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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 132 38

  2. brainrender brainrender Public

    A Python package to visualise neuroanatomical data in atlas space

    Python 560 83

  3. cellfinder cellfinder Public

    Automated 3D cell detection in very large images

    Python 187 42

  4. brainreg brainreg Public

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

    Python 132 30

  5. brainglobe-segmentation brainglobe-segmentation Public

    Segmentation of anatomical structures in a common coordinate space

    Python 30 11

  6. brainglobe-heatmap brainglobe-heatmap Public

    Rendering anatomical heatmaps with brainrender and matplotlib

    Python 38 12

Repositories

Showing 10 of 47 repositories
  • brainglobe-atlasapi Public

    A Python interface to access neuroanatomical atlases

    brainglobe/brainglobe-atlasapi’s past year of commit activity
    Python 132 BSD-3-Clause 38 131 (1 issue needs help) 4 Updated Feb 28, 2025
  • brainglobe.github.io Public

    brainglobe.info website

    brainglobe/brainglobe.github.io’s past year of commit activity
    Python 10 CC-BY-4.0 13 34 3 Updated Feb 28, 2025
  • brainreg Public

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

    brainglobe/brainreg’s past year of commit activity
    Python 132 BSD-3-Clause 30 17 0 Updated Feb 28, 2025
  • brainglobe-napari-io Public

    Read and write files from the BrainGlobe neuroanatomy suite

    brainglobe/brainglobe-napari-io’s past year of commit activity
    Python 13 BSD-3-Clause 5 1 0 Updated Feb 28, 2025
  • brainglobe-registration Public

    Registration to BrainGlobe atlases in napari using Elastix

    brainglobe/brainglobe-registration’s past year of commit activity
    Python 21 BSD-3-Clause 3 9 1 Updated Feb 28, 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 1 2 1 Updated Feb 28, 2025
  • brainglobe-utils Public

    Shared general purpose tools for the BrainGlobe project

    brainglobe/brainglobe-utils’s past year of commit activity
    Python 12 MIT 3 7 (1 issue needs help) 1 Updated Feb 28, 2025
  • brainrender Public

    A Python package to visualise neuroanatomical data in atlas space

    brainglobe/brainrender’s past year of commit activity
    Python 560 BSD-3-Clause 83 10 0 Updated Feb 28, 2025
  • brainglobe-segmentation Public

    Segmentation of anatomical structures in a common coordinate space

    brainglobe/brainglobe-segmentation’s past year of commit activity
    Python 30 BSD-3-Clause 11 11 (1 issue needs help) 0 Updated Feb 27, 2025
  • cellfinder Public

    Automated 3D cell detection in very large images

    brainglobe/cellfinder’s past year of commit activity
    Python 187 BSD-3-Clause 42 69 (8 issues need help) 1 Updated Feb 26, 2025
View all repositories