Frederic Da Vitoria wrote:
I believe horizontal control points should only be used when assembling an 
actual landscape panorama, to mark the horizon itself. I never assembled 
flatbed or microscope images, but I did some mosaic mode stitches. My remark 
could be wrong...

I use horizontal and vertical control points routinely when sitiching mosaic 
scans, most commonly on the straight edges
of rectangles (e.g. maps).

Hugin is then able to use pitch and yaw, roll to correct any perspective 
distortion of the stitch, as well as using X,Y,Z
to perform the tesselation of the sub-images.

Optimising something with this many variables MUST (IME) be done incrementally.

 BugBear

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