Dear all,

           Is there any way to stitch images together in the z direction? I have several images with similar but not identical x/y dimensions that need to be stitched in z. I used the pairwise stitching plugin to stitch the individual images together in x and y but this does not work for the z direction.

            To clarify, I am trying to stitch consecutive confocal images that were taken of the same part of a mouse brain. The slices are 50 microns thick and are taken with a saggital view, starting laterally and going medial. Unfortunately, the stacks do not have the exact same X and Y dimensions, nor the same number of z-slices (they range from 10-16 slices). There's also no true landmark present in all of the images. It would be really useful to be able to combine these images so that I can visualize this section of the brain and do neuron tracing.

Thank you for your time and help!
Sumeer