iRoCS Toolbox
Computer Vision Group @ University of Freiburg
Overview
| 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 resolutionThorsten Schmidt, Taras Pasternak, Kun Liu, Thomas Blein, Dorothée Aubry-Hivet, Alexander Dovzhenko, Jasmin Duerr, William Teale, Franck A. Ditengou, Hans Burkhardt, Olaf Ronneberger, Klaus PalmeThe Plant Journal, 2014 View paper
Similar tools
Other tools for the analysis of single-root,cell:
Description
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