1. An analysis target region setting apparatus configured to set an analysis target region that is a region analyzed by an analyzer in an observation region of a sample; comprising: a pixel information acquisition means configured to acquire pixel information on each pixel constituting the observation region; a sub-region forming means configured to classify each pixel in accordance with the pixel information and form plural sub-regions each composed of one pixel or 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 two adjacent sub-regions of the plural sub-regions based on the consolidation information, wherein the region consolidating means is configured to consolidate the two adjacent sub-regions based on the number of pixels in each sub-region 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 sub-region adjacent to the sub-region.