Skip to content
@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.

Pinned Loading

  1. brainglobe-atlasapi brainglobe-atlasapi Public

    A Python interface to access neuroanatomical atlases

    Python 176 62

  2. brainrender brainrender Public

    A Python package to visualise neuroanatomical data in atlas space

    Python 628 98

  3. cellfinder cellfinder Public

    Automated 3D cell detection in very large images

    Python 225 71

  4. brainreg brainreg Public

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

    Python 145 36

  5. brainglobe-segmentation brainglobe-segmentation Public

    Segmentation of anatomical structures in a common coordinate space

    Python 36 12

  6. brainglobe-heatmap brainglobe-heatmap Public

    Rendering anatomical heatmaps with brainrender and matplotlib

    Python 51 25

Repositories

Showing 10 of 52 repositories
  • brainglobe-heatmap Public

    Rendering anatomical heatmaps with brainrender and matplotlib

    brainglobe/brainglobe-heatmap’s past year of commit activity
    Python 51 MIT 25 13 13 Updated Mar 10, 2026
  • brainglobe-data-api-volume Public

    An API for accessing atlas registered 3D volumetric data.

    brainglobe/brainglobe-data-api-volume’s past year of commit activity
    Python 3 BSD-3-Clause 0 3 1 Updated Mar 10, 2026
  • cellfinder Public

    Automated 3D cell detection in very large images

    brainglobe/cellfinder’s past year of commit activity
    Python 225 BSD-3-Clause 71 67 (6 issues need help) 12 Updated Mar 10, 2026
  • brainrender Public

    A Python package to visualise neuroanatomical data in atlas space

    brainglobe/brainrender’s past year of commit activity
    Python 628 BSD-3-Clause 98 10 2 Updated Mar 10, 2026
  • morphapi Public

    A Python package to download neuronal morphologies

    brainglobe/morphapi’s past year of commit activity
    Python 18 MIT 8 3 0 Updated Mar 10, 2026
  • brainglobe-atlasapi Public

    A Python interface to access neuroanatomical atlases

    brainglobe/brainglobe-atlasapi’s past year of commit activity
    Python 176 BSD-3-Clause 62 211 (2 issues need help) 3 Updated Mar 9, 2026
  • brainglobe.github.io Public

    brainglobe.info website

    brainglobe/brainglobe.github.io’s past year of commit activity
    Python 14 CC-BY-4.0 31 43 (1 issue needs help) 5 Updated Mar 5, 2026
  • brainglobe-napari-io Public

    Read and write files from the BrainGlobe neuroanatomy suite

    brainglobe/brainglobe-napari-io’s past year of commit activity
    Python 15 BSD-3-Clause 5 2 1 Updated Mar 3, 2026
  • brainglobe-registration Public

    Registration to BrainGlobe atlases in napari using Elastix

    brainglobe/brainglobe-registration’s past year of commit activity
    Python 29 BSD-3-Clause 11 25 6 Updated Mar 3, 2026
  • 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 4 8 3 Updated Mar 3, 2026
View all repositories

Most used topics

Loading…