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Subs from different nights and bad framing

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Since I moved into a flat its not quite as easy to get out and image these days.. But this past weeks fantastically clear skies made it easy to not risk any wasted journeys or setting up, for the first time in a year! 

Anyway, I went for the Heart Nebula this time and I got 50x300 workable lights that didnt go wrong.. HOWEVER the last evening of shooting I accidentally cut off the top of the nebula in the framing. So my question is, What is the best way in PI to stack these subs? Create 2 separate stacks one with the correct framing and one without and somehow merge them later? Or stack all frames using the good framing as the reference and edit out the horrible stacking/alignment effects at the top edges? Or maybe something else entirely? Its roughly 33 subs correct framing, 17 badly framed.

Im a little rusty in my processing, and now only use PI. (I found PS was easier for this sort of thing)

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Not sure if this is what you are after, but it may be worth stacking them separately and creating a mosaic. Microsoft Image composite editor is pretty good

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