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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

issue of Segmentation fault #252

Closed dingxm closed 2 months ago

dingxm commented 3 months ago

I have a big tiff (19755x14552 ) for the segmentation. I met issue of "out of memory". I have 1Tb memory for my Linux server. Below is the error info: /app/entrypoint.sh: line 3: 13 Segmentation fault (core dumped) python -m steinbock "$@" Is there anyway I can change some parameter that the deepcell step will use less memory. For example change the number of thread. Thanks

Milad4849 commented 3 months ago

Hi @dingxm You cannot specify such a parameter via steinbock. I think your best bet is to try deepcell tiling directly (not via steinbock). Steinbock is primarily designed to handle imc images and not images of the size that you have.