MorphoGraphX: A platform for quantifying morphogenesis in 4D

Abstract

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

eLife digest

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