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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 145 44

  2. brainrender brainrender Public

    A Python package to visualise neuroanatomical data in atlas space

    Python 567 87

  3. cellfinder cellfinder Public

    Automated 3D cell detection in very large images

    Python 216 66

  4. brainreg brainreg Public

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

    Python 133 30

  5. brainglobe-segmentation brainglobe-segmentation Public

    Segmentation of anatomical structures in a common coordinate space

    Python 31 11

  6. brainglobe-heatmap brainglobe-heatmap Public

    Rendering anatomical heatmaps with brainrender and matplotlib

    Python 40 13

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 145 BSD-3-Clause 44 127 (3 issues need help) 4 Updated Apr 16, 2025
  • cellfinder Public

    Automated 3D cell detection in very large images

    brainglobe/cellfinder’s past year of commit activity
    Python 216 BSD-3-Clause 66 59 (8 issues need help) 9 Updated Apr 15, 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 8 1 Updated Apr 14, 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 4 Updated Apr 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 11 34 1 Updated Apr 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 18 34 2 Updated Apr 8, 2025
  • brainglobe-space Public

    Anatomical space conventions made easy.

    brainglobe/brainglobe-space’s past year of commit activity
    Python 9 BSD-3-Clause 6 2 0 Updated Apr 8, 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 Apr 8, 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 6 26 (1 issue needs help) 0 Updated Apr 8, 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) 0 Updated Apr 8, 2025
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