Comments (10)
Hey!
I am currently in holidays for another week.
I cannot see why this fails - did the generation of the subfolders in the folder data/ome
work?
Until this is figured out you can also skip this step - it is likely not that essenitai.
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Hello Votti!
Thank You for your reply!
It does generate all of the subfolders during the previous step. At least I did not find anything missing.
I have also tried to just continue with pipeline and skipping the step, however it fails to generate the ometiff-files and the folders stay empty...
Thank You for your help
Best Max
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Ah so the problem is the OME files are missing?
Can you show the output printed at the previous step?
Convert mcd containing folders into imc zip folders
In [10]:
The issue seems to be with converting the zipped mcd to ome tiff in this step.
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Ok, alright.
So this is what is showing:
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Checked it right now again, but it does not change the result. I had also checked the directory multiple times already... Cannot find an obvious mistake.
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Alternatively, while trying around and when removing "_", I am now getting following error when trying to convert the mcd into the imc zip folders... Might this be the source of the problem?
Thank You a lot for your help!
Best Max
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Hello again,
I am very sorry, as I do not have any programming experience, but I just cannot work around the issue in this step...
I have found the reasons for the previous errors and now the pipeline does find the .zip-files with the .mcd.
However now
"OSError: [Errno 22] Invalid argument: '../../data\ometiff\20201026_SK_MG_UC_biopsies_6292-1\20201026_SK_MG_UC_biopsies_6292-1_s0_slide""'
is raised and I cannot pass it.
Thanks a lot for your help!
Best, Max
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Hi Max,
Now I am back from holidays :)
So I see you managed to get a compatible ZIP folder.
From the error message I read that something in the your metadata is different than the '.mcd' files we usually get which causes this issue. It is a bit an issue that the '.mcd' format is not extremely well defined, so it can look a bit different between different versions of the machine :/
We are currently updating the way we are reading the .mcd files. Could you maybe try this more 'cutting edge' version of the pipeline that uses our new file converter? https://github.com/BodenmillerGroup/ImcSegmentationPipeline/tree/imctools2
This requires that you reinstall the conda environment using the setup/conda_imctools.yml
from that version of the repository.
If this again gives this error - would you be able to share the file such that we can adapt our converter (imctools) to support it as well?
Sorry that this is workiung so un-smooth for you!
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Hello Votti,
I have installed the imctools2 version and also the updated kernel and now it seems to work!
Thank You so much! You have helped me a ton!
Best, Max
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Related Issues (20)
- Avoid processing of hidden files HOT 12
- Error "FileNotFound" in the last step HOT 4
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- Error“Generate image stacks for downstream analyses” HOT 13
- single-cell expression data HOT 1
- Presence of undefined channels during conversion from MCD to ome-TIFF HOT 2
- Numpy float or unsigned integer in TIFF images HOT 3
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