Schmidt Thorsten, Pasternak Taras, Liu Kun, Blein Thomas, Aubry-Hivet Dorothée, Dovzhenko Alexander, Duerr Jasmin, Teale William, Ditengou Franck A, Burkhardt Hans, Ronneberger Olaf, Palme Klaus
Institute for Computer Science, Albert Ludwigs University Freiburg, Georges Köhler Allee, Gebäude 52, D-79110, Freiburg, Germany.
Plant J. 2014 Mar;77(5):806-14. doi: 10.1111/tpj.12429. Epub 2014 Feb 12.
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.
为了深入了解生物系统中的过程，必须在细胞和器官的三维（3D）背景下对细胞特征进行量化。我们描述了使用内在根坐标系（iRoCS）作为植物根尖分生组织的参考模型。iRoCS能够在单细胞分辨率下对植物群体的根尖进行直接和定量比较。iRoCS工具箱会自动将标准化坐标拟合到原始3D图像数据。它可以检测细胞核或分割细胞，自动拟合坐标系，并将细胞核/细胞分组到根的组织层中。每个细胞核的分裂状态也可以确定。唯一需要手动完成的步骤是标记静止中心。如有必要，所有中间输出都可以进行细化。通过示例学习细胞核视觉外观的能力使iRoCS工具箱能够轻松适应各种表型。iRoCS工具箱作为一个开源软件包提供，遵循GNU通用公共许可证，以便广大社区能够使用。为了展示该技术的强大功能，我们测量了拟南芥根尖分生组织内生长素通量改变引起的细胞分裂模式的细微变化。
