title: MorphoGraphX: A platform for quantifying morphogenesis in 4D.
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.
authors.affiliation: Institute of Plant Sciences, University of Bern, Bern, Switzerland.
authors.forename: Pierre
authors.initials: P
authors.lastname: Barbier de Reuille
authors.affiliation: Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany.
authors.forename: Anne-Lise
authors.initials: AL
authors.lastname: Routier-Kierzkowska
authors.affiliation: Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany.
authors.forename: Daniel
authors.initials: D
authors.lastname: Kierzkowski
authors.affiliation: School of Biosciences, University of Birmingham, Birmingham, United Kingdom.
authors.forename: George W
authors.initials: GW
authors.lastname: Bassel
authors.affiliation: Swiss Institute of Bioinformatics, Lausanne, Switzerland.
authors.forename: Thierry
authors.initials: T
authors.lastname: Schüpbach
authors.affiliation: Chair of Computational Science, ETH Zurich, Zurich, Switzerland.
authors.forename: Gerardo
authors.initials: G
authors.lastname: Tauriello
authors.affiliation: Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany.
authors.forename: Namrata
authors.initials: N
authors.lastname: Bajpai
authors.affiliation: Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany.
authors.forename: Sören
authors.initials: S
authors.lastname: Strauss
authors.affiliation: Institute of Plant Sciences, University of Bern, Bern, Switzerland.
authors.forename: Alain
authors.initials: A
authors.lastname: Weber
authors.affiliation: Reproduction et Développement des Plantes, Ecole Normale Supérieure de Lyon, Lyon, France.
authors.forename: Annamaria
authors.initials: A
authors.lastname: Kiss
authors.affiliation: Institute of Plant Sciences, University of Bern, Bern, Switzerland.
authors.forename: Agata
authors.initials: A
authors.lastname: Burian
authors.affiliation: Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany.
authors.forename: Hugo
authors.initials: H
authors.lastname: Hofhuis
authors.affiliation: Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany.
authors.forename: Aleksandra
authors.initials: A
authors.lastname: Sapala
authors.affiliation: Department of Biophysics and Morphogenesis of Plants, University of Silesia, Katowice, Poland.
authors.forename: Marcin
authors.initials: M
authors.lastname: Lipowczan
authors.affiliation: Institute of Molecular Life Sciences, Zurich, Switzerland.
authors.forename: Maria B
authors.initials: MB
authors.lastname: Heimlicher
authors.affiliation: Institute of Plant Sciences, University of Bern, Bern, Switzerland.
authors.forename: Sarah
authors.initials: S
authors.lastname: Robinson
authors.affiliation: Laboratory of Membrane Biogenesis, University of Bordeaux, Bordeaux, France.
authors.forename: Emmanuelle M
authors.initials: EM
authors.lastname: Bayer
authors.affiliation: Institute of Molecular Life Sciences, Zurich, Switzerland.
authors.forename: Konrad
authors.initials: K
authors.lastname: Basler
authors.affiliation: Chair of Computational Science, ETH Zurich, Zurich, Switzerland.
authors.forename: Petros
authors.initials: P
authors.lastname: Koumoutsakos
authors.affiliation: Weill Institute for Cell and Molecular Biology and School of Integrative Plant Science, Section of Plant Biology, Cornell University, Ithaca, United States.
authors.forename: Adrienne H K
authors.identifier: http://orcid.org/0000-0001-6685-2984
authors.initials: AH
authors.lastname: Roeder
authors.affiliation: Institute of Molecular Life Sciences, Zurich, Switzerland.
authors.forename: Tinri
authors.initials: T
authors.lastname: Aegerter-Wilmsen
authors.affiliation: Institute of Plant Sciences, University of Bern, Bern, Switzerland.
authors.forename: Naomi
authors.initials: N
authors.lastname: Nakayama
authors.affiliation: Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany.
authors.forename: Miltos
authors.initials: M
authors.lastname: Tsiantis
authors.affiliation: Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany.
authors.forename: Angela
authors.initials: A
authors.lastname: Hay
authors.affiliation: Department of Biophysics and Morphogenesis of Plants, University of Silesia, Katowice, Poland.
authors.forename: Dorota
authors.initials: D
authors.lastname: Kwiatkowska
authors.affiliation: Swiss Institute of Bioinformatics, Lausanne, Switzerland.
authors.forename: Ioannis
authors.initials: I
authors.lastname: Xenarios
authors.affiliation: Institute of Plant Sciences, University of Bern, Bern, Switzerland.
authors.forename: Cris
authors.initials: C
authors.lastname: Kuhlemeier
authors.affiliation: Institute of Plant Sciences, University of Bern, Bern, Switzerland.
authors.forename: Richard S
authors.initials: RS
authors.lastname: Smith
mesh_terms: D000465:Algorithms; D000818:Animals; D016880:Anisotropy; D017360:Arabidopsis / Q000235:genetics / Q000254:growth & development / Q000648:ultrastructure*; D002366:Cassia / Q000235:genetics / Q000254:growth & development / Q000648:ultrastructure; D049109:Cell Proliferation; D048430:Cell Shape; D004331:Drosophila melanogaster / Q000235:genetics / Q000254:growth & development / Q000648:ultrastructure; D035264:Flowers / Q000235:genetics / Q000254:growth & development / Q000648:ultrastructure; D005638:Fruit / Q000235:genetics / Q000254:growth & development / Q000648:ultrastructure; D015870:Gene Expression; D007091:Image Processing, Computer-Assisted / Q000379:methods* / Q000706:statistics & numerical data; D021621:Imaging, Three-Dimensional / Q000295:instrumentation / Q000379:methods* / Q000706:statistics & numerical data; D018551:Solanum lycopersicum / Q000235:genetics / Q000254:growth & development / Q000648:ultrastructure; D018613:Microscopy, Confocal; D008870:Microtubules / Q000235:genetics / Q000648:ultrastructure; D009024:Morphogenesis / Q000235:genetics; D063245:Plant Development / Q000235:genetics; D012984:Software; D059008:Time-Lapse Imaging / Q000295:instrumentation / Q000379:methods / Q000706:statistics & numerical data
keywords: D. melanogaster; arabidopsis; computational biology; confocal microscopy; developmental biology; image analysis; morphogenesis; mouse; quantification; software; stem cells; systems biology; tomato