angelolab / ark-analysis

Integrated pipeline for multiplexed image analysis
https://ark-analysis.readthedocs.io/en/latest/
MIT License
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Fix zero pixels #956

Closed cliu72 closed 1 year ago

cliu72 commented 1 year ago

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What is the purpose of this PR?

After removing the pixel thresholding step (to filter out low pixels), we never added back in the filter for pixels that were zero for all markers. Added that back in.

How did you implement your changes

Added one line to remove pixels that are 0 for all markers before row normalization.

Remaining issues

None