Repositories list

• HowTo

  Public
  NIU website on common software problems and their troubleshooting

  Creative Commons Attribution 4.0 International

  •1•9•12•2•Updated Nov 13, 2024Nov 13, 2024

• calcium-imaging-automation

  Public
  Automate analysis and tracking of multiple calcium imaging datasets to compare parameters choices

  Python

  •

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

  •0•0•0•1•Updated Nov 12, 2024Nov 12, 2024

• spikewrap

  Public
  A tool to streamline extracellular electrophysiology analysis using SpikeInterface

  electrophysiologyneuropixelsextracellular-electrophysiology

  Python

  •

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

  •0•13•25•3•Updated Nov 11, 2024Nov 11, 2024

• movement

  Public
  Python tools for analysing body movements across space and time

  behaviorkinematicsneuroscience+ 4behaviouranimalmotion-trackingethology

  Python

  •

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

  •8•105•82•12•Updated Nov 8, 2024Nov 8, 2024

• derotation

  Public
  Derotate images acquired via 2-photon or 3-photon calcium imaging

  Python

  •

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

  •0•7•14•4•Updated Nov 5, 2024Nov 5, 2024

• course-extracellular-ephys-analysis

  Public
  Covering how to build electrophysiology pipelines with SpikeInterface

  Python

  •

  MIT License

  •0•5•0•0•Updated Nov 5, 2024Nov 5, 2024

• python-cookiecutter

  Public
  Utility to create a basic Python project structure with tests, CI etc.

  Python

  •

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

  •3•24•14•1•Updated Nov 5, 2024Nov 5, 2024

• software-skills

  Public
  Software skills training at the Sainsbury Wellcome Centre & Gatsby Computational Neuroscience Unit

  Creative Commons Attribution 4.0 International

  •0•7•0•0•Updated Nov 5, 2024Nov 5, 2024

• swc-slack

  Public
  Tools to interface with slack

  Python

  •

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

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

• fancylog

  Public
  Fancier logging with python.

  Python

  •

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

  •4•12•5•0•Updated Nov 4, 2024Nov 4, 2024

• slurmio

  Public
  Python tools to read SLURM job parameters.

  Python

  •

  MIT License

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

• datashuttle

  Public
  Tool for the creation, validation and transfer of neuroscience project folders.

  neurosciencedata-managementneuroblueprint

  Python

  •

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

  •3•15•43•3•Updated Nov 4, 2024Nov 4, 2024

• translocator-models

  Public
  Evaluate the model for the translocator project

  Python

  •

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

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

• actions

  Public
  Re-usable GitHub Action scripts

  MIT License

  •3•10•5•0•Updated Nov 4, 2024Nov 4, 2024

• rsp-vision

  Public archive
  Analysis and visualization of calcium imaging data from retrosplenial cortex

  neuroscience-methods

  Python

  •

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

  •0•8•23•0•Updated Oct 28, 2024Oct 28, 2024

• .github

  Public
  MIT License

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

• course-behavioural-analysis

  Public
  Materials and slides for the video-based analysis of animal behaviour course.

  Jupyter Notebook

  •

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

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

• course-behaviour-hpc

  Public
  Python

  •

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

  •0•5•2•0•Updated Oct 2, 2024Oct 2, 2024

• course-software-good-practice

  Public
  Slides for NIU collaborative coding and software development good practices

  SCSS

  •

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

  •0•7•0•0•Updated Oct 2, 2024Oct 2, 2024

• slides-SWC-PhD-intro

  Public
  Slides introducing the software skills courses on the SWC/GCNU PhD course

  SCSS

  •

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

  •2•1•2•0•Updated Sep 30, 2024Sep 30, 2024

• course-data-management-neuroblueprint

  Public
  Toy examples highlighting good data management practices

  Python

  •

  MIT License

  •0•6•0•0•Updated Sep 26, 2024Sep 26, 2024

• NeuroBlueprint

  Public
  Lightweight data specification for systems neuroscience, inspired by BIDS.

  Creative Commons Attribution 4.0 International

  •1•17•9•0•Updated Sep 25, 2024Sep 25, 2024

• dashboard

  Public
  Overview of all Neuroinformatics Unit repos

  TypeScript

  •

  MIT License

  •21•1•2•0•Updated Sep 24, 2024Sep 24, 2024

• org-metrics-dashboard

  Public archive
  Overview of all NIU repos

  TypeScript

  •

  MIT License

  •21•1•0•0•Updated Sep 5, 2024Sep 5, 2024

• slides-demo-cellfinder-multiprocessing

  Public
  SCSS

  •

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

  •0•1•0•0•Updated Sep 4, 2024Sep 4, 2024

• software-practice-template

  Public template
  A template to generate repositories used to teach SE best practices

  Python

  •

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

  •0•6•0•0•Updated Sep 4, 2024Sep 4, 2024

• In2Research-2024

  Public
  Repository used as a playground for the In2Research placement we hosted in summer 2024.

  Jupyter Notebook

  •0•3•2•0•Updated Aug 28, 2024Aug 28, 2024

• course-intro-python

  Public
  Jupyter Notebook

  •

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

  •0•1•0•0•Updated Aug 15, 2024Aug 15, 2024

• nuffield-students-exercises

  Public
  A series of python exercises to make the students practice before starting the main project

  Python

  •

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

  •0•1•0•0•Updated Aug 9, 2024Aug 9, 2024

• neuroinformatics-unit.github.io

  Public
  Home website of the Neuroinformatics Unit

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

  •0•7•8•0•Updated Jul 15, 2024Jul 15, 2024