MatchPlant: An Open-Source Pipeline for UAV-Based Single-Plant Detection and Data Extraction
This provides a scalable framework for UAV-based plant-level analysis, addressing the need for efficient data-driven decision-making in plant breeding and agricultural monitoring, though it is incremental as it builds on existing object detection and geospatial methods.
The study tackled the problem of accurately identifying individual plants from UAV images for high-throughput phenotyping by developing MatchPlant, an open-source pipeline that achieved reliable detection performance with validation AP of 89.6% and test AP of 85.9%, and effectively extracted traits with high agreement to manual annotations (r = 0.87-0.97).
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.