Repositories list

• PyNutil

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

  Python

  •

  MIT License

  •1•4•14•0•Updated Nov 7, 2024Nov 7, 2024

• quint-deepzoom

  Public
  DeepZoom API app to handle pyramiding and tiles

  Python

  •1•0•0•0•Updated Nov 6, 2024Nov 6, 2024

• QUINT_workflow

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

  GNU General Public License v3.0

  •2•2•0•0•Updated Oct 25, 2024Oct 25, 2024

• LocaliZoom

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

  HTML

  •

  MIT License

  •2•3•10•0•Updated Oct 17, 2024Oct 17, 2024

• VisuAlign

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

  Java

  •

  MIT License

  •3•0•15•0•Updated Oct 9, 2024Oct 9, 2024

• 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 Oct 4, 2024Oct 4, 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•1•2•0•Updated Sep 9, 2024Sep 9, 2024

• nutil

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

  C++

  •

  GNU General Public License v3.0

  •5•12•19•1•Updated Aug 22, 2024Aug 22, 2024

• WebAlign

  Public
  https://webalign.readthedocs.io

  HTML

  •

  MIT License

  •4•5•8•0•Updated Aug 1, 2024Aug 1, 2024

• 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•7•19•0•Updated Aug 1, 2024Aug 1, 2024

• WebWarp

  Public
  https://webwarp.readthedocs.io

  JavaScript

  •

  MIT License

  •3•0•4•0•Updated Aug 1, 2024Aug 1, 2024

• tempinfo

  Public
  HTML

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

• QCAlign

  Public
  https://qcalign.readthedocs.io/

  Java

  •2•1•3•0•Updated May 29, 2024May 29, 2024

• QuickNII

  Public
  https://quicknii.readthedocs.io

  ActionScript

  •

  MIT License

  •5•7•9•0•Updated May 27, 2024May 27, 2024

• DeepSlice

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

  Python

  •

  MIT License

  •17•0•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

• Laterality

  Public
  Quantitative analysis of rat and mouse brain data

  Python

  •

  GNU General Public License v3.0

  •0•1•0•0•Updated Nov 28, 2023Nov 28, 2023

• Neural-Systems-at-UIO.github.io

  Public
  The repository for the neural systems workflow website

  HTML

  •

  Apache License 2.0

  •1•0•0•0•Updated Nov 2, 2023Nov 2, 2023

• LocareJSON

  Public
  LocareJSON is a collection of JSON schemas for defining geometrical shapes with coordinates in 3D brain atlas coordinate spaces.

  Python

  •

  Creative Commons Attribution 4.0 International

  •1•0•0•0•Updated Oct 20, 2023Oct 20, 2023

• RB-workbench

  Public
  a next generation online rodent brain workbench

  JavaScript

  •

  GNU General Public License v3.0

  •0•2•33•0•Updated Oct 17, 2023Oct 17, 2023

• pyramidio-bioformats

  Public
  Image pyramid reader and writer enhanced with bio-formats library reader

  Java

  •

  Other

  •21•0•0•0•Updated Oct 16, 2023Oct 16, 2023

• ImageIngestion

  Public
  JavaScript

  •0•2•3•0•Updated Oct 16, 2023Oct 16, 2023

• QUINT_webtools

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

  GNU General Public License v3.0

  •0•0•0•0•Updated Oct 13, 2023Oct 13, 2023

• allen2quicknii

  Public
  Download Allen mouse datasets and format them for use in QuickNII

  Python

  •2•2•0•0•Updated Oct 6, 2023Oct 6, 2023

• Multi-Image-OSd

  Public
  Multi-Image OpenSeadragon viewer

  HTML

  •

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

  •1•1•9•0•Updated Sep 15, 2023Sep 15, 2023

• xyz-converter

  Public
  A script for conversion between the local coordinate system for the pontine nuclei defined by Leergaard et al. 2000 and Waxholm Space for the SD rat brain

  Python

  •

  Other

  •2•0•0•0•Updated Aug 29, 2023Aug 29, 2023