Three-dimensional imaging of individual carbon atoms

Ptychography is a computational microscopy method that unifies crystallography and microscopy by combining coherent diffraction with iterative phase retrieval. Although multislice electron ptychography achieves deep-sub-ångström lateral resolution, its depth resolution is typically at the nanometre scale. Ptychographic atomic electron tomography (pAET) has enabled three-dimensional (3D) atomic structure determination in nanomaterials, yet reliably resolving individual light atoms remains challenging. Here, using twisted bilayer graphene as a model moiré system, we demonstrate pAET for 3D localization of 6,648 carbon atoms with a precision of 0.12 Å. The resulting 3D atomic structure reveals stacking-dependent interlayer spacing and corrugation across the moiré supercell, as well as chiral lattice distortions with meron-like, anti-meron-like and anti-skyrmion-like textures. Density functional theory calculations based on the experimentally derived structure predict electronic band narrowing and a gap at the K point relative to a relaxed model. Multislice pAET simulations further support extending the method to diamond containing a nitrogen-vacancy centre and to amorphous carbon. These results establish pAET for 3D imaging of individual carbon atoms and open a route to linking 3D atomic structure with the properties of light-element materials.