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BodenmillerGroup / ImcSegmentationPipeline

A pixel classification based multiplexed image segmentation pipeline
https://bodenmillergroup.github.io/ImcSegmentationPipeline/
MIT License
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Unexpected argument 'compress' #92

Closed Laner closed 2 years ago

Laner commented 2 years ago

I am trying to run the script and get an error when trying to convert .mcd files to .ome.tiff files.

ERROR:root:Error reading acquisition 1 from file Patient1.mcd: write() got an unexpected keyword argument 'compress'

I got this with my own data, so I tried to run the script again with the example data and got the same error.

Any suggestions on how to correct this error?

jwindhager commented 2 years ago

Please have a look at https://github.com/BodenmillerGroup/ImcSegmentationPipeline/issues/90, a fix is currently being implemented. For now, please use an older tifffile version (see https://github.com/BodenmillerGroup/ImcSegmentationPipeline/issues/90).

nilseling commented 2 years ago

Should be fixed in #91