Error“Generate image stacks for downstream analyses”

[HouPB]

Hi, I am trying to perform this ImcSegmentationPipeline with example data, but I am stuck in this step that Generate image stacks for downstream analyses. Ang help is appreciated.

[nilseling]

Hi @HouPB

did you use the download_examples.ipynb notebook to download the data? Could you also please send me a screenshot of the raw folder and the panel.csv file?

[HouPB]

Thanks for your reply. Yes, I download this file.

[nilseling]

Hmm, that's strange. I can't reproduce this error on my side. Could you please restart the kernel and try again?

[HouPB]

I will try again according to your advice. Maybe I made some mistake operation. Thank you very much.

[Milad4849]

Hi @HouPB , I also cannot reproduce the error. If the issue persists, please make sure that you have set up the conda environment according to the instructions and if so, post the output of conda list.

[HouPB]

Now, this error was already solved. Thanks for your help.

[HouPB]

Hi, Nilseling. Now, I use this pipeline to run my IMC data but I meet a new problem that is "ValueError-Pr141 is not in list".

I don't know where is the reason and hope you give me some suggestions. Sincere Thanks.

panel.csv

[nilseling]

Hi @HouPB

the error means that Pr141 was not acquired. Please double check that this channel was actually open when you performed the measurement.

[HouPB]

I checked this channel. No problem in it and I can observe the signals of Pr141-aSMA by MCD-Viewer.

[HouPB]

Now, I found the reason that there are some ROI files(such as csv that miss channel Pr141 ) presented in omitiff folder.

[nilseling]

That makes sense. The pipeline only works for acquisitions that contain the same channels. Could you try to exclude the files?

[HouPB]

Yes, I am trying to exclude these files following this form.
Thanks.

[nilseling]

Hi @HouPB

has this been resolved? If so, could you please close the issue?