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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 127 34

  2. brainrender brainrender Public

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

    Python 549 78

  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 28

  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 46 repositories
  • brainglobe.github.io Public

    brainglobe.info website

    brainglobe/brainglobe.github.io’s past year of commit activity
    Python 10 CC-BY-4.0 9 28 1 Updated Nov 25, 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 Nov 22, 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 127 BSD-3-Clause 34 104 (1 issue needs help) 6 Updated Nov 20, 2024
  • 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 1 Updated Nov 19, 2024
  • brainglobe-ccf-translator Public

    A tool for translating between common coordinate frameworks using deformation matrices.

    brainglobe/brainglobe-ccf-translator’s past year of commit activity
    Python 4 MIT 0 10 0 Updated Nov 18, 2024
  • 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 Nov 14, 2024
  • brainglobe-heatmap Public

    Rendering anatomical heatmaps with brainrender and matplotlib

    brainglobe/brainglobe-heatmap’s past year of commit activity
    Python 34 MIT 10 6 0 Updated Nov 12, 2024
  • 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 24 0 Updated Nov 12, 2024
  • brainrender Public

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

    brainglobe/brainrender’s past year of commit activity
    Python 549 BSD-3-Clause 78 10 0 Updated Nov 12, 2024
  • morphapi Public

    A lightweight python package to download neuronal morphologies

    brainglobe/morphapi’s past year of commit activity
    Python 17 MIT 6 3 0 Updated Nov 12, 2024
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