Single-Scan Three-Dimensional Atomic Imaging via Electron Ptychographic Interferometry

Abstract Resolving atomic positions in all three dimensions with high precision is central to understanding many emergent properties of quantum materials, but has remained fundamentally challenging. Existing three-dimensional (3D) imaging methods in electron microscopy are largely tomography-based, relying on geometrical parallax from tilt-series projections and high electron doses, which makes them unfriendly for beam-sensitive and structurally flexible systems such as 2D materials. Here, we introduce electron ptychographic interferometry (EPI), a single-scan 3D atomic imaging method that exploits intrinsic wave interference induced by individual atoms during electron scattering. By decoding this atom-induced interference in the amplitude of the electron exit wave into a quantitative depth-sensitive contrast, EPI retrieves full 3D atomic coordinates with picometer axial precision and deep sub-angstrom lateral resolution, without specimen tilting or model assumptions. We validate the picometer accuracy of EPI by quantifying the 2.98 Å S-S interlayer distance in monolayer MoS2, and apply it to experimentally resolve, for the first time, a ~5 pm out-of-plane structural reconstruction in AA-stacked regions of magic-angle twisted bilayer graphene. EPI thus establishes a physically distinct and experimentally accessible route to single-scan 3D atomic imaging, opening new opportunities to uncover atomic-scale origins of quantum phenomena.