Plant phenotyping methods.

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

Accurate point-cloud segmentation of cotton organs is essential for precise phenotypic characterization. However, reliable instance segmentation of cotton bolls in field-derived point clouds remains challenging because foliage occlusion, contact between adjacent bolls and incomplete reconstruction obscure instance boundaries. Here we present RQ-PointNeXt, an end-to-end framework that directly maps input point clouds to boll instance masks within a unified trainable network. Built on PointNeXt, it incorporates relative-elevation geometric channel attention in the shallow encoder to fuse global channel context with elevation and surface-normal cues. Its Query–mask branch integrates semantic guidance, center-seeded queries and a center-aware mask prior to suppress background responses, localize instances and constrain mask extent. Hungarian matching and multitask optimization establish one-to-one query–instance assignments, whereas query-based decoding produces instance masks without external geometric clustering. We evaluated the framework on 226 field-grown cotton plants containing 720 annotated boll instances reconstructed from UAV multi-view imagery using neural radiance fields. On the held-out test set, overall accuracy, mean class accuracy and mean intersection over union reached 0.8942, 0.8980 and 0.8076, respectively. AP25, AP50 and AP75 were 0.7359, 0.5585 and 0.2777, yielding an mAP25/50/75 of 0.5240. The framework provides instance-level outputs for boll counting and spatial analysis in high-throughput field phenotyping.

Why it matches plant phenotyping methods綿花ボールの点群インスタンス分割を開発・評価し、計数や空間解析に利用可能な植物器官表現型を抽出する方法が中心である。

abstractHere we present RQ-PointNeXt, an end-to-end framework that directly maps input point clouds to boll instance masks within a unified trainable network.

Sparse phenotyping for wheat grain yield enabled by multiomics prediction →

Grain yield is a central target in wheat breeding, yet accurately predicting it remains challenging because it depends on many genes and responds strongly to environmental variation. Genomic selection (GS) has improved breeding efficiency by enabling genome-based prediction of genetic merit, but predictability (PA) for grain yield is often limited under stress environments. At the same time, advances in high-throughput phenotyping (HTP) using unmanned aerial vehicles (UAVs) provide phenomic data that capture environment-responsive plant performance and may complement genomic information. In this study, we evaluated genomic and phenomic models for predicting grain yield in elite bread wheat lines across irrigated, drought, and heat-stress environments. Using a sparse phenotyping framework, we compared parametric and non-parametric models. PA was evaluated within environments and under cross-environment sparse phenotyping scenarios. Genomic models provided a stable baseline and enabled effective information sharing across environments when phenotypic data were incomplete. Phenomics-only models captured environment-specific plant responses but were more sensitive to environmental context. Multiomics models that integrated genomic and phenomic information consistently achieved the highest PA, with the largest gains observed under stress conditions. Overall, our results demonstrate that integrating genomics and UAV-based phenomics within sparse phenotyping designs offers a practical and scalable approach to improve grain yield prediction in wheat.

Why it matches plant phenotyping methodsUAV由来のフェノミクスを用いた疎な表現型取得と予測モデルを中心に、環境横断で評価しており、収量という植物形質の推定手法が主要な貢献である。

abstractadvances in high-throughput phenotyping (HTP) using unmanned aerial vehicles (UAVs) provide phenomic data that capture environment-responsive plant performance

Cognitive UAV-driven agro-surveillance framework for predicting crop stress–induced yield loss using spatio-temporal learning and adaptive irrigation control →

Precision agriculture is becoming more and more of a challenge that requires the use of intelligent systems that are able to predict stress and prevent yield loss before it is too late. Traditional methods of agricultural surveillance are predominantly reactive with irrigation demands being based on thresholds or individual yield forecasts models that do not represent the intricate spatio-temporal interactions that exist between crop physiology, soil status, and environmental stresses. Besides, the majority of the current practices do not have an autonomous decision-making approach to preventive intervention which leads to inefficient use of water and slows down the response to stress. This paper suggests a cognitive UAV-assisted agro-surveillance system to predict yield vulnerability caused by crop stress and optimize adaptive irrigation with the help of spatio-temporal deep and reinforcement learning. The framework combines UAV-obtained RGB and multispectral and thermal imagery with measurements of soil sensors and meteorological data obtained with the Crop Health and Environmental Stress Dataset. A new GeoSpatio-TRiNet model is used to acquire long-range spatial relationship, time stress development, and diffusion of stresses across agricultural regions. The model predicts the vulnerability trajectories of the stress instead of the direct yield regression, and this allows early detection of yield risk. Such predictions serve to generate a cognitive environmental state of a Soft ActorCritic (SAC) reinforcement learning agent that autonomously computes zone-based irrigation behaviors to reduce the recurrence of stress at the minimum water usage cost. As shown by the results of the experiment, the proposed framework has a stress forecasting accuracy of 96.3% and performs much better than the traditional machine learning, CNN-based, and transformer-based baselines. The system also decreases the predicted yield vulnerability by 46.6 and enhances water-use efficiency by 41.1 as compared to irrigation strategies based on rules. The results confirm the usefulness of spatio-temporal intelligence with predictive control in terms of effectiveness, and the proposed framework is a scalable and sustainable solution to precision agriculture of the next generation.

Why it matches plant phenotyping methodsUAV画像とセンサーデータから作物ストレスの時系列状態および収量脆弱性を推定する計算・センシング手法が研究の中心であり、灌漑制御への応用も技術評価の一部として記述されている。

abstractThe framework combines UAV-obtained RGB and multispectral and thermal imagery with measurements of soil sensors and meteorological data

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

Boll-opening concentration is critical for mechanical cotton harvesting, yet it is still assessed mainly by manual records and single time-point indicators that miss temporal dynamics. To bridge the lack of a unified workflow linking vision foundation models, multi-temporal boll-opening monitoring, and harvest decision-making, we developed a cross-scale UAV high-throughput phenotyping framework centered on DINO-BollGX. DINO-BollGX couples a DINO v3 backbone, a RetinaNet detection head, and an adaptive refinement-and-suppression module for robust open-boll detection under complex field conditions. Using multi-temporal UAV imagery collected over two years for 383 cultivars, we reconstructed plot-scale time series of open-boll counts, derived dynamic features describing progression and intensity changes, and proposed a Cotton Boll-Opening Temporal Stability Index (CTSI) to quantify boll-opening rhythm and concentration; CTSI was further integrated with a time-based risk function to generate harvest decision curves. Under unified data and training settings, DINO-BollGX achieved precision = 0.91, F1 = 0.88, and AP@0.50 = 0.80, and provided accurate boll-count estimation (R 2 =0.98; MAE=3.10), outperforming YOLOv11, YOLOv12, YOLOv13, and RT-DETR. On an independent cross-year dataset acquired at 5 m altitude, it obtained precision = 0.98 and F1 = 0.87. An internal consistency analysis showed that CTSI had the expected negative association with Window_days (r = −0.83) and positive associations with Max_count (r = 0.78) and the boll-opening efficiency index (r = 0.92), reflecting the co-occurrence of temporal compactness and main-phase opening intensity in the cultivar population. CTSI ranged from −2.72 to 4.69 across cultivars, enabling identification of highly synchronized boll-opening. Harvest decision curves indicated that the relative net income index peaked at day 67 after the first observation and a compact optimal harvest window near the end of monitoring; on a fixed harvest date, Kuche 130292 (CTSI=4.69) produced 486 open bolls versus 182 for Xinluzao 36 (CTSI=0.53) and 90 for Andizhan-60 (CTSI=-2.72). Overall, the framework integrates dynamic boll-opening phenotyping with harvest timing optimization, supporting scalable cultivar screening and mechanization-ready deployment, with potential extension to harvest decision scenarios in other crops.

Why it matches plant phenotyping methodsUAV画像と基盤モデルを用いて綿花の開絮を検出・定量し、時系列表現型指標を構築・検証する方法が研究の中心であるため。

abstractwe developed a cross-scale UAV high-throughput phenotyping framework centered on DINO-BollGX.

Precision monitoring of leaf area index and chlorophyll content of major field crops in Northern Europe using UAV remote sensing and radiative transfer modeling →

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).

UAV3DCrop: Benchmarking 3D Reconstruction in Repeated Multi-Angle UAV Crop Surveys →

Accurate 3D crop monitoring underpins data-driven precision agriculture by enabling field-scale analysis of plant structure, growth dynamics, and management response. Modern 3D reconstruction methods perform strongly on generic benchmarks, but rendered appearance may not translate into metrically and agronomically useful geometry in crop fields. We introduce UAV3DCrop, a public benchmark of repeated multi-angle unmanned aerial vehicle (UAV) crop surveys. It contains 88,830 RGB images at $5280 \times 3956$ pixels, with a ground sampling distance of 3.6-5.8 mm, from 91 scenes spanning corn, soybean, wheat, and oat. Track A evaluates seven scene-optimized methods -- Neural Radiance Field (NeRF) and 3D Gaussian Splatting (3DGS) variants -- on held-out views, photogrammetry-referenced depth, and canopy-height recovery. Track B tests four pretrained feed-forward models on zero-shot camera-pose and geometry estimation. The scene-optimized methods rank differently across the three targets: Splatfacto-big leads appearance, whereas Scaffold-GS leads depth and is statistically tied with Splatfacto for canopy height. Among feed-forward models, MapAnything leads on seven of the eight metrics, while the remaining models vary more across crops and fail severely on absolute scale in a way that alignment conceals. Repeated acquisitions reveal further sensitivities that differ by output type and by model, associated with position within the acquisition sequence and with tie-point multiplicity. Current 3D reconstruction methods are therefore not yet interchangeable for agronomic use: no single method wins on appearance, geometry, and canopy height at once, and only one of four feed-forward models recovers usable metric scale. The dataset is publicly available at https://link-dev.github.io/UAV3DCrop/

Why it matches plant phenotyping methods植物キャノピー高さという明示的な形質を対象に、UAV 3D再構成手法をベンチマークし、公開データセットとして提供しているため、フェノタイピング手法が中心である。

abstractWe introduce UAV3DCrop, a public benchmark of repeated multi-angle unmanned aerial vehicle (UAV) crop surveys.

From field to sky: measurement and modeling of transgenic switchgrass pollen dispersal in the atmosphere →

Accurate tracking and measurement of pollen dispersal in the atmosphere are essential for assessing cross-pollination risks, particularly in the case of genetically engineered (GE) crops. We conducted a series of unique release-recapture field studies with GE switchgrass in Oliver Springs, TN, USA. Two hundred transgenic switchgrass plants (Panicum virgatum L. "Performer") were planted at the center of a clear-cut field, with one block of 100 plants expressing orange fluorescent protein (OFP) under a switchgrass ubiquitin promoter (PvUBI1) and another block of 100 plants expressing OFP driven by a maize pollen-specific promoter (Zm13). Pollen was sampled from the atmosphere using fixed (ground-based) and mobile (drone-based) sampling devices at different distances from the source field, with Lagrangian stochastic dispersal simulations run for sampling periods using high-resolution wind measurements. The pollen emission rate was estimated by combining simulated and measured pollen concentrations, and strong diurnal trends were observed. Diurnal emission rate trends were positively correlated with wind speed, temperature, and vapor pressure deficit, while negatively correlated with relative humidity. In low-wind meandering conditions, incorporating changing wind direction into the dispersal modeling improved pollen emission rate estimation and model-measurement comparisons. This study assesses the effectiveness of high- and low-volume pollen samplers in relation to source strength up to 1 km from the source, enhancing understanding of pollen measurement techniques. Additionally, it is a proof-of-concept for drone-based pollen sampling and GMO pollen tracking using fluorescence measurements. Results from our experiments have significant implications for cross-pollination risk assessment, prediction, and management of airborne allergens.

Why it matches plant phenotyping methods固定・ドローン搭載サンプラー、蛍光測定、風況モデルを組み合わせて植物由来の花粉放出率を推定し、花粉測定技術を評価することが中心であるため、植物の生殖状態・放出特性に関するフェノタイピング手法として採用。

abstractPollen was sampled from the atmosphere using fixed (ground-based) and mobile (drone-based) sampling devices

Drones detect fine-scale vegetation structure across cover types and disturbance histories →

Introduction: Habitat restoration is necessary for the conservation and management of plant and animal species, especially in rare ecosystems. Drones may be well-suited to monitor changes in plant and animal communities in response to restoration efforts. The objective of the study was to examine whether drone imagery can detect differences in vegetation across multiple contexts. Materials and methods: Using a commercially available drone, I captured and processed aerial imagery with an open-source photogrammetric processing program. Point cloud data were processed to generate a vegetation density index, which was quantified across four cover types and compared between disturbance histories. In addition, using automated radio tracking, I compared vegetation density between used and available locations for Eastern Whip-poor-wills during the day and at night. Results: In August 2024, a drone flight covering a 3.05 km2 area of pine barrens captured 3372 images. Vegetation density differed by cover type (p = 0.001) and was greater in recently disturbed sites (p = 0.002). Scrub oak and recently burned sites had ~30% and ~12% greater vegetation density than deciduous forests and plots > 2 years post-disturbance, respectively. Vegetation density was lower at Eastern Whip-poor-will used locations than at available locations (151.0 vs. 159.7 points/m2, p < 0.001). Conclusions: Analysis of fine-scale differences in vegetation structure was important in discriminating subtle differences in habitat selection for Eastern Whip-poor-wills. This study demonstrated that drones and relatively simple image processing can be practical tools for restoration when quantifying and monitoring vegetation differences in dynamic ecosystems.

Why it matches plant phenotyping methodsドローン画像と点群処理により植生密度・植生構造を定量化する手法を中心に、異なる植生条件での適用性を評価しているため、植物表現型計測の方法適用研究に該当する。

abstractPoint cloud data were processed to generate a vegetation density index, which was quantified across four cover types and compared between disturbance histories.

LUF-net: A physically informed color calibration method for UAV RGB images based on exposure and irradiance information. →

Accurate color representation is critical for UAV-based crop phenotyping, yet UAV images are often distorted by variable illumination and camera exposure settings. Here, we propose Lite U-net FiLM (LUF-net), a lightweight U-net framework integrated with feature-wise linear modulation (FiLM) layers, which incorporates both multispectral-derived irradiance and camera exposure parameters as auxiliary inputs. This metadata-aware design enables dynamic modulation of intermediate image features, allowing the network to disentangle unified canopy color from environmental artifacts. Experiments conducted across diverse crop types (soybean, rice, maize), flight altitudes (6m, 12m, 25m, 40m), and illumination conditions (overcast skies, cloudy, sunny, early morning) demonstrate that the LUF-net model substantially reduces the mean absolute percentage error to below 5.5%, outperforming conventional Gray-world, U-net, AlexNet-MLP, and SIDBlock-MLP methods. Ablation experiments further show that both irradiance and exposure metadata provide complementary information, while FiLM-based conditioning effectively integrates these acquisition parameters into feature learning, jointly contributing to improved color reconstruction performance. Moreover, correlation analysis indicates that the model's color reconstruction errors are weakly dependent on irradiance and exposure settings, confirming that LUF-net reduces sensitivity to external imaging conditions while maintaining physically meaningful and robust corrections.

Why it matches plant phenotyping methodsUAV画像の色校正手法を開発し、複数作物・撮影条件で性能検証しており、作物フェノタイピングの画像取得・補正が中心である。

abstractAccurate color representation is critical for UAV-based crop phenotyping, yet UAV images are often distorted by variable illumination and camera exposure settings.

AI for Precision Fertilizer and Pesticide Application: An Integrated Real-Time Deep Learning and IoT-Driven Field Management System →

Abstract Blanket-rate agrochemical scheduling — a practice wherein the same quantity of fertilizer or pesticide is spread uniformly across an entire field irrespective of spatial or temporal crop need — persists as the dominant farm management paradigm across rural India and large parts of South Asia. This approach generates cascading inefficiencies: excess nitrogen drains into waterways, off-target pesticide deposits devastate pollinators, input costs erode thin profit margins, and wide-scale greenhouse gas release from soil microbial activity accelerates climate change. The study documented here addresses this challenge through a purpose-built, four-layer intelligent field management platform. The platform ingests continuous data from drone-mounted multispectral cameras, in-field IoT soil probes, a wireless weather station, and cloud-sourced Sentinel-2 satellite imagery, then passes these inputs through a cascaded AI inference stack. A fine-tuned YOLOv8-L network performs real-time pest and foliar disease localisation; a ResNet-50 backbone quantifies canopy health across five stress gradients; a two-layer stacked LSTM projects short-horizon yield trajectories; and a Deep Q-Network autonomously plans drone spray routes weighted by field-specific prescription maps. Field validation spanned two consecutive growing seasons (Rabi 2022–23 and Kharif 2023–24) across six georeferenced plots covering 4.8 ha at Baramati, Maharashtra. Outcome metrics recorded during head-to-head comparison with conventional practice included a disease detection score of 95.6% mAP, a 47.3% reduction in total nitrogen applied, a 38.1% decrease in pesticide volume, and a 22.4% uplift in harvested grain weight. Together, these field-verified numbers substantiate the operational readiness of integrated AI precision agriculture for smallholder deployment.

Why it matches plant phenotyping methodsマルチスペクトル画像・深層学習による病害局在化とキャノピー健康状態の定量化を中核機能とする統合プラットフォームであり、植物の病害状態・生育状態を直接推定して現地検証している。

abstractThe platform ingests continuous data from drone-mounted multispectral cameras, in-field IoT soil probes, a wireless weather station, and cloud-sourced Sentinel-2 satellite imagery, then passes these inputs through a cascaded AI inference stack.

MatchPlant: An Open-Source Pipeline for UAV-Based Single-Plant Detection from Undistorted Images with Orthomosaic Projection →

Accurate identification of individual plants from unmanned aerial vehicle (UAV) imagery is essential for high-throughput phenotyping and data-driven decision-making in plant breeding. This study presents MatchPlant, a modular, open-source Python pipeline with a graphical user interface for UAV-based single-plant detection and geospatial trait extraction. The pipeline integrates UAV image processing, user-guided annotation of selected undistorted images, convolutional neural network–based object-detection training, forward projection of bounding boxes onto an orthomosaic, and shapefile generation for spatial phenotypic analysis. This workflow preserves native image geometry during detection while maintaining coordinate traceability from source imagery to georeferenced outputs. Across five independent training runs using early-season maize imagery, MatchPlant achieved source-image-level detection performance of AP@0.5 = 90.3 ± 1.1% and mAP@0.5:0.95 = 43.4 ± 2.9%. Orthomosaic-level evaluation after forward projection showed AP@0.5 = 89.7 ± 0.8% and recall = 93.7 ± 1.2%, demonstrating the workflow’s ability to transfer plant detections into georeferenced outputs. Plant-level traits, including plant height derived from canopy height models and NDVI derived from vegetation index rasters, showed strong agreement with manual annotations ( r = 0.87–0.97). Detection outputs were reused across time points with minimal additional annotation, supporting temporal phenotyping during early growth. The framework was validated using maize imagery from a single site and growing season, where plant separation remained clear. By combining modular design, reproducibility, and coordinate traceability, MatchPlant provides an open-source workflow for UAV-based plant-level analysis, with broader applications requiring validation across additional crops, sensors, growth stages, GSDs, and field conditions.

Why it matches plant phenotyping methodsUAV画像から個体検出と植物形質（草高・NDVI）を抽出する、オープンソースの再利用可能なワークフローを開発・検証しており、植物フェノタイピング手法が中心である。

abstractThis study presents MatchPlant, a modular, open-source Python pipeline with a graphical user interface for UAV-based single-plant detection and geospatial trait extraction.

Optimizing SfM parameters for RGB-only individual-tree detection in loblolly pine (Pinus taeda L.) and mixed pine-hardwood stands →

Unmanned aerial vehicle (UAV) photogrammetry offers a cost-effective approach to tree-level detection, however, Structure-from-Motion (SfM) outputs are sensitive to processing choices and site conditions, which can alter canopy representation and reduce individual-tree detection accuracy. Here, we systematically evaluate how SfM reconstruction quality and depth-map filtering influence RGB-only individual-tree detection under controlled acquisition conditions. Objectives were to (i) identify an optimal SfM-derived point-cloud configuration for delineating individual trees, and (ii) implement and test a segmentation workflow (local-maxima treetop detection plus Dalponte2016 in lidR) for detecting and counting trees. We assessed RGB-only SfM for individual-tree detection (ITD) across thirteen 1.21-ha loblolly pine ( Pinus taeda ) plots located in two counties in the state of Alabama in the southeastern United States; eight even-aged plantations and five mixed pine-hardwood stands, while holding image acquisition parameters constant. Using Agisoft Metashape Professional (Agisoft LLC, St. Petersburg, Russia), dense-cloud quality (Lowest, Low, Medium, High, Ultra High) and depth-map filtering (Disabled, Mild, Moderate, Aggressive) were varied in a 5 × 4 full-factorial design; assessment metrics included point-cloud density, canopy-surface completeness, canopy-height-model (CHM) agreement with field heights, and ITD precision/recall/F1. We identified a single high-resolution configuration (Ultra High + Disabled) by screening parameter sets for structural accuracy and suppression of false peaks. Using this configuration, CHMs matched field heights in Washington County, Alabama (R 2 = 0.96; RMSE = 0.44 m; bias = − 0.01 m) and in Cullman County, Alabama (R 2 = 0.44; RMSE = 1.14 m; bias = − 0.09 m); pooled performance was R 2 = 0.98; RMSE = 0.54 m; bias = − 0.01 m. ITD accuracy at the primary 3 m match radius yielded a precision of 0.03; recall = 0.29; F1 = 0.05 in the even-aged plantations (Washington) and a precision of 0.03; recall = 0.12; F1 = 0.05 in mixed pine–hardwood stands (Cullman); pooled F1 = 0.05. The selected parameters and workflow are reproducible and transferable, provide insight into RGB-SfM ITD performance, and indicate when lidar remains preferable for crown delineation.

Why it matches plant phenotyping methodsRGB-SfMによる個体樹の検出・樹高推定と、SfM設定およびセグメンテーションワークフローの系統的評価が研究の中心であり、植物の樹冠構造・樹高という形態形質を抽出する方法を検証している。

abstractwe systematically evaluate how SfM reconstruction quality and depth-map filtering influence RGB-only individual-tree detection

A Three-Dimensional Phenotyping Framework for Quantifying Soybean Resilience to Pest Stress in the Field →

Abstract Biotic stress is a major, yet under-quantified, driver of global soybean yield losses, and field-based phenotyping under pest pressure remains a critical bottleneck for crop improvement. Using multi-temporal data from soybean genotypes grown under insecticide-protected and unprotected conditions in Brazil, we present a UAV-based, large-scale and non-invasive framework for evaluating genotype performance under natural pest pressure. We introduce a three-dimensional metric that jointly captures productivity, feature-level similarity as a proxy for tolerance, and phenological response through days to maturity. This unified formulation enables field-based quantification of pest resilience and replaces labor-intensive and often unreliable direct pest collection and counting. To operationalize this framework, we integrate vegetation indices and self-supervised visual embeddings into a common representation space linking feature stability, performance response and phenological development. This approach enables robust identification of genotypes that maintain feature integrity, minimize developmental delay and sustain yield under pest pressure, with genotypic differences peaking during the pod-fill (R3–R4) and grain-fill (R5.1–R5.5) stages. Overall, this work establishes a scalable, field-ready paradigm for quantifying crop resilience to biotic stress and provides a practical pathway to accelerate breeding for stable yields under real-world agricultural conditions.

Why it matches plant phenotyping methodsUAVによる大規模な圃場フェノタイピング基盤と、植生指数・視覚埋め込みを統合した新しい耐虫性表現型の定量手法が研究の中心である。

abstractwe present a UAV-based, large-scale and non-invasive framework for evaluating genotype performance under natural pest pressure

Multi-omics prediction for yellow rust in bread and durum wheat through conventional and Ai-based frameworks. →

Yellow rust (YR) is a major threat to both bread and durum wheat production, often causing substantial yield losses. Conventional visual scoring of YR severity, while widely adopted, is labor-intensive, time-consuming, and prone to human error. In this study, we evaluated the predictability (PA), defined as the correlation between predicted and observed values, using genomic and phenomic data for YR severity under multiple prediction scenarios in two biparental wheat populations (bread and durum). YR scoring was conducted on two dates, with YR severity visually assessed while unmanned aerial vehicle (UAV)-based high-throughput phenotyping (HTP) data were collected using a multispectral camera. HTP data were processed to extract spectral wavelengths and vegetation indices (VIs), and all lines were also genotyped using SNP arrays. We tested a diverse set of models, including parametric, machine learning, and deep learning approaches. PA increased markedly when HTP-derived data were used compared with genomic markers alone. For example, support vector regression (SVR) improved from 0.35 (markers only) to 0.87 (wavelengths only). However, integrating genomic and phenomic data did not yield further improvements, as models often plateaued when using HTP-derived features alone. Cross-crop prediction demonstrated promising generalization across bread and durum wheat, achieving PA values up to 0.83. For this last task, best linear unbiased prediction (BLUP) and multilayer perception (MLP) consistently provided robust performance across scenarios. These findings highlight the strong potential of UAV-based HTP for rapid, scalable, and accurate prediction of YR severity in wheat. While genomics retains broad utility for breeding, the practical integration of phenomics and AI-driven prediction pipelines will ultimately depend on breeding program strategies, resources, and objectives.

Why it matches plant phenotyping methodsUAV multispectral HTPによる小麦黄さび病重症度の推定と、複数の予測モデルの比較・検証が研究の中心であり、植物病害状態を直接推定する実質的なフェノタイピング手法研究である。

abstractHTP data were processed to extract spectral wavelengths and vegetation indices (VIs)

Automatic preprocessing pipeline for individual-plant level (IPL) soybean growth monitoring through UAV multisource imagery. →

Orthoimagery derived from unmanned aerial vehicles (UAVs) has become a valuable data source for crop-growth monitoring. Individual plant-level (IPL) information enables high-throughput analyses by capturing plant-to-plant variability within fields. However, reliable IPL-based analysis requires accurate extraction of plant-specific regions, which remains challenging in soybean cultivation due to weed interference and canopy overlap. This study proposed an automatic preprocessing framework for IPL soybean growth monitoring that integrates deep-learning-based semantic segmentation with a furrow-guided region of interest (ROI) generation strategy using UAV imagery. A segmentation model was developed using combinations of RGB and multispectral orthoimagery, and a furrow line detection algorithm was designed to generate IPL ROIs aligned with crop rows. The ensemble model combining U-Net, DeepLabV3+, and SegFormer achieved the most stable performance (F1-score up to 0.94 and IoU up to 0.89). The furrow-guided ROI generation algorithm also accurately estimated crop counts, showing strong agreement with manual observations (R² = 0.90 and RMSE = 6.35). The generated IPL ROIs enabled accurate quantification of growth-related features, with strong agreement between automatically generated and manually delineated ROIs (R² > 0.90). Overall, the proposed preprocessing framework provides a practical and scalable solution for UAV-based high-throughput phenotyping in soybean and other ridge-based cropping systems.

Why it matches plant phenotyping methodsUAV画像から個体単位の植物領域を抽出し、成長形質を定量化する前処理・セグメンテーション手法が研究の中心であるため。

abstractThis study proposed an automatic preprocessing framework for IPL soybean growth monitoring that integrates deep-learning-based semantic segmentation with a furrow-guided region of interest (ROI) generation strategy using UAV imagery.

Mapping peatland plant communities dynamics using multispectral indices coupled with a joint species distribution model →

Aims Climate change is altering northern peatland plant communities, shifting from Sphagnum mosses to vascular plants. This transition impacts ecological functions like carbon sequestration, making long-term vegetation monitoring at the site scale more critical than ever. However, current monitoring methods tend to focus on specific species or functional groups with limited spatial coverage. This study uses remote sensing to infer the spatial structure and temporal variations of peatland plant communities. Location Temperate peatland in Pyrenees Mountains, France (Bernadouze, Vicdessos). Methods Nine plots were selected across diverse microhabitats and sampled three times over the growing season of 2023 (May, June, and July). Plant species abundances were recorded, and 45 vegetation indices were derived from drone and Sentinel-2 multispectral imagery. Five vegetation indices were selected to fit a joint Species Distribution Model (JSDM) and a Random Forests (RF) model, and map species spatial distribution. Principal Coordinates Analysis (PCoA) identified plant community composition, and spatiotemporal variations were quantified in relation to environmental variables. Results Plant species occurrences could be predicted from multispectral imagery using the JSDM, with drone-based inferences (mean R 2 = 0.36) outperforming Sentinel-2 (mean R 2 = 0.29). Model performance was high for abundant species ( R 2 > 0.5), whereas predictions for rare species were less accurate ( R 2 R 2 > 0.65, P R 2 = 0.40; P R 2 = 0.04; P Conclusion This study demonstrates that drone multispectral imagery can be used to predict peatland vegetation richness and community composition and capture fine-scale heterogeneity in a small and fragmented peatland site, outperforming satellite data in spatial precision. Although our model was less accurate using satellite imagery, the use of Sentinel-2 imagery enabled long-term community tracking. By combining both, our predictive modelling framework provides a promising preliminary tool to monitor climate-induced shifts in species distributions, supporting targeted conservation.

Why it matches plant phenotyping methodsドローンおよび衛星マルチスペクトル画像から植物種の空間分布、植生多様性、群集組成を推定する画像・モデリング手法が研究の中心であり、植物状態の測定に直接結びつく。

abstractThis study uses remote sensing to infer the spatial structure and temporal variations of peatland plant communities.

Physiology-Driven Irrigation Scheduling in Ananas comosus via Hybrid Machine Learning: UAV-Based Phenotyping of Water-Related Traits Coupled with FAO-56 Soil Water Balance. →

Field-based phenotyping of water-related traits for precision irrigation in tropical agroecosystems poses a persistent methodological challenge, driven by high climatic variability and the complex water-use physiology of Crassulacean Acid Metabolism (CAM) crops such as pineapple (Ananas comosus var. MD2). We developed and validated a Physics-Informed Machine Learning (PIML) framework that integrates high-resolution UAV multispectral imagery, IoT-based microclimatic records, and a mechanistic soil water balance based on the FAO-56 Penman–Monteith standard to predict plot-scale soil moisture depletion as a proxy of plant water status. A six-month field campaign (March–August 2022) across 25 georeferenced commercial pineapple plots in the Colombian Orinoquia piedmont yielded a spatiotemporally balanced dataset of N=150 observations. Soil-adjusted vegetation indices (OSAVI, MSAVI) outperformed standard NDVI for capturing water-related canopy traits, effectively decoupling spectral responses from substrate noise. A Gradient Boosting regressor achieved R2=0.842 and RMSE=0.0705 on a normalized target scale, corresponding to a 7.05% error over the prediction range, while the traffic-light Decision Support System (DSS) for irrigation scheduling reached 91.1% accuracy (Cohen’s Kappa =0.91). Incorporating daily soil moisture depletion as a mechanistic feature improved predictive accuracy over a spectral-only baseline (ΔR2=+0.052) and anchored predictions within a physically consistent framework based on the FAO-56 water balance, with no false negatives observed for water deficit detection in the hold-out validation set. This framework advances high-throughput, population-scale phenotyping of water-related traits in open-canopy CAM crops, establishing a transferable methodology for operational precision irrigation under tropical savanna conditions.

Why it matches plant phenotyping methodsUAVマルチスペクトル画像と機械学習を用いて植物の水関連形質・水状態を推定する枠組みを開発・検証しており、表現型取得と予測手法が研究の中心である。

abstractWe developed and validated a Physics-Informed Machine Learning (PIML) framework that integrates high-resolution UAV multispectral imagery, IoT-based microclimatic records, and a mechanistic soil water balance based on the FAO-56 Penman–Monteith standard to predict plot-scale soil moisture depletion as a proxy of plant water status.

Transformer-based Reconstruction of Canopy Profiles from Large-Footprint Waveform LiDAR →

Spaceborne laser scanning (SLS) presents a cost-effective means for frequent, global-scale monitoring of forest ecosystem parameters. Compared to airborne laser scanning (ALS), SLS offers substantially greater spatial coverage and revisit frequency, but at the cost of larger footprints, sparser sampling, and attenuated return signals. These constraints typically result in a loss of fine-scale vertical canopy structure in large-footprint waveform LiDAR, thereby limiting the retrieval of ecologically meaningful forest structural metrics. To address this challenge, we developed an encoder–decoder Transformer architecture to reconstruct high-resolution vertical canopy profiles from large-footprint waveform LiDAR observations. Using waveform data acquired by NASA’s Land, Vegetation, and Ice Sensor (LVIS) – a high-altitude ALS instrument commonly used as a proxy for spaceborne missions – we trained the model to recover fine-scale canopy structure by leveraging overlapping ALS point clouds as reference data. The proposed Transformer leverages long-range vertical dependencies within waveform signals to infer canopy structural details that are degraded or unresolved in large-footprint, high-altitude observations. Results show that the proposed approach substantially improves the agreement between LVIS-derived and ALS-derived canopy structural complexity metrics, increasing correlations from R = 0.62 to 0.84 and from R = 0.76 to 0.90 for two representative metrics. This framework is readily transferable to current and future SLS missions, enabling the retrieval of super-resolved vertical canopy profiles and supporting large-area assessment of ecologically meaningful canopy structural metrics.

Why it matches plant phenotyping methodsLiDAR波形から植物キャノピーの垂直構造プロファイルを再構成するTransformer手法の開発と検証が研究の中心であり、植物構造形質を推定している。

abstractwe developed an encoder–decoder Transformer architecture to reconstruct high-resolution vertical canopy profiles from large-footprint waveform LiDAR observations.

Generation of spatially and temporally fine-resolution imagery using STF algorithms and CACAO post-processing. →

Spatio-Temporal Fusion (STF) has been widely used across various remote sensing applications, including environmental monitoring, land cover change detection, and water resource management by integrating multi-sensor data with different spatial and temporal resolutions. The objective of this study was to generate spatially and temporally fine-resolution imagery and to evaluate the performance of multiple STF algorithms and Consistent Adjustment of the Climatology to Actual Observations (CACAO) post-processing for parcel-level crop monitoring. The study was conducted in a soybean field located in Anseong, South Korea, covering the entire soybean growing season from late June to early November. Near-daily Planet SuperDove imagery with 3 m resolution was used to temporally enhance UAV images, which were acquired at 0.05 m resolution but only at weekly to monthly intervals. Through the downscaling process, the UAV data were converted into a daily dataset with a target spatial resolution of 0.5 m. Relative radiometric normalization was applied, followed by the implementation and comparison of four STF algorithms- Enhanced Spatial and Temporal Adaptive Reflectance Fusion Model (ESTARFM), Fitting, spatial Filtering and residual Compensation (Fit-FC), Flexible Spatiotemporal Data Fusion (FSDAF), and Variation-based Spatiotemporal Data Fusion (VSDF)-within a 4-fold cross-validation framework. CACAO post-processing was then employed to reconstruct temporally continuous Normalized Difference Vegetation Index (NDVI) and Enhanced Vegetation Index (EVI) trajectories, from which the NDVI-based Vegetation Growth Metrics (VGM)85 and the EVI-based VGMmax were derived. The validation results indicated that ESTARFM achieved the highest NDVI performance among the evaluated algorithms, with a Root Mean Square Error (RMSE) of 0.113 and the Universal Image Quality Index (UIQI) of 0.697. CACAO post-processing further improved these results, with CA-ESTARFM achieving an RMSE of 0.108 and a UIQI of 0.740, corresponding to a 4.4% reduction in RMSE and a 6.2% improvement in UIQI relative to the baseline ESTARFM. NDVI histogram and spatial analyses demonstrated that CA-ESTARFM achieved the most consistent agreement with UAV observations while preserving fine-scale spatial heterogeneity. In addition, intra-field vegetation assessment using NDVI-based VGM85 and EVI-based VGMmax showed that CA-ESTARFM remained consistent with simple linear interpolation of UAV observations while retaining finer spatial structure and reducing localized noise in the derived growth metrics. The proposed framework demonstrates strong potential for applications in comprehensive crop monitoring, precision agriculture management, and yield forecasting.

Why it matches plant phenotyping methodsUAV・衛星画像の時空間融合とCACAO処理により、NDVI/EVIおよび植生成長指標を抽出するワークフローを開発・比較検証しており、植物状態の取得手法が中心である。

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

Multi-scale predictive modeling of phenology and carotenoid content in carrots using spectral techniques, colorimetry, and artificial intelligence. →

Objective This study presents an integrated, multi-scale approach for the non-destructive estimation of phenological stages and carotenoid content in carrots by combining spectral techniques, colorimetry, and artificial intelligence. Methods Six commercial varieties, including orange, yellow, white, and purple genotypes, were evaluated under field and laboratory conditions using multispectral drone imagery, high-resolution spectroradiometric signatures, red green blue (RGB) images, and CIELAB color measurements. A hierarchical modeling framework was developed across two phases: (i) spectral modeling using uncrewed aerial vehicle (UAV)-based multispectral indices, textural and geometric metrics, and laboratory-generated hyperspectral signatures; and (ii) a colorimetric index from RGB images. Results Using UAV-based multispectral field data, phenological prediction indices achieved high classification performance (F1-scores > 0.90) when modeled with a Random Forest classifier, supported by distinct spectral signatures associated with canopy development and senescence. In parallel, carotenoid content estimation using a Random Forest regression model demonstrated strong predictive accuracy ( R 2 = 0.897; RMSE = 0.584), with the Plant Senescence Reflectance Index (PSRI) and Carotenoid Reflectance Index (CRI) identified as the most influential predictors. A complementary laboratory-based Random Forest regression model using high-resolution spectral signatures achieved near-perfect predictive performance ( R 2 = 0.987). SHapley Additive exPlanations (SHAP) analysis identified physiologically relevant wavelengths in the green (540-550 nm) and red-edge (∼700 nm) regions as the primary drivers of carotenoid concentration. Likewise, a novel colorimetric index (ICarot), derived from CIELAB parameters, enabled accurate image-based carotenoid estimation ( R 2 = 0.85). Conclusion This study introduces an innovative multi-sensor framework for precision agriculture and automated postharvest quality control, enabling rapid, objective, and scalable phenotyping in carrot production systems. Through the integration of spectral, colorimetric, and AI-based approaches, the proposed methodology effectively captures both internal nutritional attributes and external quality traits within a unified, non-destructive assessment pipeline.

Why it matches plant phenotyping methods複数センサー画像・分光計測とAIを統合し、ニンジンの生育段階およびカロテノイド含量を非破壊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ある。

abstractThis study presents an integrated, multi-scale approach for the non-destructive estimation of phenological stages and carotenoid content in carrots by combining spectral techniques, colorimetry, and artificial intelligence.

UAV-based temporal synergistic estimation of multiple alfalfa qualities integrating physics-informed network and 3D allometric operator. →

Accurately monitoring alfalfa nutritional quality is essential for optimal pasture management. Yet, current UAV remote sensing methods rely on single-temporal imagery and empirical indices, limiting their ability to handle multi-stage growth dynamics, canopy spectral saturation, and canopy-to-whole-plant scale differences. Furthermore, small sample sizes often cause purely data-driven models to overfit correlations, yielding biologically unrealistic results. Overcoming these challenges, we designed a comprehensive quality estimation framework using 127 alfalfa core germplasms, combining high-dimensional spectral mining, a physics-informed network, and a 3D allometric transfer operator. After screening 14,960 spectral operators across original and log-transformed spaces, we applied a dual dimensionality reduction strategy to isolate optimal features. Four-band dual-difference structures proved highly sensitive to fiber components (ADF/NDF, |r| = 0.896), while logarithmic decoupling operators accurately isolated protein and nitrogen signals (CP/N, |r| = 0.868). We then engineered a Physics-Informed Sparse Shallow Network (PI-SSN). By leveraging temporal attention decoupling, it adaptively assigns growth-stage weights to different components and uses carbon-nitrogen metabolic constraints to maintain biological accuracy during multi-task retrieval. Multi-stage temporal data significantly boosted accuracy over single-period spectra. PI-SSN delivered exceptional test set coefficients of determination ( R2 ) of 0.812-0.848 and RPDs >2.0 for N, CP, ADF, and NDF, easily outperforming standard baselines. To bridge the canopy-only observation gap, we introduced a 3D allometric transfer operator that incorporates canopy coverage and plant height. This effectively corrected vertical stem-leaf observation biases, enhancing Relative Feed Value (RFV) predictions. Ultimately, this approach offers a powerful new framework for high-throughput forage phenotyping.

Why it matches plant phenotyping methodsUAVリモートセンシングと物理制約ネットワーク、3Dアロメトリック演算子を統合し、アルファルファの栄養品質を推定する手法を開発・検証しており、植物表現型取得が中心である。

abstractwe designed a comprehensive quality estimation framework using 127 alfalfa core germplasms, combining high-dimensional spectral mining, a physics-informed network, and a 3D allometric transfer operator.

Methodology for Selecting Stable UAV-Based Vegetation Indices for Prediction of Agronomic Variables in Maize Using a Multispectral Sensor. →

Plant phenotyping based on unmanned aerial vehicles still faces challenges regarding the direct correlation between spectral information with field-collected variables, due to the influence of environmental factors and the considerable variation among maize phenological stages. Therefore, the objectives of this research were: I) to evaluate the interaction of nitrogen doses and evaluation environments (phenological stages and growing seasons) and variance components for field variables and vegetation indices; II) to identify the most suitable indices according to the evaluation environments; and III) to predict field variables based on relevant vegetation indices identified through the proposed methodology. The study was conducted using a randomized complete block design with four repetitions, in which treatments consisted of six nitrogen (N) topdressing doses (0, 50, 100, 200, 300, and 400 kg ha−1) during the 2022/2023 and 2023/2024 growing seasons. Evaluations of agronomic variables and image acquisition were performed in five distinct phenological stages throughout the maize crop cycle. The data were analyzed using deviance analysis and variance components, principal component analysis (PCA), and multivariate linear modeling for the prediction of field variables. Our results demonstrated that all indices were affected by the interaction between N doses and evaluation environments (phenological stages and growing seasons). Additionally, the most reliable were EXGRaw, TGI, GNDVI, NDRE, CIRE, GVI, CVI, BNDVI, PanNDVI, SRNIRRe, SFDVI, RGBindex, NDVI, SAVI, MSAVI, and OSAVI, which showed clustering patterns according to growing season condition and phenological stage. Finally, the variables predicted using the proposed methodology achieved coefficients of determination above 0.80, except for shoot biomass and 100-grain weight. Therefore, it can be concluded that vegetation indices are influenced by the evaluated environment; however, the proposed framework based on the deduction of fixed and random effects enables the prediction of field variables with high accuracy using relatively simple models.

