I have been trying to do the stitching, but the image I am getting doesn’t make sense. Please, can someone take me through the process of doing the stitching?
Which version of the microscope are you using, and which softwate version?
It looks as though you have a lot of overlap between images. What scan settings did you use?
My guess is that the mapping between camera and stage coordinates is off - it looks like those images have been positions with more or less no overlap, which suggests that the microscope is moving a shorter distance in between images than expected.
This may be a problem with the metadata saved in the images: the format of this metadata has gone through a number of incompatible versions, unfortunately, so if the microscope software is much older than the stitching program it might be difficult to make it work properly.
Possibly the easiest fix is to wait for the next alpha release of the v3 disk image, which should, I think, have stitching built in.