Easy MPE: Extraction of Quality Microplot Images for UAV-Based High-Throughput Field Phenotyping

Léa Tresch; Yue Mu; Atsushi Itoh; Akito Kaga; Kazunori Taguchi; Masayuki Hirafuji; Seishi Ninomiya; Wei Guo

doi:10.34133/2019/2591849

Easy MPE: Extraction of Quality Microplot Images for UAV-Based High-Throughput Field Phenotyping

Plant Phenomics. 2019 Nov 29:2019:2591849. doi: 10.34133/2019/2591849. eCollection 2019.

Authors

Léa Tresch^{1

2}, Yue Mu³, Atsushi Itoh⁴, Akito Kaga⁵, Kazunori Taguchi⁴, Masayuki Hirafuji¹, Seishi Ninomiya^{1

3}, Wei Guo¹

Affiliations

¹ International Field Phenomics Research Laboratory, Institute for Sustainable Agro-Ecosystem Services, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.
² Montpellier SupAgro, Montpellier, France.
³ Plant Phenomics Research Center, Nanjing Agricultural University, Nanjing, China.
⁴ Memuro Upland Farming Research Station, Hokkaido Agricultural Research Center, National Agriculture and Food Research Organization, Hokkaido, Japan.
⁵ Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba City, Ibaraki, Japan.

Abstract

Microplot extraction (PE) 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 semiautomatic 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 the 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).