To obtain the 3D atomic structure of the Au NP from the estimated number of atoms in each atomic column, we applied our proposed method to a simulated system as a validation step. We used the atom-counts procedure to generate an initial 3D model of the Au NP by arranging the atoms symmetrically around the central plane, based on the known specimen orientation ([110]) and the crystal structure. We fixed the distance between adjacent Au atoms, along the beam direction, according to the lattice parameter .