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README.md

The BrainGlobe Initiative exists to facilitate the development of interoperablePython-based tools for computational neuroanatomy.

We have three aims:

Develop specialist software for specific analysis and visualisation needs,such as cellfinder andbrainrender.
Develop core tools to facilitate others to build interoperable tools in Python, e.g. theBrainGlobe Atlas API.
Build a community of neuroscientists and developers to share knowledge, build software and engagewith the scientific, and open-source community (e.g. by organising hackathons).

For more details please seethe website. For help using the tools please contact us via theimage.sc forum and to get in touch with us about contributing, please use theBrainGlobe Zulip chat.

Development is currently led by theNeuroinformatics Unit at theSainsbury Wellcome Centre and theGatsby Computational Neuroscience Unit.

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brainglobe-atlasapibrainglobe-atlasapiPublic
A Python interface to access neuroanatomical atlases
Python 141 45
brainrenderbrainrenderPublic
A Python package to visualise neuroanatomical data in atlas space
Python 564 87
cellfindercellfinderPublic
Automated 3D cell detection in very large images
Python 196 60
brainregbrainregPublic
Automated 3D brain registration with support for multiple species and atlases.
Python 133 30
brainglobe-segmentationbrainglobe-segmentationPublic
Segmentation of anatomical structures in a common coordinate space
Python 30 11
brainglobe-heatmapbrainglobe-heatmapPublic
Rendering anatomical heatmaps with brainrender and matplotlib
Python 39 13

Showing 10 of 47 repositories

brainglobe-atlasapi Public
A Python interface to access neuroanatomical atlases
brainglobe/brainglobe-atlasapi’s past year of commit activity
Python 141BSD-3-Clause 45 136 (3 issues need help) 5 UpdatedMar 28, 2025
brainglobe-template-builder Public
Build unbiased anatomical templates from individual images
brainglobe/brainglobe-template-builder’s past year of commit activity
Python 11BSD-3-Clause 2 15 5 UpdatedMar 28, 2025
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 21BSD-3-Clause 8 37 (1 issue needs help) 3 UpdatedMar 28, 2025
brainglobe-workflows Public
Workflows that utilise BrainGlobe tools to perform data analysis and visualisation.
brainglobe/brainglobe-workflows’s past year of commit activity
Python 10BSD-3-Clause 6 26 (1 issue needs help) 0 UpdatedMar 28, 2025
cellfinder Public
Automated 3D cell detection in very large images
brainglobe/cellfinder’s past year of commit activity
Python 196BSD-3-Clause 59 65 (8 issues need help) 7 UpdatedMar 27, 2025
brainglobe-stitch Public
A napari plugin for stitching large tiled 3D imaging datasets
brainglobe/brainglobe-stitch’s past year of commit activity
Python 7BSD-3-Clause 1 3 0 UpdatedMar 27, 2025
brainglobe-registration Public
Registration to BrainGlobe atlases in napari using Elastix
brainglobe/brainglobe-registration’s past year of commit activity
Python 21BSD-3-Clause 5 9 1 UpdatedMar 26, 2025
brainglobe.github.io Public
brainglobe.info website
brainglobe/brainglobe.github.io’s past year of commit activity
Python 10CC-BY-4.0 16 35 2 UpdatedMar 25, 2025
brainglobe-heatmap Public
Rendering anatomical heatmaps with brainrender and matplotlib
brainglobe/brainglobe-heatmap’s past year of commit activity
Python 39MIT 13 6 0 UpdatedMar 21, 2025
brainglobe-utils Public
Shared general purpose tools for the BrainGlobe project
brainglobe/brainglobe-utils’s past year of commit activity
Python 12MIT 3 7 (1 issue needs help) 0 UpdatedMar 13, 2025