 6 Sept 2026
Background Rapidly estimating multiple trait indicators simultaneously, nondestructively, and with high precision is an important means of accurate diagnosis in modern phenomics. Increasing the accuracy of estimation models for rice yield-related trait indicators (leaf nitrogen concentration, LNC; leaf area index, LAI; aboveground biomass, AGB; and grain yield, GY) through a strategy of "spectral data + texture data + dimensionality reduction + machine learning" is highly important. Methods Between 2022 and 2023, hyperspectral canopy images, the LNC, LAI, AGB, and GY were collected synchronously. Then, dimensionality reduction was performed on the preprocessed spectral data using the Pearson correlation coefficient method, the successive projections algorithm (SPA), and competitive adaptive reweighted sampling (CARS) to select sensitive wavelengths. Estimation models were constructed using artificial neural networks (ANNs), support vector machine regression, one-dimensional convolutional neural networks, and long short-term memory networks. By extracting the texture features corresponding to sensitive wavelengths, high-precision estimation models were constructed using a "spectral data + texture data + dimensionality reduction + machine learning" method. Results SPA-ANN provided the best prediction for LNC (R 2 = 0.82, RMSE = 3.68 g/kg) and LAI (R 2 = 0.75, RMSE = 0.47), while CARS-ANN was optimal for AGB (R 2 = 0.90, RMSE = 79.05 g/m2) and GY (R 2 = 0.63, RMSE = 0.59 t/ha). Adding texture features increased R 2 by up to 9.9% and reduced RMSE by up to 27.2%. Conclusion The optimized method can significantly increase the accuracy of estimation models. The results provide a scientific basis and technical data for the precise diagnosis of rice yield-related traits.
Why it matches plant phenotyping methods水稲の収量関連形質を、ハイパースペクトル画像・テクスチャ特徴・次元削減・機械学習で非破壊推定する手法が研究の中心であり、植物フェノタイピング手法として明確に該当する。
abstractRapidly estimating multiple trait indicators simultaneously, nondestructively, and with high precision is an important means of accurate diagnosis in modern phenomics.
The parameterization of vegetation indices (VIs) is crucial for sustainable irrigation and horticulture management, specifically for urban green infrastructure (GI) management. However, the constraints of roadside traffic, motor and industrially related pollution, and potential public vandalism compromise the efficacy of conventional in situ monitoring systems. The shortcomings of prevalent satellites, UAVs, and manual/automated sensor measurements and monitoring systems have already been reviewed. This research proposes a novel urban GI monitoring system based on an integration of gas exchange and various VIs obtained from computer vision algorithms applied to data acquired from three novel sources: (1) Integrated gas sensor data using nine different volatile organic compounds using an electronic nose (E-nose), designed on a PCB for stable performance under variable environmental conditions; (2) Plant growth parameters including effective leaf area index (LAIe), infrared index (Ig), canopy temperature depression (CTD) and tree water stress index (TWSI); (3) Meteorological data for all measurement campaigns based on wind velocity, air temperature, rainfall, air pressure, and air humidity conditions. To account for spatial and temporal data acquisition variability, the integrated cameras and the E-nose were mounted on a vehicle roof to acquire information from 172 Elm trees planted across the Royal Parade, Melbourne. Results showed strong correlations among air contaminants, ambient conditions, and plant growth status, which can be modelled and optimized for better smart irrigation and environmental monitoring based on real-time data.
Why it matches plant phenotyping methods植物のLAI、赤外線指数、樹冠温度差、水ストレス指数を、カメラ・E-nose・コンピュータビジョンで取得する統合的な植物モニタリング手法が研究の中心である。
abstractThis research proposes a novel urban GI monitoring system based on an integration of gas exchange and various VIs obtained from computer vision algorithms
ABSTRACT Climate change is causing vegetation stress across the globe, increasing the need for reliable indicators to monitor plant health. Leaf water and carotenoid content, and the chlorophyll/carotenoid ratio, are established proxies for environmental stress that can be detected by remote sensing. Here, we evaluated the sensitivity of 11 multispectral vegetation indices (VIs) designed to monitor these three stress-related leaf traits across a broad range of environmental and vegetation conditions. For this, we combined radiative transfer modeling with cross-biome field and satellite observations from Sentinel-2, Landsat 8, and MODIS from the National Ecological Observatory Network (NEON), spanning in most major terrestrial ecosystems. Our model-based analysis showed that VIs have a low to moderate sensitivity to their target traits, ranging from water indices with 66% of their variability explained by leaf water content, to carotenoid indices with 27% variability explained by leaf carotenoid content. Surprisingly, our field-based analyses revealed minimal to no sensitivity to leaf water and carotenoid content and chlorophyll/carotenoid ratio across all VIs. In contrast, we showed that leaf area index was the dominant driver of all studied VIs, accounting for 54-74 % of their variability in the field-based analysis. Lastly, we detected that VIś sensitivity to atmospheric conditions and field sampling issues contribute to their low performance in validating ground truth observations. These findings show that improvements in the VIs formulation and field sampling strategies are needed to increase the reliability of vegetation stress monitoring from multispectral satellites and support a generalized use of VIs across ecosystems. Highlights: 3-5 bullet points, 85 characters ● Sensitivity of water and carotenoid multispectral indices was evaluated ● Analysis based on cross-biome field data and radiative transfer models ● Field data showed indices had minimal sensitivity to leaf water and carotenoid ● Leaf area index explained most cross-biome variation in water and carotenoid indices ● We propose strategies to improve stress-related index formulation and validation
Why it matches plant phenotyping methods衛星マルチスペクトル指数による葉の水分・カロテノイド等の形質推定性能を、モデル・野外・衛星データで評価し、感度と検証上の課題を分析しているため、フェノタイピング手法の検証が中心です。
abstractHere, we evaluated the sensitivity of 11 multispectral vegetation indices (VIs) designed to monitor these three stress-related leaf traits across a broad range of environmental and vegetation conditions.
Plant phenotyping relevance match · UnverifiedOpenAlex · Europe PMC · bioRxiv · checked 6 Sept 2026
Abstract In agroecosystems, the variable expression of crop functional traits is expected to play a role in key processes, including plant nutrient cycling and water acquisition, that confer ecosystem resistance and/ or resilience to environmental change. The ability to estimate crop trait data is therefore critical to predict crop responses to environmental change, enabling more informed diagnosis of crop performance and on-farm management strategies. Yet, many traditional methods for quantifying plant traits are time-consuming and resource-intensive, limiting sample sizes and study durations. In response, high-throughput phenotyping— specifically reflectance spectroscopy— has emerged as a key element of plant trait research, capable of estimating plant traits more rapidly. However, little is known about whether or not reflectance spectroscopy can detect within-species variation in resource acquisition and plant-water traits. Using wine grapes ( V. vinifera subsp. vinifera ) as a focal crop, this study aimed to assess the ability of reflectance spectroscopy and the subsequent partial least squares regression modelling approach to quantify intraspecific variation in 12 functional traits across 12 different cultivars. Results showed significant differences in traits, especially in the photosynthetic and hydraulic traits, among closely related cultivars, falling along a resource-conservative to resource-acquisitive axis of variation. We also found that reflectance differentiated this fine-scale trait variation, specifically in leaf chemical and morphological traits, contributing to higher accuracy, and indicating that this HTP approach is viable for detailed trait estimation in diverse agroecosystems.
Why it matches plant phenotyping methods反射分光とPLS回帰によるブドウの複数機能形質推定を主目的とし、ハイスループット表現型解析手法の性能・実用性を評価しているため。
abstractthis study aimed to assess the ability of reflectance spectroscopy and the subsequent partial least squares regression modelling approach to quantify intraspecific variation in 12 functional traits across 12 different cultivars.
Field / plotLeafMorphology / geometry measurementLeaf traits
We present a comprehensive dataset of qualitative and quantitative leaf functional traits for 93 dominant woody species representing two distinct leafing phenologies and three growth forms from the central Western Ghats of India. Quantitative assessments were conducted for nine key traits: leaf area (LA), mean thickness (LTH), specific leaf area (SLA), leaf dry matter content (LDMC), leaf tissue density (LTD), leaf nitrogen concentration (Leaf N), carbon-to-nitrogen ratio (C/N), and phytolith yield, following standard protocols. For each species, 30 leaves were sampled from a minimum of five individuals, totalling 2790 leaf samples. Qualitative traits, including leaf shape, margin, surface, texture, apex, base, type, and latex presence, were recorded in the field and validated using field manuals. The majority of species sampled were evergreen (74 %), with deciduous species comprising the remainder. Given the growing importance of plant functional traits in ecological research, this dataset offers valuable species-level leaf trait information at the regional scale. The phytolith yield data, in particular, represent one of the few globally available datasets, providing essential baselines for palaeoecological research and enabling quantitative reconstruction of vegetation composition and environmental change over millennial timescales.
Why it matches plant phenotyping methods植物の葉形質を標準化プロトコルで体系的に収集した再利用可能なデータセット論文であり、データセット自体が中心的な成果である。
abstractWe present a comprehensive dataset of qualitative and quantitative leaf functional traits for 93 dominant woody species
Reproduction assets foundThe paper's own leaf functional trait dataset (2790 leaves, 93 woody species, central Western Ghats) is publicly deposited on Zenodo with an explicit DOI/URL given in the article.Dataset · publicduals per species. Quantitative leaf functional traits were analyzed following the standard protocol [ 1 , 2 ].
Data source location
Country: India
Sampling site: Gerusoppa Reserve Forest, Central Western Ghats (14°12′ N to 14°24′ N and 74°36′ E to 74°48′ E)
Data accessibility
Repository name: Zenodo
Data identification number: https://doi.org/10.5281/zenodo.16717435
Direct URL to data: https://doi.org/10.5281/zenodo.16717435
Related research article
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Value of the Data
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This dataset provides high-resolution leaf-level data ( n = 2790) on 17 functional traits for 93 dominant woody species of the central Western Ghats, supporting trait-based ecological research.
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It enables assessmentOpen asset ↗Zenodo · 10.5281/zenodo.16717435lines:1-54Plant phenotyping relevance match · UnverifiedEurope PMC · checked 15 Sept 2026
Accurate assessment of cotton defoliation (DF) and boll opening (BO) is essential for optimizing yield and fiber quality during mechanized harvesting, as improper timing can reduce yield and impair fiber quality. Unmanned aerial vehicle (UAV)-based remote sensing has become an effective tool for monitoring these indicators, but most current methods rely on single-sensor data, limiting diagnostic accuracy and generalizability. To address this limitation, we propose a multi-source data fusion framework integrating RGB, multi-spectral (MS), and thermal infrared (TIR) sensors for comprehensive canopy information. The fused dataset includes vegetation indices (VIs), color indices (CIs), texture features (Tex), and canopy temperature (TC). Feature selection was performed using pearson correlation coefficients (PCCs), recursive feature elimination with cross-validation (RFECV), and the Boruta algorithm to identify key variables. Three machine learning models—partial least-squares regression (PLSR), random forest regression (RFR), and extreme gradient boosting regression (XGBR)—were developed and compared. The RFECV-selected RGB+MS+TIR features in the XGBR model achieved the highest predictive accuracy, with R² values of 0.918 for defoliation rate and 0.867 for boll opening rate, improving by 1.9 % and 4.3 %, respectively, over single-sensor models. Root mean square error (RMSE) and relative RMSE (rRMSE) were reduced by 1.11 %-1.99 % and 1.66 %-2.28 %, respectively. These findings demonstrate that multi-source UAV data fusion, combined with advanced machine learning techniques, significantly enhances the accuracy and robustness of cotton defoliation and boll opening diagnosis. This approach offers a practical solution for precision agriculture to improve harvest scheduling and defoliant management.
Why it matches plant phenotyping methodsUAVのRGB・マルチスペクトル・熱赤外データを融合し、綿花の落葉率と綿花開絮率という植物状態を推定する手法を開発・比較しており、フェノタイピング手法が研究の中心である。
abstractwe propose a multi-source data fusion framework integrating RGB, multi-spectral (MS), and thermal infrared (TIR) sensors for comprehensive canopy information.
Leaf detection and counting are essential in plant phenotyping, but traditional manual methods are slow and error prone. To improve the efficiency and accuracy of leaf counting, this study introduces a lightweight, high-precision model for leaf detection and counting based on the optimized YOLOv8 computer vision model, called MobileViT-Asymptotic Feature Pyramid Network-YOLOv8 (MAF-YOLOv8). This model integrates the MobileViT architecture and an Adaptive Feature Pyramid Network (AFPN) structure, achieving a lightweight model with enhanced feature representation capabilities, thereby improving leaf counting accuracy. In this work, we constructed a dataset consisting of 711 RGB images with a 640 × 640 resolution and expanded it to 2136 images using data augmentation methods to enhance model robustness. The MAF-YOLOv8 model was able to achieve a mean average precision (mAP) of 91.7 %, a recall of 95.0 %, and a precision of 86.5 % in leaf counting tasks. Compared to YOLOv8, mAP improved by 2.6 %, while the number of parameters was reduced by 34.1 %. Ablation experiments evaluating the contributions of each model component further confirmed that MobileViT and AFPN critically improve model performance; together, they led to a 2.3 % improvement in precision and a 3 % increase in recall. This study also validates the performance of MAF-YOLOv8 on resource-constrained mobile devices, achieving an inference time of only 5.110 s. The findings indicate that the model has superior accuracy, inference speed, and resource efficiency, which renders it suitable for extensive applications within agriculture and environmental monitoring. This study provides an efficient technological approach for plant phenotyping and precision agriculture.
Why it matches plant phenotyping methods葉の検出・計数という植物表現型を抽出する画像解析モデルを開発し、データセット、アブレーション、精度・速度評価、モバイル実装まで行っており、方法が研究の中心である。
abstractLeaf detection and counting are essential in plant phenotyping, but traditional manual methods are slow and error prone.
In the domain of plant morphological studies, three-dimensional scanning technologies have brought about a paradigm shift in the field of leaf structure modelling. Nevertheless, the high cost and operational complexity of these systems act as significant barriers to widespread adoption. To address this issue, a single-image 3D reconstruction pipeline was developed, focusing on potato leaves and optimized for use with mobile phone cameras. The algorithm begins with image preprocessing to enhance quality, followed by leaf instance segmentation to isolate the target leaf. Subsequently, a precise 2D leaf contour is extracted to capture planar geometry. Subsequently, 3D spatial features are recovered from a single image to infer depth information. Contour back-projection is a process that Links the extracted 2D contour to the estimated 3D space. The discretization of the 3D contour is enabled by boundary sampling, thereby facilitating the generation of an initial 3D polygonal mesh. Finally, mesh surface refinement is applied to optimize model accuracy and visual fidelity. The methodology employed in this study successfully reconstructed potato and other crop leaves, demonstrating minimal deviation in key morphological shape descriptors and negligible error in surface area measurements in comparison to the ground truth. The reconstructed models exhibited high geometric congruence with the original leaves. This demonstrates the potential of our technique to broaden the accessibility of conventional modelling approaches and to advance methodologies within the field of crop phenotyping.
Why it matches plant phenotyping methods単一画像から葉の3D形状を再構成し、形態形状記述子や表面積を推定・検証する手法開発であり、植物フェノタイピングが中心である。
abstracta single-image 3D reconstruction pipeline was developed, focusing on potato leaves and optimized for use with mobile phone cameras.
The low spatial resolution of satellite remote sensing has become a major limiting factor in monitoring crop growth. Existing studies have effectively enhanced the resolution of remote-sensing imagery through super-resolution reconstruction (SR) techniques. Although these methods demonstrate good generalizability across different scenarios, they do not adequately address the anisotropic spatial structural characteristics of agricultural fields, particularly the influence of crop ridge orientation distribution on reconstruction outcomes. To address this issue, this study developed a super-resolution direction-aware generative adversarial network (SRDGAN) that incorporates multi-attention mechanisms and orientation-aware convolutions specifically designed for RGB satellite imagery of cotton farmlands. Large-scale monitoring models for defoliation and boll-opening rates were developed using feature selection and machine-learning techniques. The key findings include the following: (1) Significant correlations exist between features (vegetation indices, color components, and texture features) extracted from RGB satellite images and both defoliation and boll-opening rates. (2) A comparative analysis of SR methods revealed a progressive improvement in accuracy in the order Bicubic < EDSR< HAT< SRGAN < SRDGAN. (3) The RFE-XGBoost model achieved the optimal defoliation-rate monitoring accuracy using SRDGAN-enhanced imagery, whereas the RF-XGBoost model achieved the optimal boll-opening-rate monitoring accuracy. This study innovatively addresses the inherent conflict between spatial resolution and coverage range by incorporating directional perception into traditional GAN frameworks. The proposed methodology enables high-spatial resolution and large-scale precision management of cotton defoliation effects, providing crucial technical support for ensuring high-quality and efficient mechanical cotton harvesting in Xinjiang's modern agricultural systems.
Why it matches plant phenotyping methods綿花の脱葉率・吐絮率という植物状態を衛星画像から推定する超解像および機械学習手法を開発・比較しており、表現型取得・推定が研究の中心である。
abstractthis study developed a super-resolution direction-aware generative adversarial network (SRDGAN) that incorporates multi-attention mechanisms and orientation-aware convolutions specifically designed for RGB satellite imagery of cotton farmlands.
