ISS_preprocessing index error with example Leica-data

[Sverreg]

I tried to run the preprocessing notebooks on example data from Marco Grillo (Leica 20x organoid dataset). The mipping ran successfully (the expected folders are produced with mipped images), but the leica_OME_tiff function fails with the error below.
Edit: (On ubuntu 22.04)

I followed the manual, except for one part in the environment setup - it does not run with the Python=3.7 argument. Perhaps my above error is due to using a different python version than 3.7?

Screenshot of input datastructure (pre-mip)

post-mip (note that the base2 folder also contains a coords.csv file, which the other base folders do not contain).

[mgcizzu]

Hi Sverre, How many channels are you imaging in, and what's the index of your DAPI in the list of colors? I see something strange in your mipping output, hence my question. You seem to lack a C0 channel for the first tile, is that correct? That would point to some problem with the mipping. Are you using the latest version from github? we put in a couple of updates maybe 2-3 months ago that automatically parse the number of channels in the different functions. An older version was assuming 4+DAPI channels and make a mess in the mipping step that we would drag down the pipeline causing errors as the one you have there. Let me know! Marco

…

On Thu, Sep 5, 2024 at 4:46 PM Sverre Grødem ***@***.***> wrote: I tried to run the preprocessing notebooks on example data from Marco Grillo (Leica 20x organoid dataset). The mipping ran successfully (the expected folders are produced with mipped images), but the leica_OME_tiff function fails with the error below. image.png (view on web) <https://github.com/user-attachments/assets/d9c53d6a-54b4-4f52-a04b-dca949d559c7> I followed the manual, except for one part in the environment setup - it does not run with the Python=3.7 argument. Perhaps my above error is due to using a different python version than 3.7? image.png (view on web) <https://github.com/user-attachments/assets/3720f519-71c4-46b4-9be3-863c04f8716c> Screenshot of input datastructure (pre-mip) image.png (view on web) <https://github.com/user-attachments/assets/7735b6ab-cf1a-4638-8f40-2edfeb589787> post-mip (note that the base2 folder also contains a coords.csv file, which the other base folders do not contain). image.png (view on web) <https://github.com/user-attachments/assets/83032da9-c232-43c6-98b5-4af06bfca094> — Reply to this email directly, view it on GitHub <#6>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACVSJMJ4SYTXC64GWE6XNCLZVBVETAVCNFSM6AAAAABNWVJOOOVHI2DSMVQWIX3LMV43ASLTON2WKOZSGUYDQMBRGUZDEMY> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[Sverreg]

Hi Marco,

A fresh install (6th sept 2024) appears to have resolved the issue, my output matches the example screenshots in the manual. I was using a version that was probably half a year old. Thanks for the quick response!