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MorphoGraphX: A platform for quantifying morphogenesis in 4D.
- Source :
-
ELife [Elife] 2015 May 06; Vol. 4, pp. 05864. Date of Electronic Publication: 2015 May 06. - Publication Year :
- 2015
-
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.
- Subjects :
- Animals
Anisotropy
Arabidopsis genetics
Arabidopsis growth & development
Cassia genetics
Cassia growth & development
Cassia ultrastructure
Cell Proliferation
Cell Shape
Drosophila melanogaster genetics
Drosophila melanogaster growth & development
Drosophila melanogaster ultrastructure
Flowers genetics
Flowers growth & development
Flowers ultrastructure
Fruit genetics
Fruit growth & development
Fruit ultrastructure
Gene Expression
Image Processing, Computer-Assisted statistics & numerical data
Imaging, Three-Dimensional instrumentation
Imaging, Three-Dimensional statistics & numerical data
Solanum lycopersicum genetics
Solanum lycopersicum growth & development
Solanum lycopersicum ultrastructure
Microscopy, Confocal
Microtubules genetics
Microtubules ultrastructure
Morphogenesis genetics
Plant Development genetics
Time-Lapse Imaging instrumentation
Time-Lapse Imaging methods
Time-Lapse Imaging statistics & numerical data
Algorithms
Arabidopsis ultrastructure
Image Processing, Computer-Assisted methods
Imaging, Three-Dimensional methods
Software
Subjects
Details
- Language :
- English
- ISSN :
- 2050-084X
- Volume :
- 4
- Database :
- MEDLINE
- Journal :
- ELife
- Publication Type :
- Academic Journal
- Accession number :
- 25946108
- Full Text :
- https://doi.org/10.7554/eLife.05864