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I agree with Marcus. Also CCDs do deteroriate over time. They get damaged by cosmic rays and a sensor that had virtually no defects a year ago may suddenly have new hot pixels. So you need to replace your dark library every now and then.
How old are the darks or are they fresh?
How did you combine the darks to form a master dark?
If the darks are old then try taking new darks. If the darks are fresh then perhaps the way they were taken didn't match for some reason.
Sigma reject is the usual dark combine method to get rid of non repeating elements like a random cosmic ray.
As mentioned dithering gets rid of these fixed noise patterns.
Greg.
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