A 3D adult zebrafish brain atlas (AZBA) for the digital age

  1. Justin W Kenney  Is a corresponding author
  2. Patrick E Steadman
  3. Olivia Young
  4. Meng Ting Shi
  5. Maris Polanco
  6. Saba Dubaishi
  7. Kristopher Covert
  8. Thomas Mueller
  9. Paul W Frankland  Is a corresponding author
  1. Wayne State University, United States
  2. The Hospital for Sick Children, Canada
  3. Kansas State University, United States
  4. University of Toronto, Canada

Abstract

Zebrafish have made significant contributions to our understanding of the vertebrate brain and the neural basis of behavior, earning a place as one of the most widely used model organisms in neuroscience. Their appeal arises from the marriage of low cost, early life transparency, and ease of genetic manipulation with a behavioral repertoire that becomes more sophisticated as animals transition from larvae to adults. To further enhance the use of adult zebrafish, we created the first fully segmented three-dimensional digital adult zebrafish brain atlas (AZBA). AZBA was built by combining tissue clearing, light-sheet fluorescence microscopy, and three-dimensional image registration of nuclear and antibody stains. These images were used to guide segmentation of the atlas into over 200 neuroanatomical regions comprising the entirety of the adult zebrafish brain. As an open source, online (azba.wayne.edu), updatable digital resource, AZBA will significantly enhance the use of adult zebrafish in furthering our understanding of vertebrate brain function in both health and disease.

Data availability

Data have been deposited in Dryad, accessible at: https://doi.org/10.5061/dryad.dfn2z351g

The following data sets were generated

Article and author information

Author details

  1. Justin W Kenney

    Department of Biological Sciences, Wayne State University, Detroit, United States
    For correspondence
    jkenney9@wayne.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-8790-5184
  2. Patrick E Steadman

    The Hospital for Sick Children, Toronto, Canada
    Competing interests
    The authors declare that no competing interests exist.
  3. Olivia Young

    Department of Biological Sciences, Wayne State University, Detroit, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Meng Ting Shi

    Department of Biological Sciences, Wayne State University, Detroit, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Maris Polanco

    Department of Biological Sciences, Wayne State University, Detroit, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Saba Dubaishi

    Department of Biological Sciences, Wayne State University, Detroit, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. Kristopher Covert

    Department of Biological Sciences, Wayne State University, Detroit, United States
    Competing interests
    The authors declare that no competing interests exist.
  8. Thomas Mueller

    Kansas State University, Manhattan, United States
    Competing interests
    The authors declare that no competing interests exist.
  9. Paul W Frankland

    Department of Physiology, University of Toronto, Toronto, Canada
    For correspondence
    paul.frankland@sickkids.ca
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1395-3586

Funding

Human Frontiers Science Program (LT000759/2014)

  • Justin W Kenney

National Institutes of Health (R35GM142566)

  • Justin W Kenney

Canadian Institute for Health Research (FDN143227)

  • Paul W Frankland

National Institutes of Health (P20GM113109)

  • Thomas Mueller

Human Frontiers Science Program (RGP0016/2019)

  • Thomas Mueller

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

Ethics

Animal experimentation: The study was performed in accordance with the Guide for the Care and Use of Laboratory Animals of the National Institutes of Health. All procedures were approved by the animal care committee of The Hospital for Sick Children (protocol #0000047792).

Reviewing Editor

  1. Stephen C Ekker, Mayo Clinic, United States

Publication history

  1. Received: May 3, 2021
  2. Accepted: November 21, 2021
  3. Accepted Manuscript published: November 22, 2021 (version 1)
  4. Version of Record published: December 2, 2021 (version 2)

Copyright

© 2021, Kenney 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. Justin W Kenney
  2. Patrick E Steadman
  3. Olivia Young
  4. Meng Ting Shi
  5. Maris Polanco
  6. Saba Dubaishi
  7. Kristopher Covert
  8. Thomas Mueller
  9. Paul W Frankland
(2021)
A 3D adult zebrafish brain atlas (AZBA) for the digital age
eLife 10:e69988.
https://doi.org/10.7554/eLife.69988
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