title: RootAnalyzer: A Cross-Section Image Analysis Tool for Automated Characterization of Root Cells and Tissues.
abstract: The morphology of plant root anatomical features is a key factor in effective water and nutrient uptake. Existing techniques for phenotyping root anatomical traits are often based on manual or semi-automatic segmentation and annotation of microscopic images of root cross sections. In this article, we propose a fully automated tool, hereinafter referred to as RootAnalyzer, for efficiently extracting and analyzing anatomical traits from root-cross section images. Using a range of image processing techniques such as local thresholding and nearest neighbor identification, RootAnalyzer segments the plant root from the image's background, classifies and characterizes the cortex, stele, endodermis and epidermis, and subsequently produces statistics about the morphological properties of the root cells and tissues. We use RootAnalyzer to analyze 15 images of wheat plants and one maize plant image and evaluate its performance against manually-obtained ground truth data. The comparison shows that RootAnalyzer can fully characterize most root tissue regions with over 90% accuracy.
authors.affiliation: Phenomics and Bioinformatics Research Centre, University of South Australia, Mawson Lakes, South Australia, Australia.
authors.forename: Joshua
authors.initials: J
authors.lastname: Chopin
authors.affiliation: Phenomics and Bioinformatics Research Centre, University of South Australia, Mawson Lakes, South Australia, Australia.
authors.forename: Hamid
authors.initials: H
authors.lastname: Laga
authors.affiliation: The Australian Centre for Plant Functional Genomics, Urrbrae, South Australia, Australia.
authors.forename: Chun Yuan
authors.initials: CY
authors.lastname: Huang
authors.affiliation: The Australian Centre for Plant Functional Genomics, Urrbrae, South Australia, Australia.
authors.forename: Sigrid
authors.initials: S
authors.lastname: Heuer
authors.affiliation: Phenomics and Bioinformatics Research Centre, University of South Australia, Mawson Lakes, South Australia, Australia.
authors.forename: Stanley J
authors.initials: SJ
authors.lastname: Miklavcic
mesh_terms: D000465:Algorithms; D007091:Image Processing, Computer-Assisted; D018517:Plant Roots / Q000166:cytology*; D014908:Triticum / Q000166:cytology*; D052584:Xylem / Q000166:cytology; D003313:Zea mays / Q000166:cytology*