• ADT and DIF precisely regulated elongation and thickening in tomato seedlings. • Canopy traits imaging predicted grafting traits with high accuracy (R 2 > 0.9). • CTPS-imaging integration offers real-time monitoring for grafting suitability. • First trial on tailored production with imaging for an automated grafting. Tomato seedling growth and quality are crucial determinants of the success of grafting and transplant establishment. This study aimed to investigate temperature control strategies in a closed transplant production system (CTPS) and their integration with imaging-based prediction to produce grafting-ready seedlings. Scion ‘Dotaerang Dia’ and rootstock ‘B-Blocking’ were grown under combinations of average daily temperatures (ADTs; 24 and 26 °C) and difference between day and night temperatures (DIFs; –8, –4, 0, +4, and +8 °C). Morphological traits crucial for grafting, including the epicotyl length (EPL) and diameter (EPD) of scions and hypocotyl length (HYL) and diameter (HYD) of rootstocks, and canopy traits, including leaf area index (LAI) and canopy height (CH), were evaluated. Higher ADTs and positive DIFs promoted elongation, whereas lower ADTs and negative DIFs restricted elongation and improved compactness. Compact seedlings with a higher dry matter content are advantageous for grafting, whereas seedlings with greater elongation and dimensional synchrony better meet the requirements of robotic grafting. Imaging-based monitoring using multispectral-derived LAI and light detection and ranging (LiDAR)-derived CH accurately predicted grafting-related traits ( R 2 > 0.9 for EPL, EPD, and HYD); however, HYL predictions were less reliable under negative DIFs. Leave-one-environment-out cross-validation confirmed robust performance for diameter traits across environments. These findings collectively indicate that CTPS enable precise morphological regulation of tomato scions and rootstocks through temperature control, whereas imaging-based phenotyping allows a basis for real-time prediction of grafting suitability. This integration establishes a scalable and automation-ready framework for grafted transplant production, offering a technological foundation for developing automated grafting strategies.
Why it matches plant phenotyping methods画像計測（マルチスペクトルによるLAI、LiDARによる樹冠高）から接ぎ木関連形態形質を予測・検証し、リアルタイムな接ぎ木適性評価を実現する方法が研究の中心である。
abstractCanopy traits imaging predicted grafting traits with high accuracy (R 2 > 0.9).
The rapid growth of remotely sensed earth observation data presents clear opportunities for monitoring complex ecosystem change and answering fundamental ecological questions. However, large-scale automated monitoring of ecosystems faces challenges. Data-driven models require extensive datasets and often lack generalizability when training data are unrepresentative, while process-driven models, such as radiative transfer models (RTMs), can be imprecise due to gaps in knowledge, or simplified representation of physical processes. To enhance the prediction of plant functional traits and simultaneously discover where process-driven models can be improved, we explore the potential of Physics-Informed Neural Networks (PINNs) as a hybrid approach that combines the strengths of both methodologies at the leaf scale. In contrast to data augmentation approaches, our implementation directly integrates the widely-used PROSPECT5B model into the architecture of an autoencoder framework. Our results show that our PINNs approach is able to outperform data-driven techniques even when trained on very limited training data (i.e. 17 % training vs 83 % validation). We also identified weak points in the PROSPECT5B model by progressively replacing individual components of PROSPECT5B with convolutional neural networks. Our case study indicates that especially Prospect's generalized “plate model” could be refined to improve predictive ability. Hence, our framework provides a self-diagnostic capability and identifies areas for improvement in process-driven models and their components. Thus, we conclude that PINNs 1) improve data-driven predictive accuracy while maintaining physical consistency with minimal training data while 2) being able to identify limitations in process-driven models. Hence, we believe our framework could serve as a new standard for evolving and improving radiative transfer models.
Why it matches plant phenotyping methods葉レベルの植物機能形質を推定するPINNsと放射伝達モデル統合手法を開発・検証しており、形質取得・推定法が研究の中心である。
abstractwe explore the potential of Physics-Informed Neural Networks (PINNs) as a hybrid approach that combines the strengths of both methodologies at the leaf scale.
The genus Trichoderma is a valuable source of biological control agents: useful means for sustainable crop disease management. Speeding up screening phase in the set-up of new microbial means is crucial to meet needs for managing pathogens. Functional phenomics expressing through objective spectral data the result of the plant genotype's interactions with the environment, can contribute to the performance-based selection. In this study nineteen Trichoderma spp., including strains belonging to the species T. atroviride , T. harzianum , T. longibrachiatum and T. rifaii , were screened for the biocontrol of F. oxysporum f. sp. lycopersici and S. rolfsii infections on tomato plants, with the help of phenomics measures on infected plants subjected to symptom-reducing effects of the beneficial microbial treatments, alongside the traditional method. Trichoderma spp. isolates showed an antagonistic behavior in plate assays against the two pathogens, while four and five out of total isolates significantly lowered, respectively, wilt and Southern blight symptoms on plants. Detection of the plant phenotype closer to that of the healthy ideotype, defined through the overall computation of biometric and spectral traits acquired by a multispectral dual scan platform, individuated T. harzianum T2 and PB3 as the best performing strains in controlling both tomato pathogens. Leaf area and Normalized Chlorophyll Pigment Ratio Index Average acted as engine vectors for phenotypic clustering with non-infected plants in both systems. Voxel Volume Total, 3D-Leaf area, Green Leaf Index Average, Hue Average, and Surface Angle Average assumed importance under F. oxysporum assay. Specifically, the phenomics assisted procedure contributed to prompt results in the individuation of the best performing Trichoderma strains against F. oxysporum and S. rolfsii .
Why it matches plant phenotyping methods感染植物からマルチスペクトル画像および3D・生理形質を取得し、計算的に健全表現型との近さを評価するフェノミクス手順が、Trichoderma株選抜の中心的手法として用いられている。
abstractDetection of the plant phenotype closer to that of the healthy ideotype, defined through the overall computation of biometric and spectral traits acquired by a multispectral dual scan platform
Plant domestication may create trade-offs between growth and stress tolerance, raising concerns about yield stability in future climates. Previous studies have found limited direct evidence for such trade-offs, often focusing on weakened defenses associated with higher growth rates. Trade-offs can also occur when traits optimized for favorable conditions perform less efficiently under stress. Deciphering these mechanisms is crucial for maintaining growth in changing environments. We examine one key aspect of vegetative growth, leaf elongation, in six species of grasses. We use a machine learning-enabled pipeline to extract cell dimensions and positions from leaf microscope images to study cell kinematics. We find that domesticated plants generally have longer leaves, larger division zones, and higher cell production rates. While no clear trade-off is observed between domestication and drought response in final leaf length, a trade-off occurs in development; wild species exhibit a smaller decrease in the elongation zone size under drought compared with domesticated species. This pattern points to compensatory mechanisms, such as extended elongation duration or increased cell production, mitigating drought effects in domesticated plants. These nuanced trade-offs associated with domestication highlight the importance of robustly phenotyping developmental and physiological traits, possibly informing breeding strategies to enhance crop resilience in future climates.
Why it matches plant phenotyping methods機械学習パイプラインによる葉の顕微鏡画像からの細胞寸法・位置抽出が、葉伸長と細胞動態の表現型評価の中心であるため。
abstractWe use a machine learning-enabled pipeline to extract cell dimensions and positions from leaf microscope images to study cell kinematics.
ABSTRACT As an essential species across European forests, Scots pine ( Pinus sylvestris L.) plays a vital ecological and economic role, yet its physiological variability underlying its adaptive potential remains underexplored. Understanding this intraspecific variability is crucial for uncovering the genetic basis of adaptation. Traditional genetic evaluations require large sample sizes and are time‐consuming, whereas hyperspectral sensing/imaging enables rapid, nondestructive assessment of physiological traits across many individuals, facilitating more efficient exploration of adaptive variation. We assessed needle functional traits (NFTs) linked to foliar structure, water content, and pigment composition in clonal seed orchards over two seasons, integrating hyperspectral measurements at needle and canopy levels with genotyping using a new 50 K single‐nucleotide polymorphism (SNP) array. Linear mixed models revealed substantial genetic variation, with the carotenoid‐to‐total‐chlorophyll ratio showing the highest heritability (0.29) among pigment traits, and structural/water‐related traits reaching heritability values up to 0.38. Significant genetic correlations were observed between stress‐related traits (pigment content, equivalent water thickness) and reflectance, suggesting that spectral traits could serve as proxies for indirect selection of adaptive traits or in breeding programs. Low genotype‐by‐environment interaction and stable clonal performance across years further underscore the reliability of these traits for identifying resilient genotypes. Overall, our findings highlight hyperspectral phenotyping and NFTs as promising tools for accelerating climate‐adaptive breeding in Scots pine.
Why it matches plant phenotyping methods針葉および林冠レベルのハイパースペクトル測定を用いて植物の機能形質を評価し、育種への再利用可能性を検討しており、フェノタイピング手法の適用が中心的です。
abstracthyperspectral sensing/imaging enables rapid, nondestructive assessment of physiological traits across many individuals
Reproduction assets foundThe paper's Data Availability Statement points to a public Figshare deposit (DOI 10.6084/m9.figshare.27134907.v2) containing the data supporting the study's hyperspectral phenotyping and genetic analyses. This URL is in the allowed list and the identifier occurs verbatim in the quote. No separate author analysis code, Dataset · publicThe data supporting the findings of this study are openly available in Figshare at https://doi.org/10.6084/m9.figshare.27134907.v2 .Open asset ↗Figshare · 10.6084/m9.figshare.27134907.v2lines:454-598Plant phenotyping relevance match · UnverifiedEurope PMC · checked 15 Sept 2026
Published1 Nov 2025South African journal of botany : official journal of the South African Association of Botanists = Suid-Afrikaanse tydskrif vir plantkunde : amptelike tydskrif van die Suid-Afrikaanse Genootskap van Plantkundiges
The genus Lycium L. (Solanaceae) includes economically important species such as Lycium barbarum, L. chinense, and L. ruthenicum (goji). This study focuses on the morphological characterization of L. barbarum, a recently domesticated species lacking standardized descriptors. We evaluated traits including plant habit, vigor, leaf morphology, floral structure, fruit shape, and ripening stages using both qualitative and quantitative analyses. Growth habits were evenly distributed: 33.3 % were erect, 39.3 % were expanded, and 27.4 % were pendulous. The average leaf area was 166.22 ± 79.66 mm², and discriminant analysis of leaf shape achieved 83 % classification accuracy. Floral traits were consistent, with 94.3 % of plants having five petals and 5.7 % having six petals. Fruit ripened rapidly, completing four stages in ∼11.5 days. These findings highlight key diagnostic traits for developing harmonized descriptors. These traits will support future distinctness, uniformity, and stability (DUS) testing, which is essential for cultivar protection, genebank documentation, and product traceability in the growing global market for functional foods and nutraceuticals.
Why it matches plant phenotyping methodsゴジベリーの形態・生育段階を標準化された記述子として整理し、葉形分類やDUS試験に向けた診断形質を開発することが中心であり、単なる生物学的結果測定ではない。
abstractThis study focuses on the morphological characterization of L. barbarum, a recently domesticated species lacking standardized descriptors.
Accurate estimation of agroecosystem carbon fluxes is essential for assessing cropland sustainability and climate resilience. This study integrates Leaf Area Index (LAI) retrieval from Radiative Transfer Model (RTM) inversion into AgroC, an agroecosystem model, from Unmanned Aerial System (UAS) platform to enhance carbon fluxes estimates, including Gross Primary Production (GPP), Net Ecosystem Exchange (NEE), and Total Ecosystem Respiration (TER). By replacing the internally developed LAI in the AgroC model with interpolated LAI time series derived from UAS, improved spatiotemporal representativeness of agroecosystem carbon fluxes is observed under both the Farquhar-von Caemmerer-Berry (FvCB) and the Light Use Efficiency (LUE) photosynthesis approaches. Temporally, the highest GPP accuracy was achieved by the AgroC FvCB model integrated with UAS-derived LAI (RMSE = 3.19 gC m⁻² d⁻¹, KGE = 0.89), while the best NEE estimation was obtained with the AgroC LUE model integrated with UAS-derived LAI (RMSE = 2.10 gC m⁻² d⁻¹, KGE = 0.89). Spatially, the superior performance of the AgroC FvCB model in integrating UAS-derived LAI enabled high-resolution (1 m) mapping of GPP and NEE, effectively capturing within-field spatial variations in a winter wheat field. The daily Pearson correlation coefficient ( r ) overtime ranged from 0.16 in non-vegetated areas to 0.94 in vegetated zones for GPP, and up to 0.88 for NEE. Despite the advantages taking physical basis in RTM inversion for LAI retrieval and biochemical constraints considered in FvCB approach, the limitation in TER improvement requires further investigation to refine RTM-AgroC coupling for cropland carbon fluxes modelling using UAS platforms.
Why it matches plant phenotyping methodsUAS画像からRTM逆解析でLAIという植物群落形質を推定し、その時系列をモデルへ統合・評価するワークフローが主要な技術的要素であるため、植物フェノタイピング手法の実質的応用として含める。
abstractThis study integrates Leaf Area Index (LAI) retrieval from Radiative Transfer Model (RTM) inversion into AgroC, an agroecosystem model, from Unmanned Aerial System (UAS) platform
High-throughput phenotyping of growth kinetics and organ size in the model plant Arabidopsis thaliana requires rapid and precise methods for trait estimation. To address this need, we developed the Arabidopsis Phenotypic Trait Estimation System, APTES, an open-access, high-throughput program that uses computer vision and deep learning to extract 64 leaf traits and 64 silique traits from photographs. The enhanced segmentation model Cascade Mask Region-based Convolutional Neural Network (Mask R-CNN) achieved precision (measure of positive prediction accuracy), recall (sensitivity in detection), and F1 score values (harmonic mean of precision and recall) of 0.965, 0.958, and 0.961, respectively, for individual leaf segmentation. These metrics demonstrated a consistent improvement of approximately 1 percentage point over the baseline model. For silique segmentation, our enhanced DetectoRS model for silique segmentation attained precision, recall, and F1 scores of 0.954, 0.930, and 0.942, respectively. Notably, precision increased by 1%, while the F1 score improved by 2 percentage points. Trait parameters were automatically calculated with coefficient of determination values for leaf and silique traits ranging from 0.776 to 0.976 and mean absolute percentage error values from 1.89% to 7.90%. We phenotyped 166 Arabidopsis accessions, using APTES, and subjected the resulting values to a genome-wide association study (GWAS), revealing 1,042 single-nucleotide polymorphisms (SNPs) as being significantly associated with 18 leaf and silique traits, and one significant SNP on chromosome 3 linked to silique number. Furthermore, we validated APTES across other public Arabidopsis databases and other plant species, with segmentation results demonstrating its applicability across diverse datasets. In conclusion, APTES is a valuable automated tool for leaf and silique segmentation and trait estimation, which should offer benefits to the broader plant science community. Supplementary information The online version contains supplementary material available at 10.1007/s42994-025-00239-y.
Why it matches plant phenotyping methods植物の葉・莢の形質を画像から抽出する深層学習システムを開発し、性能検証・他データセットでの妥当性確認まで行っており、フェノタイピング手法が研究の中心である。
abstractwe developed the Arabidopsis Phenotypic Trait Estimation System, APTES, an open-access, high-throughput program that uses computer vision and deep learning to extract 64 leaf traits and 64 silique traits from photographs.
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2件を確認しました。Code · publicThe executable tool and software packages are available at https://drive.google.com/drive/folders/1i9IariiIrxuFtVIaRiaIzqvb8Gfg3xTc or http://plantphenomics.hzau.edu.cn/usercrop/Rice/download .Open asset ↗lines:292-292Code · publicThe executable tool and software packages are available at https://drive.google.com/drive/folders/1i9IariiIrxuFtVIaRiaIzqvb8Gfg3xTc or http://plantphenomics.hzau.edu.cn/usercrop/Rice/download .Open asset ↗lines:292-292Code / dataset availability confirmedEurope PMC · checked 6 Sept 2026
Light intensity and spectral distribution within plant canopies provides insights into the effects of optimizing canopy architecture on light use efficiency. Breeding crop varieties with a "smart" canopy, characterized by erect upper-layer leaves and flat lower-layer leaves, can be supported with a 3D canopy model which can simulate light distribution for a particular canopy architecture. Leaf optical properties are required parameters for such canopy photosynthesis model to accurately predict canopy microclimate and hence photosynthetic efficiency. In this study, we developed a strategy to estimate the leaf optical properties based on leaf anatomical features. We developed a Directional Spectrum Detection Instrument (DSDI) system and associated Bidirectional Reflectance Distribution Function (BRDF) analysis software to precisely describe leaf light distribution. BRDF parameters were quantified with high accuracy ( R2>0.95 ) for adaxial and abaxial surfaces of maize, rice, cotton, and poplar leaves across canopy layers. Leaf phenotypic traits, surface roughness, pigments content, specific leaf weight and thickness were also assessed. Ensemble learning (EL) model showed excellent predictive performance for leaf optical properties based on phenotypic traits with R 2 between 0.83 and 0.99. Compared to existing BRDF measurement systems, the DSDI achieves broader angular coverage (-π/36 to 35π/36) via mechanical rotation design, and the ensemble learning model establishes the first direct predictive relationship between BRDF parameters and leaf phenotypic traits. This work presents a new approach to quantify leaf optical properties and offers predictive models for leaf optical properties, which can support canopy light distribution prediction and hence support design leaf features for higher canopy photosynthesis efficiency.
Why it matches plant phenotyping methods葉の光学特性と表現型形質を取得・予測する測定機器、BRDF解析ソフトウェア、機械学習モデルを開発しており、植物フェノタイピング手法が研究の中心である。
abstractthe ensemble learning model establishes the first direct predictive relationship between BRDF parameters and leaf phenotypic traits.
