Merging many microscopic images taken from optical microscope

Hello everyone,
Im' new in this group.
I'd like to know if you know a practical way to merge many images
(40+) in an unique one, possibly in an automated way.
My problem is that I have an optical trinocular microscope to which I
attached my Canon EOS camera, and took 40+ images of a slide to cover
the entire object, but then I'm unable to merge them in a simple way
to form a unique photo.
Can you help me?
Thank you,

Emanuele (Italy)
.

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