Barbier de Reuille Pierre, Routier-Kierzkowska Anne-Lise, Kierzkowski Daniel, Bassel George W, Schüpbach Thierry, Tauriello Gerardo, Bajpai Namrata, Strauss Sören, Weber Alain, Kiss Annamaria, Burian Agata, Hofhuis Hugo, Sapala Aleksandra, Lipowczan Marcin, Heimlicher Maria B, Robinson Sarah, Bayer Emmanuelle M, Basler Konrad, Koumoutsakos Petros, Roeder Adrienne H K, Aegerter-Wilmsen Tinri, Nakayama Naomi, Tsiantis Miltos, Hay Angela, Kwiatkowska Dorota, Xenarios Ioannis, Kuhlemeier Cris, Smith Richard S
Institute of Plant Sciences, University of Bern, Bern, Switzerland.
Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany.
Elife. 2015 May 6;4:05864. doi: 10.7554/eLife.05864.
Morphogenesis emerges from complex multiscale interactions between genetic and mechanical processes. To understand these processes, the evolution of cell shape, proliferation and gene expression must be quantified. This quantification is usually performed either in full 3D, which is computationally expensive and technically challenging, or on 2D planar projections, which introduces geometrical artifacts on highly curved organs. Here we present MorphoGraphX ( www.MorphoGraphX.org), a software that bridges this gap by working directly with curved surface images extracted from 3D data. In addition to traditional 3D image analysis, we have developed algorithms to operate on curved surfaces, such as cell segmentation, lineage tracking and fluorescence signal quantification. The software's modular design makes it easy to include existing libraries, or to implement new algorithms. Cell geometries extracted with MorphoGraphX can be exported and used as templates for simulation models, providing a powerful platform to investigate the interactions between shape, genes and growth.
形态发生源于遗传和机械过程之间复杂的多尺度相互作用。为了理解这些过程，必须对细胞形状、增殖和基因表达的演变进行量化。这种量化通常在完整的三维空间中进行，这在计算上成本高昂且技术上具有挑战性，或者在二维平面投影上进行，这会在高度弯曲的器官上引入几何伪影。在这里，我们展示了MorphoGraphX（www.MorphoGraphX.org），这是一款通过直接处理从三维数据中提取的曲面图像来弥合这一差距的软件。除了传统的三维图像分析，我们还开发了在曲面上运行的算法，如细胞分割、谱系追踪和荧光信号量化。该软件的模块化设计使其易于纳入现有库或实现新算法。用MorphoGraphX提取的细胞几何形状可以导出并用作模拟模型的模板，为研究形状、基因和生长之间的相互作用提供了一个强大的平台。
