Switch use of readimc in pipeline

BodenmillerGroup / ImcSegmentationPipeline

A pixel classification based multiplexed image segmentation pipeline

https://bodenmillergroup.github.io/ImcSegmentationPipeline/

MIT License

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Switch use of readimc in pipeline #122

Closed nilseling closed 1 year ago

nilseling commented 1 year ago

With the newest version of readimc I get the error:

/Users/nils/opt/anaconda3/envs/imcsegpipe/lib/python3.9/site-packages/readimc/mcd_file.py:35: UserWarning: `MCDFile.metadata` will be removed in future readimc releases; use `MCDFile.schema_xml` instead

We would need to switch from MCDFile.metadata to MCDFile.schema_xml soon.

nilseling commented 1 year ago

Fixed in #126