IJ_Rhizo


Alain Pierret @ Institut de Recherche pour le Developpement

Overview

Measured variables length, diameter
Operating system windows, mac, linux
Licence open-source
Automation level automated
Plant requirements any
Export formats txt
Other information -

Scientific article(s)

IJ_Rhizo: an open-source software to measure scanned images of root samples
Alain Pierret, Santimaitree Gonkhamdee, Christophe Jourdan, Jean-Luc Maeght
Plant and Soil, 2017 View paper

Description

IJ_Rhizo is an ImageJ macro for the batch processing of scanned images of root samples physically separated from soil by washing. IJ_Rhizo automatically generates root length and radius measurements. Being based on a public domain, Java image processing package, IJ_Rhizo is free of charge and platform-independent. IJ_Rhizo 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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