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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.
Honestly, hugin already does pretty good job. I did this one with hugin. Not the highest resolution, but it's also a very dense IC (Wii U GPU). Literally just pushing the die around with tweezers. https://marcan.st/transf/latte_stitched.jpg …
how many images did you stitch it out of? because when working with the switch PCB I ran in to several issues. required a huge amount of manual work to get something more complete. admittedly, my microscope was a piece of shit, lighting was terrible, etc etc.
I think that one was 15 images (3x5 probably)
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