MorphoGraphX: A platform for quantifying morphogenesis in 4D

Barbier de Reuille, Pierre; Routier-Kierzkowska, Anne-Lise; Kierzkowski, Daniel; Bassel, George W; Schüpbach, Thierry; Tauriello, Gerardo; Bajpai, Namrata; Strauss, Sören; Weber, Alain; Kiss, Annamaria; Burian, Agata Maria; Hofhuis, Hugo; Sapala, Aleksandra; Lipowczan, Marcin; Heimlicher, Maria B; Robinson, Sarah Jane; Bayer, Emmanuelle M.; Basler, Konrad; Koumoutsakos, Petros; Roeder, Adrienne HK; ... (2015). MorphoGraphX: A platform for quantifying morphogenesis in 4D. eLife, 4, e05864. eLife Sciences Publications 10.7554/eLife.05864

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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.DOI: http://dx.doi.org/10.7554/eLife.05864.001Author keywordsResearch organism

Item Type:

Journal Article (Original Article)

Division/Institute:

08 Faculty of Science > Department of Biology > Institute of Plant Sciences (IPS) > Plant Development
08 Faculty of Science > Department of Biology > Institute of Plant Sciences (IPS)

UniBE Contributor:

Barbier de Reuille, Pierre; Routier, Anne-Lise; Kierzkowski, Daniel; Weber, Alain; Burian, Agata Maria; Robinson, Sarah Jane; Bayer, Emmanuelle; Nakayama, Naomi; Kuhlemeier, Cris and Smith, Richard Simon

Subjects:

500 Science > 580 Plants (Botany)

ISSN:

2050-084X

Publisher:

eLife Sciences Publications

Language:

English

Submitter:

Peter Alfred von Ballmoos-Haas

Date Deposited:

08 Jun 2015 14:52

Last Modified:

08 Jun 2015 16:24

Publisher DOI:

10.7554/eLife.05864

BORIS DOI:

10.7892/boris.69212

URI:

https://boris.unibe.ch/id/eprint/69212

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