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I typically start by running all of the frames through CCDInspector, it can be a quick and easy way to cull ones that have a really soft focus (higher FWHM) or elongation higher than I'd like.
Sometimes only taking out the really bad ones and leaving some of the okay ones isn't a bad thing too. If you have a lot of subs to work with and you get a good rejection going when stacking, it can improve the SNR without effecting star shape.
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