PT  - JOURNAL ARTICLE
AU  - Yinglun Li
AU  - Weiliang Wen
AU  - Xinyu Guo
AU  - Zetao Yu
AU  - Shenghao Gu
AU  - Haipeng Yan
AU  - Chunjiang Zhao
TI  - High-throughput phenotyping analysis of maize at the seedling stage using end-to-end segmentation network
AID  - 10.1101/2020.10.19.345199
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 2020.10.19.345199
4099  - http://biorxiv.org/content/early/2020/10/19/2020.10.19.345199.short
4100  - http://biorxiv.org/content/early/2020/10/19/2020.10.19.345199.full
AB  - Image processing technologies are available for high-throughput acquisition and analysis of phenotypes for crop populations, which is of great significance for crop growth monitoring, evaluation of seedling condition, and cultivation management. However, existing methods rely on empirical segmentation thresholds, thus can have insufficient accuracy of extracted phenotypes. Taking maize as an example crop, we propose a phenotype extraction approach from top-view images at the seedling stage. An end-to-end segmentation network, named PlantU-net, which uses a small amount of training data, was explored to realize automatic segmentation of top-view images of a maize population at the seedling stage. Morphological and color related phenotypes were automatic extracted, including maize shoot coverage, circumscribed radius, aspect ratio, and plant azimuth plane angle. The results show that the approach can segment the shoots at the seedling stage from top-view images, obtained either from the UAV or ground high-throughput phenotyping platform. The average segmentation accuracy, recall rate, and F1 score are 0.96, 0.98, and 0.97, respectively. The extracted phenotypes, including maize shoot coverage, circumscribed radius, aspect ratio, and plant azimuth plane angle, are highly correlated with manual measurements (R2=0.96-0.99). This approach requires less training data and thus has better expansibility. It provides practical means for high-throughput phenotyping analysis of early growth stage crop populations.