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I 'save all uncombined images' in FITS3P format. This will save every image you take as well as the final stacked image. I do it this way because I might have a few goes at drizzle after capturing (I might change the alignment stars, or change the drizzle settings). I have AIP4WIN, an astro image processing package that comes with the book 'Handbook of Astronomical Image Processing', so I can stack and process the frames in that, too.
Depending on what image processing software you have, you might prefer to save all uncombined images in a different format (TIFF would probably be the best non-astro format) that your IP software 'understands'.
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