title: The iRoCS Toolbox--3D analysis of the plant root apical meristem at cellular resolution.
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.
authors.affiliation: Institute for Computer Science, Albert Ludwigs University Freiburg, Georges Köhler Allee, Gebäude 52, D-79110, Freiburg, Germany.
authors.forename: Thorsten
authors.initials: T
authors.lastname: Schmidt
authors.forename: Taras
authors.initials: T
authors.lastname: Pasternak
authors.forename: Kun
authors.initials: K
authors.lastname: Liu
authors.forename: Thomas
authors.initials: T
authors.lastname: Blein
authors.forename: Dorothée
authors.initials: D
authors.lastname: Aubry-Hivet
authors.forename: Alexander
authors.initials: A
authors.lastname: Dovzhenko
authors.forename: Jasmin
authors.initials: J
authors.lastname: Duerr
authors.forename: William
authors.initials: W
authors.lastname: Teale
authors.forename: Franck A
authors.initials: FA
authors.lastname: Ditengou
authors.forename: Hans
authors.initials: H
authors.lastname: Burkhardt
authors.forename: Olaf
authors.initials: O
authors.lastname: Ronneberger
authors.forename: Klaus
authors.initials: K
authors.lastname: Palme
mesh_terms: D017360:Arabidopsis / Q000166:cytology*; D021621:Imaging, Three-Dimensional; D018519:Meristem / Q000166:cytology*; D008938:Mitosis; D018517:Plant Roots / Q000166:cytology
keywords: Arabidopsis thaliana; automated image analysis; confocal microscopy; pin mutants; population studies; root modelling; technical advance