Multi-feature data repository development and analytics for image cosegmentation in high-throughput plant phenotyping

PLoS One. 2021 Sep 2;16(9):e0257001. doi: 10.1371/journal.pone.0257001. eCollection 2021.

Abstract

Cosegmentation is a newly emerging computer vision technique used to segment an object from the background by processing multiple images at the same time. Traditional plant phenotyping analysis uses thresholding segmentation methods which result in high segmentation accuracy. Although there are proposed machine learning and deep learning algorithms for plant segmentation, predictions rely on the specific features being present in the training set. The need for a multi-featured dataset and analytics for cosegmentation becomes critical to better understand and predict plants' responses to the environment. High-throughput phenotyping produces an abundance of data that can be leveraged to improve segmentation accuracy and plant phenotyping. This paper introduces four datasets consisting of two plant species, Buckwheat and Sunflower, each split into control and drought conditions. Each dataset has three modalities (Fluorescence, Infrared, and Visible) with 7 to 14 temporal images that are collected in a high-throughput facility at the University of Nebraska-Lincoln. The four datasets (which will be collected under the CosegPP data repository in this paper) are evaluated using three cosegmentation algorithms: Markov random fields-based, Clustering-based, and Deep learning-based cosegmentation, and one commonly used segmentation approach in plant phenotyping. The integration of CosegPP with advanced cosegmentation methods will be the latest benchmark in comparing segmentation accuracy and finding areas of improvement for cosegmentation methodology.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Benchmarking
  • Cluster Analysis
  • Crop Production
  • Crops, Agricultural / genetics*
  • Deep Learning*
  • Fagopyrum / genetics*
  • Helianthus / genetics*
  • Humans
  • Image Processing, Computer-Assisted / methods*
  • Markov Chains
  • Phenotype*

Grants and funding

This material is based upon work supported by the National Science Foundation under Grant No. DGE-1735362. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation. Also, the authors acknowledge the support provided by the Agriculture and Food Research Initiative Grant number NEB-21-176 and NEB-21-166 from the USDA National Institute of Food and Agriculture, Plant Health and Production and Plant Products: Plant Breeding for Agricultural Production.