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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 measure neighbors very slow #229

Closed dingxm closed 6 months ago

dingxm commented 7 months ago

Hi I have a sample from AKOYA (15K pixel X 15K pixel) and around 200K cells were identified after segmentation. Then I run $steinbock measure neighbors --type borders --dmax 4. It is very slow and it is still running after 24 hours. Is there anyway I can speed up this step. Thanks Xiangming

Milad4849 commented 7 months ago

Hi @dingxm

You can see if the --mmap option of steinbock measure neighbors helps. In general steinbock is optimized for operating on IMC images and benchmarked against using their associated masks.

Milad4849 commented 6 months ago

Closing due to inactivity