MorphoGraphX: A platform for quantifying morphogenesis in 4D.
MorphoGraphX: A platform for quantifying morphogenesis in 4D.
复制标题
DOI：
10.7554/elife.05864
复制
发表时间：
2015-05-06
期刊：
影响因子：
7.7
通讯作者：
Smith RS
中科院分区：
文献类型：
--
作者：
Barbier de Reuille P;Routier-Kierzkowska AL;Kierzkowski D;Bassel GW;Schüpbach T;Tauriello G;Bajpai N;Strauss S;Weber A;Kiss A;Burian A;Hofhuis H;Sapala A;Lipowczan M;Heimlicher MB;Robinson S;Bayer EM;Basler K;Koumoutsakos P;Roeder AH;Aegerter-Wilmsen T;Nakayama N;Tsiantis M;Hay A;Kwiatkowska D;Xenarios I;Kuhlemeier C;Smith RS
形态发生是遗传过程和机械过程之间复杂的多尺度相互作用的结果。为了理解这些过程，必须量化细胞形状、增殖和基因表达的进化。这种量化通常是在全3D下进行的，这是计算昂贵且具有技术挑战性的，或者是在2D平面投影上执行的，这在高度弯曲的器官上引入了几何伪影。在这里，我们介绍了MorPhoGraphX(www.MorPhoGraphX.org)，这是一款通过直接处理从3D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3D图像分析，我们还开发了在曲面上操作的算法，如细胞分割、谱系跟踪和荧光信号量化。该软件的模块化设计使其很容易包含现有的库，或实现新的算法。用Morphy GraphX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。DOI：http://dx.doi.org/10.7554/eLife.05864.001动物、植物和其他多细胞生物在生长过程中形成独特的三维形状。这一过程被称为形态发生，受到许多基因的影响，涉及细胞之间的通讯，以控制单个细胞分裂和生长的能力。特定细胞中事件的准确时间和位置对于确定生物体的最终形状非常重要。研究形态发生的常用技术是用显微镜拍摄活细胞的二维(2D)和三维(3D)延时视频。荧光标签使科学家能够观察特定的蛋白质、细胞边界和单个细胞之间的相互作用。这些成像技术可以产生大量的数据，需要使用计算机进行分析，并将其合并到计算机模拟中，以预测生物体内的组织或器官如何生长以形成最终形状。目前，大多数形态发生的计算模型工作在2D模板上，并且关注组织和器官是如何形成的。但是，许多阵列事件发生在弯曲或折叠的曲面上，因此2D模型可能会丢失重要的细节。开发3D模型将提供更准确的图像，但这些模型制作成本高昂，而且在技术上具有挑战性。为了解决这个问题，Barbier de Ruille，Routier-Kierzkowska等人。介绍一个开源的、可定制的软件平台，名为Morphy GraphX。该软件从3D数据中提取图像，以重建曲面。Barbier de Ruille，Routier-Kierkowska等人。还开发了算法来帮助分析这些曲线图像中的生长和基因活动，这些数据可以导出并用于计算机模拟。一些科学家已经在他们的研究中使用了这个软件，但Barbier de Ruille，Routier-Kierzkowska等人。现在已经使该软件更广泛地可用，并对其工作原理提供了完整的解释。还描述了科学家如何扩展和定制Morphy GraphX以回答他们自己独特的研究问题。预计Morphy GraphX将成为开放共享研究形态发生的计算工具的流行平台。DOI：http://dx.doi.org/10.7554/eLife.05864.002
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. DOI: http://dx.doi.org/10.7554/eLife.05864.001 Animals, plants and other multicellular organisms develop their distinctive three-dimensional shapes as they grow. This process—called morphogenesis—is influenced by many genes and involves communication between cells to control the ability of individual cells to divide and grow. The precise timing and location of events in particular cells is very important in determining the final shape of the organism. Common techniques for studying morphogenesis use microscopes to take 2-dimensional (2D) and 3-dimensional (3D) time-lapse videos of living cells. Fluorescent tags allow scientists to observe specific proteins, cell boundaries, and interactions between individual cells. These imaging techniques can produce large sets of data that need to be analyzed using a computer and incorporated into computer simulations that predict how a tissue or organ within an organism grows to form its final shape. Currently, most computational models of morphogenesis work on 2D templates and focus on how tissues and organs form. However, many patterning events occur on surfaces that are curved or folded, so 2D models may lose important details. Developing 3D models would provide a more accurate picture, but these models are expensive and technically challenging to make. To address this problem, Barbier de Reuille, Routier-Kierzkowska et al. present an open-source, customizable software platform called MorphoGraphX. This software extracts images from 3D data to recreate curved 2D surfaces. Barbier de Reuille, Routier-Kierkowska et al. have also developed algorithms to help analyze growth and gene activity in these curved images, and the data can be exported and used in computer simulations. Several scientists have already used this software in their studies, but Barbier de Reuille, Routier-Kierzkowska et al. have now made the software more widely available and have provided a full explanation of how it works. How scientists can extend and customize MorphoGraphX to answer their own unique research questions is also described. It is anticipated that MorphoGraphX will become a popular platform for the open sharing of computational tools to study morphogenesis. DOI: http://dx.doi.org/10.7554/eLife.05864.002