An image analysis apparatus comprising: an image acquisition unit adapted to acquire a first fluorescence image indicating an observation target including a plurality of types of cells, each of which has a first region stained by first staining, and a second fluorescence image indicating the observation target in which a second region of a specific cell among the plurality of types of cells is stained by second staining different from the first staining; a first determination unit adapted to extract a contour of the first region from the first fluorescence image, to extract a contour of the second region from the second fluorescence image, to set a first reference point on the contour of the first region, to set a first outward unit normal vector which passes the first reference point as first information, to set an intersection point of an extension line of the first unit normal vector and the contour of the second region as a second reference point, the intersection point being adjacent to the first reference point, to set a second outward unit normal vector which passes the second reference point as second information, to determine whether or not the first region is included in the second region in a superimposed image obtained by superimposing the first fluorescence image and the second fluorescence image on the basis of the first information, the second information and third information indicating a distance between the first reference point and the second reference point, and to acquire a first determination result for each of the first regions; and a second determination unit adapted to determine the type of cell included in the observation target on the basis of the first determination result, wherein the first fluorescence image and the second fluorescence image are fluorescence images captured by an imaging apparatus. an image acquisition unit adapted to acquire a first fluorescence image indicating an observation target including a plurality of types of cells, each of which has a first region stained by first staining, and a second fluorescence image indicating the observation target in which a second region of a specific cell among the plurality of types of cells is stained by second staining different from the first staining; a first determination unit adapted to extract a contour of the first region from the first fluorescence image, to extract a contour of the second region from the second fluorescence image, to set a first reference point on the contour of the first region, to set a first outward unit normal vector which passes the first reference point as first information, to set an intersection point of an extension line of the first unit normal vector and the contour of the second region as a second reference point, the intersection point being adjacent to the first reference point, to set a second outward unit normal vector which passes the second reference point as second information, to determine whether or not the first region is included in the second region in a superimposed image obtained by superimposing the first fluorescence image and the second fluorescence image on the basis of the first information, the second information and third information indicating a distance between the first reference point and the second reference point, and to acquire a first determination result for each of the first regions; and a second determination unit adapted to determine the type of cell included in the observation target on the basis of the first determination result, wherein the first fluorescence image and the second fluorescence image are fluorescence images captured by an imaging apparatus.