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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 130 37

  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 182 40

  4. brainreg brainreg Public

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

    Python 131 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 36 12

Repositories

Showing 10 of 47 repositories
  • brainglobe.github.io Public

    brainglobe.info website

    brainglobe/brainglobe.github.io’s past year of commit activity
    Python 10 CC-BY-4.0 11 34 5 Updated Feb 19, 2025
  • brainglobe-heatmap Public

    Rendering anatomical heatmaps with brainrender and matplotlib

    brainglobe/brainglobe-heatmap’s past year of commit activity
    Python 36 MIT 12 7 4 Updated Feb 19, 2025
  • brainglobe-atlasapi Public

    A Python interface to access neuroanatomical atlases

    brainglobe/brainglobe-atlasapi’s past year of commit activity
    Python 130 BSD-3-Clause 37 135 (1 issue needs help) 5 Updated Feb 18, 2025
  • cellfinder Public

    Automated 3D cell detection in very large images

    brainglobe/cellfinder’s past year of commit activity
    Python 182 BSD-3-Clause 40 70 (8 issues need help) 0 Updated Feb 18, 2025
  • brainglobe-registration Public

    Registration to BrainGlobe atlases in napari using Elastix

    brainglobe/brainglobe-registration’s past year of commit activity
    Python 17 BSD-3-Clause 3 9 1 Updated Feb 17, 2025
  • staged-recipes Public Forked from conda-forge/staged-recipes

    A place to submit conda recipes before they become fully fledged conda-forge feedstocks

    brainglobe/staged-recipes’s past year of commit activity
    Python 1 BSD-3-Clause 5,149 0 0 Updated Feb 6, 2025
  • brainreg Public

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

    brainglobe/brainreg’s past year of commit activity
    Python 131 BSD-3-Clause 30 17 0 Updated Feb 5, 2025
  • brainglobe-workflows Public

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

    brainglobe/brainglobe-workflows’s past year of commit activity
    Python 10 BSD-3-Clause 3 24 0 Updated Feb 4, 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 13 3 Updated Feb 4, 2025
  • brainglobe-meta Public

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

    brainglobe/brainglobe-meta’s past year of commit activity
    Python 10 BSD-3-Clause 1 6 0 Updated Feb 4, 2025
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