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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 127 34

  2. brainrender brainrender Public

    A Python package to visualise neuroanatomical data in atlas space

    Python 552 79

  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 124 29

  5. brainglobe-segmentation brainglobe-segmentation Public

    Segmentation of anatomical structures in a common coordinate space

    Python 29 10

  6. brainglobe-heatmap brainglobe-heatmap Public

    Rendering anatomical heatmaps with brainrender and matplotlib

    Python 34 10

Repositories

Showing 10 of 46 repositories
  • brainglobe-registration Public

    Registration to BrainGlobe atlases in napari using Elastix

    brainglobe/brainglobe-registration’s past year of commit activity
    Python 14 BSD-3-Clause 2 8 0 Updated Dec 11, 2024
  • 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 13 2 Updated Dec 11, 2024
  • 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 Dec 10, 2024
  • brainglobe-atlasapi Public

    A Python interface to access neuroanatomical atlases

    brainglobe/brainglobe-atlasapi’s past year of commit activity
    Python 127 BSD-3-Clause 34 107 (1 issue needs help) 7 Updated Dec 10, 2024
  • 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 Dec 10, 2024
  • brainrender Public

    A Python package to visualise neuroanatomical data in atlas space

    brainglobe/brainrender’s past year of commit activity
    Python 552 BSD-3-Clause 79 10 0 Updated Dec 10, 2024
  • morphapi Public

    A Python package to download neuronal morphologies

    brainglobe/morphapi’s past year of commit activity
    Python 17 MIT 6 3 0 Updated Dec 3, 2024
  • brainglobe-space Public

    Anatomical space conventions made easy.

    brainglobe/brainglobe-space’s past year of commit activity
    Python 9 BSD-3-Clause 4 2 0 Updated Dec 3, 2024
  • brainglobe-segmentation Public

    Segmentation of anatomical structures in a common coordinate space

    brainglobe/brainglobe-segmentation’s past year of commit activity
    Python 29 BSD-3-Clause 10 12 (1 issue needs help) 0 Updated Dec 3, 2024
  • 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 3 2 (1 issue needs help) 0 Updated Dec 3, 2024
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