Our group is developing a laser scanning module in Micro-Manager and
recently we have been working on a feature that needs to create z stack with
different number of z and also different central z positions in each tile.
We did this by creating positions containing all x, y, z positions in the
positionlist, and execute all the positions in MDA mode (with the default z
slice option disabled). However, after all the images are collected we have
trouble stitching them in ImageJ/FIJI stitcher since in this case our images
are all separated files (even if they are actually many z stack images) and
the stitching plugin treats them each as a 3D image.
Anyone has similar experience with creating varying z stacks or there is any
other way to stitch those images?