PUBLICATION
Origami: Single-cell 3D shape dynamics oriented along the apico-basal axis of folding epithelia from fluorescence microscopy data
- Authors
- Mendonca, T., Jones, A.A., Pozo, J.M., Baxendale, S., Whitfield, T.T., Frangi, A.F.
- ID
- ZDB-PUB-211103-1
- Date
- 2021
- Source
- PLoS Computational Biology 17: e1009063 (Journal)
- Registered Authors
- Baxendale, Sarah, Whitfield, Tanya T.
- Keywords
- none
- MeSH Terms
-
- Animals
- Biomechanical Phenomena
- Cell Polarity
- Cell Shape/physiology*
- Computational Biology
- Computer Simulation
- Ear, Inner/embryology
- Epithelium/embryology
- Image Processing, Computer-Assisted/statistics & numerical data*
- Imaging, Three-Dimensional
- Microscopy, Fluorescence
- Models, Biological*
- Morphogenesis
- Proof of Concept Study
- Software
- Zebrafish/embryology
- PubMed
- 34723957 Full text @ PLoS Comput. Biol.
Citation
Mendonca, T., Jones, A.A., Pozo, J.M., Baxendale, S., Whitfield, T.T., Frangi, A.F. (2021) Origami: Single-cell 3D shape dynamics oriented along the apico-basal axis of folding epithelia from fluorescence microscopy data. PLoS Computational Biology. 17:e1009063.
Abstract
A common feature of morphogenesis is the formation of three-dimensional structures from the folding of two-dimensional epithelial sheets, aided by cell shape changes at the cellular-level. Changes in cell shape must be studied in the context of cell-polarised biomechanical processes within the epithelial sheet. In epithelia with highly curved surfaces, finding single-cell alignment along a biological axis can be difficult to automate in silico. We present 'Origami', a MATLAB-based image analysis pipeline to compute direction-variant cell shape features along the epithelial apico-basal axis. Our automated method accurately computed direction vectors denoting the apico-basal axis in regions with opposing curvature in synthetic epithelia and fluorescence images of zebrafish embryos. As proof of concept, we identified different cell shape signatures in the developing zebrafish inner ear, where the epithelium deforms in opposite orientations to form different structures. Origami is designed to be user-friendly and is generally applicable to fluorescence images of curved epithelia.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping