Plant Image Analysis Plant Image Analysis

RootTrace

Center for Plant Integrative Biology @ University of Nottingham
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Scientific article
High-throughput quantification of root growth using a novel image-analysis tool.
A. French, S. Ubeda-Tomás, TJ. Holman, MJ. Bennett, T. Pridmore,
2009 , Plant Physiol. , 150(4), 1784
View at publisher | Download PDF


High-throughput feature counting and measurement of roots.
A. Naeem, AP. French, DM. Wells, TP. Pridmore,
2011 , Bioinformatics , 27(9), 1337
View at publisher | Download PDF


Description

RootTrace is a software tool being developed at CPIB to allow the automatic and high throughput measure of root length, and extra associated measures such as curvature.

The user must supply start points for each root, and exemplar patches of nearby background. The software will then trace the main root to the tip, in every image in a timeseries, and record the results.

The original RootTrace tool has proved successful in measuring primary root lengths across time series image data. Biologists have shown interest in using the tool to address further problems, namely counting lateral roots to use as parameters in screening studies, and measuring highly curved roots. To address this, the software has been extended to count emerged lateral roots, and the tracking model extended so that strongly curved and agravitropic roots can be now be recovered.



Source: RootTrace website (CPIB)

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Overview
Operating system
windows,

Licence
open-source, freeware,

Measured variables
length, curvature, n-branches,

Automation level
automated,

Plant requirements
Arabidopsis, seedling,

Image requirements
time-series,

Export formats
csv,

Other information
-

Similar software
Other tools for the analysis of root-system, single-root: