A microscope system comprises: a stage carrying a sample; an optical system forming an sample image; a driver driving at least the optical system or stage to relatively moves the sample and optical system; an imaging section capturing a reference viewing field image as an image of a predetermined viewing field range of the sample and peripheral viewing field images each being an image of a peripheral viewing field range containing a predetermined region in the predetermined viewing field range and different from the predetermined viewing field range, by the driver moving the relative position of the sample; a correction gain calculator calculating a correction gain of each pixel of the reference viewing field image based on the reference viewing field image and peripheral viewing field image; and a corrector performing shading correction on the reference viewing field image based on the calculated correction gain.