A robot-assisted imaging pipeline for tracking the growths of maize ear and silks in a high-throughput phenotyping platform

Abstract

Background In maize, silks are hundreds of filaments that simultaneously emerge from the ear for collecting pollen over a period of 1-7 days, which largely determines grain number especially under water deficit. Silk growth is a major trait for drought tolerance in maize, but its phenotyping is difficult at throughputs needed for genetic analyses. Results We have developed a reproducible pipeline that follows ear and silk growths every day for hundreds of plants, based on an ear detection algorithm that drives a robotized camera for obtaining detailed images of ears and silks. We first select, among 12 whole-plant side views, those best suited for detecting ear position. Images are segmented, the stem pixels are labelled and the ear position is identified based on changes in width along the stem. A mobile camera is then automatically positioned in real time at 30 cm from the ear, for a detailed picture in which silks are identified based on texture and colour. This allows analysis of the time course of ear and silk growths of thousands of plants. The pipeline was tested on a panel of 60 maize hybrids in the PHENOARCH phenotyping platform. Over 360 plants, ear position was correctly estimated in 86% of cases, before it could be visually assessed. Silk growth rate, estimated on all plants, decreased with time consistent with literature. The pipeline allowed clear identification of the effects of genotypes and water deficit on the rate and duration of silk growth. Conclusions The pipeline presented here, which combines computer vision, machine learning and robotics, provides a powerful tool for large-scale genetic analyses of the control of reproductive growth to changes in environmental conditions in a non-invasive and automatized way. It is available as Open Source software in the OpenAlea platform.

Plant phenotyping relevance

トウモロコシの穂と絹糸の成長形質を高スループットに取得する画像・ロボティクス・機械学習パイプラインを開発し、精度検証と遺伝子型・水分欠 deficitへの適用を行っているため、植物表現型計測法が中心である。

Code and data availability

The paper's ear/silk phenotyping pipeline code (eartrack) is publicly available on GitHub with documentation, and the authors deposited subsets of the whole-plant images and ear images with the Ilastik project/outputs on Zenodo. All are paper-specific, public, and actionable.