The invention provides a microscope system including a correction-gain storage portion that calculates a correction gain for performing shading correction of an image related to optical images of a specimen, obtained by a microscope, and stores specimen information indicating features of the specimen and optical information at the time of obtaining the image in association with the correction gain; a correction-gain selecting portion that selects the correction gain for use when performing the shading correction of the image to be corrected; and a correction portion that performs the shading correction of the image to be corrected, on the basis of the selected correction gain, wherein the correction-gain selecting portion selects, on the basis of the specimen information or a result of the shading correction with the plurality of correction gains, the correction gain to be used in the shading correction of the image to be corrected.