1. A microscope system, comprising: an image acquiring unit that acquires a specimen image by capturing a single image of a specimen using a microscope configured for at least bright field observation, 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 detects stain intensity of the element identification pigment staining a corresponding position on the specimen and a stain intensity 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 detected stain intensity of the element identification pigment; an expression portion extraction unit that extracts expression portions of the plurality of target molecules in the cell constituent element, on the basis of the detected stain intensity of the molecule target pigment at at least one pixel in the identified 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 identified area of the cell; a display image generating unit that generates a display image in which the classified area of the cell is labeled and displayed differently from other areas of the cell, and in which each of the plurality of expression patterns of the target molecules is labeled and displayed, wherein the generated display image also represents a staining state of the specimen stained by the element identification pigment on the basis of the detected stain intensity of the element identification pigment at each pixel in the captured single specimen image, and wherein the display image is generated by replacing a pixel value of the area of the cell classified into the expression pattern of the target molecules in the captured single specimen image with a predetermined display color; and a display processing unit that displays the display image.