High-Throughput Quantification of Root Growth Using a Novel Image-Analysis Tool
- 10 June 2009
- journal article
- Published by Oxford University Press (OUP) in Plant Physiology
- Vol. 150 (4), 1784-1795
- https://doi.org/10.1104/pp.109.140558
Abstract
Measuring the dynamics of plant growth is fundamental to the understanding of plant development processes. This paper describes a high-throughput, automatic method to trace Arabidopsis (Arabidopsis thaliana) seedling roots grown on agarose plates. From the trace, additional software can quantify length, curvature, and stimulus response parameters such as onset of gravitropism. The method combines a particle-filtering algorithm with a graph-based method to trace the center line of a root. This top-down approach is robust to a variety of noise effects and is reasonably flexible across different image sets. The resulting tool requires minimal interaction from the user and is able to process long time-lapse sequences with user interaction only required on the first frame. The tool is described first, followed by its use on two sample data sets, one measuring root length and the other additionally analyzing the gravitropic response and curvature. The tool, RootTrace, is open source; both the program and source code will be available online.Keywords
This publication has 34 references indexed in Scilit:
- HYPOTrace: Image Analysis Software for Measuring Hypocotyl Growth and Shape Demonstrated on Arabidopsis Seedlings Undergoing PhotomorphogenesisPlant Physiology, 2009
- Spatio‐temporal quantification of differential growth processes in root growth zones based on a novel combination of image sequence processing and refined concepts describing curvature productionNew Phytologist, 2007
- A Novel Image-Analysis Technique for Kinematic Study of Growth and CurvaturePlant Physiology, 2007
- RootLM: a simple color image analysis program for length measurement of primary roots in ArabidopsisPlant Root, 2007
- Structure-Function Analysis of the Presumptive Arabidopsis Auxin Permease AUX1[W]THE PLANT CELL ONLINE, 2004
- A New Algorithm for Computational Image Analysis of Deformable Motion at High Spatial and Temporal Resolution Applied to Root Growth. Roughly Uniform Elongation in the Meristem and Also, after an Abrupt Acceleration, in the Elongation ZonePlant Physiology, 2003
- Mutations in the AXR3 gene of Arabidopsis result in altered auxin response including ectopic expression from the SAUR‐AC1 promoterThe Plant Journal, 1996
- Arabidopsis auxin-resistance gene AXR1 encodes a protein related to ubiquitin-activating enzyme E1Nature, 1993
- A Revised Medium for Rapid Growth and Bio Assays with Tobacco Tissue CulturesPhysiologia Plantarum, 1962
- A note on two problems in connexion with graphsNumerische Mathematik, 1959