eLife (May 2015)
MorphoGraphX: A platform for quantifying morphogenesis in 4D
- Pierre Barbier de Reuille,
- Anne-Lise Routier-Kierzkowska,
- Daniel Kierzkowski,
- George W Bassel,
- Thierry Schüpbach,
- Gerardo Tauriello,
- Namrata Bajpai,
- Sören Strauss,
- Alain Weber,
- Annamaria Kiss,
- Agata Burian,
- Hugo Hofhuis,
- Aleksandra Sapala,
- Marcin Lipowczan,
- Maria B Heimlicher,
- Sarah Robinson,
- Emmanuelle M Bayer,
- Konrad Basler,
- Petros Koumoutsakos,
- Adrienne HK Roeder,
- Tinri Aegerter-Wilmsen,
- Naomi Nakayama,
- Miltos Tsiantis,
- Angela Hay,
- Dorota Kwiatkowska,
- Ioannis Xenarios,
- Cris Kuhlemeier,
- Richard S Smith
Affiliations
- Pierre Barbier de Reuille
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
- Anne-Lise Routier-Kierzkowska
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Daniel Kierzkowski
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- George W Bassel
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
- Thierry Schüpbach
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Gerardo Tauriello
- Chair of Computational Science, ETH Zurich, Zurich, Switzerland
- Namrata Bajpai
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Sören Strauss
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Alain Weber
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
- Annamaria Kiss
- Reproduction et Développement des Plantes, Ecole Normale Supérieure de Lyon, Lyon, France; Laboratoire Joliot Curie, Ecole Normale Supérieure de Lyon, Lyon, France
- Agata Burian
- Institute of Plant Sciences, University of Bern, Bern, Switzerland; Department of Biophysics and Morphogenesis of Plants, University of Silesia, Katowice, Poland
- Hugo Hofhuis
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Aleksandra Sapala
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Marcin Lipowczan
- Department of Biophysics and Morphogenesis of Plants, University of Silesia, Katowice, Poland
- Maria B Heimlicher
- Institute of Molecular Life Sciences, Zurich, Switzerland
- Sarah Robinson
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
- Emmanuelle M Bayer
- Laboratory of Membrane Biogenesis, University of Bordeaux, Bordeaux, France
- Konrad Basler
- Institute of Molecular Life Sciences, Zurich, Switzerland
- Petros Koumoutsakos
- Chair of Computational Science, ETH Zurich, Zurich, Switzerland
- Adrienne HK Roeder
- ORCiD
- Weill Institute for Cell and Molecular Biology and School of Integrative Plant Science, Section of Plant Biology, Cornell University, Ithaca, United States
- Tinri Aegerter-Wilmsen
- Institute of Molecular Life Sciences, Zurich, Switzerland
- Naomi Nakayama
- Institute of Plant Sciences, University of Bern, Bern, Switzerland; Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, United Kingdom
- Miltos Tsiantis
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Angela Hay
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Dorota Kwiatkowska
- Department of Biophysics and Morphogenesis of Plants, University of Silesia, Katowice, Poland
- Ioannis Xenarios
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Cris Kuhlemeier
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
- Richard S Smith
- Institute of Plant Sciences, University of Bern, Bern, Switzerland; Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- DOI
- https://doi.org/10.7554/eLife.05864
- Journal volume & issue
-
Vol. 4
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
