1. A microscope system comprising: an objective lens that forms an image of a specimen; an image sensor that captures the image of the specimen formed by the objective lens; and a processor comprising hardware, the processor being configured to: identify a background region other than a region containing the specimen in the image acquired by the image sensor; generate calibration data for correcting shading contained in the image on the basis of a luminance distribution of the identified background region; and correct a luminance of the image by using the generated calibration data, wherein the generating of the calibration data comprises: estimating a luminance distribution of an entire region of the image on the basis of the luminance distribution of the identified background region, calculating correction values for individual pixels of the image so that the estimated luminance distribution becomes uniform, and generating the calibration data constituted of the calculated correction values.