1. A microscope system, comprising: an image acquiring unit that acquires a specimen image obtained by capturing an image of a specimen using a microscope, the specimen being stained by an element identification pigment visualizing one or more cell constituent elements constituting a cell and by a molecule target pigment visualizing a plurality of target molecules; a pigment amount acquiring unit that acquires a pigment amount of the element identification pigment staining a corresponding position on the specimen and a pigment amount of the molecule target pigment, for each pixel of the specimen image; an element area identification unit that identifies an area of the cell constituent element in the specimen image, on the basis of the pigment amount of the element identification pigment; an expression portion extraction unit that extracts expression portions of the plurality of target molecules on the cell constituent element, on the basis of the pigment amount of the molecule target pigment at a pixel in the area of the cell constituent element; an expression pattern setting unit that sets an expression pattern of the target molecules including a combination of presence/absence of expression of the plurality of target molecules; an expression pattern classification unit that classifies an area of a cell corresponding to the expression pattern of the target molecules having been set, on the basis of a combination of expression portions of the plurality of target molecules included in the area of the cell; a display image generating unit that generates a display image in which the area of the cell classified into the expression pattern of the target molecules is labeled and displayed differently from other areas of cells; and a display processing unit that displays the display image.