Abstract Atomic electron tomography (AET) determines the three-dimensional (3D) coordinates and chemical identities of individual atoms from a series of scanning transmission electron microscopy images taken at different tilt angles. However, under dose-limited conditions, particularly at electron doses lower than those typically used for standard AET of beam-robust inorganic nanoparticles, the reduced signal-to-noise ratio forces a trade-off among accuracy, robustness, and throughput.