Quantification of these changes is important if the developmental process is to be understood ( Chavarría-Krauser et al., 2007). Plant development is a highly complex process involving many physiological changes. The tool, RootTrace, is open source both the program and source code will be available online. 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 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. This top-down approach is robust to a variety of noise effects and is reasonably flexible across different image sets. The method combines a particle-filtering algorithm with a graph-based method to trace the center line of a root. From the trace, additional software can quantify length, curvature, and stimulus response parameters such as onset of gravitropism. This paper describes a high-throughput, automatic method to trace Arabidopsis ( Arabidopsis thaliana) seedling roots grown on agarose plates. Measuring the dynamics of plant growth is fundamental to the understanding of plant development processes.
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