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Are you using a one shot colour camera or a monochrome and filters? Maxim will do pretty much anything you ask it too. From what you are saying I think you are using a monochrome ccd with filters and you are using maxim to make a colour frame for each set of subexposures?
like making red green and blue 1 into RGB1, doing this with each subframe set and then stacking the RGB subframes?
so in DSS you stack this?
RGB1
RGB2
RGB3
ect ect
I am using DSS and maxim and I stack all of the filters frames together including any calibration frames and then take the calibrated stacked frames into maxim to do my RGB combine.
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