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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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imwrite() got an unexpected keyword argument 'compress' #100

Closed ingros closed 2 years ago

ingros commented 2 years ago

Hi! I am completely new to python and programming and are running the pre-processing pipeline for the first time. I get the error message: imwrite() got an unexpected keyword argument 'compress'.

I see from previous issues that others have had the same problem and that the solution was to use an updated xtiff package. I checked which version I have (2022.5.4) so that should not be the problem.

The error occurs when I try to run the cell converting ome.tiffs to a HistoCAT compatible format, but I also get the same error message further down when I try to generate the analysis stacks. image

Any idea what could be the problem?:)

jwindhager commented 2 years ago

Hi @ingros, thanks for reaching out! Could you please post the output of conda list here (uncomment & run the last cell in imc_preprocessing.ipynb)? I'd assume you have an outdated version of xtiff installed (current versions: 0.7.8).

ingros commented 2 years ago

Hi and thank you for quick answer!

It seems as if I have the right version of xtiff? image

jwindhager commented 2 years ago

Oh, apologies! Just realized that you're running an old version of the IMC Segmentation Pipeline! @nilseling would you be able to help out?

ingros commented 2 years ago

Ah I see. But would it then be better to just download the newest version and start over? If that makes me avoid the problem? This is the first time I am trying out the pipeline and only with some test run-data:) So I will not loose a lot of work anyhow!

nilseling commented 2 years ago

Hi @ingros yeah I would say please set up a fresh environment with the newest version of the pipeline (release 3.4) and see if that resolves the issue. Let us know how this goes.

ingros commented 2 years ago

Okay, so I have downloaded the 3.4 release! Had no problems setting up and activating the environment in anaconda as described. However, I am no longer able to run the first cell in jupyter (importing sys). I get this error: image

Probably something really basic I dont understand, hope you can help me! Thank you for helping! :)

nilseling commented 2 years ago

Hmm, this line should be commented out. At least in the notebook on Github this is still the case. Please comment it out and ignore the first chunk.

ingros commented 2 years ago

Ah yes, that worked! Perfect, thank you:))!

nilseling commented 2 years ago

Great! Closing this now