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angelolab / ark-analysis

Integrated pipeline for multiplexed image analysis
https://ark-analysis.readthedocs.io/en/latest/
MIT License
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Pixie cell clustering should ignore cells that don't contain any pixel clusters in it #1046

Closed cliu72 closed 12 months ago

cliu72 commented 1 year ago

Please refer to our FAQ and look at our known issues before opening a bug report.

Describe the bug Cells that do not have any pixel clusters in them are still being included in the cell clustering. These cells should be removed prior to clustering.

Expected behavior In cluster_count_size_norm, check for cells where all pixel cluster counts are 0 and remove those before cell clustering.

alex-l-kong commented 1 year ago

Any reason we need to keep these blank cells in the cluster_count (un-normalized) table as well? Or can we remove those from there too?

cliu72 commented 1 year ago

Any reason we need to keep these blank cells in the cluster_count (un-normalized) table as well? Or can we remove those from there too?

Hmm it's not a huge deal since it's just for reference and not used for clustering. We can remove those to be consistent.