Reproduction assets foundThe paper's BRDF analysis code (adaptive grid search fitting and Roughness Calculator) is publicly available at github.com/PlantSystemsBiology/brdf, and the modified fastTracer ray tracing software used for canopy light simulations is at github.com/PlantSystemsBiology/fastTracerPublic. Phenotype/measurement data are '…Code · publicAn adaptive grid search algorithm was developed in this study, and this algorithm utilized a 2-layered grid (step sizes of 1 × 10 − 2 and 1 × 10 − 4 respectively) structure to incrementally optimize each parameter, providing a more precise approximation of true values. By iteratively narrowing the search range and increasing resolution, this method gradually converges on the optimal solution. The source code of Python for adaptive grid search algorithm was available at https://github.com/PlantSystemsBiology/brdf .Open asset ↗PlantSystemsBiology/brdflines:212-227Plant phenotyping relevance match · UnverifiedCrossref · checked 15 Sept 2026
Climate change has led growers with uncertainty on crop growth, development, quality and yield. Thus there is a critical need to set up proper tools to help growers follow up their crop during the growth period and ensure better production at the end. In this context we used predictive machine learning models for predictions of Okra development in a controlled lighting environment based on UV-VIS-NIR spectroscopy. Fluorescence and reflectance spectroscopy data was collected from several leaves of Okra grown under different artificial lighting condition, then vegetation spectral indices were computed and used as features for the prediction of four growth and development parameters namely Plant Height (PH), Leaf Number (LN), stem diameter (SD) and Leaf Area Index (LAI). The different trained machine learning models explicitly Linear regression, K-nearest Neighbor, Support Vector Machine, Single Tree, Random Forest, Gradient Boosting, extreme Gradient Boosting (XGBoost), Light Gradient Boosting Machine (LightGBM) and Categorical Boosting (CatBoost) give good performance in the prediction of PH (R2 ranged from 0.93 to 0.97), LN (R2 ranged from 0.88 to 0.94), SD (R2 ranged from 0.95 to 0.98) with the tree-based algorithm outperformed the others. However, these trained models give poor performance on the prediction of LAI (R2 ranged from 0.25 to 0.37). Furthermore, the most responsive features and vegetation spectral indices were also identified using Shapley Additive Explanations. This work aims to help growers to follow up their crops development and moreover intend to be used as a decision tool in an overall horticultural management process to engineer their crop development.
Why it matches plant phenotyping methodsUV-VIS-NIRおよび蛍光・反射分光データから、機械学習でオクラの草丈、葉数、茎径、LAIを推定する手法が研究の中心であり、性能評価も実施しているため。
abstractwe used predictive machine learning models for predictions of Okra development in a controlled lighting environment based on UV-VIS-NIR spectroscopy.
Introduction: Leaf phenotypes are key indicators of plant growth status. Existing deep learning-based leaf skeletonization typically requires extensive manual labeling, long training, and predefined keypoints, which limits scalability. We developed a training-free and label-free approach that connects spontaneously detected keypoints to generate leaf skeletons for leafy plants. Methods: The method comprises random seed-point generation and adaptive keypoint connection. For plants with random leaf morphology, we determine a threshold for the angle difference among any three consecutive adjacent points and iteratively identify keypoints within circular search neighborhoods to trace leaf skeletons. For plants with regular leaf morphology, we fit the skeleton trajectory by minimizing curvature. We validated the approach on vertical and front-view images of orchids (covering random and regular morphological cases) and extracted five phenotypic parameters from the resulting skeletons. Generalization was further assessed on a maize image dataset. Results: On orchid images, the proposed approach achieved an average curvature fitting error of 0.12 and an average leaf recall of 92%. Five orchid phenotypic parameters were accurately derived from the skeletons. The method also showed effective skeletonization on maize, indicating cross-species applicability. Discussion: By eliminating manual labels and training, this approach reduces annotation effort and computational overhead while enabling precise geometric phenotype calculation from skeleton-based keypoints. Its effectiveness on both randomly distributed and regularly shaped leafy plants suggests suitability for high-throughput plant phenotyping workflows.
Why it matches plant phenotyping methods葉の骨格化とフェノタイプ抽出のための画像解析手法を開発し、複数植物種で検証しているため、植物フェノタイピング手法が中心的である。
abstractWe developed a training-free and label-free approach that connects spontaneously detected keypoints to generate leaf skeletons for leafy plants.
Reproduction assets foundThe paper uses a publicly available single-plant maize image dataset (hosted on datasetninja) as its generalization-test input; the orchid images and the authors' algorithm code have no stated public deposit in the supplied blocks.Dataset · publicUsing the publicly available single-plant maize dataset (Dataset URL: https://datasetninja.com/maize-whole-plant-image-dataset ), which captured images of a single maize plant over 113 days—with 1 vertical view and 12 front view images taken each day—the spontaneous keypoints connection algorithm was applied to both a front view ( Figure 9 ) and a vertical view image ( Figure 9 ) from 10 different daysOpen asset ↗datasetninja · maize-whole-plant-image-datasetlines:429-438Code / dataset availability confirmedEurope PMC · bioRxiv · Crossref · checked 14 Sept 2026
ABSTRACT The development of remote sensing methods to estimate plant functional diversity is limited by mismatches between ecology and remote sensing sampling schemes, and the limited representativeness of local field campaigns. The Biodiversity Observing System Simulation Experiment (BOSSE) provides a modeling framework for benchmarking new methodologies. We used BOSSE to simulate 180 different synthetic “Scenes” encompassing a two-year-long time series of plant trait maps and imagery of hyperspectral reflectance factors, spectral indices, sun-induced chlorophyll fluorescence, land surface temperature, and estimates of plant traits (optical traits). We used these simulations to answer five fundamental, yet unsolved, questions: Q1. How should remote sensing characterize functional diversity in large surfaces (sites)? Diversity metric values saturate with the number of pixels involved, hampering comparisons between plant traits and remote sensing estimates in large areas. The average value of metrics computed over small samples should be used instead. Q2. Which sources of spectral information (or combinations thereof) can best capture plant functional diversity at the site scale? Accounting for background effects is the key. Optical traits (remote sensing estimates of plant traits) are the best estimators for plant functional diversity. Other variables succeed when filtered out of the soil pixels; their combination did not yield additional advantages. Q3. How should remote sensing estimates be validated/compared with plant functional diversity measurements? Leaf area index (LAI) is a better proxy of abundance than the pixel for Q Rao, but not for variance-based partitioning. It is more sensitive to sample size, but also more resistant to suboptimal spatial resolution. Q4. When (in the phenological year) can remote sensing best capture site-scale plant functional diversity? The estimation error decreased with LAI and stabilized at values above 1 m²/m². Q5. Which approaches and remote sensing variables are more resistant to the effects of suboptimal spatial resolution? Optical traits, fluorescence, and reflectance factors were the most robust variables. Still, field data resolution needs to be degraded to match the sensor’s resolution. We found a relative spatial resolution threshold of ∼30 % (where the pixel is around three times larger than the plants). Simulation frameworks like BOSSE enable testing methodologies beyond local contexts and address the current shortage of suitable global datasets, supporting the application and development of methods for assessing plant functional diversity with remote sensing. In the future, BOSSE could contribute to understanding observational results, refining and pre-testing new methodologies, and supporting the development of comparable experimental datasets.
Why it matches plant phenotyping methodsBOSSEを用いてリモートセンシングによる植物形質・機能多様性推定手法をシミュレーションベンチマークし、検証・比較する研究であり、植物フェノタイピング手法が中心である。
abstractThe Biodiversity Observing System Simulation Experiment (BOSSE) provides a modeling framework for benchmarking new methodologies.
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 · publicvariables, we used the “pyGNDiv” package (https://github.com/JavierPachecoLabrador/pyGNDiv-Open asset ↗JavierPachecoLabrador/pyGNDiv- · pyGNDivpdf-page:11 lines:1-60Code / dataset availability confirmedEurope PMC · checked 6 Sept 2026
Rapid prediction and control of flowering time is essential for breeding crops resilient to changing climates. Current models often fail to predict flowering time in new cultivars because molecular models lack integration of environmental signals, while physiological models inadequately capture the interactions of vernalization, photoperiod and temperature. This leads to mischaracterized genotypes and inaccurate forecasts. A new Cereal Anthesis Molecular Phenology (CAMP) model was developed for wheat. It explicitly integrates the regulatory roles of three major 'virtual' flowering genes (Vrn1, Vrn2, and Vrn3) with environmental cues. A novel phenotyping strategy based on main stem leaf number was introduced to shorten the time required for data collection and model calibration. CAMP predicted flowering time within 4-7 d across 64 genetically diverse wheat cultivars grown under contrasting environments. The leaf-number phenotyping method reduced phenotyping time by more than 80%, offering a practical alternative to resource-intensive field trials. Together, these advances enable accurate cultivar characterization and scalable prediction of flowering behaviour. CAMP enables the ability to predict flowering time directly from genotypic data (e.g. SNPs), eliminating the need for costly controlled-environment experiments. This represents a step change in molecular-physiological modelling, supporting faster deployment of new cultivars and more effective design of wheat for future climates.
Why it matches plant phenotyping methods主茎葉数に基づく新規フェノタイピング手法とCAMPモデルを開発し、多様なコムギ品種・環境で開花期予測を検証している。表現型取得の効率化が中心的貢献である。
abstractA novel phenotyping strategy based on main stem leaf number was introduced to shorten the time required for data collection and model calibration.
Reproduction assets foundThe paper's Data availability statement explicitly provides public repositories containing the CAMP model source code and analysis scripts used for the phenotyping data analysis and flowering-time prediction: the APSIM Next Generation framework repository, the standalone Python CAMP model and analysis scripts, and theCCode · publicAll the data and the source code of the model are freely accessible for research use through the APSIM General Use License at: https://github.com/apsimInitiative/apsimxOpen asset ↗apsimInitiative/apsimxlines:295-475Code · publicPython code and analysis scripts can be found at https://github.com/HamishBrownPFR/CAMPOpen asset ↗HamishBrownPFR/CAMPlines:295-475Code · publicC# implementation is available at https://github.com/APSIMInitiative/ApsimX/tree/master/Models/PMF/Phenology/CAMPOpen asset ↗APSIMInitiative/ApsimXlines:295-475Plant phenotyping relevance match · UnverifiedCrossref · checked 14 Sept 2026
Climate change and evolving land management practices are reshaping soil–plant interactions critical for sustainable viticulture. These interactions are driven by soil texture, hydrogeochemical gradients, and climatic conditions, influencing grapevine traits like nutrient and water content. Integrating innovative methods, this study explores the relationship between soil variability and grapevine characteristics in the Médoc wine region, France. The research combines hyperspectral imaging, electromagnetic induction (EMI), and electrical resistivity tomography (ERT) with traditional soil and leaf sampling. Hyperspectral data, using visible-near infrared (VNIR) wavelengths, reliably estimated leaf traits such as nitrogen and water content, yielding strong predictive relationships (R2 up to 0.8). These findings suggest VNIR-based indices are cost-effective for monitoring grapevine physiology. Geophysical data revealed significant soil textural gradients, delineating sand, transitional (loam, sandy loam), and clay textural soil classes. Apparent electrical conductivity (ECa) and inverted electrical conductivity (EC) correlated with soil texture and grapevine traits, particularly at depths around 50 cm, aligning with primary root zones. However, interannual variability in correlations emphasised the influence of weather conditions and phenological stages, highlighting the need to align data acquisition with vine growth phases. The integration of hyperspectral imaging and geophysical methods provides a novel framework for linking soil and plant parameters. This interdisciplinary approach enhances the spatial resolution and scalability of vineyard monitoring, offering actionable insights for precision viticulture. Future work should expand datasets and refine predictive models to improve the understanding of soil–plant dynamics under changing environmental conditions. These findings underscore the potential of combining hyperspectral and geophysical data to develop climate-resilient vineyard management strategies, advancing precision agriculture, and sustainable viticulture practices.
Why it matches plant phenotyping methodsハイパースペクトル画像によりブドウ葉の窒素・水分などの植物形質を推定し、予測性能を評価している。土壌調査も含むが、植物形質の取得・推定手法が主要な技術的貢献である。
abstractHyperspectral data, using visible-near infrared (VNIR) wavelengths, reliably estimated leaf traits such as nitrogen and water content, yielding strong predictive relationships (R2 up to 0.8).
Accurate leaf area measurement is essential for plant growth monitoring and ecological research; however, it is often challenged by perspective distortion and color inconsistencies resulting from variations in shooting conditions and plant status. To address these issues, this study proposes a visual and semi-automatic measurement system. The system utilizes Hough transform-based perspective transformation to correct perspective distortions and incorporates manually sampled points to obtain prior color information, effectively mitigating color inconsistency. Based on this prior knowledge, the level-set function is automatically initialized. The leaf extraction is achieved through level-set curve evolution that minimizes an energy function derived from a multivariate Gaussian distribution model, and the evolution process allows visual monitoring of the leaf extraction progress. Experimental results demonstrate robust performance under diverse conditions: the standard deviation remains below 1 cm2, the relative error is under 1%, the coefficient of variation is less than 3%, and processing time is under 10 s for most images. Compared to the traditional labor-intensive and time-consuming manual photocopy-weighing approach, as well as OpenPheno (which lacks parameter adjustability) and ImageJ 1.54g (whose results are highly operator-dependent), the proposed system provides a more flexible, controllable, and robust semi-automatic solution. It significantly reduces operational barriers while enhancing measurement stability, demonstrating considerable practical application value.
Why it matches plant phenotyping methods葉面積という植物形態形質を画像から抽出する半自動手法を開発し、精度・再現性・処理時間を評価しているため、方法が研究の中心である。
abstractthis study proposes a visual and semi-automatic measurement system
To explore the feasibility of using UAV-LiDAR for measuring the leaf area index (LAI) of crop canopies, we employed UAV-LiDAR to scan sugarcane canopies during the tillering and elongation stages, acquiring canopy point cloud data. Subsequently, features such as average row height, projected row area, point cloud density at different canopy layers, and the ratios between these parameters were extracted. Three feature selection methods-partial least squares regression (PLSR), XGBoost feature importance (XGBoost-FI), and random forest-recursive feature elimination (RF-RFE)-were adopted to evaluate and identify the optimal input variables for modeling. With these selected variables, LAI inversion models were developed based on random forest (RF) and adaptive boosting (AdaBoost) algorithms, and their performance was assessed. Among the extracted features, the projected row area S p and the total row point count C total exhibited strong correlations with LAI, with correlation coefficients of 0.73 and 0.72, respectively. The AdaBoost-based LAI inversion model, using the projected row area S p , average height H avg , mid-layer point cloud density C m , and total row point count C total as input variables, achieved the best performance, with a coefficient of determination ( R v ²) of 0.713 and a root mean square error ( RMSE v ) of 0.25 on the validation set. This study provides an effective method for high-throughput acquisition of LAI in field crops, offering valuable scientific support for sugarcane field management and breeding efforts.
Why it matches plant phenotyping methodsUAV-LiDARによるサトウキビ群落LAIの取得・推定手法を開発し、特徴量選択と機械学習モデルの性能評価まで行っており、フェノタイピング手法が中心である。
abstractusing UAV-LiDAR for measuring the leaf area index (LAI) of crop canopies
Accurate estimation of total leaf area (TLA) is essential for assessing plant growth, photosynthetic activity, and transpiration, but remains a challenge for bushy plants like dwarf tomatoes. Traditional destructive methods and imaging-based techniques often fall short due to labor intensity, plant damage, or the inability to capture complex canopies. This study evaluated a non-destructive method combining sequential 3D reconstructions from RGB images and machine learning to estimate TLA for three dwarf tomato cultivars—Mohamed, Hahms Gelbe Topftomate, and Red Robin—grown under controlled greenhouse conditions. Two experiments, conducted in spring–summer and autumn–winter, included 73 plants, yielding 418 TLA measurements using an “onion” approach, where layers of leaves were sequentially removed and scanned. High-resolution videos were recorded from multiple angles for each plant, and 500 frames were extracted per plant for 3D reconstruction. Point clouds were created and processed, four reconstruction algorithms (Alpha Shape, Marching Cubes, Poisson’s, and Ball Pivoting) were tested, and meshes were evaluated using seven regression models: Multivariable Linear Regression (MLR), Lasso Regression (Lasso), Ridge Regression (Ridge-Reg), Elastic Net Regression (ENR), Random Forest (RF), extreme gradient boosting (XGBoost), and Multilayer Perceptron (MLP). The Alpha Shape reconstruction (α = 3) combined with XGBoost yielded the best performance, achieving an R² of 0.80 and MAE of 489 cm², with significant results across other model combinations. Results were lower when using data from different experiments as train and test datasets (R² = 0.56 and MAE = 579 cm²). Feature importance analysis identified height, width, and surface area as the most predictive features. These findings demonstrate the robustness of our approach across variable environmental conditions and canopy structures. This scalable, automated TLA estimation method is particularly suited for urban farming and precision agriculture, offering practical implications for automated pruning, improved resource efficiency, and sustainable food production.
Why it matches plant phenotyping methodsRGB画像からの3D再構成と機械学習により植物の総葉面積を推定する手法を開発・評価しており、表現型取得が研究の中心です。
abstractThis study evaluated a non-destructive method combining sequential 3D reconstructions from RGB images and machine learning to estimate TLA
Satellite remote sensing is widely used for Leaf Area Index (LAI) retrievals, but calibration and validation efforts require ground Plant Area Index (PAI) values that may be converted to LAI. Digital Cover Photography (DCP) presents an affordable means for covering large regions (∼2 × 33² km²) and multiple years. The Soil Moisture Active Passive Validation Experiment conducted from 2019–2022 (SMAPVEX19–22) utilized DCP data to study vegetation impacts on soil moisture retrievals in forests. This work reports on the DCP tool “EzPAI”, its outputs for SMAPVEX19–22, and clear sky PAI bias identification and its correction. EzPAI features sky condition tracking, multi-tier data screening, data quality flagging, and two-corner thresholding. We found that PAI is overestimated in clear conditions, and our bias correction approach reduced this by 0.2 on average. Massachusetts (‘MA’) and New York (‘MB’) networks attained comparable results for cloudiness (∼67 %) and poor data quality (21 %). Benchmark comparisons to other approaches (DCP tools, Sentinel-2 LAI, LAI-2200c) showed good agreement and performance. EzPAI showed similar results for in situ and Sentinel-2 LAI comparisons, achieving R∼0.9, and some bias (MD= <0.53). For comparisons to the coveR DCP tool the correlation was 0.73 and bias 0.26. For summer PAI totals, CoveR, coverPy, EzPAI and LAI-220c obtained nearly identical results: 4.08±0.35 4.08±0.33, 4.12±0.33 and 4.16±0.77. Differences may be explained in part due to image quality issues (noted at needleleaf canopies), the LAI-2200c data being noisy (σₛₚᵣᵢₙg=0.43, σₛᵤₘₘₑᵣ=0.72), the different measurement modalities used (satellite, handheld hemispherical, DCP), and our assumption of a constant extinction coefficient (k = 0.65) across 144 site-years. PAI values ranged from 2.73 to 5.16 (3.92 average) and 2.44 to 4.96 (3.80 average) for MA and MB, respectively. Processing time on a Dell Precision Laptop 7560 was 0.87 per image, which was about 3x speedier than coveR.
