Normalising fluorescence microscopy data across slices, replicates and location

I have a piece of tissue. I am taking slices at regular intervals from that tissue and using fluorescent staining to detect some protein of interest. I do this for all slices. A set of slices is a replicate. I collect 3 replicates. Now the data I have sometimes has some outliers where some pixels are disproportionately high and sometimes there is some illumination issue because of the location of the tissue on the microscopy slide. I use a CNN to extract the intensity values at the points of interest. What would be a principled way to normalise this data so that I compare these results across slices and replicates. I would appreciate any literature sources as well as I am quite new to this field and dont know where to start. Thanks a lot for your help.

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Were you looking to model this in Stan? The is a better place for general stats questions or experimental design.

yes i was looking to model this in stan or for that matter pyro as well. But i guess you are right