A microscope system including an objective lens, a camera for capturing an image of light that comes from a specimen and that is collected by the objective lens, a stage for moving the specimen and the objective lens relative to each other in a direction perpendicular to an optical axis, a controller implementing a VS-image generation for generating a VS image by joining a plurality of microscope-image groups that are acquired while moving the objective lens and the specimen relative to each other, a correction-region search for searching for a correction region for acquiring a correction image, a correction-data generation for generating shading-correction data based on the correction image acquired for the searched-for correction region, and a shading correction for performing correction by using the generated shading-correction data.