1. A microscope apparatus comprising: an observation optical system having an objective lens and observing a cell; a driving section adjusting a relative positional relationship between the cell and a focal position of the observation optical system in a direction of an optical axis; an imaging section having a plurality of pixels corresponding to a shooting screen, capturing the cell being observed via the observation optical system, and obtaining image data of the shooting screen, the obtained image data corresponding to a phase difference image based on the focal position; a controlling section controlling the driving section and the imaging section to capture the cell while relatively moving the cell and the focal position of the observation optical system in the direction of the optical axis, and storing and associating a plurality of the obtained image data with focal position information in the direction of the optical axis, the plurality of the obtained image data corresponding to a plurality of phase difference images, the plurality of phase difference images being obtained without irradiation of an excitation light; a focusing position calculating section finding a focusing position of the observation optical system in a pixel of the shooting screen by image processing a plurality of output signals based on the plurality of the obtained image data, the output signals being obtained with respect to the pixel in a same position of the shooting screen under conditions in which the positional relationship of the direction of the optical axis differ; and a three dimensional information calculating section finding position information of the pixel of the shooting screen and information of the focusing position in the pixel and generating three dimensional information of the cell including a height of a contour surface of the cell, based on output information of the focusing position calculating section, wherein the observation optical system forms an image by converting the plurality of obtained image data corresponding to the plurality of phase difference images into brightness variance values, the region separating section obtains a brightness variance value in each position in the field from a plurality of the image data and separates a first region and a second region based on the brightness variance values, and the three dimensional information calculating section identifies a floating cell and an attached cell by using the three dimensional information of the cell.