A microscopy system includes: an imaging unit that acquires an image by capturing an object image generated by an observation optical system; a shift unit that shifts a focal plane and a position of a field of view of the observation optical system; an imaging control unit that causes the imaging unit to acquire a multi-focus superimposed image including image information on planes in an optical axis direction of the observation optical system by shifting the focal plane and the position of the field of view during one exposure period; a shift amount acquisition processing unit that acquires a shift amount by which the position of the field of view is shifted; an all-in-focus image generation unit that generates all-in-focus images based on multi-focus superimposed images, respectively, acquired under conditions in which the shift amounts are different; and a display unit that displays the all-in-focus images.