An analysis target region setting apparatus comprising: an analysis target region setting means configured to set an analysis target region that is a region to be analyzed by an analyzer in an observation region of a sample, and to set a position, size, and orientation of an illumination aperture of the analyzer based on the set analysis target region; a pixel information acquisition means configured to acquire pixel information on each pixel constituting an observation image of the observation region; a sub-region forming means configured to classify each pixel in accordance with the pixel information and form one sub-region or plural sub-regions composed of pixels that belong to a same classification and are adjacent to each other; a consolidation information calculating means configured to obtain a characteristic value regarding a part or whole of pixels in each sub-region as consolidation information; and a region consolidating means configured to consolidate the sub-region with one sub-region adjacent to the sub-region based on the consolidation information; wherein the region consolidating means is configured to consolidate two adjacent sub-regions based on: whether the length of a boundary between the adjacent sub-regions is greater than or equal to a predetermined value, and a statistic of a difference of the pixel information on adjacent pixels on the boundary, in each sub-region, wherein the length of the boundary is calculated based on the number of pixels positioned on the boundary; or whether the number of pixels in each sub-region is less than or equal to a predetermined value, and a difference between a statistic of the pixel information on entire pixels in each sub-region and a statistic of the pixel information on entire pixels in a 22 sub-region adjacent to the sub-region; or whether a degree of circularity is less than or equal to a predetermined value, the degree of circularity being calculated from the number of pixels in each sub-region and the number of pixels on a boundary between the sub-region and neighboring sub-regions. an analysis target region setting means configured to set an analysis target region that is a region to be analyzed by an analyzer in an observation region of a sample, and to set a position, size, and orientation of an illumination aperture of the analyzer based on the set analysis target region; a pixel information acquisition means configured to acquire pixel information on each pixel constituting an observation image of the observation region; a sub-region forming means configured to classify each pixel in accordance with the pixel information and form one sub-region or plural sub-regions composed of pixels that belong to a same classification and are adjacent to each other; a consolidation information calculating means configured to obtain a characteristic value regarding a part or whole of pixels in each sub-region as consolidation information; and a region consolidating means configured to consolidate the sub-region with one sub-region adjacent to the sub-region based on the consolidation information; wherein the region consolidating means is configured to consolidate two adjacent sub-regions based on: whether the length of a boundary between the adjacent sub-regions is greater than or equal to a predetermined value, and a statistic of a difference of the pixel information on adjacent pixels on the boundary, in each sub-region, wherein the length of the boundary is calculated based on the number of pixels positioned on the boundary; or whether the number of pixels in each sub-region is less than or equal to a predetermined value, and a difference between a statistic of the pixel information on entire pixels in each sub-region and a statistic of the pixel information on entire pixels in a 22 sub-region adjacent to the sub-region; or whether a degree of circularity is less than or equal to a predetermined value, the degree of circularity being calculated from the number of pixels in each sub-region and the number of pixels on a boundary between the sub-region and neighboring sub-regions. whether the length of a boundary between the adjacent sub-regions is greater than or equal to a predetermined value, and a statistic of a difference of the pixel information on adjacent pixels on the boundary, in each sub-region, wherein the length of the boundary is calculated based on the number of pixels positioned on the boundary; or whether the number of pixels in each sub-region is less than or equal to a predetermined value, and a difference between a statistic of the pixel information on entire pixels in each sub-region and a statistic of the pixel information on entire pixels in a 22 sub-region adjacent to the sub-region; or whether a degree of circularity is less than or equal to a predetermined value, the degree of circularity being calculated from the number of pixels in each sub-region and the number of pixels on a boundary between the sub-region and neighboring sub-regions.