Plant Image Analysis Plant Image Analysis

IJ_Rhizo

Alain Pierret @ Institut de Recherche pour le Developpement


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Scientific article

IJ_Rhizo: an open-source software to measure scanned images of root samples
Alain Pierret & Santimaitree Gonkhamdee & Christophe Jourdan & Jean-Luc Maeght
2013 Plant Soil

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Description

IJRhizo is an ImageJ macro for the batch processing of scanned images of root samples physically separated from soil by washing. IJRhizo automatically generates root length and radius measurements. Being based on a public domain, Java image processing package, IJRhizo is free of charge and platform-independent. IJRhizo offers a simple GUI so that it can be used by end-users with limited computer literacy. This GUI allows to customize: image resolution; the size of image border to be excluded from processing; background particle cleaning; root length correction including the Kimura estimator; and the choice of automatic versus user-defined thresholding. In addition, the macro is also fully modifiable to accommodate the specific needs of more advanced users. IJ_Rhizo generates, in addition to the main “ResultAll.txt” output file and for each image analyzed, a root radius distribution file, stored as a text file and named using the input image name exclusive of the original extension.

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Overview
Operating system
windows, mac, linux,

Licence
open-source,

Measured variables
length, diameter,

Automation level
automated,

Plant requirements
any,

Image requirements
jpg,

Export formats
txt,

Other information
-

Additional information

ImageJ must be installed prior to running the script as a macro. Morphological Operators for ImageJ must be installed (download as a single zip file from: http://www.dentistry.bham.ac.uk/landinig/ and copy to ImageJ's "plugins" directory)