1. A microscope apparatus comprising: a microscopic optical system converting a phase difference produced by an observation object in a field into a brightness difference to form an image; a driving section adjusting a distance between a cultured cell as the observation object and a focal position of the microscopic optical system in a direction of an optical axis; an imaging section capturing a plurality of microscope images with a light flux having passed through the microscopic optical system, the plurality of microscope images each having the focal position which differs in the field being same; 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 the field by using the plurality of the microscope images; a focusing position calculating section finding 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; 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 in the target pixel.