iRoCS Toolbox

Computer Vision Group @ University of Freiburg


Measured variables 3D-reconstruction, localisation, diameter, volume
Operating system windows, linux
Licence open-source, freeware
Automation level automated, semi-automated
Plant requirements Arabidopsis
Export formats -
Other information -

Scientific article(s)

The iRoCS Toolbox - 3D analysis of the plant root apical meristem at cellular resolution
Thorsten Schmidt, Taras Pasternak, Kun Liu, Thomas Blein, Dorothée Aubry-Hivet, Alexander Dovzhenko, Jasmin Duerr, William Teale, Franck A. Ditengou, Hans Burkhardt, Olaf Ronneberger, Klaus Palme
The Plant Journal, 2014 View paper

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The iRoCS Toolbox is an interactive Qt4 analysis tool for attaching the intrinsic Root Coordinate System (iRoCS) to 3-D confocal recordings of the Arabidopsis root apical meristem (RAM). This allows quantitative comparative studies of root populations in a sound and intuitive context. Main features are: - 3-D Visualization of the volume in an orthographic view. - Manual annotation of anatomical reference structures (QC, nuclei) - Automatic detection and annotation of cells and/or nuclei with several meaningful properties, like position, radius, tissue, cell file, cell cycle state, volume. - Full control. Any step can be manually corrected and re-fed into the modeling. - Retrieval and localization of key events like cell divisions

Source: iRoCS website @ University of Freiburg

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