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Hi Paul,
Looking at your picture, it looks like noise, not hot pixels.
I usually rune each sub through the hot pixel removal process straight after calibration. So in CCDStack go to Process->Data Reject->Remove hot/cold pixels. I use a strength of 5 and an ADU count of 100000. Then do an impute rejected pixels, width 0.2, 3 iterations.
Then go on to align and stack your images.
Cheers
Stuart
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