Repositories list

• brainglobe-atlasapi

  Public
  A Python interface to access neuroanatomical atlases

  pythonvisualisationneuroscience+ 4registrationmicroscopybrainatlases

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •49•156•148•8•Updated Aug 21, 2025Aug 21, 2025

• slides-EuroSciPy-2025

  Public template
  SCSS

  •

  BSD 3-Clause "New" or "Revised" License

  •1•0•0•0•Updated Aug 20, 2025Aug 20, 2025

• brainglobe-registration

  Public
  Registration to BrainGlobe atlases in napari using Elastix

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •9•22•18•2•Updated Aug 19, 2025Aug 19, 2025

• brainglobe-template-builder

  Public
  Build unbiased anatomical templates from individual images

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •2•11•16•3•Updated Aug 19, 2025Aug 19, 2025

• brainglobe.github.io

  Public
  brainglobe.info website

  brainglobe

  Python

  •

  Creative Commons Attribution 4.0 International

  •20•10•39•3•Updated Aug 19, 2025Aug 19, 2025

• course-whole-brain-microscopy-analysis

  Public
  Materials for the Whole brain microscopy analysis with BrainGlobe and napari course

  JavaScript

  •

  BSD 3-Clause "New" or "Revised" License

  •2•4•3•0•Updated Aug 13, 2025Aug 13, 2025

• brainglobe-heatmap

  Public
  Rendering anatomical heatmaps with brainrender and matplotlib

  visualizationatlasneuroanatomy+ 1brainglobe

  Python

  •

  MIT License

  •15•44•8•0•Updated Aug 7, 2025Aug 7, 2025

• brainglobe-ccf-translator

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

  Python

  •

  MIT License

  •0•7•11•0•Updated Aug 7, 2025Aug 7, 2025

• brainrender-napari

  Public
  A napari plugin to render BrainGlobe atlases and associated data as layers.

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •13•22•31•0•Updated Aug 7, 2025Aug 7, 2025

• napari-experimental

  Public
  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •1•4•4•0•Updated Aug 7, 2025Aug 7, 2025

• morphapi

  Public
  A Python package to download neuronal morphologies

  Python

  •

  MIT License

  •7•17•3•0•Updated Aug 5, 2025Aug 5, 2025

• brainglobe-space

  Public
  Anatomical space conventions made easy.

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •7•10•2•0•Updated Aug 5, 2025Aug 5, 2025

• brainglobe-stitch

  Public
  A napari plugin for stitching large tiled 3D imaging datasets

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •2•7•8•0•Updated Aug 5, 2025Aug 5, 2025

• brainglobe-workflows

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

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •8•10•27•2•Updated Aug 5, 2025Aug 5, 2025

• brainglobe-meta

  Public
  (Meta-)package repository for BrainGlobe's Python tools for computational neuroanatomy.

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •1•10•6•0•Updated Aug 5, 2025Aug 5, 2025

• brainglobe-napari-io

  Public
  Read and write files from the BrainGlobe neuroanatomy suite

  napari-plugin

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •6•14•4•2•Updated Aug 5, 2025Aug 5, 2025

• brainrender

  Public
  A Python package to visualise neuroanatomical data in atlas space

  visualizationpythonneuroscience+ 1anatomy

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •89•594•11•0•Updated Aug 5, 2025Aug 5, 2025

• brainglobe-utils

  Public
  Shared general purpose tools for the BrainGlobe project

  Python

  •

  MIT License

  •3•12•9•2•Updated Aug 5, 2025Aug 5, 2025

• brainglobe-segmentation

  Public
  Segmentation of anatomical structures in a common coordinate space

  neurosciencesegmentationneuroanatomy+ 3naparibrainregcellfinder

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •12•33•12•0•Updated Aug 5, 2025Aug 5, 2025

• brainreg

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

  neuroscienceregistrationmicroscopy+ 3brainneuroanatomyatlases

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •32•136•19•0•Updated Aug 5, 2025Aug 5, 2025

• cellfinder

  Public
  Automated 3D cell detection in very large images

  pythondeep-learningneuroscience+ 5image-analysismicroscopyimagingneuroanatomycell-detection

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •63•217•68•5•Updated Aug 5, 2025Aug 5, 2025

• BrainGlobe

  Public
  General information, resources and dicussions for the BrainGlobe project.

  1•11•24•0•Updated Feb 21, 2025Feb 21, 2025

• staged-recipes

  Public
  A place to submit conda recipes before they become fully fledged conda-forge feedstocks

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •5.4k•1•0•0•Updated Feb 6, 2025Feb 6, 2025

• slides-AI2-austria-2025

  Public
  SCSS

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•0•0•Updated Jan 27, 2025Jan 27, 2025

• slides-neuropixels-aligning-spikes-histology

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

  JavaScript

  •

  BSD 3-Clause "New" or "Revised" License

  •0•1•0•0•Updated Oct 15, 2024Oct 15, 2024

• .github

  Public
  Common templates for BrainGlobe repositories.

  0•6•0•0•Updated Oct 8, 2024Oct 8, 2024

• brainrender-docs

  Public archive
  docsneuroscienceanatomy+ 1brainrender

  CSS

  •4•9•0•0•Updated Sep 16, 2024Sep 16, 2024

• micrometa

  Public archive
  Parsing of whole-brain microscopy metadata

  Python

  •

  MIT License

  •0•2•0•0•Updated Jul 4, 2024Jul 4, 2024

• stack-to-chunk

  Public
  Convert stacks of images to chunked datasets

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •1•2•0•0•Updated May 28, 2024May 28, 2024

• bg-atlasgen

  Public archive
  Tools for packaging atlases for use with BrainGlobe

  pythonneuroscienceregistration+ 2brainatlas

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •25•12•0•0•Updated Feb 21, 2024Feb 21, 2024