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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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write() got an unexpected keyword argument 'compress' #90

Closed olivierbortolotti closed 2 years ago

olivierbortolotti commented 2 years ago

Hi,

I'm having troubles running the script. I'm getting this error even with example data: "ERROR:root:Error reading acquisition 1 from file Patient1.mcd: write() got an unexpected keyword argument 'compress' ERROR:root:Error restoring acquisition 1 for file Patient1.mcd from file C:\Users\Olivier\AppData\Local\Temp\tmp922yv41a\Patient1\Patient1_pos1_1_1.txt: write() got an unexpected keyword argument 'compress'"

Could you help me?

image

jwindhager commented 2 years ago

Hi @olivierbortolotti, thanks for checking in! This sounds like a Python package dependency issue to me. Could you please post the output of the last notebook cell (conda list) here? Cheers

olivierbortolotti commented 2 years ago

Hi @jwindhager,

Thank you for your answer.

I checked Python packages and the code of the pipeline and found that xtiff (https://github.com/BodenmillerGroup/xtiff) uses tifffile and they deprecated compress since the 2022.4.22 release.

The workaround is to use tifffile 2022.4.8.

Cheers

jwindhager commented 2 years ago

Thanks for investigating and for filing https://github.com/BodenmillerGroup/xtiff/issues/10!

nilseling commented 2 years ago

I merged #91 - could you please test if this solved the issue?