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Title: MorphoGraphX : a platform for quantifying morphogenesis in 4D
Authors: de Reuille, Pierre Barbier
Routier-Kierzkowska, Anne-Lise
Kierzkowski, Daniel
Bassel, George W.
Schupbach, Thierry
Tauriello, Gerardo
Bajpai, Namrata
Strauss, Soren
Weber, Alain
Kiss, Annamaria
Burian, Agata
Hofhuis, Hugo
Sapala, Aleksandra
Lipowczan, Marcin
Heimlicher, Maria B.
Robinson, Sarah
Bayer, Emmanuelle M.
Basler, Konrad
Koumoutsakos, Petros
Roeder, Adrienne HK
Aegerter-Wilmsen, Tinri
Nakayama, Naomi
Tsiantis, Miltos
Hay, Angela
Kwiatkowska, Dorota
Xenarios, Ioannis
Kuhlemeier, Cris
Smith, Richard S.
Keywords: morphogenesis; MorphoGraphX
Issue Date: 2015
Citation: eLife, Vol. 4 (2015), art. no e05864
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 (, 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: 10.7554/eLife.05864
ISSN: 2050-084X
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