The iRoCS Toolbox – 3D Analysis of the Plant Root Apical Meristem at Cellular Resolution

Thorsten Schmidt, T. Pasternak, Kun Liu, T. Blein, D. Aubry-Hivet, A. Dovzhenko, J. Dürr, W. Teale, F. Ditengou, Hans Burkhardt, Olaf Ronneberger, K. Palme
The Plant Journal, 77(5): 806--814, Mar 2014

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 introduce the intrinsic Root Coordinate System (iRoCS) as a reference model for the root apical meristem (RAM) of plants. iRoCS enables direct and quantitative comparison between the root tips of plant populations at single cell resolution.

The iRoCS Toolbox automatically fits standardised 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 can also be determined. The only manual step required is to mark the quiescent centre, the origin of iRoCS. All intermediate outputs can be refined if necessary. The ability to learn the visual appearance of nuclei by example allows the iRoCS Toolbox to be easily adapted to different phenotypes. We provide the iRoCS Toolbox as open source software package, licensed under the GNU General Public License (GPL) 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 RAM.

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  author       = "T. Schmidt and T. Pasternak and K. Liu and T. Blein and D. Aubry-Hivet and A. Dovzhenko and J. D{\"u}rr and W. Teale and F. A. Ditengou and H. Burkhardt and O. Ronneberger and K. Palme",
  title        = "The iRoCS Toolbox – 3D Analysis of the Plant Root Apical Meristem at Cellular Resolution",
  journal      = "The Plant Journal",
  number       = "5",
  volume       = "77",
  pages        = "806--814",
  month        = "Mar",
  year         = "2014",
  keywords     = "Arabidopsis thaliana, root modelling, biological atlas, automated image analysis, registration, high content, confocal microscopy, population studies, pin mutants, mitosis distribution",
  url          = "http://lmb.informatik.uni-freiburg.de/Publications/2014/SLBR14"

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