Why it matches plant phenotyping methodsUAVマルチスペクトル画像から植生指数を選定し、農業形質を予測する方法論の開発・評価が研究の中心であり、植物形質の取得・推定に直接関与している。

titleMethodology for Selecting Stable UAV-Based Vegetation Indices for Prediction of Agronomic Variables in Maize Using a Multispectral Sensor.

Estimation of SPAD values in litchi based on improved LSTM with fusion of IoT and multispectral image texture features. →

Litchi is an important economic fruit in southern China, and its precision management relies on the rapid and accurate estimation of the Soil and Plant Analyzer Development (SPAD) values in leaves. Addressing the limitations of existing SPAD detection methods, such as limited rapid coverage, inadequate modeling of dynamic environmental interference, and shallow fusion of multi-source data, this study constructed an Internet of Things (IoT) system to collect real-time environmental data from a litchi orchard, combined with unmanned aerial vehicle (UAV) multispectral imagery to obtain canopy vegetation index and texture features. A Long Short-Term Memory (LSTM) network model integrated with a feature level attention mechanism (MLSTM) was proposed to fuse IoT time-series data, vegetation index, and high dimensional texture features for dynamic SPAD value prediction. The results indicate that multi-source feature fusion significantly improves SPAD estimation accuracy. The MLSTM model achieved optimal performance under the all-features situation, with a coefficient of determination (R²) of 0.897 and a root mean square error (RMSE) of 2.638, outperforming other comparative models. The attention mechanism effectively enhanced the model's focus on key features, improving feature utilization efficiency and model interpretability. The multi-source data fusion method and MLSTM model proposed in this study enable high precision, dynamic estimation of SPAD values in litchi leaves, providing reliable data support for precision fertilization, stress diagnosis, and yield prediction in litchi orchards, as well as theoretical support for promoting the practical application of this technology in smart agriculture.

Why it matches plant phenotyping methodsIoT・UAVマルチスペクトル画像から葉のSPAD値を推定するデータ融合システムとMLSTMモデルを開発・評価しており、植物形質取得手法が研究の中心です。

abstractthis study constructed an Internet of Things (IoT) system to collect real-time environmental data from a litchi orchard, combined with unmanned aerial vehicle (UAV) multispectral imagery to obtain canopy vegetation index and texture features.

Variability in crop responses as a function of environment affects the NDVI relationship with grain yield in wheat. →

Advancing wheat breeding requires reliable digital traits that capture genotype × environment interactions and improve yield prediction across diverse growing conditions. Although vegetation indices such as the normalized difference vegetation index (NDVI) are widely used, their performance relative to yield variability and environmental stress remains underexplored in multi-environment trials. This study utilized unmanned aerial vehicle multispectral imagery to derive NDVI and assess its relationship with grain yield in 34 spring and winter wheat variety trials. These trials included data across seven Washington State locations in different precipitation zones, five years (2019 to 2023), and some irrigated trials. Environments were grouped into high-, moderate-, and low-stress clusters based primarily on precipitation and temperature. Variability was quantified using the coefficient of variation, and correlations between grain yield and NDVI were evaluated within and between varieties across environments based on market classes (hard and soft spring and winter wheat). Across all environments and varieties, NDVI strongly correlated with grain yield ( r = 0.79-0.82, p r = 0.72 in hard spring, r = 0.53 in soft spring). These conditions also improved discrimination between varieties. Although heritability patterns were not clearly differentiated by stress clusters, environments with higher genetic control of yield also tended to show stronger NDVI heritability. Overall, NDVI reliably captured wheat grain yield, which is governed by the genotype × environment driven variability, with its predictive value strongest in stress-prone conditions. These findings underline NDVI's usability as a practical digital trait for improving variety testing and guiding breeding decisions in challenging environments.

Why it matches plant phenotyping methodsUAVマルチスペクトル画像からNDVIを抽出し、複数環境・品種で収量との関係、予測性、遺伝率を評価しており、デジタル植物形質の測定・検証が中心である。

abstractThis study utilized unmanned aerial vehicle multispectral imagery to derive NDVI and assess its relationship with grain yield in 34 spring and winter wheat variety trials.

Ecological insights from transferable plant biomass mapping across the arctic using high-resolution structure-from-motion and LiDAR data →

Abstract Warmer temperatures, permafrost thaw, and increased wildfire activity are driving rapid ecological change across the Arctic, significantly altering plant productivity and aboveground biomass (AGB). These rapid changes highlight the urgent need to improve monitoring of vegetation dynamics in the Earth’s northern ecosystems, where high spatiotemporal heterogeneity occurs at scales finer than those captured by traditional satellite observations. The growing use of unoccupied aerial systems (UASs) presents an opportunity to overcome this limitation. Yet, the diversity of UAS platforms, sensors, and data collection and processing workflows presents challenges for developing standardized, generalizable approaches. To address this challenge, we compiled 672 AGB plots co-located with 183 UAS-based structure-from-motion (SfM) or light detection and ranging (LiDAR) surveys collected across the Arctic. Here, we: (1) evaluated the generalizability of UAS-derived canopy structure derived from high-resolution SfM and LiDAR for estimating AGB, (2) assessed scaling errors and their sources in two recent satellite-based AGB products derived from Landsat and moderate resolution imaging spectroradiometer, and (3) demonstrated the use of high-resolution AGB maps to quantify biomass variation across tundra plant functional types (PFTs) and to monitor post-fire recovery. Our results show that both SfM and LiDAR accurately captured AGB and its variability across tundra PFTs using a random forest model (overall root mean squared error: 0.332 kg m –2 ), with mapping performance varying slightly by region and data source. Using UAS-derived AGB maps as a benchmark, we identified systematic biases in satellite-derived AGB products, largely attributable to the magnitude of AGB and structural heterogeneity within coarse-resolution pixels. Applying our model to repeat UAS surveys following a tundra fire on Seward Peninsula, we observed rapid AGB recovery in non-shrub patches, with biomass recovering to pre-fire levels within two years. In contrast, shrub patches recovered more slowly, with AGB gains continuing over 2–4 years through both in-patch growth and lateral expansion (via dispersal) into remaining burned areas. Overall, these findings support the generalizability of UAS-based SfM and LiDAR data for estimating tundra AGB and highlight the need for broader collection and synthesis of such data to improve ecological monitoring and model benchmarking in the Arctic.

Why it matches plant phenotyping methodsUASのSfMおよびLiDARから植物群落の地上部 biomass (AGB) を推定する手法の一般化性能を評価し、衛星推定値のベンチマークにも用いており、植物形質取得が研究の中心である。

abstractevaluated the generalizability of UAS-derived canopy structure derived from high-resolution SfM and LiDAR for estimating AGB

Rapid modeling of 3D rice canopy structure considering vertical heterogeneity and analysis of spectral response →

The vertical heterogeneity of rice canopy structure limits the accuracy of inverting leaf physicochemical parameters using traditional radiative transfer models, while LiDAR-based 3D reconstruction remains costly for large-scale applications. To address these challenges, this study proposes a method for constructing 3D rice canopy scenes using "Precision Mode" and "Rapid Mode" strategies. The Precision Mode builds detailed structural models based on measured morphological parameters, validated via the LESS 3D radiative transfer model. To overcome the limitations of obtaining detailed morphology via UAV remote sensing, the Rapid Mode employs machine learning algorithms-specifically Support Vector Machine (SVM), Random Forest (RF), and XGBoost-to map easily accessible parameters (LAI, Above-ground Biomass, Plant Height, and Transplanting Date) to detailed 3D structural parameters. Results indicate that XGBoost achieves the highest accuracy in the Rapid Mode. Furthermore, simulated spectra under both modes showed high consistency with measured spectra, yielding average RMSE values of 0.0104 (R 2 = 0.9965) for the Precision Mode and 0.0307 (R 2 = 0.9694) for the Rapid Mode. Although the spectral accuracy of the Rapid Mode is slightly lower, its modeling efficiency is significantly enhanced, retaining a strong capability to reproduce spectral response characteristics across growth stages. This approach provides an effective tool for analyzing vertical spectral response mechanisms and offers an efficient data simulation scheme for UAV remote sensing parameter inversion based on 3D radiative transfer models.

Why it matches plant phenotyping methodsイネ群落の3D構造を構築・推定する手法を開発し、放射伝達モデルと実測スペクトルで検証しており、植物形質の取得・再現が研究の中心です。

abstractthis study proposes a method for constructing 3D rice canopy scenes using "Precision Mode" and "Rapid Mode" strategies.

Multi-scale spatial-temporal remote sensing fusion for phenology identification in rice germplasm resources. →

Crop phenology is a critical determinant for yield prediction and germplasm evaluation. However, precise phenological monitoring in large-scale rice breeding trials faces significant challenges due to the inherent phenological asynchrony among hundreds of cultivars and the trade-off between spatial resolution and temporal continuity in unmanned aerial vehicle (UAV) remote sensing. To address these issues, this study proposes a multi-scale temporal deep learning framework that integrates high-frequency medium-resolution (MR) images as temporal anchor with sparse high-resolution (HR) images as spatial enhancement. We introduce a Missing Aware Gated Fusion (MAGF) mechanism to dynamically integrate multi-resolution features on non-aligned timelines, enabling robust modeling under irregular sampling conditions. Validated on a massive dataset covering approximately 500 rice cultivars and over 100,000 images across 2023 and 2024 growing seasons, the proposed method significantly outperformed single-temporal-scale baselines despite multiple growth stages coexisting within the same dates. The integration of multi-spatial-scale fusion with LSTM temporal modeling yielded superior performance considering efficiency, achieving an Overall Accuracy (OA) and F1-score of 0.873, with a Kappa coefficient of 0.84. A hybrid sampling strategy (daily MR image combined with weekly HR image) demonstrates that weekly flight time can be reduced from 28 h to approximately 6 h while maintaining high accuracy. Notably, even when HR acquisition was reduced to a once every 14 days frequency, the fusion performance remained significantly superior to that of daily MR monitoring alone. The model exhibited strong generalization capabilities. When directly applying the model trained on 2024 data to the 2023 dataset, it maintained an OA of 0.774 and an F1-score of 0.738 under a 3-day error tolerance, with recall for the maturity stage consistently exceeding 0.96. This framework offers a flexible, scalable, and cost-effective solution for high-throughput phenotyping in precision breeding.

Why it matches plant phenotyping methodsUAVリモートセンシング画像と深層学習によるイネの生育ステージ（フェノロジー）推定手法を開発・検証し、大規模育種データで性能評価しているため、フェノタイピング手法が中心である。

abstractTo address these issues, this study proposes a multi-scale temporal deep learning framework that integrates high-frequency medium-resolution (MR) images as temporal anchor with sparse high-resolution (HR) images as spatial enhancement.

Quantifying Growth and Lodging in Tef ( Eragrostis tef ) With Uncrewed Aerial Systems (UAS) →

ABSTRACT Lodging is a major contributor to decreased yield in tef, a staple cereal crop in Ethiopia. Semidwarf varieties have been developed with a goal to increase yield through reduced lodging, but studying lodging susceptibility currently requires a labor‐intensive, imprecise, manual scoring method. Here we present workflows for analyzing tef stand height from UAS sensors across time to both predict lodging later in the season with early height and to measure the severity of lodging after a storm event. We compare 3D point clouds generated by photogrammetry from RGB images with those generated from LiDAR to estimate height, demonstrating that they produce similar results, despite differences in cost. Stand height and lodging can both be accurately measured with low‐cost UAS, reducing the need for manual measurements and increasing precision and temporal resolution in plant breeding programs.

Why it matches plant phenotyping methodsUAS画像・LiDARによるテフの草高と倒伏程度の推定ワークフローを開発・比較し、育種での測定精度向上を示す中心的な表現型計測研究。

abstractHere we present workflows for analyzing tef stand height from UAS sensors across time to both predict lodging later in the season with early height and to measure the severity of lodging after a storm event.

AI-driven multi-agent framework for smart irrigation and crop health monitoring in Indian rice and sugarcane farming →

Disease prevention and water management are important to all the crops, particularly rice and sugarcane production in India. The article proposes a reinforcement learning (RL) based intelligent irrigation management system that is capable of optimising water consumption and crop nutrition in response to the changing agricultural climatic conditions. Decentralised reinforcement learning (RL) is used in a network of irrigation agents that utilise soil and microclimate sensor networks to set the terms of water allocation, water use efficiency (WUE) and crop health. At the same time, deep convolutional networks can be used to differentiate between plant stress/disease and leaf images and take applicable proactive actions. It is a framework that incorporates satellite-derived indices (NDVI, EVI, land surface temperature) with local sensor measurements and image-based health measurements through multimodal deep learning. Far-reaching simulations (including Indian climate and crop calendars) demonstrate that the multi-agent system lowers water consumption and preserves the yields and properly notifies stressed plants. The scores of disease detection with plantvillage-based fine-tuned on rice (120 (3 disease types) and 3829 (5 disease types) and sugarcane (2569 images for all disease types, Convolutional Neural Network (CNN) yield results of >98 % accuracy. Crop mapping (rice/sugarcane) Satellite/LSTM-based crop mapping (with Sentinel-1 / Sentinel-2) achieves more than 97 % accuracy. The suggested structure provides a data-driven, scalable system for precision agriculture to enhance the management of irrigation periods and crop health. Simulation experiments show that the RL-based controller can reduce water consumption while preserving optimal soil moisture levels when compared to rule-based irrigation strategies.

Why it matches plant phenotyping methods画像・衛星・センサーを統合して植物ストレス／病害状態を推定するマルチモーダル基盤が提案され、病害検出性能も評価されているため、植物表現型推定が実質的な構成要素である。

abstractdeep convolutional networks can be used to differentiate between plant stress/disease and leaf images

AI-Powered Yield Prediction, Bacterial Blight and Crop Health Classification in Common Bean (Phaseolus vulgaris L.) Using Drone RGB and Multispectral Imaging →

Phenotyping plant traits using UAV-based multispectral imaging offers a robust and unbiased approach to assessing crop status. With approximately 70% of smallholder farmers in East and Southern Africa cultivating common beans as a key source of food and income, there is a critical need for accurate and timely measurements of crop health and yield to support data-driven management decisions and disease mitigation. Traditional phenotyping methods are labor-intensive, and existing remote sensing and machine learning approaches remain limited. This study presents a comprehensive framework for plot-level assessment of common bean health and yield using time-series RGB and multispectral imagery. Data collected over three growing seasons (2022–2024) were used to extract canopy variables and vegetation indices (VIs) across phenological stages. For yield prediction, traditional machine learning models achieved a root mean squared error (RMSE) of 242.33 kg ha⁻¹ and an R² of 0.66 using an Extra Trees Regressor. A novel BY-GRU architecture improved performance, achieving an RMSE of 242.40 kg ha⁻¹ and an R² of 0.79. The analysis also identified 45–60 days after sowing as the optimal window for prediction. To address limitations in conventional plant health assessments, this study introduces a novel Health Index. Comparative analysis demonstrated its robustness across genotypes and stronger correlation with yield. Machine learning and deep learning models, including MaxViT, were applied to estimate the Health Index, achieving improved predictive performance. Overall, this work integrates UAV sensing and modelling to provide scalable tools for phenomics, crop management, and breeding.

Why it matches plant phenotyping methodsUAVのRGB・マルチスペクトル画像から作物の健康状態、収量、キャノピー形質を推定するセンシング・機械学習フレームワークが研究の中心であり、植物フェノタイピング手法として適格です。

abstractThis study presents a comprehensive framework for plot-level assessment of common bean health and yield using time-series RGB and multispectral imagery.

drone2report: A Configuration-Driven Multi-Sensor Batch-Processing Engine for UAV-Based Plot Analysis in Precision Agriculture →

Unmanned aerial vehicles (UAVs) have become indispensable tools in precision agriculture and plant phenotyping, enabling the rapid, non-destructive assessment of crop traits across space and time. Equipped with RGB, multispectral, thermal, and other sensors, UAVs provide detailed information on canopy structure, physiology, and stress responses that can guide management decisions and accelerate breeding programs. Despite these advances, the downstream processing of UAV imagery remains technically demanding. Converting orthomosaics into standardized, biologically meaningful data often requires a combination of photogrammetry, geospatial analysis, and custom scripting, which can limit reproducibility and accessibility across research groups. We present drone2report, an open-source python-based software that processes orthomosaics from UAV flights to generate vegetation indices, summary statistics, derived subimages, and text (html) reports, supporting both research and applied crop breeding needs. Alongside the basic structure and functioning of drone2report, we also present five case studies that illustrate practical applications common in UAV-/drone-phenotyping of plants: (i) thresholding to remove background noise and highlight regions of interest; (ii) monitoring plant phenotypes over time; (iii) extracting information on plant height to detect events like lodging or the falling over of spikes; (iv) integrating multiple sensors (cameras) to construct and optimize new synthetic indices; (v) integrate a trained deep learning network to implement a classification task. These examples demonstrate the tool’s ability to automate analysis, integrate heterogeneous data and models, and support reproducible computation of agronomically relevant traits. drone2report streamlines orthorectified UAV-image processing for precision agriculture by linking orthomosaics to standardized, plot-level outputs. Its modular, configuration-driven design allows transparent workflows, easy customization, and integration of multiple sensors within a unified analytical framework. By facilitating reproducible, multi-modal image analysis, drone2report lowers technical barriers to UAV-based phenotyping and opens the way to robust, data-driven crop monitoring and breeding applications.

Why it matches plant phenotyping methods植物表現型取得のためのUAV画像処理ソフトウェアを開発し、植物高・倒伏などの形質抽出、マルチセンサー統合、再現可能な解析ワークフローを中心的に提示している。

abstractWe present drone2report, an open-source python-based software that processes orthomosaics from UAV flights to generate vegetation indices, summary statistics, derived subimages, and text (html) reports

Drone-based assessment of multifunctionality in mixed cropping systems →

Abstract Modern agriculture faces the dual challenge of sustainably increasing food production while mitigating the environmental impact of intensive monocultures. Mixed cropping, which is the cultivation of multiple species or varieties, may provide ecological benefits that address productivity and environmental sustainability challenges. However, evaluating its multifunctionality in conventional agricultural field experiments is costly and labour-intensive, and small sample sizes and high spatial variability often make it difficult to detect the statistical significance of mixed cropping effects. This study aims to introduce and validate a high-throughput field phenotyping (HTP) framework that integrates aerial imagery obtained from unmanned aerial vehicles (UAVs) to efficiently assess the multifunctionality of mixed cropping systems. We conducted a field experiment comparing monocultures of oat, rye, and barley; intraspecific mixed cropping combining three oat varieties; and interspecific mixed cropping combining oat, rye, and barley. Using UAV-derived data across the entire field, including vegetation cover, plant height, and the normalised difference vegetation index, we evaluated five multifunctionalities (biomass production, spatial variability in biomass production, early canopy closure, lodging resistance, and lodging resilience). This framework reveals that mixed cropping outperforms monocropping in several key ecological functions. The proposed UAV-based HTP approach enables cost-effective, robust, and scalable evaluation of mixed cropping systems, facilitating their optimisation for multifunctionality and contributing to the advancement of sustainable agriculture.

Why it matches plant phenotyping methodsUAV画像を用いた高スループット圃場フェノタイピング枠組みを導入・検証し、植生被覆、草丈、NDVIから複数の植物形質・状態を抽出しており、フェノタイピング手法が中心的です。

abstractThis study aims to introduce and validate a high-throughput field phenotyping (HTP) framework that integrates aerial imagery obtained from unmanned aerial vehicles (UAVs)

Country-wide, high-resolution monitoring of forest browning with Sentinel-2 →

Natural and anthropogenic disturbances are impacting the health of forests worldwide. Monitoring forest disturbances at scale is important to inform conservation efforts. Here, we present a scalable approach for country-wide mapping of forest greenness anomalies at the 10 m resolution of Sentinel-2. Using relevant ecological and topographical context and an established representation of the vegetation cycle, we learn a predictive quantile model of the normalised difference vegetation index (NDVI) derived from Sentinel-2 data. The resulting expected seasonal cycles are used to detect NDVI anomalies across Switzerland between April 2017 and August 2025. Goodness-of-fit evaluations show that the conditional model explains 65% of the observed variations in the median seasonal cycle. The model consistently benefits from the local context information, particularly during the green-up period. The approach produces coherent spatial anomaly patterns and enables country-wide quantification of forest browning. Case studies with independent reference data from known events illustrate that the model reliably detects different types of disturbances.

Why it matches plant phenotyping methodsSentinel-2 NDVIを用いて森林キャノピーの季節変動から褐変・攪乱状態を推定する手法を開発し、適合度と独立参照データで検証しているため、単なる森林地図作成ではなく植物状態の取得・評価が中心である。

abstractwe present a scalable approach for country-wide mapping of forest greenness anomalies at the 10 m resolution of Sentinel-2.

AI-IoT-Enabled Crop Monitoring Through Crop Stage and Leaf Disease Identification Using PECFIS and DGBESCNN →

The aspect of crop monitoring takes into consideration the timely detection of crop stages, leaf disorders, and deficiencies to enhance crop yield and decrease losses in agriculture. However, most of the current methods are limited to either disease detection or nutrient evaluation and do not examine the conditions of crops at various stages of growth, even though several AI -IoT-based solutions have been suggested to be applied to crop health monitoring. In addition, the estimation of the severity of the diseases is neglected, and this restricts decision-making in favor of the farmers. To address these constraints, the paper presents a Parametrized Elliptical Cauchy Fuzzy Inference System (PECFIS) combined with a Deep Glorot Bessel Elliott Softplus Convolutional Neural Network (DGBESCNN), proposed as an AI-based solution for crop monitoring and IoT support. The IoT devices in the form of drones are used to get real-time field images, and they are preprocessed in terms of noise reduction, contrast enhancement by LHM-CLAHE, conversion to HSV color space, and feature discrimination by vegetation indexing, as well as C3MEK-Means. PECFIS is used to determine eight key stages of rice growth and the severity of leaf diseases, whereas DGBESCNN provides proper classification of leaf diseases and nutrient deficiencies at each growth stage. The evaluation of the proposed framework was conducted using publicly available datasets on rice leaf disease and nutrient deficiency. The results of the experiments show that the system achieves high classification performance, with an accuracy of 98.82, a precision of 98.65, a recall of 98.73, an F1-score of 98.59, and low error rates (MSE = 0.0135, RMSE = 0.116). The findings show that the developed AI-IoT system is superior to available approaches and can serve as a dependable, real-time, and scalable solution in precision agriculture and intelligent crop monitoring.

Why it matches plant phenotyping methodsドローン画像からイネの生育段階と葉病害の重症度を推定・分類するAI-IoT手法が研究の中心であり、植物状態の取得・抽出方法を技術的に評価している。

abstractThe IoT devices in the form of drones are used to get real-time field images

Hierarchically scaled remote sensing and field datasets for three-dimensional wildland fuel characterization →

Abstract Background: Next-generation models of fire behavior and smoke production rely on gridded, 3D inputs of wildland fuel complexes. We used a hierarchically scaled sampling design to characterize canopy and surface fuels that are common to prescribed burning programs in the southeastern and western US. Sampling included airborne laser scanning, terrestrial laser scanning, close-range photogrammetry, and destructive field sampling. The objective of this study was to use a combination of airborne laser scanning (ALS), terrestrial laser scanning (TLS), structure-from-motion photogrammetry (SfM), and field observations to create co-located 3D datasets of live and dead understory fuels for use in wildland fuel mapping and prescribed burn decision support Results: Using our integrated, co-located methods, we produced hierarchically-scaled datasets detailing the structure and composition of canopy and surface fuels across 9 southeastern pine sites, 5 western pine sites, and 4 western grassland sites. These are now publicly available at within the Wildland Fire Science Initiative data repository (https://doi.org/10.60594/W4859C). In this paper, we detail methods and the repository structure. Conclusions: The study was designed to evaluate and advance methods for 3D fuel characterization and to provide consistently scaled and labelled datasets for model training and evaluation. More specifically, machine learning models can be used to parse 3D point clouds collected from ALS, TLS, and structure-from-motion photogrammetry into fuel objects and metrics. Calibration with field plots will allow our hierarchically-scaled datasets to be used as the foundation for synthetic fuelbed mapping, starting with fine-scale objects such as individual shrubs or downed wood and scaling to vegetation patches and operational burn units.

Why it matches plant phenotyping methodsALS、TLS、SfMと現地観測を統合して植物群落の3D構造・燃料特性を取得し、手法の評価・改良と公開データセット構築を主目的としているため、植物形質計測法が中心である。

abstractThe objective of this study was to use a combination of airborne laser scanning (ALS), terrestrial laser scanning (TLS), structure-from-motion photogrammetry (SfM), and field observations to create co-located 3D datasets of live and dead understory fuels for use in wildland fuel mapping and prescribed burn decision support

Vegetation dynamics inside Mediterranean vineyards: A dataset for tracking changes using unmanned aerial vehicles. →

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.

From Field to Sky: Measurement and Modeling of Transgenic Switchgrass Pollen Dispersal in the Atmosphere →

Abstract Accurate tracking and measurement of pollen dispersal in the atmosphere are essential for assessing cross-pollination risks, particularly in the case of genetically engineered (GE) crops. We conducted a series of unique release-recapture field studies with GE switchgrass in Oliver Springs, Tennessee, USA. Two hundred transgenic switchgrass plants ({\it Panicum virgatum L.} `Performer') were planted at the center of a clear-cut field, with one block of 100 plants expressing orange fluorescent protein (OFP) under a maize ubiquitin promoter (PvUBI1) and another block of 100 plants expressing OFP driven by a maize pollen-specific promoter (Zm13). Pollen was sampled from the atmosphere using fixed (ground-based) and mobile (drone-based) sampling devices at different distances from the source field, with Lagrangian Stochastic dispersal simulations run for sampling periods using high-resolution wind measurements. The pollen emission rate was estimated by combining simulated and measured pollen concentrations, and strong diurnal trends were observed. Diurnal emission rate trends were positively correlated with wind speed, temperature, and vapor pressure deficit, while negatively correlated with relative humidity. In low-wind meandering conditions, incorporating changing wind direction into the dispersal modeling improved pollen emission rate estimation and model-measurement comparisons. This study assesses the effectiveness of high and low volume pollen samplers in relation to source strength up to 1 km from the source, enhancing understanding of pollen measurement techniques. Additionally, it is a proof-of-concept for drone-based pollen sampling and GMO pollen tracking using fluorescence measurements. Results from our experiments have significant implications for cross-pollination risk assessment, prediction, and management of airborne allergens.

Why it matches plant phenotyping methods固定・ドローン型サンプラーと蛍光測定、分散モデルを用いて植物由来花粉の放出量を推定し、サンプリング技術を評価することが中心であるため。

abstractPollen was sampled from the atmosphere using fixed (ground-based) and mobile (drone-based) sampling devices

A new plant association of the alliance Saxifragion australis described by drone-based phytosociology in northeastern Sicily (Peloritani Mountains) →

Although the chasmophytic vegetation of Sicily has been examined previously, it remains insufficiently explored due to the formidable challenges associated with accessing vertical cliff habitats. This study employed drone-based surveys combined with Braun-Blanquet methodology to investigate cliff vegetation in the Peloritani and Madonie Mountains. High-resolution aerial imagery enabled species identification and cover estimation on inaccessible rock faces. Twenty-three new relevés were combined with 33 literature records for multivariate analysis. Cluster analysis and DCA revealed floristic differentiation between Peloritani and Madonie phytocoenoses, contrasting with communities from Apennines that we used as an outgroup. We describe Athamanto siculae-Saxifragetum australis for the calcareous cliffs of Rocca Salvatesta (Peloritani), characterized by Athamanta sicula , Hypochaeris laevigata , and Saxifraga callosa subsp. australis . Additionally, we propose to change the name Asperuletum gussonei to Cynanchicetum gussonei for the high-elevation vegetation of the Madonie dominated by Cynanchica gussonei . Drone methodology proved effective for documenting cliff vegetation, offering a safe and replicable approach for advancing phytosociological knowledge in extreme habitats. This research contributes to the syntaxonomic revision of Mediterranean chasmophytic vegetation within the alliance Saxifragion australis .

Why it matches plant phenotyping methodsドローン画像を用いてアクセス困難な崖面の植物種同定と被覆率推定を行う手法が、植生調査・分類の中心的手段として明示されているため。

abstractHigh-resolution aerial imagery enabled species identification and cover estimation on inaccessible rock faces.

Low-annotation apple flower counting: A color-SAM enhanced and uncertainty-guided semi-supervised framework. →

Accurate flower-load assessment is critical for informed thinning strategies in orchard management. UAV-based deep learning automated counting offers efficiency advantages, yet precise counting is heavily dependent on abundant annotated data, which is scarce and costly to obtain in agricultural settings. While semi-supervised learning alleviates dependency on manual annotation, its application to UAV-based orchard imagery faces challenges: complex backgrounds and small target sizes, which undermine pseudo-label reliability. To address these challenges, this study proposes a two-stage framework to achieve separate counting of apple flowers at different phenological stages. First, a color-SAM flower extractor (CSAM-FE) is proposed to preprocess images using a strategy combining color thresholding with the Segment Anything Model (SAM), suppressing background noise and extracting high-quality flower clusters, thereby providing purified inputs for the subsequent counting network. Second, an uncertainty-guided semi-supervised flower counting network (USCount-Net) is proposed for accurate stage-specific flower counting with limited labeled data. The USCount-Net incorporates two key components: an adaptive pseudo-label filtering (PLF) mechanism based on frequent forward uncertainty estimation (FFUE) is designed to dynamically suppress noisy gradient backpropagation, mitigating error propagation from unreliable pseudo-labels; and a noise-sensitive adaptive gated fusion (AGF) module is introduced to fuse cross-scale features without redundancy, addressing significant scale variations across phenological stages and observation angles. Comparative experiments on a self-built apple flower counting dataset demonstrate that USCount-Net achieves lower MAE and RMSE than state-of-the-art methods at 10%, 30%, and 50% labeling ratios. The results demonstrate that the proposed methodology serves as methodological support for rapid and precise apple flower counting in low-annotation agricultural scenarios.

Why it matches plant phenotyping methodsリンゴ花の画像抽出・計数手法と半教師あり解析ネットワークを開発し、データセット上で比較評価しているため、植物表現型取得が中心である。

abstractthis study proposes a two-stage framework to achieve separate counting of apple flowers at different phenological stages.

A novel point cloud completion model for three-dimensional reconstruction of complex, dynamic population-level crop canopy architecture →

Quantitative characterization of complete canopy architecture is essential for accurate evaluation of crop photosynthesis and yield potential, thereby supporting crop ideotype design. Although various sensing technologies enable three-dimensional (3D) reconstruction of individual plants and canopies, they often fail to describe canopy architecture accurately because of severe occlusion in dense populations. To address this limitation, we developed an effective framework for the 3D reconstruction of complex and dynamic population-scale canopy architecture in rapeseed using unmanned aerial vehicle multi-view imagery combined with a novel point cloud completion model. A complete point cloud generation pipeline was first established to enable automated training data annotation, allowing discrimination between surface points and occluded points within the canopy. The proposed crop population point cloud completion network (CP-PCN) integrates a multi-resolution dynamic graph convolutional encoder, a point pyramid decoder, a dynamic graph convolutional feature extractor, and a generative adversarial network-based loss function to predict occluded canopy points. CP-PCN achieved chamfer distance values of 3.35 to 4.51 cm across four growth stages, outperforming the state-of-the-art transformer-based method PoinTr. Ablation analyses confirmed that each of the four modules contributes to overall model accuracy. In addition, validation experiments showed that the improved architectural completeness achieved by CP-PCN resulted in more accurate yield estimation compared with incomplete and PoinTr-completed point clouds. CP-PCN also demonstrated strong cross-crop generalizability by successfully reconstructing mature rice canopies. Overall, this framework provides a scalable approach for quantitative analysis of complex canopy architectures in field-grown crops.

Why it matches plant phenotyping methodsUAVマルチビュー画像から遮蔽点を補完し、作物群落の3Dキャノピー構造を再構成する手法を開発・検証しており、植物表現型取得が研究の中心です。

abstractwe developed an effective framework for the 3D reconstruction of complex and dynamic population-scale canopy architecture in rapeseed using unmanned aerial vehicle multi-view imagery combined with a novel point cloud completion model

Design and implementation of a deep learning framework for automated crop classification and health diagnosis in precision agriculture. →

This paper presents a three-phase deep learning framework comprising (i) multi-modal data acquisition from drones and satellites, (ii) standardized pre-processing including interpolation for missing temporal data, and (iii) CNN-based feature extraction for real-time health classification. This framework relies on a mathematical model based on neural networks that classifies and detects the condition of agriculture, removing the reliance on manual tasks and subjective diagnosis. This paper focuses on three main aspects of our framework: data acquisition, training and prediction. Data is collected using sensors like drones, cameras, and satellite imagery and is pre-processed to filter out noise and improve quality. The training part uses CNN to learn features from the data and become more meaningful. The prediction part of the task classifies, and diagnoses crop health through the trained model using the features. The framework accuracy for crops such as maize, potato, and wheat has been tested and yielded over 90% accuracy. The novelty of this work resides in the development of a multi-modal deep learning architecture that fuses macro-scale satellite imagery with micro-scale drone and IoT sensor data to improve diagnostic reliability. The framework was validated on a multi-source agricultural dataset using a 70% training, 15% validation, and 15% testing protocol. Experimental results demonstrate an accuracy exceeding 90% for staple crops. Using this framework can increase the visibility and quality of information maintained for crop health and improve the decision-making routine of farmers in real time. Additionally, automation of this process can significantly reduce labor costs and increase productivity per crop. Implementing this framework can contribute to precision agriculture and sustainable management practices.

Why it matches plant phenotyping methods作物の健康状態を植物の表現型・状態として推定するマルチモーダル画像・センサ基盤と深層学習手法を開発し、複数作物・データセットで検証しているため、方法が中心である。

abstractThis paper presents a three-phase deep learning framework comprising (i) multi-modal data acquisition from drones and satellites, (ii) standardized pre-processing including interpolation for missing temporal data, and (iii) CNN-based feature extraction for real-time health classification.

A novel leaf counting method for field tobacco plants based on UAV imagery and an improved PointNext →

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

Precise tea leaf disease detection using UAV low-altitude remote sensing and optimized YOLO11 model. →

Tea leaf diseases seriously affect its yield and quality, and consequently there is an urgent need for intelligent detection methods with high precision and edge deployment capabilities. To address low detection accuracy in complex backgrounds, overfitting due to limited data, and redundant parameters for existing methods, this paper proposes an improved lightweight detection model FCHE-YOLO based on the YOLO11, which aims to achieve rapid and accurate identification of tea leaf disease combining low altitude remote sensing with unmanned aerial vehicle (UAV). The model has made three key optimizations in the structure: Introduce the self-developed lightweight backbone module FC_C3K2, which significantly reduces computation and parameter count while enhancing the robustness of the model to complex scenarios; construct an efficient feature fusion structure HSFPN, optimizing multi-scale information integration and compressing model volume; design the detection head Efficient Head, integrating group convolution and lightweight attention mechanism to improve detection accuracy and suppress overfitting. The experimental results from the self built tea gardens show that the FCHE-YOLO improves the average accuracy (mAP) from 94.1% to 98.1% compared to the benchmark model YOLO11, with an improvement of 4.0 percentage points. Meanwhile, the inference speed of the model increases from 43.3 FPS to 47.5 FPS, with an increase of 9.0%, meeting the real-time detection requirements. More importantly, by network structure optimization, the model's computational complexity is significantly reduced: The floating-point operations per second (FLOPs) decreases from 6.4 G to 4.2 G, with a decrease of 34.3%, and the parameter count decreases from 2.59 M to 1.46 M, with the compression rate reaching 38.9%, which makes the model more suitable for deployment on resource-constrained UAV edge devices. The final test show that the FCHE-YOLO significantly reduces the missed-detection rate, owns better detection accuracy and deployment practicality, and is suitable for real-time monitoring scenarios of tea leaf diseases with UAVs.

Why it matches plant phenotyping methods茶葉の病害状態をUAV画像から検出する軽量深層学習手法を開発・評価しており、植物病害表現型の取得が中心的な技術貢献である。

abstractthis paper proposes an improved lightweight detection model FCHE-YOLO based on the YOLO11, which aims to achieve rapid and accurate identification of tea leaf disease combining low altitude remote sensing with unmanned aerial vehicle (UAV).

Synchronized UAV multi-angle inversion of canopy structure parameters in wheat breeding materials. →

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.

In Situ Crop and Soil Data and UAV Imagery from Winter Wheat Fields in a Bulgarian Site →

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.

Branch architecture reconstruction and phenotypic trait analysis of poplar trees using low-cost UAV LiDAR point clouds. →

Poplars are essential to China's forestry, contributing to timber production, ecological restoration, and shelterbelt construction. Branch architecture critically influences tree growth, demanding scalable solutions beyond manual methods to assess phenotypic variation in large-scale poplar breeding programs. Unmanned aerial vehicle light detection and ranging (UAV LiDAR) provides an efficient alternative; however, existing methods focus on conifers, leaving a gap in approaches for the more complex morphology of poplar branches. This study proposes a poplar branch reconstruction algorithm utilizing material transport flux and object-level geometric features from low-cost UAV LiDAR data. First, a voxel-based near-centroid method is used to extract skeleton points from tree point clouds. Next, a material transport flux model identifies individual branches, and geometric features of transport paths, including path length and curvature, are used to reconstruct each branch. Finally, branch parameters are estimated based on reconstructed branches. Data from a 5-ha plot were collected using the DJI Zenmuse L1 UAV LiDAR at the Shishou National Poplar Breeding Station, Hubei Province, China. Results demonstrate the proposed algorithm achieves high accuracy in first-order branch identification (F1-score = 1), with second-order branches having an average F1-score of 0.69. Branch length estimation demonstrates an RMSE of 0.47 m, while branch angles show an RMSE of 7.06°. The study also reveals structural variability in branch traits, with the highest variability observed in the second-order branch length (coefficient of variation = 29.68%), and a moderate positive correlation between first- and second-order branch lengths (correlation coefficient = 0.34), providing insights into tree growth patterns. This approach offers a framework for high-throughput phenotyping, which provides an efficient solution towrads advanced tree breeding using UAV LiDAR.

Why it matches plant phenotyping methodsUAV LiDARによるポプラの枝構造再構成と枝長・枝角度などの形質推定アルゴリズムを開発し、精度検証まで行っており、フェノタイピング手法が研究の中心である。

abstractThis study proposes a poplar branch reconstruction algorithm utilizing material transport flux and object-level geometric features from low-cost UAV LiDAR data.

Unsupervised Tree Detection from UAV Imagery and 3D Point Clouds via Distance Transform-Based Circle Estimation and AIC Optimization →

This work proposes a novel tree detection methodology, named DTCD (Distance Transform Circle Detection), based on a fast circle detection method via Distance Transform and Akaike Information Criterion (AIC) optimization. More specifically, a visible-band vegetation index (RGBVI) is calculated to enhance canopy regions, followed by morphological filtering to delineate individual tree crowns. The Euclidean Distance Transform is then applied, and the local maxima of the smoothed distance map are extracted as candidate tree locations. The final detections are iteratively refined using the AIC to optimize the number of trees with respect to canopy coverage efficiency. Additionally, this work introduces DTCD-PC, a modified algorithm tailored for point clouds, which significantly enhances detection accuracy in complex environments. This work makes a significant contribution to tree detection in the following ways: (1) by creating a tree detection framework entirely based on an unsupervised technique, which outperforms state-of-the-art unsupervised and supervised tree detection methods; (2) by introducing a new urban dataset, named AgiosNikolaos-3, that consists of orthomosaics and photogrammetrically reconstructed 3D point clouds, allowing the assessment of the proposed method in complex urban environments. The proposed DTCD approach was evaluated on the Acacia-6 dataset, consisting of UAV images of six-month-old Acacia trees in Southeast Asia, demonstrating superior detection performance compared to existing state-of-the-art techniques, both unsupervised and supervised. Additional experiments were conducted in the custom-developed Urban Dataset, confirming the robustness and generalizability of the DTCD-PC method in heterogeneous environments.

Why it matches plant phenotyping methodsUAV画像・3D点群から個体樹冠を抽出する新規手法を開発し、複数データセットで精度・頑健性を評価しているため、植物形態の取得・抽出が中心である。

abstractThis work proposes a novel tree detection methodology, named DTCD (Distance Transform Circle Detection), based on a fast circle detection method via Distance Transform and Akaike Information Criterion (AIC) optimization.

