The iRoCS Toolbox – 3D analysis of the plant root apical meristem at cellular resolution |
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Authors: | 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 |
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Institution: | 1. Institute for Computer Science, Albert Ludwigs University Freiburg, , D–79110 Freiburg, Germany;2. Institute for Biology II, Albert Ludwigs University Freiburg, , D–79104 Freiburg, Germany;3. Center for Applied Biosciences (Zentrum für angewandte Biowissenschaften), Albert Ludwigs University Freiburg, , D–79104 Freiburg, Germany;4. Centre for Biological Signalling Studies, Albert Ludwigs University Freiburg, , D–79104 Freiburg, Germany;5. Freiburg Centre for Advanced Studies, Albert Ludwigs University Freiburg, , D–79104 Freiburg, Germany;6. Freiburg Initiative for Systems Biology, Faculty for Biology, Albert Ludwigs University Freiburg, , D–79104 Freiburg, Germany |
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Abstract: | To achieve a detailed understanding of processes in biological systems, cellular features must be quantified in the three‐dimensional (3D) context of cells and organs. We described use of the intrinsic root coordinate system (iRoCS) as a reference model for the root apical meristem of plants. iRoCS enables direct and quantitative comparison between the root tips of plant populations at single‐cell resolution. The iRoCS Toolbox automatically fits standardized coordinates to raw 3D image data. It detects nuclei or segments cells, automatically fits the coordinate system, and groups the nuclei/cells into the root's tissue layers. The division status of each nucleus may also be determined. The only manual step required is to mark the quiescent centre. All intermediate outputs may be refined if necessary. The ability to learn the visual appearance of nuclei by example allows the iRoCS Toolbox to be easily adapted to various phenotypes. The iRoCS Toolbox is provided as an open‐source software package, licensed under the GNU General Public License, to make it accessible to a broad community. To demonstrate the power of the technique, we measured subtle changes in cell division patterns caused by modified auxin flux within the Arabidopsis thaliana root apical meristem. |
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Keywords: |
Arabidopsis thaliana
root modelling automated image analysis confocal microscopy population studies pin mutants technical advance |
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