Easy MPE: Extraction of quality microplot images for UAV-based high-throughput field phenotyping

Abstract

Microplot extraction (MPE) is a necessary image-processing step in unmanned aerial vehicle (UAV)-based research on breeding fields. At present, it is manually using ArcGIS, QGIS or other GIS-based software, but achieving the desired accuracy is time-consuming. We therefore developed an intuitive, easy-to-use semi-automatic program for MPE called Easy MPE to enable researchers and others to access reliable plot data UAV images of whole fields under variable field conditions. The program uses four major steps: (1). Binary segmentation, (2). Microplot extraction, (3). Production of *.shp files to enable further file manipulation, and (4). Projection of individual microplots generated from the orthomosaic back onto the raw aerial UAV images to preserve the image quality. Crop rows were successfully identified in all trial fields. The performance of proposed method was evaluated by calculating the intersection-over-union (IOU) ratio between microplots determined manually and by Easy MPE: The average IOU ({+/-}SD) of all trials was 91% ({+/-}3).

Plant phenotyping relevance

UAV画像から育種圃場のマイクロプロットを半自動抽出する画像処理手法を開発し、手動結果とのIoUで性能検証しており、植物表現型取得ワークフローが中心です。

Code and data availability

The paper's Easy MPE microplot-extraction Python code is publicly available in the authors' GitHub repository, linked in the Data Availability section.