Why it matches plant phenotyping methods植物面積指数（PAI）を画像から推定するDCP処理ツールEzPAIの開発、品質管理・バイアス補正、他手法とのベンチマークを中心に扱っており、植物フェノタイピング手法が明確に中心である。
abstractThis work reports on the DCP tool “EzPAI”, its outputs for SMAPVEX19–22, and clear sky PAI bias identification and its correction.
Methods based on upward canopy gap fractions are widely employed to measure in-situ effective LAI (Le) as an alternative to destructive sampling. However, these measurements are limited to point-level and are not practical for scaling up to larger areas. To address the point-to-landscape gap, this study introduces an innovative approach, named NeRF-LAI, for corn and soybean Le estimation that combines gap-fraction theory with the neural radiance field (NeRF) technology, an emerging neural network-based method for implicitly representing 3D scenes using multi-angle 2D images. The trained NeRF-LAI can render downward photorealistic hemispherical depth images from an arbitrary viewpoint in the 3D scene, and then calculate gap fractions to estimate Le. To investigate the intrinsic difference between upward and downward gaps estimations, initial tests on virtual corn fields demonstrated that the downward Le matches well with the upward Le, and the viewpoint height is insensitive to Le estimation for a homogeneous field. Furthermore, we conducted intensive real-world experiments at controlled plots and farmer-managed fields to test the effectiveness and transferability of NeRF-LAI in real-world scenarios, where multi-angle UAV oblique images from different phenological stages were collected for corn and soybeans. Results showed the NeRF-LAI is able to render photorealistic synthetic images with an average peak signal-to-noise ratio (PSNR) of 18.94 for the controlled corn plots and 19.10 for the controlled soybean plots. We further explored three methods to estimate Le from calculated gap fractions: the 57.5° method, the five-ring-based method, and the cell-based method. Among these, the cell-based method achieved the best performance, with the r² ranging from 0.674 to 0.780 and RRMSE ranging from 1.95 % to 5.58 %. The Le estimates are sensitive to viewpoint height in heterogeneous fields due to the difference in the observable foliage volume, but they exhibit less sensitivity to relatively homogeneous fields. Additionally, the cross-site testing for pixel-level LAI mapping showed the NeRF-LAI significantly outperforms the VI-based models, with a small variation of RMSE (0.71 to 0.95 m²/m²) for spatial resolution from 0.5 m to 2.0 m. This study extends the application of gap fraction-based Le estimation from a discrete point scale to a continuous field scale by leveraging implicit 3D neural representations learned by NeRF. The NeRF-LAI method can map Le from raw multi-angle 2D images without prior information, offering a potential alternative to the traditional in-situ plant canopy analyzer with a more flexible and efficient solution.
Why it matches plant phenotyping methodsNeRFとUAV多視点画像を組み合わせ、トウモロコシ・ダイズの葉面積指数を推定・マッピングする手法を開発し、実圃場で性能検証しているため、植物表現型取得が中心である。
abstractthis study introduces an innovative approach, named NeRF-LAI, for corn and soybean Le estimation that combines gap-fraction theory with the neural radiance field (NeRF) technology
Advanced phenotyping techniques are required in the breeding and management of maize, which is crucial for global food security. Traditional in situ three-dimensional (3D) field phenotyping entails labour-intensive data acquisition. Light detection and ranging technology offers high-resolution maize canopy point clouds under outdoor field conditions, establishing a technical foundation for automated phenotypic trait extraction. However, accurately segmenting individual plants from dense and structurally complex canopy point clouds for single-plant trait analysis is challenging. To address this challenge, we propose a novel framework named Paired-Attention Central Axis Aggregation Network (PACANet) for 3D point cloud-based plant segmentation. Firstly, a 3D paired-attention backbone network is introduced to enhance point-wise feature representations by integrating spatial and channel information, thereby enabling effective learning of high-dimensional point cloud features. Secondly, a projection-based central axis aggregation strategy is incorporated to guide instance separation by projecting plant point clouds onto their respective central axis skeletons, which improves the spatial coherence of segmentation. Additionally, a simulation-based point cloud generation approach is proposed to reduce reliance on large-scale manual annotations, facilitating model training in scenarios with limited real-world population data. Comprehensive experimental evaluations across multiple datasets demonstrate that PACANet consistently outperforms existing plant population segmentation methods. Notably, when trained solely on simulated data, PACANet achieves a state-of-the-art average precision of 0.9246. Finally, based on the segmentation results, phenotypic traits at both the individual plant and organ levels are analyzed under various planting densities, including the field-level distributions of plant height, plant width, leaf base angle and leaf inclination angle, all of which exhibit strong consistency with the validation data. These results highlight the potential of PACANet as a robust and scalable solution for high-throughput phenotyping in smart breeding and precision agriculture. This study provides a new tool for smart breeding and precision agriculture, and the source code and data are available at https://github.com/yangxin6/3D-PACA-Network.git.
Why it matches plant phenotyping methods3D点群による個体分割と形質抽出ネットワークを開発し、複数データセットで性能評価・検証しているため、植物フェノタイピング手法が中心である。
abstractwe propose a novel framework named Paired-Attention Central Axis Aggregation Network (PACANet) for 3D point cloud-based plant segmentation.
Leaves play a fundamental role in the plant body by performing photosynthesis. Their morphological characteristics, leaf area and other surface parameters, can help to explain various processes, such as climate change, ecological relationships, and agricultural productivity. However, most existing methods for measuring leaf surface dimensions are expensive and often complicated. Additionally, several methods employ destructive approaches, preventing the monitoring of plant growth. In this work, we introduce a new deep neural network to estimate bean’s leaf area from images containing a salient leaf and a marker. Our method is based on the DeepLabv3+ architecture for semantic segmentation and comprises one encoder and two decoders, which estimate the image segmentation and the pixel areas of the objects of interest. An extensive quantitative and qualitative analysis was conducted with the model’s predictions on 3374 images of 300 different leaves. Results indicate that the trained model is capable of estimating the leaf and marker areas with only one input image.
Why it matches plant phenotyping methods画像から葉面積を非破壊推定する深層学習手法を開発し、多数画像で評価しており、植物表現型の取得・抽出が研究の中心である。
titleNon-destructive leaf area estimation based on a semantic segmentation deep neural network
A precise and timely assessment of the cotton leaf area index (LAI) plays a critical role in advancing precision agriculture practices. Verticillium wilt reduces LAI by disrupting leaf structure and physiological functions.Verticillium wilt is a significant disease that constrains the yield potential of cotton. The emergence of unmanned aerial vehicle (UAV) technology offers a revolutionary technology for cost-effective, fine-scale inversion of the LAI in cotton under Verticillium wilt stress. The study investigated the relevant potential of classical-based algorithms and deep learning-based algorithms to estimate the LAI using multi-spectral images acquired by drones under Verticillium wilt stress. Prior to constructing the model, Gaussian blur was applied to enhance the original images. Inputs to the Random Forest (RF) and Extreme Learning Machine (ELM) algorithms included vegetation indices (VI) and texture features (TF), and the LAI of cotton under Verticillium wilt stress was estimated in conjunction with ground-measured LAI data. The enhanced images were used as input to the Convolutional Neural Network (CNN) algorithm to estimate the LAI of cotton under Verticillium wilt stress. The results demonstrated that, in the classical-based models, the prediction accuracy of LAI inversion using both VI and TF was slightly higher than that achieved using VI or TF alone. After Gaussian blur processing, the accuracy of RF, ELM, and CNN models showed significant improvement. Among these, the CNN model based on Gaussian blur achieved the highest LAI inversion accuracy (R²≥0.88), followed by the LSM model (R²=0.83) and the RF model (R²=0.82). Consequently, the CNN model under Gaussian blur is employed to achieve rapid and accurate inversion of the LAI of cotton under Verticillium wilt stress. This finding of the study provides a significant reference for real-time monitoring of cotton growth and effective field management under Verticillium wilt conditions.
Why it matches plant phenotyping methodsUAVマルチスペクトル画像から綿花のLAIを推定する画像解析・機械学習手法の比較と精度評価が研究の中心であり、植物表現型の取得方法に該当する。
abstractThe study investigated the relevant potential of classical-based algorithms and deep learning-based algorithms to estimate the LAI using multi-spectral images acquired by drones under Verticillium wilt stress.
Continuous information on soil water content (SWC) and plant development is crucial for environmental monitoring, agricultural management, and beyond. Cosmic-ray neutron sensors (CRNS), widely used to estimate SWC, also have the potential to monitor field-scale variations in vegetation properties. In this study, a CRNS measured both epithermal (EN) and thermal (TN) neutron intensities over a 10-year period at an ICOS Class 1 ecosystem station in Selhausen (Germany). Compared to nearby point-scale sensors, the CRNS provided more representative SWC estimates within the monitoring area of the adjacent eddy covariance (EC) station. A general co-development was observed between TN and gross primary productivity (GPP), but differences during senescence and desiccation suggest that factors beyond plant water content can influence TN. An extensive dataset of plant height (PH), leaf area index (LAI), and dry above-ground biomass (AGB) was used to evaluate the ability of TN to monitor plant development. TN was found to be more closely related to vegetation dynamics than to changes in SWC. CRNS estimations of PH, LAI, and AGB yielded relatively good agreement with reference data (RMSE of 0.13 m, 1.01 m²/m², and 0.27 kg/m², respectively). The RMSE obtained with a leave-one-out cross validation generally confirmed these findings. Although CRNS estimates generally had lower accuracy than traditional methods, they have the key advantages of being continuous, non-invasive, and non-laborious. Combined with simultaneous estimation of SWC at a relevant spatial scale, CRNS becomes a particularly interesting tool among long-term monitoring platforms with further potential in modelling, remote sensing, and decision-making in agriculture.
Why it matches plant phenotyping methodsCRNSを用いて植物高、LAI、地上部乾物量を推定し、基準データおよび交差検証で性能評価しており、植物形質取得法が研究の中心です。
abstractAn extensive dataset of plant height (PH), leaf area index (LAI), and dry above-ground biomass (AGB) was used to evaluate the ability of TN to monitor plant development.
While tobacco plays a significant role in the global economy, research on regional tobacco growth simulation remains limited. This study integrates the WOFOST crop model with satellite remote sensing data, focusing on the data assimilation (DA) of leaf area index (LAI) to enhance the accuracy of regional tobacco growth simulations. Field survey data were used for model calibration, providing the foundation for the analysis. The performance of four 4-Dimensional Variational Assimilation algorithms (4DVAs)—Particle Swarm Optimization (PSO), Simulated Annealing (SA), Shuffled Complex Evolution-University of Arizona (SCE-UA), and Gray Wolf Optimization (GWO)—was compared with four sequential DA algorithms (SDAs)—Ensemble Kalman Filter (EnKF), Ensemble Variational (EnVar), Ensemble Square Root Filter (EnSRF), and Particle Filter (PF). The 4DVAs were developed by integrating constraint DA Algorithms (CDAs) into the 4D-Var framework, enhancing their capability to optimize model states over a time window. Additionally, the performance of their coupled DA algorithms was evaluated. The results indicated that the coupled of SA and PF (SA-PF) achieved the best performance in terms of model accuracy. Compared to field survey data for biomass, stem mass and leaf mass, our method achieved the coefficient of determination (R²) values of 0.89, 0.86, and 0.81, respectively, with normalized root mean square error (NRMSE) values of 0.12, 0.10, and 0.09. The SA-PF coupling algorithm also performs better than some new DA algorithms. This study provides a valuable reference for regional tobacco growth simulation and data assimilation, improving the accuracy and applicability of crop growth models.
Why it matches plant phenotyping methods衛星リモートセンシングのLAIを作物モデルへ同化し、バイオマス・茎重・葉重を推定するデータ同化手法を開発・比較・検証しており、植物形質推定が中心である。
abstractThis study integrates the WOFOST crop model with satellite remote sensing data, focusing on the data assimilation (DA) of leaf area index (LAI) to enhance the accuracy of regional tobacco growth simulations.
Plant phenotyping relevance match · UnverifiedOpenAlex · Crossref · Europe PMC · checked 6 Sept 2026
Introduction: Accurate 3D reconstruction is essential for plant phenotyping. However, point clouds generated directly by binocular cameras using single-shot mode often suffer from distortion, while self-occlusion among plant organs complicates complete data acquisition. Methods: To address these challenges, this study proposes and validates an integrated, two-phase plant 3D reconstruction workflow. In the first phase, we bypass the integrated depth estimation module on camera and instead apply Structure from Motion (SfM) and Multi-View Stereo (MVS) techniques to the captured high-resolution images. It produces high-fidelity, single-view point clouds, effectively avoiding distortion and drift. In the second phase, to overcome self-occlusion, we register point clouds from six viewpoints into a complete plant model. This process involves a rapid coarse alignment using a marker-based Self-Registration (SR) method, followed by fine alignment with the Iterative Closest Point (ICP) algorithm. Results: The workflow was validated on two Ilex species (Ilex verticillata and Ilex salicina). The results demonstrate the high accuracy and reliability of the workflow. Furthermore, key phenotypic parameters extracted from the models show a strong correlation with manual measurements, with coefficients of determination (R²) exceeding 0.92 for plant height and crown width, and ranging from 0.72 to 0.89 for leaf parameters. Discussion: These findings validate our workflow as an accurate, reliable, and accessible tool for quantitative 3D plant phenotyping.
Why it matches plant phenotyping methods植物の3D再構成と形質抽出ワークフロー自体を開発・検証しており、植物形質計測が中心的な方法論的貢献である。
abstractthis study proposes and validates an integrated, two-phase plant 3D reconstruction workflow
Plant phenotyping relevance match · UnverifiedOpenAlex · Europe PMC · bioRxiv · checked 6 Sept 2026
Abstract Stand count, the number of plants per unit ground area, and leaf area index (LAI), the ratio of leaf area to ground area, are critical traits for crop research but are traditionally measured using labor-intensive methods. While new sensing technologies are being developed, quantifying improvement in measurement efficiency and data quality, relative to traditional techniques, is lacking. In this study, we use LiDAR to generate 3D scans of corn and soybean plots and evaluate two computational methods: a gap fraction approach to estimate LAI and a persistent homology algorithm to estimate stand count by detecting structural peaks in the canopy. Validation experiments and statistical comparisons of bias and variance demonstrate that LiDAR-derived LAI estimates in corn are comparable in quality to those from established instruments. However, in soybean, the LiDAR method performs poorly, likely due to dense canopies limiting light penetration and structural differentiation. Stand count estimations in corn closely match manual counts, with the added benefit of full-plot coverage and significantly faster data collection. In soybean, stand count estimates are unreliable under dense canopy conditions. These results offer practical guidance for the use of LiDAR in field phenotyping and highlight both its current capabilities and limitations. While a trade-off between speed and precision remains, particularly in high-density canopies, LiDAR’s scalability and multi-trait potential make it a promising tool for high-throughput breeding programs. Continued improvements in LiDAR hardware and algorithm design may further enhance measurement accuracy and extend applicability across crops and growth stages.
Why it matches plant phenotyping methodsLiDARによるLAI・立ち株数推定を開発・比較検証し、バイアス、分散、精度、適用限界を評価しており、植物表現型取得法が研究の中心である。
abstractwe use LiDAR to generate 3D scans of corn and soybean plots and evaluate two computational methods: a gap fraction approach to estimate LAI and a persistent homology algorithm to estimate stand count by detecting structural peaks in the canopy.
The vertical projection leaf area (VPA) of cabbage (Brassica oleracea var. capitata) is an important phenotypic trait that is closely related to total leaf area, biomass, and head weight (yield). Developing a high-throughput method to measure individual VPAs of cabbage can assist in monitoring growth conditions in the field and improve the prediction of crop growth. High-throughput phenotyping using drones that can extract phenotypic crop traits from aerial images is widely used. Here, an R program was developed to detect and segment cabbages in images and calculate each cabbage’s VPA. The detection error and precision of the method were evaluated by using orthoimages collected from cabbage fields of NARO, Kannondai, Tsukuba, Ibaraki, Japan. The average detection error was 3.93%–5.40% and the average detection accuracy was 93.03%–96.35%. The accuracy of the VPA generated by the method was sufficient to be used in a cabbage growth prediction model and has the potential to predict yields of individual cabbages.
Why it matches plant phenotyping methodsキャベツの航空画像から個体を検出・セグメンテーションし、垂直投影葉面積という表現型形質を算出するRプログラムを開発・評価しており、表現型取得手法が研究の中心である。
abstractHere, an R program was developed to detect and segment cabbages in images and calculate each cabbage’s VPA.
Plant phenotyping relevance match · UnverifiedCrossref · Europe PMC · checked 6 Sept 2026
Aiming to address the issues of low efficiency and large errors in the manual measurement process of phenotypic parameters in Schima Superba seedlings, an automated non-destructive method for acquiring phenotypic parameters based on three-dimensional point clouds is proposed, which includes the main steps of alignment, skeleton extraction, and automatic phenotypic calculation. Aiming to overcome the technical challenges of stem and leaf separation in Schima Superba , a density-weighted voxel centroid method is proposed to extract skeleton points, combined with minimum spanning tree (MST) and principal component analysis (PCA) techniques to accurately identify the stem skeleton point cloud, effectively addressing the problem of stem-leaf separation. The separation process encounters difficulties at the stem-leaf junction, resulting in suboptimal separation accuracy. An improved K-means++ algorithm is proposed to initially estimate the number of adhering leaves based on coarse segmentation, followed by fine segmentation to achieve higher precision in leaf segmentation, effectively improving the accuracy and efficiency of the segmentation process. Following the completion of stem and leaf segmentation, a fully automated phenotypic characterization method based on the segmented point cloud is proposed for the first time. The method automatically outputs relevant phenotypic parameters, including plant height, stem length, stem diameter, and leaf area. The predicted correlation coefficients for the experimental phenotypes were 0.994, 0.992, 0.938, and 0.873, meeting the requirements for on-site measurement of phenotypic parameters in Schima Superba and providing strong technical support for plantation management and cultivar improvement.