Cross-modal data integration and spectral optimization for enhanced individual apple tree canopy nitrogen concentration estimation using UAV remote sensing. →

Precision management in high-density orchards requires individual-tree, nondestructive monitoring of canopy nitrogen concentration (CNC), but hyperspectral applications are limited by two factors: unmodeled vertical stratification of CNC within 3D canopies and mixed-pixel effects near canopy boundaries. We develop a cross-modal framework that co-registers RGB-derived 3D point clouds with hyperspectral orthomosaics, enabling individual-tree localization in dense orchards. With this framework, we quantified layer-specific nitrogen-spectral relationships and assessed mixed-pixel effects across canopy positions. Stratified sampling, continuous wavelet transform (CWT), and partial least squares regression (PLSR) with variable importance in projection (VIP)-based band selection were used for spectral optimization, and K-means was applied to isolate representative canopy pixels. Field experiments over two consecutive years (2023-2024) revealed consistent CNC gradients, with the lower canopy exceeding the upper by 0.5-9.5 % across fertilization treatments. CWT-2 delivered the most accurate and robust performance across years. VIP-PLSR indicated layer-dependent CNC-informative wavelengths spanning the visible, red-edge, and near-infrared regions, with scale-dependent cross-layer overlap after CWT. Pixel clustering revealed distinct spatial structure: canopy-interior pixels exhibited characteristic vegetation spectra and achieved R 2 val of 0.69-0.76, substantially outperforming boundary-affected pixels with R 2 val of 0.48-0.57. These results demonstrate that coupling spectral feature optimization with layer-specific modeling and clustering-based pixel screening improves the accuracy of tree-level CNC estimation in complex canopies. The proposed framework provides a mechanistic and operational basis for robust biochemical retrieval in structurally complex orchard systems.

Why it matches plant phenotyping methodsUAVのRGB・ハイパースペクトルデータを統合し、個体樹の樹冠窒素濃度という植物形質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す。

abstractWe develop a cross-modal framework that co-registers RGB-derived 3D point clouds with hyperspectral orthomosaics, enabling individual-tree localization in dense orchards.

3D reconstruction analysis of maize-soybean intercropping competition under water stress. →

Maize-soybean intercropping is a sustainable intensive agroecosystem, though the productivity is constrained by interspecific competition for water and light resources. To enhance the water use efficiency in this intercropping system and understand canopy structure dynamics under the water-limited conditions of arid northwest China, this study proposes a novel optimization strategy that synchronizes deficit irrigation scheduling with crop-specific water requirements during critical phenological phases. Four irrigation regimes were implemented: W1 (full irrigation for both maize and soybean crops), W2 (maize-full and soybean-deficit), W3 (maize-deficit and soybean-full), and W4 (dual deficit). Through UAV-based high-resolution 3D canopy reconstruction (R = 0.98 for plant height validation), 14 spatial-geometric descriptors were quantified. The W2 strategy demonstrated superior competitive coordination, enhancing aggressivity of maize (Ams) by 85.9 % through strategic canopy reconfiguration: 11.8 % reduction in maize maximum leaf layer width position (MLLWP), 28.3 % decrease in inter-specific canopy overlap area (COA), and 40.0 % compression of shading convex hull volume (SCHV). These optimized structural adaptations synergistically enhanced photosynthetically active radiation interception (+13.4 %) while achieving concurrent reductions in crop evapotranspiration (ET, -19.7 %) without yield penalty, thereby elevating irrigation water use efficiency (IWUE) by 14.4 % and water equivalent ratio (WER) by 15.9 %. This work provides mechanistic insights into canopy architecture-mediated resource competition mitigation and establishes a technological framework for sustainable intensification in water-limited environments.

Why it matches plant phenotyping methodsUAVによる3Dキャノピー再構成を用いた植物構造形質の取得と検証が、灌漑試験の主要な解析基盤として明示されているため、実質的なフェノタイピング手法の応用に該当する。

abstractThrough UAV-based high-resolution 3D canopy reconstruction (R = 0.98 for plant height validation), 14 spatial-geometric descriptors were quantified.

The Multi-Sensor and Multi-Temporal Dataset of Multiple Crops for In-Field Phenotyping and Monitoring →

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

Quantifying growth and lodging in Tef ( Eragrostis tef ) with Uncrewed Aerial Systems (UAS) →

Lodging is a major contributor to decreased yield in tef, a staple cereal crop in Ethiopia. Semidwarf varieties have been developed with a goal to increase yield through reduced lodging, but studying lodging susceptibility currently requires a labor-intensive, imprecise, manual scoring method. Here we present workflows for analyzing tef stand height from UAS sensors across time to both predict lodging later in the season with early height and to measure the severity of lodging after a storm event. We compare 3D point clouds generated by photogrammetry from RGB images with those generated from LiDAR to estimate height, demonstrating that they produce similar results, despite differences in cost. Stand height and lodging can both be accurately measured with low-cost UAS, reducing the need for manual measurements and increasing precision and temporal resolution in plant breeding programs. Significance Statement Extreme weather or heavy grain can cause plant stems to bend, a process called lodging. Lodging significantly reduces crop yields globally, particularly in grain crops such as tef ( Eragrostis tef ). Semidwarf crops have previously been reported to be lodging-resistant, increasing crop yields. Here, we used uncrewed aerial systems (UAS) to measure plant growth, height, and lodging in gene edited semidwarf tef lines, and compared the results to ground-truth data. Using a UAS equipped with a red-green-blue (RGB) camera or LiDAR sensor, we measured plant height and lodging, and found that early-season height measurements could predict future lodging potential. The tools used were contributed to the open-source software PlantCV-Geospatial for community use. This work contributes to a broader understanding of genetic resistance to lodging, providing valuable insights for tef crop improvement and reduces the need for labor-intensive manual measurements.

Why it matches plant phenotyping methodsUASのRGB画像・LiDARから3D点群を生成し、植物の草高と倒伏を定量化・検証するワークフロー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。

abstractHere we present workflows for analyzing tef stand height from UAS sensors across time to both predict lodging later in the season with early height and to measure the severity of lodging after a storm event.

Utilizing high‐throughput phenotyping to identify metribuzin tolerance in winter wheat →

Abstract Plant breeders and weed scientists address weed management collaboratively by selecting for herbicide tolerance in breeding programs. Metribuzin, a Group 5 PSII‐inhibiting herbicide, is labeled for use in wheat ( Triticum aestivum L.). However, application to currently available lines results in frequent, variable, and unpredictable crop injury. Breeding for enhanced metribuzin tolerance would allow growers to utilize this herbicide effectively while minimizing the risk of crop injury. Incorporating an additional herbicide mode of action in winter wheat production would enhance rotational flexibility and weed resistance management. Selection for improved herbicide tolerance in crops has traditionally relied on visual estimation, yet assessments can be variable. The objective of this study was to improve the accuracy and efficiency of selecting for herbicide tolerance in a breeding program by utilizing a drone‐mounted multispectral sensor. Multispectral data were collected on paired rows of an diversity panel and advanced generation lines grown in paired plot yield trials. Vegetation indices calculated include normalized difference vegetation index (NDVI), normalized difference red edge (NDRE), transformed chlorophyll absorption reflectance index, normalized water index, and modified triangular vegetation index. Visual assessments of injury, plant height, and grain yield were also recorded. Correlations between reflectance indices and grain yield were stronger than those between visual injury assessments and grain yield. The top 10 lines overlapped 45%–53% when selected by highest yield and highest NDVI or NDRE, respectively, in treated plots. The relationship between yield and index differences in treated and nontreated plots showed that the difference in indices (multiple R 2 = 0.0802–0.5434) explained more yield variation than visual assessments (multiple R 2 = 0.0003–0.1915). These results suggest that multispectral analysis at the plot level is a more accurate and efficient indicator of herbicide injury in winter wheat than traditional visual assessments.

Why it matches plant phenotyping methodsドローン搭載マルチスペクトルセンサーと植生指数を用いて、冬コムギの除草剤傷害・耐性を従来の目視評価より高精度かつ効率的に推定する方法を実証しており、表現型取得法が研究の中心である。

abstractThe objective of this study was to improve the accuracy and efficiency of selecting for herbicide tolerance in a breeding program by utilizing a drone‐mounted multispectral sensor.

In-season estimation of aboveground biomass and yield in winter wheat with a UAV-based LUE model and machine learning. →

Timely and accurate in-season estimation of aboveground biomass (AGB) and yield in winter wheat is crucial for optimizing resources and ensuring food security. Light use efficiency (LUE) models have proven effective in estimating crop gross primary productivity and yield across sites and years due to their strong physiological and ecological mechanisms. However, existing studies are limited to satellite applications and have not utilized unmanned aerial vehicle (UAV) imagery. This study proposed a practical framework for accurate in-season estimation of AGB and yield in winter wheat from UAV imagery by combining a LUE model and machine learning (LUE-ML) across five plot experiments. Subsequently, the scalability of the LUE-ML yield prediction approach was assessed in farmer's fields from five counties of Jiangsu Province, China. The results demonstrated that while the AGB for the heading stage was estimated by combining the retrieved LAI and 20-day accumulated meteorological features, the AGB during the post-heading period could be estimated accurately using the stage-skipping or stage-progressive strategy, with the latter ( R val 2 = 0.93) outperforming the former ( R val 2 = 0.84). The combination of one spectral index, LUE-derived AGB, and three 20-day accumulated relative meteorological features (Comb. #6) performed the best ( R cal 2 = 0.89; R val 2 ≥ 0.79) for yield prediction among all combinations. When extended to farmer-field yield prediction across the province, Comb. #6 also achieved acceptable performance. This study suggests the use of LUE-ML models represents a significant step forward towards mechanistic estimation of AGB and yield for cereal crops from UAV imagery.

Why it matches plant phenotyping methodsUAV画像から冬コムギの地上部バイオマスと収量を推定するLUE-ML手法を開発・評価し、圃場で性能検証しているため、植物形質取得・推定が研究の中心である。

abstractThis study proposed a practical framework for accurate in-season estimation of AGB and yield in winter wheat from UAV imagery by combining a LUE model and machine learning (LUE-ML) across five plot experiments.

Deep learning framework using UAV imagery for multi-disease detection in cereal crops. →

Agriculture is a cornerstone of the economies of many countries, and wheat is a staple cereal crop that sustains nearly half of the worldwide population. However, production of wheat is highly vulnerable to biotic stress such as pathogens and pests, as well as adverse environmental conditions. These factors significantly affect yield and quality, posing critical threats to food security and economic resilience. Conventional disease detection methods often involve intense human labor, prolonged procedures, and are predisposed to subjectivity. Therefore, the development of an automated, accurate, and real-time disease monitoring system is imperative for modern precision agriculture. We propose a hybrid deep learning based Multi-Disease Detection Framework for Wheat Diseases (MDDM-WD) for the identification of multiple wheat diseases using UAV imagery. The framework leverages the pre-trained VGG-16 convolutional neural network for deep feature extraction via a transfer learning approach. These features are subsequently classified using Support Vector Machine (SVM), Random Forest (RF), Decision Tree (DT), XGBoost, and Bernoulli Naïve Bayes (BNB) algorithms of machine learning. The model is trained and evaluated on a custom-curated dataset, containing wheat diseases: stripe rust, powdery mildew, scab (Fusarium head blight), and yellow dwarf. Evaluation of experiments demonstrates that the classification performance is enhanced significantly through our hybrid approach, with accuracy ranging from 74 to 97%, precision from 73 to 96%, and recall from 73 to 95.7%. The SVM-based variant of the model achieved the highest performance, yielding 96% precision, 95.7% recall, 96% F1-score, and 97% accuracy. The proposed two-phase fine-tuned system demonstrates its effectiveness and efficiency in detecting multiple wheat diseases. The MDDM-WD model offers a resource-efficient and scalable approach for early disease detection, supporting informed decision-making for farmers, agronomists, and policymakers in advancing sustainable agriculture.

Why it matches plant phenotyping methodsUAV画像からコムギの病徴・病害状態を直接推定する深層学習フレームワークを開発・評価しており、植物表現型取得法が中心です。

abstractWe propose a hybrid deep learning based Multi-Disease Detection Framework for Wheat Diseases (MDDM-WD) for the identification of multiple wheat diseases using UAV imagery.

A 0.6-meter resolution canopy height and structure model for the contiguous United States →

Above-ground vertical structure is a critical variable for ecosystem monitoring, carbon accounting, and land management. However, the high cost and limited coverage of airborne lidar hinder its widespread application. To address this, we developed NAIP-CHM, a 0.6-meter resolution canopy height and structure model (CHM) covering the contiguous United States, derived from National Agriculture Imagery Program (NAIP) aerial imagery. Unlike forestry-specific models that exclude human-made features, NAIP-CHM characterizes the full vertical structure of the landscape including vegetation, buildings, and infrastructure. We utilized a U-Net convolutional neural network with attention mechanisms and environmental conditioning, training and validating the model with a peer-reviewed, publicly available dataset of 22.8 million co-registered NAIP imagery and lidar-derived CHM pairs, with stratified sampling to ensure robustness in open-canopy ecosystems. The model achieved a pixel-wise root mean square error (RMSE) of 2.28 meters and an r2 of 0.87. Forested sites alone produced an r2 of 0.82 and RMSE of 3.82 meters. We provide the dataset, source code, and cloud-based tools to enable broad application without requiring specialized computational resources.

Why it matches plant phenotyping methods植生を含む景観の樹冠高・構造を航空画像から推定するモデルを開発し、公開データセットで検証している。植物キャノピーの明示的な構造形質推定が中心だが、建造物等も含むため植物以外の構造も対象とする点には留意が必要。

abstractwe developed NAIP-CHM, a 0.6-meter resolution canopy height and structure model (CHM) covering the contiguous United States, derived from National Agriculture Imagery Program (NAIP) aerial imagery.

Deep learning for sorghum yield forecasting using uncrewed aerial systems and lab-derived imagery. →

The AI revolution, advanced Graphics Processing Units (GPUs), and open-source platforms have enabled Machine Learning (ML) and Deep Learning (DL) algorithms to rapidly and accurately extract phenotypic features from imagery. Such advancements have led to phenotypic digitization and made rapid yield forecasting possible. Yield predictions are critical to assess the merit of genotypes to propel cultivar development. This trial followed a three-replicated Randomized Complete Block Design (RCBD) with 36 diverse sorghum genotypes in 2023 at Ashland Bottoms, Kansas. The field images were captured 6 m above using a DJI M300 drone at 90° nadir and 45° oblique angles. This research trained YOLO and Faster R-CNN (Detectron2) models to harness yield attributes from UAS field and lab images. The YOLO models outperformed the Faster R-CNN in detecting sorghum panicles, achieving a mean average precision at 50 % IoU (mAP@0.50) scores of 0.92-0.98, compared to 0.61-0.89 for Faster R-CNN. Panicle detection from field imagery showed a linear correlation of 0.86 with ground truth field panicle counts. Lab imagery analyses measured panicle area, seed counts, and seed area with correlation coefficients of 0.79, 0.94, and 0.25 with respective ground truth observations. Support Vector Regression (SVR), Random Forest Regression (RFR), and Decision Tree Regression (DTR) were used to predict yield with correlation coefficients of 0.74, 0.71, and 0.78, respectively, and SHapley Additive exPlanation (SHAP) analysis revealed panicle seed count as the primary driver of yield prediction. We observed YOLO models are well-suited for extracting yield-predictive features from pertinent images. Such features can then be incorporated into ML regression models to predict yield per se performance with greater accuracy. The GitHub link is provided in the Data availability section.

Why it matches plant phenotyping methodsUAS・実験室画像から穂数、穂面積、種子数・面積などの植物形質を深層学習で抽出し、検出精度を検証して収量予測へ利用する方法が研究の中心である。

abstractThis research trained YOLO and Faster R-CNN (Detectron2) models to harness yield attributes from UAS field and lab images.

Machine learning-enabled UAV hyperspectral identification of tomato spotted wilt virus in tobacco. →

Problems Tomato Spotted Wilt Virus (TSWV) severely affects tobacco yield and quality, creating an urgent need for accurate, rapid, non-destructive monitoring to support disease management. While existing TSWV detection methods perform well at the leaf scale, their field-scale application remains challenging. Due to complex crop canopy structures, spectral characteristics at the field level differ significantly from leaf-level observations, and TSWV-sensitive spectral features are still unclear. This study therefore aims to develop a field-scale TSWV identification model using UAV-based hyperspectral imaging to enable targeted disease control. Methodology A UAV-mounted hyperspectral camera (400-1000 nm) was deployed to capture imagery of tobacco plants at the rosette stage, enabling comparative spectral analysis between healthy and infected specimens. To identify sensitive features associated with tobacco plants infected with TSWV, six distinct feature extraction methodologies encompassing traditional statistical approaches (spectral ratio, correlation analysis, and principal component analysis [PCA]), machine learning-based techniques (relevant features [Relief], successive projections algorithm) and vegetation indices were utilized. Subsequently, we conducted a systematic evaluation of 18 classification models developed using three machine learning algorithms-support vector machine (SVM), k-nearest neighbors, and extreme gradient boosting -with the derived feature variables. Results This study demonstrates that while all integrated models combining Relief- and Correlation- selected feature bands with three machine learning algorithms delivered excellent performance, the SVM-Relief model achieved the most outstanding results (OA = 97.3%, AUC = 0.994, Kappa=0.947). Based on the SVM-Relief combination, a proposed method called RPR -which integrates PCA with recursive feature elimination- was further employed to reduce the number of feature indicators from 15 to 4 (775.6/772.9/781.1/756.4 nm). The resulting SVM-RPR combination model achieved performance (OA = 97.3%, AUC = 0.990, Kappa=0.947) comparable to that of the SVM-Relief model. Contribution This indicated that red-edge bands were of significant value in distinguishing healthy and TSWV-infected tobacco plants. Our study indicates the significant potential of integrating UAV-based hyperspectral imaging with machine learning techniques for rapid, non-destructive detection of tobacco TSWV at the field scale. The proposed approach offers a novel and efficient pathway for remote sensing-based monitoring of viral diseases in crops, with implications for precision agriculture and plant disease management.

Why it matches plant phenotyping methodsUAVハイパースペクトル画像と機械学習により、タバコ個体のウイルス感染状態を圃場規模で推定する手法の開発・評価が研究の中心であるため。

abstractThis study therefore aims to develop a field-scale TSWV identification model using UAV-based hyperspectral imaging to enable targeted disease control.

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

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

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

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

DP-MaizeTrack: a software for tracking the number of maize plants and leaves information from UAV image. →

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

UAV‐based high‐throughput phenotyping for crop growth analysis and seed yield prediction in a nested association mapping population of lentils →

Abstract Unoccupied aerial vehicle (UAV)‐based high‐throughput phenotyping provides scalable and cost‐effective access to phenotypic information for crop improvement, yet its application in minor crops such as lentil ( Lens culinaris Medik.) remains limited. This study applied UAV‐derived canopy traits and crop growth regression modeling to a nested association mapping population developed from CDC Redberry crossed with 32 diverse founder lines. UAV imagery collected across four site‐years was used to capture canopy height, crop area, and crop volume per plot basis at multiple time points. Crop growth regression models were fitted to derive crop growth parameters, maximum canopy size, growth rate, and cumulative growth anchored to phenological stages. These static and time‐series traits were evaluated for seed yield prediction using partial least squares regression with a 70:20:10 data split and 10‐fold cross‐validation. Static traits such as maximum crop volume and maximum crop area were consistently associated with yield. Dynamic trait‐based models improved prediction accuracy and identified the swollen pod stage (R5–R6) as the most informative forecasting window. External validation using an independent trial confirmed the generalizability of the approach. This study presents a UAV phenotyping framework that supports crop growth dissection and early yield prediction and downstream trait discovery in lentil.

Why it matches plant phenotyping methodsUAV画像から作物の形態・成長形質を抽出し、時系列成長モデルと収量予測を検証するフレームワークが研究の中心であるため。

abstractUAV imagery collected across four site‐years was used to capture canopy height, crop area, and crop volume per plot basis at multiple time points.

Countrywide digital surface models and vegetation height models from historical aerial images →

Abstract. Historical aerial images, captured by film cameras in the previous century, are valuable resources for quantifying Earth's surface and landscape changes over time. In the post-war period, these images were often acquired to create topographic maps, resulting in the acquisition of large-scale aerial photographs with stereo coverage. Photogrammetric techniques applied to these stereo images enable the extraction of 3D information to reconstruct digital surface models (DSMs) and orthoimages. Here, we present a highly automated photogrammetric approach for generating countrywide DSMs of Switzerland, at a 1 m resolution, from approximately 32 000 scanned aerial stereo images acquired between 1979 and 2006, with known exterior and interior orientation. We derived four countrywide DSMs for the epochs 1979–1985, 1985–1991, 1991–1998, and 1998–2006. From the DSMs, we generated corresponding countrywide vegetation height models (VHMs). We assessed the quality of the historical DSMs at the country scale and within six representative study sites, evaluating the vertical accuracy and the completeness of image matching across different land cover types. Mean completeness ranged from 64 % for “glacial and perpetual snow” to 98 % for “sealed surfaces”, with a value of 93 % for the “closed forest” class. Across Switzerland, the median elevation accuracy of the historical DSMs compared with a reference digital terrain model (DTM) on sealed surface points ranged from 0.08 to 0.16 m, with a normalized median absolute deviation (NMAD) of around 0.8 m and a maximum root mean square error (RMSE) of 1.20 m. Similar accuracies are obtained when comparing historical DSMs with measured geodetic points. The VHMs generated in this study enabled the detection of major changes in forest areas due to windstorm damage, forest dynamics, and growth. This work demonstrates the feasibility of generating accurate, very-high-resolution DSM time series (spanning three decades) and VHMs from historical aerial images of the entire surface of Switzerland in a highly automated manner. The VHMs are already being used to estimate countrywide biomass changes. The countrywide DSMs and VHMs for the four epochs, along with auxiliary data, are available online at https://doi.org/10.16904/envidat.528 (Marty et al., 2024) and can be used to quantify long-term elevation changes and related processes across different surfaces.

Why it matches plant phenotyping methods歴史的航空画像から植生高モデルを生成する自動写真測量法を開発・精度評価し、森林の高さ変化という植物キャノピー形質を抽出しているため、測定法が中心的である。

abstractFrom the DSMs, we generated corresponding countrywide vegetation height models (VHMs).

Aerial imagery and Segment Anything Model for architectural trait phenotyping to support genetic analysis in peanut breeding. →

Unmanned aerial systems (UAS) are reliable tools for field phenotyping, enabling rapid, large-scale, and cost-effective data collection to support breeding programs. However, many UAS-based approaches rely on manual data processing, limiting scalability and efficiency. This study presents a fully automated pipeline for high-throughput phenotyping (HTP) of peanut crop architectural traits, including canopy height (CH), growth habit (GH), and mainstem prominence (MP) by integrating UAS imagery, a vision foundation model-Segment Anything Model (SAM), and convolutional neural networks (CNN). SAM auto-mask generator mode was used to identify field extent and orientation, while SAM interactive mode enabled individual plot segmentation using auto-generated point prompts. Terrain points automatically sampled near each plot were used to model the ground surface and compute the canopy height model, allowing CH estimations at the plot level. CH estimations showed strong agreement with manual measurements (R² ​= ​0.78, RMSE ​= ​3 ​cm, MAPE ​= ​10 ​%). For MP and GH estimation, three pre-trained CNN models (AlexNet, ResNet18, and EfficientNet-B0) were evaluated, with AlexNet achieving the highest accuracy (89 ​% for GH, 83 ​% for MP). To assess the feasibility of using these HTP-derived estimations in plant breeding, quantitative trait loci (QTL) analysis was performed, identifying major-effect loci associated with these traits. The results were consistent with conventional QTL mapping methods, demonstrating that UAS-based phenotyping provides reliable trait data for genetic studies in peanut breeding. Overall, our deep learning-based data processing workflow minimizes manual efforts, providing an efficient and scalable approach that can accelerate genetic studies and trait selection in large-scale breeding programs.

Why it matches plant phenotyping methodsUAS画像、SAM、CNNを統合したピーナッツの草冠高・生育型・主茎優勢度の自動推定パイプラインを開発・検証しており、表現型取得と抽出手法が研究の中心である。

abstractThis study presents a fully automated pipeline for high-throughput phenotyping (HTP) of peanut crop architectural traits, including canopy height (CH), growth habit (GH), and mainstem prominence (MP) by integrating UAS imagery, a vision foundation model-Segment Anything Model (SAM), and convolutional neural networks (CNN).

Agri-DSSA: A Dual Self-Supervised Attention Framework for Multisource Crop Health Analysis Using Hyperspectral and Image-Based Benchmarks →

Recent advances in hyperspectral imaging (HSI) and multimodal deep learning have opened new opportunities for crop health analysis; however, most existing models remain limited by dataset scope, lack of interpretability, and weak cross-domain generalization. To overcome these limitations, this study introduces Agri-DSSA, a novel Dual Self-Supervised Attention (DSSA) framework that simultaneously models spectral and spatial dependencies through two complementary self-attention branches. The proposed architecture enables robust and interpretable feature learning across heterogeneous data sources, facilitating the estimation of spectral proxies of chlorophyll content, plant vigor, and disease stress indicators rather than direct physiological measurements. Experiments were performed on seven publicly available benchmark datasets encompassing diverse spectral and visual domains: three hyperspectral datasets (Indian Pines with 16 classes and 10,366 labeled samples; Pavia University with 9 classes and 42,776 samples; and Kennedy Space Center with 13 classes and 5211 samples), two plant disease datasets (PlantVillage with 54,000 labeled leaf images covering 38 diseases across 14 crop species, and the New Plant Diseases dataset with over 30,000 field images captured under natural conditions), and two chlorophyll content datasets (the Global Leaf Chlorophyll Content Dataset (GLCC), derived from MERIS and OLCI satellite data between 2003–2020, and the Leaf Chlorophyll Content Dataset for Crops, which includes paired spectrophotometric and multispectral measurements collected from multiple crop species). To ensure statistical rigor and spatial independence, a block-based spatial cross-validation scheme was employed across five independent runs with fixed random seeds. Model performance was evaluated using R2, RMSE, F1-score, AUC-ROC, and AUC-PR, each reported as mean ± standard deviation with 95% confidence intervals. Results show that Agri-DSSA consistently outperforms baseline models (PLSR, RF, 3D-CNN, and HybridSN), achieving up to R2=0.86 for chlorophyll content estimation and F1-scores above 0.95 for plant disease detection. The attention distributions highlight physiologically meaningful spectral regions (550–710 nm) associated with chlorophyll absorption, confirming the interpretability of the model’s learned representations. This study serves as a methodological foundation for UAV-based and field-deployable crop monitoring systems. By unifying hyperspectral, chlorophyll, and visual disease datasets, Agri-DSSA provides an interpretable and generalizable framework for proxy-based vegetation stress estimation. Future work will extend the model to real UAV campaigns and in-field spectrophotometric validation to achieve full agronomic reliability.

Why it matches plant phenotyping methods植物のクロロフィル含量・活力・病害ストレスを画像／ハイパースペクトルから推定する新規深層学習フレームワークを開発・評価しており、植物表現型の取得・推定が中心である。

abstractthis study introduces Agri-DSSA, a novel Dual Self-Supervised Attention (DSSA) framework that simultaneously models spectral and spatial dependencies through two complementary self-attention branches.

Integration of UAV and Remote Sensing Data for Early Diagnosis and Severity Mapping of Diseases in Maize Crop Through Deep Learning and Reinforcement Learning →

Accurate and timely prediction of diseases in water-intensive crops is critical for sustainable agriculture and food security. AI-based crop disease management tools are essential for an optimized approach, as they offer significant potential for enhancing yield and sustainability. This study centers on maize, training deep learning models on UAV imagery and satellite remote-sensing data to detect and predict disease. The performance of multiple convolutional neural networks, such as ResNet-50, DenseNet-121, etc., is evaluated by their ability to classify maize diseases such as Northern Leaf Blight, Gray Leaf Spot, Common Rust, and Blight using UAV drone data. Remotely sensed MODIS satellite data was used to generate spatial severity maps over a uniform grid by implementing time-series modeling. Furthermore, reinforcement learning techniques were used to identify hotspots and prioritize the next locations for inspection by analyzing spatial and temporal patterns, identifying critical factors that affect disease progression, and enabling better decision-making. The integrated pipeline automates data ingestion and delivers farm-level condition views without manual uploads. The combination of multiple remotely sensed data sources leads to an efficient and scalable solution for early disease detection.

Why it matches plant phenotyping methodsトウモロコシの病徴・病害重症度をUAV画像および衛星データから推定する深層学習・時系列解析パイプラインが研究の中心であり、植物状態の取得・評価手法に該当する。

abstracttraining deep learning models on UAV imagery and satellite remote-sensing data to detect and predict disease

Ortho-Fuse: Orthomosaic Generation for Sparse High-Resolution Crop Health Maps Through Intermediate Optical Flow Estimation →

AI-driven crop health mapping systems offer substantial advantages over conventional monitoring approaches through accelerated data acquisition and cost reduction. However, widespread farmer adoption remains constrained by technical limitations in orthomosaic generation from sparse aerial imagery datasets. Traditional photogrammetric reconstruction requires 70-80\% inter-image overlap to establish sufficient feature correspondences for accurate geometric registration. AI-driven systems operating under resource-constrained conditions cannot consistently achieve these overlap thresholds, resulting in degraded reconstruction quality that undermines user confidence in autonomous monitoring technologies. In this paper, we present Ortho-Fuse, an optical flow-based framework that enables the generation of a reliable orthomosaic with reduced overlap requirements. Our approach employs intermediate flow estimation to synthesize transitional imagery between consecutive aerial frames, artificially augmenting feature correspondences for improved geometric reconstruction. Experimental validation demonstrates a 20\% reduction in minimum overlap requirements. We further analyze adoption barriers in precision agriculture to identify pathways for enhanced integration of AI-driven monitoring systems.

Why it matches plant phenotyping methods作物の健康状態マップ作成を目的とする航空画像のオルソモザイク生成法を開発し、重複率低減を実験検証しており、画像取得・再構成手法が中心である。

titleOrtho-Fuse: Orthomosaic Generation for Sparse High-Resolution Crop Health Maps Through Intermediate Optical Flow Estimation

Deep learning model BiFPN-YOLOv8m for tree counting in mango orchards using satellite remote sensing data​. →

Mango is a fruit of great economic importance in India. India is the top mango-producing nation in the world, accounting for over half of global mango output. In order to determine the production capability of the insured orchards, a complete inventory is carried out in situ every three years. The inventory includes counting number of trees, grouping them into yield categories, and assessing damaged ones. Satellite Remote Sensing proves to be a vital tool for estimating ecological parameters such as population density, tree health, volume, biomass, and carbon sequestration rates. The significance of tree counting extends beyond orchard evaluations, playing a vital role in environmental protection, agricultural planning, and crop yield forecast. unfortunately, conventional tree counting methods often require very expensive feature engineering, which leads to more errors as well as lower overall optimization. In order to overcome these obstacles, deep learning-based methods have been used to count trees, exhibiting cutting-edge results in this crucial activity. This paper introduces a novel approach employing deep learning for Image-Based Mango Tree counting in high-resolution satellite imagery data. The proposed model, named Bi-directional Feature Pyramid Network (BiFPN)-YOLOv8m an improved version of YOLOv8, employs object detection to effectively separate, locate, and count mango trees with in orchards. A dataset of 1700 training and 300 testing images of mango orchards with trees of various ages is used to evaluate the various YOLOv8 variants, YOLOv8n, YOLOv8s, YOLOv8m, YOLOv8l, YOLOv8x, including YOLOv9, YOLOv10, and BiFPN-YOLOv8m, with a focus on computational efficiency, accuracy, and speed. Experimental findings show that, even under difficult circumstances, the proposed method continuously outperforms state-of-the-art techniques.

Why it matches plant phenotyping methods衛星画像からマンゴー樹木を分離・位置推定・計数する深層学習手法を開発・評価しており、植物個体数という観測可能な形態・構造形質の抽出が中心である。

abstractThis paper introduces a novel approach employing deep learning for Image-Based Mango Tree counting in high-resolution satellite imagery data.

YOLOv8-FDA: lightweight wheat ear detection and counting in drone images based on improved YOLOv8. →

Introduction Wheat is a vital global staple crop, where accurate ear detection and counting are essential for yield prediction and field management. However, the complexity of field environments poses significant challenges to achieving lightweight yet high-precision detection. Methods This study proposes YOLOv8-FDA, a lightweight detection and counting method based on YOLOv8. The approach integrates RFAConv for enhanced feature extraction, DySample for efficient multi-scale upsampling, HWD for compressed and accelerated model training, and the SDL loss for improved bounding box regression. Results Experimental results on the GWHD dataset show that YOLOv8-FDA achieves a precision of 86.3%, recall of 77.5%, and mAP@0.5 of 84.9%, outperforming the original YOLOv8n by significant margins. The model size is 2.96MB with a computational cost of 8.3 GFLOPs, and it operates at 19.2 FPS, enabling real-time counting with over 97.5% accuracy using cross-row segmentation. Discussion The proposed YOLOv8-FDA model demonstrates strong detection performance, lightweight characteristics, and efficient real-time capability, indicating its high practicality and suitability for deployment in real-world agricultural applications.

Why it matches plant phenotyping methodsコムギ穂の検出・計数という植物器官形質の画像ベース抽出法をYOLOv8改良モデルとして開発し、データセット上で性能検証しているため、方法が研究の中心である。

abstractThis study proposes YOLOv8-FDA, a lightweight detection and counting method based on YOLOv8.

Drone-based assessment of multifunctionality in mixed cropping systems →

Abstract Modern agriculture faces the dual challenge of sustainably increasing food production while mitigating the environmental impact of intensive monocultures. Mixed cropping, which is the cultivation of multiple species or varieties, may provide ecological benefits that address productivity and environmental sustainability challenges. However, evaluating its multifunctionality in conventional agricultural field experiments is costly and labour-intensive, and small sample sizes and high spatial variability often make it difficult to detect the statistical significance of mixed cropping effects. This study aims to introduce and validate a high-throughput field phenotyping (HTP) framework that integrates aerial imagery obtained from unmanned aerial vehicles (UAVs) to efficiently assess the multifunctionality of mixed cropping systems. We conducted a field experiment comparing monocultures of oat, rye, and barley; intraspecific mixed cropping combining three oat varieties; and interspecific mixed cropping combining oat, rye, and barley. Using UAV-derived data across the entire field, including vegetation cover, plant height, and the normalised difference vegetation index, we evaluated five multifunctionalities (biomass production, spatial variability in biomass production, early canopy closure, lodging resistance, and lodging resilience). This framework reveals that mixed cropping outperforms monocropping in several key ecological functions. The proposed UAV-based HTP approach enables cost-effective, robust, and scalable evaluation of mixed cropping systems, facilitating their optimisation for multifunctionality and contributing to the advancement of sustainable agriculture.

Why it matches plant phenotyping methodsUAV画像から植被率・草高・NDVIなどの植物形質を取得する高スループット表現型解析フレームワークを導入・検証しており、フェノタイピング手法が研究の中心です。

abstractThis study aims to introduce and validate a high-throughput field phenotyping (HTP) framework that integrates aerial imagery obtained from unmanned aerial vehicles (UAVs)

Establishment of a high-throughput field defoliation data survey strategy combined with genome-wide association studies to reveal the genetic basis of defoliation in cotton. →

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

Precise Image Color Correction Based on Dual Unmanned Aerial Vehicle Cooperative Flight. →

Color accuracy and consistency in remote sensing imagery are crucial for reliable plant health monitoring, precise growth stage identification, and stress detection. However, without effective color correction, variations in lighting and sensor sensitivity often cause color distortions between images, compromising data quality and analysis. This study introduces a novel in-flight color correction approach for RGB imagery using cooperative dual unmanned aerial vehicle (UAV) flights integrated with a color chart (CoF-CC). The method employs a master UAV equipped with an RGB camera for image acquisition and a synchronized secondary UAV carrying a ColorChecker (X-Rite) chart, ensuring persistent visibility of the chart within the imaging field of the master UAV for the calculation of a color correction matrix (CCM) for in-flight image correction. Field experiments validated the method by analyzing cross-sensor color consistency, assessing color measurement accuracy on field-grown rice leaves, and demonstrating its practical applications using rice maturity estimation as an example. The results indicated that the CCM significantly enhanced color accuracy, with a 66.1 ​% reduction in the average CIE 2000 color difference (ΔE), and improved color consistency among the six RGB sensors, with a 70.2 ​% increase in the intracluster distance. CoF-CC subsequently reduced ΔE from 18.2 to 5.0 between the corrected rice leaf color and ground-truth measurements, indicating that the color differences were nearly perceptible to the human eye. Moreover, the corrected imagery significantly enhanced the rice maturity prediction accuracy, improving the R 2 from 0.28 to 0.67. In summary, the CoF-CC method standardizes RGB images across diverse lighting conditions and sensors, demonstrating robust performance in color analysis and interpretation under open-field conditions.

Why it matches plant phenotyping methods植物葉の色および成熟度を推定するためのUAV画像色補正法を開発し、圃場で精度検証と成熟度推定への適用を行っており、フェノタイピング手法が中心である。

abstractThis study introduces a novel in-flight color correction approach for RGB imagery using cooperative dual unmanned aerial vehicle (UAV) flights integrated with a color chart (CoF-CC).

Leveraging unmanned aerial vehicle derived multispectral data for improved genomic prediction in potato (Solanum tuberosum). →

Multispectral leaf canopy reflectance as measured by unmanned aerial vehicles is the result of genetic and environmental interactions driving plant physiochemical processes. These measures can then be used to construct relationship matrices for modeling genetic main effects. This type of phenotypic prediction is particularly relevant for trials with many entries, such as those used in early generation potato (Solanum tuberosum) breeding. We compared three methods for making predictions in our potato breeding program: first, using multispectral-derived relationship matrices; second, using the traditional approach based on genomic derived relationships; and third, using a combination of both. Multispectral bands were collected at five different time points for two market classes of potato: chipping and fresh market. We modeled genetic main effects for yield and quality traits at each time point and all stages combined. Models with multispectral relationship matrices exhibited better prediction accuracy for yield and roundness than genomic only models and models featuring spectra plus genomic kernels outperformed both single-kernel predictions in terms of accuracy for most traits. Time points were variably informative depending on the trait measured, however, for all traits combining across time points performed as well or better than single time point models. Similarly, using feature selection to limit our models to important variables did not improve prediction accuracy significantly. This work highlights two potential uses for spectral data in genomic prediction: first, as an alternative to genetic data and second, in combination with genetic data to increase precision of selection.

Why it matches plant phenotyping methodsUAVマルチスペクトルセンシングを用いたキャノピー反射データをゲノム予測に組み込み、複数手法と予測精度を比較しており、植物表現型取得・推定ワークフローが研究の中心です。

abstractMultispectral leaf canopy reflectance as measured by unmanned aerial vehicles is the result of genetic and environmental interactions driving plant physiochemical processes.

Mapping multiple dimensions of forest diversity using spaceborne spectroscopy →

Observing biodiversity across space and time is essential for advancing and verifying conservation efforts toward global biodiversity and sustainability goals. Spaceborne imaging spectroscopy has emerged as a revolutionary tool for quantifying and tracking forest diversity, yet its application at large spatial scales remains a central challenge. We develop a framework to map multiple dimensions of forest community composition and diversity by integrating imaging spectroscopy from two spaceborne sensors (DESIS and EMIT) with taxonomic, phylogenetic, and functional trait datasets, and 43,155 forest inventory plots across the Eastern United States. We find that spectral dissimilarity among forest communities is positively correlated with β-diversity matrices of compositional dissimilarity. We then show that imaging spectroscopy can be used to predict ordination axes of β-diversity and to map multiple dimensions of forest diversity at high spatial resolution (30 or 60 m). Predicted β-diversity axes can be used to model forest attributes, including forest types, plant lineages, and community plant traits. On average, β-diversity axes explain more than 48% of the variance—outperforming climatic and topographic predictors—and enable accurate mapping of 95 forest attributes. Our framework shows that spaceborne imaging spectroscopy, when combined with inventory data, allows indirect yet comprehensive observation of forest diversity attributes across broad spatial extents. This integrative approach sets the stage for scalable forest monitoring in support of global biodiversity conservation and forthcoming satellite missions.

Why it matches plant phenotyping methods宇宙空間イメージング分光と在庫データを統合し、森林群集の多様性や植物形質を推定・マッピングする枠組みが研究の中心であり、植物状態の大規模な表現型推定に該当する。

abstractWe develop a framework to map multiple dimensions of forest community composition and diversity by integrating imaging spectroscopy from two spaceborne sensors (DESIS and EMIT) with taxonomic, phylogenetic, and functional trait datasets, and 43,155 forest inventory plots across the Eastern United States.

TTADDA-UAV: A multi-season RGB and multispectral UAV dataset of potato fields collected in Japan and the Netherlands. →

The Transition to a Data-Driven Agriculture (TTADDA) project focuses on advancing the shift toward high-tech, circular agriculture. By developing cutting-edge sensor technologies and AI-driven tools, the project aims to boost productivity through a data-centric potato production system that supports circular agricultural practices. Potato phenotyping is crucial for creating high-yielding, resilient, and sustainable potato crops, which are essential in global food systems. Specifically in the Netherlands, the global leader in seed potato production and Japan that produces certified seed potatoes under strict quality controls and phytosanitary regulations. A multi-season drone dataset from five potato trials-three in Japan and two in the Netherlands was collected. Each trial field was divided into small plots, each planted with a specific cultivar to assess varietal performance. Data included drone imagery (RGB and multispectral), manual yield and ground coverage measurements, and weather data. The combination of sensor versatility, diverse potato varieties, and varying climate and soil conditions between Japan and the Netherlands makes this dataset highly valuable and potentially reusable for a wide range of applications. Using MIAPPE for this dataset ensures consistent, clear documentation of sensors, varieties, and conditions, making the data findable, reusable, and easy to integrate with other studies. It also supports reproducibility and automated analysis across the multi-location trials.

Why it matches plant phenotyping methodsジャガイモの表現型解析を目的としたUAV RGB・マルチスペクトル画像と圃場測定を含む、多季節・多地点の再利用可能なデータセットの構築・標準化が中心である。

abstractA multi-season drone dataset from five potato trials-three in Japan and two in the Netherlands was collected.

