steinbock icon indicating copy to clipboard operation
steinbock copied to clipboard

Published 20 hours ago • verified publisher icon BodenmillerGroup

Develop

Open Milad4849 opened this issue 1 year ago • 5 comments

  • Cellpose added as an app ( steinbock/_cli/apps.py ).
  • Cellpose model training added (steinbock/segmentation/_cli/train.py', 'steinbock/segmentation/train.py, 'Steinbock/segmentation/_cli/_cli.py').
  • Cellpose default parameters changed (steinbock/segmentation/cellpose.py).
  • Cellpose model zoo added (steinbock/segmentation/_cli/cellpose.py).
  • List of contributors updated (CONTRIBUTORS.md).
  • CHANGELOG.md updated.
  • Segmentation doc updated (docs/cli/segmentation.md).
  • Utils doc updated (docs/cli/utils.md).
  • Docker doc updated (docs/install-docker.md).
  • Opencv-python==4.8.0.74 added to requirements, it was needed to run cellpose training (requirements.txt).
  • Unifying how panel column datatypes are handled (steinbock/preprocessing/imc.py).
  • Fixed No neighborhood Data in h5ad (#210)

Milad4849 avatar Aug 24 '23 14:08 Milad4849

The recent push includes change and fixes to address all the issues raised. I will now move on to test the Docker containers. After this PR is merged I will move on to address other issues via feature branches.

Milad4849 avatar Aug 31 '23 09:08 Milad4849

Hi @Jonas, how should we proceed with this PR?

nilseling avatar Oct 10 '23 11:10 nilseling

Hi both, sorry for not getting back to you earlier. As commented, I've only reviewed the documentation-related issues so far. Will now take a closer look at the code changes and get back to you asap.

jwindhager avatar Oct 10 '23 13:10 jwindhager

Hi @Milad4849! Apologies for the delay, I completely missed that you re-requested a review. Will do it asap, latest at the end of this week.

CC @SchulzDan

jwindhager avatar Jan 17 '24 16:01 jwindhager

Also, the code still contains #TODO for list-like options

jwindhager avatar Jan 26 '24 22:01 jwindhager