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BodenmillerGroup / steinbock

A toolkit for processing multiplexed tissue images
https://bodenmillergroup.github.io/steinbock
MIT License
49 stars 14 forks source link

qptiff format #236

Closed alexeykb closed 5 months ago

alexeykb commented 6 months ago

Hello!

I was wondering if it is possible to use qptiff as an input format for steinbock ? If not, what is the preferable way to transform it to appropriate tiff?

Thank you Best regards Alexey

Milad4849 commented 6 months ago

@alexeykb Thank you for reaching out! External images need to be in a format supported by imageio (see External images in the relevant part of the documentation). I am not aware of the best practices for qptiff conversion. You would need to convert them into a iamgeio supported format and then convert them to steinbock-compatible TIFF files using steinbock preprocess external images.

Milad4849 commented 5 months ago

Closing this due to inactivity

alexeykb commented 5 months ago

Hello, I have an update on current issue (still doesnt work): I am facing the issue with segmenting the ome.tiff using steinbock. I have original CODEX files in the format of qptiff. I have transformed qptiff to ome.tiff using BioFormats: https://docs.openmicroscopy.org/bio-formats/6.10.1/users/comlinetools/index.html What increased my original file from 25 gb to 75gb and stored it to: path/to/publication/steinbock/external

I further have tried to input it to the IMC pipline (starting with steinbock), by using this command:

steinbock preprocess external images --img /data/external --imgout /data/images --infoout /data/images/images.csv

Unfortunatelly , it doesnt work and return the error: WARNING steinbock.preprocessing.external - Unsupported file format: /data/external/scanone.ome.tiff

However, originally, the channel names from the ome.tiff I have extracted the channel names from the ome.tiff file and those are in the form Channel:0:0 Channel:0:1 etc

Which is not acceptable for steinbock, so i changed it to the 0 1 etc

What should be my steps now ? Should I open ome.tiff through qptiff and manually rename channels or the problem is in ome.tiff file, and not in channels names. If it is ome.tiff fault, how can I overpass it ? I also tried to transform qptiff thorugh QPath and it didi not give any positive results either.

Thank you Best Alexey