An interesting application. I agree, if they used one of the small microscope cameras, they could use it to capture the data inside the sterile environement and bring our the video/image to a bigger screen. I like the idea of using the Legos. They would help you set up different types of dish sizes for the scanning. It would be very easy for them to set up an X-Y dish extractor and use the legos to build a matrix of the cultures being grown. The dish extractor could cycle through the matrix, pull out each dish, take it over to the camera, take the picture, return the dish and go to the next.
A simple Arduino or MSP430 could handle software. You already have many designs for and X-Y motor driven device. The rest is a simple robot sampling task.
Just a thought,