Journal article
RootAnalyzer: A Cross-Section image analysis tool for automated characterization of root cells and tissues
PloS one, Vol.10(9), e0143270
2015
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.
Details
- Title
- RootAnalyzer: A Cross-Section image analysis tool for automated characterization of root cells and tissues
- Authors/Creators
- J. Chopin (Author/Creator)H. Laga (Author/Creator)C.Y. Huang (Author/Creator)Sigrid Heuer (Author/Creator)Stanley J. Miklavcic (Author/Creator)
- Publication Details
- PloS one, Vol.10(9), e0143270
- Publisher
- Public Library of Science
- Identifiers
- 991005542200807891
- Copyright
- © 2015 Chopin et al.
- Murdoch Affiliation
- Murdoch University
- Language
- English
- Resource Type
- Journal article
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- Collaboration types
- Domestic collaboration
- Citation topics
- 4 Electrical Engineering, Electronics & Computer Science
- 4.17 Computer Vision & Graphics
- 4.17.282 Image Segmentation
- Web Of Science research areas
- Plant Sciences
- ESI research areas
- Plant & Animal Science