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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

ome-tiff issue #197

Open paulrbuckley-kcl opened 1 year ago

paulrbuckley-kcl commented 1 year ago

Hi,

I am running 'steinbock preprocess external images' on a CODEX-generated .ome.tiff, which has been exported from QuPath. When converting to 'steinbock file format' I receive the following warning and nothing is processed:

I noticed there is a recent bug, so I am using the most recent version of the docker image - 0.16.1 - the below code is used to run this in singularity:

steinbock="singularity run -B /X/$FOLDER:/data --env STEINBOCK_MASK_DTYPE=uint32 docker://ghcr.io/bodenmillergroup/steinbock:0.16.1 where $FOLDER has been defined previously. then the following code is generates the issue: $steinbock preprocess external images --img /data/external --imgout /data/images --infoout /data/images/images.csv I assume its something simple like I have not received the updated code given the recent bug? But not entirely sure. Any help would be really appreciated

Thanks

Paul

jwindhager commented 1 year ago

Hi @paulrbuckley-kcl!

Your commands look right to me. I suspect that the TIFF shape is not compatible with steinbock (expected dimension order: CYX, optionally with additional dimensions of size 1 at the beginning/end). This would for example be the case if the CODEX-generated TIFFs are channels-last instead of channels-first. Unfortunately, the steinbock logging for this particular problem is currently broken, which is why the error message is so uninformative. Sorry about that.

@Milad4849: Could you maybe investigate this further/help out @paulrbuckley-kcl? And what's your opinion on adding a --channels-last option to the steinbock preprocess external command (feature request)?

PS @paulrbuckley-kcl: Really nice to see that you are using steinbock with Singularity!

paulrbuckley-kcl commented 1 year ago

Thanks for getting back to me. Yes that makes sense. I've exported in two different ways (imagej format which i assume is CYX) and all appears to be working but will keep you updated. Also yes it works very cleanly using singularity! bit of a lifesaver to be honest!

Milad4849 commented 1 year ago

@jwindhager, sure I will look into this together with #199, adding channel last makes sense to me, will update you on this.