Hi,

Thanks for being interested in using our plugins. The istitch plugin we've developed for stitching 2D/3D/4D images with merely "translations" (x,y, and z shifts). From your messages, it looks like there might be also rotations and possibly deformable transformations between the consecutive sections. Your "stitching" issues are more like "alignment/registration" problems instead of image stitching problems we solved here. To clarify your real problems, you can send us a link of your data or screen shots so that we can further help.

Best,
Yang