Origami: Single-cell 3D shape dynamics oriented along the apico-basal axis of folding epithelia from fluorescence microscopy data.

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 epith...

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Autores principales:	Tania Mendonca, Ana A Jones, Jose M Pozo, Sarah Baxendale, Tanya T Whitfield, Alejandro F Frangi
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/08d61221602043068260cd1f1cff142f
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spelling	oai:doaj.org-article:08d61221602043068260cd1f1cff142f2021-12-02T19:57:40ZOrigami: Single-cell 3D shape dynamics oriented along the apico-basal axis of folding epithelia from fluorescence microscopy data.1553-734X1553-735810.1371/journal.pcbi.1009063https://doaj.org/article/08d61221602043068260cd1f1cff142f2021-11-01T00:00:00Zhttps://doi.org/10.1371/journal.pcbi.1009063https://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358A 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.Tania MendoncaAna A JonesJose M PozoSarah BaxendaleTanya T WhitfieldAlejandro F FrangiPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 17, Iss 11, p e1009063 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Tania Mendonca Ana A Jones Jose M Pozo Sarah Baxendale Tanya T Whitfield Alejandro F Frangi Origami: Single-cell 3D shape dynamics oriented along the apico-basal axis of folding epithelia from fluorescence microscopy data.
description	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.
format	article
author	Tania Mendonca Ana A Jones Jose M Pozo Sarah Baxendale Tanya T Whitfield Alejandro F Frangi
author_facet	Tania Mendonca Ana A Jones Jose M Pozo Sarah Baxendale Tanya T Whitfield Alejandro F Frangi
author_sort	Tania Mendonca
title	Origami: Single-cell 3D shape dynamics oriented along the apico-basal axis of folding epithelia from fluorescence microscopy data.
title_short	Origami: Single-cell 3D shape dynamics oriented along the apico-basal axis of folding epithelia from fluorescence microscopy data.
title_full	Origami: Single-cell 3D shape dynamics oriented along the apico-basal axis of folding epithelia from fluorescence microscopy data.
title_fullStr	Origami: Single-cell 3D shape dynamics oriented along the apico-basal axis of folding epithelia from fluorescence microscopy data.
title_full_unstemmed	Origami: Single-cell 3D shape dynamics oriented along the apico-basal axis of folding epithelia from fluorescence microscopy data.
title_sort	origami: single-cell 3d shape dynamics oriented along the apico-basal axis of folding epithelia from fluorescence microscopy data.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/08d61221602043068260cd1f1cff142f
work_keys_str_mv	AT taniamendonca origamisinglecell3dshapedynamicsorientedalongtheapicobasalaxisoffoldingepitheliafromfluorescencemicroscopydata AT anaajones origamisinglecell3dshapedynamicsorientedalongtheapicobasalaxisoffoldingepitheliafromfluorescencemicroscopydata AT josempozo origamisinglecell3dshapedynamicsorientedalongtheapicobasalaxisoffoldingepitheliafromfluorescencemicroscopydata AT sarahbaxendale origamisinglecell3dshapedynamicsorientedalongtheapicobasalaxisoffoldingepitheliafromfluorescencemicroscopydata AT tanyatwhitfield origamisinglecell3dshapedynamicsorientedalongtheapicobasalaxisoffoldingepitheliafromfluorescencemicroscopydata AT alejandroffrangi origamisinglecell3dshapedynamicsorientedalongtheapicobasalaxisoffoldingepitheliafromfluorescencemicroscopydata
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Origami: Single-cell 3D shape dynamics oriented along the apico-basal axis of folding epithelia from fluorescence microscopy data.

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