Assessment of plant diversity index in degraded desert grassland using UAV hyperspectral multimodal data and Encoder-CNN. →

The biodiversity function of the desert steppe ecosystem faces many challenges under the pressure of climate change and human activities. Accurate and efficient assessment of plant diversity is critical for guiding desert steppe restoration efforts. However, desert steppe vegetation has sparse leaves and sparse distribution. It is difficult to accurately distinguish micro-vegetation types based on a single spectrum, vegetation index or texture feature, and the resolution of satellite remote sensing cannot meet the needs of high-precision diversity assessment. To this end, this study proposed a novel method for assessing plant diversity index in degraded desert grassland based on multimodal UAV hyperspectral data and Encoder-CNN. Through experiments on different modal feature combinations, spatial spectra, vegetation indices and texture features were targeted and fused. Channel Attention Fusion (CAF) was introduced into Encoder to achieve cross-layer "soft" residual fusion, the Encoder and CNN models were fused to construct a global-local co-expression structure, and finally the quantitative calculation of the plant diversity index at the pixel level was realized. The results show that the vegetation types determined by the fusion of multimodal data and deep learning are consistent with the existing species, dominant species and sub-dominant species of the actual community, and the calculated diversity index results are also consistent with the actual situation. The use of multimodal data combining spatial spectral features with index features, combined with the Encode-CNN model, can provide the most accurate information on community composition. The overall accuracy of sparse vegetation classification can reach 90.01%, and the average accuracy can reach 85.23%, which is better than single mode or traditional 3DCNN, VIT models. This study demonstrates the application potential of UAV hyperspectral multimodal technology and deep learning in the assessment of desert steppe plant diversity, providing important technical support for ecological protection and conservation.

Why it matches plant phenotyping methodsUAVハイパースペクトルとEncoder-CNNを用いて、植物多様性指数を画素レベルで定量推定する手法を開発・評価しており、植物状態の取得・抽出が研究の中心である。

abstractthis study proposed a novel method for assessing plant diversity index in degraded desert grassland based on multimodal UAV hyperspectral data and Encoder-CNN.

Dissecting lentil crop growth in contrasting environments using digital imaging and genome‐wide association studies →

Abstract The development of high‐throughput phenotyping platforms to capture time‐series data on large, diverse populations holds promise for crop researchers and breeders investigating growth‐related traits. We used imagery from unoccupied aerial vehicles (UAVs) with red/green/blue (RGB) and multispectral cameras flown over multiple site‐years in Saskatchewan, Canada, and Metaponto, Italy, to gather data for crop height, area, and volume in a lentil diversity panel (324 genotypes). The temporal nature of the UAV image‐derived data enabled the modeling of growth curves for volume, height, and area, something that would be impractical under traditional phenotyping procedures in such a large population grown in multiple environments. A principal component analysis and hierarchical clustering revealed differential growth patterns across contrasting environments, with large variations in temperature and photoperiod, within our lentil diversity panel. Combining this analysis with genome‐wide genotyping data, we identified markers, from an exome capture array (267,845 single nucleotide polymorphisms), associated with crop growth that could be used for marker‐assisted selection. Our study demonstrates the potential for UAV‐based imaging to obtain large‐scale time‐series data across multiple environments to model growth curves and investigate genotype‐by‐environment interactions. In addition, we can now use phenotypic traits that were once impractical to collect and derive novel phenotypes to improve our understanding of crop growth and the genetics underlying adaptation in lentil, approaches that will be useful for both researchers and breeders.

Why it matches plant phenotyping methodsUAV画像からレンティルの高さ・面積・体積を時系列推定し、大規模集団で成長曲線をモデル化するフェノタイピング手法の実質的な適用・評価が中心である。

abstractThe development of high‐throughput phenotyping platforms to capture time‐series data on large, diverse populations holds promise for crop researchers and breeders investigating growth‐related traits.

Detecting and Mapping Invasive Species Across Riparian Corridors via Object Detection Approaches in UAV Imagery: An Example of Impatiens glandulifera . →

Riparian zones in the United Kingdom have high species diversity but are prone to anthropogenic changes and alien plant invasions, like Impatiens glandulifera . However, identification can be challenging due to poor accessibility or visibility via tree canopies. UAVs provide a means to access previously inaccessible areas and capture imagery of the area. In this study, a method is introduced to identify the flowers of invasive species ( Impatiens glandulifera ) and map their locations using a computer vision framework and oblique image capture methods. The process includes thresholding images, image masking, blurring, ellipsoid shape search, noise reduction, and contour extraction. Locations are determined using camera parameters, EXIF data, and the average flower size, then converted into vector format for GIS software. This method is wrapped into a single executable program named the semi-automatic thresholding tool (SATT). A validation set of 312 UAV images from the River Elwy, North Wales, showed high precision (79%-96%) and mean average precision (mAP) scores of 73%-86%. This demonstrates that the SATT consistently and correctly identifies Impatiens glandulifera flowers from UAV imagery, making it effective for identifying hotspots and targeting management techniques along riparian corridors. The tool has been wrapped into a single-file executable program with a graphical user interface, enabling nonexperts to use the tool without the need of any software installation. Overall, the tool obtains consistent detection levels of abundance/or flower density across the study site. The tool also does not require an extensive amount of training data, and the intuitive design of the software enables nonexperts to utilize the tool and modify parameter values to adapt it to their needs.

Why it matches plant phenotyping methodsUAV画像から花を検出・抽出し、花の存在位置だけでなく個体群の abundance／flower density を推定する手法と実行可能なツールを開発・検証しており、植物器官形質の取得が中心です。

abstracta method is introduced to identify the flowers of invasive species ( Impatiens glandulifera ) and map their locations using a computer vision framework and oblique image capture methods.

From aerial drone to quantitative trait locus: leveraging next-generation phenotyping to reveal the genetics of color and height in field-grown Lactuca sativa. →

In recent years, accurate and low-cost variant calling has enabled the genotyping of large diversity panels for genome-wide association studies. As a result, phenotyping rather than genotyping is now the rate-limiting step, especially in field experiments. This has created a strong need for high-throughput, accurate, and low-cost in-field phenotyping. Here, we present a genome-wide association study (GWAS) study on 194 field-grown accessions of lettuce (Lactuca sativa). These accessions were non-destructively phenotyped at two time points 15 days apart using a drone equipped with an RGB and multispectral (MSP) camera. Our high-throughput phenotyping approach integrates an RGB- and MSP camera to measure the color and height of lettuce in this large-scale field experiment. We used the mean and other summary statistics, such as median, quantiles, skewness, kurtosis, minimum, and maximum to quantify different aspects of color and height variation in lettuce from the drone images. Using these summary statistics as traits for GWAS, we confirm several previously described genetic associations, now under field conditions, and identify additional novel associations for color and height traits in lettuce.

Why it matches plant phenotyping methodsドローン搭載RGB・マルチスペクトルカメラを用いて、レタスの色と高さを大規模・非破壊・定量測定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への応用も行っている。

abstractHere, we present a genome-wide association study (GWAS) study on 194 field-grown accessions of lettuce (Lactuca sativa). These accessions were non-destructively phenotyped at two time points 15 days apart using a drone equipped with an RGB and multispectral (MSP) camera.

RsegNet: An Advanced Methodology for Individual Rubber Tree Segmentation and Structural Parameter Extraction from UAV LiDAR Point Clouds. →

As an important tropical cash crop, rubber trees play a key role in the rubber industry and ecosystem. However, a significant challenge in precision agriculture and refined management of rubber plantation lies in the limitations of traditional point cloud segmentation methods, which struggle to accurately extract structural parameters and capture the spatial layout of individual rubber trees. Therefore, we propose an optimized dual-channel clustering method for the UAV LiDAR-based Rubber Tree Point Cloud Segmentation Network (RsegNet) for improved assessment of rubber tree architecture and traits. Firstly, we designed a cosine feature extraction network, termed CosineU-Net, to address the branch-and-leaf overlap problem by calculating the cosine similarity of the spatial and positional features of each point, leveraging deep learning approaches to improve feature representation. Secondly, we constructed a dual-channel clustering module reducing prediction error in rubber tree point cloud data, integrating multi-class association and background classification to tackle background interference. The cluster identification and separation accuracy in high-dimensional data processing is enhanced through a dynamic clustering optimization algorithm. In our self-built dataset and across five regions of the FOR-instance forest dataset, RsegNet achieved the best performance compared to five state-of-the-art networks, reaching an F-score of 86.1%. This method calculated structural attributes including height, crown diameter, and volume for rubber trees in three areas under different environments in Danzhou City, Hainan Province, providing robust support for precise monitoring, plantation management, and health assessment.

Why it matches plant phenotyping methodsUAV LiDAR点群の個体分割・構造形質抽出手法を開発し、精度比較と樹高・樹冠径・体積の算出まで行っており、植物フェノタイピング手法が中心である。

abstractwe propose an optimized dual-channel clustering method for the UAV LiDAR-based Rubber Tree Point Cloud Segmentation Network (RsegNet) for improved assessment of rubber tree architecture and traits.

UAV-based estimation of post-sowing rice plant density using RGB imagery and deep learning across multiple altitudes →

This study presents a novel and efficient approach to accurately assess post-sowing rice plant density by leveraging unmanned aerial vehicles (UAVs) equipped with high-resolution RGB cameras. In contrast to labor-intensive and spatially limited traditional methods that rely on manual sampling and extrapolation, our proposed methodology uses UAVs to rapidly and comprehensively survey entire paddy fields at optimized altitudes (4, 6, 8, and 10 m). Aerial imagery was autonomously acquired 17 days post-sowing, following a pre-defined flight path. The robust rice plant density estimation process incorporates two key innovations: first, a dynamic system of 12 adaptive segmentation thresholding blocks that effectively detects rice seed presence across diverse and variable background conditions. Second, a tailored three-layer convolutional neural network (CNN) accurately classifies vegetative situations. To maximize the training efficiency and performance, we implemented both a pretrained model and a deep learning model, conducting a rigorous comparative analysis against the state-of-the-art YOLOv10. Notably, under favorable imaging conditions, our findings indicate that a 6-m flight altitude yields optimal results, achieving a high degree of accuracy with rice plant density estimates that closely align with those obtained through traditional ground-based methods. This investigation unequivocally highlights the significant advantages of UAV-based monitoring as an economically viable, spatially comprehensive, and demonstrably accurate tool for precise rice field management, ultimately contributing to enhanced crop yields, improved food security, and the promotion of sustainable agricultural practices.

Why it matches plant phenotyping methodsUAV RGB画像と適応的セグメンテーション、CNNを用いてイネ個体密度を推定する手法を開発・比較・検証しており、植物形質の取得が研究の中心です。

abstractThis study presents a novel and efficient approach to accurately assess post-sowing rice plant density by leveraging unmanned aerial vehicles (UAVs) equipped with high-resolution RGB cameras.

Phenomics‐driven insights into zoysiagrass drought resistance using small unmanned aircraft systems (sUAS)‐based hyperspectral images →

Abstract The application of small unmanned aircraft systems (sUAS)‐based high‐throughput phenotyping in plant breeding has advanced significantly over the past decade. Hyperspectral images and machine learning approaches offer potential to enhance drought resistance screening in turfgrass. However, large‐scale field applications remain limited, and the transition from controlled environments to real‐world phenotyping is not well understood. This study aimed to develop an sUAS‐based hyperspectral image workflow to monitor changes in turfgrass canopy reflectance during drought, validate previously reported indices from controlled environment studies in a large‐scale field study, and estimate visual turfgrass quality (TQ) from hyperspectral images. Images were collected from a zoysiagrass ( Zoysia spp.) mapping population at three dates under varying soil moisture conditions. Vegetation indices (VIs) related to light use efficiency, leaf pigments, senescence, water status, and green vegetation were computed and compared. Top‐performing genotypes under drought exhibited greater absorption in blue and red wavelengths and higher near‐infrared reflectance than poor‐performing ones. The photochemical reflectance index and plant senescence reflectance index were highly correlated with TQ ( r = 0.84 and −0.76), showed higher coefficient of variation (range 18%–37%), and had higher broad‐sense heritability (0.73–0.74) than normalized difference vegetation index (0.69), warranting their use in large‐scale field study. Machine learning models estimated TQ with a mean absolute error of 0.46. These findings highlight the importance of integrating VIs related to light use efficiency, leaf pigments, senescence, and water status to gain deeper insights into turfgrass drought response and support breeding for stress tolerance.

Why it matches plant phenotyping methodssUASハイパースペクトル画像によるキャノピー形質取得ワークフローを開発し、指標を検証して芝草品質を推定しており、フェノタイピング手法が中心である。

abstractThis study aimed to develop an sUAS‐based hyperspectral image workflow to monitor changes in turfgrass canopy reflectance during drought, validate previously reported indices from controlled environment studies in a large‐scale field study, and estimate visual turfgrass quality (TQ) from hyperspectral images.

Evaluating UAV LiDAR and Field Spectroscopy for Estimating Residual Dry Matter Across Conservation Grazing Lands →

Residual dry matter (RDM) is a term used in rangeland management to describe the non-photosynthetic plant material left on the soil surface at the end of the growing season. RDM measurements are used by agencies and conservation entities for managing grazing and fire fuels. Measuring the RDM using traditional methods is labor-intensive, costly, and subjective, making consistent sampling challenging. Previous studies have assessed the use of multispectral remote sensing to estimate the RDM, but with limited success across space and time. The existing approaches may be improved through the use of spectroscopic (hyperspectral) sensors, capable of capturing the cellulose and lignin present in dry grass, as well as Unmanned Aerial Vehicle (UAV)-mounted Light Detection and Ranging (LiDAR) sensors, capable of capturing centimeter-scale 3D vegetation structures. Here, we evaluate the relationships between the RDM and spectral and LiDAR data across the Jack and Laura Dangermond Preserve (Santa Barbara County, CA, USA), which uses grazing and prescribed fire for rangeland management. The spectral indices did not correlate with the RDM (R2

Why it matches plant phenotyping methodsUAV LiDARとフィールド分光法を用いて、植生残渣量（RDM）という植物状態を推定するセンサー手法の評価が研究の中心であり、単なる農業実験での routine measurement ではない。

titleEvaluating UAV LiDAR and Field Spectroscopy for Estimating Residual Dry Matter Across Conservation Grazing Lands

Photothermal Integration of Multi-Spectral Imaging Data via UAS Improves Prediction of Target Traits in Oat Breeding Trials →

The modelling and prediction of important agronomic traits using remotely sensed data is an evolving science and an attractive concept for plant breeders, as manual crop phenotyping is both expensive and time consuming. Major limiting factors in creating robust prediction models include the appropriate integration of data across different years and sites, and the availability of sufficient genetic and phenotypic diversity. Variable weather patterns, especially at higher latitudes, add to the complexity of this integration. This study introduces a novel approach by using photothermal time units to align spectral data from unmanned aerial system images of spring, winter, and facultative oat (Avena sativa) trials conducted over different years at a trial site at Aberystwyth, on the western Atlantic seaboard of the UK. The resulting regression and classification models for various agronomic traits are of significant interest to oat breeding programmes. The potential applications of these findings include optimising breeding strategies, improving crop yield predictions, and enhancing the efficiency of resource allocation in breeding programmes.

Why it matches plant phenotyping methodsUASマルチスペクトル画像とフォトサーマル時間単位を統合し、オート育種試験の農業形質を予測する手法が研究の中心である。

abstractThis study introduces a novel approach by using photothermal time units to align spectral data from unmanned aerial system images

On the Minimum Dataset Requirements for Fine-Tuning an Object Detector for Arable Crop Plant Counting: A Case Study on Maize Seedlings →

Object detection is essential for precision agriculture applications like automated plant counting, but the minimum dataset requirements for effective model deployment remain poorly understood for arable crop seedling detection on orthomosaics. This study investigated how much annotated data is required to achieve standard counting accuracy (R2 = 0.85) for maize seedlings across different object detection approaches. We systematically evaluated traditional deep learning models requiring many training examples (YOLOv5, YOLOv8, YOLO11, RT-DETR), newer approaches requiring few examples (CD-ViTO), and methods requiring zero labeled examples (OWLv2) using drone-captured orthomosaic RGB imagery. We also implemented a handcrafted computer graphics algorithm as baseline. Models were tested with varying training sources (in-domain vs. out-of-distribution data), training dataset sizes (10–150 images), and annotation quality levels (10–100%). Our results demonstrate that no model trained on out-of-distribution data achieved acceptable performance, regardless of dataset size. In contrast, models trained on in-domain data reached the benchmark with as few as 60–130 annotated images, depending on architecture. Transformer-based models (RT-DETR) required significantly fewer samples (60) than CNN-based models (110–130), though they showed different tolerances to annotation quality reduction. Models maintained acceptable performance with only 65–90% of original annotation quality. Despite recent advances, neither few-shot nor zero-shot approaches met minimum performance requirements for precision agriculture deployment. These findings provide practical guidance for developing maize seedling detection systems, demonstrating that successful deployment requires in-domain training data, with minimum dataset requirements varying by model architecture.

Why it matches plant phenotyping methodsトウモロコシ幼苗の個体数という植物形質を画像から推定する物体検出手法について、複数モデル、データ量、アノテーション品質を系統的に比較・評価しており、手法の性能検証が中心である。

abstractThis study investigated how much annotated data is required to achieve standard counting accuracy (R2 = 0.85) for maize seedlings across different object detection approaches.

Drone-based, multispectral photogrammetric point clouds to classify fire severity at differing canopy height strata →

Abstract Background Remote sensing techniques for assessing fire severity using two-dimensional imagery, such as satellite data, are limited to a single severity value per pixel, typically at a 30-m resolution. This often leads to an underestimation of understory fire severity, as live tree crowns can obscure the extent of the burned area beneath. By leveraging the three-dimensional capabilities of drone imagery, a more comprehensive assessment of fire severity across different canopy height strata can be achieved. Methods We show how drone digital aerial photogrammetry (dDAP), also known as structure from motion, can be used to generate three-dimensional multispectral photogrammetric point clouds for quantifying fire effects at various canopy height strata as well as classify ground cover below normally occluding overstory trees. Conducted during prescribed fires at Fort Jackson, South Carolina, RGB and multispectral imagery were collected via drone both pre- and post-fire at five plots, with two additional unburned plots flown to serve as controls. Multispectral photogrammetric point clouds were generated and NDVI values were calculated for each point. Point clouds were segmented into 2-m height stratum layers, to compare NDVI values for different canopy height strata pre- and post-fire. Orthoimages of the understory, overstory, and traditional nadir views were generated. Conclusions Findings showed that prescribed fire had a substantial effect on NDVI values up to 6 m in height, with only minor effects observed above 6 m. Ground cover under the canopy, typically occluded from overhead imagery, was classified with 87% accuracy. This study demonstrated the ability to digitally remove occluding tall vegetation using dDAP and to derive a more precise assessment of fire effects on ground and understory vegetation compared to two-dimensional satellite imagery.

Why it matches plant phenotyping methodsドローンの3次元マルチスペクトル点群を用いて、植物の樹冠層別の火災影響・NDVI・地被状態を抽出する手法が研究の中心であり、単なる生物学的測定ではない。

abstractcan be used to generate three-dimensional multispectral photogrammetric point clouds for quantifying fire effects at various canopy height strata as well as classify ground cover below normally occluding overstory trees

MatchPlant: An Open-Source Pipeline for UAV-Based Single-Plant Detection and Data Extraction →

Accurate identification of individual plants from unmanned aerial vehicle (UAV) images is essential for advancing high-throughput phenotyping and supporting data-driven decision-making in plant breeding. This study presents MatchPlant, a modular, graphical user interface-supported, open-source Python pipeline for UAV-based single-plant detection and geospatial trait extraction. MatchPlant enables end-to-end workflows by integrating UAV image processing, user-guided annotation, Convolutional Neural Network model training for object detection, forward projection of bounding boxes onto an orthomosaic, and shapefile generation for spatial phenotypic analysis. In an early-season maize case study, MatchPlant achieved reliable detection performance (validation AP: 89.6%, test AP: 85.9%) and effectively projected bounding boxes, covering 89.8% of manually annotated boxes with 87.5% of projections achieving an Intersection over Union (IoU) greater than 0.5. Trait values extracted from predicted bounding instances showed high agreement with manual annotations (r = 0.87-0.97, IoU >= 0.4). Detection outputs were reused across time points to extract plant height and Normalized Difference Vegetation Index with minimal additional annotation, facilitating efficient temporal phenotyping. By combining modular design, reproducibility, and geospatial precision, MatchPlant offers a scalable framework for UAV-based plant-level analysis with broad applicability in agricultural and environmental monitoring.

Why it matches plant phenotyping methodsUAV画像から個体検出・地理空間的形質抽出を行うオープンソース基盤の開発と性能検証が中心であり、植物形質（草丈・NDVI）を抽出する再利用可能なワークフローを提供している。

abstractThis study presents MatchPlant, a modular, graphical user interface-supported, open-source Python pipeline for UAV-based single-plant detection and geospatial trait extraction.

Performance of stacking machine learning and volume model for improving corn above ground biomass prediction. →

The aboveground biomass (AGB) of crops is an essential metric for monitoring crop growth, making timely and accurate AGB forecasting critical for effective agricultural management. The introduction of Unmanned Aerial Vehicles (UAVs) and advanced sensor technologies has revolutionized traditional AGB prediction techniques. Currently, machine learning (ML) combined with UAV data are commonly utilized, along with the Vegetation Index Weighted Canopy Volume Model (CVM VI ) for AGB prediction. Nevertheless, there is limited investigation into how these methods perform across different agricultural conditions. This study aims to fill this gap by creating specific methodologies for estimating corn AGB under diverse fertilization and irrigation treatments. We utilized LiDAR, multispectral (MS), thermal infrared (TIR), along with measured AGB and Leaf Area Index (LAI) data from various growth stages to develop a stacking ensemble learning model. This model effectively integrates data from multiple sources, resulting in a strong prediction performance with R 2 of 0.86, Mean Absolute Error (MAE) of 1.54 ​t/ha, and Root Mean Square Error (RMSE) of 2.06 ​t/ha. Meanwhile, the analysis of the accuracy of CVM VI revealed its efficacy during the early-stage when corn is short, with its predictive capability diminishing as AGB increases. Consequently, we recommend the CVM VI for early-stage AGB prediction, which can streamline data collection and computational efforts. In contrast, the ML approach, which benefits from data fusion, is more appropriate for predicting AGB during the mid to late growth stages. This study enhances AGB prediction accuracy and speed, providing critical understanding of regional AGB dynamics and supporting better agricultural decision-making.

Why it matches plant phenotyping methodsUAVのLiDAR・マルチスペクトル・熱赤外データを統合し、トウモロコシの地上部バイオマスを推定するモデルを開発・比較・評価しており、植物形質取得手法が中心である。

abstractThis study aims to fill this gap by creating specific methodologies for estimating corn AGB under diverse fertilization and irrigation treatments.

FRPNet: A Lightweight Multi-Altitude Field Rice Panicle Detection and Counting Network Based on Unmanned Aerial Vehicle Images →

Rice panicle detection is a key technology for improving rice yield and agricultural management levels. Traditional manual counting methods are labor-intensive and inefficient, making them unsuitable for large-scale farmlands. This paper proposes FRPNet, a novel lightweight convolutional neural network optimized for multi-altitude rice panicle detection in UAV images. The architecture integrates three core innovations: a CSP-ScConv backbone with self-calibrating convolutions for efficient multi-scale feature extraction; a Feature Pyramid Shared Convolution (FPSC) module that replaces pooling with multi-branch dilated convolutions to preserve fine-grained spatial information; and a Dynamic Bidirectional Feature Pyramid Network (DynamicBiFPN) employing input-adaptive kernels to optimize cross-scale feature fusion. The model was trained and evaluated on the open-access Dense Rice Panicle Detection (DRPD) dataset, which comprises UAV images captured at 7 m, 12 m, and 20 m altitudes. Experimental results demonstrate that our method significantly outperforms existing advanced models, achieving an AP50 of 0.8931 and an F2 score of 0.8377 on the test set. While ensuring model accuracy, the parameters of the proposed model decreased by 42.87% and the GFLOPs by 48.95% compared to Panicle-AI. Grad-CAM visualizations reveal that FRPNet exhibits superior background noise suppression in 20 m altitude images compared to mainstream models. This work establishes an accuracy-efficiency balanced solution for UAV-based field phenotyping.

Why it matches plant phenotyping methodsUAV画像からイネ穂の検出・計数という植物形質を抽出する軽量深層学習手法を開発し、公開データセットで評価しており、表現型取得手法が中心である。

abstractThis paper proposes FRPNet, a novel lightweight convolutional neural network optimized for multi-altitude rice panicle detection in UAV images.

An Indian UAV and leaf image dataset for integrated crop health assessment of soybean crop. →

Soybean is an important oilseed crop, rich in protein and oil, often referred to as a ``cash crop'' or ``gold bean'' by Indian farmers. In Maharashtra, soybean cultivation spans over approximately 3.8 million hectares, producing 3.07 million tons, placing the state second in India for overall soybean production. However, despite of its significance, several issues such as weeds, diseases, and pests hamper the overall productivity of soybean. Addressing these challenges faced by soybean growers it is essential to enhance yield and improve the crop's overall potential Currently, the farming sector is transitioning towards Agriculture 5.0, also known as digital farming. This approach utilizes data-driven technologies, such as artificial intelligence and computer vision, to transform the agriculture sector. These technologies enable the automation of several farming tasks. To develop accurate and robust machine learning/deep learning models high quality datasets are needed. With this aim, we have created a comprehensive dataset of soybean crop images affected by diseases and pest attacks from original fields of Maharashtra region located in India. Data acquisition was conducted across two seasons through aerial as well as ground-based approaches. The dataset is enriched with 4 types of diseases and 1 pest attack. The proposed dataset will serve as a valuable resource for training and testing machine learning and deep learning models ,enabling accurate detection and classification of diseases and pests attack damage.

Why it matches plant phenotyping methods大豆の病害・害虫被害を対象とした航空・地上画像データセットの構築が中心で、植物の病害状態を画像から評価する再利用可能な資源であるため。

abstractwe have created a comprehensive dataset of soybean crop images affected by diseases and pest attacks from original fields of Maharashtra region located in India.

High-Throughput Field Phenotyping Using Unmanned Aerial Vehicles (UAVs) for Rapid Estimation of Photosynthetic Traits. →

​= ​0.63). Our findings demonstrate that UAV-acquired multispectral data can effectively map photosynthetic traits with high spatial resolution, establishing it as a valuable tool for rapid phenotyping and spatial assessment of photosynthetic capacity in crop fields.

Why it matches plant phenotyping methodsUAVマルチスペクトルデータで作物の光合成形質を推定する高スループット表現型解析が中心であり、センサープラットフォームの実質的な適用に該当する。

titleHigh-Throughput Field Phenotyping Using Unmanned Aerial Vehicles (UAVs) for Rapid Estimation of Photosynthetic Traits.

Integrating UAV multispectral imaging and proximal sensing for high-precision cereal crop monitoring. →

Multispectral optical data significantly enhances cereal crop monitoring by enabling precise tracking of growth stages, early detection of germination issues, and assessment of plant health. This study evaluates the potential of integrating UAV multispectral sensor with the handheld Plant-O-Meter device for high-precision crop monitoring. The aim was to determine the optimal UAV imaging timing that aligns with proximal sensor measurements to improve growth stage assessments. Experiments were conducted on 41 cereal genotypes, including ancient and modern varieties, under two nitrogen top-dress dosages across 130 plots. The top ten performing genotypes were analyzed to identify resilient varieties adaptable to climate change and evolving field conditions. Our results demonstrate that vegetation indices during booting and spike emergence stages consistently predict yield potential, offering a robust framework for early-stage yield estimation. Additionally, we provide a comparative analysis of UAV and handheld sensor data, highlighting their respective strengths and limitations. Three vegetation indices, GRDVI, NDVI and SAVI demonstrated a very strong average positive correlation: 0.957, 0.954 and 0.944 across the selected genotypes from different performance levels. The combined dataset supports improved fertilization strategies, optimized seeding cycles, and identification of genotypes with stable agronomic traits. This study underscores the synergistic potential of aerial and proximal sensing technologies for next-generation cereal crop management and precision agriculture.

Why it matches plant phenotyping methodsUAVマルチスペクトル画像と近接センサーを統合し、画像取得時期、センサーデータの比較、植物生育段階・収量予測を評価しており、植物形質取得手法が研究の中心である。

abstractThis study evaluates the potential of integrating UAV multispectral sensor with the handheld Plant-O-Meter device for high-precision crop monitoring.

Evaluating UAV captured RGB and multispectral imagery as a proxy for visual rating of leaf spot in cultivated peanut →

Abstract Leaf spot is a devastating disease in cultivated peanut ( Arachis hypogaea L.) that can lead to significant yield losses without chemical controls. Multiple disease symptoms, two causal organisms, inconsistent testing environments, and genotype by environment interactions are all components that make breeding for leaf spot‐resistant peanuts challenging. To better understand this disease, and make gains in breeding for disease resistance, an accurate and objective phenotyping strategy must be implemented. In this work, data derived from leaf scans, unoccupied aerial vehicle‐captured red, green, blue and multispectral imagery were evaluated as a replacement for the subjective visual rating scale used at present. Standard operating procedures are detailed for all digital methods evaluated in this paper, and all digital phenotypes are fully characterized with descriptive statistics. Feature importance and post hoc proof of concept studies are conducted to further evaluate the new digital methods. Ultimately, “visible atmospherically resistant index” was selected as the most appropriate proxy for visual ratings and should be deployed by researchers and plant breeders in the peanut community for the objective evaluation of leaf spot resistance.

Why it matches plant phenotyping methods落花生葉斑病の客観的表現型評価を目的に、葉スキャンおよびUAVのRGB・マルチスペクトル画像を用いるデジタル手法を評価・標準化しており、病害表現型の取得法が中心である。

abstractan accurate and objective phenotyping strategy must be implemented

SMICGS: A novel snapshot multispectral imaging sensor for quantitative monitoring of crop growth. →

Unmanned aerial vehicle (UAV)-based multispectral imaging is one of the most widely used technologies for rapid crop monitoring, essential for crop-growth management. However, the technology's complex optical structure and difficulty in interpreting real-time crop-growth information seriously restrict its application. This paper presents a newly designed UAV-based snapshot multispectral imaging crop-growth sensor (SMICGS) aimed at simplifying the optical structure and realizing the online interpretation of crop spectral information. Mosaic filters based on the special spectral characteristics of crops were designed to achieve multiband co-optical imaging. A spectral crosstalk correction method based on the pixel response characteristics of SMICGS was proposed, and a processing system based on the coupling of sensor information and crop-growth monitoring models was developed to realize real-time online processing of crop spectral information. Field experiments showed that the vegetation indices obtained by SMICGS combined with the machine learning algorithm random forest (RF) achieved better results in predicting leaf area index (LAI) and above-ground biomass (AGB) for wheat and rice. For wheat, the R 2 and root mean square error (RMSE) values for the LAI and AGB prediction models were 0.81 and 0.85, and 0.682 and 1.127 ​t/ha, respectively. For rice, the R 2 and RMSE values for the LAI and AGB prediction models were 0.89 and 0.93, and 0.818 and 0.866 ​t/ha, respectively. Overall, SMICGS provides a reliable foundational tool for real-time, non-destructive monitoring of field crop growth information, offering significant potential for the precise management of agricultural production.

Why it matches plant phenotyping methods作物生育情報を定量化するUAVマルチスペクトルセンサー、補正法、処理システムを開発し、LAIと地上部バイオマス推定を検証しており、植物フェノタイピング手法が中心である。

abstractThis paper presents a newly designed UAV-based snapshot multispectral imaging crop-growth sensor (SMICGS)

Plant recognition of maize seedling stage in UAV remote sensing images based on H-RT-DETR. →

The real-time monitoring and counting of maize seed germination at seedling stage is of great significance for seed quality detection, field management and yield estimation. Traditional manual monitoring and counting is very time-consuming, cumbersome and error-prone. In order to quickly and accurately identify and count maize seedlings in a complex field environment, this study proposes an end-to-end maize seedling plant detection model H-RT-DETR (Hierarchical-Real-Time DEtection TRansformer) based on hierarchical feature extraction and RT-DETR (Real-Time DEtection TRansformer). H-RT-DETR uses Hierarchical Feature Representation and Efficient Self-Attention as the backbone network for feature extraction, thereby improving the network's ability to extract features of maize seedling stage in UAV remote sensing images. Through experiments on the UAV remote sensing data set of maize seedling stage, the mean Average Precision mAP0.5-0.95, mAP0.5 and mAP0.75 of the improved H-RT-DETR model reached 51.2%, 94.7% and 48.1%, respectively, and the Average Recall (AR) reached 68.5%. In order to verify the efficiency of the proposed method, H-RT-DETR is compared with the widely used and advanced target recognition methods. The results show that the detection accuracy of H-RT-DETR is better than that of the comparison methods. In terms of detection speed, the H-RT-DETR model does not require Non-Maximum Suppression (NMS) post-processing operations, the Frames Per Second (FPS) on the test dataset reaches 84f/s, which is 19,12,11 and 21 higher than that of YOLOv5, YOLOv7, YOLOv8 and YOLOX, respectively, under the same hardware environment. This model can provide technical support for real-time detection of maize seedlings under UAV remote sensing images in terms of both detection accuracy and speed (see https://github.com/wylSUGAR/H-RT-DETR for model implementation and results).

Why it matches plant phenotyping methodsUAV画像からトウモロコシ幼苗を検出・計数する深層学習手法を開発し、既存手法と精度・速度を比較検証しているため、植物フェノタイピング手法が中心である。

abstractIn order to quickly and accurately identify and count maize seedlings in a complex field environment, this study proposes an end-to-end maize seedling plant detection model H-RT-DETR

Detecting olive quick decline syndrome: A satellite-based dataset for a case study in Apulia Region. →

The bacterium Xylella fastidiosa (Xf) is a plant pathogen first identified in Europe in 2013, specifically in olive groves in the Apulia region (south-eastern Italy). It is now spreading across the Mediterranean basin and poses a serious threat to the local economy by causing branch desiccation and the rapid death of olive trees, a condition known as olive quick decline syndrome (OQDS). Several studies have investigated the potential of remote sensing (RS) technology to monitor OQDS over time and space; however, accurate and reliable data on OQDS occurrence remain scarce. To enhance the distribution data of Xf-infected trees in the Apulia region, we investigated an infection hotspot of 25 km² area in the province of Brindisi, where records of infections were documented in 2019 and 2020. Three very high resolution, commercial WorldView-2 images were acquired and segmented, resulting in a dataset of 76637 olive trees. Through visual interpretation, 2340 trees were identified most likely as either infected or removed due to OQDS. This dataset provides a valuable resource for developing or validating RS techniques for early detection of OQDS. Furthermore, it could support studies aimed to evaluate spectral bands or indices most correlated with infection presence. Finally, the dataset can be integrated with other Xf-infection presence data to support species distribution model studies.

Why it matches plant phenotyping methods衛星画像のセグメンテーションと感染・枯死オリーブ樹のラベル化による、植物病害状態の検出・検証用データセットが研究の中心である。

abstractThree very high resolution, commercial WorldView-2 images were acquired and segmented, resulting in a dataset of 76637 olive trees.

Simplifying drone-based aboveground carbon density measurements to support community forestry. →

Community-based forest restoration has the potential to sequester large amounts of atmospheric carbon, avoid forest degradation, and support sustainable development. However, if partnered with international funders, such projects often require robust and transparent aboveground carbon measurements to secure payments, and current monitoring approaches are not necessarily appropriate due to costs, scale, and complexity. The use of consumer-grade drones in combination with open source structure-from-motion photogrammetry may provide a solution. In this study, we tested the suitability of a simplified drone-based method for measuring aboveground carbon density in heavily degraded tropical forests at a 2 ha restoration site in Sabah, Malaysia, comparing our results against established field-based methods. We used structure-from-motion photogrammetry to generate canopy height models from drone imagery, and applied multiple pre-published plot-aggregate allometric equations to examine the importance of utilising regionally calibrated allometric equations. Our results suggest that this simplified method can produce aboveground carbon density measurements of a similar magnitude to field-based methods, quickly and only with a single input metric. However, there are greater levels of uncertainty in carbon density measurements due to errors associated with canopy height measurements from drones. Our findings also highlight the importance of selecting regionally calibrated allometric equations for this approach. At scales between 1 and 100 ha, drone-based methods provide an appealing option for data acquisition and carbon measurement, balancing trade-offs between accuracy, simplicity, and cost effectiveness and coinciding well with the needs of community-scale aboveground carbon measurement. Of importance, we also discuss considerations relating to the accessibility of this method for community use, beyond purchasing a drone, that must not be overlooked. Nevertheless, the method presented here lays the foundations for a simple workflow for measuring aboveground carbon density at a community scale that can be refined in future studies.

Why it matches plant phenotyping methodsドローン画像とSfMから森林キャノピー高モデルを生成し、地上部炭素密度を推定する測定ワークフローを開発・検証しており、植物群落の形態・状態の取得が研究の中心である。

abstractWe used structure-from-motion photogrammetry to generate canopy height models from drone imagery

Semantic segmentation model of multi-source remote sensing images was used to extract winter wheat at tillering stage. →

In complex farmland environments, wheat canopy coverage is insufficient at the tillering stage, posing a considerable challenge to the accurate extraction of its canopy using UAV(unmanned air vehicle) remote sensing images. In this paper, an end-to-end semantic segmentation method based on visible light (RGB) and thermal infrared (TIR) images, Tiff-SegFormer, which fused spectral features and temperature features effectively, is proposed for accurate pixel-level classification of winter wheat at the tillering stage images taken by UAV to segment the wheat canopy and background. Tiff-SegFormer utilizes hierarchical feature representation and efficient self-attention in the encoder stage to extract features of detail contours of RGB images and temperature changes of TIFF images, respectively. In the decoder stage, the features are concatenated and then the channel and spatial attention mechanisms are superimposed, aiming to further improve the segmentation accuracy and efficiency of winter wheat at the tillering stage in UAV remote sensing images. The results show that Tiff-SegFormer can achieve accurate segmentation of wheat canopy and background from UAV images of winter wheat at the tillering stage (mIoU = 84.28%, mPA = 88.97%, accuracy = 94.55%). In order to verify the efficiency of the proposed method, Tiff-SegFormer is compared with four widely used semantic segmentation methods, all of which show better performance. The four methods are UNet, DeepLabv3+, HRNet, SegFormer and four-channel (RGB + TIFF) Segformer. The generalization test shows that the proposed Tiff-SegFormer also achieves better performance than other comparison methods (mIoU = 84.94%, mPA = 91.46%, accuracy = 94.71%). Tiff-SegFormer provides a robust and efficient tool for segmenting winter wheat canopy from UAV remote sensing images of winter wheat at the tillering stage, and has great potential in applications (model implementation and results can be found at https://github.com/wylSUGAR/Tiff-SegFormer ).

Why it matches plant phenotyping methodsUAVのRGB・熱赤外画像から冬コムギのキャノピーを抽出するセマンティックセグメンテーション手法を開発し、複数手法との比較および汎化性能検証を行っており、植物状態の取得方法が中心である。

abstractan end-to-end semantic segmentation method based on visible light (RGB) and thermal infrared (TIR) images, Tiff-SegFormer, which fused spectral features and temperature features effectively, is proposed for accurate pixel-level classification of winter wheat at the tillering stage images taken by UAV to segment the wheat canopy and background.

Characterization of N variations in different organs of winter wheat and mapping NUE using low altitude UAV-based remote sensing →

Although unmanned aerial vehicle (UAV) remote sensing is widely used for high-throughput crop monitoring, few attempts have been made to assess nitrogen content (NC) at the organ level and its association with nitrogen use efficiency (NUE). Also, little is known about the performance of UAV-based image texture features of different spectral bands in monitoring crop nitrogen and NUE. In this study, multi-spectral images were collected throughout different stages of winter wheat in two independent field trials - a single-variety field trial and a multi-variety trial in 2021 and 2022, respectively in China and Germany. Forty-three multispectral vegetation indices (VIs) and forty texture features (TFs) were calculated from images and fed into the partial least squares regression (PLSR) and random forest (RF) regression models for predicting nitrogen-related indicators. Our main objectives were to (1) assess the potential of UAV-based multispectral imagery for predicting NC in different organs of winter wheat, (2) explore the transferability of different image features (VI and TF) and trained machine learning models in predicting NC, and (3) propose a technical workflow for mapping NUE using UAV imagery. The results showed that the correlation between different features (VIs and TFs) and NC in different organs varied between the pre-anthesis and post-anthesis stages. PLSR latent variables extracted from those VIs and TFs could be a great predictor for nitrogen agronomic efficiency (NAE). While adding TFs to VI-based models enhanced the model performance in predicting NC, inconsistency arose when applying the TF-based models trained based on one dataset to the other independent dataset that involved different varieties, UAVs, and cameras. Unsurprisingly, models trained with the multi-variety dataset show better transferability than the models trained with the single-variety dataset. This study not only demonstrates the promise of applying UAV-based imaging to estimate NC in different organs and map NUE in winter wheat but also highlights the importance of conducting model evaluations based on independent datasets.

Why it matches plant phenotyping methodsUAVマルチスペクトル画像から小麦の器官別窒素含量と窒素利用効率を推定する技術ワークフローを開発・検証しており、特徴量、機械学習モデル、独立データセットでの転移性評価が中心である。

abstractOur main objectives were to (1) assess the potential of UAV-based multispectral imagery for predicting NC in different organs of winter wheat, (2) explore the transferability of different image features (VI and TF) and trained machine learning models in predicting NC, and (3) propose a technical workflow for mapping NUE using UAV imagery.

