general notes

[ph4s3r]

• when loaded echino wsis, needed to use openslide backend, otherwise it will be processed with bioformats by default then pipelines will fail with not being able to process the number of channels...
• don't use WSL!! it was unstable and unpredictable because of resource handling
• why py instead of jupyter notebooks?:
  • on windows debugging did not work properly. You only need notebooks if you want to rerun parts of your code sequentially and don't want to re-execute everything, also display results nicely and in a structured way
  • there is a nice profiler set up for python in .vscode/launch.json works with snakeviz
• how to install on windows:
  • install latest anaconda
  • create new env named pathml with python 3.9x
  • make sure that the openslide importer is working (download binary and set path)
  • install latest cuda (11.2 was used here) that is supported by the latest pytorch (they need to be in sync):
  • install torch with going to their website and grabbing the appropriate install commands