An image processing apparatus includes an area specifying unit that specifies a closed area emitting fluorescence in a fluorescence image as a cell area in a cell population including a number of dispersed cells. The fluorescence image is generated from fluorescence emitted by the cell population irradiated with a scanning laser beam. The apparatus also includes a nucleus data removing unit that removes data corresponding to a nucleus in the cell area; an overlapping cell specifying unit that specifies an overlapping cell area where cells overlap, based on a fluorescence intensity of a cytoplasm portion corresponding to an image where the data corresponding to the nucleus is removed; and an analyzed image generating unit that generates an analyzed image where data of the overlapping cell area is removed from the fluorescence image.