1. A microscope system comprising: a microscope including a motorized stage on which is mounted at least one container that contains a specimen and which can adjust a position of the container, a scanner that scans laser light radiated onto the specimen in the container mounted on the motorized stage, an objective lens that focuses the laser light scanned by the scanner onto the specimen, an image-acquisition unit that acquires an image of the specimen by detecting fluorescence produced in the specimen by laser light irradiation with the objective lens, and a dark box that contains these components; a storage unit that stores a mounting position of the container; an image-acquisition-position setting unit that sets acquisition positions of partial images of inside of the container, to be acquired by the image-acquisition unit, based on the mounting position of the container stored in the storage unit; a control section that controls the microscope so as to acquire a plurality of the partial images for each container based on the acquisition positions set by the image-acquisition-position setting unit; and a map-image generating section that arranges the plurality of partial images acquired for each container to generate a map image.