A dynamic and expandable Digital 3D-Atlas MAKER for monitoring the temporal changes in tissue growth during hindbrain morphogenesis

  1. Matthias Blanc
  2. Giovanni Dalmasso
  3. Frederic Udina
  4. Cristina Pujades  Is a corresponding author
  1. Universitat Pompeu Fabra, Spain
  2. European Molecular Biology Laboratory, Spain

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 in vivo 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 in vivo 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.

Data availability

All data generated or analysed during this study are included in the manuscript or in the supplementary files.All code is available in https://github.com/cristinapujades/Blanc-et-al.-2022.

Article and author information

Author details

  1. Matthias Blanc

    Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
    Competing interests
    The authors declare that no competing interests exist.
  2. Giovanni Dalmasso

    European Molecular Biology Laboratory, Barcelona, Spain
    Competing interests
    The authors declare that no competing interests exist.
  3. Frederic Udina

    Department of Economics and Business, Universitat Pompeu Fabra, Barcelona, Spain
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7155-4153
  4. Cristina Pujades

    Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
    For correspondence
    cristina.pujades@upf.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-6423-7451

Funding

Agencia Estatal de Investigación (PGC2018-095663-B-I00)

  • Cristina Pujades

Agencia Estatal de Investigación (PGC2018-101643-B-I00)

  • Frederic Udina

Agencia Estatal de Investigación (CEX2018-000792-M)

  • Matthias Blanc
  • Cristina Pujades

Institució Catalana de Recerca i Estudis Avançats

  • Cristina Pujades

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Kristin Tessmar-Raible, University of Vienna, Austria

Ethics

Animal experimentation: Zebrafish (Dario rerio) were treated according to the Spanish/European regulations for the handling of animals in research. All protocols were approved by the Institutional Animal Care and Use Ethic Committee (Comitè Etica en Experimentació Animal, PRBB) and the Generalitat of Catalonia (Departament de Territori i Sostenibilitat), and they were implemented according to European regulations. The Project Licenses covering the proposed work (Ref 10642, Ref 10477, GC) pay particular attention to the 3Rs (Replacement, Reduction, Refinement).

Version history

  1. Preprint posted: March 30, 2021 (view preprint)
  2. Received: March 1, 2022
  3. Accepted: September 27, 2022
  4. Accepted Manuscript published: September 28, 2022 (version 1)
  5. Version of Record published: November 4, 2022 (version 2)

Copyright

© 2022, Blanc et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Matthias Blanc
  2. Giovanni Dalmasso
  3. Frederic Udina
  4. Cristina Pujades
(2022)
A dynamic and expandable Digital 3D-Atlas MAKER for monitoring the temporal changes in tissue growth during hindbrain morphogenesis
eLife 11:e78300.
https://doi.org/10.7554/eLife.78300

Share this article

https://doi.org/10.7554/eLife.78300

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