A microscope system includes an acquisition unit that obtains a specimen image acquired by capturing the specimen stained by an element identification dye that visualizes a predetermined cell constituent element and a molecule target dye that visualizes a predetermined target molecule by using a microscope; a dye amount unit that obtains dye amounts of the element identification dye and the molecule target dye that stain corresponding positions on the specimen for each pixel of the image; an element area identification unit that identifies an area of the cell constituent element based on the dye amount of the element identification dye; a condition setting unit that sets the presence or absence of the predetermined target molecule on the cell constituent element as a condition; and an extraction unit that extracts an area of a target portion that satisfies the condition based on the dye amount of the molecule target dye.