Semantic Segmentation of Sorghum Using Hyperspectral Data Identifies Genetic Associations.

Abstract

This study describes the evaluation of a range of approaches to semantic segmentation of hyperspectral images of sorghum plants, classifying each pixel as either nonplant or belonging to one of the three organ types (leaf, stalk, panicle). While many current methods for segmentation focus on separating plant pixels from background, organ-specific segmentation makes it feasible to measure a wider range of plant properties. Manually scored training data for a set of hyperspectral images collected from a sorghum association population was used to train and evaluate a set of supervised classification models. Many algorithms show acceptable accuracy for this classification task. Algorithms trained on sorghum data are able to accurately classify maize leaves and stalks, but fail to accurately classify maize reproductive organs which are not directly equivalent to sorghum panicles. Trait measurements extracted from semantic segmentation of sorghum organs can be used to identify both genes known to be controlling variation in a previously measured phenotypes (e.g., panicle size and plant height) as well as identify signals for genes controlling traits not previously quantified in this population (e.g., stalk/leaf ratio). Organ level semantic segmentation provides opportunities to identify genes controlling variation in a wide range of morphological phenotypes in sorghum, maize, and other related grain crops.

Plant phenotyping relevance

イネ科植物のハイパースペクトル画像から器官をセグメンテーションし、形態形質を抽出する手法を開発・評価しており、表現型取得法が研究の中心です。

Code and data availability

The paper deposits its authors' analysis code, extracted phenotypes, and manually annotated sorghum/maize pixel data in a public GitHub repository, and its Zooniverse crowdsourcing project (used to generate the pixel annotations) is publicly accessible. Both are paper-specific, public, and actionable.