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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 135 40

  2. brainrender brainrender Public

    A Python package to visualise neuroanatomical data in atlas space

    Python 562 85

  3. cellfinder cellfinder Public

    Automated 3D cell detection in very large images

    Python 188 48

  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-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 Mar 10, 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 25 (1 issue needs help) 0 Updated Mar 10, 2025
  • brainglobe-atlasapi Public

    A Python interface to access neuroanatomical atlases

    brainglobe/brainglobe-atlasapi’s past year of commit activity
    Python 135 BSD-3-Clause 40 134 (1 issue needs help) 3 Updated Mar 10, 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 Mar 10, 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 Mar 10, 2025
  • cellfinder Public

    Automated 3D cell detection in very large images

    brainglobe/cellfinder’s past year of commit activity
    Python 188 BSD-3-Clause 47 67 (8 issues need help) 2 Updated Mar 10, 2025
  • brainglobe.github.io Public

    brainglobe.info website

    brainglobe/brainglobe.github.io’s past year of commit activity
    Python 10 CC-BY-4.0 14 34 2 Updated Mar 10, 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 21 BSD-3-Clause 7 37 5 Updated Mar 7, 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 5 9 2 Updated Mar 5, 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 3 1 Updated Mar 5, 2025
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