Pre-processing error

[ssaintsoon]

Hello. I'm new user for coding and IMC, and have some troubles i cannot solve :(

I'm currently using Anaconda and Jupyter-lab, and trying to make histoCAT works. I tried with my own data, and it was successfully pre-processed, segmented and analyzed. But in histoCAT, Run Phenograph seems doesn't work for my desktop (Windows 10) while t-SNE or other analyzes works well. I suspected space in filenames, so removed space and retried but it failed.

So I tried example data, named "Patient1.zip" from https://zenodo.org/record/5949116/files/Patient.zip It is stored in "raw" folder, and I ran pre-processing pipeline.

But this error occured:

I deleted panel.csv file and re-made manually typing every mass channel and target proteins, full, ilastik column, but it still didn't work. (I made it manually because when I did with my own data, it worked)

Why this error was occured?

[nilseling]

Hi @ssaintsoon

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

[ssaintsoon]

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")?

[nilseling]

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

[ssaintsoon]

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

[caucheteux]

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.

[ssaintsoon]

@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.

[ssaintsoon]

@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!

[nilseling]

Great, thanks for the update! Closing this issue now