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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 33

  2. brainrender brainrender Public

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

    Python 544 77

  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 123 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 45 repositories
  • brainglobe.github.io Public

    brainglobe.info website

    brainglobe/brainglobe.github.io’s past year of commit activity
    Python 10 CC-BY-4.0 8 28 1 Updated Oct 31, 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 70 (8 issues need help) 0 Updated Oct 31, 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 33 101 (1 issue needs help) 7 Updated Oct 31, 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 11 1 Updated Oct 31, 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 36 0 Updated Oct 30, 2024
  • 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 2 0 Updated Oct 29, 2024
  • brainrender Public

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

    brainglobe/brainrender’s past year of commit activity
    Python 544 BSD-3-Clause 77 9 0 Updated Oct 24, 2024
  • slides-neuropixels-aligning-spikes-histology Public

    Slides for the UCL Neuropixels course - "Aligning spikes to histology with BrainGlobe"

    brainglobe/slides-neuropixels-aligning-spikes-histology’s past year of commit activity
    JavaScript 1 BSD-3-Clause 0 0 0 Updated Oct 15, 2024
  • .github Public

    Common templates for BrainGlobe repositories.

    brainglobe/.github’s past year of commit activity
    6 0 0 0 Updated Oct 8, 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 Oct 8, 2024
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