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I've done a repro tonight, this time with some dark-flats. I also realised that I didn't have the star selection set correctly in my original stacking. The background looks a lot less noisy in this one. I also did some analysis of how uniform the illumination is in my light box by comparing two sets of flats taken with the light box rotated 90 degrees and I'm happy to report the flats look identical in the two images when layered in PS with difference.
Bring on the new moon!
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