I recently had a similar, but more complex, problem and managed to solve it
satisfactorily using the stackreg and turboreg plugins for imageJ
<http://bigwww.epfl.ch/algorithms.html> together with a panorama software
called Stitcher <www.realviz.com>. Stitcher has the advantages of a good GUI
and that uses templates and is scriptable, which greatly speeds up stitching
of multiple images.
> I had posted question regarding aligning two stacks. I did find a plugin Align
> 3 TP. Using this I was able to align slices from two stacks, but the final
> images size is same as the original image. I am basically thinking of
> stitching two stacks after they are aligned. I am not even sure if I explained
> my problem correctly. I have two stacks each of hundred images. if I pick up
> the first slice in both the stacks, I will see a small overlapping region. I
> want to stitch these two slices and want to stitch the remaining 99 pairs,
> which finally would increase the size of each slice. Can anyone please help me
> with this.. It is very important that I get this thing going for my research
> to start. Any help will be greatly appreciated.