Generalized masking - Githubissues

angelolab / ark-analysis

Integrated pipeline for multiplexed image analysis

https://ark-analysis.readthedocs.io/en/latest/

MIT License

70 stars 25 forks source link

Generalized masking #1092

Closed camisowers closed 4 months ago

camisowers commented 8 months ago

If you haven't already, please read through our contributing guidelines before opening your PR

What is the purpose of this PR?

Closes #1091.

How did you implement your changes

Add two user functions, generate_signal_masks() and generate_cell_masks() for either signal based masking or cell based masking.

Remaining issues

[x] create masking notebook

review-notebook-app[bot] commented 8 months ago

Check out this pull request on

See visual diffs & provide feedback on Jupyter Notebooks.

Powered by ReviewNB

camisowers commented 8 months ago

I still need to write the notebook tests, but would love any preliminary input on the masking functionalities you have helped write or seen lab members use. @alex-l-kong @srivarra

camisowers commented 4 months ago

Updated to use the already built ezseg functions. Decided to forego the notebook tests, since it's just a utility notebook with only top-level function calls that are already tested.