hugin tries to take 2 images that you tell it are adjacent, and use a set of key pairs of points to distort, deblur, etc using excess information. You can get somewhat decent results, but not better than what you can get with a hi-res scanner, which should absolutely be doable.
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mmmk. its going to be pretty simple, mostly leaning towards 80/20 frame, prolly not a lot of room to work with, but enough to do some Scary Chemical Shit (tm) without fear
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Honestly, nothing I'm likely to work with will be more than a couple cm on a side, or need many reagents/steps or a complicated apparetus.
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