In this paper, we propose an algorithm to obtain a three-dimensional reconstruction of a single nanoparticle based on the method of atom counting. The location of atoms in three dimensions has been successfully performed using simulations of high-angle-annular-dark-field images from only three zone-axis projections, [110], [310] and [211], for a face-centred cubic particle. These three orientations are typically accessible by low-tilt holders often used in high-performance scanning transmission electron microscopes.