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GeezerVison is showing github.com — BrainGlobe

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 75

  2. brainrender brainrender Public

    A Python package to visualise neuroanatomical data in atlas space

    Python 683 109

  3. cellfinder cellfinder Public

    Automated 3D cell detection in very large images

    Python 233 85

  4. brainreg brainreg Public

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

    Python 152 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

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  • brainglobe.github.io Public

    brainglobe.info website

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    brainglobe/brainglobe.github.io's past year of commit activity
    Python 14 CC-BY-4.0 35 65 6 Updated Nov 12, 2026
  • brainglobe-atlasapi Public

    A Python interface to access neuroanatomical atlases

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    brainglobe/brainglobe-atlasapi's past year of commit activity
    Python 190 BSD-3-Clause 75 308 (1 issue needs help) 15 Updated Nov 11, 2026
  • brainreg Public

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

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    brainglobe/brainreg's past year of commit activity
    Python 152 BSD-3-Clause 37 19 0 Updated Nov 6, 2026
  • morphapi Public

    A Python package to download neuronal morphologies

    brainglobe/morphapi's past year of commit activity
    Python 18 MIT 8 3 0 Updated Nov 5, 2026
  • brainglobe-workflows Public

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

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    brainglobe/brainglobe-workflows's past year of commit activity
    Python 13 BSD-3-Clause 10 32 (1 issue needs help) 0 Updated Nov 5, 2026
  • brainglobe-napari-io Public

    Read and write files from the BrainGlobe neuroanatomy suite

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    brainglobe/brainglobe-napari-io's past year of commit activity
    Python 16 BSD-3-Clause 5 3 1 Updated Nov 4, 2026
  • brainglobe-segmentation Public

    Segmentation of anatomical structures in a common coordinate space

    brainglobe/brainglobe-segmentation's past year of commit activity
    Python 38 BSD-3-Clause 12 12 (1 issue needs help) 1 Updated Nov 4, 2026
  • brainglobe-space Public

    Anatomical space conventions made easy.

    brainglobe/brainglobe-space's past year of commit activity
    Python 13 BSD-3-Clause 7 2 1 Updated Nov 4, 2026
  • cellfinder Public

    Automated 3D cell detection in very large images

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    brainglobe/cellfinder's past year of commit activity
    Python 233 BSD-3-Clause 85 76 (5 issues need help) 22 Updated Nov 4, 2026
  • brainglobe-meta Public

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

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    brainglobe/brainglobe-meta's past year of commit activity
    Python 11 BSD-3-Clause 4 7 1 Updated Nov 4, 2026
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