A microscope apparatus comprises a focusing unit for changing the relative position between a specimen and the focus position of an object lens; and a setup unit for setting a plurality of import regions in the optical axis of the object lens, with a position at which a specimen is focused being established as a reference. It further comprises a control unit for obtaining a plurality of extended time exposure images by changing the relative positions from each respective start position to the end position of each of the plurality of import regions by means of the focusing unit under an import condition determined by desired exposure time and emission light volume; and an image generation unit for generating a focal-depth enlarged image by adding together the obtained plurality of extended time exposure images.