1. A microscope system, comprising: an image information obtainment unit for obtaining image information of the entirety, or a part, of a sample by moving an object lens and a sample relatively to each other in the perpendicular direction against an optical axis; a specific zone designation unit for designating a specific zone of the image information 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; 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.