Plant Image Analysis Plant Image Analysis

iRoCS Toolbox

Computer Vision Group @ University of Freiburg

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Scientific article
The iRoCS Toolbox - 3D Analysis of the Plant Root Apical Meristem at Cellular Resolution.
T. Schmidt, T. Pasternak, K. Liu, T. Blein, D. Aubry-Hivet, A. Dovzhenko, J. Duerr, W. Teale, FA. Ditengou, H. Burkhardt, O. Ronneberger, K. Palme,
2014 , Plant J. , 0(0), 0
View at publisher | Download PDF


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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Operating system
windows, linux,

open-source, freeware,

Measured variables
3D-reconstruction, localisation, diameter, volume,

Automation level
automated, semi-automated,

Plant requirements

Image requirements
3D image stack,

Export formats

Other information

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