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That's interesting Peter about Maxim, with DSS, Astro Art and Nebulosity you don't have to do any pre-conditioning of the flats.
You do have to tell those programs which subs are the flats though, so the chosen program itself may do some pre-conditioning in the background.
The Nebulosity manual mentions that a 2x2 median filter is applied to all flats when they are stacked.
Cheers
Bill
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