I have lots of microscope images and I would like to stitch together. These images were created by an automatic stage so positions of images are very exact. I used 10 % overlapping. However, there is a little backlash so it needs a small reposition. I used the import Gigapan option because it seem very similar strategy of microscope scanning (rows :downward). I set rows, columns and overlapping. This preview seems pretty, but result is terrible. The program tried to stretch and transform images and created some cubist picture
So my question is how can I set that it makes only an image reposition (maybe a little vignette removing) ?
There was a bug in the GIGAPan import module. Did you use the latest version of APG V3.0 B1? Have you try to stitch them without using import modules?
Then on microscope, normally the lens infos are missing. What have you set as focal length? If you set a microscopic value as 2mm, APG must fail Don't set fisheye characteristic. For planar images like you have, use a long focal lenght >100mm
Is the orientation of all the images correct? On microscope, normally the camera is mounted vertically. So the orientation sensor fails and you can not differ between landscape and portrait mode. But APG is looking to this informations in EXIF. What kind of motiv you have? Are there really identificable points in it? Best is to show us a screenshot.