The Unstable Relationship Between Drought Status and Leaf Water Content Complicates the Remote Sensing of Tree Drought Stress. →

Remote sensing holds promise for ecosystem-level monitoring of plant drought stress but is limited by uncertain linkages between physiological stress and remotely sensed metrics of water content. Here, we investigate the stability of relationships between water potential (Ψ) and water content (measured in situ and via repeat airborne VSWIR imaging) over diel, seasonal, and spatial variation in two xeric oak tree species. We also compare these field-based relationships with ones established in laboratory settings that might be used as calibration. Due to confounding physiological processes related to growth, both in situ and remotely sensed metrics lacked consistent relationships with stress when measured across space or through time. Relationships between water content and physiological drought stress measured over the growing season were stronger and more closely related to established laboratory-based drydown methods than those measured across space (i.e., between wet trees and dry trees). These results provide insight into the utility of "space for time" approaches in remote sensing and demonstrate both important limitations and the potential power of high temporal resolution remote sensing for detecting drought stress.

Why it matches plant phenotyping methods樹木の干ばつストレスを対象に、航空機VSWIR画像による含水量推定と水ポテンシャルとの関係を時空間的に検証しており、リモートセンシング手法の妥当性・限界評価が中心です。

abstractwater content (measured in situ and via repeat airborne VSWIR imaging)

Detection of Banana Diseases Based on Landsat-8 Data and Machine Learning →

Banana is an important cash and food crop worldwide. Recent outbreaks of banana diseases are threatening the global banana industry and smallholder livelihoods. Remote sensing data offer the potential to detect the presence of disease, but there is a need for formal analysis to compare inferred with observed disease data. Here we use Landsat-8 data to investigate the detection of two banana diseases: banana bunchy top disease (BBTD) and Fusarium wilt Tropical Race 4 (TR4). We use satellite imagery to develop meteorology-driven predictive models for vegetation phenology, specifically based on healthy crops. Machine learning is then applied to identify anomalies associated with diseased plants by comparing the predicted vegetation indices of healthy crops with the observed indices from published data when disease is present. Our results show a correlation between changes in vegetation indices and the number of infected cases, highlighting the potential of this approach for large-scale disease surveillance.

Why it matches plant phenotyping methods衛星画像と機械学習により、バナナの病害に伴う植生指数の異常を推定する手法を開発・適用しており、感染植物の状態を大規模に評価することが中心です。

abstractWe use satellite imagery to develop meteorology-driven predictive models for vegetation phenology, specifically based on healthy crops.

Breaking the barrier of human-annotated training data for machine learning-aided plant research using aerial imagery →

Abstract Machine learning (ML) can accelerate biological research. However, the adoption of such tools to facilitate phenotyping based on sensor data has been limited by (i) the need for a large amount of human-annotated training data for each context in which the tool is used and (ii) phenotypes varying across contexts defined in terms of genetics and environment. This is a major bottleneck because acquiring training data is generally costly and time-consuming. This study demonstrates how a ML approach can address these challenges by minimizing the amount of human supervision needed for tool building. A case study was performed to compare ML approaches that examine images collected by an uncrewed aerial vehicle to determine the presence/absence of panicles (i.e. “heading”) across thousands of field plots containing genetically diverse breeding populations of 2 Miscanthus species. Automated analysis of aerial imagery enabled the identification of heading approximately 9 times faster than in-field visual inspection by humans. Leveraging an Efficiently Supervised Generative Adversarial Network (ESGAN) learning strategy reduced the requirement for human-annotated data by 1 to 2 orders of magnitude compared to traditional, fully supervised learning approaches. The ESGAN model learned the salient features of the data set by using thousands of unlabeled images to inform the discriminative ability of a classifier so that it required minimal human-labeled training data. This method can accelerate the phenotyping of heading date as a measure of flowering time in Miscanthus across diverse contexts (e.g. in multistate trials) and opens avenues to promote the broad adoption of ML tools.

Why it matches plant phenotyping methods航空画像とESGANを用いて、ススキの出穂（開花期）を低アノテーションで自動推定する手法を開発・比較しており、植物表現型取得が中心である。

abstractThis study demonstrates how a ML approach can address these challenges by minimizing the amount of human supervision needed for tool building.

Lightweight highland barley detection based on improved YOLOv5. →

Accurate and efficient assessment of highland barley (Hordeum vulgare L.) density is crucial for optimizing cultivation and management practices. However, challenges such as overlapping spikes in unmanned aerial vehicle (UAV) images and the computational requirements for high-resolution image analysis hinder real-time detection capabilities. To address these issues, this study proposes an improved lightweight YOLOv5 model for highland barley spike detection. We chose depthwise separable convolution (DSConv) and ghost convolution (GhostConv) for the backbone and neck networks, respectively, to reduce the parameter and computational complexity. In addition, the integration of convolutional block attention module (CBAM) enhances the model's ability to focus on target object in complex backgrounds. The results show that the improved YOLOv5 model has a significant improvement in detection performance. Precision and recall increased by 3.1% to 92.2% and 86.2%, respectively, with an F1 score of 0.892. The AP0.5 reaches 92.7% and 93.5% for highland barley in the growth and maturation stages, respectively, and the overall mAP0.5 improved to 93.1%. Compared to the baseline YOLOv5n model, the number of parameters and floating-point operations (FLOPs) were reduced by 70.6% and 75.6%, respectively, enabling lightweight deployment without compromising accuracy. In addition,the proposed model outperformed mainstream object detection algorithms such as Faster R-CNN, Mask R-CNN, RetinaNet, YOLOv7, and YOLOv8, in terms of detection accuracy and computational efficiency. Although this study also suffers from limitations such as insufficient generalization under varying lighting conditions and reliance on rectangular annotations, it provides valuable support and reference for the development of real-time highland barley spike detection systems, which can help to improve agricultural management.

Why it matches plant phenotyping methodsUAV画像からハダンオオムギの穂を検出し密度評価に用いる軽量化画像解析モデルを開発・比較しており、植物形質状態の取得手法が中心である。

abstractthis study proposes an improved lightweight YOLOv5 model for highland barley spike detection

OliveTreeCrownsDb: A high-resolution UAV dataset for detection and segmentation in agricultural computer vision. →

This article introduces OliveTreeCrownsDb, a comprehensive dataset of high-resolution images captured by a DJI Phantom 4 RTK drone. The dataset includes 46 images covering an entire olive farm, focusing on the detection and analysis of olive tree crowns and supporting segmentation tasks. Each image is accompanied by detailed metadata, such as focal distance, capture altitude, GPS coordinates, and other essential parameters for accurate tree mapping and localization. OliveTreeCrownsDb is publicly accessible, promoting research in precision agriculture, including tree crown detection, segmentation, geometric shape analysis, automation, yield estimation, and computer vision applications. It facilitates the development of innovative algorithms to optimize resource allocation and improve crop management. By enabling studies on tree crown analysis and farm monitoring, OliveTreeCrownsDb advances agricultural technologies and enhances management practices in olive cultivation.

Why it matches plant phenotyping methodsオリーブ樹冠の画像検出・セグメンテーションと幾何形状解析を可能にする公開データセットが研究の中心であり、植物の樹冠形態を抽出する再利用可能な基盤に該当する。

abstractThis article introduces OliveTreeCrownsDb, a comprehensive dataset of high-resolution images captured by a DJI Phantom 4 RTK drone.

Soybean yield estimation and lodging discrimination based on lightweight UAV and point cloud deep learning →

The unmanned aerial vehicle (UAV) platform has emerged as a powerful tool in soybean (Glycine max (L.) Merr.) breeding phenotype research due to its high throughput and adaptability. However, previous studies have predominantly relied on statistical features like vegetation indices and textures, overlooking the crucial structural information embedded in the data. Feature fusion has often been confined to a one-dimensional exponential form, which can decouple spatial and spectral information and neglect their interactions at the data level. In this study, we leverage our team's cross-circling oblique (CCO) route photography and Structure-from-Motion with Multi-View Stereo (SfM-MVS) techniques to reconstruct the three-dimensional (3D) structure of soybean canopies. Newly point cloud deep learning models SoyNet and SoyNet-Res were further created with two novel data-level fusion that integrate spatial structure and color information. Our results reveal that incorporating RGB color and vegetation index (VI) spectral information with spatial structure information, leads to a significant reduction in root mean square error (RMSE) for yield estimation (22.55 ​kg ​ha -1 ) and an improvement in F1-score for five-class lodging discrimination (0.06) at S7 growth stage. The SoyNet-Res model employing multi-task learning exhibits better accuracy in both yield estimation (RMSE: 349.45 ​kg ​ha -1 ) when compared to the H2O-AutoML. Furthermore, our findings indicate that multi-task deep learning outperforms single-task learning in lodging discrimination, achieving an accuracy top-2 of 0.87 and accuracy top-3 of 0.97 for five-class. In conclusion, the point cloud deep learning method exhibits tremendous potential in learning multi-phenotype tasks, laying the foundation for optimizing soybean breeding programs.

Why it matches plant phenotyping methodsUAV・SfM-MVSによるダイズ群落の3D構造再構成と、収量推定・倒伏判別のための専用深層学習モデル開発が研究の中心であり、再利用可能な表現型取得・推定手法に該当する。

abstractIn this study, we leverage our team's cross-circling oblique (CCO) route photography and Structure-from-Motion with Multi-View Stereo (SfM-MVS) techniques to reconstruct the three-dimensional (3D) structure of soybean canopies.

From smartphones to satellites: Uniting crowdsourced biodiversity monitoring and Earth observation to fill the gaps in global plant trait mapping →

Plant functional traits are fundamental to ecosystem dynamics and Earth system processes, but their global characterization is limited by the availability of field surveys and trait measurements. Recent expansions in biodiversity data aggregation, including large collections of vegetation surveys, citizen science observations, and trait measurements, offer new opportunities to overcome these constraints. Here we demonstrate that combining these diverse data sources with high-resolution Earth observation data enables accurate modeling of key plant traits at up to 1 km resolution. Our approach achieves high predictive power, reaching correlations up to 0.63 (15 of 31 traits exceeding 0.50) and improved spatial transferability, effectively bridging gaps in under-sampled regions. By capturing a broad range of traits with high spatial coverage, these maps can enhance our understanding of plant community properties and ecosystem functioning globally, and can serve as useful tools in modeling global biogeochemical processes and informing worldwide conservation efforts. Ultimately, our framework highlights the power and necessity of crowdsourced biodiversity data in high-resolution plant trait modeling. We anticipate that advancements in biodiversity data collection and remote sensing capabilities will further refine global trait mapping, fostering a dynamic trait-based understanding of the biosphere.

Why it matches plant phenotyping methods地球観測データと生物多様性データを統合し、植物機能形質を空間的に推定・検証する方法が研究の中心であり、単なる生態学的測定ではない。

abstractcombining these diverse data sources with high-resolution Earth observation data enables accurate modeling of key plant traits at up to 1 km resolution

Photogrammetry to Assess the Recovery of a Forest: Case Study of Guadalupe Island →

This study employs photogrammetry to evaluate and monitor the recovery of the cypress forest on Guadalupe Island, Mexico, an ecosystem significantly impacted by fires and overgrazing. Two drone surveys were conducted over the forest area during the summers of 2016 and 2019 using natural color (RGB) and near-infrared (NIR) cameras. This work presents the first complete 3D reconstruction of the cypress forest on the island. The image processing products include the canopy height model (CHM), digital surface model (DSM), and digital terrain model (DTM), which were utilized to calculate the number, density, height and crown projected areas of trees. The CHM showed a high correlation with the forest's structure (R = 0.92), based on field measurements of tree heights. Our study accounted for approximately 67,340 trees taller than two meters in 2019. Over 90% of the cypress population consisted of young trees between 2 and 3 meters tall, which have recovered significantly following a fire in 2008 that burned 70% of its extent. A horizontal expansion of 134 hectares was observed from 2016 to 2019 in the regeneration process.

Why it matches plant phenotyping methodsドローン画像のフォトグラメトリによる3D再構成を用いて樹木の高さ・密度・樹冠面積を推定し、現地測定との相関で検証しているため、植物形質の取得手法が中心です。

abstractThis study employs photogrammetry to evaluate and monitor the recovery of the cypress forest on Guadalupe Island, Mexico

Image-based yield prediction for tall fescue using random forests and convolutional neural networks →

In the early stages of selection, many plant breeding programmes still rely on visual evaluations of traits by experienced breeders. While this approach has proven to be effective, it requires considerable time, labour and expertise. Moreover, its subjective nature makes it difficult to reproduce and compare evaluations. The field of automated high-throughput phenotyping aims to resolve these issues. A widely adopted strategy uses drone images processed by machine learning algorithms to characterise phenotypes. This approach was used in the present study to assess the dry matter yield of tall fescue and its accuracy was compared to that of the breeder's evaluations, using field measurements as ground truth. RGB images of tall fescue individuals were processed by two types of predictive models: a random forest and convolutional neural network. In addition to computing dry matter yield, the two methods were applied to identify the top 10% highest-yielding plants and predict the breeder's score. The convolutional neural network outperformed the random forest method and exceeded the predictive power of the breeder's eye. It predicted dry matter yield with an R² of 0.62, which surpassed the accuracy of the breeder's score by 8 percentage points. Additionally, the algorithm demonstrated strong performance in identifying top-performing plants and estimating the breeder's score, achieving balanced accuracies of 0.81 and 0.74, respectively. These findings indicate that the tested automated phenotyping approach could not only offer improvements in cost, time efficiency and objectivity, but also enhance selection accuracy. As a result, this technique has the potential to increase overall breeding efficiency, accelerate genetic progress, and shorten the time to market. To conclude, phenotyping by means of RGB-based machine learning models provides a reliable alternative or addition to the visual evaluation of selection candidates in a tall fescue breeding programme.

Why it matches plant phenotyping methodsRGBドローン画像と機械学習により乾物収量などの植物形質を推定し、育種家評価および実測値と比較検証しており、フェノタイピング手法が中心である。

abstractThe field of automated high-throughput phenotyping aims to resolve these issues.

Improved Detection and Location of Small Crop Organs by Fusing UAV Orthophoto Maps and Raw Images →

Extracting the quantity and geolocation data of small objects at the organ level via large-scale aerial drone monitoring is both essential and challenging for precision agriculture. The quality of reconstructed digital orthophoto maps (DOMs) often suffers from seamline distortion and ghost effects, making it difficult to meet the requirements for organ-level detection. While raw images do not exhibit these issues, they pose challenges in accurately obtaining the geolocation data of detected small objects. The detection of small objects was improved in this study through the fusion of orthophoto maps with raw images using the EasyIDP tool, thereby establishing a mapping relationship from the raw images to geolocation data. Small object detection was conducted by using the Slicing-Aided Hyper Inference (SAHI) framework and YOLOv10n on raw images to accelerate the inferencing speed for large-scale farmland. As a result, comparing detection directly using a DOM, the speed of detection was accelerated and the accuracy was improved. The proposed SAHI-YOLOv10n achieved precision and mean average precision (mAP) scores of 0.825 and 0.864, respectively. It also achieved a processing latency of 1.84 milliseconds on 640×640 resolution frames for large-scale application. Subsequently, a novel crop canopy organ-level object detection dataset (CCOD-Dataset) was created via interactive annotation with SAHI-YOLOv10n, featuring 3986 images and 410,910 annotated boxes. The proposed fusion method demonstrated feasibility for detecting small objects at the organ level in three large-scale in-field farmlands, potentially benefiting future wide-range applications.

Why it matches plant phenotyping methodsUAV画像と生画像の融合、SAHI-YOLOv10nによる作物器官の検出・位置推定を中心に開発・評価し、器官レベルの大規模データセットも構築しているため、植物表現型取得法が研究の中心である。

abstractThe detection of small objects was improved in this study through the fusion of orthophoto maps with raw images using the EasyIDP tool, thereby establishing a mapping relationship from the raw images to geolocation data.

Unlocking the potential of Airborne LiDAR for direct assessment of fuel bulk density and load distributions for wildfire hazard mapping →

Large-scale mapping of fuel load and fuel vertical distribution is essential for assessing fire danger, setting strategic goals and actions, and determining long-term resource needs. The Airborne LiDAR system can fulfil such goal by accurately capturing the three-dimensional arrangement of vegetation at regional and national scales. We developed a novel method to estimate multiple metrics of fuel load and vertical bulk density distribution for any type of vegetation. The approach uses Beer-Lambert law for inverting the ALS point cloud into vertical plant area density profiles, which are converted into vertical bulk density distribution profiles using species-specific plant traits. The approach is evaluated by comparing ALS-based vegetation profiles and fuel metrics with field-based data from southeastern France, Spain, and Portugal for a range of vegetation types. ALS-based and field-based vertical vegetation profiles were consistent. The range of values of fuel load metrics was also consistent with field data. Good correlations and low bias were attained for simple stratified structure with R² of 0.6, 0.42 and 0.68 and bias of -5 %, -2 % and -3.3 % for canopy base height, canopy fuel load, and canopy bulk density respectively. However, correlations were low for complex vertical structures. The use of species-specific plant traits appeared relevant by lowering the deviation between field and ALS-based values for most species. Our field-independent fuel metric estimation shows comparable performance to results in the literature based on classification approaches trained on field metrics, highlighting the generality of our direct approach. We demonstrated how our approach is more relevant than field data for defining vertical vegetation strata in complex forest structures. We showed an application of the methods by mapping multiple metrics at regional scale (6343 km²) such as canopy base height, fuel strata gap, and canopy and understory fuel loads. Our approach is adequate for feeding next generation models of wildfire risk assessment systems, enhanced by more flexible and accurate fuel data than the existing fuel typologies.

Why it matches plant phenotyping methods航空LiDAR点群から植生の垂直構造、燃料負荷、バルク密度などの植物・キャノピー形質を推定する手法を開発し、野外データで評価して地域適用しているため、植物フェノタイピング手法が中心である。

abstractWe developed a novel method to estimate multiple metrics of fuel load and vertical bulk density distribution for any type of vegetation.

Enhancing genomic-based forward prediction accuracy in wheat by integrating UAV-derived hyperspectral and environmental data with machine learning under heat-stressed environments. →

Integrating genomic, hyperspectral imaging (HSI), and environmental data enhances wheat yield predictions, with HSI providing detailed spectral insights for predicting complex grain yield (GY) traits. Incorporating HSI data with single nucleotide polymorphic markers (SNPs) resulted in a substantial improvement in predictive ability compared to the conventional genomic prediction models. Over the course of several years, the prediction ability varied due to diverse weather conditions. The most comprehensive parametric model tested, which included SNPs, HSI, and environmental covariates data, consistently achieved the best results, closely followed by machine learning (ML) approaches when considering the same omics data. For example, the most comprehensive model (M9), under the forward prediction cross-validation scheme, predicted the GY of the 2023 growing season using data from 2021 and 2022 for a correlation between predicted and observed values of 0.53. This model demonstrated superior performance compared to less complex models, emphasizing the advantage of integrating numerous data sources and their interactive effects. Furthermore, when comparing the top 25% of the predicted lines versus the corresponding observed lines with the highest GY, the M9 model returned a coincide index (CI) of 55% (i.e., in both sets, 55% of the top 25% values were common), whereas for the highest performing ML model (gradient boosting regression), the CI was of 46%. This study highlights the potential of multi-data source approaches to accelerate the selection of heat-tolerant wheat genotypes.

Why it matches plant phenotyping methodsUAVハイパースペクトル画像を用いた小麦収量形質の推定を、ゲノム・環境データとの統合モデルで検証しており、形質予測性能の比較が研究の中心である。

abstractIntegrating genomic, hyperspectral imaging (HSI), and environmental data enhances wheat yield predictions, with HSI providing detailed spectral insights for predicting complex grain yield (GY) traits.

Drone-based dataset of annotated sunflower images from Bangladesh. →

Accurate and automated detection of sunflower plants, along with assessments of their growth stages and health conditions, is crucial for enabling precision agriculture and improving crop management. In this work, we present a drone-based dataset of annotated sunflower images, derived from high-resolution videos captured at two distinct locations in Bangladesh. The original dataset comprises 1649 images extracted from drone footage of the BARI Surjomukhi-3 variety under various orientations, health conditions, and weather scenarios. After meticulous annotation using the Roboflow platform and augmentation with seven distinct techniques, the dataset expanded to 4286 images in Pascal VOC format. Detailed metadata-including geospatial coordinates, timestamped acquisition conditions, and camera settings-accompanies the dataset to support reproducibility and model generalization. By offering a comprehensive suite of annotated and augmented images, this dataset provides a valuable resource for developing and refining computer vision models geared toward sunflower detection, maturity evaluation, and yield prediction, ultimately advancing sustainable farming practices and decision-making tools in agricultural research.

Why it matches plant phenotyping methodsヒマワリ画像を注釈付きデータセットとして構築し、成長段階・健康状態・成熟度などの植物状態推定を支援することが中心であり、再利用可能な画像ベース表現型データセットに該当する。

abstractwe present a drone-based dataset of annotated sunflower images

Combining machine learning and publicly available aerial data (NAIP and NEON) to achieve high-resolution remote sensing of grass-shrub-tree mosaics in the Central Great Plains (U.S.A.) →

Woody plant encroachment (WPE)—a phenomenon similar to species invasion—is shifting many grasslands and savannas into shrub and evergreen-dominated ecosystems. Tracking WPE is difficult because shrubs and small trees are much smaller than the coarse resolution of common remote sensing platforms (> 10 m 2 ) and the impassibility of encroaching woody thickets slows ground-based approaches. Many agencies have been investing in fine resolution ( 90%), with the NEON-based models a few percent more accurate than NAIP. A model using both inputs had the highest accuracy. However, the accuracies of NAIP and NEON models differed for woody vegetation: compared to NEON, NAIP accuracy was, 82-93% compared to 94-98% for shrubs, 72-92% compared to 93-98% for deciduous trees, and 52-78% compared to 83-86% for evergreen trees (specifically Juniperus virginiana ). NEON-based models relied on canopy height (LiDAR) to make classifications, whereas the several bands of light make similar contributions to accuracy in the NAIP models. Finally, we found that both machine learning approaches had similar accuracy, but random forests ran substantially faster. We conclude that with large training datasets, publicly available aerial imagery and similar products (e.g., UAVs, micro-satellites) can produce fine-scale, high-accuracy remote sensing of WPE in this region with low up-front costs.

Why it matches plant phenotyping methods航空画像・LiDARと機械学習を用いて低木・樹木の植生状態を高解像度で推定し、NAIPとNEONおよび手法間の精度を比較しており、植物状態の取得・推定法が研究の中心である。

abstractTracking WPE is difficult because shrubs and small trees are much smaller than the coarse resolution of common remote sensing platforms

SugarViT-Multi-objective regression of UAV images with Vision Transformers and Deep Label Distribution Learning demonstrated on disease severity prediction in sugar beet. →

Remote sensing and artificial intelligence are pivotal technologies of precision agriculture nowadays. The efficient retrieval of large-scale field imagery combined with machine learning techniques shows success in various tasks like phenotyping, weeding, cropping, and disease control. This work will introduce a machine learning framework for automatized large-scale plant-specific trait annotation for the use case of disease severity scoring for CLS in sugar beet. With concepts of DLDL, special loss functions, and a tailored model architecture, we develop an efficient Vision Transformer based model for disease severity scoring called SugarViT. One novelty in this work is the combination of remote sensing data with environmental parameters of the experimental sites for disease severity prediction. Although the model is evaluated on this special use case, it is held as generic as possible to also be applicable to various image-based classification and regression tasks. With our framework, it is even possible to learn models on multi-objective problems, as we show by a pretraining on environmental metadata. Furthermore, we perform several comparison experiments with state-of-the-art methods and models to constitute our modeling and preprocessing choices.

Why it matches plant phenotyping methods植物病害重症度をUAV画像から自動推定するVision Transformerベースの手法を開発・比較評価しており、植物表現型取得が中心である。

abstractThis work will introduce a machine learning framework for automatized large-scale plant-specific trait annotation for the use case of disease severity scoring for CLS in sugar beet.

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

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

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

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

Adaptive spatial-channel feature fusion and self-calibrated convolution for early maize seedlings counting in UAV images. →

Accurate counting of crop plants is essential for agricultural science, particularly for yield forecasting, field management, and experimental studies. Traditional methods are labor-intensive and prone to errors. Unmanned Aerial Vehicle (UAV) technology offers a promising alternative; however, varying UAV altitudes can impact image quality, leading to blurred features and reduced accuracy in early maize seedling counts. To address these challenges, we developed RC-Dino, a deep learning methodology based on DINO, specifically designed to enhance the precision of seedling counts from UAV-acquired images. RC-Dino introduces two innovative components: a novel self-calibrating convolutional layer named RSCconv and an adaptive spatial feature fusion module called ASCFF. The RSCconv layer improves the representation of early maize seedlings compared to non-seedling elements within feature maps by calibrating spatial domain features. The ASCFF module enhances the discriminability of early maize seedlings by adaptively fusing feature maps extracted from different layers of the backbone network. Additionally, transfer learning was employed to integrate pre-trained weights with RSCconv, facilitating faster convergence and improved accuracy. The efficacy of our approach was validated using the Early Maize Seedlings Dataset (EMSD), comprising 1,233 annotated images of early maize seedlings, totaling 83,404 individual annotations. Testing on this dataset demonstrated that RC-Dino outperformed existing models, including DINO, Faster R-CNN, RetinaNet, YOLOX, and Deformable DETR. Specifically, RC-Dino achieved improvements of 16.29% in Average Precision (AP) and 8.19% in Recall compared to the DINO model. Our method also exhibited superior coefficient of determination (R²) values across different datasets for seedling counting. By integrating RSCconv and ASCFF into other detection frameworks such as Faster R-CNN, RetinaNet, and Deformable DETR, we observed enhanced detection and counting accuracy, further validating the effectiveness of our proposed method. These advancements make RC-Dino particularly suitable for accurate early maize seedling counting in the field. The source code for RSCconv and ASCFF is publicly available at https://github.com/collapser-AI/RC-Dino, promoting further research and practical applications.

Why it matches plant phenotyping methodsUAV画像からトウモロコシ幼苗数を抽出する深層学習手法を開発し、公開データセット上で既存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す。

abstractwe developed RC-Dino, a deep learning methodology based on DINO, specifically designed to enhance the precision of seedling counts from UAV-acquired images.

Countrywide Digital Surface Models and Vegetation Height Models from Historical Aerial Images →

Abstract. Historical aerial images, captured by film cameras in the previous century, are valuable resources for quantifying Earth’s surface and landscape changes over time. In the post-war period, these images were often acquired to create topographic maps, resulting in the acquisition of large-scale aerial photographs with stereo coverage. Photogrammetric techniques applied to these stereo images enable the extraction of 3D information to reconstruct digital surface models (DSMs) and orthoimages. Here, we present a highly automated photogrammetric approach for generating countrywide DSMs of Switzerland, at a 1 m resolution, from approximately 40,000 scanned aerial stereo images acquired between 1979 and 2006, with known exterior and interior orientation. We derived four countrywide DSMs for the epochs 1979–1985, 1985–1991, 1991–1998, and 1998–2006. From the DSMs, we generated corresponding countrywide vegetation height models (VHMs). We assessed the quality of the historical DSMs at the country scale and within six representative study sites, evaluating the vertical accuracy and the completeness of image-matching across different land cover types. Mean completeness ranged from 64 % for ‘glacial and perpetual snow’ to 98 % for ‘sealed surfaces’, with a value of 93 % for the ‘closed forest’ class. Across Switzerland, the median elevation accuracy of the historical DSMs compared with a reference digital terrain model (DTM) on sealed surface points ranged from 0.28 to 0.53 m, with a normalised median absolute deviation (NMAD) of around 1 m and a maximum root mean square error (RMSE) of 3.90 m. The same analysis between geodetic points and historical DSMs showed higher accuracies, with median values of ≤ 0.05 m and an NMAD < 1 m. The VHMs generated in this study enabled the detection of major changes in forest areas due to windstorm damage, forest dynamics, and growth. This work demonstrates the feasibility of generating accurate, very high-resolution DSM time series (spanning three decades) and VHMs from historical aerial images of the entire surface of Switzerland in a highly automated manner. The VHMs are already being used to estimate countrywide biomass changes. The countrywide DSMs and VHMs for the four epochs, along with auxiliary data, are available online at https://doi.org/10.16904/envidat.528 (Marty et al., 2024) and can be used to quantify long-term elevation changes and related processes across different surfaces.

Why it matches plant phenotyping methods歴史航空画像から植生高モデルを自動生成するフォトグラメトリ手法を開発・精度評価し、森林の高さ変化という植物状態を測定するデータセットも提供しているため、植物フェノタイピング手法が中心である。

abstractFrom the DSMs, we generated corresponding countrywide vegetation height models (VHMs).

Plant diversity across dimensions: Coupling biodiversity measures from the ground and the sky →

Tracking biodiversity across biomes over space and time has emerged as an imperative in unified global efforts to manage our living planet for a sustainable future for humanity. We harness the National Ecological Observatory Network to develop routines using airborne spectroscopic imagery to predict multiple dimensions of plant biodiversity at continental scale across biomes in the US. Our findings show strong and positive associations between diversity metrics based on spectral species and ground-based plant species richness and other dimensions of plant diversity, whereas metrics based on distance matrices did not. We found that spectral diversity consistently predicts analogous metrics of plant taxonomic, functional, and phylogenetic dimensions of biodiversity across biomes. The approach demonstrates promise for monitoring dimensions of biodiversity globally by integrating ground-based measures of biodiversity with imaging spectroscopy and advances capacity toward a Global Biodiversity Observing System.

Why it matches plant phenotyping methods航空分光画像を用いて植物多様性を予測するルーチンを開発し、地上データとの関連を評価しており、植物状態の推定手法が研究の中心である。

abstractWe harness the National Ecological Observatory Network to develop routines using airborne spectroscopic imagery to predict multiple dimensions of plant biodiversity at continental scale across biomes in the US.

Plant Detection in RGB Images from Unmanned Aerial Vehicles Using Segmentation by Deep Learning and an Impact of Model Accuracy on Downstream Analysis →

Crop field monitoring using unmanned aerial vehicles (UAVs) is one of the most important technologies for plant growth control in modern precision agriculture. One of the important and widely used tasks in field monitoring is plant stand counting. The accurate identification of plants in field images provides estimates of plant number per unit area, detects missing seedlings, and predicts crop yield. Current methods are based on the detection of plants in images obtained from UAVs by means of computer vision algorithms and deep learning neural networks. These approaches depend on image spatial resolution and the quality of plant markup. The performance of automatic plant detection may affect the efficiency of downstream analysis of a field cropping pattern. In the present work, a method is presented for detecting the plants of five species in images acquired via a UAV on the basis of image segmentation by deep learning algorithms (convolutional neural networks). Twelve orthomosaics were collected and marked at several sites in Russia to train and test the neural network algorithms. Additionally, 17 existing datasets of various spatial resolutions and markup quality levels from the Roboflow service were used to extend training image sets. Finally, we compared several texture features between manually evaluated and neural-network-estimated plant masks. It was demonstrated that adding images to the training sample (even those of lower resolution and markup quality) improves plant stand counting significantly. The work indicates how the accuracy of plant detection in field images may affect their cropping pattern evaluation by means of texture characteristics. For some of the characteristics (GLCM mean, GLRM long run, GLRM run ratio) the estimates between images marked manually and automatically are close. For others, the differences are large and may lead to erroneous conclusions about the properties of field cropping patterns. Nonetheless, overall, plant detection algorithms with a higher accuracy show better agreement with the estimates of texture parameters obtained from manually marked images.

Why it matches plant phenotyping methodsUAV画像から植物個体をセグメンテーションし、株数・欠株などの植物状態を推定する画像解析手法を開発・評価しており、手法が研究の中心です。

abstractIn the present work, a method is presented for detecting the plants of five species in images acquired via a UAV on the basis of image segmentation by deep learning algorithms (convolutional neural networks).

High‐throughput phenotyping of stay‐green in a sorghum breeding program using unmanned aerial vehicles and machine learning →

Abstract As climate change continues to influence global weather patterns, the frequency and severity of drought conditions are expected to increase, posing a significant challenge to crop production. In sorghum ( Sorghum bicolor L. Moench), a key cereal crop, the stay‐green trait is of particular importance as a measure of how well a genotype can tolerate post‐anthesis drought conditions, which are critical for harvestable yield. Despite its importance, there is a pressing need for a more efficient, accurate, and precise method to phenotype stay‐green in sorghum to enhance breeding efforts. To address this need, this study explores the application of random forest and XGBoost machine learning models for phenotyping the stay‐green trait in sorghum. These models provide quantitative measurements that have the potential to enhance genomic studies and offer additional benefits. Although correlations with vegetation indices were occasionally high, they were not sufficiently reliable to be used exclusively. The machine learning models, in contrast, showed high percentages of genetic variation explained and had high repeatability. The values generated by these algorithms enable plant breeders to efficiently make selections in their stay‐green breeding programs. Further research is needed to assess the robustness of these models across different environments and genetic material. Additionally, comparing these models with other machine learning approaches will help determine if decision tree‐based models are the most effective for this application. Overall, the models presented in this study serve as a promising foundation for improving the efficiency of stay‐green breeding programs in sorghum, but they require further validation and comparison with alternative approaches.

Why it matches plant phenotyping methodsソルガムのstay-green形質をUAV画像と機械学習で定量化する手法を開発・評価しており、表現型取得・抽出が研究の中心である。反復性や遺伝的変異の説明率も評価している。

abstractthere is a pressing need for a more efficient, accurate, and precise method to phenotype stay‐green in sorghum

Integrating remote sensing data assimilation, deep learning and large language model for interactive wheat breeding yield prediction →

Yield is one of the core goals of crop breeding. By predicting the potential yield of different breeding materials, breeders can screen these materials at various growth stages to select the best performing. Based on unmanned aerial vehicle remote sensing technology, high-throughput crop phenotyping data in breeding areas is collected to provide data support for the breeding decisions of breeders. However, the accuracy of current yield predictions still requires improvement, and the usability and user-friendliness of yield forecasting tools remain suboptimal. To address these challenges, this study introduces a hybrid method and tool for crop yield prediction, designed to allow breeders to interactively and accurately predict wheat yield by chatting with a large language model (LLM). First, the newly designed data assimilation algorithm is used to assimilate the leaf area index into the WOFOST model. Then, selected outputs from the assimilation process, along with remote sensing inversion results, are used to drive the time-series temporal fusion transformer model for wheat yield prediction. Finally, based on this hybrid method and leveraging an LLM with retrieval augmented generation technology, we developed an interactive yield prediction Web tool that is user-friendly and supports sustainable data updates. This tool integrates multi-source data to assist breeding decision-making. This study aims to accelerate the identification of high-yield materials in the breeding process, enhance breeding efficiency, and enable more scientific and smart breeding decisions.

Why it matches plant phenotyping methodsUAVリモートセンシングによる作物フェノタイピングデータを基盤に、収量推定手法と対話型Webツールを開発しており、植物形質（小麦収量）の取得・推定が研究の中心である。

abstractBased on unmanned aerial vehicle remote sensing technology, high-throughput crop phenotyping data in breeding areas is collected to provide data support for the breeding decisions of breeders.

Temporal field phenomics of transgenic maize events subjected to drought stress: Cross‐validation scenarios and machine learning models →

Abstract Global climate change has driven breeding programs to develop abiotic stress‐resilient plant varieties. Traditionally, assessing drought resilience involves labor‐intensive and time‐consuming processes. This study used an unmanned aerial system (UAS) to predict key phenotyping traits in maize ( Zea mays L.) and monitor plant response to drought during the crop cycle. We grew transgenic maize hybrids in two trials, one irrigated and another subjected to drought stress, and used a drone equipped with red–green–blue (RGB) and multispectral sensors to capture images of the plots over time. Machine learning models and various prediction scenarios revealed significant correlations between vegetation indices over time. Interestingly, the RGB sensor outperformed the multispectral sensor in trait prediction. Prediction accuracy across scenarios with untested genotypes and environments ranged from 0.40 to 0.70 for grain yield, 0.43 to 0.69 for days to anthesis, 0.51 to 0.67 for days to silking, and 0.35 to 0.57 for plant height. Ridge and random forest models consistently delivered the most accurate predictions across traits and environments. The vegetation indices normalized green–red difference index, VARI, and RCC also effectively predicted and captured the plant response to drought. This study highlights the value of UAS phenotyping as a practical tool for assessing abiotic stress due to its straightforward implementation.

Why it matches plant phenotyping methodsUASによるRGB・マルチスペクトル画像と機械学習で、作物形質および干ばつ応答を予測するフェノタイピング手法を、複数環境・遺伝子型で検証しているため。

abstractThis study used an unmanned aerial system (UAS) to predict key phenotyping traits in maize ( Zea mays L.) and monitor plant response to drought during the crop cycle.

Annotated image dataset with different stages of European pear rust for UAV-based automated symptom detection in orchards. →

The evaluation of fruit genetic resources regarding a resistance to pathogens is an essential basis for subsequent selection in fruit breeding. Both genetic analysis and phenotyping of defined traits are important tools and provide decision data in the evaluation process. However, the phenotyping of plants is often carried out 'by hand' and remains the bottleneck in fruit breeding and fruit growing. The development of a digital and UAV (unmanned aerial vehicle)-based phenotyping method for the assessment of genotype-specific susceptibility or resistance against diseases in orchards would significantly increase the efficiency of plant breeding. In this framework, a workflow for drone-based monitoring of pathogens in orchards was developed using the European pear rust ( Gymnosporangium sabinae ) as model pathogen. Pear rust is widespread in orchards and causes conspicuous, clearly visible, yellow to orange-colored disease symptoms. In this paper, we provide a dataset with expert-annotated high-resolution RGB images with pear rust symptoms. For data collection, ten UAV-flight campaigns were realized between 2021 and 2023 under various weather conditions and with different flight parameters in the experimental orchard of the Julius Kühn-Institute for Breeding Research on Fruit Crops in Dresden-Pillnitz (Germany). 1394 images were captured of different pear genotypes, including varieties, wild species and progeny from breeding. The dataset contains manually labelled images with a size of 768 × 768 pixels of leaves infected with pear rust at different stages of development, labelled as class GYMNSA, as well as background images without symptoms. Each leaf with pear rust symptoms was annotated with the drawing method by two points (bounding boxes) using the Computer Vision Annotation Tool (CVAT, v1.1.0) [1] and presented in YOLO 1.1 file format (.txt files). A total of 584 annotated images and 162 background images, organized into a training and validation set, are included in the GYMNSA dataset. This GYMNSA dataset can be used as a resource for researchers and developers working on drone-based plant disease monitoring systems.

Why it matches plant phenotyping methodsナシさび病の植物症状をUAV画像から検出するための注釈付きデータセットを提供しており、植物病害状態の画像ベース表現型取得・解析ワークフローが中心的です。

abstractThe development of a digital and UAV (unmanned aerial vehicle)-based phenotyping method for the assessment of genotype-specific susceptibility or resistance against diseases in orchards would significantly increase the efficiency of plant breeding.

Evaluation of Height Changes in Uneven-Aged Spruce–Fir–Beech Forest with Freely Available Nationwide Lidar and Aerial Photogrammetry Data →

Tree height and vertical forest structure are important attributes in forestry, but their traditional measurement or assessment in the field is expensive, time-consuming, and often inaccurate. One of the main advantages of using remote sensing data to estimate vertical forest structure is the ability to obtain accurate data for larger areas in a more time- and cost-efficient manner. Temporal changes are also important for estimating and analysing tree heights, and in many countries, national airborne laser scanning (ALS) surveys have been conducted either only once or at specific, longer intervals, whereas aerial surveys are more often arranged in cycles with shorter intervals. In this study, we reviewed all freely available national airborne remote sensing data describing three-dimensional forest structures in Slovenia and compared them with traditional field measurements in an area dominated by uneven-aged forests. The comparison of ALS and digital aerial photogrammetry (DAP) data revealed that freely available national ALS data provide better estimates of dominant forest heights, vertical structural diversity, and their changes compared to cyclic DAP data, but they are still useful due to their temporally dense data. Up-to-date data are very important for forest management and the study of forest resilience and resistance to disturbance. Based on field measurements (2013 and 2023) and all remote sensing data, dominant and maximum heights are statistically significantly higher in uneven-aged forests than in mature, even-aged forests. Canopy height diversity (CHD) information, derived from lidar ALS and DAP data, has also proven to be suitable for distinguishing between even-aged and uneven-aged forests. The CHDALS 2023 was 1.64, and the CHDCAS 2022 was 1.38 in uneven-aged stands, which were statistically significantly higher than in even-aged forest stands.

Why it matches plant phenotyping methodsALSと航空写真測量による樹高・森林垂直構造・樹冠高多様性の推定を現地測定と比較検証しており、植物（森林）の形態形質測定が研究の中心です。

abstractThe comparison of ALS and digital aerial photogrammetry (DAP) data revealed that freely available national ALS data provide better estimates of dominant forest heights, vertical structural diversity, and their changes compared to cyclic DAP data

Dataset of aerial photographs acquired with UAV using a multispectral (green, red and near-infrared) camera for cherry tomato ( Solanum lycopersicum var. cerasiforme ) monitoring. →

A dataset of aerial photographs acquired with an Unmanned Aerial Vehicle (UAV) DJI Phantom 4 Pro is presented for monitoring a cherry tomato ( Solanum lycopersicum var. cerasiforme ) crop in Navolato, Mexico. Seven photogrammetric flights were carried out to assess the plant growth using a Mapir Survey 3W multispectral camera. Multispectral images with an approximate spatial resolution of 1.83 cm/px were obtained in each photogrammetric flight. These images were acquired every 15 days starting on October 15, 2021, and ending on January 23, 2022. The dataset contains the radiometrically calibrated images of the tomato crop divided into 2 open field parcels. The dataset also includes the processed photogrammetric products (ortho-mosaics) using a binary mask to exclude the soil from the plant area. The dataset was originally acquired to assess plant growth, stress levels, and overall crop health. However, this multispectral imagery dataset can also have various uses, such as creating training datasets with accurate labels or classes which can then be used to develop, train, and/or validate machine learning algorithms for image classification, object detection tasks, or change detection analysis.

