Pre-processing error about imcsegmentationpipeline HOT 8 CLOSED

Hi @ssaintsoon

for using the example data, please run the download_examples.ipynb first. It will retrieve all needed example data.

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Thanks @nilseling , I will try it.
But I still wonder why only Patient1.zip doesn't work because it has its own .mcd and .txt file right?
I ran download_examples.ipynb for Patient1.zip and panel.csv. not entirely.

May I have to indicate Path as Path("C:\Users\Username\Desktop\raw")?

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My guess is that somehow the panel didn't match. I can't reproduce the error on my side yet.

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My guess is that somehow the panel didn't match. I can't reproduce the error on my side yet.

Thanks for your kind reply. I'll keep trying

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Hi @ssaintsoon Looking at your error, it says In113 is not in list, isnt it? Make sure your channel list match 100% panel.csv with mcd and txt files. Im not sure about the path/to/folder on PC, but on my computer, all 3 files (panel, csv, mcd) are in the raw folder.

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@caucheteux Hi. I added In113 in my panel.csv when I saw this error, and it seems like it isn't recognized well. I totally re-started processes and it's fine now. Thanks for your comment.

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@nilseling I also solved my problem that 'Run Phenograph' didn't work. When histoCAT is started, a window appears that selects where to store the custom gate, and when I specified this path to the same place as my data folder(in this case, 'analyze' folder), the problem was solved. I hope this can be helpful for others :) Thanks @nilseling , and have a good day!

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Great, thanks for the update! Closing this issue now

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