1Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, USA
2Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA
3Quantitative Life Sciences Initiative, University of Nebraska-Lincoln, Lincoln, NE, USA
4Department of Mathematics and Statistics, Wright State University, Dayton, OH, USA
| Received 26 Nov 2019 |
Accepted 17 Jan 2020 |
Published 04 Feb 2020 |
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.
