I'm scanning maps in patches for later stitching and realized that many 
flatbed scanners give slightly non-square pixels. (When scanning a circle I 
get an oval). Hugin has no ability to optimize for this parameter. My 
solution would be to manually adjust each image in Photoshop before loading 
into Hugin. Is there no elegant way of correcting this? Any ideas?

Some old HP models are very poor in this regard. My Canon Canoscan 4400F 
gives perfect square pixels but I had to replace it because when 
painstakingly dismounting the lid, I introduced dust somewhere which 
resulted in colored lines that I have been unable to get rid of despite 
cleaning repeatedly. I then bought a used Canoscan 8800F. It outputs very 
slightly non-square pixels, though not much at all so I figured I can live 
with it. Still, I assume it should be impossible to get a perfect stitch.

Are we really certain that all cameras have square pixels?

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