NIU Open Software Summer School

Welcome!

Neuroinformatics Unit

Code of Conduct

  • Reminder: please follow the code of conduct
  • Summary: be kind, respectful and professional
  • Contacts: Adam, Sofia, Niko or Alessandro

Schedule

Maps

Ask a member of NIU for a quiet space

Ask for help

  • Ask any member of NIU
  • Use the OSSS-2026 channel on Zulip
  • Work together
  • Let Adam know if you don’t want to appear in photos

AI policy

During teaching & exercises

  • Learning requires friction!
  • No AI assistants inside your IDE or terminal (Copilot, Cursor, Claude Code, etc.)
  • Chat-based tools are fine for looking things up, like a search engine

During collaboration days

  • AI use is up to you
  • If working on a joint project, agree on it with your collaborators first

Join the socials

Week 1

  • Tuesday 18th August: Celtic folk music near King’s Cross
  • Thursday 20th August: Walk to Primrose Hill

Week 2

  • Tuesday 25th August: Celtic folk music near King’s Cross
  • Thursday 27th August: Run
  • Friday 28th August: Walk to Primrose Hill

Made possible by

Enjoy!

Collaboration days

Our definition of collaboration

Work together on a small project in quick, dirty and fun way

Schedule

  • Thursday 10:00 - 17:00
  • Friday 10:00 - 17:00

Thursday (approximate)

10:00 - 11:15: Intro to collaboration, getting started

11:30 - 13:00: Git course (part 1) / collaboration

14:00 - 15:30: Git course (part 2) / collaboration

15:30 - 15:45: Data management with datashuttle (Joe Ziminski) / collaboration

15:45 - 17:00: collaboration

17:45 Running social: meet Wolf outside SWC in running gear.

Friday (approximate)

Collaboration 10:00-16:00

11:00 A high-level introduction to whole-brain image analysis with BrainGlobe (Alessandro Felder); Adapting cellfinder to single-channel and 2.5-D data (Soumya Snigdha Kundu)

14:00 QUINT workflow (Harry Carey)

16:00 Lightning talks

17:45 Walk to Primrose Hill

Goal

Enable knowledge exchange through hands-on work

Focus on collaboration:

  • Active listening
  • Being inclusive
  • Taking initiative
  • Planning
  • Stepping out of your comfort zone

Opportunity to foster:

  • Collaborative skills
  • Coding skills
  • Creativity skills
  • Social skills
  • Time-management skills

Collaboration tips

Everyone gets opportunity to contribute

  • Be flexible and inclusive
  • Code is not the only thing that needs doing
  • Planning, documenting, organizing, presenting, reading, time-keeping…

Working together

  • Start by introducing yourself, your work and your skills to the group
  • Make use of GitHub, Shared google doc
  • Keep in touch with the group throughout

Look after yourself

  • Take breaks, stretch, rest your eyes
  • Enjoy

Collaboration tips

  • Settle on doable plan

Things will go wrong – that’s OK!

  • Work incrementally and version-control your work
  • You have a very short amount of time!
  • Focus on minimum viable “product”

Report back in short lightning presentations at 4 PM (joint slide-deck)

  • What you did
  • What you learnt
  • Future work

We will check in regularly

What’s next

GitHub project board

Have fun!