Why it matches plant phenotyping methods植物の生育・ストレス・健全性評価を目的とした、放射補正済みマルチスペクトル画像とオルソモザイクを含む再利用可能なデータセットであり、植物表現型取得基盤が中心です。

abstractThe dataset contains the radiometrically calibrated images of the tomato crop divided into 2 open field parcels.

From Images to Loci: Applying 3D Deep Learning to Enable Multivariate and Multitemporal Digital Phenotyping and Mapping the Genetics Underlying Nitrogen Use Efficiency in Wheat →

The selection and promotion of high-yielding and nitrogen-efficient wheat varieties can reduce nitrogen fertilizer application while ensuring wheat yield and quality and contribute to the sustainable development of agriculture; thus, the mining and localization of nitrogen use efficiency (NUE) genes is particularly important, but the localization of NUE genes requires a large amount of phenotypic data support. In view of this, we propose the use of low-altitude aerial photography to acquire field images at a large scale, generate 3-dimensional (3D) point clouds and multispectral images of wheat plots, propose a wheat 3D plot segmentation dataset, quantify the plot canopy height via combination with PointNet++, and generate 4 nitrogen utilization-related vegetation indices via index calculations. Six height-related and 24 vegetation-index-related dynamic digital phenotypes were extracted from the digital phenotypes collected at different time points and fitted to generate dynamic curves. We applied height-derived dynamic numerical phenotypes to genome-wide association studies of 160 wheat cultivars (660,000 single-nucleotide polymorphisms) and found that we were able to locate reliable loci associated with height and NUE, some of which were consistent with published studies. Finally, dynamic phenotypes derived from plant indices can also be applied to genome-wide association studies and ultimately locate NUE- and growth-related loci. In conclusion, we believe that our work demonstrates valuable advances in 3D digital dynamic phenotyping for locating genes for NUE in wheat and provides breeders with accurate phenotypic data for the selection and breeding of nitrogen-efficient wheat varieties.

Why it matches plant phenotyping methods航空画像・3D点群・マルチスペクトル画像から小麦区画の草冠高と植生指数を抽出するデジタルフェノタイピング手法を開発・適用しており、表現型取得が研究の中心である。

abstractwe propose the use of low-altitude aerial photography to acquire field images at a large scale, generate 3-dimensional (3D) point clouds and multispectral images of wheat plots

YH-RTYO: an end-to-end object detection method for crop growth anomaly detection in UAV scenarios. →

Background Small object detection via unmanned Aerial vehicle (UAV) is crucial for smart agriculture, enhancing yield and efficiency. Methods This study addresses the issue of missed detections in crowded environments by developing an efficient algorithm tailored for precise, real-time small object detection. The proposed Yield Health Robust Transformer-YOLO (YH-RTYO) model incorporates several key innovations to advance conventional convolutional models. The model features an efficient convolutional expansion module that captures additional feature information through extended branches while maintaining parameter efficiency by consolidating features into a single convolution during validation. It also includes a local feature pyramid module designed to suppress background interference during feature interaction. Furthermore, the loss function is optimized to accommodate various object scales in different scenes by adjusting the regression box size and incorporating angle factors. These enhancements collectively contribute to improved detection performance and address the limitations of traditional methods. Result Compared to YOLOv8-L, the YH-RTYO model achieves superior performance in all key accuracy metrics, with a 13% reduction in the scale of model. Experimental results demonstrate that the YH-RTYO model outperforms others in key detection metrics. The model reduces the number of parameters by 13%, facilitating deployment while maintaining accuracy. On the OilPalmUAV dataset, it achieves a 3.97% improvement in average precision (AP). Additionally, the model shows strong generalization on the RFRB dataset, with AP 50 and AP values exceeding those of the YOLOv8 baseline by 3.8% and 2.7%, respectively.

Why it matches plant phenotyping methods作物の生育異常検出を目的とする画像ベースの物体検出モデルを開発し、複数データセットで性能評価しており、表現型状態の抽出法が中心である。

titleYH-RTYO: an end-to-end object detection method for crop growth anomaly detection in UAV scenarios.

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

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

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

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

Estimation of nitrogen uptake, biomass, and nitrogen concentration, in cover crop monocultures and mixtures from optical UAV images →

Cover crops (CC) immobilize mineral soil N in their biomass, preventing N losses during crop rotation intervals. As the CC biomass is incorporated into the soil and decomposes, N is released for the following main crop. The efficiency of CC N uptake and release depends on CC quantity and quality, which can be enhanced in mixtures. Traditional N uptake measurements are labour-intensive and limited in capturing spatial variability. We calibrated relationships between traditional measurements and multispectral data from an Unmanned Aerial Vehicle (UAV) to quantify CC traits with minimal disturbance and high spatial resolution in both monocultures and mixtures. This innovative approach combined vegetation indices, textural features, and a photogrammetry-derived canopy surface model to predict CC traits. Linear models were trained for biomass, N uptake, and C:N predictions, while a K-Nearest-Neighbour model was trained for N concentration. When evaluated on the test set, the calibrated remote sensing models accurately predicted CC aboveground biomass (R 2 : 0.71, RMSE: 287.1 kg/ha, NRMSE: 11.74 %), N concentration (R 2 : 0.80, RMSE: 1.77 gN /kg, NRMSE: 6.96 %), N uptake (R 2 : 0.56, RMSE: 9.38 kgN /ha, NRMSE: 15.08 %), and C:N ratio (R 2 : 0.62, RMSE: 1.86, NRMSE: 10.98 %). The field experiment included monocultures, bi-, and tri-species mixtures of common vetch ( Vicia sativa ), black oat ( Avena strigosa ), and fodder radish ( Raphanus sativus ). N uptake was similar between treatments, yet the CC species differed in strategies, producing high biomass with low N concentration or vice versa. This study provides a basis for spatially predicting key CC traits using UAV optical data.

Why it matches plant phenotyping methodsUAVマルチスペクトル画像、テクスチャ特徴、フォトグラメトリ由来モデルを用いて、植物のバイオマス、窒素濃度、窒素吸収量、C:N比を推定する手法を開発・検証しており、表現型取得が研究の中心である。

abstractWe calibrated relationships between traditional measurements and multispectral data from an Unmanned Aerial Vehicle (UAV) to quantify CC traits with minimal disturbance and high spatial resolution in both monocultures and mixtures.

Drone-Based Digital Phenotyping to Evaluating Relative Maturity, Stand Count, and Plant Height in Dry Beans (Phaseolus vulgaris L.) →

Substantial effort has been made in manually tracking plant maturity and to measure early-stage plant density and crop height in experimental fields. In this study, RGB drone imagery and deep learning (DL) approaches are explored to measure relative maturity (RM), stand count (SC), and plant height (PH), potentially offering higher throughput, accuracy, and cost-effectiveness than traditional methods. A time series of drone images was utilized to estimate dry bean RM employing a hybrid convolutional neural network (CNN) and long short-term memory (LSTM) model. For early-stage SC assessment, Faster RCNN object detection algorithm was evaluated. Flight frequencies, image resolution, and data augmentation techniques were investigated to enhance DL model performance. PH was obtained using a quantile method from digital surface model (DSM) and point cloud (PC) data sources. The CNN-LSTM model showed high accuracy in RM prediction across various conditions, outperforming traditional image preprocessing approaches. The inclusion of growing degree days (GDD) data improved the model's performance under specific environmental stresses. The Faster R-CNN model effectively identified early-stage bean plants, demonstrating superior accuracy over traditional methods and consistency across different flight altitudes. For PH estimation, moderate correlations with ground-truth data were observed across both datasets analyzed. The choice between PC and DSM source data may depend on specific environmental and flight conditions. Overall, the CNN-LSTM and Faster R-CNN models proved more effective than conventional techniques in quantifying RM and SC. The subtraction method proposed for estimating PH without accurate ground elevation data yielded results comparable to the difference-based method. Additionally, the pipeline and open-source software developed hold potential to significantly benefit the phenotyping community.

Why it matches plant phenotyping methodsドローン画像と深層学習を用いて成熟度、株数、草丈を推定する手法を開発・評価し、パイプラインとオープンソースソフトウェアも提示しており、植物表現型取得が研究の中心である。

abstractIn this study, RGB drone imagery and deep learning (DL) approaches are explored to measure relative maturity (RM), stand count (SC), and plant height (PH)

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

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

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

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

From aerial drone to QTL: Leveraging next-generation phenotyping to reveal the genetics of color and height in field-grown Lactuca sativa →

Abstract In recent years, the automation of genotyping has significantly enhanced the efficiency of genome-wide association studies. As a result, phenotyping rather than genotyping is now the rate-limiting step, especially in field experiments. For this reason, there is a strong need to further automate in-field phenotyping. Here we present a GWAS study on 194 field-grown accessions of lettuce ( Lactuca sativa ). These accessions were non-destructively phenotyped at two time points 15 days apart using an unmanned aerial vehicle. Our high throughput phenotyping approach integrates an RGB camera, a multispectral camera to measure the reflectance at 5 wavelengths (blue, green, red, red edge, near-infrared), and precise height estimation. We used the mean and other descriptives such as median, quantiles, minimum and maximum to quantify different aspects of color and height variation in lettuce from the drone images. Using this approach, we confirm several previously described QTLs, now in populations grown under field conditions, and identify several new QTLs for plant-height and color.

Why it matches plant phenotyping methodsドローン搭載RGB・マルチスペクトルカメラと高さ推定を統合した圃場フェノタイピング手法を開発・適用し、画像からレタスの色と草丈を定量化しているため、方法が研究の中心です。

abstractOur high throughput phenotyping approach integrates an RGB camera, a multispectral camera to measure the reflectance at 5 wavelengths (blue, green, red, red edge, near-infrared), and precise height estimation.

Counting Canola: Toward Generalizable Aerial Plant Detection Models. →

Plant population counts are highly valued by crop producers as important early-season indicators of field health. Traditionally, emergence rate estimates have been acquired through manual counting, an approach that is labor-intensive and relies heavily on sampling techniques. By applying deep learning-based object detection models to aerial field imagery, accurate plant population counts can be obtained for much larger areas of a field. Unfortunately, current detection models often perform poorly when they are faced with image conditions that do not closely resemble the data found in their training sets. In this paper, we explore how specific facets of a plant detector's training set can affect its ability to generalize to unseen image sets. In particular, we examine how a plant detection model's generalizability is influenced by the size, diversity, and quality of its training data. Our experiments show that the gap between in-distribution and out-of-distribution performance cannot be closed by merely increasing the size of a model's training set. We also demonstrate the importance of training set diversity in producing generalizable models, and show how different types of annotation noise can elicit different model behaviors in out-of-distribution test sets. We conduct our investigations with a large and diverse dataset of canola field imagery that we assembled over several years. We also present a new web tool, Canola Counter, which is specifically designed for remote-sensed aerial plant detection tasks. We use the Canola Counter tool to prepare our annotated canola seedling dataset and conduct our experiments. Both our dataset and web tool are publicly available.

Why it matches plant phenotyping methods航空画像からカノーラ個体数（個体群密度）を推定する検出モデルの汎化性能を検証し、注釈付きデータセットと専用Webツールを提示しており、植物表現型取得手法が中心である。

abstractBy applying deep learning-based object detection models to aerial field imagery, accurate plant population counts can be obtained for much larger areas of a field.

MS-YOLOv8: multi-scale adaptive recognition and counting model for peanut seedlings under salt-alkali stress from remote sensing. →

Introduction The emergence rate of crop seedlings is an important indicator for variety selection, evaluation, field management, and yield prediction. To address the low recognition accuracy caused by the uneven size and varying growth conditions of crop seedlings under salt-alkali stress, this research proposes a peanut seedling recognition model, MS-YOLOv8. Methods This research employs close-range remote sensing from unmanned aerial vehicles (UAVs) to rapidly recognize and count peanut seedlings. First, a lightweight adaptive feature fusion module (called MSModule) is constructed, which groups the channels of input feature maps and feeds them into different convolutional layers for multi-scale feature extraction. Additionally, the module automatically adjusts the channel weights of each group based on their contribution, improving the feature fusion effect. Second, the neck network structure is reconstructed to enhance recognition capabilities for small objects, and the MPDIoU loss function is introduced to effectively optimize the detection boxes for seedlings with scattered branch growth. Results Experimental results demonstrate that the proposed MS-YOLOv8 model achieves an AP50 of 97.5% for peanut seedling detection, which is 12.9%, 9.8%, 4.7%, 5.0%, 11.2%, 5.0%, and 3.6% higher than Faster R-CNN, EfficientDet, YOLOv5, YOLOv6, YOLOv7, YOLOv8, and RT-DETR, respectively. Discussion This research provides valuable insights for crop recognition under extreme environmental stress and lays a theoretical foundation for the development of intelligent production equipment.

Why it matches plant phenotyping methodsUAVリモートセンシング画像からピーナッツ幼苗を認識・計数するモデルを開発し、検出性能を比較検証している。幼苗数・出現率という植物状態の推定が研究の中心である。

abstractthis research proposes a peanut seedling recognition model, MS-YOLOv8

RGB‐based indices for estimating cover crop biomass, nitrogen content, and carbon:nitrogen ratio →

Plant cover and biochemical composition are essential parameters for evaluating cover crop management. Destructive sampling or estimates with aerial imagery require substantial labor, time, expertise, or instrumentation cost. Using low-cost consumer and mobile phone cameras to estimate plant canopy coverage and biochemical composition could broaden the use of high-throughput technologies in research and crop management. Here, we estimated canopy development, tissue nitrogen, and biomass of medium red clover (Trifolium pratense L.), a perennial forage legume and common cover crop, using red-green-blue (RGB) indices collected with standard settings in non-standardized field conditions. Pixels were classified as plant or background using combinations of four RGB indices with both unsupervised machine learning and preset thresholds. The excess green minus red (ExGR) index with a preset threshold of zero was the best index and threshold combination. It correctly identified pixels as plant or background 86.25% of the time. This combination also provided accurate estimates of crop growth and quality: Canopy coverage correlated with red clover biomass (R² = 0.554, root mean square error [RMSE] = 219.29 kg ha⁻¹), and ExGR index values of vegetation pixels were highly correlated with clover nitrogen content (R² = 0.573, RMSE = 3.5 g kg⁻¹) and carbon:nitrogen ratio (R² = 0.574, RMSE = 1.29 g g⁻¹). Data collection were simple to implement and stable across imaging conditions. Pending testing across different sensors, sites, and crop species, this method contributes to a growing and open set of decision support tools for agricultural research and management.

Why it matches plant phenotyping methods低コストRGB画像と画素分類を用いて、植物被覆、バイオマス、窒素含量、C:N比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。

abstractUsing low-cost consumer and mobile phone cameras to estimate plant canopy coverage and biochemical composition could broaden the use of high-throughput technologies in research and crop management.

Benchmarking of Individual Tree Segmentation Methods in Mediterranean Forest Based on Point Clouds from Unmanned Aerial Vehicle Imagery and Low-Density Airborne Laser Scanning →

Three raster-based (RB) and one point cloud-based (PCB) algorithms were tested to segment individual Aleppo pine trees and extract their tree height (H) and crown diameter (CD) using two types of point clouds generated from two different techniques: (1) Low-Density (≈1.5 points/m2) Airborne Laser Scanning (LD-ALS) and (2) photogrammetry based on high-resolution unmanned aerial vehicle (UAV) images. Through intensive experiments, it was concluded that the tested RB algorithms performed best in the case of UAV point clouds (F1-score > 80.57%, H Pearson’s r > 0.97, and CD Pearson´s r > 0.73), while the PCB algorithm yielded the best results when working with LD-ALS point clouds (F1-score = 89.51%, H Pearson´s r = 0.94, and CD Pearson´s r = 0.57). The best set of algorithm parameters was applied to all plots, i.e., it was not optimized for each plot, in order to develop an automatic pipeline for mapping large areas of Mediterranean forests. In this case, tree detection and height estimation showed good results for both UAV and LD-ALS (F1-score > 85% and >76%, and H Pearson´s r > 0.96 and >0.93, respectively). However, very poor results were found when estimating crown diameter (CD Pearson´s r around 0.20 for both approaches).

Why it matches plant phenotyping methods個体樹のセグメンテーション手法を比較・検証し、樹高と樹冠径という植物形質を点群から推定する自動パイプラインを評価しており、フェノタイピング手法が中心です。

titleBenchmarking of Individual Tree Segmentation Methods in Mediterranean Forest Based on Point Clouds from Unmanned Aerial Vehicle Imagery and Low-Density Airborne Laser Scanning

Estimating Carbon Stock in Unmanaged Forests Using Field Data and Remote Sensing →

Unmanaged forest ecosystems play a critical role in addressing the ongoing climate and biodiversity crises. As there is no commercial interest in monitoring the health and development of such inaccessible habitats, low-cost assessment approaches are needed. We used a method combining RGB imagery acquired using an Unmanned Aerial Vehicle (UAV), Sentinel-2 data, and field surveys to determine the carbon stock of an unmanaged forest in the UNESCO World Heritage Site wilderness area Dürrenstein-Lassingtal in Austria. The entry-level consumer drone (DJI Mavic Mini) and freely available Sentinel-2 multispectral datasets were used for the evaluation. We merged the Sentinel-2 derived vegetation index NDVI with aerial photogrammetry data and used an orthomosaic and a Digital Surface Model (DSM) to map the extent of woodland in the study area. The Random Forest (RF) machine learning (ML) algorithm was used to classify land cover. Based on the acquired field data, the average carbon stock per hectare of forest was determined to be 371.423 ± 51.106 t of CO2 and applied to the ML-generated class Forest. An overall accuracy of 80.8% with a Cohen’s kappa value of 0.74 was achieved for the land cover classification, while the carbon stock of the living above-ground biomass (AGB) was estimated with an accuracy within 5.9% of field measurements. The proposed approach demonstrated that the combination of low-cost remote sensing data and field work can predict above-ground biomass with high accuracy. The results and the estimation error distribution highlight the importance of accurate field data.

Why it matches plant phenotyping methodsUAV・衛星リモートセンシングと機械学習により森林の地上部バイオマス（炭素蓄積量）を推定し、現地測定と精度検証しているため、植物群落レベルの形質推定手法が中心です。

abstractWe used a method combining RGB imagery acquired using an Unmanned Aerial Vehicle (UAV), Sentinel-2 data, and field surveys to determine the carbon stock of an unmanaged forest

Influence of Structure from Motion Algorithm Parameters on Metrics for Individual Tree Detection Accuracy and Precision →

Uncrewed aerial system (UAS) structure from motion (SfM) monitoring strategies for individual trees has rapidly expanded in the early 21st century. It has become common for studies to report accuracies for individual tree heights and DBH, along with stand density metrics. This study evaluates individual tree detection and stand basal area accuracy and precision in five ponderosa pine sites against the range of SfM parameters in the Agisoft Metashape, Pix4DMapper, and OpenDroneMap algorithms. The study is designed to frame UAS-SfM individual tree monitoring accuracy in the context of data processing and storage demands as a function of SfM algorithm parameter levels. Results show that when SfM algorithms are properly tuned, differences between software types are negligible, with Metashape providing a median F-score improvement over OpenDroneMap of 0.02 and PIX4DMapper of 0.06. However, tree extraction performance varied greatly across algorithm parameters, with the greatest extraction rates typically coming from parameters causing increased density in dense point clouds and minimal point cloud filtering. Transferring UAS-SfM forest monitoring into management will require tradeoffs between accuracy and efficiency. Our analysis shows that a one-step reduction in dense point cloud quality saves 77–86% in point cloud processing time without decreasing tree extraction (F-score) or basal area precision using Metashape and PIX4DMapper but the same parameter change for OpenDroneMap caused a ~5% loss in precision. Providing reproducible processing strategies is a vital step in successfully transferring these technologies into usage as management tools.

Why it matches plant phenotyping methodsUAS-SfMの処理パラメータと複数ソフトウェアを比較し、個体樹の抽出精度、樹高・DBH、林分断面積を評価する技術検証が中心である。

abstractThis study evaluates individual tree detection and stand basal area accuracy and precision in five ponderosa pine sites against the range of SfM parameters in the Agisoft Metashape, Pix4DMapper, and OpenDroneMap algorithms.

A Coffee Plant Counting Method Based on Dual-Channel NMS and YOLOv9 Leveraging UAV Multispectral Imaging →

Accurate coffee plant counting is a crucial metric for yield estimation and a key component of precision agriculture. While multispectral UAV technology provides more accurate crop growth data, the varying spectral characteristics of coffee plants across different phenological stages complicate automatic plant counting. This study compared the performance of mainstream YOLO models for coffee detection and segmentation, identifying YOLOv9 as the best-performing model, with it achieving high precision in both detection (P = 89.3%, mAP50 = 94.6%) and segmentation performance (P = 88.9%, mAP50 = 94.8%). Furthermore, we studied various spectral combinations from UAV data and found that RGB was most effective during the flowering stage, while RGN (Red, Green, Near-infrared) was more suitable for non-flowering periods. Based on these findings, we proposed an innovative dual-channel non-maximum suppression method (dual-channel NMS), which merges YOLOv9 detection results from both RGB and RGN data, leveraging the strengths of each spectral combination to enhance detection accuracy and achieving a final counting accuracy of 98.4%. This study highlights the importance of integrating UAV multispectral technology with deep learning for coffee detection and offers new insights for the implementation of precision agriculture.

Why it matches plant phenotyping methodsUAVマルチスペクトル画像とYOLOv9、二重チャネルNMSを用いてコーヒー植物の検出・セグメンテーション・個体数推定手法を開発し、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。

titleA Coffee Plant Counting Method Based on Dual-Channel NMS and YOLOv9 Leveraging UAV Multispectral Imaging

Influence of Vegetation Phenology on the Temporal Effect of Crop Fractional Vegetation Cover Derived from Moderate-Resolution Imaging Spectroradiometer Nadir Bidirectional Reflectance Distribution Function–Adjusted Reflectance →

Moderate-Resolution Imaging Spectroradiometer (MODIS) Nadir Bidirectional Reflectance Distribution Function (BRDF)-Adjusted Reflectance (NBAR) products are being increasingly used for the quantitative remote sensing of vegetation. However, the assumption underlying the MODIS NBAR product’s inversion model—that surface anisotropy remains unchanged over the 16-day retrieval period—may be unreliable, especially since the canopy structure of vegetation undergoes stark changes at the start of season (SOS) and the end of season (EOS). Therefore, to investigate the MODIS NBAR product’s temporal effect on the quantitative remote sensing of crops at different stages of the growing seasons, this study selected typical phenological parameters, namely SOS, EOS, and the intervening stable growth of season (SGOS). The PROBA-V bioGEOphysical product Version 3 (GEOV3) Fractional Vegetation Cover (FVC) served as verification data, and the Pearson correlation coefficient (PCC) was used to compare and analyze the retrieval accuracy of FVC derived from the MODIS NBAR product and MODIS Surface Reflectance product. The Anisotropic Flat Index (AFX) was further employed to explore the influence of vegetation type and mixed pixel distribution characteristics on the BRDF shape under different stages of the growing seasons and different FVC; that was then combined with an NDVI spatial distribution map to assess the feasibility of using the reflectance of other characteristic directions besides NBAR for FVC correction. The results revealed the following: (1) Generally, at the SOSs and EOSs, the differences in PCCs before vs. after the NBAR correction mainly ranged from 0 to 0.1. This implies that the accuracy of FVC derived from MODIS NBAR is lower than that derived from MODIS Surface Reflectance. Conversely, during the SGOSs, the differences in PCCs before vs. after the NBAR correction ranged between –0.2 and 0, suggesting the accuracy of FVC derived from MODIS NBAR surpasses that derived from MODIS Surface Reflectance. (2) As vegetation phenology shifts, the ensuing differences in NDVI patterning and AFX can offer auxiliary information for enhanced vegetation classification and interpretation of mixed pixel distribution characteristics, which, when combined with NDVI at characteristic directional reflectance, could enable the accurate retrieval of FVC. Our results provide data support for the BRDF correction timescale effect of various stages of the growing seasons, highlighting the potential importance of considering how they differentially influence the temporal effect of NBAR corrections prior to monitoring vegetation when using the MODIS NBAR product.

Why it matches plant phenotyping methodsMODIS反射率から作物のFVCを推定するリモートセンシング手法について、NBAR補正の時期効果を比較・検証しており、植物形質推定が研究の中心である。

abstractThe PROBA-V bioGEOphysical product Version 3 (GEOV3) Fractional Vegetation Cover (FVC) served as verification data, and the Pearson correlation coefficient (PCC) was used to compare and analyze the retrieval accuracy of FVC derived from the MODIS NBAR product and MODIS Surface Reflectance product.

Estimation of corn crop damage caused by wildlife in UAV images →

PURPOSE: This paper proposes a low-cost and low-effort solution for determining the area of corn crops damaged by the wildlife facility utilising field images collected by an unmanned aerial vehicle (UAV). The proposed solution allows for the determination of the percentage of the damaged crops and their location. METHODS: The method utilises image segmentation models based on deep convolutional neural networks (e.g., UNet family) and transformers (SegFormer) trained on over 300 hectares of diverse corn fields in western Poland. A range of neural network architectures was tested to select the most accurate final solution. RESULTS: The tests show that despite using only easily accessible RGB data available from inexpensive, consumer-grade UAVs, the method achieves sufficient accuracy to be applied in practical solutions for agriculture-related tasks, as the IoU (Intersection over Union) metric for segmentation of healthy and damaged crop reaches 0.88. CONCLUSION: The proposed method allows for easy calculation of the total percentage and visualisation of the corn crop damages. The processing code and trained model are shared publicly.

Why it matches plant phenotyping methodsUAV画像からトウモロコシの健全・損傷状態をセグメンテーションし、損傷面積率と位置を推定する手法が研究の中心であり、植物状態の定量的フェノタイピングに該当する。

abstractThis paper proposes a low-cost and low-effort solution for determining the area of corn crops damaged by the wildlife facility utilising field images collected by an unmanned aerial vehicle (UAV).

Enhancing Crop Yield Estimation from Remote Sensing Data: A Comparative Study of the Quartile Clean Image Method and Vision Transformer →

Abstract The use of high-altitude remote sensing (RS) data from aerial and satellite platforms presents considerable challenges for agricultural monitoring and crop yield estimation due to the presence of noise caused by atmospheric interference, sensor anomalies, and outlier pixel values. This paper introduces a "Quartile Clean Image" pre-processing technique to address these data issues by analyzing quartile pixel values in local neighborhoods to identify and adjust outliers. Applying this technique to 20,946 Moderate Resolution Imaging Spectroradiometer (MODIS) images from 2003 to 2015 improved the mean peak signal-to-noise ratio (PSNR) to 40.91 dB. Integrating Quartile Clean data with Convolutional Neural Networks (CNN) models with exponential decay learning rate scheduling achieved RMSE improvements up to 5.88% for soybeans and 21.85% for corn, while Long Short-Term Memory (LSTM) models demonstrated RMSE reductions up to 11.52% for soybeans and 29.92% for corn using exponential decay learning rates. To compare the proposed method with state-of-the-art techniques, we introduce the Vision Transformer (ViT) model for crop yield estimation. The ViT model, applied to the same dataset, achieves remarkable performance without explicit pre-processing, with R 2 scores ranging from 0.9752 to 0.9875 for soybean and 0.9540 to 0.9888 for corn yield estimation. The RMSE values range from 7.75086 to 9.76838 for soybean and 26.25265 to 34.20382 for corn, demonstrating the ViT model's robustness. This research contributes by (1) introducing the Quartile Clean Image method for enhancing RS data quality and improving crop yield estimation accuracy, and (2) comparing it with the state-of-the-art ViT model. The results demonstrate the effectiveness of the proposed approach and highlight the potential of the ViT model for crop yield estimation, representing a valuable advancement in processing high-altitude imagery for precision agriculture applications.

Why it matches plant phenotyping methods作物収量という植物形質を遠隔センシング画像から推定する前処理法を開発し、CNN・LSTM・ViTとの比較で性能を検証しており、フェノタイピング手法が中心です。

abstractThis paper introduces a "Quartile Clean Image" pre-processing technique to address these data issues by analyzing quartile pixel values in local neighborhoods to identify and adjust outliers.

Lidar-derived structural-complexity data across four experimental forests. →

Structural complexity refers to the three-dimensional arrangement and variability of both biotic and abiotic components of an ecosystem. Metrics that characterize structural complexity are often used to manage various aspects of ecosystem function, such as light transmittance, wildlife habitat, and biological diversity. Additionally, these metrics aid in evaluating resilience to disturbance events, including hurricanes, bark-beetle outbreaks, and wildfire. Recent advances in wildland fire modelling have facilitated the integration of forest structural complexity metrics into the QUIC-Fire model, enabling real-time prediction of fire spread and behaviour by simulating interactions between fire, weather, topography, and forest structure. While QUIC-Fire is designed to be highly adaptable, model performance depends on the availability and accuracy of local data inputs. Expanding the model's usability across different regions can be facilitated by the availability of more comprehensive and high-quality data. Thus, the primary goal behind the data products we developed was to establish a basis for collaborative research across various disciplines, particularly within the focal areas of the Southern Research Station, such as forestry, wildland fire, hydrology, soil science, and cultural resources at Bent Creek, Coweeta, Escambia, and Hitchiti Experimental Forests (EFs). Airborne laser scanning (ALS) was used to collect point-cloud data for each EF during the leaf-off season to minimize interference from foliage. Subsequent processing of the raw lidar data involved outlier detection and filtering, ground and non-ground classification, and the computation of a variety of metrics representing various aspects of topography and forest structure at both the pixel-level and the tree-level. Pixel-level topographic data products include: digital elevation model (DEM), slope, aspect, topographic position index (TPI), topographic roughness index (TRI), roughness, and flow direction. Forest structural-complexity metrics include canopy height, foliar height diversity (FHD), vertical distribution ratio (VDR), canopy rugosity, crown relief ratio (CRR), understory complexity index (UCI), vertical complexity index (VCI), canopy cover, mean vegetation height, and the standard deviation of vegetation height. Tree-level data products were computed from the point cloud using multiple algorithms to perform individual tree detection (ITD) and individual tree segmentation (ITS). The datasets have been harmonized and are openly accessible through the USDA Forest Service Research Data Archive.

Why it matches plant phenotyping methods航空レーザースキャンから樹冠高、植生高、樹冠構造、個体樹木を抽出した再利用可能なデータセットであり、植物の構造形質取得と処理が中心です。

abstractAirborne laser scanning (ALS) was used to collect point-cloud data for each EF during the leaf-off season

Crop Growth Analysis Using Automatic Annotations and Transfer Learning in Multi-Date Aerial Images and Ortho-Mosaics →

Growth monitoring of crops is a crucial aspect of precision agriculture, essential for optimal yield prediction and resource allocation. Traditional crop growth monitoring methods are labor-intensive and prone to errors. This study introduces an automated segmentation pipeline utilizing multi-date aerial images and ortho-mosaics to monitor the growth of cauliflower crops (Brassica Oleracea var. Botrytis) using an object-based image analysis approach. The methodology employs YOLOv8, a Grounding Detection Transformer with Improved Denoising Anchor Boxes (DINO), and the Segment Anything Model (SAM) for automatic annotation and segmentation. The YOLOv8 model was trained using aerial image datasets, which then facilitated the training of the Grounded Segment Anything Model framework. This approach generated automatic annotations and segmentation masks, classifying crop rows for temporal monitoring and growth estimation. The study’s findings utilized a multi-modal monitoring approach to highlight the efficiency of this automated system in providing accurate crop growth analysis, promoting informed decision-making in crop management and sustainable agricultural practices. The results indicate consistent and comparable growth patterns between aerial images and ortho-mosaics, with significant periods of rapid expansion and minor fluctuations over time. The results also indicated a correlation between the time and method of observation which paves a future possibility of integration of such techniques aimed at increasing the accuracy in crop growth monitoring based on automatically derived temporal crop row segmentation masks.

Why it matches plant phenotyping methods航空画像・オルソモザイクから作物列を自動セグメンテーションし、時系列の生育・成長を推定する画像解析パイプラインが研究の中心であり、植物形質の取得手法として適格。

abstractThis study introduces an automated segmentation pipeline utilizing multi-date aerial images and ortho-mosaics to monitor the growth of cauliflower crops

YOLOTree-Individual Tree Spatial Positioning and Crown Volume Calculation Using UAV-RGB Imagery and LiDAR Data →

Individual tree canopy extraction plays an important role in downstream studies such as plant phenotyping, panoptic segmentation and growth monitoring. Canopy volume calculation is an essential part of these studies. However, existing volume calculation methods based on LiDAR or based on UAV-RGB imagery cannot balance accuracy and real-time performance. Thus, we propose a two-step individual tree volumetric modeling method: first, we use RGB remote sensing images to obtain the crown volume information, and then we use spatially aligned point cloud data to obtain the height information to automate the calculation of the crown volume. After introducing the point cloud information, our method outperforms the RGB image-only based method in 62.5% of the volumetric accuracy. The AbsoluteError of tree crown volume is decreased by 8.304. Compared with the traditional 2.5D volume calculation method using cloud point data only, the proposed method is decreased by 93.306. Our method also achieves fast extraction of vegetation over a large area. Moreover, the proposed YOLOTree model is more comprehensive than the existing YOLO series in tree detection, with 0.81% improvement in precision, and ranks second in the whole series for mAP50-95 metrics. We sample and open-source the TreeLD dataset to contribute to research migration.

Why it matches plant phenotyping methodsUAV-RGB画像とLiDARを用いて個体樹冠体積を推定する手法を開発・評価しており、単なる樹木位置検出を超えた植物形態形質の抽出が中心です。データセット公開も行っています。

abstractwe propose a two-step individual tree volumetric modeling method

High temporal resolution unoccupied aerial systems phenotyping provides unique information between flight dates →

Abstract Unoccupied aerial systems (UAS, unoccupied aerial vehicle, and drone) are high‐throughput phenotyping tools that can provide transformational insights into biological and agricultural research, but practical and scientific questions remain. The utility of dense versus sparse temporal collections (e.g., daily, weekly, and monthly flights) has important implications for experimental design, resource allocation, and the scope of scientific questions investigated through UAS. UAS‐derived image data were collected on over 1500 maize hybrid yield trial plots with a temporal (longitudinal, 4D) sampling density of 2.8 days on average between 43 flights throughout the growing season. Correlations of vegetation index (VI) phenomic features between flight dates were generally high between flights separated by only 1 or 2 days but dropped when 3, 4, or more days separated the flights. These varied depending on specific dates and the VI used. Correlations between flights were lower around flowering time than during other parts of the season indicating the phenotypic uniqueness of this developmental period. The cross‐validation accuracy of end of season yields prediction models on untested genotypes from the UAS data (0.59 and 0.62) far exceeded genomic prediction accuracy (0.24) for the same test set hybrids regardless of whether all flight dates were used for prediction or only dates before flowering. Phenomic prediction accuracy marginally increased as additional flight dates were added throughout the season.

Why it matches plant phenotyping methodsUAS画像を用いた高頻度植物フェノタイピングの時間分解能と予測性能を評価しており、取得・解析方法の技術的検証が中心です。

abstractUnoccupied aerial systems (UAS, unoccupied aerial vehicle, and drone) are high‐throughput phenotyping tools

Phenology and Plant Functional Type Link Optical Properties of Vegetation Canopies to Patterns of Vertical Vegetation Complexity →

Vegetation vertical complexity influences biodiversity and ecosystem productivity. Rapid warming in the boreal region is altering patterns of vertical complexity. LiDAR sensors offer novel structural metrics for quantifying these changes, but their spatiotemporal limitations and their need for ecological context complicate their application and interpretation. Satellite variables can estimate LiDAR metrics, but retrievals of vegetation structure using optical reflectance can lack interpretability and accuracy. We compare vertical complexity from the airborne LiDAR Land Vegetation and Ice Sensor (LVIS) in boreal Canada and Alaska to plant functional type, optical, and phenological variables. We show that spring onset and green season length from satellite phenology algorithms are more strongly correlated with vegetation vertical complexity (R = 0.43–0.63) than optical reflectance (R = 0.03–0.43). Median annual temperature explained patterns of vegetation vertical complexity (R = 0.45), but only when paired with plant functional type data. Random forest models effectively learned patterns of vegetation vertical complexity using plant functional type and phenological variables, but the validation performance depended on the validation methodology (R2 = 0.50–0.80). In correlating satellite phenology, plant functional type, and vegetation vertical complexity, we propose new methods of retrieving vertical complexity with satellite data.

Why it matches plant phenotyping methods植生キャノピーの垂直複雑性という明示的な植物構造形質を、LiDAR・衛星フェノロジー・機械学習で推定し、検証する方法研究であり、測定手法が中心的です。

abstractLiDAR sensors offer novel structural metrics for quantifying these changes

Modeling soybean growth: A mixed model approach. →

The evaluation of plant and animal growth, separately for genetic and environmental effects, is necessary for genetic understanding and genetic improvement of environmental responses of plants and animals. We propose to extend an existing approach that combines nonlinear mixed-effects model (NLMEM) and the stochastic approximation of the Expectation-Maximization algorithm (SAEM) to analyze genetic and environmental effects on plant growth. These tools are widely used in many fields but very rarely in plant biology. During model formulation, a nonlinear function describes the shape of growth, and random effects describe genetic and environmental effects and their variability. Genetic relationships among the varieties were also integrated into the model using a genetic relationship matrix. The SAEM algorithm was chosen as an efficient alternative to MCMC methods, which are more commonly used in the domain. It was implemented to infer the expected growth patterns in the analyzed population and the expected curves for each variety through a maximum-likelihood and a maximum-a-posteriori approaches, respectively. The obtained estimates can be used to predict the growth curves for each variety. We illustrate the strengths of the proposed approach using simulated data and soybean plant growth data obtained from a soybean cultivation experiment conducted at the Arid Land Research Center, Tottori University. In this experiment, plant height was measured daily using drones, and the growth was monitored for approximately 200 soybean cultivars for which whole-genome sequence data were available. The NLMEM approach improved our understanding of the determinants of soybean growth and can be successfully used for the genomic prediction of growth pattern characteristics.

Why it matches plant phenotyping methods植物成長を対象に、遺伝・環境効果を分離し、品種別の成長曲線を推定するNLMEM/SAEM手法を中心的に提案・適用しているため、成長形質の計算的推定に該当する。

abstractWe propose to extend an existing approach that combines nonlinear mixed-effects model (NLMEM) and the stochastic approximation of the Expectation-Maximization algorithm (SAEM) to analyze genetic and environmental effects on plant growth.

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

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

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

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

Field-based high-throughput phenotyping enhances phenomic and genomic predictions for grain yield and plant height across years in maize →

Field-based phenomic prediction employs novel features, like vegetation indices (VIs) from drone images, to predict key agronomic traits in maize, despite challenges in matching biomarker measurement time points across years or environments. This study utilized functional principal component analysis (FPCA) to summarize the variation of temporal VIs, uniquely allowing the integration of this data into phenomic prediction models tested across multiple years (2018-2021) and environments. The models, which included 1 genomic, 2 phenomic, 2 multikernel, and 1 multitrait type, were evaluated in 4 prediction scenarios (CV2, CV1, CV0, and CV00), relevant for plant breeding programs, assessing both tested and untested genotypes in observed and unobserved environments. Two hybrid populations (415 and 220 hybrids) demonstrated the visible atmospherically resistant index's strong temporal correlation with grain yield (up to 0.59) and plant height. The first 2 FPCAs explained 59.3 ± 13.9% and 74.2 ± 9.0% of the temporal variation of temporal data of VIs, respectively, facilitating predictions where flight times varied. Phenomic data, particularly when combined with genomic data, often were comparable to or numerically exceeded the base genomic model in prediction accuracy, particularly for grain yield in untested hybrids, although no significant differences in these models' performance were consistently observed. Overall, this approach underscores the effectiveness of FPCA and combined models in enhancing the prediction of grain yield and plant height across environments and diverse agricultural settings.

Why it matches plant phenotyping methodsドローン画像由来の時系列植生指数をFPCAで要約し、穀粒収量・草丈予測へ統合するフェノタイピング手法と予測モデルを複数年・環境で評価しており、表現型取得・抽出と技術的評価が中心である。

titleField-based high-throughput phenotyping enhances phenomic and genomic predictions for grain yield and plant height across years in maize

Plant height defined growth curves during vegetative development have the potential to predict end of season maize yield and assist with mid-season management decisions →

Precision farming has been developing with the intention of identifying within field variability to adjust management strategies and maximize end of season yield and profitability and minimize negative environmental impacts. The development of quick, easy, and low cost methods to quantify field level variation is essential to successful implementation of precision agriculture at scale. Temporal plant height and growth rates collected with unoccupied aerial vehicles mounted with red, green, blue sensors have the potential to predict end of season grain yield, which could facilitate mid-season management decisions. Image-based plant height data was collected weekly from commercial maize fields in three growing seasons to assess variation within fields and the relationship with grain yield variation. Plant height, growth rate, and grain yield had variable relationships depending on the time point and growth environment. Models developed using temporal traits predicted grain yield variation within a commercial field up to r = 0.7, though insufficient water affected the prediction accuracy in one field due to the limited representation of drought environments in the model development. In the future, with more data from stress environments, such as drought, this method has potential for high accuracy grain yield prediction across a range of environmental conditions. This study demonstrates the potential of using unoccupied aerial vehicles to derive vegetative growth patterns and model within field variations, and has application in making mid-season management decisions.

