MorphoGraphX: A platform for quantifying morphogenesis in 4D

被引：339

作者：

de Reuille, Pierre Barbier ^{[1
]}

Routier-Kierzkowska, Anne-Lise ^{[2
]}

Kierzkowski, Daniel ^{[2
]}

Bassel, George W. ^{[3
]}

Schuepbach, Thierry ^{[4
]}

Tauriello, Gerardo ^{[5
]}

Bajpai, Namrata ^{[2
]}

Strauss, Soeren ^{[2
]}

Weber, Alain ^{[1
]}

Kiss, Annamaria ^{[6
,7
]}

Burian, Agata ^{[1
,8
]}

Hofhuis, Hugo ^{[2
]}

Sapala, Aleksandra ^{[2
]}

Lipowczan, Marcin ^{[8
]}

Heimlicher, Maria B. ^{[9
]}

Robinson, Sarah ^{[1
]}

Bayer, Emmanuelle M. ^{[10
]}

Basler, Konrad ^{[9
]}

Koumoutsakos, Petros

Roeder, Adrienne H. K. ^{[11
,12
]}

Aegerter-Wilmsen, Tinri ^{[9
]}

Nakayama, Naomi ^{[1
,13
]}

Tsiantis, Miltos ^{[2
]}

Hay, Angela ^{[2
]}

Kwiatkowska, Dorota ^{[8
]}

Xenarios, Ioannis ^{[4
]}

Kuhlemeier, Cris ^{[1
]}

Smith, Richard S. ^{[1
,2
]}

机构：

[1] Univ Bern, Inst Plant Sci, Bern, Switzerland

[2] Max Planck Inst Plant Breeding Res, Dept Comparat Dev & Genet, Cologne, Germany

[3] Univ Birmingham, Sch Biosci, Birmingham, W Midlands, England

[4] Swiss Inst Bioinformat, Lausanne, Switzerland

[5] ETH, Chair Computat Sci, Zurich, Switzerland

[6] Ecole Normale Super Lyon, Reproduct & Dev Plantes, F-69364 Lyon, France

[7] Ecole Normale Super Lyon, Lab Joliot Curie, F-69364 Lyon, France

[8] Univ Silesia, Dept Biophys & Morphogenesis Plants, Katowice, Poland

[9] Inst Mol Life Sci, Zurich, Switzerland

[10] Univ Bordeaux, Lab Membrane Biogenesis, Bordeaux, France

[11] Cornell Univ, Weill Inst Cell & Mol Biol, Ithaca, NY USA

[12] Cornell Univ, Plant Biol Sect, Sch Integrat Plant Sci, Ithaca, NY 14853 USA

[13] Univ Edinburgh, Inst Mol Plant Sci, Edinburgh, Midlothian, Scotland

来源：

ELIFE | 2015年 / 4卷

基金：

欧洲研究理事会; 英国生物技术与生命科学研究理事会;

关键词：

SHOOT APICAL MERISTEM; ARABIDOPSIS-THALIANA; QUANTITATIVE-ANALYSIS; SURFACE GROWTH; COMPUTATIONAL MORPHODYNAMICS; MODELING FRAMEWORK; PLANT DEVELOPMENT; VEGETATIVE SHOOT; CELL-GROWTH; LEAF SHAPE;

D O I：

10.7554/eLife.05864

中图分类号：

Q [生物科学];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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.

引用

页码：1 / 20

页数：20

共 68 条

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