Why it matches plant phenotyping methods3D点群による茎葉分離、骨格抽出、形質自動計算を開発・検証しており、植物表現型取得手法が研究の中心である。
abstractan automated non-destructive method for acquiring phenotypic parameters based on three-dimensional point clouds is proposed
Understanding how plant populations respond to environmental variation through functional leaf traits remains challenging due to limitations of traditional phenotyping approaches. Hyperspectral reflectance offers a rapid, non-destructive and high-throughput method to capture functional trait variation and detect signatures of local adaptation across populations. We combined hyperspectral data, inverse modeling, and network analysis to investigate population-level variation in Streptanthus tortuosus. Using a common garden experiment with four geographically distinct populations, we applied partial least square discriminant analysis (PLS-DA) and ridge regression for population discrimination, inverse PROSPECT modeling to estimate leaf biochemical traits, and canonical correlation analysis to examine trait-climate relationships across historical (1900-1994) and recent (1995-2024) periods. We developed a spectral network approach treating wavelength correlations as biologically meaningful trait networks. Populations showed distinct, heritable spectral signatures with high classification accuracy. Significant population differences emerged in anthocyanins, carotenoids, chlorophyll, and water content. Trait-climate correlations shifted between time periods, consistent with historical climate adaptation. Network analysis revealed population-specific integration patterns, with more variable environments displaying greater spectral modularity. Hyperspectral signatures provide a high-throughput tool for detecting population-level adaptation and trait coordination. Our findings provide a framework to investigate how plant populations respond to climate change through evolved shifts in trait networks rather than isolated traits alone.
Why it matches plant phenotyping methodsハイパースペクトル計測と逆モデリングを用いて葉の機能形質を推定し、集団間比較・適応評価を行う手法が研究の中心であるため。
abstractHyperspectral reflectance offers a rapid, non-destructive and high-throughput method to capture functional trait variation
Reproduction assets foundThe paper's Data availability statement explicitly deposits raw hyperspectral data and source code in a public GitHub repository, which is an allowed URL.Code · publicRR, JL; Formal Analysis:
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References
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Albert R, Barabási A-L. 2002. Statistical mechanics of complex networks. Reviews of Modern
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Physics 74: 47–97.
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Anderson JT, DeMarche ML, Denney DA, Breckheimer I, Santangelo J, Wadgymar SM.
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2025. Adaptation and gene flow are insufficient to rescue a montane plant under climate change.
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ScieOpen asset ↗rishavray/spectral-networkpdf-raw-page:23 lines:1-60Code / dataset availability confirmedEurope PMC · bioRxiv · checked 15 Sept 2026
Understanding how plants capture light and maintain their energy balance is crucial for predicting how ecosystems respond to environmental changes. By monitoring leaf inclination angle distributions (LIADs), we can gain insights into plant behaviour that directly influences ecosystem functioning. LIADs affect radiative transfer processes and reflectance signals, which are essential components of satellite-based vegetation monitoring. Despite their importance, scalable methods for continuously observing these dynamics across different plant species throughout day-night cycles are limited. We present AngleCam V2, a deep learning model that estimates LIADs from both RGB and near-infrared (NIR) night-vision imagery. We compiled a dataset of over 4,500 images across 200 globally distributed species to facilitate generalization across taxa. Moreover, we developed a method to simulate pseudo-NIR imagery from RGB imagery to enable an efficient training of a deep learning model for tracking LIADs across day and night. The model is based on a vision transformer architecture with mixed-modality training using the RGB and the synthetic NIR images. AngleCam V2 achieved substantial improvements in generalization compared to AngleCam V1 (R 2 = 0.62 vs 0.12 on the same holdout dataset). Phylogenetic analysis across 100 genera revealed no systematic taxonomic bias in prediction errors. Testing against leaf angle dynamics obtained from multitemporal terrestrial laser scanning demonstrated the reliable tracking of diurnal leaf movements (R 2 = 0.61-0.75) and the successful detection of water limitation-induced changes over a 14-day monitoring period. This method enables continuous monitoring of leaf angle dynamics using conventional cameras, enabling applications in ecosystem monitoring networks, plant stress detection, interpreting satellite vegetation signals, and citizen science platforms for global-scale understanding of plant structural responses.
Why it matches plant phenotyping methods葉の傾斜角分布という植物形質を画像から推定する深層学習手法を開発し、大規模データセット、既存モデル比較、レーザースキャンによる検証、水ストレス下での追跡評価まで実施しており、フェノタイピング手法が研究の中心です。
abstractWe present AngleCam V2, a deep learning model that estimates LIADs from both RGB and near-infrared (NIR) night-vision imagery.
Reproduction assets foundThe paper's Data Availability Statement explicitly provides public access to the authors' analysis code (Anonymous GitHub), the phenotyping image/trait dataset (Zenodo), and the pretrained AngleCam V2 model weights (Zenodo). All three are paper-specific, public, and actionable.Code · publicLK and TK conceived the ideas, designed the methodology, and led the analysis. TK, JP, RR, JF, LK,
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Conflicts of Interest
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All authors declare that they have no conflicts of interest.
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at (https://doi.org/10.5281/zenodo.17101166).32
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All authors declare that they have no conflicts of interest.
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preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in
The copyright holder for tOpen asset ↗zenodo · 10.5281/zenodo.17101166pdf-raw-page:2 lines:1-30Plant phenotyping relevance match · UnverifiedCrossref · checked 8 Sept 2026
Field / plotLiDAR / point cloudLeafWhole plant / canopy / plot / fieldMorphology / geometry measurement2D/3D reconstructionVisualization / data managementBiomass / plant weightGrowth / development / phenologyLeaf traits
The acquisition of plant ecological indicators, such as leaf area index and leaf area density values, typically relies on labor-intensive field sampling and measurements, which are often time-consuming and hinder large-scale application. As different plant ecological indicators are closely related to plants’ geometric characteristics, the development of dynamic correlation and prediction methods for relevant indicators has become an important research topic. However, existing 3D plant models are mainly used for visualization purposes, which cannot accurately reflect the plant’s growth process or geometric characteristics. This study presents a workflow for parametric 3D plant modeling and ecological indicator analysis, integrating dynamic plant modeling, indicator calculation, and microclimate simulation. With the established plant model, a method for calculating and analyzing ecological indicators, including the leaf area index, leaf area density, aboveground biomass, and aboveground carbon storage, was then proposed. A method for exporting the model-generated data into ENVI-met v.5.0 to simulate the microclimate environment was also established. Then, by taking Daijia Lake Park as an example, this study utilized site planting construction drawings and field survey data to perform parametric modeling of 21,685 on-site trees from 65 species at three different growth stages using Blender v.4.0 and The Grove plugin v.10. The generated plant model’s accuracy was then verified using the 3D IoU ratio between the models and on-site scanned point cloud data. Plant ecological indicators at various stages were then extracted and exported to ENVI-met for microclimate analysis. The workflow integrates the simulation of plant growth dynamics and their interactions with environmental factors. It can also be used for scenario-based predictions in planting design and serves as a basis for urban green space monitoring and management.
Why it matches plant phenotyping methods3D植物モデルを用いて葉面積指数・葉面積密度・地上部バイオマス等の植物形質を抽出するワークフローを開発し、点群データとの3D IoUで精度検証しているため、方法が中心である。
abstractThis study presents a workflow for parametric 3D plant modeling and ecological indicator analysis, integrating dynamic plant modeling, indicator calculation, and microclimate simulation.
Efficient and non-destructive extraction of organ-level phenotypic parameters of sesame ( Sesamum indicum L.) plants is a key bottleneck in current sesame phenotyping research. To address this issue, this study proposes a method for organ segmentation and phenotypic parameter extraction based on CAVF-PointNet++ and geometric clustering. First, this method constructs a high-precision 3D point cloud using multi-view RGB image sequences. Based on the PointNet++ model, a CAVF-PointNet++ model is designed to perform feature learning on point cloud data and realize the automatic segmentation of stems, petioles, and leaves. Meanwhile, different leaves are segmented using curvature-density clustering technology. Based on the results of segmentation, this study extracted a total of six organ-level phenotypic parameters, including plant height, stem diameter, leaf length, leaf width, leaf angle, and leaf area. The experimental results show that in the segmentation tasks of stems, petioles, and leaves, the overall accuracy of CAVF-PointNet++ reaches 96.93%, and the mean intersection over union is 82.56%, which are 1.72% and 3.64% higher than those of PointNet++, demonstrating excellent segmentation performance. Compared with the results of manual segmentation of different leaves, the proposed clustering method achieves high levels in terms of precision, recall, and F1-score, and the segmentation results are highly consistent. In terms of phenotypic parameter measurement, the coefficients of determination between manual measurement values and algorithmic measurement values are 0.984, 0.926, 0.962, 0.942, 0.914, and 0.984 in sequence, with root-mean-square errors of 5.9 cm, 1.24 mm, 1.9 cm, 1.2 cm, 3.5°, and 6.22 cm 2 , respectively. The measurement results of the proposed method show a strong correlation with the actual values, providing strong technical support for sesame phenotyping research and precision agriculture. It is expected to provide reference and support for the automated 3D phenotypic analysis of other crops in the future.
Why it matches plant phenotyping methods3D画像・点群分割と幾何クラスタリングにより、ゴマの器官分割および6種類の表現型形質抽出法を開発し、手動測定との精度検証も行っているため、方法が中心的である。
abstractthis study proposes a method for organ segmentation and phenotypic parameter extraction based on CAVF-PointNet++ and geometric clustering.
Pre-harvest defoliation of cotton is a key agricultural measure to improve mechanical harvesting efficiency and raw cotton purity. Collecting data on cotton defoliation traits for genetic localization and thus breeding defoliation-prone varieties is an essential alternative to traditional defoliant spraying. Nevertheless, it is hampered by low throughput and artificial error in manual field surveys. In this study, a framework for collecting high-throughput defoliation data in large fields was established. Three spectral indices (MTCI, VDVI, CI) and leaf area index (LAI) were first screened as core predictors through hierarchical segmentation analysis in three levels: leaf number (LN), leaf number difference (LND), and defoliation rate (DR). Four deep learning architectures (CNN, BiGRU, CNN-BiGRU, and CNN-BiGRU-Attention) were developed, and the CNN-BiGRU-Attention hybrid model demonstrated superior performance at all three levels, with R 2 values exceeding 0.85. Importantly, the inversion accuracy of this model at the LN and LND levels was superior to that at the DR level, which was also confirmed by the results of the genome-wide association study (GWAS). We combined GWAS and transcriptome results to identify a new gene, GhDR_UAV1 , associated with defoliation traits. The overexpression of GhDR_UAV1 significantly promoted the wilting of cotton leaves, indicating that GhDR_UAV1 plays a positive regulatory role in cotton defoliation. This study proposed a strategy to invert cotton defoliation data at three levels using deep learning fusion of UAV remote sensing data and LAI data and confirmed that LND can provide accurate phenotypic data for GWAS analysis. This study provides a new theoretical basis for cotton defoliation regulation and genetic improvement by integrating cotton high-throughput defoliation phenomics and genomics from an innovative perspective.
Why it matches plant phenotyping methodsUAVリモートセンシング、LAI、深層学習を統合し、ワタの落葉形質を高スループット推定する方法を開発・評価しており、表現型取得が研究の中心である。
abstracta framework for collecting high-throughput defoliation data in large fields was established
Reproduction assets foundThe paper's Data Availability statement explicitly deposits the study's data and code (UAV/LAI defoliation phenotyping data and analysis code) in a public GitHub repository, which matches an allowed URL.Code · publicThe data and code utilized in this study are available at GitHub ( https://github.com/xbw322/Data_upload.git ).Open asset ↗https://github.com/xbw322/Data_upload.gitlines:169-205Plant phenotyping relevance match · UnverifiedOpenAlex · checked 15 Sept 2026
Accurate prediction of maize ( Zea mays L.) yield and design of density-tolerant ideotypes are crucial for crop management and yield improvement. Three-dimensional (3D) phenotypic traits are closely related to light interception efficiency and yield formation, theoretically serving as important indicators for yield prediction and plant architecture optimization. However, studies utilizing 3D phenotypic traits for yield prediction and ideotype design remain limited. In this study, a two-year (2023–2024) field experiment was conducted with 10 maize hybrids grown under three planting densities (37,500 (low density, LD), 67,500 (medium density, MD), and 97,500 (high density, HD)) plants ha -1 . Plant 3D phenotypic traits at the silking stage were captured using the MVS-Pheno platform. The results showed that increasing planting density led to more compact plant architecture and significant changes in 3D phenotypic traits. A partial least squares regression model integrating 3D phenotypic traits with canopy light interception data achieved high prediction accuracy for yield (R 2 = 0.91, RMSE = 0.49 Mg ha -1 ). Feature sensitivity and correlation analyses further identified projected area (PJA) and plant side width (PSW) as critical indicators for designing varieties tolerant to high density. Furthermore, a strategy is proposed to match plant ideotype to different planting densities: under MD, the leaf area per plant (LAP) and PJA increased, whereas the PSW and leaf orientation value (LOV) decreased; under HD, the LAP, PJA, and PSW decreased, whereas the LOV increased. These findings provide an effective model for yield prediction and a valuable reference for breeding maize with optimal architecture for high-density cultivation. • Partial least squares regression model combining point cloud parameters with canopy light interception predicted yield well. • Plant side width and projected area stand out as pivotal traits influencing maize grain yield. • Plant type optimization under 37,500 and 67,500 plants ha -1 aimed to enhance population light interception. • Plant type optimization focused on improving canopy light distribution under 97,500 plants ha -1 .
Why it matches plant phenotyping methodsMVS-Phenoによる3D形態形質の取得と、収量予測・品種設計への解析が研究の中心であり、形質抽出および予測手法を実質的に評価している。
abstractPlant 3D phenotypic traits at the silking stage were captured using the MVS-Pheno platform.
This study addresses the critical need for efficient phenotyping methods in plant ecology by exploring predictive models for total leaf area per shoot ( A T ) and total leaf dry mass per shoot ( M T ), which are both key determinants of photosynthetic capacity and carbon allocation, using two fast-growing bamboo species ( Indocalamus decorus and I. longiauritus ) as proof of concept. Traditional approaches to measuring these traits are destructive and labor-intensive, motivating our exploration of non-destructive proxies based on one-dimensional leaf metrics. We validated the Montgomery equation for individual leaves, confirming a robust proportional relationship between leaf area ( A ) and the product of length and width ( LW ) in both Indocalamus species ( k ≈ 0.72). Extending this to the shoot level, the Montgomery-Koyama-Smith equation (MKSE) revealed significant proportionality between total leaf area ( A T ) and the composite metric L KS W KS (where L KS denotes the sum of leaf widths and W KS denotes maximum leaf length, and the subscript "KS" stands for Koyama-Smith). However, power-law scaling analysis demonstrated allometric, non-isometric relationships for A T vs. L KS W KS (with a scaling exponent α A T vs. total leaf dry mass ( M T ) (α < 1), indicating an increased biomass investment per unit area (i.e., increasing leaf mass per unit area) in larger shoots. These findings validate using simplified one-dimensional metrics that enable accurate, non-destructive predictions of shoot-level functional traits, advancing phenotyping in bamboo ecology, which may hold true more generally for other types of plant species.
Why it matches plant phenotyping methods一方向の葉形質からシュート葉面積・乾物量を非破壊推定する予測法を開発・検証しており、植物フェノタイピング手法が中心である。
abstractThis study addresses the critical need for efficient phenotyping methods in plant ecology by exploring predictive models for total leaf area per shoot ( A T ) and total leaf dry mass per shoot ( M T )
Sericulture is the multi- dimensional activity and Mulberry (Morus spp) is the sole food for silkworm Bombyx mori. It is very important to study the physiology of mulberry for the betterment of sericulture productivity and screening of better performing lines to withstand biotic and abiotic stress. It is necessary to monitor the crop growing status continuously and non-destructively to make decisions as to changed environmental conditions. High-throughput screening, defined as the automation and scaling of experimental analyses, enables rapid, reproducible, and large-scale measurements of plant traits. Importantly, these approaches allow continuous and non-destructive monitoring of crop growth, providing valuable insights for adaptive management under variable environmental conditions. Recent technological advances have introduced a wide range of high-throughput tools into mulberry research. Phenotyping platforms such as leaf area meters, chlorophyll fluorescence imaging, and portable photosynthetic systems allow rapid assessment of photosynthetic efficiency and stress responses. High-throughput sequencing methods, including RNA-Sequencing and genome-wide association studies (GWAS), have deepened genetic insights, while genome editing technologies like CRISPR/Cas9 open avenues for targeted improvement. Remote, hyperspectral, and multispectral sensing technologies enable large-scale monitoring of canopy health, nutrient status, and early stress detection. This review synthesizes how these tools facilitate early stress detection, genotype screening, and integration with molecular datasets for precision breeding. Case studies highlight their use under drought, waterlogging, nutrient imbalances, etc. This review concludes that high-throughput phenotyping not only enhances physiological understanding but also offers a pathway to accelerated mulberry improvement programs, bridging the gap between research and practical sericulture applications.
Why it matches plant phenotyping methodsマルベリーの生理・ストレス応答を対象に、ハイスループット表現型解析ツールとプラットフォーム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す。
abstractPhenotyping platforms such as leaf area meters, chlorophyll fluorescence imaging, and portable photosynthetic systems allow rapid assessment of photosynthetic efficiency and stress responses.
