1. An analysis apparatus, comprising: a two-dimensional coordinate detecting unit configured to detect, with respect to a captured image group obtained by capturing an analysis specimen including an analysis target object at a plurality of focal depths, a two-dimensional coordinate candidate being a candidate of a plane coordinate of the analysis target object in each captured image; and a three-dimensional coordinate determining unit configured to determine, based on a position relationship of the plane coordinate candidates between the captured images, a three-dimensional coordinate candidate being a candidate of a three-dimensional coordinate of the analysis target object, wherein the two-dimensional coordinate detecting unit is configured to extract a first feature amount from the captured image, detect a preliminary two-dimensional coordinate candidate based on the first feature amount, set a comparison range around the preliminary two-dimensional coordinate candidate, extract a second feature amount from the captured image included in the comparison range, and compare a feature amount of a template with the second feature amount of the captured image in a range overlapping with the template when moving the template in the comparison range, to thereby detect the two-dimensional coordinate candidate.