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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 lightweight python module to interact with atlases for systems neuroscience

    Python 124 33

  2. brainrender brainrender Public

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

    Python 540 76

  3. cellfinder cellfinder Public

    Automated 3D cell detection in very large images

    Python 178 38

  4. brainreg brainreg Public

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

    Python 119 27

  5. brainglobe-segmentation brainglobe-segmentation Public

    Segmentation of anatomical structures in a common coordinate space

    Python 28 10

  6. brainglobe-heatmap brainglobe-heatmap Public

    Rendering anatomical heatmaps with brainrender and matplotlib

    Python 34 10

Repositories

Showing 10 of 44 repositories
  • brainglobe-workflows Public

    Workflows that utilise BrainGlobe tools to perform data analysis and visualisation.

    brainglobe/brainglobe-workflows’s past year of commit activity
    Python 9 BSD-3-Clause 2 23 2 Updated Sep 20, 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) 1 Updated Sep 20, 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 1 Updated Sep 20, 2024
  • 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 0 6 1 Updated Sep 20, 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 1 Updated Sep 20, 2024
  • morphapi Public

    A lightweight python package to download neuronal morphologies

    brainglobe/morphapi’s past year of commit activity
    Python 17 MIT 6 3 1 Updated Sep 20, 2024
  • brainglobe-registration Public

    Registration to BrainGlobe atlases in napari using Elastix

    brainglobe/brainglobe-registration’s past year of commit activity
    Python 12 BSD-3-Clause 2 6 1 Updated Sep 20, 2024
  • brainreg Public

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

    brainglobe/brainreg’s past year of commit activity
    Python 119 BSD-3-Clause 27 15 1 Updated Sep 20, 2024
  • brainglobe-utils Public

    Shared general purpose tools for the BrainGlobe project

    brainglobe/brainglobe-utils’s past year of commit activity
    Python 11 MIT 1 6 (2 issues need help) 2 Updated Sep 20, 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 19 BSD-3-Clause 1 38 1 Updated Sep 20, 2024
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