1. A method for database construction comprising the following steps: (a) providing more than one three-dimensional (3D) network motif images; (b) aligning and correcting 3D images generated in (a) according to a 3D standardized coordinate, wherein each point registered to the 3D images is assigned a coordinate location (x, y, z) to indicate its position in the standardized space area; (c) dividing 3D images in (b) with individual voxel or a self-defined brick consisting various voxels, wherein voxel is a volume element, representing 1×1×1 unit on a regular grid in the standardized space area; (d) categorizing space information of each coordinate point registered to the 3D images within voxels; (e) storing processed 3D network motif images in (c) and space information in (d) into a computer-readable recording medium; and (f) providing skeletal forms of said 3D network motif images processed with path tracing algorithm.