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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

Steinbock preprocess IMC produces empty TIFF files #230

Closed Dmitry-Khochanskiy closed 6 months ago

Dmitry-Khochanskiy commented 7 months ago

Steinbock does not preprocess correctly imc sample images (https://zenodo.org/record/7575859/files/Patient*.zip) It shows "warnings.warn( 2023-12-09 19:46:53,407 INFO steinbock - img/Patient4_005.tiff /opt/steinbock-venv/lib/python3.8/site-packages/tifffile/tifffile.py:2060: UserWarning: <tifffile.TiffWriter 'Patient4_006.tiff'> writing zero-size array to nonconformant TIFF" and outputs correct images.csv and empty tiff files. Command used - doskey steinbock=docker run -p 8888:8888 -v E://data:/data ghcr.io/bodenmillergroup/steinbock:0.16.1 $* steinbock preprocess imc images --hpf 50 OS - Windows 11

nilseling commented 7 months ago

Could it be that the download failed and you are processing a corrupt file? Maybe try downloading it again and see if that helps.

Milad4849 commented 6 months ago

Closing due to inactivity