Repositories list

• MeshView-for-Brain-Atlases

  Public
  WebGL based mesh viewer with solid slicing and point cloud support. User documentation https://meshview-for-brain-atlases.readthedocs.io

  JavaScript

  •

  MIT License

  •5•9•21•0•Updated Sep 10, 2025Sep 10, 2025

• QUINT_webtools

  Public
  https://quint-webtools.readthedocs.io

  GNU General Public License v3.0

  •0•0•0•0•Updated Sep 5, 2025Sep 5, 2025

• SHAREbrain

  Public
  SHAREbrain is a workflow aimed to help researchers prepare data and metadata in a standardised manner for sharing via the EBRAINS Data & Knowledge service

  MATLAB

  •

  GNU General Public License v2.0

  •1•0•0•0•Updated Sep 1, 2025Sep 1, 2025

• QuickNII

  Public
  https://quicknii.readthedocs.io

  ActionScript

  •

  MIT License

  •5•8•12•0•Updated Aug 20, 2025Aug 20, 2025

• LocaliZoom

  Public
  Localizoom viewer https://localizoom.readthedocs.io

  HTML

  •

  MIT License

  •2•3•13•0•Updated Aug 20, 2025Aug 20, 2025

• spatial_brain_maps

  Public
  tools for exploring 3D maps of features in the brain

  Python

  •

  MIT License

  •0•1•0•0•Updated Aug 19, 2025Aug 19, 2025

• webilastik

  Public
  A revision of classic ilastik to drop legacy stuff and make it portable

  Python

  •

  MIT License

  •3•0•0•0•Updated Aug 19, 2025Aug 19, 2025

• neuroglancer

  Public
  neuroglancer fork for build after cscs change

  TypeScript

  •

  Apache License 2.0

  •1•0•0•0•Updated Aug 19, 2025Aug 19, 2025

• ebrains-2025_metadata-wizard

  Public
  rewriting wizard in vite

  JavaScript

  •1•0•0•0•Updated Jul 3, 2025Jul 3, 2025

• nutil

  Public
  https://nutil.readthedocs.io/en/latest/

  C++

  •

  GNU General Public License v3.0

  •7•13•21•1•Updated Jul 2, 2025Jul 2, 2025

• PyNutil

  Public
  Python library for brain-wide quantification and spatial analysis.

  Python

  •

  MIT License

  •2•8•9•0•Updated Jun 26, 2025Jun 26, 2025

• QUINT_workflow

  Public
  Documentation: https://quint-workflow.readthedocs.io

  GNU General Public License v3.0

  •2•3•1•0•Updated Jun 11, 2025Jun 11, 2025

• CreateZoom

  Public
  CreateZoom API app to handle pyramiding and tiles

  Python

  •

  MIT License

  •2•0•0•0•Updated Jun 10, 2025Jun 10, 2025

• SeriesZoom

  Public
  HTML

  •

  MIT License

  •1•0•0•0•Updated May 27, 2025May 27, 2025

• restrictedaccess_request

  Public
  Automatic email to data custodian informing about submitted request to access externally hosted data

  JavaScript

  •1•0•0•0•Updated May 23, 2025May 23, 2025

• QCAlign

  Public
  https://qcalign.readthedocs.io/

  Java

  •

  MIT License

  •2•1•4•0•Updated May 7, 2025May 7, 2025

• WebAlign

  Public
  https://webalign.readthedocs.io

  HTML

  •

  MIT License

  •4•5•8•0•Updated May 7, 2025May 7, 2025

• VisuAlign

  Public
  Online manual: https://visualign.readthedocs.io

  Java

  •

  MIT License

  •4•0•16•0•Updated May 7, 2025May 7, 2025

• WebWarp

  Public
  https://webwarp.readthedocs.io

  JavaScript

  •

  MIT License

  •3•0•4•0•Updated May 7, 2025May 7, 2025

• Laterality

  Public
  Quantitative analysis of rat and mouse brain data

  Python

  •

  GNU General Public License v3.0

  •0•1•0•0•Updated Feb 13, 2025Feb 13, 2025

• ebrains_wizard

  Public
  JavaScript

  •3•0•0•0•Updated Jan 9, 2025Jan 9, 2025

• tar-svc

  Public
  a test of using using tarred dzi files directly with our viewers

  JavaScript

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Nov 12, 2024Nov 12, 2024

• 3d-point-clouds

  Public
  Scripts and notebooks for the Copodata paper Øvsthus et al.

  Jupyter Notebook

  •

  MIT License

  •3•0•0•0•Updated Sep 27, 2024Sep 27, 2024

• PyNutilWeb

  Public
  a web interface for PyNutil

  JavaScript

  •

  GNU General Public License v3.0

  •0•2•2•0•Updated Sep 9, 2024Sep 9, 2024

• tempinfo

  Public
  HTML

  •0•0•0•0•Updated Jun 6, 2024Jun 6, 2024

• DeepSlice

  Public
  A python package which aligns histology to the Allen Brain Atlas and Waxholm rat atlas using deep learning.

  Python

  •

  MIT License

  •25•1•0•0•Updated Feb 21, 2024Feb 21, 2024

• BRAINSPACE

  Public
  Files and script relating to the BRAINSPACE project

  R

  •

  GNU General Public License v3.0

  •1•0•0•0•Updated Jan 12, 2024Jan 12, 2024

• ImageMagick-scripts

  Public
  Collection of ImageMagick scripts for mass processing of images.

  1•0•0•0•Updated Jan 5, 2024Jan 5, 2024

• QuickNII-extras

  Public
  Code snippets and tools for working with QuickNII output

  Java

  •

  MIT License

  •2•0•0•0•Updated Nov 28, 2023Nov 28, 2023

• QuickMaskNL

  Public
  Mask-generator (black/white PNG) for VisuAlign

  Java

  •

  MIT License

  •2•0•0•0•Updated Nov 28, 2023Nov 28, 2023