Pixel Clustering - Run without segmentaiton files

angelolab / ark-analysis

Integrated pipeline for multiplexed image analysis

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

MIT License

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Pixel Clustering - Run without segmentaiton files #998

Closed srivarra closed 1 year ago

srivarra commented 1 year ago

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What is the purpose of this PR?

Allows pixel clustering without segmentation files.

How did you implement your changes

Added a variable called pixie_seg_dir which evaluates to the full path of the segmentation_dir if it exists, or None when segmentation_dir is None.

Slightly modified a check for None in pixie_preprocesing.py.

Remaining issues

None.

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