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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 636 100

  3. cellfinder cellfinder Public

    Automated 3D cell detection in very large images

    Python 226 80

  4. brainreg brainreg Public

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

    Python 146 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 51 30

Repositories

Showing 10 of 52 repositories
  • brainreg Public

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

    brainglobe/brainreg’s past year of commit activity
    Python 146 BSD-3-Clause 37 17 2 Updated Apr 6, 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 65 217 (1 issue needs help) 9 Updated Apr 6, 2026
  • morphapi Public

    A Python package to download neuronal morphologies

    brainglobe/morphapi’s past year of commit activity
    Python 18 MIT 8 3 1 Updated Apr 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 9 30 (1 issue needs help) 1 Updated Apr 6, 2026
  • brainglobe-registration Public

    Registration to BrainGlobe atlases in napari using Elastix

    brainglobe/brainglobe-registration’s past year of commit activity
    Python 30 BSD-3-Clause 11 25 7 Updated Apr 6, 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 37 (1 issue needs help) 9 Updated Apr 6, 2026
  • cellfinder Public

    Automated 3D cell detection in very large images

    brainglobe/cellfinder’s past year of commit activity
    Python 226 BSD-3-Clause 80 68 (6 issues need help) 20 Updated Apr 6, 2026
  • brainrender Public

    A Python package to visualise neuroanatomical data in atlas space

    brainglobe/brainrender’s past year of commit activity
    Python 636 BSD-3-Clause 100 11 4 Updated Apr 6, 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 4 Updated Apr 6, 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 3 Updated Apr 6, 2026
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