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BodenmillerGroup / steinbock

A toolkit for processing multiplexed tissue images
https://bodenmillergroup.github.io/steinbock
MIT License
50 stars 15 forks source link

Measure intensities of user-defined loci #270

Closed Shhsvri closed 1 day ago

Shhsvri commented 1 week ago

I am working on skin tissue samples. I am using steinbock with deepcell. I was wondering if there is functionality to measure intensities by user defined borders? My goal is to measure intensities in the epidermis and compare with signal from the dermis.

Milad4849 commented 2 days ago

@Shhsvri Steinbock operates on segmented objects. You would have to make segmented objects out of whatever you want to quantify the signal based on. If what you are interested in are not cells, then you likely have to find another way, such as training a model via ilastik, to achieve your desired segmentation.