Plant phenotyping relevance match · UnverifiedOpenAlex · Europe PMC · checked 6 Sept 2026
Introduction: With the advancement of imaging technologies, the efficiency of acquiring plant phenotypic information has significantly improved. The integration of deep learning has further enhanced the automatic recognition of plant structures and the accuracy of phenotypic parameter extraction. To enable efficient monitoring of tomato water stress, this study developed a deep learning-based framework for phenotypic trait extraction and parameter computation, applied to tomato images collected under varying water stress conditions. Methods: Based on the You Only Look Once version 11 nano (YOLOv11n) object detection model, adaptive kernel convolution (AKConv) was integrated into the backbone's C3 module with kernel size 2 convolution (C3k2), and a recalibration feature pyramid detection head based on the P2 layer was designed. Results and discussion: Results showed that the improved model achieved a 4.1% increase in recall, a 2.7% increase in mAP50, and a 5.4% increase in mAP50-95 for tomato phenotype recognition. Using the bounding box information extracted by the model, key phenotype parameters were further calculated through geometric analysis. The average relative error for plant height was 6.9%, and the error in petiole count was 10.12%, indicating good applicability and accuracy for non-destructive crop phenotype analysis. Based on these extracted traits, multiple sets of weighted combinations were constructed as input features for classification. Seven classification algorithms-Logistic Regression, Support Vector Machine, Random Forest, Decision Tree, K-Nearest Neighbors, Naive Bayes, and Gradient Boosting-were used to differentiate tomato plants under different water stress conditions. The results showed that Random Forest consistently performed the best across all combinations, with the highest classification accuracy reaching 98%. This integrated approach provides a novel approach and technical support for the early identification of water stress and the advancement of precision irrigation.
Why it matches plant phenotyping methodsトマト画像から植物高や葉柄数などの表現型形質を抽出・計算する深層学習フレームワークを開発し、精度評価も行っており、表現型取得手法が研究の中心である。
abstractthis study developed a deep learning-based framework for phenotypic trait extraction and parameter computation
Leaves are the key organs in photosynthesis and nutrient production, and leaf counting is an important indicator of banana plant health and growth rate. However, in complex orchard environments, leaves often overlap, the background is cluttered, and illumination varies, making accurate segmentation and detection challenging. To address these issues, we propose a lightweight banana leaf detection and counting method deployable on embedded devices, which integrates a space–depth-collaborative reasoning strategy with multi-scale feature enhancement to achieve efficient and precise leaf identification and counting. For complex background interference and occlusion, we design a multi-scale attention guided feature enhancement mechanism that employs a Mixed Local Channel Attention (MLCA) module and a Self-Ensembling Attention Mechanism (SEAM) to strengthen local salient feature representation, suppress background noise, and improve discriminability under occlusion. To mitigate feature drift caused by environmental changes, we introduce a task-aware dynamic scale adaptive detection head (DyHead) combined with multi-rate depthwise separable dilated convolutions (DWR_Conv) to enhance multi-scale contextual awareness and adaptive feature recognition. Furthermore, to tackle instance differentiation and counting under occlusion and overlap, we develop a detection-guided space–depth position modeling method that, based on object detection, effectively models the distribution of occluded instances through space–depth feature description, outlier removal, and adaptive clustering analysis. Experimental results demonstrate that our YOLOv8n MDSD model outperforms the baseline by 2.08% in mAP50-95, and achieves a mean absolute error (MAE) of 0.67 and a root mean square error (RMSE) of 1.01 in leaf counting, exhibiting excellent accuracy and robustness for automated banana leaf statistics.
Why it matches plant phenotyping methodsバナナ葉の検出・計数という植物形態・生育指標を対象に、複雑環境での画像解析手法を開発し、精度評価しているため、植物フェノタイピング手法が中心である。
abstractwe propose a lightweight banana leaf detection and counting method deployable on embedded devices
Accurate and non-destructive estimation of leaf area index (LAI) is crucial for monitoring rice growth and predicting yield. This study tested the applicability of non-destructive method for estimating rice canopy LAI using the ratio of near-infrared to photosynthetically active radiation (NIR/PAR) transmitted through the rice canopy to four rice cultivars with different leaf characteristics and plant architectures. We further compared the accuracy of the present method with a conventional plant canopy analyzer estimation. The NIR/PAR method accurately estimated LAI across all cultivars regardless of leaf characteristics (nitrogen content, leaf mass per area) or plant architecture (height, stem number, biomass). Furthermore, the NIR/PAR method accurately estimated LAI even in dense canopies (> 8 m 2 m −2 ) where the plant canopy analyzer underestimated LAI. These findings demonstrate the robustness and accuracy of the NIR/PAR method for rice LAI estimation, suggesting its potential for improving growth assessment, yield prediction, and developing smart agriculture technologies.
Why it matches plant phenotyping methodsイネ群落のLAIという植物形質を、NIR/PAR透過光比で非破壊推定する手法の適用性・精度・頑健性を品種間で検証し、従来法とも比較しているため、方法が研究の中心です。
abstractThis study tested the applicability of non-destructive method for estimating rice canopy LAI using the ratio of near-infrared to photosynthetically active radiation (NIR/PAR) transmitted through the rice canopy to four rice cultivars with different leaf characteristics and plant architectures.
Quantifying crop responses to increasing temperatures is critical for predicting the productivity and sustainability of agricultural systems under environmental change. Physiological trait data associated with maximum Rubisco carboxylation ( V cmax ) and maximum electron transport ( J max ) rates are especially important predictors of crop response to elevated temperatures. However, when generating V cmax and J max data, steady-state methods of gas exchange measurements are time-consuming; thus, non-steady-state methods have been developed to obtain these measurements faster, prospectively allowing for trait data collection of considerably more varieties of crops. Globally important and geographically widespread vineyards are of particular interest due to the high economic value and the susceptibility of these managed systems to climate warming, especially in Canada, where the annual rate of warming far exceeds global averages. In this study, we examined the efficacy of the high-throughput, non-steady-state dynamic assimilation technique (DAT) for obtaining V cmax and J max data from wine grapes. Specifically, we measured V cmax and J max (alongside leaf nitrogen [N] concentrations and leaf mass per unit area [LMA]) across seven of the world's most common wine grape ( Vitis vinifera L.) varieties, namely, Cabernet franc, Cabernet sauvignon, Merlot, Pinot noir, Riesling, Sauvignon blanc, and Viognier. Our results show that V cmax and J max estimates derived from the DAT were strongly correlated to those obtained through the steady-state method ( r 2 = 0.748 and 0.908, respectively), and J max did not differ significantly between the two methods. Additionally, leaf N explained 43%-46% and 56%-58% of the variation in V cmax and J max , respectively, across both methods. Our results suggest that the DAT represents a viable tool for rapidly estimating intraspecific variation in important physiological traits and allows for increased replication and the inclusion of additional varieties when evaluating the responses of wine grape and other crops to climate warming.
Why it matches plant phenotyping methodsワインブドウの生理形質を高速取得する動的同化技術（DAT）を定常法と比較検証しており、植物表現型の測定法が中心的である。
abstractwe examined the efficacy of the high-throughput, non-steady-state dynamic assimilation technique (DAT) for obtaining V cmax and J max data from wine grapes.
Reproduction assets foundThe paper's physiological trait data (Vcmax, Jmax, leaf N, LMA for seven wine grape varieties) are openly deposited in the University of Toronto Borealis Dataverse, per the Data Availability Statement. No author analysis code or trained models are reported.Dataset · publicThe data that support the findings of this study are openly available in the Borealis Repository—University of Toronto Dataverse at https://doi.org/10.5683/SP3/URPVFF .Open asset ↗Borealis Repository—University of Toronto Dataverse · 10.5683/SP3/URPVFFlines:277-347Plant phenotyping relevance match · UnverifiedOpenAlex · Crossref · Europe PMC · checked 6 Sept 2026
Accurate acquisition of tobacco phenotypic traits is crucial for growth monitoring, cultivar selection, and other scientific management practices. Traditional manual measurements are time-consuming and labor-intensive, making them unsuitable for large-scale, high-throughput field phenotyping. The integration of 3D reconstruction and stem-leaf segmentation techniques offers an effective approach for crop phenotypic data acquisition. In this study, we propose a tobacco phenotyping method that combines unmanned aerial vehicle (UAV) remote sensing with an improved PointNet++ model. First, a 3D point-cloud dataset of field-grown tobacco plants was generated using multi-view UAV imagery. Next, the PointNet++ architecture was enhanced by incorporating a Local Spatial Encoding (LSE) module and a Density-Aware Pooling (DAP) module to improve the accuracy of stem and leaf segmentation. Finally, based on the segmentation results, an automated pipeline was developed to compute key phenotypic traits, including plant height, leaf length, leaf width, leaf number, and internode length. Experimental results demonstrated that the improved PointNet++ model achieved an overall accuracy (OA) of 95.25% and a mean intersection over union (mIoU) of 93.97% for tobacco plant segmentation-improvements of 5.12% and 5.55%, respectively, over the original PointNet++ model. Moreover, using the segmentation results from the improved PointNet++ model, the predicted phenotypic values exhibited strong agreement with ground-truth measurements, with coefficients of determination (R²) ranging from 0.86 to 0.95 and root mean square errors (RMSE) between 0.31 and 2.27 cm. This study provides a technical foundation for high-throughput phenotyping of tobacco and presents a transferable framework for phenotypic analysis in other crops.
Why it matches plant phenotyping methodsUAV 3D点群、改良PointNet++による茎葉分割と形質推定パイプラインが研究の中心であり、複数のタバコ形質を自動取得・検証している。
abstractIn this study, we propose a tobacco phenotyping method that combines unmanned aerial vehicle (UAV) remote sensing with an improved PointNet++ model.
WheatGrowth chamberLeafPhysiological trait estimationGrowth / development / phenologyLeaf traits
Summary Disentangling genotype × environment (G×E) effects is critical to understand the performance of wheat across different environments. A framework for doing this was previously presented in a model that integrated knowledge of crop physiology and the Vrn gene feedback loop to explain and predict the time of anthesis. The aims of this study were: 1) provide an updated description of the Cereal Anthesis Molecular Phenology (CAMP) model; 2) to verify the model’s assumptions regarding the relationship between Vrn gene expression and the timing of phenological stages in a set of diverse genotypes and environments; 3) to use the CAMP model to establish a phenotyping strategy for use in genetic studies and model parameterisation. Six wheat genotypes with a range of cool temperature and photoperiod sensitivities were evaluated. Apical development, final leaf number (FLN) and temporal expression of Vrn1, Vrn2 and Vrn3 were compared with model predictions. There was a clear relationship between FLN responses to cool temperature and photoperiod, the timing of phenological events and the patterns of Vrn gene expression for all genotypes. There was general agreement between the temporal patterns of foliar gene expression observed with those assumed by CAMP, but some obvious discrepancies. These may be related to differences between gene expression in foliar (observed) and apical (assumed by the model) parts of the plant, or differences in the way observed and modelled gene expression are scaled. Overall, the model described all the observed development responses to environment and provides a basis for building quantitative predictions of field-based development from genotypic and environmental data. A protocol is presented for phenotyping wheat using FLN measured in specific combinations of temperature and photoperiod. It allows easy and unconfounded measure of key developmental phenotypes that clearly relate to the genetic make-up of the plants and underlying gene expression profiles.
Why it matches plant phenotyping methodsCAMPモデルの更新・検証と、FLNを用いた小麦発育形質のフェノタイピングプロトコル提示が研究の中心であり、単なる生物学的測定ではない。
abstractto use the CAMP model to establish a phenotyping strategy for use in genetic studies and model parameterisation.
Reproduction assets foundThe paper's CAMP model code, analysis scripts, and data are explicitly stated as publicly available on the authors' GitHub repository, with specific URLs for the model notebook and the test/plotting script.Code · publicwere also validated and the best-performing sets selected. A
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description of each of the primers used in this study is given in the supplementary material
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2.9.1 Model set-up and operation.
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The CAMP model was coded into a Python script which is available at
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https://github.com/HamishBrownPFR/CAMP/blob/master/CAMP.ipynb. A formal
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description of the code and parameterisation scheme is given in the supplementary material.
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The FLN developmental phenotypes measured for each genotype (Section 3.1) were used to
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derive the Vrn expression parameters needed for CAMP. Each of the treatments was
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simulated using CAMP wOpen asset ↗https://github.com/HamishBrownPFR/CAMP/pdf-raw-page:14 lines:1-70Code · publicpression parameters needed for CAMP. Each of the treatments was
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simulated using CAMP with its corresponding daily temperature and Pp, so its predictions of
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Vrn gene expression could be compared with those observed. The script running the CAMP
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code and producing the graphs displayed in this paper can be viewed at
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https://github.com/HamishBrownPFR/CAMP/blob/master/Tests/CAMPCETests.py.360
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CC-BY-NC 4.0 International license
available under a
(which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made
The copyright holder for this preprint
this version posted September 12, 2025.
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https://doiOpen asset ↗https://github.com/HamishBrownPFR/CAMP/pdf-raw-page:14 lines:1-70Code · publicnd testing of the model in
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broader contexts. EW contributed substantially to the improvement of model concepts and the
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manuscript and all authors provided final checking.
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8. Data Availability
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All the data and scripts used to analyse data and produce graphs as well as CAMP model code are
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Allard V, Otto V, Bela K, Rousset M, Le Gouis J, Martre P. 2012. The quantitative
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response of wheat vernalization to environmental variables indicates that vernalization is not
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a response to cold temperature. Journal of Experimental Botany 63: 847–857.
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Baumont M, Parent B, Manceau L, Brown HE, DOpen asset ↗https://github.com/HamishBrownPFR/CAMP/pdf-raw-page:31 lines:1-68Plant phenotyping relevance match · UnverifiedOpenAlex · arXiv · checked 6 Sept 2026
Plant phenotyping involves analyzing observable characteristics of plants to better understand their growth, health, and development. In the context of deep learning, this analysis is often approached through single-view classification or regression models. However, these methods often fail to capture all information required for accurate estimation of target phenotypic traits, which can adversely affect plant health assessment and harvest readiness prediction. To address this, the Growth Modelling (GroMo) Grand Challenge at ACM Multimedia 2025 provides a multi-view dataset featuring multiple plants and two tasks: Plant Age Prediction and Leaf Count Estimation. Each plant is photographed from multiple heights and angles, leading to significant overlap and redundancy in the captured information. To learn view-invariant embeddings, we incorporate 24 views, referred to as the selection vector, in a random selection. Our ViewSparsifier approach won both tasks. For further improvement and as a direction for future research, we also experimented with randomized view selection across all five height levels (120 views total), referred to as selection matrices.
Why it matches plant phenotyping methods多視点画像から植物年齢と葉数を推定する手法を開発・評価し、ベンチマーク課題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。
abstractTo learn view-invariant embeddings, we incorporate 24 views, referred to as the selection vector, in a random selection.
Why it matches plant phenotyping methodsスマートフォンLiDAR・写真測量による樹体3D計測法を開発・精度検証し、樹高・幹径・葉面積という植物形態形質へ適用しており、フェノタイピング手法が中心である。
abstractThis study investigates the performances of a low-cost, consumer-grade device-the iPhone 13 Pro equipped with an integrated LiDAR sensor and RGB camera-for 3D scanning of fruit tree structures.
Plant phenotyping relevance match · UnverifiedbioRxiv · Europe PMC · checked 6 Sept 2026
O_LISeasonal and spatial variations in leaf area index (LAI) are challenging to detect in tropical forests due to dynamic lighting conditions and the subtle differences in the variation. Many existing LAI software tools offer one-click processing of all images through auto-threshold segmentation (e.g., HemispheR, HemiPy and Hemisfer), but they produce results with large discrepancies. Some software (e.g. CAN-EYE) requires manual tuning of each image, making large-scale analysis impractical. C_LIO_LIWe analysed 19,000 images from four tropical forest subtypes and found that using coding-free AI software to process hemispherical images can significantly improve the consistency of leaf-sky segmentation, thereby enhancing LAI outcomes. C_LIO_LIThe results show that replacing the auto-threshold with AI substantially reduced inter-software disagreement and delineated correct seasonal and spatial patterns. CAN-EYE was able to identify seasonal patterns but produced less accurate results than the CAN-EYE-AI integrated approach due to subjective user bias. C_LIO_LIThe high consistency achieved through AI integration enables reliable cross-site and cross-operator comparisons. As users can customise the AI model according to local images and combine the AI model with other LAI software, our integrated, affordable, and coding-free method offers wide applicability and high consistency of LAI measurements, facilitating the advancement of tropical forest monitoring and research. C_LI Data/Code for peer review statementOne of the key features of this method is coding-free. The method is explained in Protocolv20251118.docx. We have uploaded R codes for drawing figures in a zip pack. These codes and the protocol will be deposited in the Zenodo (or figshare) database under accession link [TBC]. Since Zenodo allows authors to archive updated versions after publication, we may update the protocol by uploading a revised version to Zenodo. Please check the Zenodo archive for any new versions. In the protocol, we note that users can use Image_conversion_20220407.m and lets_change_values.R instead of the Renormalise function of ilastik to modify values in the classification output images. These codes are not essential for users following our protocol, but could be useful for integrating ilastik with other LAI software not covered in this paper. Additionally, the protocol mentions that Gather_LAI_fapar_from_caneye.R can be used to consolidate output Excel files, eliminating the need to manually open each file. Field measurements of LAI and GCC are available on request.
Why it matches plant phenotyping methods森林のLAIという植物形態・構造形質を、AIによる画像セグメンテーションで推定する方法の開発・統合・比較評価が中心であり、植物フェノタイピング手法に該当する。
abstractusing coding-free AI software to process hemispherical images can significantly improve the consistency of leaf-sky segmentation, thereby enhancing LAI outcomes.
The vertical distribution of leaves plays a crucial role in the growth process of maize. Understanding the vertical spectral characteristics of maize leaves is crucial for monitoring their growth. However, accurate estimation of the vertical distribution of leaf area remains a significant challenge in practical investigations. To address this, we used a 3D RTM to simulate the layered canopy spectra of maize, revealing the impact of canopy structure on remote sensing penetration depth across different growth stages and planting densities. The results of this study revealed differences in detection depth across growth stages. During the early growth stage, the depth was concentrated in the bottom 1 to 3 leaves of the canopy, reaching 1 to 4 leaves at the ear stage and 1 to 7 leaves during the grain-filling stage. The planting density had a notable effect on the detection depth at the bottom of the canopy. Moreover, compared with the other spectral bands, the near-infrared spectral range exhibited greater sensitivity to density variations. In terms of LAI inversion, a FuseBell-Hybrid model was constructed. We analyzed VIs across different planting density and canopy structural scenarios and found that compared with lower layers, increased density reduced the relative change rate in the upper leaf layers. The sensitivity patterns differed between plant architectures: VIred exhibited density-dependent sensitivity, with distinct responses between plant types, and MTVI2 demonstrated optimal performance for mid-canopy monitoring. This study highlights the influence of the heterogeneous structural characteristics of maize canopies on remote sensing detection depth during different phenological stages, providing theoretical support for enhancing multilayer crop monitoring in precision agriculture.
