Mendonca, T, Jones, AA, Pozo, JM et al. (3 more authors) (2021) Origami: Single-cell oriented 3D shape dynamics of folding epithelia from fluorescence microscopy images. [Preprint - bioRXiv]
Abstract
A common feature of morphogenesis is the formation of three-dimensional structures from the folding of two-dimensional epithelial sheets aided by spatio-temporal cell shape changes at the cellular-level. Studying cell shape dynamics and polarised processes that underpin them, requires orienting cells within the epithelial sheet. In epithelia with highly curved surfaces, assigning cell orientation can be difficult to automate in silico. We present ‘Origami’, a MATLAB-based image analysis pipeline to compute oriented cell shape-features. Our automated method accurately computed cell orientation 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.
Metadata
Item Type: | Preprint |
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Authors/Creators: |
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Copyright, Publisher and Additional Information: | The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license. |
Dates: |
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Institution: | The University of Leeds |
Academic Units: | The University of Leeds > Faculty of Engineering & Physical Sciences (Leeds) > School of Computing (Leeds) |
Depositing User: | Symplectic Publications |
Date Deposited: | 11 Dec 2024 15:53 |
Last Modified: | 11 Dec 2024 15:53 |
Published Version: | https://www.biorxiv.org/content/10.1101/2021.05.13... |
Identification Number: | 10.1101/2021.05.13.443974 |
Open Archives Initiative ID (OAI ID): | oai:eprints.whiterose.ac.uk:176702 |
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Licence: CC-BY 4.0