I typically use Affinity Photo for my pano stitching, but that's assuming all the images are undistorted, and parallel to each other (ie, I didn't change the angle of my camera, only the position).
If your images are distorted, Hugin should be quite capable of fixing them.
How much overlap do you have between the images?
If you take 3 images with a regular rectilinear lens by pivoting the camera, with some overlap between images, then there are going to be changes in the perspective between images, which have to be undone to overlap them. This occurs even if you rotate about the ideal point of the lens (nodal point, entrance pupil, whatever). You see this as distortion by the merging program, but it is due to the rectilinear perspective of the lenses.
When we try to merge them into a panorama, we're mapping a series of rectilinear images onto a cylindrical perspective. The effect can be made less by taking more exposures and rotating by less in between each one (using a longer focal length lens will enforce this). It is similar to the way that a 12-gon is a better approximation of a circle than a hexagon, which is better than a square.
Most of the people in this thread are talking about taking individual 35mm photos pivoting the camera
Personally, I shift the position of the negative relative to the camera. No pivoting involved. Stitching is also simple, although I use Affinity's auto-stitch utility.
Why the OP is getting distortion out of an image scanner, which by default, should be producing flat images, I don't know.
I have been using the Photomerge tool in Photoshop CS5 and CS6 for Hasselblad XPan frames:
I am not getting distortion from scanning. I am getting distortion stitching with different softwares.
This is why I need a simple 2d stitching. Nothing that changes the geometry of the pictures.
I can't see a way to use 'reposition' mode for stitching in Lightroom. 'Perspective' is not a stitching mode to use when you want to just align multiple parts of the same frame. It will be close, but not perfect. 'Cylindrical', I suspect, would be better, but still probably not pixel perfect. In 'reposition' mode every single pixel remains in place, only the blending masks are employed at the overlap areas.
You can check this is true with pasting partial scans as separate layers into the stitched panorama and carefully manually adjust their position over the stitched layer. Turning the partial scan layers on/off should be unnoticeable (in the regions that were part of the stitching overlap) if there was no distortion employed during stitching.
Full resolution psd file for demonstration....
With 'reposition' the overlapping area will "suffer" if your partial scans are not uniform. For example left hand scan is slightly tilted in one direction and the right hand scan tilted in another direction (maybe because your scanner's film feed/transport is not 100% stable). 'Collage' is the opposite.
If you have a decent scanner and you are not sloppy with film loading, 'reposition' is the mode to use. I'd rather have imperfections (potentially slight decrease in sharpness) in the overlap area than skewed everything else because that makes overlap area to fit together better.
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