Why it matches plant phenotyping methodsUAV画像から植物高と成長率を抽出し、時系列形質による圃場内収量変動予測を評価しており、植物表現型の取得・解析手法が研究の中心です。

abstractTemporal plant height and growth rates collected with unoccupied aerial vehicles mounted with red, green, blue sensors have the potential to predict end of season grain yield

A global dataset for assessing nitrogen-related plant traits using drone imagery in major field crop species →

Abstract Enhancing rapid phenotyping for key plant traits, such as biomass and nitrogen content, is critical for effectively monitoring crop growth and maximizing yield. Studies have explored the relationship between vegetation indices (VIs) and plant traits using drone imagery. However, there is a gap in the literature regarding data availability, accessible datasets. Based on this context, we conducted a systematic review to retrieve relevant data worldwide on the state of the art in drone-based plant trait assessment. The final dataset consists of 41 peer-reviewed papers with 11,189 observations for 11 major crop species distributed across 13 countries. It focuses on the association of plant traits with VIs at different growth/phenological stages. This dataset provides foundational knowledge on the key VIs to focus for phenotyping key plant traits. In addition, future updates to this dataset may include new open datasets. Our goal is to continually update this dataset, encourage collaboration and data inclusion, and thereby facilitate a more rapid advance of phenotyping for critical plant traits to increase yield gains over time.

Why it matches plant phenotyping methodsドローン画像と植生指数に基づく作物形質評価研究を体系的に収集・統合したデータセットであり、植物フェノタイピングの再利用可能な資源が中心です。

titleA global dataset for assessing nitrogen-related plant traits using drone imagery in major field crop species

GobhiSet: Dataset of raw, manually, and automatically annotated RGB images across phenology of Brassica oleracea var. Botrytis . →

This research introduces an extensive dataset of unprocessed aerial RGB images and orthomosaics of Brassica oleracea crops, captured via a DJI Phantom 4. The dataset, publicly accessible, comprises 244 raw RGB images, acquired over six distinct dates in October and November of 2020 as well as 6 orthomosaics from an experimental farm located in Portici, Italy. The images, uniformly distributed across crop spaces, have undergone both manual and automatic annotations, to facilitate the detection, segmentation, and growth modelling of crops. Manual annotations were performed using bounding boxes via the Visual Geometry Group Image Annotator (VIA) and exported in the Common Objects in Context (COCO) segmentation format. The automated annotations were generated using a framework of Grounding DINO + Segment Anything Model (SAM) facilitated by YOLOv8x-seg pretrained weights obtained after training manually annotated images dated 8 October, 21 October, and 29 October 2020. The automated annotations were archived in Pascal Visual Object Classes (PASCAL VOC) format. Seven classes, designated as Row 1 through Row 7, have been identified for crop labelling. Additional attributes such as individual crop ID and the repetitiveness of individual crop specimens are delineated in the Comma Separated Values (CSV) version of the manual annotation. This dataset not only furnishes annotation information but also assists in the refinement of various machine learning models, thereby contributing significantly to the field of smart agriculture. The transparency and reproducibility of the processes are ensured by making the utilized codes accessible. This research marks a significant stride in leveraging technology for vision-based crop growth monitoring.

Why it matches plant phenotyping methods作物の生育モニタリングを目的としたRGB画像・オルソモザイクの公開データセットで、手動／自動アノテーションと成長モデリングを中心的に扱っているため、植物フェノタイピング手法・データセットに該当する。

abstractThis research introduces an extensive dataset of unprocessed aerial RGB images and orthomosaics of Brassica oleracea crops

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

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

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

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

Spatio-temporal modeling of high-throughput multispectral aerial images improves agronomic trait genomic prediction in hybrid maize →

Design randomizations and spatial corrections have increased understanding of genotypic, spatial, and residual effects in field experiments, but precisely measuring spatial heterogeneity in the field remains a challenge. To this end, our study evaluated approaches to improve spatial modeling using high-throughput phenotypes (HTP) via unoccupied aerial vehicle (UAV) imagery. The normalized difference vegetation index was measured by a multispectral MicaSense camera and processed using ImageBreed. Contrasting to baseline agronomic trait spatial correction and a baseline multitrait model, a two-stage approach was proposed. Using longitudinal normalized difference vegetation index data, plot level permanent environment effects estimated spatial patterns in the field throughout the growing season. Normalized difference vegetation index permanent environment were separated from additive genetic effects using 2D spline, separable autoregressive models, or random regression models. The Permanent environment were leveraged within agronomic trait genomic best linear unbiased prediction either modeling an empirical covariance for random effects, or by modeling fixed effects as an average of permanent environment across time or split among three growth phases. Modeling approaches were tested using simulation data and Genomes-to-Fields hybrid maize (Zea mays L.) field experiments in 2015, 2017, 2019, and 2020 for grain yield, grain moisture, and ear height. The two-stage approach improved heritability, model fit, and genotypic effect estimation compared to baseline models. Electrical conductance and elevation from a 2019 soil survey significantly improved model fit, while 2D spline permanent environment were most strongly correlated with the soil parameters. Simulation of field effects demonstrated improved specificity for random regression models. In summary, the use of longitudinal normalized difference vegetation index measurements increased experimental accuracy and understanding of field spatio-temporal heterogeneity.

Why it matches plant phenotyping methodsUAVマルチスペクトル画像から得た縦断的NDVIを植物・圃場プロットの表現型として用い、空間・時系列モデリング手法を提案・評価しており、表現型取得と解析ワークフローが研究の中心です。

abstractour study evaluated approaches to improve spatial modeling using high-throughput phenotypes (HTP) via unoccupied aerial vehicle (UAV) imagery.

Using UAV-Based Temporal Spectral Indices to Dissect Changes in the Stay-Green Trait in Wheat. →

Stay-green (SG) in wheat is a beneficial trait that increases yield and stress tolerance. However, conventional phenotyping techniques limited the understanding of its genetic basis. Spectral indices (SIs) as non-destructive tools to evaluate crop temporal senescence provide an alternative strategy. Here, we applied SIs to monitor the senescence dynamics of 565 diverse wheat accessions from anthesis to maturation stages over 2 field seasons. Four SIs (normalized difference vegetation index, green normalized difference vegetation index, normalized difference red edge index, and optimized soil-adjusted vegetation index) were normalized to develop relative stay-green scores (RSGS) as the SG indicators. An RSGS-based genome-wide association study identified 47 high-confidence quantitative trait loci (QTL) harboring 3,079 single-nucleotide polymorphisms associated with SG and 1,085 corresponding candidate genes. Among them, 15 QTL overlapped or were adjacent to known SG-related QTL/genes, while the remaining QTL were novel. Notably, a set of favorable haplotypes of SG-related candidate genes such as TraesCS2A03G1081100 , TracesCS6B03G0356400 , and TracesCS2B03G1299500 are increasing following the Green Revolution, further validating the feasibility of the pipeline. This study provided a valuable reference for further quantitative SG and genetic research in diverse wheat panels.

Why it matches plant phenotyping methodsUAV時系列スペクトル指標を用いてコムギのstay-green（老化動態）を定量化し、RSGS指標と解析パイプラインを開発・適用しており、表現型取得法が研究の中心である。

abstractSpectral indices (SIs) as non-destructive tools to evaluate crop temporal senescence provide an alternative strategy.

A dataset of unmanned aerial vehicle multispectral images acquired over a field to identify nitrogen requirements. →

The technique of detecting and tracking an area's physical properties from a distance by measuring its reflected and emitted radiation is known as remote sensing. It gathered data accurately in near real-time. For this purpose, multispectral cameras mounted on UAVs that capture images with different bands can be used to generate vegetation indexes (NDVI, NDRE), which are useful in precision agriculture. In this study UAV image dataset contains 336 multispectral images from a 0.06 ha paddy field with three different phonological cycles of the crop (vegetative, reproductive, and ripening) in the north-western province of Sri Lanka. The selected sample rice variety is BG300. The images were taken over five days, starting from August 14 to October 5, 2023. The UAV flight took place at 30 m from the canopy level with the multispectral camera titled at an angle of 900. The SPAD Chlorophyll Meter was used to collect ground truth data, which is proportional to the nitrogen level of the leaf. There were 50 randomly selected readings throughout the paddy field. Relevant climate data for five days was provided by the Rice Research and Development Institute, Bathalagoda, which belongs to the paddy field. The purpose of this data creation was to aid researchers who are generally interested in disease diagnosis. Moreover, this dataset allows for studying the effect of using different tilt angles on the 3D reconstruction of the paddy fields and the generation of orthomosaics.

Why it matches plant phenotyping methodsUAVマルチスペクトル画像とSPADによる地上真値を含む、植物キャノピーの状態推定に再利用可能なデータセットであり、画像取得・オルソモザイク生成・3D再構成が中心的な方法的貢献です。

abstractIn this study UAV image dataset contains 336 multispectral images from a 0.06 ha paddy field with three different phonological cycles of the crop (vegetative, reproductive, and ripening)

The Uncertainty Assessment by the Monte Carlo Analysis of NDVI Measurements Based on Multispectral UAV Imagery. →

This paper proposes a workflow to assess the uncertainty of the Normalized Difference Vegetation Index (NDVI), a critical index used in precision agriculture to determine plant health. From a metrological perspective, it is crucial to evaluate the quality of vegetation indices, which are usually obtained by processing multispectral images for measuring vegetation, soil, and environmental parameters. For this reason, it is important to assess how the NVDI measurement is affected by the camera characteristics, light environmental conditions, as well as atmospheric and seasonal/weather conditions. The proposed study investigates the impact of atmospheric conditions on solar irradiation and vegetation reflection captured by a multispectral UAV camera in the red and near-infrared bands and the variation of the nominal wavelengths of the camera in these bands. Specifically, the study examines the influence of atmospheric conditions in three scenarios: dry-clear, humid-hazy, and a combination of both. Furthermore, this investigation takes into account solar irradiance variability and the signal-to-noise ratio (SNR) of the camera. Through Monte Carlo simulations, a sensitivity analysis is carried out against each of the above-mentioned uncertainty sources and their combination. The obtained results demonstrate that the main contributors to the NVDI uncertainty are the atmospheric conditions, the nominal wavelength tolerance of the camera, and the variability of the NDVI values within the considered leaf conditions (dry and fresh).

Why it matches plant phenotyping methodsUAVマルチスペクトル画像から植物状態を示すNDVIを取得する測定ワークフローについて、不確かさ評価・感度分析を中心に扱っており、測定法の技術的検証が主題である。

abstractThis paper proposes a workflow to assess the uncertainty of the Normalized Difference Vegetation Index (NDVI), a critical index used in precision agriculture to determine plant health.

Crop Canopy Nitrogen Estimation from Mixed Pixels in Agricultural Lands Using Imaging Spectroscopy →

Accurate retrieval of canopy nutrient content has been made possible using visible-to-shortwave infrared (VSWIR) imaging spectroscopy. While this strategy has often been tested on closed green plant canopies, little is known about how nutrient content estimates perform when applied to pixels not dominated by photosynthetic vegetation (PV). In such cases, contributions of bare soil (BS) and non-photosynthetic vegetation (NPV), may significantly and nonlinearly reduce the spectral features relied upon for nutrient content retrieval. We attempted to define the loss of prediction accuracy under reduced PV fractional cover levels. To do so, we utilized VSWIR imaging spectroscopy data from the Global Airborne Observatory (GAO) and a large collection of lab-calibrated field samples of nitrogen (N) content collected across numerous crop species grown in several farming regions of the United States. Fractional cover values of PV, NPV, and BS were estimated from the GAO data using the Automated Monte Carlo Unmixing algorithm (AutoMCU). Errors in prediction from a partial least squares N model applied to the spectral data were examined in relation to the fractional cover of the unmixed components. We found that the most important factor in the accuracy of the partial least squares regression (PLSR) model is the fraction of photosynthetic vegetation (PV) cover, with pixels greater than 60% cover performing at the optimal level, where the coefficient of determination (R2) peaks to 0.66 for PV fractions of more than 60% and bare soil (BS) fractions of less than 20%. Our findings guide future spaceborne imaging spectroscopy missions as applied to agricultural cropland N monitoring.

Why it matches plant phenotyping methodsVSWIR画像分光とスペクトル混合分解・PLSRを用いて作物キャノピー窒素含量の推定精度を検証しており、植物形質取得法が研究の中心である。

abstractAccurate retrieval of canopy nutrient content has been made possible using visible-to-shortwave infrared (VSWIR) imaging spectroscopy.

Large‐scale breeding applications of unoccupied aircraft systems enabled genomic prediction →

Abstract Breeding for improved, reliable cultivars despite growing environmental irregularity can be challenging. Unoccupied aircraft systems (UAS) are a popular high‐throughput phenotyping technology that has been shown to help interpret the mechanisms associated with crop productivity and environmental response, creating potential for improved breeding strategies. Spectral reflectance indices (SRIs), encompassing both vegetation and water indices like normalized difference vegetation index (NDVI), normalized difference red‐edge index, and normalized water index, were employed to assess 4094 winter wheat genotypes across 11,593 breeding plots at Washington State University from 2019 through 2022. SRIs were then used with genomic data in univariate models as covariates and multivariate models as secondary response variables for predictions of grain yield. The prediction accuracy of models was evaluated using a leave‐one‐year‐out validation strategy against a base genomic prediction method. Including SRI data as fixed effects in univariate genomic prediction models can improve prediction accuracy over the control but is unreliable across years. When used in multivariate models, SRIs improve prediction performance across years but require high‐performance computational resources that could limit feasibility. In univariate models, when test year NDVI data were available and used to calculate breeding values, prediction performance was at least 16% better than the control, ranging in prediction accuracy from 0.54 in 2019 to 0.93 in 2020. This study highlights the limited reliability of SRI use in genomic prediction of untested environments and locations. However, a significant application for the technology can be found in early‐season UAS data collection to aid accurate predictions in late season, a helpful tool in tight turnaround times commonly experienced in winter crop breeding programs.

Why it matches plant phenotyping methodsUASによる大規模なスペクトル形質取得を用い、SRIの予測性能を年次交差検証しており、植物フェノタイピング手法の実質的な適用・評価が中心である。

abstractUnoccupied aircraft systems (UAS) are a popular high‐throughput phenotyping technology

Image Filtering to Improve Maize Tassel Detection Accuracy Using Machine Learning Algorithms. →

Unmanned aerial vehicle (UAV)-based imagery has become widely used to collect time-series agronomic data, which are then incorporated into plant breeding programs to enhance crop improvements. To make efficient analysis possible, in this study, by leveraging an aerial photography dataset for a field trial of 233 different inbred lines from the maize diversity panel, we developed machine learning methods for obtaining automated tassel counts at the plot level. We employed both an object-based counting-by-detection (CBD) approach and a density-based counting-by-regression (CBR) approach. Using an image segmentation method that removes most of the pixels not associated with the plant tassels, the results showed a dramatic improvement in the accuracy of object-based (CBD) detection, with the cross-validation prediction accuracy ( r 2 ) peaking at 0.7033 on a detector trained with images with a filter threshold of 90. The CBR approach showed the greatest accuracy when using unfiltered images, with a mean absolute error (MAE) of 7.99. However, when using bootstrapping, images filtered at a threshold of 90 showed a slightly better MAE (8.65) than the unfiltered images (8.90). These methods will allow for accurate estimates of flowering-related traits and help to make breeding decisions for crop improvement.

Why it matches plant phenotyping methodsトウモロコシ雄穂を画像から自動計数し、画像セグメンテーションと2種類の機械学習手法の精度を検証する研究であり、植物表現型取得法が中心である。

abstractwe developed machine learning methods for obtaining automated tassel counts at the plot level.

An applied framework to unlocking multi-angular UAV reflectance data: a case study for classification of plant parameters in maize (Zea mays) →

Abstract Optical sensors, mounted on uncrewed aerial vehicles (UAVs), are typically pointed straight downward to simplify structure-from-motion and image processing. High horizontal and vertical image overlap during UAV missions effectively leads to each object being measured from a range of different view angles, resulting in a rich multi-angular reflectance dataset. We propose a method to extract reflectance data, and their associated distinct view zenith angles (VZA) and view azimuth angles (VAA), from UAV-mounted optical cameras; enhancing plant parameter classification compared to standard orthomosaic reflectance retrieval. A standard (nadir) and a multi-angular, 10-band multispectral dataset was collected for maize using a UAV on two different days. Reflectance data was grouped by VZA and VAA (on average 2594 spectra/plot/day for the multi-angular data and 890 spectra/plot/day for nadir flights only, 13 spectra/plot/day for a standard orthomosaic), serving as predictor variables for leaf chlorophyll content (LCC), leaf area index (LAI), green leaf area index (GLAI), and nitrogen balanced index (NBI) classification. Results consistently showed higher accuracy using grouped VZA/VAA reflectance compared to the standard orthomosaic data. Pooling all reflectance values across viewing directions did not yield satisfactory results. Performing multiple flights to obtain a multi-angular dataset did not improve performance over a multi-angular dataset obtained from a single nadir flight, highlighting its sufficiency. Our openly shared code ( https://github.com/ReneHeim/proj_on_uav ) facilitates access to reflectance data from pre-defined VZA/VAA groups, benefiting cross-disciplinary and agriculture scientists in harnessing the potential of multi-angular datasets. Graphical abstract

Why it matches plant phenotyping methodsUAVマルチアングル反射データから植物形質を抽出・分類する方法を提案し、標準オルソモザイクと精度比較しているため、表現型取得手法が中心である。

abstractWe propose a method to extract reflectance data, and their associated distinct view zenith angles (VZA) and view azimuth angles (VAA), from UAV-mounted optical cameras; enhancing plant parameter classification compared to standard orthomosaic reflectance retrieval.

Using drone-retrieved multispectral data for phenomic selection in potato breeding. →

Predictive breeding approaches, like phenomic or genomic selection, have the potential to increase the selection gain for potato breeding programs which are characterized by very large numbers of entries in early stages and the availability of very few tubers per entry in these stages. The objectives of this study were to (i) explore the capabilities of phenomic prediction based on drone-derived multispectral reflectance data in potato breeding by testing different prediction scenarios on a diverse panel of tetraploid potato material from all market segments and considering a broad range of traits, (ii) compare the performance of phenomic and genomic predictions, and (iii) assess the predictive power of mixed relationship matrices utilizing weighted SNP array and multispectral reflectance data. Predictive abilities of phenomic prediction scenarios varied greatly within a range of - 0.15 and 0.88 and were strongly dependent on the environment, predicted trait, and considered prediction scenario. We observed high predictive abilities with phenomic prediction for yield (0.45), maturity (0.88), foliage development (0.73), and emergence (0.73), while all other traits achieved higher predictive ability with genomic compared to phenomic prediction. When a mixed relationship matrix was used for prediction, higher predictive abilities were observed for 20 out of 22 traits, showcasing that phenomic and genomic data contained complementary information. We see the main application of phenomic selection in potato breeding programs to allow for the use of the principle of predictive breeding in the pot seedling or single hill stage where genotyping is not recommended due to high costs.

Why it matches plant phenotyping methodsドローン由来マルチスペクトルデータを用いたフェノミック予測をジャガイモ育種に適用し、複数の予測シナリオやゲノム予測との性能比較を行っており、植物形質推定法が中心である。

abstractexplore the capabilities of phenomic prediction based on drone-derived multispectral reflectance data in potato breeding

High-throughput UAV-based rice panicle detection and genetic mapping of heading-date-related traits. →

Introduction: ) serves as a vital staple crop that feeds over half the world's population. Optimizing rice breeding for increasing grain yield is critical for global food security. Heading-date-related or Flowering-time-related traits, is a key factor determining yield potential. However, traditional manual phenotyping methods for these traits are time-consuming and labor-intensive. Method: Here we show that aerial imagery from unmanned aerial vehicles (UAVs), when combined with deep learning-based panicle detection, enables high-throughput phenotyping of heading-date-related traits. We systematically evaluated various state-of-the-art object detectors on rice panicle counting and identified YOLOv8-X as the optimal detector. Results: Applying YOLOv8-X to UAV time-series images of 294 rice recombinant inbred lines (RILs) allowed accurate quantification of six heading-date-related traits. Utilizing these phenotypes, we identified quantitative trait loci (QTL), including verified loci and novel loci, associated with heading date. Discussion: Our optimized UAV phenotyping and computer vision pipeline may facilitate scalable molecular identification of heading-date-related genes and guide enhancements in rice yield and adaptation.

Why it matches plant phenotyping methodsUAV画像と深層学習によるイネ穂検出・計数を中核とし、出穂関連形質を高スループットに定量するフェノタイピング手法およびワークフローを評価・適用している。

abstractaerial imagery from unmanned aerial vehicles (UAVs), when combined with deep learning-based panicle detection, enables high-throughput phenotyping of heading-date-related traits

Identifying Regenerated Saplings by Stratifying Forest Overstory Using Airborne LiDAR Data. →

Identifying the spatiotemporal distributions and phenotypic characteristics of understory saplings is beneficial in exploring the internal mechanisms of plant regeneration and providing technical assistances for continues cover forest management. However, it is challenging to detect the understory saplings using 2-dimensional (2D) spectral information produced by conventional optical remotely sensed data. This study proposed an automatic method to detect the regenerated understory saplings based on the 3D structural information from aerial laser scanning (ALS) data. By delineating individual tree crown using the improved spectral clustering algorithm, we successfully removed the overstory canopy and associated trunk points. Then, individual understory saplings were segmented using an adaptive-mean-shift-based clustering algorithm. This method was tested in an experimental forest farm of North China. Our results showed that the detection rates of understory saplings ranged from 94.41% to 152.78%, and the matching rates increased from 62.59% to 95.65% as canopy closure went down. The ALS-based sapling heights well captured the variations of field measurements [ R 2 = 0.71, N = 3,241, root mean square error (RMSE) = 0.26 m, P R 2 = 0.78, N =443, RMSE = 0.23 m, P R 2 = 0.64, N = 443, RMSE = 0.24 m). This study provides a solution for the quantification of understory saplings, which can be used to improve forest ecosystem resilence through regulating the dynamics of forest gaps to better utilize light resources.

Why it matches plant phenotyping methods航空LiDARの3D構造情報を用いて林冠下の実生を自動検出・分割し、樹高を野外測定と検証する手法が研究の中心であるため。

abstractThis study proposed an automatic method to detect the regenerated understory saplings based on the 3D structural information from aerial laser scanning (ALS) data.

AdaTreeFormer: Few Shot Domain Adaptation for Tree Counting from a Single High-Resolution Image →

The process of estimating and counting tree density using only a single aerial or satellite image is a difficult task in the fields of photogrammetry and remote sensing. However, it plays a crucial role in the management of forests. The huge variety of trees in varied topography severely hinders tree counting models to perform well. The purpose of this paper is to propose a framework that is learnt from the source domain with sufficient labeled trees and is adapted to the target domain with only a limited number of labeled trees. Our method, termed as AdaTreeFormer, contains one shared encoder with a hierarchical feature extraction scheme to extract robust features from the source and target domains. It also consists of three subnets: two for extracting self-domain attention maps from source and target domains respectively and one for extracting cross-domain attention maps. For the latter, an attention-to-adapt mechanism is introduced to distill relevant information from different domains while generating tree density maps; a hierarchical cross-domain feature alignment scheme is proposed that progressively aligns the features from the source and target domains. We also adopt adversarial learning into the framework to further reduce the gap between source and target domains. Our AdaTreeFormer is evaluated on six designed domain adaptation tasks using three tree counting datasets, \ie Jiangsu, Yosemite, and London. Experimental results show that AdaTreeFormer significantly surpasses the state of the art, \eg in the cross domain from the Yosemite to Jiangsu dataset, it achieves a reduction of 15.9 points in terms of the absolute counting errors and an increase of 10.8\% in the accuracy of the detected trees' locations. The codes and datasets are available at https://github.com/HAAClassic/AdaTreeFormer.

Why it matches plant phenotyping methods単一の航空・衛星画像から樹木数・密度を推定する画像解析手法を開発し、複数データセットとドメイン適応タスクで評価しており、植物形質の取得が中心である。

abstractThe purpose of this paper is to propose a framework that is learnt from the source domain with sufficient labeled trees and is adapted to the target domain with only a limited number of labeled trees.

Remote Sensing Evaluation Drone Herbicide Application Effectiveness for Controlling Echinochloa spp. in Rice Crop in Valencia (Spain) →

Rice (Oryza sativa L.) is a staple cereal in the diet of more than half of the world’s population. Within the European Union, Spain is a leader in rice production due to its climate and tradition, accounting for 26% of total EU production in 2020. The Valencian rice area covers around 15,000 hectares and is strongly influenced by biotic and abiotic factors. An important biotic factor affecting rice production is weeds, which compete with rice for sunlight, water and nutrients. The dominant weed in Spain is Echinochloa spp., although wild rice is becoming increasingly important. Rice cultivation in Valencia takes place in the area of L’Albufera de Valencia, which is a natural park, i.e., a special protection area. In this natural area, the use of phytosanitary products is limited, so it is necessary to use the minimum amount possible. Therefore, the objective of this work is to evaluate the possibility of using remote sensing effectively to determine the effectiveness of the application of the herbicide cyhalofop-butyl by drone for the control of Echinochloa spp. in rice crops in Valencia. The results will be compared with those obtained by using sterilisation machines (electric backpack sprayers) to apply the herbicide. To evaluate the effectiveness of the application, the reflectance obtained by the satellite sensors in the red and near infrared (NIR) wavelengths, as well as the normalised difference vegetation index (NDVI), were used. The remote sensing results were analysed and complemented by the number of rice plants and weeds per area, plant dry weight, leaf area, BBCH phenological state, SPAD index values, chlorophyll content and relative growth rate. Remote sensing is validated as an effective tool for determining the efficacy of an herbicide in controlling weeds applied by both the drone and the electric backpack sprayer. The weeds slowed down their development after the treatment. Depending on the phenological state of the crop and the active ingredient of the herbicide, these results are applicable to other areas with different climatic and environmental conditions.

Why it matches plant phenotyping methodsドローン・衛星リモートセンシングとNDVI等を用いて除草剤効果を評価し、その手法を有効な評価ツールとして検証しているため、植物状態の取得・評価方法が中心である。

abstractTherefore, the objective of this work is to evaluate the possibility of using remote sensing effectively to determine the effectiveness of the application of the herbicide cyhalofop-butyl by drone for the control of Echinochloa spp. in rice crops in Valencia.

Crop growth dynamics: Fast automatic analysis of LiDAR images in field-plot experiments by specialized software ALFA →

Repeated measurements of crop height to observe plant growth dynamics in real field conditions represent a challenging task. Although there are ways to collect data using sensors on UAV systems, proper data processing and analysis are the key to reliable results. As there is need for specialized software solutions for agricultural research and breeding purposes, we present here a fast algorithm ALFA for the processing of UAV LiDAR derived point-clouds to extract the information on crop height at many individual cereal field-plots at multiple time points. Seven scanning flights were performed over 3 blocks of experimental barley field plots between April and June 2021. Resulting point-clouds were processed by the new algorithm ALFA. The software converts point-cloud data into a digital image and extracts the traits of interest–the median crop height at individual field plots. The entire analysis of 144 field plots of dimension 80 x 33 meters measured at 7 time points (approx. 100 million LiDAR points) takes about 3 minutes at a standard PC. The Root Mean Square Deviation of the software-computed crop height from the manual measurement is 5.7 cm. Logistic growth model is fitted to the measured data by means of nonlinear regression. Three different ways of crop-height data visualization are provided by the software to enable further analysis of the variability in growth parameters. We show that the presented software solution is a fast and reliable tool for automatic extraction of plant height from LiDAR images of individual field-plots. We offer this tool freely to the scientific community for non-commercial use.

Why it matches plant phenotyping methodsUAV LiDAR点群から圃場区画ごとの作物高を自動抽出するソフトウェアと処理アルゴリズムを開発・検証しており、植物形質取得が研究の中心である。

abstractwe present here a fast algorithm ALFA for the processing of UAV LiDAR derived point-clouds to extract the information on crop height at many individual cereal field-plots at multiple time points.

Estimating the frost damage index in lettuce using UAV-based RGB and multispectral images. →

Introduction The cold stress is one of the most important factors for affecting production throughout year, so effectively evaluating frost damage is great significant to the determination of the frost tolerance in lettuce. Methods We proposed a high-throughput method to estimate lettuce FDI based on remote sensing. Red-Green-Blue (RGB) and multispectral images of open-field lettuce suffered from frost damage were captured by Unmanned Aerial Vehicle platform. Pearson correlation analysis was employed to select FDI-sensitive features from RGB and multispectral images. Then the models were established for different FDI-sensitive features based on sensor types and different groups according to lettuce colors using multiple linear regression, support vector machine and neural network algorithms, respectively. Results and discussion Digital number of blue and red channels, spectral reflectance at blue, red and near-infrared bands as well as six vegetation indexes (VIs) were found to be significantly related to the FDI of all lettuce groups. The high sensitivity of four modified VIs to frost damage of all lettuce groups was confirmed. The average accuracy of models were improved by 3% to 14% through a combination of multisource features. Color of lettuce had a certain impact on the monitoring of frost damage by FDI prediction models, because the accuracy of models based on green lettuce group were generally higher. The MULTISURCE-GREEN-NN model with R 2 of 0.715 and RMSE of 0.014 had the best performance, providing a high-throughput and efficient technical tool for frost damage investigation which will assist the identification of cold-resistant green lettuce germplasm and related breeding.

Why it matches plant phenotyping methodsUAV画像と機械学習を用いてレタスの霜害指数という植物状態を推定する高スループット手法を開発・評価しており、フェノタイピング手法が中心です。

abstractWe proposed a high-throughput method to estimate lettuce FDI based on remote sensing.

Temporal image sandwiches enable link between functional data analysis and deep learning for single-plant cotton senescence →

Abstract Abstract. Senescence is a highly ordered biological process involving resource redistribution away from ageing tissues that affects yield and quality in annuals and perennials. Images from 14 unmanned/unoccupied/uncrewed aerial system/vehicle (UAS, UAV and drone) flights captured the senescence window across two experiments while functional principal component analysis effectively reduced the dimensionality of temporal visual senescence ratings (VSRs) and two vegetation indices: the red chromatic coordinate (RCC) index and the transformed normalized difference green and red (TNDGR) index. Convolutional neural networks trained on temporally concatenated, or ‘sandwiched’, UAS images of individual cotton plants (Gossypium hirsutum L.), allowed single-plant analysis. The first functional principal component scores (FPC1) served as the regression target across six CNN models (M1–M6). Model performance was strongest for FPC1 scores from VSRs (R2 = 0.857 and 0.886 for M1 and M4), strong for TNDGR (R2 = 0.743 and 0.745 for M3 and M6), and strong-to-moderate for RCC index (R2 = 0.619 and 0.435 for M2 and M5), with deep learning attention of each model confirmed by activation of plant pixels within saliency maps. Single-plant UAS image analysis across time enabled translatable implementations of high-throughput phenotyping by linking deep learning with functional data analysis. This has applications for fundamental plant biology, monitoring orchards or other spaced plantings, plant breeding, and genetic research.

Why it matches plant phenotyping methods単一個体の綿花について、時系列UAS画像とCNN・機能的データ解析を用いて老化表現型を推定する方法が研究の中心であり、性能評価も実施している。

abstractConvolutional neural networks trained on temporally concatenated, or ‘sandwiched’, UAS images of individual cotton plants (Gossypium hirsutum L.), allowed single-plant analysis.

A pulse crop dataset of agronomic traits and multispectral images from multiple environments. →

Crop yield potential in breeding trials can be captured using unmanned aerial vehicle (UAV) based multispectral imagery. Several digital traits or phenotypes such as vegetation indices can represent canopy crop vigor and overall plant health, which can be used to evaluate differences in performance across varieties in crop breeding programs. This dataset contains agronomic data for named cultivars and breeding lines of spring-sown dry pea and chickpea, and over 275 multispectral images from advanced and preliminary breeding trials. The breeding trials were located at three locations in the "Palouse" region of Eastern Washington and Northern Idaho of the United States across 2017, 2018 and 2019 cropping seasons. The multispectral images were captured using a UAV integrated with a 5-band multispectral camera at multiple time points from early vegetative growth through pod development stages during each cropping season. This dataset details seed yield information from trials of dry peas and chickpea that were obtained from each location, as well as additional agronomic and phenological data recorded at one location (mostly Pullman, WA) for each cropping season. The dataset also includes 20-78 megabytes (MB) Tagged Image Format (TIF) uncalibrated stitched orthomosaic images generated from the photogrammetric software. The images can be processed using any convenient image processing algorithm to obtain vegetation indices and other useful information.

Why it matches plant phenotyping methodsUAVマルチスペクトル画像と抽出可能なデジタル形質を含む、育種利用可能な植物表現型データセットとして構築・公開されているため。

abstractThis dataset contains agronomic data for named cultivars and breeding lines of spring-sown dry pea and chickpea, and over 275 multispectral images from advanced and preliminary breeding trials.

The Dissection of Nitrogen Response Traits Using Drone Phenotyping and Dynamic Phenotypic Analysis to Explore N Responsiveness and Associated Genetic Loci in Wheat. →

Inefficient nitrogen (N) utilization in agricultural production has led to many negative impacts such as excessive use of N fertilizers, redundant plant growth, greenhouse gases, long-lasting toxicity in ecosystem, and even effect on human health, indicating the importance to optimize N applications in cropping systems. Here, we present a multiseasonal study that focused on measuring phenotypic changes in wheat plants when they were responding to different N treatments under field conditions. Powered by drone-based aerial phenotyping and the AirMeasurer platform, we first quantified 6 N response-related traits as targets using plot-based morphological, spectral, and textural signals collected from 54 winter wheat varieties. Then, we developed dynamic phenotypic analysis using curve fitting to establish profile curves of the traits during the season, which enabled us to compute static phenotypes at key growth stages and dynamic phenotypes (i.e., phenotypic changes) during N response. After that, we combine 12 yield production and N-utilization indices manually measured to produce N efficiency comprehensive scores (NECS), based on which we classified the varieties into 4 N responsiveness (i.e., N-dependent yield increase) groups. The NECS ranking facilitated us to establish a tailored machine learning model for N responsiveness-related varietal classification just using N-response phenotypes with high accuracies. Finally, we employed the Wheat55K SNP Array to map single-nucleotide polymorphisms using N response-related static and dynamic phenotypes, helping us explore genetic components underlying N responsiveness in wheat. In summary, we believe that our work demonstrates valuable advances in N response-related plant research, which could have major implications for improving N sustainability in wheat breeding and production.

Why it matches plant phenotyping methodsドローン画像とAirMeasurerを用いた作物形態・スペクトル・テクスチャ形質の取得、および曲線フィッティングによる動的表現型抽出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応用・解析である。

abstractPowered by drone-based aerial phenotyping and the AirMeasurer platform, we first quantified 6 N response-related traits as targets using plot-based morphological, spectral, and textural signals collected from 54 winter wheat varieties.

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

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

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

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

"Flower power": how flowering affects spectral diversity metrics and their relationship with plant diversity →

Abstract Biodiversity monitoring is constrained by cost- and labour-intensive field sampling methods. Increasing evidence suggests that remotely sensed spectral diversity (SD) is linked to plant diversity, holding promise for monitoring applications. However, studies testing such a relationship reported conflicting findings, especially in challenging ecosystems such as grasslands, due to their high temporal dynamism and variety. It follows that a thorough investigation of the key factors, such as the metrics applied (i.e., continuous, categorical) and phenology (e.g., flowering), influencing such a relationship is necessary. Thus, this study aims to assess the applicability of SD for plant diversity monitoring at the local scale by testing six different SD metrics while considering the effect of the presence of flowering on the relationship and resampling the original data to assess how spatial resolution affects the results. Taxonomic diversity was calculated based on data collected in 159 plots with 1.5 m ×1.5 m experimental mesic grassland communities. Spectral information was collected using a UAV-borne sensor measuring reflectance across six bands in the visible and near-infrared range at ∼2 cm spatial resolution. Our results show that, in the presence of flowering, the relationship is significant and positive only when SD is calculated using categorical metrics. Despite the observed significance, the variance explained by the models had very low values, with no evident differences when resampling spectral data to coarser pixel sizes. Such findings suggest that new insights into the possible confounding effects on the SD∼plant diversity in grassland communities are needed to use SD for monitoring purposes.

Why it matches plant phenotyping methodsUAV搭載センサーによるスペクトル情報から植物多様性を推定し、複数のスペクトル多様性指標と空間解像度を比較検証しているため、植物フェノタイピング手法の応用・評価が中心です。

abstractThus, this study aims to assess the applicability of SD for plant diversity monitoring at the local scale by testing six different SD metrics

G-DMD: A Gated Recurrent Unit-Based Digital Elevation Model for Crop Height Measurement from Multispectral Drone Images →

Crop height is a vital indicator of growth conditions. Traditional drone image-based crop height measurement methods primarily rely on calculating the difference between the Digital Elevation Model (DEM) and the Digital Terrain Model (DTM). The calculation often needs more ground information, which remains labour-intensive and time-consuming. Moreover, the variations of terrains can further compromise the reliability of these ground models. In response to these challenges, we introduce G-DMD, a novel method based on Gated Recurrent Units (GRUs) using DEM and multispectral drone images to calculate the crop height. Our method enables the model to recognize the relation between crop height, elevation, and growth stages, eliminating reliance on DTM and thereby mitigating the effects of varied terrains. We also introduce a data preparation process to handle the unique DEM and multispectral image. Upon evaluation using a cotton dataset, our G-DMD method demonstrates a notable increase in accuracy for both maximum and average cotton height measurements, achieving a 34% and 72% reduction in Root Mean Square Error (RMSE) when compared with the traditional method. Compared to other combinations of model inputs, using DEM and multispectral drone images together as inputs results in the lowest error for estimating maximum cotton height. This approach demonstrates the potential of integrating deep learning techniques with drone-based remote sensing to achieve a more accurate, labour-efficient, and streamlined crop height assessment across varied terrains.

Why it matches plant phenotyping methodsドローンのDEM・マルチスペクトル画像から作物高を推定する手法を開発し、従来法と精度比較・検証しており、植物表現型取得が中心である。

abstractwe introduce G-DMD, a novel method based on Gated Recurrent Units (GRUs) using DEM and multispectral drone images to calculate the crop height.

UAV-based individual Chinese cabbage weight prediction using multi-temporal data. →

The use of unmanned aerial vehicles (UAVs) has facilitated crop canopy monitoring, enabling yield prediction by integrating regression models. However, the application of UAV-based data to individual-level harvest weight prediction is limited by the effectiveness of obtaining individual features. In this study, we propose a method that automatically detects and extracts multitemporal individual plant features derived from UAV-based data to predict harvest weight. We acquired data from an experimental field sown with 1196 Chinese cabbage plants, using two cameras (RGB and multi-spectral) mounted on UAVs. First, we used three RGB orthomosaic images and an object detection algorithm to detect more than 95% of the individual plants. Next, we used feature selection methods and five different multi-temporal resolutions to predict individual plant weights, achieving a coefficient of determination (R 2 ) of 0.86 and a root mean square error (RMSE) of 436 g/plant. Furthermore, we achieved predictions with an R 2 greater than 0.72 and an RMSE less than 560 g/plant up to 53 days prior to harvest. These results demonstrate the feasibility of accurately predicting individual Chinese cabbage harvest weight using UAV-based data and the efficacy of utilizing multi-temporal features to predict plant weight more than one month prior to harvest.

Why it matches plant phenotyping methodsUAV画像から個体特徴を自動抽出し、収穫重量という植物形質を予測する手法が研究の中心であるため。

abstractwe propose a method that automatically detects and extracts multitemporal individual plant features derived from UAV-based data to predict harvest weight.

Probabilistic assimilation of optical satellite data with physiologically based growth functions improves crop trait time series reconstruction →

A sound understanding of plant growth is critical to maintaining future crop productivity under ongoing climate change. Remotely sensed time series of crop functional traits from optical satellite imagery are an invaluable tool for deriving appropriate management practices that facilitate risk mitigation and increase the resilience of agroecosystems. However, the availability of imagery is limited by atmospheric disturbances that cause large temporal gaps and noise in the trait time series. Therefore, time series reconstruction methods are required for accurate crop growth modelling. Physiological priors, such as the fact that plant growth is mainly controlled by a few environmental covariates, among which air temperature plays a prominent role, represent a promising approach to improve the representation of crop growth. Here, a novel approach is proposed that combines Sentinel-2 Green Leaf Area Index (GLAI) observations with three dose response curve approaches describing the a priori physiological relationship between growth and temperature in winter wheat. A probabilistic ensemble Kalman filtering data assimilation scheme allows the combination of high temporal resolution air temperature data and satellite imagery, which also allows quantification of uncertainties. The proposed approach requires a smaller number of satellite observations compared to conventional remote sensing time series algorithms, making it suitable for agricultural areas with high cloud cover, and is considerably less complex than a mechanistic crop growth model. Validation was carried out using in-situ data collected on winter wheat plots in Switzerland in two consecutive years. The validation results suggest that the proposed assimilation of Sentinel-2 GLAI and temperature-response-based growth rates allows the reconstruction of physiologically meaningful GLAI time series. In particular, the systematic underestimation of high in-situ GLAI values (> 5 m^2 m^-2) often prevalent in purely remote sensing driven GLAI time series reconstruction was reduced. Thus, the proposed approach is advantageous compared to state-of-the-art remote sensing approach based on wide-spread logistic functions by means of physiological plausibility, fitting requirements and representation of high in-situ GLAI values. This has great potential to increase the reliability of remotely sensed crop productivity assessment.

