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A dynamic and expandable digital 3D-atlas maker for monitoring the temporal changes in tissue growth during hindbrain morphogenesis

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dc.contributor.author Blanc, Matthias
dc.contributor.author Dalmasso, Giovanni
dc.contributor.author Udina, Frederic
dc.contributor.author Pujades Corbi, Cristina
dc.date.accessioned 2022-11-16T07:37:52Z
dc.date.available 2022-11-16T07:37:52Z
dc.date.issued 2022
dc.identifier.citation Blanc M, Dalmasso G, Udina F, Pujades C. A dynamic and expandable digital 3D-atlas maker for monitoring the temporal changes in tissue growth during hindbrain morphogenesis. Elife. 2022 Sep 28;11:e78300. DOI: 10.7554/eLife.78300
dc.identifier.issn 2050-084X
dc.identifier.uri http://hdl.handle.net/10230/54884
dc.description.abstract Reconstruction of prototypic three-dimensional (3D) atlases at the scale of whole tissues or organs requires specific methods to be developed. We have established a digital 3D-atlas maker (DAMAKER) and built a digital 3D-atlas to monitor the changes in the growth of the neuronal differentiation domain in the zebrafish hindbrain upon time. DAMAKER integrates spatial and temporal data of cell populations, neuronal differentiation and brain morphogenesis, through <i>in vivo</i> imaging techniques paired with image analyses and segmentation tools. First, we generated a 3D-reference from several imaged hindbrains and segmented them using a trainable tool; these were aligned using rigid registration, revealing distribution of neuronal differentiation growth patterns along the axes. Second, we quantified the dynamic growth of the neuronal differentiation domain by <i>in vivo</i> neuronal birthdating experiments. We generated digital neuronal birthdating 3D-maps and revealed that the temporal order of neuronal differentiation prefigured the spatial distribution of neurons in the tissue, with an inner-outer differentiation gradient. Last, we applied it to specific differentiated neuronal populations such as glutamatergic and GABAergic neurons, as proof-of-concept that the digital birthdating 3D-maps could be used as a proxy to infer neuronal birthdate. As this protocol uses open-access tools and algorithms, it can be shared for standardized, accessible, tissue-wide cell population atlas construction.
dc.description.sponsorship This work was funded by grants PGC2018-095663-B-I00 and RED2018-102553-T to CP and PGC2018-101643-B-I00 to FU, from Spanish MCIN/AEI (DOI: 10.13039/501100011033) and Fondo Europeo de Desarrollo Regional (FEDER). Department of Medicine and Life Sciences UPF is a Unidad de Excelencia María de Maeztu funded by the Spanish MCIN/AEI (DOI: 10.13039/501100011033), Ref CEX2018-000792-M. CP is a recipient of ICREA Academia award (Generalitat de Catalunya).
dc.format.mimetype application/pdf
dc.language.iso eng
dc.publisher eLife
dc.relation.ispartof Elife. 2022 Sep 28;11:e78300
dc.rights © 2022, Blanc et al. This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.
dc.rights.uri http://creativecommons.org/licenses/by/4.0/
dc.title A dynamic and expandable digital 3D-atlas maker for monitoring the temporal changes in tissue growth during hindbrain morphogenesis
dc.type info:eu-repo/semantics/article
dc.identifier.doi http://dx.doi.org/10.7554/eLife.78300
dc.subject.keyword Developmental biology
dc.subject.keyword Hindbrain
dc.subject.keyword Morphogenesis
dc.subject.keyword Neural progenitors
dc.subject.keyword Neuronal differentiation
dc.subject.keyword Neuroscience
dc.subject.keyword Temporal 3D-imaging
dc.subject.keyword Tissue growth
dc.subject.keyword Zebrafish
dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/PGC2018-095663-B-I00
dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/RED2018-102553-T
dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/PGC2018-101643-B-I00
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.type.version info:eu-repo/semantics/publishedVersion


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