1. A three-dimensional image reconstructing apparatus for reconstructing a three-dimensional image showing a three-dimensional structure of an object based on an image of the object which is obtained by image-capturing the object, comprising: an image-capturing section that captures a plurality of transmission-type images by transmitting an electron beam through the object from a plurality of different angles, the captured transmission-type images each being represented by densities of different levels and including the object; a characteristic region selecting section that selects a plurality of characteristic regions included in the object in each of the transmission-type images; a characteristic region distribution calculating section that calculates respective spatial positions of the characteristic regions in the whole object based on respective positions of the characteristic regions, in the each of the transmission-type images, which are selected in the each of the transmission-type images, so as to calculate a spatial distribution of the characteristic regions in the whole object; and a three-dimensional image reconstructing section that, when reconstructing the three-dimensional image which shows the three-dimensional structure of the object and in which the densities of different levels are allocated to the whole object by integrating the transmission-type images, allocates the densities of different levels of the transmission-type images to respective positions, in the three-dimensional image, of the characteristic regions based on the spatial distribution of the characteristic regions in the whole object, so as to reconstruct the three-dimensional image in which a three-dimensional structure in each of the characteristic regions is shown.