Why it matches plant phenotyping methods衛星光学データと生理モデルを統合して作物GLAI時系列を再構築する手法を提案し、圃場データで検証しており、植物形質推定が研究の中心である。

abstractHere, a novel approach is proposed that combines Sentinel-2 Green Leaf Area Index (GLAI) observations with three dose response curve approaches describing the a priori physiological relationship between growth and temperature in winter wheat.

Optimizing Drone-Based Surface Models for Prescribed Fire Monitoring →

Prescribed burning and pyric herbivory play pivotal roles in mitigating wildfire risks, underscoring the imperative of consistent biomass monitoring for assessing fuel load reductions. Drone-derived surface models promise uninterrupted biomass surveillance but require complex photogrammetric processing. In a Mediterranean mountain shrubland burning experiment, we refined a Structure from Motion (SfM) and Multi-View Stereopsis (MVS) workflow to diminish biases in 3D modeling and RGB drone imagery-based surface reconstructions. Given the multitude of SfM-MVS processing alternatives, stringent quality oversight becomes paramount. We executed the following steps: (i) calculated Root Mean Square Error (RMSE) between Global Navigation Satellite System (GNSS) checkpoints to assess SfM sparse cloud optimization during georeferencing; (ii) evaluated elevation accuracy by comparing the Mean Absolute Error (MAE) of six surface and thirty terrain clouds against GNSS readings and known box dimensions; and (iii) complemented a dense cloud quality assessment with density metrics. Balancing overall accuracy and density, we selected surface and terrain cloud versions for high-resolution (2 cm pixel size) and accurate (DSM, MAE = 57 mm; DTM, MAE = 48 mm) Digital Elevation Model (DEM) generation. These DEMs, along with exceptional height and volume models (height, MAE = 12 mm; volume, MAE = 909.20 cm3) segmented by reference box true surface area, substantially contribute to burn impact assessment and vegetation monitoring in fire management systems.

Why it matches plant phenotyping methodsドローン画像のSfM-MVS処理を改良・精度検証し、植生の高さ・体積・バイオマス監視に用いる手法が研究の中心である。

abstractwe refined a Structure from Motion (SfM) and Multi-View Stereopsis (MVS) workflow to diminish biases in 3D modeling and RGB drone imagery-based surface reconstructions.

Panicle-Cloud: An Open and AI-Powered Cloud Computing Platform for Quantifying Rice Panicles from Drone-Collected Imagery to Enable the Classification of Yield Production in Rice. →

Rice ( Oryza sativa ) is an essential stable food for many rice consumption nations in the world and, thus, the importance to improve its yield production under global climate changes. To evaluate different rice varieties' yield performance, key yield-related traits such as panicle number per unit area (PNpM 2 ) are key indicators, which have attracted much attention by many plant research groups. Nevertheless, it is still challenging to conduct large-scale screening of rice panicles to quantify the PNpM 2 trait due to complex field conditions, a large variation of rice cultivars, and their panicle morphological features. Here, we present Panicle-Cloud, an open and artificial intelligence (AI)-powered cloud computing platform that is capable of quantifying rice panicles from drone-collected imagery. To facilitate the development of AI-powered detection models, we first established an open diverse rice panicle detection dataset that was annotated by a group of rice specialists; then, we integrated several state-of-the-art deep learning models (including a preferred model called Panicle-AI) into the Panicle-Cloud platform, so that nonexpert users could select a pretrained model to detect rice panicles from their own aerial images. We trialed the AI models with images collected at different attitudes and growth stages, through which the right timing and preferred image resolutions for phenotyping rice panicles in the field were identified. Then, we applied the platform in a 2-season rice breeding trial to valid its biological relevance and classified yield production using the platform-derived PNpM 2 trait from hundreds of rice varieties. Through correlation analysis between computational analysis and manual scoring, we found that the platform could quantify the PNpM 2 trait reliably, based on which yield production was classified with high accuracy. Hence, we trust that our work demonstrates a valuable advance in phenotyping the PNpM 2 trait in rice, which provides a useful toolkit to enable rice breeders to screen and select desired rice varieties under field conditions.

Why it matches plant phenotyping methodsイネ穂数という植物形質をドローン画像から定量化するAIプラットフォーム、データセット、検出モデルを開発・検証しており、表現型取得手法が研究の中心である。

abstractwe present Panicle-Cloud, an open and artificial intelligence (AI)-powered cloud computing platform that is capable of quantifying rice panicles from drone-collected imagery.

Remote sensing continuity: a comparison of HTP platforms and potential challenges with field applications. →

In an era of climate change and increased environmental variability, breeders are looking for tools to maintain and increase genetic gain and overall efficiency. In recent years the field of high throughput phenotyping (HTP) has received increased attention as an option to meet this need. There are many platform options in HTP, but ground-based handheld and remote aerial systems are two popular options. While many HTP setups have similar specifications, it is not always clear if data from different systems can be treated interchangeably. In this research, we evaluated two handheld radiometer platforms, Cropscan MSR16R and Spectra Vista Corp (SVC) HR-1024i, as well as a UAS-based system with a Sentera Quad Multispectral Sensor. Each handheld radiometer was used for two years simultaneously with the unoccupied aircraft systems (UAS) in collecting winter wheat breeding trials between 2018-2021. Spectral reflectance indices (SRI) were calculated for each system. SRI heritability and correlation were analyzed in evaluating the platform and SRI usability for breeding applications. Correlations of SRIs were low against UAS SRI and grain yield while using the Cropscan system in 2018 and 2019. Dissimilarly, the SVC system in 2020 and 2021 produced moderate correlations across UAS SRI and grain yield. UAS SRI were consistently more heritable, with broad-sense heritability ranging from 0.58 to 0.80. Data standardization and collection windows are important to consider in ensuring reliable data. Furthermore, practical aspects and best practices for these HTP platforms, relative to applied breeding applications, are highlighted and discussed. The findings of this study can be a framework to build upon when considering the implementation of HTP technology in an applied breeding program.

Why it matches plant phenotyping methods複数の地上・UAS型HTPセンサープラットフォームを比較評価し、スペクトル形質の相関・遺伝率・標準化を検証しており、フェノタイピング手法が研究の中心です。

abstractwe evaluated two handheld radiometer platforms, Cropscan MSR16R and Spectra Vista Corp (SVC) HR-1024i, as well as a UAS-based system with a Sentera Quad Multispectral Sensor.

Drone-Based Harvest Data Prediction Can Reduce On-Farm Food Loss and Improve Farmer Income. →

On-farm food loss (i.e., grade-out vegetables) is a difficult challenge in sustainable agricultural systems. The simplest method to reduce the number of grade-out vegetables is to monitor and predict the size of all individuals in the vegetable field and determine the optimal harvest date with the smallest grade-out number and highest profit, which is not cost-effective by conventional methods. Here, we developed a full pipeline to accurately estimate and predict every broccoli head size ( n > 3,000) automatically and nondestructively using drone remote sensing and image analysis. The individual sizes were fed to the temperature-based growth model and predicted the optimal harvesting date. Two years of field experiments revealed that our pipeline successfully estimated and predicted the head size of all broccolis with high accuracy. We also found that a deviation of only 1 to 2 days from the optimal date can considerably increase grade-out and reduce farmer's profits. This is an unequivocal demonstration of the utility of these approaches to economic crop optimization and minimization of food losses.

Why it matches plant phenotyping methodsドローンリモートセンシングと画像解析により、個々のブロッコリー頭部サイズを自動・非破壊推定するパイプラインを開発・検証しており、植物形質取得が中心的です。

abstractwe developed a full pipeline to accurately estimate and predict every broccoli head size ( n > 3,000) automatically and nondestructively using drone remote sensing and image analysis.

Consumer-grade UAV imagery facilitates semantic segmentation of species-rich savanna tree layers. →

Conventional forest inventories are labour-intensive. This limits the spatial extent and temporal frequency at which woody vegetation is usually monitored. Remote sensing provides cost-effective solutions that enable extensive spatial coverage and high sampling frequency. Recent studies indicate that convolutional neural networks (CNNs) can classify woody forests, plantations, and urban vegetation at the species level using consumer-grade unmanned aerial vehicle (UAV) imagery. However, whether such an approach is feasible in species-rich savanna ecosystems remains unclear. Here, we tested whether small data sets of high-resolution RGB orthomosaics suffice to train U-Net, FC-DenseNet, and DeepLabv3 + in semantic segmentation of savanna tree species. We trained these models on an 18-ha training area and explored whether models could be transferred across space and time. These models could recognise trees in adjacent (mean F1-Score = 0.68) and distant areas (mean F1-Score = 0.61) alike. Over time, a change in plant morphology resulted in a decrease of model accuracy. Our results show that CNN-based tree mapping using consumer-grade UAV imagery is possible in savanna ecosystems. Still, larger and more heterogeneous data sets can further improve model robustness to capture variation in plant morphology across time and space.

Why it matches plant phenotyping methodsUAV画像とCNNによる樹木の空間的な認識・セグメンテーション手法を開発・評価し、植物形態の時空間変動に対する頑健性も検証しているため、手法が中心である。

abstractwe tested whether small data sets of high-resolution RGB orthomosaics suffice to train U-Net, FC-DenseNet, and DeepLabv3 + in semantic segmentation of savanna tree species.

Analysis of key factors affecting maize tassels detection and construction of shared dataset based on UAV →

Background: Rapid and accurate detection of tassels is of great significance for maize breeding, seed production and the acquisition of key growth stage. To liberate manpower and improve the efficiency of production management, many automatic detection methods with acceptable accuracy have been proposed. However, images acquisition parameters of these methods were quite different, so they cannot provide an operable standard for practical applications. In this study, based on multi-temporal unmanned aerial vehicle (UAV) RGB images with maize flowering stage, we created UAV Maize Tassel Detection (UAVMTD) dataset, and used Faster R-CNN to answer what are the key factors affecting detection accuracy from two aspects of efficient use of samples and data acquisition standards. Based on the detection results, we estimated tasseling date of different plots and analyzed varieties’ differences. Results: The results show that model performance would not be greatly affected before the amount of training data changed by orders of magnitude, but it can be improved effectively by adjusting sub-images’ sizes, and the final model was selected with AP@0.5IOU was 0.916; images obtained at 12 pm were more suitable for tassels detection, AP@0.5IOU, recall and precision were 3%, 2% and 6% higher than that at 8 am; optimal spatial resolution was around 1cm for tassels detection by considering the recognition effect and data acquisition efficiency. Conclusions: This study analyzed key factors affecting maize tassels detection and provided a reasonable reference for future applications, which is helpful to screen out varieties from large-scale breeding materials.

Why it matches plant phenotyping methodsUAV画像によるトウモロコシ雄穂検出のデータセット構築、検出精度の検証、撮影条件の最適化を中心とする植物フェノタイピング研究である。

abstractwe created UAV Maize Tassel Detection (UAVMTD) dataset, and used Faster R-CNN to answer what are the key factors affecting detection accuracy

Digital Phenotyping in Plant Breeding: Evaluating Relative Maturity, Stand Count, and Plant Height in Dry Beans (Phaseolus vulgaris L.) via RGB Drone-Based Imagery and Deep Learning Approaches →

Abstract Background Significant effort has been made in manually tracking plant maturity and to measure early-stage plant density, and crop height in experimental breeding plots. Agronomic traits such as relative maturity (RM), stand count (SC) and plant height (PH) are essential to cultivar development, production recommendations and management practices. The use of RGB images collected via drones may replace traditional measurements in field trials with improved throughput, accuracy, and reduced cost. Recent advances in deep learning (DL) approaches have enabled the development of automated high-throughput phenotyping (HTP) systems that can quickly and accurately measure target traits using low-cost RGB drones. In this study, a time series of drone images was employed to estimate dry bean relative maturity (RM) using a hybrid model combining Convolutional Neural Networks (CNN) and Long Short-Term Memory (LSTM) for features extraction and capturing the sequential behavior of time series data. The performance of the Faster-RCNN object detection algorithm was also examined for stand count (SC) assessment during the early growth stages of dry beans. Various factors, such as flight frequencies, image resolution, and data augmentation, along with pseudo-labeling techniques, were investigated to enhance the performance and accuracy of DL models. Traditional methods involving pre-processing of images were also compared to the DL models employed in this study. Moreover, plant architecture was analyzed to extract plant height (PH) using digital surface model (DSM) and point cloud (PC) data sources. Results The CNN-LSTM model demonstrated high performance in predicting the RM of plots across diverse environments and flight datasets, regardless of image size or flight frequency. The DL model consistently outperformed the pre-processing images approach using traditional analysis (LOESS and SEG models), particularly when comparing errors using mean absolute error (MAE), providing less than two days of error in prediction across all environments. When growing degree days (GDD) data was incorporated into the CNN-LSTM model, the performance improved in certain environments, especially under unfavorable environmental conditions or weather stress. However, in other environments, the CNN-LSTM model performed similarly to or slightly better than the CNN-LSTM + GDD model. Consequently, incorporating GDD may not be necessary unless weather conditions are extreme. The Faster R-CNN model employed in this study was successful in accurately identifying bean plants at early growth stages, with correlations between the predicted SC and ground truth (GT) measurements of 0.8. The model performed consistently across various flight altitudes, and its accuracy was better compared to traditional segmentation methods using pre-processing images in OpenCV and the watershed algorithm. An appropriate growth stage should be carefully targeted for optimal results, as well as precise boundary box annotations. On average, the PC data source marginally outperformed the CSM/DSM data to estimating PH, with average correlation results of 0.55 for PC and 0.52 for CSM/DSM. The choice between them may depend on the specific environment and flight conditions, as the PH performance estimation is similar in the analyzed scenarios. However, the ground and vegetation elevation estimates can be optimized by deploying different thresholds and metrics to classify the data and perform the height extraction, respectively. Conclusions The results demonstrate that the CNN-LSTM and Faster R-CNN deep learning models outperforms other state-of-the-art techniques to quantify, respectively, RM and SC. The subtraction method proposed for estimating PH in the absence of accurate ground elevation data yielded results comparable to the difference-based method. In addition, open-source software developed to conduct the PH and RM analyses can contribute greatly to the phenotyping community.

Why it matches plant phenotyping methodsRGBドローン画像と深層学習を用いて、乾燥豆の成熟期、株数、草高を推定する手法を開発・比較・検証しており、表現型取得が研究の中心である。

abstractThe use of RGB images collected via drones may replace traditional measurements in field trials with improved throughput, accuracy, and reduced cost.

TreeFormer: a Semi-Supervised Transformer-based Framework for Tree Counting from a Single High Resolution Image →

Automatic tree density estimation and counting using single aerial and satellite images is a challenging task in photogrammetry and remote sensing, yet has an important role in forest management. In this paper, we propose the first semisupervised transformer-based framework for tree counting which reduces the expensive tree annotations for remote sensing images. Our method, termed as TreeFormer, first develops a pyramid tree representation module based on transformer blocks to extract multi-scale features during the encoding stage. Contextual attention-based feature fusion and tree density regressor modules are further designed to utilize the robust features from the encoder to estimate tree density maps in the decoder. Moreover, we propose a pyramid learning strategy that includes local tree density consistency and local tree count ranking losses to utilize unlabeled images into the training process. Finally, the tree counter token is introduced to regulate the network by computing the global tree counts for both labeled and unlabeled images. Our model was evaluated on two benchmark tree counting datasets, Jiangsu, and Yosemite, as well as a new dataset, KCL-London, created by ourselves. Our TreeFormer outperforms the state of the art semi-supervised methods under the same setting and exceeds the fully-supervised methods using the same number of labeled images. The codes and datasets are available at https://github.com/HAAClassic/TreeFormer.

Why it matches plant phenotyping methods樹木の個体数・密度という植物状態を航空・衛星画像から推定する画像解析手法を開発し、複数データセット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。

abstractAutomatic tree density estimation and counting using single aerial and satellite images is a challenging task

Data on three-year flowering intensity monitoring in an apple orchard: A collection of RGB images acquired from unmanned aerial vehicles. →

There is a growing body of literature that recognises the importance of UAVs in precision agriculture tasks. Currently, flowering thinning tasks in orchard management rely on the decisions derived from time-consuming manual flower cluster counting in the field by an agrotechnician. Yet it is hard to guarantee the counting accuracy due to numerous human factors. The present dataset contains UAV images during the full blooming period of an apple orchard for three consecutive years, 2018, 2019, and 2020. It is directly linked to a research article entitled "Feasibility assessment of tree-level flower intensity quantification from UAV RGB imagery: A triennial study in an apple orchard". The data collection site was an apple orchard located at Randwijk, Overbetuwe, The Netherlands (51.938, 5.7068 in WGS84 UTM 31U). Moreover, the flower cluster number and floridity ground truth are also provided in one row from the orchard. The UAV flights were conducted with different flying altitudes, camera resolutions, and lighting conditions. This dataset aims to support researchers focussing on remote sensing, machine vision, deep learning, and image classification, and the stakeholders interested in precision horticulture and orchard management. It can be used for flowering intensity estimation and prediction, and spatial and temporal flowering variability mapping by using digital photogrammetry and 3D reconstruction.

Why it matches plant phenotyping methodsリンゴ樹の開花強度という植物形質をUAV RGB画像から推定するための3年間の画像・地上真値データセットであり、再利用可能なフェノタイピング基盤として中心的です。

abstractThe present dataset contains UAV images during the full blooming period of an apple orchard for three consecutive years, 2018, 2019, and 2020.

Image-based phenomic prediction can provide valuable decision support in wheat breeding. →

KEY MESSAGE: Genotype-by-environment interactions of secondary traits based on high-throughput field phenotyping are less complex than those of target traits, allowing for a phenomic selection in unreplicated early generation trials. Traditionally, breeders' selection decisions in early generations are largely based on visual observations in the field. With the advent of affordable genome sequencing and high-throughput phenotyping technologies, enhancing breeders' ratings with such information became attractive. In this research, it is hypothesized that G[Formula: see text]E interactions of secondary traits (i.e., growth dynamics' traits) are less complex than those of related target traits (e.g., yield). Thus, phenomic selection (PS) may allow selecting for genotypes with beneficial response-pattern in a defined population of environments. A set of 45 winter wheat varieties was grown at 5 year-sites and analyzed with linear and factor-analytic (FA) mixed models to estimate G[Formula: see text]E interactions of secondary and target traits. The dynamic development of drone-derived plant height, leaf area and tiller density estimations was used to estimate the timing of key stages, quantities at defined time points and temperature dose-response curve parameters. Most of these secondary traits and grain protein content showed little G[Formula: see text]E interactions. In contrast, the modeling of G[Formula: see text]E for yield required a FA model with two factors. A trained PS model predicted overall yield performance, yield stability and grain protein content with correlations of 0.43, 0.30 and 0.34. While these accuracies are modest and do not outperform well-trained GS models, PS additionally provided insights into the physiological basis of target traits. An ideotype was identified that potentially avoids the negative pleiotropic effects between yield and protein content.

Why it matches plant phenotyping methodsドローン画像から植物高・葉面積・分げつ密度を推定し、これらを用いたフェノミック選抜モデルを評価しており、形質取得と解析ワークフローが研究の中心である。

abstractThe dynamic development of drone-derived plant height, leaf area and tiller density estimations was used to estimate the timing of key stages, quantities at defined time points and temperature dose-response curve parameters.

Row selection in remote sensing from four-row plots of maize and sorghum based on repeatability and predictive modeling. →

Remote sensing enables the rapid assessment of many traits that provide valuable information to plant breeders throughout the growing season to improve genetic gain. These traits are often extracted from remote sensing data on a row segment (rows within a plot) basis enabling the quantitative assessment of any row-wise subset of plants in a plot, rather than a few individual representative plants, as is commonly done in field-based phenotyping. Nevertheless, which rows to include in analysis is still a matter of debate. The objective of this experiment was to evaluate row selection and plot trimming in field trials conducted using four-row plots with remote sensing traits extracted from RGB (red-green-blue), LiDAR (light detection and ranging), and VNIR (visible near infrared) hyperspectral data. Uncrewed aerial vehicle flights were conducted throughout the growing seasons of 2018 to 2021 with data collected on three years of a sorghum experiment and two years of a maize experiment. Traits were extracted from each plot based on all four row segments (RS) (RS1234), inner rows (RS23), outer rows (RS14), and individual rows (RS1, RS2, RS3, and RS4). Plot end trimming of 40 cm was an additional factor tested. Repeatability and predictive modeling of end-season yield were used to evaluate performance of these methodologies. Plot trimming was never shown to result in significantly different outcomes from non-trimmed plots. Significant differences were often observed based on differences in row selection. Plots with more row segments were often favorable for increasing repeatability, and excluding outer rows improved predictive modeling. These results support long-standing principles of experimental design in agronomy and should be considered in breeding programs that incorporate remote sensing.

Why it matches plant phenotyping methodsRGB・LiDAR・VNIRリモートセンシングによる作物形質抽出について、行選択とプロットトリミングを反復性・収量予測で評価しており、フェノタイピング手法の技術評価が中心である。

abstractThe objective of this experiment was to evaluate row selection and plot trimming in field trials conducted using four-row plots with remote sensing traits extracted from RGB (red-green-blue), LiDAR (light detection and ranging), and VNIR (visible near infrared) hyperspectral data.

CropQuant-Air: an AI-powered system to enable phenotypic analysis of yield- and performance-related traits using wheat canopy imagery collected by low-cost drones. →

As one of the most consumed stable foods around the world, wheat plays a crucial role in ensuring global food security. The ability to quantify key yield components under complex field conditions can help breeders and researchers assess wheat’s yield performance effectively. Nevertheless, it is still challenging to conduct large-scale phenotyping to analyse canopy-level wheat spikes and relevant performance traits, in the field and in an automated manner. Here, we present CropQuant-Air, an AI-powered software system that combines state-of-the-art deep learning (DL) models and image processing algorithms to enable the detection of wheat spikes and phenotypic analysis using wheat canopy images acquired by low-cost drones. The system includes the YOLACT-Plot model for plot segmentation, an optimised YOLOv7 model for quantifying the spike number per m2(SNpM2) trait, and performance-related trait analysis using spectral and texture features at the canopy level. Besides using our labelled dataset for model training, we also employed the Global Wheat Head Detection dataset to incorporate varietal features into the DL models, facilitating us to perform reliable yield-based analysis from hundreds of varieties selected from main wheat production regions in China. Finally, we employed the SNpM2and performance traits to develop a yield classification model using the Extreme Gradient Boosting (XGBoost) ensemble and obtained significant positive correlations between the computational analysis results and manual scoring, indicating the reliability of CropQuant-Air. To ensure that our work could reach wider researchers, we created a graphical user interface for CropQuant-Air, so that non-expert users could readily use our work. We believe that our work represents valuable advances in yield-based field phenotyping and phenotypic analysis, providing useful and reliable toolkits to enable breeders, researchers, growers, and farmers to assess crop-yield performance in a cost-effective approach.

Why it matches plant phenotyping methodsドローン画像からコムギ穂数や収量関連形質を抽出・検証するAIソフトウェア／表現型解析システムが研究の中心であり、植物フェノタイピング手法に該当する。

abstractwe present CropQuant-Air, an AI-powered software system that combines state-of-the-art deep learning (DL) models and image processing algorithms to enable the detection of wheat spikes and phenotypic analysis using wheat canopy images acquired by low-cost drones.

Multi-modal deep learning improves grain yield prediction in wheat breeding by fusing genomics and phenomics →

Motivation Developing new crop varieties with superior performance is highly important to ensure robust and sustainable global food security. The speed of variety development is limited by long field cycles and advanced generation selections in plant breeding programs. While methods to predict yield from genotype or phenotype data have been proposed, improved performance and integrated models are needed. Results We propose a machine learning model that leverages both genotype and phenotype measurements by fusing genetic variants with multiple data sources collected by unmanned aerial systems. We use a deep multiple instance learning framework with an attention mechanism that sheds light on the importance given to each input during prediction, enhancing interpretability. Our model reaches 0.754 ± 0.024 Pearson correlation coefficient when predicting yield in similar environmental conditions; a 34.8% improvement over the genotype-only linear baseline (0.559 ± 0.050). We further predict yield on new lines in an unseen environment using only genotypes, obtaining a prediction accuracy of 0.386 ± 0.010, a 13.5% improvement over the linear baseline. Our multi-modal deep learning architecture efficiently accounts for plant health and environment, distilling the genetic contribution and providing excellent predictions. Yield prediction algorithms leveraging phenotypic observations during training therefore promise to improve breeding programs, ultimately speeding up delivery of improved varieties. Availability and implementation Available at https://github.com/BorgwardtLab/PheGeMIL (code) and https://doi.org/doi:10.5061/dryad.kprr4xh5p (data).

Why it matches plant phenotyping methodsUAS由来の植物表現型データを用いて収量を推定する深層学習手法を開発・評価しており、表現型の取得・統合・推定が研究の中心である。

abstractWe propose a machine learning model that leverages both genotype and phenotype measurements by fusing genetic variants with multiple data sources collected by unmanned aerial systems.

A Generic Model to Estimate Wheat LAI over Growing Season Regardless of the Soil-Type Background. →

It is valuable to develop a generic model that can accurately estimate the leaf area index (LAI) of wheat from unmanned aerial vehicle-based multispectral data for diverse soil backgrounds without any ground calibration. To achieve this objective, 2 strategies were investigated to improve our existing random forest regression (RFR) model, which was trained with simulations from a radiative transfer model (PROSAIL). The 2 strategies consisted of (a) broadening the reflectance domain of soil background to generate training data and (b) finding an appropriate set of indicators (band reflectance and/or vegetation indices) as inputs of the RFR model. The RFR models were tested in diverse soils representing varying soil types in Australia. Simulation analysis indicated that adopting both strategies resulted in a generic model that can provide accurate estimation for wheat LAI and is resistant to changes in soil background. From validation on 2 years of field trials, this model achieved high prediction accuracy for LAI over the entire crop cycle (LAI up to 7 m 2 m -2 ) (root mean square error (RMSE): 0.23 to 0.89 m 2 m -2 ), including for sparse canopy (LAI less than 0.3 m 2 m -2 ) grown on different soil types (RMSE: 0.02 to 0.25 m 2 m -2 ). The model reliably captured the seasonal pattern of LAI dynamics for different treatments in terms of genotypes, plant densities, and water-nitrogen managements (correlation coefficient: 0.82 to 0.98). With appropriate adaptations, this framework can be adjusted to any type of sensors to estimate various traits for various species (including but not limited to LAI of wheat) in associated disciplines, e.g., crop breeding, precision agriculture, etc.

Why it matches plant phenotyping methodsUAVマルチスペクトルデータから小麦LAIを推定する汎用モデルを開発し、異なる土壌・圃場試験で検証しており、植物形質取得手法が中心である。

abstractdevelop a generic model that can accurately estimate the leaf area index (LAI) of wheat from unmanned aerial vehicle-based multispectral data

Digital whole-community phenotyping: tracking morphological and physiological responses of plant communities to environmental changes in the field →

Plant traits are informative for ecosystem functions and processes and help to derive general rules and predictions about responses to environmental gradients, global change and perturbations. Ecological field studies often use 'low-throughput' methods to assess plant phenotypes and integrate species-specific traits to community-wide indices. In contrast, agricultural greenhouse or lab-based studies often employ 'high-throughput phenotyping' to assess plant individuals tracking their growth or fertilizer and water demand. In ecological field studies, remote sensing makes use of freely movable devices like satellites or unmanned aerial vehicles (UAVs) which provide large-scale spatial and temporal data. Adopting such methods for community ecology on a smaller scale may provide novel insights on the phenotypic properties of plant communities and fill the gap between traditional field measurements and airborne remote sensing. However, the trade-off between spatial resolution, temporal resolution and scope of the respective study requires highly specific setups so that the measurements fit the scientific question. We introduce small-scale, high-resolution digital automated phenotyping as a novel source of quantitative trait data in ecological field studies that provides complementary multi-faceted data of plant communities. We customized an automated plant phenotyping system for its mobile application in the field for 'digital whole-community phenotyping' (DWCP), capturing the 3-dimensional structure and multispectral information of plant communities. We demonstrated the potential of DWCP by recording plant community responses to experimental land-use treatments over two years. DWCP captured changes in morphological and physiological community properties in response to mowing and fertilizer treatments and thus reliably informed about changes in land-use. In contrast, manually measured community-weighted mean traits and species composition remained largely unaffected and were not informative about these treatments. DWCP proved to be an efficient method for characterizing plant communities, complements other methods in trait-based ecology, provides indicators of ecosystem states, and may help to forecast tipping points in plant communities often associated with irreversible changes in ecosystems.

Why it matches plant phenotyping methods植物群集の3次元構造とマルチスペクトル情報を取得する自動フェノタイピングシステムをフィールド用に改変・実証しており、植物表現型取得法が研究の中心である。

abstractWe introduce small-scale, high-resolution digital automated phenotyping as a novel source of quantitative trait data in ecological field studies

Automatic rape flower cluster counting method based on low-cost labelling and UAV-RGB images. →

Background The flowering period is a critical time for the growth of rape plants. Counting rape flower clusters can help farmers to predict the yield information of the corresponding rape fields. However, counting in-field is a time-consuming and labor-intensive task. To address this, we explored a deep learning counting method based on unmanned aircraft vehicle (UAV). The proposed method developed the in-field counting of rape flower clusters as a density estimation problem. It is different from the object detection method of counting the bounding boxes. The crucial step of the density map estimation using deep learning is to train a deep neural network that maps from an input image to the corresponding annotated density map. Results We explored a rape flower cluster counting network series: RapeNet and RapeNet+. A rectangular box labeling-based rape flower clusters dataset (RFRB) and a centroid labeling-based rape flower clusters dataset (RFCP) were used for network model training. To verify the performance of RapeNet series, the paper compares the counting result with the real values of manual annotation. The average accuracy (Acc), relative root mean square error (rrMSE) and [Formula: see text] of the metrics are up to 0.9062, 12.03 and 0.9635 on the dataset RFRB, and 0.9538, 5.61 and 0.9826 on the dataset RFCP, respectively. The resolution has little influence for the proposed model. In addition, the visualization results have some interpretability. Conclusions Extensive experimental results demonstrate that the RapeNet series outperforms other state-of-the-art counting approaches. The proposed method provides an important technical support for the crop counting statistics of rape flower clusters in field.

Why it matches plant phenotyping methodsUAV-RGB画像から菜種の花房数という植物器官形質を推定する深層学習手法を開発・評価しており、フェノタイピング手法が中心である。

abstractwe explored a deep learning counting method based on unmanned aircraft vehicle (UAV).

High-precision plant height measurement by drone with RTK-GNSS and single camera for real-time processing →

Conventional crop height measurements performed using aerial drone images require 3D reconstruction results of several aerial images obtained through structure from motion. Therefore, they require extensive computation time and their measurement accuracy is not high; if the 3D reconstruction result fails, several aerial photos must be captured again. To overcome these challenges, this study proposes a high-precision measurement method that uses a drone equipped with a monocular camera and real-time kinematic global navigation satellite system (RTK-GNSS) for real-time processing. This method performs high-precision stereo matching based on long-baseline lengths (approximately 1 m) during the flight by linking the RTK-GNSS and aerial image capture points. As the baseline length of a typical stereo camera is fixed, once the camera is calibrated on the ground, it does not need to be calibrated again during the flight. However, the proposed system requires quick calibration in flight because the baseline length is not fixed. A new calibration method that is based on zero-mean normalized cross-correlation and two stages least square method, is proposed to further improve the accuracy and stereo matching speed. The proposed method was compared with two conventional methods in natural world environments. It was observed that error rates reduced by 62.2% and 69.4%, for flight altitudes between 10 and 20 m respectively. Moreover, a depth resolution of 1.6 mm and reduction of 44.4% and 63.0% in the error rates were achieved at an altitude of 4.1 m, and the execution time was 88 ms for images with a size of 5472 × 3468 pixels, which is sufficiently fast for real-time measurement.

Why it matches plant phenotyping methodsドローン画像とRTK-GNSSを用いた植物高のリアルタイム測定法を開発し、既存法との精度・処理時間比較で検証しており、植物表現型取得が研究の中心である。

abstractA new calibration method that is based on zero-mean normalized cross-correlation and two stages least square method, is proposed to further improve the accuracy and stereo matching speed.

Lightweight Detection System with Global Attention Network (GloAN) for Rice Lodging. →

Rice lodging seriously affects rice quality and production. Traditional manual methods of detecting rice lodging are labour-intensive and can result in delayed action, leading to production loss. With the development of the Internet of Things (IoT), unmanned aerial vehicles (UAVs) provide imminent assistance for crop stress monitoring. In this paper, we proposed a novel lightweight detection system with UAVs for rice lodging. We leverage UAVs to acquire the distribution of rice growth, and then our proposed global attention network (GloAN) utilizes the acquisition to detect the lodging areas efficiently and accurately. Our methods aim to accelerate the processing of diagnosis and reduce production loss caused by lodging. The experimental results show that our GloAN can lead to a significant increase in accuracy with negligible computational costs. We further tested the generalization ability of our GloAN and the results show that the GloAN generalizes well in peers' models (Xception, VGG, ResNet, and MobileNetV2) with knowledge distillation and obtains the optimal mean intersection over union (mIoU) of 92.85%. The experimental results show the flexibility of GloAN in rice lodging detection.

Why it matches plant phenotyping methodsUAV画像からイネの倒伏領域（植物状態）を抽出する軽量な検出システムとGloANを提案・評価しており、表現型取得・推定手法が中心である。

abstractwe proposed a novel lightweight detection system with UAVs for rice lodging.

Using High-Resolution UAV Imaging to Measure Canopy Height of Diverse Cover Crops and Predict Biomass →

Remote-sensing data has become essential for site-specific farming methods. It is also a powerful tool for monitoring the agroecosystem services offered by integrating cover crops (CC) into crop rotations. This study presents a method to determine the canopy height (CH), defined as the average height of the crop stand surface, including tops and gaps, of heterogeneous and multi-species CC using commercial unmanned aerial vehicles (UAVs). Images captured with red–green–blue cameras mounted on UAVs in two missions varying in ground sample distances were used as input for generating three-dimensional point clouds using the structure-from-motion approach. These point clouds were then compared to manual ground measurements. The results showed that the agreement between the methods was closest when CC presented dense and smooth canopies. However, stands with rough canopies or gaps showed substantial differences between the UAV method and ground measurements. We conclude that the UAV method is substantially more precise and accurate in determining CH than measurements taken with a ruler since the UAV introduces additional dimensions with greatly increased resolution. CH can be a reliable indicator of biomass yield, but no differences between the investigated methods were found, probably due to allometric variations of different CC species. We propose the presented UAV method as a promising tool to include site-specific information on CC in crop production strategies.

Why it matches plant phenotyping methodsUAV画像とSfM点群を用いて被覆作物の群落高を推定する手法を提示し、地上測定と比較検証しており、植物形質取得法が研究の中心である。

abstractThis study presents a method to determine the canopy height (CH), defined as the average height of the crop stand surface, including tops and gaps, of heterogeneous and multi-species CC using commercial unmanned aerial vehicles (UAVs).

PhytoOracle: Scalable, modular phenomics data processing pipelines →

As phenomics data volume and dimensionality increase due to advancements in sensor technology, there is an urgent need to develop and implement scalable data processing pipelines. Current phenomics data processing pipelines lack modularity, extensibility, and processing distribution across sensor modalities and phenotyping platforms. To address these challenges, we developed PhytoOracle (PO), a suite of modular, scalable pipelines for processing large volumes of field phenomics RGB, thermal, PSII chlorophyll fluorescence 2D images, and 3D point clouds. PhytoOracle aims to ( i ) improve data processing efficiency; ( ii ) provide an extensible, reproducible computing framework; and ( iii ) enable data fusion of multi-modal phenomics data. PhytoOracle integrates open-source distributed computing frameworks for parallel processing on high-performance computing, cloud, and local computing environments. Each pipeline component is available as a standalone container, providing transferability, extensibility, and reproducibility. The PO pipeline extracts and associates individual plant traits across sensor modalities and collection time points, representing a unique multi-system approach to addressing the genotype-phenotype gap. To date, PO supports lettuce and sorghum phenotypic trait extraction, with a goal of widening the range of supported species in the future. At the maximum number of cores tested in this study (1,024 cores), PO processing times were: 235 minutes for 9,270 RGB images (140.7 GB), 235 minutes for 9,270 thermal images (5.4 GB), and 13 minutes for 39,678 PSII images (86.2 GB). These processing times represent end-to-end processing, from raw data to fully processed numerical phenotypic trait data. Repeatability values of 0.39-0.95 (bounding area), 0.81-0.95 (axis-aligned bounding volume), 0.79-0.94 (oriented bounding volume), 0.83-0.95 (plant height), and 0.81-0.95 (number of points) were observed in Field Scanalyzer data. We also show the ability of PO to process drone data with a repeatability of 0.55-0.95 (bounding area).

Why it matches plant phenotyping methods植物フェノミクスのマルチモーダル画像・点群から形質を抽出する、スケーラブルで再現可能な処理パイプラインの開発と反復性評価が中心である。

abstractwe developed PhytoOracle (PO), a suite of modular, scalable pipelines for processing large volumes of field phenomics RGB, thermal, PSII chlorophyll fluorescence 2D images, and 3D point clouds.

Automatic counting of rapeseed inflorescences using deep learning method and UAV RGB imagery. →

Flowering is a crucial developing stage for rapeseed ( Brassica napus L.) plants. Flowers develop on the main and branch inflorescences of rapeseed plants and then grow into siliques. The seed yield of rapeseed heavily depends on the total flower numbers per area throughout the whole flowering period. The number of rapeseed inflorescences can reflect the richness of rapeseed flowers and provide useful information for yield prediction. To count rapeseed inflorescences automatically, we transferred the counting problem to a detection task. Then, we developed a low-cost approach for counting rapeseed inflorescences using YOLOv5 with the Convolutional Block Attention Module (CBAM) based on unmanned aerial vehicle (UAV) Red-Green-Blue (RGB) imagery. Moreover, we constructed a Rapeseed Inflorescence Benchmark (RIB) to verify the effectiveness of our model. The RIB dataset captured by DJI Phantom 4 Pro V2.0, including 165 plot images and 60,000 manual labels, is to be released. Experimental results showed that indicators R 2 for counting and the mean Average Precision (mAP) for location were over 0.96 and 92%, respectively. Compared with Faster R-CNN, YOLOv4, CenterNet, and TasselNetV2+, the proposed method achieved state-of-the-art counting performance on RIB and had advantages in location accuracy. The counting results revealed a quantitative dynamic change in the number of rapeseed inflorescences in the time dimension. Furthermore, a significant positive correlation between the actual crop yield and the automatically obtained rapeseed inflorescence total number on a field plot level was identified. Thus, a set of UAV- assisted methods for better determination of the flower richness was developed, which can greatly support the breeding of high-yield rapeseed varieties.

Why it matches plant phenotyping methodsUAV RGB画像と深層学習を用いてナタネの花序数を自動計数する手法を開発し、ベンチマークデータセットで検証しているため、植物表現型取得が中心である。

abstractwe developed a low-cost approach for counting rapeseed inflorescences using YOLOv5 with the Convolutional Block Attention Module (CBAM) based on unmanned aerial vehicle (UAV) Red-Green-Blue (RGB) imagery.

Rice Plant Counting, Locating, and Sizing Method Based on High-Throughput UAV RGB Images →

Rice plant counting is crucial for many applications in rice production, such as yield estimation, growth diagnosis, disaster loss assessment, etc. Currently, rice counting still heavily relies on tedious and time-consuming manual operation. To alleviate the workload of rice counting, we employed an UAV (unmanned aerial vehicle) to collect the RGB images of the paddy field. Then, we proposed a new rice plant counting, locating, and sizing method (RiceNet), which consists of one feature extractor frontend and 3 feature decoder modules, namely, density map estimator, plant location detector, and plant size estimator. In RiceNet, rice plant attention mechanism and positive-negative loss are designed to improve the ability to distinguish plants from background and the quality of the estimated density maps. To verify the validity of our method, we propose a new UAV-based rice counting dataset, which contains 355 images and 257,793 manual labeled points. Experiment results show that the mean absolute error and root mean square error of the proposed RiceNet are 8.6 and 11.2, respectively. Moreover, we validated the performance of our method with two other popular crop datasets. On these three datasets, our method significantly outperforms state-of-the-art methods. Results suggest that RiceNet can accurately and efficiently estimate the number of rice plants and replace the traditional manual method.

Why it matches plant phenotyping methodsUAV画像からイネ個体の位置・サイズ・個体数を推定する手法RiceNetを開発し、データセット構築と性能検証まで行っており、植物表現型取得が研究の中心です。

abstractwe proposed a new rice plant counting, locating, and sizing method (RiceNet)

Gap geometry, seasonality and associated losses of biomass – combining UAV imagery and field data from a Central Amazon forest →

Abstract. Understanding mechanisms of tree mortality and geometric patterns of canopy gaps is relevant for robust estimates of carbon stocks and balance in tropical forests, and for assessing how they are responding to climate change. We combined monthly RGB images acquired from an unmanned aerial vehicle with field surveys to identify gaps in an 18-ha permanent plot in an old-growth Central Amazon forest over a period of 28 months. In addition to detecting, we measured the size and shape of gaps, and analyzed their temporal variation and correlation with rainfall. We further described associated modes of tree mortality or branch fall and quantified associated losses of biomass. Overall, the sensitivity of gap detection differed between field surveys and imagery data. In total, we detected 32 gaps either in the images and field, ranging in area from 9 m2 to 835 m2. Relatively small gaps (

Why it matches plant phenotyping methodsUAV画像とフィールド調査を用いて森林キャノピーギャップを検出・定量化し、検出感度を比較しており、植物群落の構造状態を測定する方法の適用・検証が中心的です。

abstractWe combined monthly RGB images acquired from an unmanned aerial vehicle with field surveys to identify gaps

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

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

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

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

Prediction of heading date, culm length, and biomass from canopy-height-related parameters derived from time-series UAV observations of rice. →