MorphoGraphX: A platform for quantifying morphogenesis in 4D

Elife. 2015 May 6;4:05864. doi: 10.7554/eLife.05864.

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.

Keywords: D. melanogaster; arabidopsis; computational biology; confocal microscopy; developmental biology; image analysis; morphogenesis; mouse; quantification; software; stem cells; systems biology; tomato.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Animals
  • Anisotropy
  • Arabidopsis / genetics
  • Arabidopsis / growth & development
  • Arabidopsis / ultrastructure*
  • Cassia / genetics
  • Cassia / growth & development
  • Cassia / ultrastructure
  • Cell Proliferation
  • Cell Shape
  • Drosophila melanogaster / genetics
  • Drosophila melanogaster / growth & development
  • Drosophila melanogaster / ultrastructure
  • Flowers / genetics
  • Flowers / growth & development
  • Flowers / ultrastructure
  • Fruit / genetics
  • Fruit / growth & development
  • Fruit / ultrastructure
  • Gene Expression
  • Image Processing, Computer-Assisted / methods*
  • Image Processing, Computer-Assisted / statistics & numerical data
  • Imaging, Three-Dimensional / instrumentation
  • Imaging, Three-Dimensional / methods*
  • Imaging, Three-Dimensional / statistics & numerical data
  • Lycopersicon esculentum / genetics
  • Lycopersicon esculentum / growth & development
  • Lycopersicon esculentum / ultrastructure
  • Microscopy, Confocal
  • Microtubules / genetics
  • Microtubules / ultrastructure
  • Morphogenesis / genetics
  • Plant Development / genetics
  • Software*
  • Time-Lapse Imaging / instrumentation
  • Time-Lapse Imaging / methods
  • Time-Lapse Imaging / statistics & numerical data