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@brainglobe

BrainGlobe

Interoperable Python-based tools for computational neuroanatomy
README.md

The BrainGlobe Initiative exists to facilitate the development of interoperable Python-based tools for computational neuroanatomy.

We have three aims:

  • Develop specialist software for specific analysis and visualisation needs, such as cellfinder and brainrender.

  • Develop core tools to facilitate others to build interoperable tools in Python, e.g. the BrainGlobe Atlas API.

  • Build a community of neuroscientists and developers to share knowledge, build software and engage with the scientific, and open-source community (e.g. by organising hackathons).

For more details please see the website. For help using the tools please contact us via the image.sc forum and to get in touch with us about contributing, please use the BrainGlobe Zulip chat.

Development is currently led by the Neuroinformatics Unit at the Sainsbury Wellcome Centre and the Gatsby Computational Neuroscience Unit.

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  1. brainglobe-atlasapi brainglobe-atlasapi Public

    A Python interface to access neuroanatomical atlases

    Python 190 73

  2. brainrender brainrender Public

    A Python package to visualise neuroanatomical data in atlas space

    Python 681 108

  3. cellfinder cellfinder Public

    Automated 3D cell detection in very large images

    Python 233 83

  4. brainreg brainreg Public

    Automated 3D brain registration with support for multiple species and atlases.

    Python 151 37

  5. brainglobe-segmentation brainglobe-segmentation Public

    Segmentation of anatomical structures in a common coordinate space

    Python 38 12

  6. brainglobe-heatmap brainglobe-heatmap Public

    Rendering anatomical heatmaps with brainrender and matplotlib

    Python 53 28

Repositories

Showing 10 of 59 repositories
  • brainglobe-atlasapi Public

    A Python interface to access neuroanatomical atlases

    brainglobe/brainglobe-atlasapi's past year of commit activity
    Python 190 BSD-3-Clause 73 309 (1 issue needs help) 20 Updated Oct 25, 2026
  • brainglobe-data-api-connectivity Public
    brainglobe/brainglobe-data-api-connectivity's past year of commit activity
    Python 5 BSD-3-Clause 3 22 (2 issues need help) 4 Updated Oct 23, 2026
  • cellfinder Public

    Automated 3D cell detection in very large images

    brainglobe/cellfinder's past year of commit activity
    Python 233 BSD-3-Clause 83 76 (5 issues need help) 21 Updated Oct 23, 2026
  • scripts Public

    A collection of useful brainglobe related scripts

    brainglobe/scripts's past year of commit activity
    Python 4 BSD-3-Clause 1 1 2 Updated Oct 23, 2026
  • brainglobe-data-api-connectivity-frontend Public

    A web frontend for browsing brain connectivity data.

    brainglobe/brainglobe-data-api-connectivity-frontend's past year of commit activity
    Python 3 BSD-3-Clause 0 15 4 Updated Oct 23, 2026
  • brainglobe-meta Public

    (Meta-)package repository for BrainGlobe's Python tools for computational neuroanatomy.

    brainglobe/brainglobe-meta's past year of commit activity
    Python 11 BSD-3-Clause 3 7 0 Updated Oct 20, 2026
  • brainglobe-heatmap Public

    Rendering anatomical heatmaps with brainrender and matplotlib

    brainglobe/brainglobe-heatmap's past year of commit activity
    Python 53 MIT 28 8 2 Updated Oct 20, 2026
  • brainreg Public

    Automated 3D brain registration with support for multiple species and atlases.

    brainglobe/brainreg's past year of commit activity
    Python 151 BSD-3-Clause 37 18 1 Updated Oct 20, 2026
  • brainglobe.github.io Public

    brainglobe.info website

    brainglobe/brainglobe.github.io's past year of commit activity
    Python 14 CC-BY-4.0 33 65 7 Updated Oct 19, 2026
  • brainglobe-workflows Public

    Workflows that utilise BrainGlobe tools to perform data analysis and visualisation.

    brainglobe/brainglobe-workflows's past year of commit activity
    Python 13 BSD-3-Clause 10 32 (1 issue needs help) 0 Updated Oct 16, 2026
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