Why it matches plant phenotyping methods分光計測と3D放射伝達モデルを用いてトウモロコシ冠層の検出深度およびLAI推定法を構築・評価しており、植物形質取得手法が研究の中心である。
abstractTo address this, we used a 3D RTM to simulate the layered canopy spectra of maize
Reproduction assets foundThe paper states its analysis code was uploaded to a public GitHub repository, which qualifies as an authors' public code asset for the LAI phenotyping analysis. No separate phenotype dataset or model checkpoint deposit is explicitly stated.Code · publicData availability
The code have been uploaded to Github: https://github.com/aaawitch/code .Open asset ↗https://github.com/aaawitch/codelines:290-311Code / dataset availability confirmedOpenAlex · checked 14 Sept 2026
Leaf area is a critical trait in plant physiology and agronomy, yet conventional measurement approaches such as those using ImageJ remain labor-intensive, user-dependent, and difficult to scale for high-throughput phenotyping. To address these limitations, we developed a fully automated, open-source Python tool for quantifying citrus leaf area from scanned images using multi-mask HSV segmentation, contour-hierarchy filtering, and batch calibration. The tool was validated against ImageJ across 11 citrus cultivars (n = 412 leaves), representing a broad range of leaf sizes and morphologies. Agreement between methods was near perfect, with correlation coefficients exceeding 0.997, mean bias within ±0.14 cm2, and error rates below 2.5%. Bland–Altman analysis confirmed narrow limits of agreement (±0.3 cm2) while scatter plots showed robust performance across both small and large leaves. Importantly, the Python tool successfully handled challenging imaging conditions, including low-contrast leaves and edge-aligned specimens, where ImageJ required manual intervention. Processing efficiency was markedly improved, with the full dataset analyzed in 7 s compared with over 3 h using ImageJ, representing a >1600-fold speed increase. By eliminating manual thresholding and reducing user variability, this tool provides a reliable, efficient, and accessible framework for high-throughput leaf area quantification, advancing reproducibility and scalability in digital phenotyping.
Why it matches plant phenotyping methods柑橘葉面積の画像ベース測定ツールを開発し、ImageJとの比較検証と高スループット性能評価を行っており、植物フェノタイピング手法が研究の中心である。
abstractwe developed a fully automated, open-source Python tool for quantifying citrus leaf area from scanned images using multi-mask HSV segmentation, contour-hierarchy filtering, and batch calibration.
Reproduction assets foundThe paper's authors publicly released the Python leaf-area analysis tool (source code and documentation) on GitHub with an archived citable version on Zenodo, as stated in the Data Availability Statement.Code · publich received no external funding.
Institutional Review Board Statement: Not applicable.
Informed Consent Statement: Not applicable.
Data Availability Statement: The Python-based tool created in this study for automated leaf area
analysis, along with its source code and documentation, is publicly available on GitHub and Zenodo
at: https://github.com/esuarez-12/Leaf-Area-Analyzer, accessed on 26 August 2025, and a perma-
nent, citable version of the tool, corresponding to version v1.0.0, has been archived on Zenodo with
the following DOI: https://doi.org/10.5281/zenodo.16951132. These materials are openly accessible
and provided under an open-source license to support reproducibility and furtherOpen asset ↗esuarez-12/Leaf-Area-Analyzer · Leaf-Area-Analyzerpdf-raw-page:16 lines:1-45Code · publicmated leaf area
analysis, along with its source code and documentation, is publicly available on GitHub and Zenodo
at: https://github.com/esuarez-12/Leaf-Area-Analyzer, accessed on 26 August 2025, and a perma-
nent, citable version of the tool, corresponding to version v1.0.0, has been archived on Zenodo with
the following DOI: https://doi.org/10.5281/zenodo.16951132. These materials are openly accessible
and provided under an open-source license to support reproducibility and further research.
Acknowledgments: The authors would like to thank Jake Price and the UGA Cooperative Extension
Lowndes County Office for the use of their citrus trees. The UGA Citrus Lab is committed to
advancing citOpen asset ↗10.5281/zenodo.16951132pdf-raw-page:16 lines:1-45Code / dataset availability confirmedOpenAlex · Europe PMC · checked 6 Sept 2026
Field / plotMultispectral / hyperspectralLeafSegmentationLeaf traits
Abstract Accurate segmentation of leaf area is a critical task in plant phenotyping and precision agriculture, as it directly impacts yield estimation, disease monitoring, and weed management. Conventional Convolutional Neural Networks (CNNs), such as UNet and its variants, often struggle with capturing long range contextual dependencies and preserving fine structural boundaries, while pure transformer based architectures like the Vision Transformer (ViT) suffer from poor inductive bias and limited data efficiency. To overcome these challenges , we propose a SegFormer inspired model that integrates Edge Gated Multi Head Spectral Attention (EG MHSA) for robust leaf area segmentation. The spectral attention mechanism captures discriminative frequency domain representations across spectral bands, while the edge gating module enhances boundary preservation by adaptively fusing multiscale edge features. Evaluated on the benchmark CWFID dataset, the proposed model achieves superior performance with an F1score of 97.33%, IoU of 95.84%, and the lowest loss of 0.0395, outperforming UNet variants and transformer based baselines. Qualitative analysis further demonstrates its effectiveness in accurately delineating fine leaf boundaries under complex field conditions. The ablation results highlight the complementary contributions of spectral attention and edge gating in boosting segmentation performance. With its lightweight architecture, edge focused refinement, and strong generalization capability, the proposed approach sets a new benchmark for leaf area segmentation and provides a practical, scalable solution for agricultural applications.
Why it matches plant phenotyping methods葉面積の画像セグメンテーション手法を開発・ベンチマーク評価しており、植物フェノタイピングにおける形態形質抽出が中心である。
abstractAccurate segmentation of leaf area is a critical task in plant phenotyping and precision agriculture
Reproduction assets foundThe paper evaluates its leaf area segmentation model on the public CWFID dataset (60 field images with pixel-level annotations), and the authors explicitly state the datasets are publicly available at the cwfid GitHub repository. No author analysis code or trained model checkpoints are reported.Dataset · publicThe datasets used in the study are publicly available in the repository: https://github.com/cwfid/Open asset ↗https://github.com/cwfid/pdf-page:22 lines:1-27Plant phenotyping relevance match · UnverifiedOpenAlex · Crossref · checked 6 Sept 2026
The development of effective selection criteria and models under hydroponic salinity screening can be used image-based phenotyping (IBP) and statistical analysis to detect double-haploid rice with high adaptability to saline environments. Therefore, this study aimed to identify the IBP selection criteria and develop a model for potential tolerance in double-haploid rice under hydroponic salinity screening. The experimental design was a split-plot randomized complete block design. The main plot was NaCl concentration (0 mM and 120 mM), and the subplots contained ten genotypes with three replications. Selection criteria and model development were identified systematically and comprehensively through the best linear unbiased estimation, stress tolerance index, principal component analysis, factor analysis, and selection index. In addition, validation was also carried out based on conventional morphological characteristics, physiology, Na + and K + contents, and yield in saline land. The results showed that there are two tolerance index models: a morphometric (geometric) index represented by the total area and green area, and a colorimetric index defined by the green area percentage, CIVE, and GLI. The interaction of these indices effectively mapped the double-haploid rice genotypes based on their tolerance levels and adaptability to salinity stress. The colorimetric index was a reliable indicator of the potential adaptability of double-haploid rice lines in saline fields. This study provides a novel approach for developing effective selection criteria and models for rice tolerance, especially double-haploid line, under hydroponic salinity screening, which can accelerate the identification of genotypes with high adaptability to saline environments.
Why it matches plant phenotyping methods画像ベース表現型測定から形態・色彩指標と選抜モデルを開発し、形態・生理・収量等で検証しており、表現型取得・抽出手法が研究の中心である。
abstractthis study aimed to identify the IBP selection criteria and develop a model for potential tolerance in double-haploid rice under hydroponic salinity screening.
The precise segmentation of crop organs plays a crucial role in optimizing crop cultivation strategies and enhancing yield potential. This study proposes a novel deep learning network, CotSegNet, which enables precise and non-destructive segmentation of cotton organs facilitating the extraction of phenotypic characteristics. In CotSegNet, an improved attention mechanism known as CGLUConvFormer is designed. This mechanism significantly improves segmentation accuracy by emphasizing important features while diminishing redundant information. Furthermore, CotSegNet integrates the SegNext attention mechanism. This mechanism facilitates the efficient extraction and integration of multi-scale features, thereby significantly enhancing the ability of CotSegNet to comprehend and segment point cloud data. To address issues related to leaf adhesion and coplanarity that lead to over-segmentation problems, this study proposes an improved region-growing algorithm. This algorithm enhances the accuracy of leaf instance segmentation through the incorporation of distance constraints. In comparative experiments with five advanced deep learning networks (PointNet, PointNet++, DGCNN, SPoTr and CurveNet), CotSegNet demonstrated outstanding performance. Its Precision, Recall, F1-score, and IoU reached 95.06 %, 93.32 %, 94.61 %, and 89.80 %, respectively. The experimental results demonstrated that the proposed method effectively extracted the phenotypic parameters of stem height, leaf length, leaf width, and leaf area in cotton plants. These measurements exhibited a high degree of consistency with manual assessments, yielding determination coefficients of 0.947, 0.948, 0.955, and 0.961 for each parameter respectively. The corresponding root mean square errors were recorded as 0.852 cm, 0.492 cm, 0.551 cm, and 1.674 cm² respectively. The research findings demonstrate that this approach offers essential technical support for the collection and analysis of high throughput phenotyping data in field crops.
Why it matches plant phenotyping methods綿花器官の点群セグメンテーションと表現型形質抽出のためのCotSegNetおよび改良領域成長法を開発し、手動測定との検証も行っており、表現型取得が研究の中心である。
abstractThis study proposes a novel deep learning network, CotSegNet, which enables precise and non-destructive segmentation of cotton organs facilitating the extraction of phenotypic characteristics.
This study integrates a dynamic plant growth model with a three-dimensional (3D) radiative transfer model (RTM) for maize traits retrieval using high spatial–spectral resolution airborne data. The research combines the Discrete Anisotropic Radiative Transfer (DART) model with the Dynamic L-System-based Architectural maize (DLAmaize) growth model to simulate field reflectance. Comparison with the 1D RTM SAIL revealed limitations in representing row structure effects, field slope, and complex light–canopy interactions. Novel Global Sensitivity Analyses (GSA) were carried out using dependence-based methods to overcome limitations of traditional variance-based approaches, enabling better characterization of hyperspectral sensitivity to changes in leaf biochemistry, canopy architecture, and soil moisture. GSA provided complementary results to assess estimation uncertainties of the proposed traits retrieval method across growth stages. A hybrid inversion framework combining DART simulations with an active learning strategy using Kernel Ridge Regression was implemented for traits estimation. The approach was validated using ground data and HyPlant-DUAL airborne hyperspectral images from two field campaigns in 2018 and achieved high retrieval accuracy of key maize traits: leaf area index (LAI, R 2 =0.91, RMSE=0.42 m 2 /m 2 ), leaf chlorophyll content (LCC, R 2 =0.61, RMSE=3.89 μ g/cm 2 ), leaf nitrogen content (LNC, R 2 =0.86, RMSE=1.13 × 10 −2 mg/cm 2 ), leaf dry matter content (LMA, R 2 =0.84, RMSE=0.15 mg/cm 2 ), and leaf water content (LWC, R 2 =0.78, RMSE=0.88 mg/cm 2 ). The validated models were used to generate two-date 10 m resolution maps, showing good spatial consistency and traits dynamics. The findings demonstrate that integrating 3D RTMs with dynamic growth models is suited for maize trait mapping from hyperspectral data in varying growing conditions.
Why it matches plant phenotyping methods3D放射伝達モデル、動的生長モデル、ハイパースペクトル画像、機械学習を統合し、トウモロコシ形質推定法を開発・検証しており、形質取得が研究の中心である。
abstractThis study integrates a dynamic plant growth model with a three-dimensional (3D) radiative transfer model (RTM) for maize traits retrieval using high spatial–spectral resolution airborne data.
Implementing high spectral resolution imaging from the Environmental Mapping and Analysis Program (EnMAP) paved the way for detailed retrieval of agricultural traits for accurate crop monitoring and management. The proposed methodology involves the integration and detailed analysis of Radiative Transfer Modelling (RTM) with an integrated approach of machine learning (ML) and Active Learning (AL) algorithms for the retrieval of the Leaf Chlorophyll Content (LCC), Carotenoids (Car) and Leaf Area index (LAI) of wheat cropland from the continuous three years of the dataset. Reflectance values of leaf were collected using Analytical Spectral Device (ASD) − Spectroradiometer data ranging from 350-2500 nm and EnMAP satellite hyperspectral data extends spectral data range varies between 420 nm to 1000 nm in the visible and near-infrared (VNIR) of EMR region, and from 900 nm to 2450 nm in the shortwave infrared (SWIR) region for crop parameters mapping for a larger spatial area of Varanasi district, Uttar Pradesh, India. The PROSPECT + SAIL (PROSAIL) RTM was employed to simulate spectral (reflectance) data, and fourteen ML algorithms were assessed for implementation into a hybrid model. Kernel Ridge regression (KRR) was combined with Euclidean-based Diversity (EBD) algorithms to retrieve crop characteristics due to their exceptional accuracy and reduced uncertainty. Spectral profiles were further used to train hybrid models using PCA (Principal Component Analysis) feature selection, and combined techniques (ML + AL) were applied to retrieve LCC, Car, and LAI. Afterwards, biophysical and biochemical spatial large-scale estimation were provided through atmospherically corrected, and noise-removed EnMAP hyperspectral data with the help of a trained and tested hybrid (ML + AL) model and validated with the ground-measured datasets. The performance indicators showed significantly very high values of correlation during calibration (LCC = 0.99, Car = 0.74, and LAI = 0.99) and validation (LCC = 0.66, Car = 0.57, and LAI= 0.88). The work showed that the optimized hybrid (KRR + AL) models customized for EnMAP hyperspectral data can efficiently estimate the wheat biophysical and biochemical parameters in near-real time therefore, expanding this workflow to agricultural fields may enable more effective monitoring and management of wheat crops.
Why it matches plant phenotyping methodsEnMAPハイパースペクトルデータ、PROSAIL、機械学習・アクティブラーニングを統合し、コムギのLCC、カロテノイド、LAIを推定・検証する手法が研究の中心である。
abstractThe proposed methodology involves the integration and detailed analysis of Radiative Transfer Modelling (RTM) with an integrated approach of machine learning (ML) and Active Learning (AL) algorithms for the retrieval of the Leaf Chlorophyll Content (LCC), Carotenoids (Car) and Leaf Area index (LAI) of wheat cropland
Leaf Area Index (LAI) is a key parameter that reflects canopy structure and influences photosynthetic activity. Traditional remote sensing methods using spectral indices usually struggle with saturation at LAI > 3.0 m² m–² in crop fields. Light detection and ranging (LiDAR) systems offer a solution by capturing detailed canopy structures. This study used drone-based LiDAR and hyperspectral imagery to predict LAI across 60 plots in five wheat fields in Israel. Field LAI, assessed using a handheld optical sensor, ranged from 0.25 to 7.7 m² m–². LiDAR-derived metrics, including height, gap fraction, and canopy volume features, were combined with spectral indices for LAI prediction. These metrics were used in simple linear regression (SLR) and five machine learning (ML) models: artificial neural network (ANN), random forest, ridge regression, relevance vector machine, and extreme gradient boosting. Shapley’s additive explanations identified key predictive features. Results show that ML models significantly improved prediction performance (R² = 0.59–0.90) compared to single metric SLR models (R² = 0.09–0.67). Combined LiDAR-spectral models outperformed spectral- and LiDAR-only models. ANN achieved the best results, with a mean R² of 0.90, normalized RMSE of 6 %, and residual prediction deviation (RPD) score of 3.34, accurately predicting LAI up to 5.5 m² m–². LiDAR alone or in combination with spectral metrics improved LAI predictions. While some spectral metrics ranked high, LiDAR-derived metrics, particularly canopy volume-related, consistently emerged among the most important features, with gap fraction and height metrics also contributing to the models. This study demonstrates the efficacy of drone-based LiDAR for non-destructively predicting LAI in wheat fields, offering a valuable tool for crop model calibration and evaluation and addressing the challenge of scaling from leaf to canopy.
Why it matches plant phenotyping methodsドローン由来のLiDAR・ハイパースペクトル画像から小麦群落のLAIを推定する手法を開発・比較し、機械学習モデルの性能を評価しているため、植物表現型取得が中心である。
abstractThis study used drone-based LiDAR and hyperspectral imagery to predict LAI across 60 plots in five wheat fields in Israel.
