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Have you taken Bias frames?
Take some then use the adaptive dark settings in CCDStack. I use the RMS value. You need bias frames to calibrate the master dark frame. This should clear most of these overcompensated dark pixels (which are really bright pixels). Also, takes lots of really long darkframes. I use 30 minute darks for everything up to 30 minute subs. A nice cold cloudy night is perfect for making lots of long darks.
Cheers
Stuart
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