Format

Send to

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

MorphoGraphX: A platform for quantifying morphogenesis in 4D.

Author information

1
Institute of Plant Sciences, University of Bern, Bern, Switzerland.
2
Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany.
3
School of Biosciences, University of Birmingham, Birmingham, United Kingdom.
4
Swiss Institute of Bioinformatics, Lausanne, Switzerland.
5
Chair of Computational Science, ETH Zurich, Zurich, Switzerland.
6
Reproduction et Développement des Plantes, Ecole Normale Supérieure de Lyon, Lyon, France.
7
Department of Biophysics and Morphogenesis of Plants, University of Silesia, Katowice, Poland.
8
Institute of Molecular Life Sciences, Zurich, Switzerland.
9
Laboratory of Membrane Biogenesis, University of Bordeaux, Bordeaux, France.
10
Weill Institute for Cell and Molecular Biology and School of Integrative Plant Science, Section of Plant Biology, Cornell University, Ithaca, United States.

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

PMID:
25946108
PMCID:
PMC4421794
DOI:
10.7554/eLife.05864
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for eLife Sciences Publications, Ltd Icon for PubMed Central
Loading ...
Support Center