Repositories list

• brainglobe-atlasapi

  Public
  A Python interface to access neuroanatomical atlases

  pythonvisualisationneuroscience+ 4registrationmicroscopybrainatlases

  Python

  •

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

  •37•129•136•6•Updated Feb 14, 2025Feb 14, 2025

• cellfinder

  Public
  Automated 3D cell detection in very large images

  pythondeep-learningneuroscience+ 5image-analysismicroscopyimagingneuroanatomycell-detection

  Python

  •

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

  •40•182•71•0•Updated Feb 12, 2025Feb 12, 2025

• brainglobe-registration

  Public
  Registration to BrainGlobe atlases in napari using Elastix

  Python

  •

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

  •2•17•9•1•Updated Feb 11, 2025Feb 11, 2025

• brainglobe.github.io

  Public
  brainglobe.info website

  brainglobe

  Python

  •

  Creative Commons Attribution 4.0 International

  •11•10•34•5•Updated Feb 7, 2025Feb 7, 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

  •5.1k•1•0•0•Updated Feb 6, 2025Feb 6, 2025

• brainreg

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

  neuroscienceregistrationmicroscopy+ 3brainneuroanatomyatlases

  Python

  •

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

  •30•130•17•0•Updated Feb 5, 2025Feb 5, 2025

• brainglobe-workflows

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

  Python

  •

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

  •3•10•24•0•Updated Feb 4, 2025Feb 4, 2025

• brainglobe-template-builder

  Public
  Build unbiased anatomical templates from individual images

  Python

  •

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

  •2•11•13•3•Updated Feb 4, 2025Feb 4, 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 Feb 4, 2025Feb 4, 2025

• brainglobe-stitch

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

  Python

  •

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

  •1•7•2•1•Updated Feb 4, 2025Feb 4, 2025

• brainglobe-utils

  Public
  Shared general purpose tools for the BrainGlobe project

  Python

  •

  MIT License

  •3•11•7•1•Updated Feb 4, 2025Feb 4, 2025

• brainrender-napari

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

  Python

  •

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

  •3•20•36•0•Updated Feb 4, 2025Feb 4, 2025

• brainglobe-space

  Public
  Anatomical space conventions made easy.

  Python

  •

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

  •6•9•2•0•Updated Feb 4, 2025Feb 4, 2025

• brainglobe-segmentation

  Public
  Segmentation of anatomical structures in a common coordinate space

  neurosciencesegmentationneuroanatomy+ 3naparibrainregcellfinder

  Python

  •

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

  •11•30•11•0•Updated Feb 4, 2025Feb 4, 2025

• brainglobe-heatmap

  Public
  Rendering anatomical heatmaps with brainrender and matplotlib

  visualizationatlasneuroanatomy+ 1brainglobe

  Python

  •

  MIT License

  •12•35•7•2•Updated Feb 4, 2025Feb 4, 2025

• morphapi

  Public
  A Python package to download neuronal morphologies

  Python

  •

  MIT License

  •7•17•3•0•Updated Feb 4, 2025Feb 4, 2025

• brainglobe-napari-io

  Public
  Read and write files from the BrainGlobe neuroanatomy suite

  napari-plugin

  Python

  •

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

  •5•13•2•0•Updated Feb 4, 2025Feb 4, 2025

• brainrender

  Public
  A Python package to visualise neuroanatomical data in atlas space

  visualizationpythonneuroscience+ 1anatomy

  Python

  •

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

  •83•559•10•0•Updated Feb 4, 2025Feb 4, 2025

• slides-AI2-austria-2025

  Public
  SCSS

  •

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

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

• napari-experimental

  Public
  Python

  •

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

  •1•3•4•0•Updated Jan 13, 2025Jan 13, 2025

• brainglobe-ccf-translator

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

  Python

  •

  MIT License

  •0•5•10•0•Updated Nov 18, 2024Nov 18, 2024

• 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

• 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•1•0•0•Updated Oct 7, 2024Oct 7, 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

  •24•12•0•0•Updated Feb 21, 2024Feb 21, 2024

• imio

  Public archive
  Loading and saving of image data.

  tiffimage-processingloading+ 3savingniftitiff-series

  Python

  •

  MIT License

  •3•10•0•0•Updated Feb 9, 2024Feb 9, 2024

• brainreg-napari

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

  neuroscienceregistrationmicroscopy+ 4brainanatomyatlasesnapari

  Python

  •

  MIT License

  •6•15•0•0•Updated Jan 5, 2024Jan 5, 2024