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First published online June 10, 2009; 10.1104/pp.109.140558

Plant Physiology 150:1784-1795 (2009)
© 2009 American Society of Plant Biologists

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BREAKTHROUGH TECHNOLOGIES

High-Throughput Quantification of Root Growth Using a Novel Image-Analysis Tool1,[C],[W]

Andrew French*, Susana Ubeda-Tomás, Tara J. Holman, Malcolm J. Bennett and Tony Pridmore

Centre for Plant Integrative Biology, University of Nottingham, Nottingham LE12 5RD, United Kingdom (A.F., S.U.-T., T.J.H., M.J.B., T.P.); and School of Computer Science, Jubilee Campus, University of Nottingham, Nottingham NG8 1BB, United Kingdom (T.P.)

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.

1 This work was supported by the Biotechnology and Biological Sciences Research Council and the Engineering and Physical Sciences Research Council as part of their Systems Biology Initiative to establish a number of Centres for Integrative Systems Biology.

The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantphysiol.org) is: Andrew French (andrew.french{at}cpib.ac.uk).

[C] Some figures in this article are displayed in color online but in black and white in the print edition.

[W] The online version of this article contains Web-only data.

www.plantphysiol.org/cgi/doi/10.1104/pp.109.140558

* Corresponding author; e-mail andrew.french{at}cpib.ac.uk.

Received May 7, 2009; accepted June 5, 2009; published June 10, 2009.

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