search

angelolab / ark-analysis

Integrated pipeline for multiplexed image analysis
https://ark-analysis.readthedocs.io/en/latest/
MIT License
71 stars 25 forks source link

Allow FOVs to contain various maximum clusters #1021

Closed srivarra closed 1 year ago

srivarra commented 1 year ago

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

What is the purpose of this PR?

Keeps the segmentation consistent across all FOVs in a cohort, even if a FOV does not have a particular phenotype / cluster when compared to others in its cohort. Adds the fix for cell clustering, neighborhood clustering, and for Mantis ingestion.

How did you implement your changes

Created a new dataclass CellClusterMaskData which contains all the cell data, cluster column, segmentation column for a particular cohort (or all FOVs used for the cell table).

Remaining issues

Partially addresses #857.

review-notebook-app[bot] commented 1 year ago

Check out this pull request on  ReviewNB

See visual diffs & provide feedback on Jupyter Notebooks.

Powered by ReviewNB