1. A microscope system, comprising: a microscope unit; and a control computer unit; wherein the control computer unit comprises: an image information obtainment unit for obtaining a plurality of first adjacent microscope images on a first plane and obtaining image information of an entirety, or a part, of a sample by combining the plurality of first adjacent microscope images, and for obtaining a plurality of second adjacent microscope images on a second plane whose focus position is different in a direction of an optical axis and obtaining image information of the entirety, or the part, of the sample by combining the plurality of second adjacent microscope images, to thereby obtain three-dimensional image information of the entirety, or the part, of the sample, by moving an object lens and the sample relatively to each other in both a direction perpendicular to the optical axis and in the direction of the optical axis; a specific zone designation unit for designating a specific zone out of the image information of either the first plane or the second plane obtained by the image information obtainment unit; a specific zone image storage unit for storing image information of the specific zone designated by the specific zone designation unit, the image information of the specific zone retaining original image information of the first plane and the second plane; an image information reduction unit for reducing an information volume of image information being not designated by the specific zone designation unit among the image information obtained by the image information obtainment unit; a reduction image storage unit for storing the image information reduced by the image information reduction unit; and an image position relationship storage unit for storing a positional relationship between the image information stored by the specific zone image storage unit and the image information stored by the reduction image storage unit; wherein the image information stored in the specific zone image storage unit retains original image information in which images on the first plane and the second plane that correspond to the specific zone are integrated into a single image.