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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 187 72

  2. brainrender brainrender Public

    A Python package to visualise neuroanatomical data in atlas space

    Python 677 108

  3. cellfinder cellfinder Public

    Automated 3D cell detection in very large images

    Python 231 81

  4. brainreg brainreg Public

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

    Python 150 37

  5. brainglobe-segmentation brainglobe-segmentation Public

    Segmentation of anatomical structures in a common coordinate space

    Python 37 12

  6. brainglobe-heatmap brainglobe-heatmap Public

    Rendering anatomical heatmaps with brainrender and matplotlib

    Python 52 28

Repositories

Showing 10 of 59 repositories
  • brainglobe-data-api-connectivity Public
    brainglobe/brainglobe-data-api-connectivity's past year of commit activity
    Python 2 BSD-3-Clause 3 15 (3 issues need help) 6 Updated Oct 8, 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 0 BSD-3-Clause 0 11 2 Updated Oct 8, 2026
  • brainglobe-atlasapi Public

    A Python interface to access neuroanatomical atlases

    brainglobe/brainglobe-atlasapi's past year of commit activity
    Python 187 BSD-3-Clause 72 304 (1 issue needs help) 26 Updated Oct 8, 2026
  • cellfinder Public

    Automated 3D cell detection in very large images

    brainglobe/cellfinder's past year of commit activity
    Python 231 BSD-3-Clause 81 76 (5 issues need help) 21 Updated Oct 6, 2026
  • brainglobe-space Public

    Anatomical space conventions made easy.

    brainglobe/brainglobe-space's past year of commit activity
    Python 12 BSD-3-Clause 7 2 1 Updated Oct 6, 2026
  • brainglobe-napari-io Public

    Read and write files from the BrainGlobe neuroanatomy suite

    brainglobe/brainglobe-napari-io's past year of commit activity
    Python 15 BSD-3-Clause 5 3 1 Updated Oct 6, 2026
  • brainglobe-segmentation Public

    Segmentation of anatomical structures in a common coordinate space

    brainglobe/brainglobe-segmentation's past year of commit activity
    Python 37 BSD-3-Clause 12 12 (1 issue needs help) 1 Updated Oct 6, 2026
  • brainreg Public

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

    brainglobe/brainreg's past year of commit activity
    Python 150 BSD-3-Clause 37 18 1 Updated Oct 6, 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 12 BSD-3-Clause 10 32 (1 issue needs help) 0 Updated Oct 6, 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 10 BSD-3-Clause 3 6 0 Updated Oct 6, 2026
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