The BigBrainWarp toolbox for integration of BigBrain 3D histology with multimodal neuroimaging

  1. Casey Paquola  Is a corresponding author
  2. Jessica Royer
  3. Lindsay B Lewis
  4. Claude Lepage
  5. Tristan Glatard
  6. Konrad Wagstyl
  7. Jordan DeKraker
  8. Paule-Joanne Toussaint
  9. Sofie Louise Valk
  10. D Louis Collins
  11. Ali Khan
  12. Katrin Amunts
  13. Alan C Evans
  14. Timo Dickscheid
  15. Boris C Bernhardt  Is a corresponding author
  1. McGill University, Canada
  2. Concordia University, Canada
  3. UCL, United Kingdom
  4. University of Western Ontario, Canada
  5. Max Planck Institute Leipzig, Germany
  6. Montreal Neurological Institute and Hospital, Canada
  7. Heinrich Heine University, Germany
  8. Forschungszentrum Jülich, Germany

Abstract

Neuroimaging stands to benefit from emerging ultrahigh-resolution 3D histological atlases of the human brain; the first of which is 'BigBrain'. Here, we review recent methodological advances for the integration of BigBrain with multi-modal neuroimaging and introduce a toolbox, 'BigBrainWarp', that combines these developments. The aim of BigBrainWarp is to simplify workflows and support the adoption of best practices. This is accomplished with a simple wrapper function that allows users to easily map data between BigBrain and standard MRI spaces. The function automatically pulls specialised transformation procedures, based on ongoing research from a wide collaborative network of researchers. Additionally, the toolbox improves accessibility of histological information through dissemination of ready-to-use cytoarchitectural features. Finally, we demonstrate the utility of BigBrainWarp with three tutorials and discuss the potential of the toolbox to support multi-scale investigations of brain organisation.

Data availability

All data generated or analysed during this study are included in the BigBrainWarp repository (https://github.com/caseypaquola/BigBrainWarp).

The following previously published data sets were used

Article and author information

Author details

  1. Casey Paquola

    Neurology and Neurosurgery, McGill University, Montréal, Canada
    For correspondence
    casey.paquola@gmail.com
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0190-4103
  2. Jessica Royer

    Neurology and Neurosurgery, McGill University, Montreal, Canada
    Competing interests
    The authors declare that no competing interests exist.
  3. Lindsay B Lewis

    Neurology and Neurosurgery, McGill University, Montreal, Canada
    Competing interests
    The authors declare that no competing interests exist.
  4. Claude Lepage

    Neurology and Neurosurgery, McGill University, Montreal, Canada
    Competing interests
    The authors declare that no competing interests exist.
  5. Tristan Glatard

    Concordia University, Montreal, Canada
    Competing interests
    The authors declare that no competing interests exist.
  6. Konrad Wagstyl

    Wellcome Centre for Human Neuroimaging, UCL, London, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  7. Jordan DeKraker

    Brain and Mind Institute, University of Western Ontario, London, Canada
    Competing interests
    The authors declare that no competing interests exist.
  8. Paule-Joanne Toussaint

    Neurology and Neurosurgery, McGill University, Montreal, Canada
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7446-150X
  9. Sofie Louise Valk

    Cognitive Neurogenetics, Max Planck Institute Leipzig, Leipzig, Germany
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2998-6849
  10. D Louis Collins

    McConnell Brain Imaging Centre, Montreal Neurological Institute, Montreal Neurological Institute and Hospital, Montreal, Canada
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-8432-7021
  11. Ali Khan

    Brain and Mind Institute, University of Western Ontario, London, Canada
    Competing interests
    The authors declare that no competing interests exist.
  12. Katrin Amunts

    Heinrich Heine University, Düsseldorf, Germany
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-5828-0867
  13. Alan C Evans

    Neurology and Neurosurgery, McGill University, Montreal, Canada
    Competing interests
    The authors declare that no competing interests exist.
  14. Timo Dickscheid

    Forschungszentrum Jülich, Jülich, Germany
    Competing interests
    The authors declare that no competing interests exist.
  15. Boris C Bernhardt

    Neurology and Neurosurgery, McGill University, Montreal, Canada
    For correspondence
    boris.bernhardt@mcgill.ca
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-9256-6041

Funding

Helmholtz Association

  • Casey Paquola
  • Lindsay B Lewis
  • Claude Lepage
  • Jordan DeKraker
  • Paule-Joanne Toussaint
  • Sofie Louise Valk
  • D Louis Collins
  • Katrin Amunts
  • Alan C Evans
  • Timo Dickscheid
  • Boris C Bernhardt

Fonds de Recherche du Québec - Santé

  • Casey Paquola
  • Boris C Bernhardt

National Science and Engineering Research Council of Canada

  • Ali Khan
  • Boris C Bernhardt

Canadian Institutes of Health Research

  • Jessica Royer
  • Ali Khan
  • Boris C Bernhardt

SickKids Foundation

  • Boris C Bernhardt

Azrieli Center for Autism Research

  • Boris C Bernhardt

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

Reviewing Editor

  1. Saad Jbabdi, University of Oxford, United Kingdom

Publication history

  1. Preprint posted: May 5, 2021 (view preprint)
  2. Received: May 6, 2021
  3. Accepted: August 23, 2021
  4. Accepted Manuscript published: August 25, 2021 (version 1)
  5. Version of Record published: September 16, 2021 (version 2)

Copyright

© 2021, Paquola 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. Casey Paquola
  2. Jessica Royer
  3. Lindsay B Lewis
  4. Claude Lepage
  5. Tristan Glatard
  6. Konrad Wagstyl
  7. Jordan DeKraker
  8. Paule-Joanne Toussaint
  9. Sofie Louise Valk
  10. D Louis Collins
  11. Ali Khan
  12. Katrin Amunts
  13. Alan C Evans
  14. Timo Dickscheid
  15. Boris C Bernhardt
(2021)
The BigBrainWarp toolbox for integration of BigBrain 3D histology with multimodal neuroimaging
eLife 10:e70119.
https://doi.org/10.7554/eLife.70119

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