Error loading zipped mcd/txt file

[Bunmi0616]

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,

[votti]

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.

[plankter]

This issue is fixed in version 2.0.1

[Bunmi0616]

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

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/BodenmillerGroup/ImcSegmentationPipeline/issues/46#issuecomment-690245158, or unsubscribe https://github.com/notifications/unsubscribe-auth/AQ55QAQBDMQFJVRLMSSHVA3SFDAR5ANCNFSM4RCYTTQQ .

-- Bunmi Olaloye M.D UTMB Pediatrics PGY-3

[plankter]

Hi Bunmi,

Could you please describe what kind of issue it is?

Best regards, Anton

[KaWingLee9]

Recently I got IMC data from my partner. He just gave me a .mcd file. Can I use this pipeline under this condition?

[Bunmi0616]

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

[nilseling]

Closing under the assumption that this is not relevant anymore. Please reopen if issues persist.

[KaWingLee9]

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！