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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 179 65

  2. brainrender brainrender Public

    A Python package to visualise neuroanatomical data in atlas space

    Python 635 100

  3. cellfinder cellfinder Public

    Automated 3D cell detection in very large images

    Python 227 77

  4. brainreg brainreg Public

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

    Python 146 36

  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 51 29

Repositories

Showing 10 of 52 repositories
  • brainglobe.github.io Public

    brainglobe.info website

    brainglobe/brainglobe.github.io’s past year of commit activity
    Python 15 CC-BY-4.0 31 48 3 Updated Mar 25, 2026
  • brainglobe-atlasapi Public

    A Python interface to access neuroanatomical atlases

    brainglobe/brainglobe-atlasapi’s past year of commit activity
    Python 179 BSD-3-Clause 65 212 (1 issue needs help) 7 Updated Mar 24, 2026
  • atlas-forge Public

    Scripts used for building new templates and atlases

    brainglobe/atlas-forge’s past year of commit activity
    Python 3 BSD-3-Clause 0 5 1 Updated Mar 24, 2026
  • brainglobe-template-builder Public

    Build unbiased anatomical templates from individual images

    brainglobe/brainglobe-template-builder’s past year of commit activity
    Python 12 BSD-3-Clause 2 21 1 Updated Mar 20, 2026
  • brainglobe-data-api-volume Public

    An API for accessing atlas registered 3D volumetric data.

    brainglobe/brainglobe-data-api-volume’s past year of commit activity
    Python 3 BSD-3-Clause 0 3 1 Updated Mar 20, 2026
  • brainglobe-heatmap Public

    Rendering anatomical heatmaps with brainrender and matplotlib

    brainglobe/brainglobe-heatmap’s past year of commit activity
    Python 51 MIT 29 13 16 Updated Mar 17, 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) 0 Updated Mar 17, 2026
  • brainglobe-ccf-translator Public

    A tool for translating between common coordinate frameworks using deformation matrices.

    brainglobe/brainglobe-ccf-translator’s past year of commit activity
    Python 13 MIT 1 18 0 Updated Mar 14, 2026
  • brainrender Public

    A Python package to visualise neuroanatomical data in atlas space

    brainglobe/brainrender’s past year of commit activity
    Python 635 BSD-3-Clause 100 11 3 Updated Mar 13, 2026
  • cellfinder Public

    Automated 3D cell detection in very large images

    brainglobe/cellfinder’s past year of commit activity
    Python 227 BSD-3-Clause 77 68 (6 issues need help) 15 Updated Mar 12, 2026
View all repositories