To properly specify an area of a desired cell constituent element and to display the presence or absence of expression of a desired target molecule on this cell constituent element with a good visibility.

In the microscope system 1, a high resolution image acquisition processing unit 453 acquires a VS image of a target specimen S stained with a staining dye containing a dye for cell component identification and a molecule target dye. A dye amount calculation unit 457 calculates, for each pixel of the VS image, a dye amount of each staining dye that stains corresponding positions on the specimen. A cell component identification processing unit 458 identifies a cell component based on the dye amount of the dye for cell component identification. An extraction condition setting unit 459 sets the presence or absence of a target molecule in the area of the cell component as an extraction condition. A target portion extraction unit 460 extracts an area of a target portion in the target specimen S that satisfies the extraction condition. A display image generator 462 generates a display image of the VS image representing the area of the target portion.