A microscope system comprises a microscope body, an imaging unit connected to the microscope body and including an image sensor for capturing a microscopic image, and an XY stage configured to place a slide and move in an X direction and a Y direction. The microscope system changes an arrangement of the image sensor with respect to the microscope body so as to cause a direction defined by a pixel arrangement of the image sensor to align with one of the X direction and the Y direction of the XY stage.