> the pattern changes depending on which line-pair is used. but the output is > not necessarily any better... > > I see. So it looks like pixel fixed-pattern noise. There are two ways how to fight it.
One is to resurrect another part of unused FPGA code - the one that can subtract/multiply the fixed values from the image pixels (that will also need some calibration). Second - with post-processing. In that case you should rather use jp46 format where pixels are not interpolated. First step - eliminate additive parameter - you can get it if you average multiple line pairs of the grey card or (even better) - disable autoexposure and white balance (if you use them) and close the lens. For such measurements you need to un-apply gamma (you can do it in ImageJ plugin) so the background subtraction will take place with linear pixel values (setting gamma=1 in the camera would kill the dynamic range) Andrey
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