Direct imaging and chemical identification of all the atoms in a material with unknown three-dimensional structure would constitute a very powerful general analysis tool. Transmission electron microscopy should in principle be able to fulfil this role, as many scientists including Feynman realized early on. It images matter with electrons that scatter strongly from individual atoms and whose wavelengths are about 50 times smaller than an atom. Recently the technique has advanced greatly owing to the introduction of aberration-corrected optics. However, neither electron microscopy nor any other experimental technique has yet been able to resolve and identify all the atoms in a non-periodic material consisting of several atomic species. Here we show that annular dark-field imaging in an aberration-corrected scanning transmission electron microscope optimized for low voltage operation can resolve and identify the chemical type of every atom in monolayer hexagonal boron nitride that contains substitutional defects. Three types of atomic substitutions were found and identified: carbon substituting for boron, carbon substituting for nitrogen, and oxygen substituting for nitrogen. The substitutions caused in-plane distortions in the boron nitride monolayer of about 0.1 A magnitude, which were directly resolved, and verified by density functional theory calculations. The results demonstrate that atom-by-atom structural and chemical analysis of all radiation-damage-resistant atoms present in, and on top of, ultra-thin sheets has now become possible.

Using a fifth-order aberration-corrected scanning transmission electron microscope, which provides a factor of 100 increase in signal over an uncorrected instrument, we demonstrated two-dimensional elemental and valence-sensitive imaging at atomic resolution by means of electron energy-loss spectroscopy, with acquisition times of well under a minute (for a 4096-pixel image). Applying this method to the study of a La(0.7)Sr(0.3)MnO3/SrTiO3 multilayer, we found an asymmetry between the chemical intermixing on the manganese-titanium and lanthanum-strontium sublattices. The measured changes in the titanium bonding as the local environment changed allowed us to distinguish chemical interdiffusion from imaging artifacts.