Future Update Megathread

[WhoIsJack]

A list of stuff I want to update/improve to get the tutorial back in shape.

Major points

• Change to a more interesting dataset (multiple channels, more cell diversity)
  • Option 1: data from the Allen Cell Explorer [WIP; see Hackday 2021 local]
  • Option 2: IDR-0072: data, publication
• Add a section on ML-based segmentation (using stardist or cellpose)
• Finalize & incorporate the data analysis / data science notebook [WIP; see Hackday 2021 local?]
• Update the lecture slides
  • New/better examples at the start
  • More on machine learning
  • Revisit and streamline existing content
  • Modern look
  • Bonus: less basic ML, more advanced stuff
• Record the lectures & put them on YouTube

Minor points

• Ensure all instructions and the solutions code are up to date (+streamline a bit where possible)
• Better handling of input/output data [Done; see Hackday 2021 branch]
  • Put input data on figshare and write code that pulls it from there on first execution (may pull from elsewhere with new data)
  • Create outputs dir and ignore everything in it with an added new .gitignore, then change file writing funcs to write there
• Provide more and updated links to other materials
• Switch to (or at least introduce) napari for interactive image viewing?
• Convenience: Automatic install of all dependencies?
  • At least provide an environment.yml to facilitate install [Done; see Hackday 2021 branch]
• Convenience: Make notebook metadata ignore conda version & co.?
• Convenience: Add binder as a way of looking at and testing the materials without install/download? [WIP; see Hackday 2021 branch]