This study integrates a dynamic plant growth model with a three-dimensional (3D) radiative transfer model (RTM) for maize traits retrieval using high spatial–spectral resolution airborne data. The research combines the Discrete Anisotropic Radiative Transfer (DART) model with the Dynamic L-System-based Architectural maize (DLAmaize) growth model to simulate field reflectance. Comparison with the 1D RTM SAIL revealed limitations in representing row structure effects, field slope, and complex light–canopy interactions. Novel Global Sensitivity Analyses (GSA) were carried out using dependence-based methods to overcome limitations of traditional variance-based approaches, enabling better characterization of hyperspectral sensitivity to changes in leaf biochemistry, canopy architecture, and soil moisture. GSA provided complementary results to assess estimation uncertainties of the proposed traits retrieval method across growth stages. A hybrid inversion framework combining DART simulations with an active learning strategy using Kernel Ridge Regression was implemented for traits estimation. The approach was validated using ground data and HyPlant-DUAL airborne hyperspectral images from two field campaigns in 2018 and achieved high retrieval accuracy of key maize traits: leaf area index (LAI, R²=0.91, RMSE=0.42 m²/m²), leaf chlorophyll content (LCC, R²=0.61, RMSE=3.89 μg/cm²), leaf nitrogen content (LNC, R²=0.86, RMSE=1.13 × 10⁻² mg/cm²), leaf dry matter content (LMA, R²=0.84, RMSE=0.15 mg/cm²), and leaf water content (LWC, R²=0.78, RMSE=0.88 mg/cm²). The validated models were used to generate two-date 10 m resolution maps, showing good spatial consistency and traits dynamics. The findings demonstrate that integrating 3D RTMs with dynamic growth models is suited for maize trait mapping from hyperspectral data in varying growing conditions.
Why it matches plant phenotyping methods3D放射伝達モデル、成長モデル、ハイパースペクトル画像、機械学習を統合し、トウモロコシの複数形質を推定する手法を開発・検証しており、植物表現型取得が研究の中心である。
abstractThis study integrates a dynamic plant growth model with a three-dimensional (3D) radiative transfer model (RTM) for maize traits retrieval using high spatial–spectral resolution airborne data.
Areca catechu L. (Arecaceae) is an important cash crop in Taiwan(China), Hainan (China), and several South Asian countries. Areca palm yellow leaf disease (YLD) poses a severe threat, leading to reduced yields and eventual plant mortality. The current study differentiates areca palm damage solely based on spectral features. We are the first to integrate LiDAR point clouds with multispectral imagery to distinguish between different damage levels. We standardized the geographic coordinate systems of the LiDAR data and multispectral images, then aligned them using the control point method. During YLD infestation, areca palm leaves turn yellow and eventually fall off. We surveyed over 1000 trees, counting the number of leaves and calculating the proportion of the canopy area covered by yellowing foliage. Based on crown color changes and leaf count, we classified areca palm damage into five levels: healthy, slightly damaged, moderately damaged, severely damaged, and dying/dead. Meanwhile, this study optimized the individual tree segmentation process for areca palm. Using trunk point clouds, we generated seed points and applied region-growing cluster segmentation to achieve a more accurate individual tree profile compared to the traditional watershed algorithm. Based on the segmentation results and crown contours, we extracted the structural and spectral characteristics of individual trees. Multiple algorithms were then applied to classify areca palms into four damage levels: healthy, slightly damaged, moderately damaged, and severely damaged. The classification achieved an overall accuracy of 86.46% and a kappa value of 0.819. The inclusion of LiDAR data improved the overall accuracy by 23.94% compared to using only spectral features. Comparatively, past studies have relied only on spectral differences to determine the area of leaf yellowing and thus further determine the level of damage. In this study, we further noted the structural changes in the canopy caused by leaf abscission, provided a more realistic description of the different damage levels, and constructed more accurate models. The proposed method demonstrates great potential in YLD damage classification and provides an important basis for precise management of plantations.
Why it matches plant phenotyping methodsLiDAR・UAVマルチスペクトル画像から個体樹の構造・スペクトル形質を抽出し、葉黄化と葉落による植物病害の被害レベルを分類する手法が研究の中心であり、個体セグメンテーションの最適化と精度評価も行っている。
abstractWe are the first to integrate LiDAR point clouds with multispectral imagery to distinguish between different damage levels.
Plant phenotyping relevance match · UnverifiedCrossref · OpenAlex · Europe PMC · checked 15 Sept 2026
With the increasing global demand for food, breeding soybean varieties resistant to dense planting is crucial for achieving high and stable yields. Traditional phenotyping methods are limited by insufficient temporal resolution and challenges in dynamic modeling continuity, making it difficult to elucidate the intrinsic relationship between canopy development rate and yield stability. Moreover, existing machine learning models often neglect temporal dependencies in time series predictions, leading to insufficient biological interpretability. This study proposes an innovative approach integrating spatiotemporal deep learning and dynamic modeling to quantify the dynamic changes in canopy parameters using UAV high-throughput phenotyping technology, revealing the key regulatory mechanisms of traits associated with resistance to dense planting. Based on a two-year field experiment (2022-2023) in northeast China (Qiqihaer, black soil region), this study set high (50w plants/ha) and low density (30w plants/ha) treatments across 208 soybean varieties, combined with multispectral UAV imagery (15-18 times per season) and ground-truth data, to develop a time series prediction model for leaf area index (LAI). Comparing the performance of spatiotemporal residual networks (ST-ResNet), long short-term memory networks (LSTM), and traditional random forests (RF), the ST-ResNet model demonstrated significantly superior prediction accuracy (R 2 = 0.90, RMSE = 0.23 m 2 /m 2 ), effectively capturing the continuous dynamics of canopy growth through its spatiotemporal feature fusion ability. By fitting the time series curves of LAI, canopy cover (CC), and plant height (PH) with P-spline, 15 intermediate traits (e.g., ΔMean LAI-mid ) were extracted. Mixed models and SHAP interpretability analysis showed that ΔMean LAI-mid was most correlated with the dense planting yield index (ΔYield, r = 0.51). Furthermore, the high-frequency data acquisition and automated analysis framework using UAVs enabled high-throughput phenotypic screening for 208 varieties per year, significantly improving efficiency compared to traditional methods that rely on manual sampling. This study pioneers the integration of spatiotemporal deep learning with dynamic trait modeling, markedly improving the temporal continuity and stability of LAI estimation compared to traditional single-time-point prediction methods. This advancement allows for more precise quantification of canopy development rates across various growth stages, enabling a systematic analysis of how these dynamic patterns influence resistance to dense planting. By elucidating the dynamic relationship between intermediate traits and yield, this approach offers a high-precision, interpretable phenotypic analysis framework for effectively screening soybean varieties resilient to dense planting.
Why it matches plant phenotyping methodsUAV画像と時系列深層学習・動的モデリングを用いてLAI、群落被覆、草丈などの植物形質を推定し、高スループット表現型スクリーニング基盤を開発・検証しているため、方法が研究の中心である。
abstractThis study proposes an innovative approach integrating spatiotemporal deep learning and dynamic modeling to quantify the dynamic changes in canopy parameters using UAV high-throughput phenotyping technology
Crop water stress (CWS) monitoring using UAV remote sensing has traditionally been limited to empirical models and specific growth stages, restricting dynamic, season-long assessment. This study proposes an integrated framework combining multispectral UAV observations with the SAFYE crop model via Ensemble Kalman Filter -based data assimilation (DA) to improve maize growth simulation and enable continuous CWS monitoring. Based on three years of field experiments, accurate inversion models for leaf area index (LAI; R 2 = 0.837, RMSE = 0.397) and aboveground biomass (AGB; R 2 = 0.862, RMSE = 224 g m −2 ) were developed using a random forest algorithm. Model parameters were calibrated using particle swarm optimization, and UAV-derived data were assimilated to optimize simulations of crop growth and actual evapotranspiration (ET c act ). Results show that DA significantly enhanced model performance: LAI simulation RMSE decreased from 0.29–0.61–0.11–0.36 (NRMSE: 3.57–11.56 %), AGB simulation RMSE from 148.2–255.7–49.3–136.8 g m −2 (NRMSE: 5.39–14.27 %), and agreement index (d) exceeded 0.92. ET c act simulations accurately reflected responses to irrigation and rainfall, with only 4.97 % relative error under full irrigation (W4). The developed crop water stress index (CWSI) effectively quantified water stress under different irrigation treatments. A significant negative correlation was observed between CWSI reduction and irrigation amount, while the severity of water deficit was positively correlated with the peak value of CWSI differences in terms of both timing and magnitude. This study establishes a robust UAV–crop model DA framework for dynamic, season-long CWS diagnosis and assessment.
Why it matches plant phenotyping methodsUAV画像からLAI・AGB・作物水ストレスを推定し、作物モデルとのデータ同化で季節を通じて評価する技術的フレームワークが研究の中心である。
abstractThis study proposes an integrated framework combining multispectral UAV observations with the SAFYE crop model via Ensemble Kalman Filter -based data assimilation (DA) to improve maize growth simulation and enable continuous CWS monitoring.
Abstract Spatiotemporal fusion addresses challenges in crop growth monitoring: namely, spatial discreteness of high‐resolution imagery and spectral mixing in high‐temporal‐frequency data. These can hinder accurate yield and phenology estimates, especially in fragmented semi‐arid landscapes. To improve winter wheat monitoring, we quantitatively and qualitatively evaluated two normalized differential vegetation index (NDVI) fusion methods: the spatial and temporal nonlocal filter‐based fusion model (STNLFFM) and enhanced spatial and temporal adaptive reflectance fusion model (ESTARFM). Our primary focus was to address the limitations of MODIS data in crop phenology monitoring, specifically to resolve the challenges of spatial and temporal resolution. STNLFFM, incorporating inter‐image coefficients and temporal variation, outperformed ESTARFM by eliminating stripe artifacts from prolonged high‐resolution data gaps. Additionally, assimilating NDVI data via the four‐dimensional variational (4DVAR) method resulted in improved accuracy, with a 6.001% mean absolute percentage error in leaf area index (LAI) estimation, compared with 6.285% using the CERES‐Wheat model. Yield estimation accuracy was enhanced by 2.734% through the 4DVAR‐assimilated LAI, particularly in addressing inaccuracies in mountain‐cropland transition zones. This study addresses this gap by providing an integrated spatiotemporal fusion framework that mitigates data quality and scale mismatches, thereby improving the accuracy of crop growth monitoring and yield predictions. This study highlights the following: (1) the operational advantages of STNLFFM in fragmented landscapes and (2) the potential of variational assimilation to reduce model uncertainties. The proposed approach is applicable to precision agriculture in topographically complex regions and provides a scalable solution for addressing mixed‐pixel challenges in the Earth's observational data.
Why it matches plant phenotyping methods冬小麦のフェノロジー・LAI・収量を推定する時空間融合と4DVAR同化フレームワークを開発・比較・評価しており、植物形質推定手法が研究の中心である。
abstractwe quantitatively and qualitatively evaluated two normalized differential vegetation index (NDVI) fusion methods: the spatial and temporal nonlocal filter‐based fusion model (STNLFFM) and enhanced spatial and temporal adaptive reflectance fusion model (ESTARFM).
Canopy chlorophyll content (CCC) is a critical indicator for assessing crop photosynthetic capacity, nitrogen status, and the occurrence of diseases. Accurate estimation of CCC holds significant importance for precision agriculture, providing a scientific basis for crop management, yield prediction, and stress detection. CCC is commonly defined as the product of leaf area index (LAI) and leaf chlorophyll content (LCC). Traditional methods of acquiring CCC rely on destructive sampling, which limits large-scale application. Hyperspectral remote sensing enables non-destructive acquisition of rich spectral information from the crop canopy across the visible to near-infrared spectrum, offering a promising approach for CCC estimation. This study proposes a convolutional neural network-based model, CanopyChlNet, to jointly estimate LAI and LCC, thereby deriving CCC. The model utilizes a one-dimensional CNN structure to effectively extract deep spectral features from hyperspectral data, improving estimation accuracy. Field-measured canopy hyperspectral reflectance and corresponding LAI and LCC data from winter wheat and potato were used to train and validate the model. The CanopyChlNet model outperformed both Random Forest (RF) and Partial Least Squares Regression (PLSR) in estimating LAI, LCC, and CCC, achieving R2 values of 0.709, 0.775, and 0.718, with RMSE values of 0.803 m2 ·m−2, 5.288 µg·cm− 2, and 34.938 µg·cm− 2, respectively. In comparison, RF yielded R2 values of 0.636, 0.685, and 0.667, and RMSE values of 0.896 m2 ·m− 2, 6.396 µg·cm− 2, and 37.901 µg·cm− 2. PLSR achieved R2 values of 0.522, 0.709, and 0.586, with RMSE values of 1.029 m2 ·m− 2, 6.042 µg·cm− 2, and 42.332 µg·cm− 2.These results demonstrate that CanopyChlNet is a high-precision model for estimating crop LCC and CCC. This study demonstrates that integrating deep learning with hyperspectral remote sensing significantly enhances the estimation accuracy of key crop parameters, providing an effective tool for crop growth monitoring.
Why it matches plant phenotyping methods作物キャノピーのLAI・LCC・CCCという植物形質を、ハイパースペクトルデータとCNNで推定する手法を開発・検証しており、フェノタイピング手法が研究の中心である。
abstractThis study proposes a convolutional neural network-based model, CanopyChlNet, to jointly estimate LAI and LCC, thereby deriving CCC.
Plant phenotyping relevance match · UnverifiedOpenAlex · Europe PMC · checked 6 Sept 2026
Introduction: The phenotypic traits of tomato plants reflect their growth status, and investigating these characteristics can improve tomato production. Traditional deep learning models face challenges such as excessive parameters, high complexity, and susceptibility to overfitting in point cloud segmentation tasks. To address these limitations, this paper proposes a lightweight improved model based on the ResNet architecture. Methods: The proposed network optimizes the traditional residual block by integrating bottleneck modules and downsampling techniques. Additionally, by combining curvature features and geometric characteristics, we custom-designed specialized convolutional layers to enhance segmentation accuracy for tomato stem and leaf point clouds. The model further employs adaptive average pooling to improve generalization and robustness. Results: Experimental validation demonstrated that the optimized model achieved a training accuracy of 95.11%, a 3.26% improvement over the traditional ResNet18 model. Testing time was reduced to 4.02 seconds (25% faster than ResNet18's 5.37 seconds). Phenotypic parameter extraction yielded high correlation with manual measurements, with coefficients of determination (R²) of 0.941 (plant height), 0.752 (stem diameter), 0.945 (leaf area), and 0.943 (leaf inclination angle). The root mean square errors (RMSE) were 0.506, 0.129, 0.980, and 3.619, respectively, while absolute percentage errors (APE) remained below 6% (1.965%-5.526%). Discussion: The proposed X-ResNet model exhibits superior segmentation performance, demonstrating high accuracy in phenotypic trait extraction. The strong correlations and low errors between extracted and manually measured data validate the feasibility of 3D point cloud technology for tomato phenotyping. This study provides a valuable benchmark for plant phenotyping research, with significant practical and theoretical implications.
Why it matches plant phenotyping methodsトマトの3D点群から茎・葉を分割し、草丈・茎径・葉面積・葉傾斜角を抽出する手法を開発・検証しており、植物表現型取得が研究の中心である。
abstractPhenotypic parameter extraction yielded high correlation with manual measurements
• In this study, we take tomato as an example and propose an improved deep learning combined with clustering algorithm for plant point cloud segmentation. First, a multi-temporal tomato point cloud dataset is constructed by combining multi-view image sequences with neural radiation field (NeRF), and preprocessing and labeling are completed; second, single channel attention (SCA) and global feature aggregation module (GFA) are introduced into the PointNet++ model, respectively, to construct the TomatoSegNet model, which improves the tomato dataset's semantic segmentation performance, while the edge filter was added to the DBSCAN algorithm to improve it and enhance the instance segmentation performance of canopy leaves; finally, a total of six phenotypic parameters were extracted based on the segmented organs. The experimental results show that the TomatoSegNet model has an average precision (mP) of 97.82%, an average recall (mR) of 98.62%, an average F1 score (mF1) of 97.97%, an average intersection and merger ratio (mIoU) of 96.84%, and an overall accuracy (OA) of 94.22% in the tomato dataset, which proves that the use of semantic segmentation algorithms feasibility of stem and leaf segmentation; the improved DBSCAN algorithm achieved an instance segmentation accuracy of 96.03% for leaves, which improved the segmentation accuracy of overlapping leaves; the coefficients of determination between the measured and calculated values of the six phenotypic parameters (plant height, stem thickness, leaf inclination, leaf length, leaf width, and leaf area) were 0.983, 0.903, 0.916, 0.962, 0.951, and 0.978. The method proposed in this study realizes the accurate segmentation and extraction of phenotypic parameters from the 3D point cloud of plants, which provides a valuable reference for automated phenotypic analysis of plants.. In plant phenotyping research, accurate organ segmentation and phenotype extraction is the key to accelerate the process of big data analysis and intelligent breeding.In this study, we take tomato as an example and propose an improved deep learning combined with clustering algorithm for plant point cloud segmentation. First, a multi-temporal tomato point cloud dataset is constructed by combining multi-view image sequences with neural radiation field (NeRF), and preprocessing and labeling are completed; second, single channel attention (SCA) and global feature aggregation module (GFA) are introduced into the PointNet++ model, respectively, to construct the TomatoSegNet model, which improves the tomato dataset's semantic segmentation performance, while the edge filter was added to the DBSCAN algorithm to improve it and enhance the instance segmentation performance of canopy leaves; finally, a total of six phenotypic parameters were extracted based on the segmented organs. The experimental results show that the TomatoSegNet model has an average precision (mP) of 97.82%, an average recall (mR) of 98.62%, an average F1 score (mF1) of 97.97%, an average intersection and merger ratio (mIoU) of 96.84%, and an overall accuracy (OA) of 94.22% in the tomato dataset, which proves that the use of semantic segmentation algorithms feasibility of stem and leaf segmentation; the improved DBSCAN algorithm achieved an instance segmentation accuracy of 96.03% for leaves, which improved the segmentation accuracy of overlapping leaves; the coefficients of determination between the measured and calculated values of the six phenotypic parameters (plant height, stem thickness, leaf inclination, leaf length, leaf width, and leaf area) were 0.983, 0.903, 0.916, 0.962, 0.951, and 0.978. The method proposed in this study realizes the accurate segmentation and extraction of phenotypic parameters from the 3D point cloud of plants, which provides a valuable reference for automated phenotypic analysis of plants.
Why it matches plant phenotyping methods3D点群の生成、深層学習・クラスタリングによる器官分割、6種類の植物表現型抽出を中心に開発・検証した研究であり、植物フェノタイピング手法が明確に中核である。
abstractpropose an improved deep learning combined with clustering algorithm for plant point cloud segmentation