Dear ImageJ Forum,
I am trying to modify the Stitching plugin to stitch a regular grid of tiles, taking into account the pecularities of our microscope, but I regularly get tile misalignments that I really can’t explain.
To ensure this wasn’t due to the fact that I fiddled with the internals of the stitcher, I took two tiles that would end up misaligned, saved the (roughly) overlapping regions as individual tiffs and aligned them using the normal “pairwise stitching” plugin. The options used were “Compute Overlap” and I set “Check Peaks” to a value of 10.
Below are the links to the original 16bit tiffs (preview is not working on them, sorry) and the results from Matlab’s phase correlation alignment module (imregcorr) compared to ImageJ’s stitching result (click on the preview to see the full image). I would appreciate if anyone could shed some light on what’s happening there.