A multiple scattering algorithm for three dimensional phase contrast atomic electron tomography

Abstract

Electron tomography is used in both materials science and structural biology to image features well below the optical resolution limit. Here, we present a new method for high-resolution 3D transmission electron microscopy (TEM) which approximately reconstructs the electrostatic potential of a sample at atomic resolution in all three dimensions. We use phase contrast images captured through-focus and at varying tilt angles, along with an implicit phase retrieval algorithm that accounts for dynamical and strong scattering, providing more accurate results with much lower electron doses than current atomic electron tomography methods. We test our algorithm using simulated images of a synthetic needle geometry dataset composed of an amorphous silicon dioxide shell around a silicon core. By simulating various levels of electron dose, tilt and defocus, missing projections, and regularization methods, we identify a configuration that allows us to accurately determine both atomic positions and species. We also test the ability of our method to recover randomly positioned vacancies in light elements such as silicon, and to accurately reconstruct strongly-scattering elements such as tungsten.