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 H K RoederTinri Aegerter-Wilmsen, Naomi Nakayama, Miltos Tsiantis, Angela Hay, Dorota Kwiatkowska, Ioannis Xenarios, Cris Kuhlemeier, Richard S Smith

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish
Article number05864
Number of pages20
Publication statusPublished - 6 May 2015


  • algorithms
  • animals
  • anisotropy
  • arabidopsis
  • cassia
  • cell proliferation
  • cell shape
  • drosophila melanogaster
  • flowers
  • fruit
  • gene expression
  • image processing
  • imaging
  • lycopersicon esculentum
  • microscopy
  • microtubules
  • morphogenesis
  • plant development
  • software
  • time-lapse imaging
  • Confocal/methods
  • computer-assisted
  • three-dimensional

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