1. A microscope system comprising: an imaging portion that forms an image of a specimen; an image-acquisition portion that captures the image of the specimen formed by the imaging portion; a background identifying portion that identifies a background region other than a region containing the specimen in the image acquired by the image-acquisition portion; a calibration-data generating portion that generates calibration data for correcting shading contained in the image on the basis of a luminance distribution of the background region identified by the background identifying portion; and a shading correcting portion that corrects a luminance of the image by using the calibration data generated by the calibration-data generating portion.