Hey Lewis,
I use DSS 3.3 beta for debayering (it reads them in the lights list) so when I click on them they convert to colour and I can see the details when I adjust the sliders.
It means they dont need to be debayered before stacking as DSS takes care of it all.
If it looks wrong, I simply adjust the FITS settings for debayering until its correct, I use generic GRBG for my Sony sensored Atik.
DSS beta 3.3.3 rocks and gives me an output that requires very little post processing.
Give it a go.
Cheers
Chris
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