An imaging section of a microscope apparatus captures a plurality of microscope images each having the focal position which differs in the field being same with a light flux having passed through a microscopic optical system. A region separating section separates a cellular region from a non-cellular region by using the plurality of the microscope images. A focusing position calculating section finds a focusing position in a target pixel included in the cellular region based on a brightness change in the position being same in the plurality of the microscope images. A three dimensional information generating section generates three dimensional information of a cultured cell based on a position of the cellular region and the focusing position in the target pixel.