GiA Roots: software for the high throughput analysis of plant root system architecture
Open Access
- 26 July 2012
- journal article
- Published by Springer Science and Business Media LLC in BMC Plant Biology
- Vol. 12 (1), 116
- https://doi.org/10.1186/1471-2229-12-116
Abstract
Background: Characterizing root system architecture (RSA) is essential to understanding the development and function of vascular plants. Identifying RSA-associated genes also represents an underexplored opportunity for crop improvement. Software tools are needed to accelerate the pace at which quantitative traits of RSA are estimated from images of root networks. Results: We have developed GiA Roots (General Image Analysis of Roots), a semi-automated software tool designed specifically for the high-throughput analysis of root system images. GiA Roots includes user-assisted algorithms to distinguish root from background and a fully automated pipeline that extracts dozens of root system phenotypes. Quantitative information on each phenotype, along with intermediate steps for full reproducibility, is returned to the end-user for downstream analysis. GiA Roots has a GUI front end and a command-line interface for interweaving the software into large-scale workflows. GiA Roots can also be extended to estimate novel phenotypes specified by the end-user. Conclusions: We demonstrate the use of GiA Roots on a set of 2393 images of rice roots representing 12 genotypes from the species Oryza sativa. We validate trait measurements against prior analyses of this image set that demonstrated that RSA traits are likely heritable and associated with genotypic differences. Moreover, we demonstrate that GiA Roots is extensible and an end-user can add functionality so that GiA Roots can estimate novel RSA traits. In summary, we show that the software can function as an efficient tool as part of a workflow to move from large numbers of root images to downstream analysis.Keywords
This publication has 36 references indexed in Scilit:
- A Novel Image-Analysis Toolbox Enabling Quantitative Analysis of Root System ArchitecturePlant Physiology, 2011
- Three-Dimensional Root Phenotyping with a Novel Imaging and Software PlatformPlant Physiology, 2011
- High-throughput phenotyping of multicellular organisms: finding the link between genotype and phenotypeGenome Biology, 2011
- Leaf Extraction and Analysis Framework Graphical User Interface: Segmenting and Analyzing the Structure of Leaf Veins and AreolesPlant Physiology, 2010
- Imaging and Analysis Platform for Automatic Phenotyping and Trait Ranking of Plant Root SystemsPlant Physiology, 2010
- MRI of intact plantsPhotosynthesis Research, 2009
- High-Throughput Quantification of Root Growth Using a Novel Image-Analysis ToolPlant Physiology, 2009
- LAMINA: a tool for rapid quantification of leaf size and shape parametersBMC Plant Biology, 2008
- A review on image segmentation techniquesPattern Recognition, 1993
- The Scaling of Root AnchorageJournal of Theoretical Biology, 1993