A microscopy system includes: an image acquisition unit configured to acquire slice images generated by capturing an object image while shifting a focal position along an optical axis of an observation optical system included in a microscope; an image shift processing configured to relatively shift, with respect to one slice image among the slice images, another slice image in a plane including the one slice image; an all-in-focus image generation unit configured to generate all-in-focus images by combining the one slice image and the other slice image relatively shifted with respect to the one slice image under conditions in which shift amounts of the other slice image with respect to the one slice image are different; and a display unit configured to display the all-in-focus images.