Ptychographic atomic electron tomography: Towards three-dimensional imaging of individual light atoms in materials

Through numerical simulations, we demonstrate the combination of ptychography and atomic electron tomography as an effective method for low dose imaging of individual low-Z atoms in three dimensions. After generating noisy diffraction patterns with multislice simulations of an aberration-corrected scanning transmission electron microscope through a 5-nm zinc-oxide nanoparticle, we have achieved three-dimensional (3D) imaging of individual zinc and oxygen atoms and their defects by performing tomography on ptychographic projections. The methodology has also been simulated in 2D materials, resolving individual sulfur atoms in vertical $\mathrm{W}{\mathrm{S}}_2/\mathrm{WS}{\mathrm{e}}_2$ van der Waals heterostructure with a low total electron dose where annular-dark-field images fail to resolve. We envision that the development of this method could be instrumental in studying the precise 3D atomic structures of radiation sensitive systems and low-$Z$ atomic structures such as 2D heterostructures, catalysts, functional oxides, and glasses.

Figure 1

Numerical experiment on ptychography- and ADF-STEM-based atomic electron tomography of a 5-nm ZnO nanoparticle. (a) 2D logarithmic heat map of the average of 15 625 diffraction patterns from a tilt series. The diffraction patterns simulate a dose per projection of $3.0\times {10}^{4}e/{\AA }^2$. (b) A representative ptychographic phase projection (left) and an ADF-STEM projection (right). Both projections were reconstructed with the same diffraction patterns seen in (a). (c) 3D isosurface rendering of the volume after tomographic reconstruction of ptychographic phase projections. (d) Magnified isosurface rendering of the core of the volume in (c). Individual oxygen atoms rendered as smaller spheres are observed. Note that the zinc atoms look disproportionately large due to the isosurface rendering effect. (e) A 2.0-Å-thick central slice of the volume in the [0001] direction reconstructed with ptychographic phase projections (left) and with ADF-STEM projections (right). (f) A magnified image of (e), indicating an oxygen defect with a red arrow. (g) A 2.0-Å-thick slice through the missing wedge direction of the reconstruction performed with ptychographic projections (left) and with ADF projections (right). (h) A magnified image of (g), demonstrating greater missing wedge artifacts in the reconstruction when performing tomography with ADF-STEM projections. Scale bars in (b), (c), (e), and (g) indicate 5 Å, scale bar in (d) indicates 1 Å, and scale bars in (f) and (h) indicate 2 Å.

Figure 2

Quantitative comparison of normalized atomic contrast from C to Xe between ptychography and ADF for three different electron beam energies (60, 120, and 240 keV). Normalized peak heights from Hartree-Fock potential estimations are also plotted. Atoms where valence shells become fully filled (Ne, Ar, Zn, and Kr) are indicated to explain fluctuations in the potential peaks.

Figure 3

Contrast per atom when imaging along the zone axis with ADF/HAADF and ptychography. (a) An experimental schematic of multislice simulation of an 80-keV electron beam probe and 24-mrad semi-convergence angle imaging a column of $N$ Si atoms separated by distance of 3 Å. Five different combinations of inner and outer angles were simulated. (b) Contrast per atom in atomic columns when measured with various ADF angles. The horizontal gray line plotted at 1 indicates the ideal linear projection. (c) Similar experimental schematic as (a) except the substitution of ADF detectors with a pixel array detector, allowing for ptychographic reconstruction. (d) Contrast per atom in columns when reconstructed with ptychography.

Figure 4

Numerical experiment on ptychography- and ADF-STEM-based AET of a vertical $\mathrm{W}{\mathrm{S}}_2/\mathrm{WS}{\mathrm{e}}_2$ van der Waals heterostructure. (a) 2.0-Å-thick slices of each atomic layer when simulated with a total electron dose of $5.1\times {10}^{4}e/{\AA }^2$ and reconstructed with ePIE and RESIRE. Tilt angle of 12.5° between the two tungsten layers was recovered, indicated by colored lines. (b) 2.0-Å-thick slices of the same experiment as (a) when reconstructed with ADF and RESIRE. Scale bars, 2 Å.