EasyIDP: A Python Package for Intermediate Data Processing in UAV-Based Plant Phenotyping

Abstract

Unmanned aerial vehicle (UAV) and structure from motion (SfM) photogrammetry techniques are widely used for field-based, high-throughput plant phenotyping nowadays, but some of the intermediate processes throughout the workflow remain manual. For example, geographic information system (GIS) software is used to manually assess the 2D/3D field reconstruction quality and cropping region of interests (ROIs) from the whole field. In addition, extracting phenotypic traits from raw UAV images is more competitive than directly from the digital orthomosaic (DOM). Currently, no easy-to-use tools are available to implement previous tasks for commonly used commercial SfM software, such as Pix4D and Agisoft Metashape. Hence, an open source software package called easy intermediate data processor (EasyIDP; MIT license) was developed to decrease the workload in intermediate data processing mentioned above. The functions of the proposed package include (1) an ROI cropping module, assisting in reconstruction quality assessment and cropping ROIs from the whole field, and (2) an ROI reversing module, projecting ROIs to relative raw images. The result showed that both cropping and reversing modules work as expected. Moreover, the effects of ROI height selection and reversed ROI position on raw images to reverse calculation were discussed. This tool shows great potential for decreasing workload in data annotation for machine learning applications.

Plant phenotyping relevance

UAV植物フェノタイピングの中間データ処理を担うオープンソースPythonパッケージを開発しており、ROI抽出・逆投影などの画像解析ワークフローが中心である。

Code and data availability

The paper's own analysis software, the EasyIDP Python package implementing the ROI cropping and reversing modules used for the UAV phenotyping measurements, is explicitly stated to be publicly downloadable under an MIT license from the authors' GitHub repository.