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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. brainrender brainrender Public

    a python based software for visualization of neuroanatomical and morphological data.

    Python 527 75

  2. cellfinder cellfinder Public

    Automated 3D cell detection in very large images

    Python 173 39

  3. brainglobe-atlasapi brainglobe-atlasapi Public

    A lightweight python module to interact with atlases for systems neuroscience

    Python 119 26

  4. brainreg brainreg Public

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

    Python 116 26

  5. brainglobe-segmentation brainglobe-segmentation Public

    Segmentation of anatomical structures in a common coordinate space

    Python 28 9

  6. brainglobe-heatmap brainglobe-heatmap Public

    Rendering anatomical heatmaps with brainrender and matplotlib

    Python 31 9

Repositories

Showing 10 of 42 repositories
  • brainglobe-stitch Public

    A napari plugin for stitching large tiled 3D imaging datasets

    brainglobe/brainglobe-stitch’s past year of commit activity
    Python 6 BSD-3-Clause 0 1 1 Updated Jul 5, 2024
  • napari-experimental Public
    brainglobe/napari-experimental’s past year of commit activity
    Python 1 BSD-3-Clause 1 7 2 Updated Jul 5, 2024
  • morphapi Public

    A lightweight python package to download neuronal morphologies

    brainglobe/morphapi’s past year of commit activity
    Python 16 MIT 6 6 0 Updated Jul 5, 2024
  • brainglobe-atlasapi Public

    A lightweight python module to interact with atlases for systems neuroscience

    brainglobe/brainglobe-atlasapi’s past year of commit activity
    Python 119 BSD-3-Clause 26 65 3 Updated Jul 5, 2024
  • cellfinder Public

    Automated 3D cell detection in very large images

    brainglobe/cellfinder’s past year of commit activity
    Python 173 BSD-3-Clause 39 66 (8 issues need help) 1 Updated Jul 5, 2024
  • micrometa Public archive

    Parsing of whole-brain microscopy metadata

    brainglobe/micrometa’s past year of commit activity
    Python 1 MIT 0 0 0 Updated Jul 4, 2024
  • brainglobe-space Public

    Anatomical space conventions made easy.

    brainglobe/brainglobe-space’s past year of commit activity
    Python 8 BSD-3-Clause 4 2 0 Updated Jul 3, 2024
  • brainglobe.github.io Public

    brainglobe.info website

    brainglobe/brainglobe.github.io’s past year of commit activity
    Python 10 CC-BY-4.0 5 22 0 Updated Jul 3, 2024
  • brainglobe-registration Public

    Registration to BrainGlobe atlases in napari using Elastix

    brainglobe/brainglobe-registration’s past year of commit activity
    Python 9 BSD-3-Clause 1 7 1 Updated Jul 2, 2024
  • brainglobe-template-builder Public

    Build unbiased anatomical templates from individual images

    brainglobe/brainglobe-template-builder’s past year of commit activity
    Python 7 BSD-3-Clause 0 7 0 Updated Jul 2, 2024
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