1. A microscope apparatus comprising: a microscopic optical system; a driving section adjusting a distance between a cultured cell as an observation object and a focal position of the microscopic optical system in a direction of an optical axis; a region separating section separating a cellular region in which the cultured cell is located from a non-cellular region in which the cultured cell is not located in a field by using a plurality of microscope images, each having the focal position which differs in the field which is the same; a focusing position calculating section finding a focusing position of a target pixel included in the cellular region based on the focusing position being the same in the plurality of the microscope images; and a three dimensional information calculating section generating three dimensional information of the cultured cell based on a position of the cellular region and the focusing position of the target pixel.