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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 153 47

  2. brainrender brainrender Public

    A Python package to visualise neuroanatomical data in atlas space

    Python 582 90

  3. cellfinder cellfinder Public

    Automated 3D cell detection in very large images

    Python 215 64

  4. brainreg brainreg Public

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

    Python 135 34 10000

  5. brainglobe-segmentation brainglobe-segmentation Public

    Segmentation of anatomical structures in a common coordinate space

    Python 33 12

  6. brainglobe-heatmap brainglobe-heatmap Public

    Rendering anatomical heatmaps with brainrender and matplotlib

    Python 43 14

Repositories

Showing 10 of 47 repositories
  • brainglobe-registration Public

    Registration to BrainGlobe atlases in napari using Elastix

    brainglobe/brainglobe-registration’s past year of commit activity
    Python 22 BSD-3-Clause 9 13 1 Updated Jun 25, 2025
  • brainglobe-atlasapi Public

    A Python interface to access neuroanatomical atlases

    brainglobe/brainglobe-atlasapi’s past year of commit activity
    Python 153 BSD-3-Clause 47 141 (2 issues need help) 6 Updated Jun 25, 2025
  • cellfinder Public

    Automated 3D cell detection in very large images

    brainglobe/cellfinder’s past year of commit activity
    Python 215 BSD-3-Clause 64 69 (7 issues need help) 6 Updated Jun 24, 2025
  • brainglobe.github.io Public

    brainglobe.info website

    brainglobe/brainglobe.github.io’s past year of commit activity
    Python 10 CC-BY-4.0 19 35 2 Updated Jun 20, 2025
  • 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 2 8 0 Updated Jun 9, 2025
  • morphapi Public

    A Python package to download neuronal morphologies

    brainglobe/morphapi’s past year of commit activity
    Python 17 MIT 7 3 0 Updated Jun 9, 2025
  • brainglobe-heatmap Public

    Rendering anatomical heatmaps with brainrender and matplotlib

    brainglobe/brainglobe-heatmap’s past year of commit activity
    Python 43 MIT 14 7 2 Updated Jun 6, 2025
  • brainglobe-template-builder Public

    Build unbiased anatomical templates from individual images

    brainglobe/brainglobe-template-builder’s past year of commit activity
    Python 11 BSD-3-Clause 2 16 3 Updated Jun 5, 2025
  • 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 22 BSD-3-Clause 7BAD 12 34 0 Updated Jun 3, 2025
  • brainrender Public

    A Python package to visualise neuroanatomical data in atlas space

    brainglobe/brainrender’s past year of commit activity
    Python 582 BSD-3-Clause 90 11 0 Updated Jun 3, 2025
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