I’d imagine any of the command line tools of dt or RT would do it, if you can specify a constant crop window that’ll work for each image.
I’m getting ready to do a similar exercise, and what I’m thinking of doing is putting some sort of marker in the slide holder that I can use to register the slide when I insert it. It’d show up in the capture, but I could use it with one capture to manually determine the top-left, for instance, and build my crop window with that. Maybe a needle taped to the diffusion screen…