1. A three-dimensional structure verification supporting apparatus for supporting verification of a three dimensional structure by verifying properness of a three-dimensional image indicating the three dimensional structure of a substance, comprising: a comparison image generating unit for generating a three-dimensional comparison image by adjusting image quality of the three-dimensional image with image quality of a reference image of the substance which is obtained experimentally; and a degree-of-image coincidence computing unit for computing degree of image coincidence between the three-dimensional comparison image and the reference image of the substance.