RT Journal Article
SR Electronic
T1 Rhizonet: Image Segmentation for Plant Root in Hydroponic Ecosystem
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2023.11.20.565580
DO 10.1101/2023.11.20.565580
A1 Ushizima, Daniela
A1 Sordo, Zineb
A1 Andeer, Peter
A1 Sethian, James
A1 Northen, Trent
YR 2023
UL http://biorxiv.org/content/early/2023/11/21/2023.11.20.565580.abstract
AB Digital cameras have the ability to capture daily images of plant roots, allowing for the estimation of root biomass. However, the complexities of root structures and noisy image backgrounds pose challenges for advanced phenotyping. Manual segmentation methods are laborious and prone to errors, which hinders experiments involving several plants. This paper introduces Rhizonet, a supervised deep learning approach for semantic segmentation of plant root images. Rhizonet harnesses a Residual U-Net backbone to enhance prediction accuracy, incorporating a convex hull operation to precisely outline the largest connected component. The primary objective is to accurately segment the biomass of the roots and analyze their growth over time. The input data comprises color images of various plant samples within a hydroponic environment known as EcoFAB, subject to specific nutrition treatments. Validation tests demonstrate the robust generalization of the model across experiments. This research pioneers advances in root segmentation and phenotype analysis by standardizing processes and facilitating the analysis of thousands of images while reducing subjectivity. The proposed root segmentation algorithms contribute significantly to the precise assessment of the dynamics of root growth under diverse plant conditions.Competing Interest StatementThe authors have declared no competing interest.