A microscope system is provided with a microscope that acquires images at least at a first magnification and a second magnification higher than the first magnification, and a processor. The processor is configured to specify a type of a container in which a specimen is placed, and when starting observation of the specimen placed in the container at the second magnification, the processor is configured to specify a map region corresponding to a map image constructed by stitching together a plurality of second images acquired by the microscope at a higher magnification than the first magnification by performing object detection according to the type of the container on a first image that includes the container acquired by the microscope at the first magnification, and cause a display unit to display the first image and a range of the map region on the first image.