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Through numerical simulations, we demonstrate the combination of ptychography and atomic electron tomography as an effective method for low dose imaging of individual low-Z atoms in three dimensions. After generating noisy diffraction patterns with multislice simulations of an aberration-corrected scanning transmission electron microscope through a 5-nm zinc-oxide nanoparticle, we have achieved three-dimensional (3D) imaging of individual zinc and oxygen atoms and their defects by performing tomography on ptychographic projections. The methodology has also been simulated in 2D materials, resolving individual sulfur atoms in vertical $\mathrm{W}{\mathrm{S}}_{2}/\mathrm{WS}{\mathrm{e}}_{2}$ van der Waals heterostructure with a low total electron dose where annular-dark-field images fail to resolve. We envision that the development of this method could be instrumental in studying the precise 3D atomic structures of radiation sensitive systems and low-$Z$ atomic structures such as 2D heterostructures, catalysts, functional oxides, and glasses.

Ptychographic atomic electron tomography: Towards three-dimensional imaging of individual light atoms in materials