Closed Bunmi0616 closed 2 years ago
Hi @Bunmi0616 ,
This is due to an annoying issue that Mac generates hidden .mcd files when creating a ZIP archive. (See https://github.com/BodenmillerGroup/ImcSegmentationPipeline/issues/33).
Deleting these hidden .zip files from the archive does fix this issue.
This will be definitely fixed in future versions of this workflow when porting everything to the imctools
version 2 library.
This issue is fixed in version 2.0.1
Hi Anton,
Thanks for your reply. I had an issue getting version 2.0.1 to load on my Mac. So I ran the pipeline on 1.0.8.
Bunmi
On Thu, Sep 10, 2020 at 8:25 AM Anton Rau notifications@github.com wrote:
This issue is fixed in version 2.0.1
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-- Bunmi Olaloye M.D UTMB Pediatrics PGY-3
Hi Bunmi,
Could you please describe what kind of issue it is?
Best regards, Anton
Recently I got IMC data from my partner. He just gave me a .mcd file. Can I use this pipeline under this condition?
Hi Anton,
I could not get the the notebook to run even after loading in the imctools environment. Attempting to download imctools using pip install the version 2.0.1 i get an error message about pip dependencies.
After running the pipeline, (without the 3_measure mask in CP) the histocat folder does not contain the masks for the designated files even though I ran the "generate histocat folder with masks" function.
Thanks for your help, Bunmi
Closing under the assumption that this is not relevant anymore. Please reopen if issues persist.
您的邮件我已收到,但如果重要通知请以我亲自回复收到为准!感谢!
I was able to run the pipeline without any major issues with the example data. However, I am getting an assertion error. The folder contains files from each run "filename.mcd" and "filename_R01_001_1.txt" in a zipped file titled filename.zip. I zipped using the compress function on my mac. We don't have multiple regions (just one per mcd). I am not sure why I keep getting this error:
ERROR:root:Error in ../data/1155NEC.zip Traceback (most recent call last): File "", line 11, in
File "/Users/Bunmi/.conda/envs/imctools/lib/python3.6/site-packages/imctools/scripts/convertfolder2imcfolder.py", line 45, in convert_folder2imcfolder
assert len(mcd_files) == 1
AssertionError
Thanks,