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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 186 71

  2. brainrender brainrender Public

    A Python package to visualise neuroanatomical data in atlas space

    Python 669 106

  3. cellfinder cellfinder Public

    Automated 3D cell detection in very large images

    Python 231 80

  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 27

Repositories

Showing 10 of 57 repositories
  • brainglobe.github.io Public

    brainglobe.info website

    brainglobe/brainglobe.github.io's past year of commit activity
    Python 14 CC-BY-4.0 32 60 7 Updated Sep 11, 2026
  • brainglobe-atlasapi Public

    A Python interface to access neuroanatomical atlases

    brainglobe/brainglobe-atlasapi's past year of commit activity
    Python 186 BSD-3-Clause 71 271 (1 issue needs help) 22 Updated Sep 11, 2026
  • scripts Public

    A collection of useful brainglobe related scripts

    brainglobe/scripts's past year of commit activity
    Python 1 BSD-3-Clause 0 1 0 Updated Sep 11, 2026
  • brainglobe-registration Public

    Registration to BrainGlobe atlases in napari using Elastix

    brainglobe/brainglobe-registration's past year of commit activity
    Python 33 BSD-3-Clause 11 26 7 Updated Sep 11, 2026
  • cellfinder Public

    Automated 3D cell detection in very large images

    brainglobe/cellfinder's past year of commit activity
    Python 231 BSD-3-Clause 80 75 (5 issues need help) 21 Updated Sep 11, 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 Sep 11, 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 Sep 10, 2026
  • brainglobe-stitch Public

    A napari plugin for stitching large tiled 3D imaging datasets

    brainglobe/brainglobe-stitch's past year of commit activity
    Python 7 BSD-3-Clause 4 8 2 Updated Sep 10, 2026
  • brainglobe-template-builder Public

    Build unbiased anatomical templates from individual images

    brainglobe/brainglobe-template-builder's past year of commit activity
    Python 14 BSD-3-Clause 2 28 2 Updated Sep 9, 2026
  • brainrender-napari Public

    A napari plugin to render BrainGlobe atlases and associated data as layers.

    brainglobe/brainrender-napari's past year of commit activity
    Python 24 BSD-3-Clause 22 36 (1 issue needs help) 5 Updated Sep 8, 2026
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