I don't recall finding hugin when I did my (short) research on image stitching tool. Thanks to you, I've read the scanned image stitching documentation and I suppose it could work.

However, the process seems quite complicated and slow, asking you to draw control points and all that.

Microscope pictures have the particularity that there are nearly no deformation to the image but you have a lot of them, so you want the process to be as automatic as possible. That was the goal of my tool, make the simplest gui anf process possible for the task at hand.