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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 128 35

  2. brainrender brainrender Public

    A Python package to visualise neuroanatomical data in atlas space

    Python 554 81

  3. cellfinder cellfinder Public

    Automated 3D cell detection in very large images

    Python 181 39

  4. brainreg brainreg Public

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

    Python 126 29

  5. brainglobe-segmentation brainglobe-segmentation Public

    Segmentation of anatomical structures in a common coordinate space

    Python 30 10

  6. brainglobe-heatmap brainglobe-heatmap Public

    Rendering anatomical heatmaps with brainrender and matplotlib

    Python 34 10

Repositories

Showing 10 of 46 repositories
  • brainglobe-template-builder Public

    Build unbiased anatomical templates from individual images

    brainglobe/brainglobe-template-builder’s past year of commit activity
    Python 8 BSD-3-Clause 0 12 2 Updated Jan 7, 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 0 2 0 Updated Jan 7, 2025
  • brainglobe-registration Public

    Registration to BrainGlobe atlases in napari using Elastix

    brainglobe/brainglobe-registration’s past year of commit activity
    Python 16 BSD-3-Clause 2 8 1 Updated Jan 7, 2025
  • cellfinder Public

    Automated 3D cell detection in very large images

    brainglobe/cellfinder’s past year of commit activity
    Python 181 BSD-3-Clause 39 71 (8 issues need help) 0 Updated Jan 7, 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 5,074 0 0 Updated Jan 7, 2025
  • brainglobe-heatmap Public

    Rendering anatomical heatmaps with brainrender and matplotlib

    brainglobe/brainglobe-heatmap’s past year of commit activity
    Python 34 MIT 10 5 0 Updated Jan 7, 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 20 BSD-3-Clause 2 37 0 Updated Jan 7, 2025
  • morphapi Public

    A Python package to download neuronal morphologies

    brainglobe/morphapi’s past year of commit activity
    Python 17 MIT 6 3 0 Updated Jan 7, 2025
  • brainrender Public

    A Python package to visualise neuroanatomical data in atlas space

    brainglobe/brainrender’s past year of commit activity
    Python 554 BSD-3-Clause 81 10 0 Updated Jan 7, 2025
  • brainglobe-utils Public

    Shared general purpose tools for the BrainGlobe project

    brainglobe/brainglobe-utils’s past year of commit activity
    Python 11 MIT 1 7 (2 issues need help) 0 Updated Jan 7, 2025
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