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We describe the development, operation, and application of the 4D Camera-a 576 by 576 pixel active pixel sensor for scanning/transmission electron microscopy which operates at 87,000 Hz. The detector generates data at ∼480 Gbit/s which is captured by dedicated receiver computers with a parallelized software infrastructure that has been implemented to process the resulting 10-700 Gigabyte-sized raw datasets. The back illuminated detector provides the ability to detect single electron events at accelerating voltages from 30 to 300 kV. Through electron counting, the resulting sparse data sets are reduced in size by 10--300× compared to the raw data, and open-source sparsity-based processing algorithms offer rapid data analysis. The high frame rate allows for large and complex scanning diffraction experiments to be accomplished with typical scanning transmission electron microscopy scanning parameters.

In recent years, there has been an increasing focus on 2D nongraphene materials that range from insulators to semiconductors to metals. As a single-elemental van der Waals semiconductor, tellurium (Te) has captivating anisotropic physical properties. Recent work demonstrated growth of ultrathin Te on WSe2 with the atomic chains of Te aligned with the armchair directions of the substrate using physical vapor deposition (PVD). In this system, a moiré superlattice is formed where micrometer-scale Te flakes sit on top of the continuous WSe2 film. Here, we determined the precise orientation of the Te flakes with respect to the substrate and detailed structure of the resulting moiré lattice by combining electron microscopy with image simulations. We directly visualized the moiré lattice using center of mass-differential phase contrast (CoM-DPC). We also investigated the local strain within the Te/WSe2 layered materials using scanning nanodiffraction techniques. There is a significant tensile strain at the edges of flakes along the direction perpendicular to the Te chain direction, which is an indication of the preferred orientation for the growth of Te on WSe2. In addition, we observed local strain relaxation regions within the Te film, specifically attributed to misfit dislocations, which we characterize as having a screw-like nature. The detailed structural analysis gives insight into the growth mechanisms and strain relaxation in this moiré heterostructure.

Transmission electron microscopy (TEM) is essential for determining atomic scale structures in structural biology and materials science. In structural biology, three-dimensional structures of proteins are routinely determined from thousands of identical particles using phase-contrast TEM. In materials science, three-dimensional atomic structures of complex nanomaterials have been determined using atomic electron tomography (AET). However, neither of these methods can determine the three-dimensional atomic structure of heterogeneous nanomaterials containing light elements. Here, we perform ptychographic electron tomography from 34.5 million diffraction patterns to reconstruct an atomic resolution tilt series of a double wall-carbon nanotube (DW-CNT) encapsulating a complex ZrTe sandwich structure. Class averaging the resulting tilt series images and subpixel localization of the atomic peaks reveals a Zr11Te50 structure containing a previously unobserved ZrTe2 phase in the core. The experimental realization of atomic resolution ptychographic electron tomography will allow for the structural determination of a wide range of beam-sensitive nanomaterials containing light elements.

Four-dimensional scanning transmission electron microscopy (4D-STEM) has recently gained widespread attention for its ability to image atomic electric fields with sub-Ångstrom spatial resolution. These electric field maps represent the integrated effect of the nucleus, core electrons and valence electrons, and separating their contributions is non-trivial. In this paper, we utilized simultaneously acquired 4D-STEM center of mass (CoM) images and annular dark field (ADF) images to determine the projected electron charge density in monolayer MoS2. We evaluate the contributions of both the core electrons and the valence electrons to the derived electron charge density; however, due to blurring by the probe shape, the valence electron contribution forms a nearly featureless background while most of the spatial modulation comes from the core electrons. Our findings highlight the importance of probe shape in interpreting charge densities derived from 4D-STEM and the need for smaller electron probes.

Increasing interest in three-dimensional nanostructures adds impetus to electron microscopy techniques capable of imaging at or below the nanoscale in three dimensions. We present a reconstruction algorithm that takes as input a focal series of four-dimensional scanning transmission electron microscopy (4D-STEM) data. We apply the approach to a lead iridate, PbIrO, and yttrium-stabilized zirconia, YZrO, heterostructure from data acquired with the specimen in a single plan-view orientation, with the epitaxial layers stacked along the beam direction. We demonstrate that Pb-Ir atomic columns are visible in the uppermost layers of the reconstructed volume. We compare this approach to the alternative techniques of depth sectioning using differential phase contrast scanning transmission electron microscopy (DPC-STEM) and multislice ptychographic reconstruction.

The arrival of direct electron detectors (DEDs) with high frame rates in the field of scanning transmission electron microscopy (TEM) has enabled many experimental techniques that require collection of a full diffraction pattern at each scan position, a field which is subsumed under the name four-dimensional scanning transmission electron microscopy (4D-STEM). DED frame rates approaching 100 kHz require data transmission rates and data storage capabilities that exceed those of the commonly available computing infrastructures. Current commercial DEDs allow the user to make compromises in pixel bit depth, detector binning, or windowing to reduce the per-frame file size and allow higher frame rates. This change in detector specifications requires decisions to be made before data acquisition that may reduce or lose information that could have been advantageous during data analysis.

Metal-organic layers (MOLs) are highly attractive for application in catalysis, separation, sensing and biomedicine, owing to their tunable framework structure. However, it is challenging to obtain comprehensive information about the formation and local structures of MOLs using standard electron microscopy methods due to serious damage under electron beam irradiation. Here, we investigate the growth processes and local structures of MOLs utilizing a combination of liquid-phase transmission electron microscopy, cryogenic electron microscopy and electron ptychography. Our results show a multistep formation process, where precursor clusters first form in solution, then they are complexed with ligands to form non-crystalline solids, followed by the arrangement of the cluster-ligand complex into crystalline sheets, with additional possible growth by the addition of clusters to surface edges. Moreover, high-resolution imaging allows us to identify missing clusters, dislocations, loop and flat surface terminations and ligand connectors in the MOLs. Our observations provide insights into controllable MOL crystal morphology, defect engineering, and surface modification, thus assisting novel MOL design and synthesis.

Scanning transmission electron microscopy (STEM), where a converged electron probe is scanned over a sample's surface and an imaging, diffraction, or spectroscopic signal is measured as a function of probe position, is an extremely powerful tool for materials characterization. The widespread adoption of hardware aberration correction, direct electron detectors, and computational imaging methods have made STEM one of the most important tools for atomic-resolution materials science. Many of these imaging methods rely on accurate imaging and diffraction simulations in order to interpret experimental results. However, STEM simulations have traditionally required large calculation times, as modeling the electron scattering requires a separate simulation for each of the typically millions of probe positions. We have created the Prismatic simulation code for fast simulation of STEM experiments with support for multi-CPU and multi-GPU (graphics processing unit) systems, using both the conventional multislice and our recently-introduced PRISM method. In this paper, we introduce Prismatic version 2.0, which adds many new algorithmic improvements, an updated graphical user interface (GUI), post-processing of simulation data, and additional operating modes such as plane-wave TEM. We review various aspects of the simulation methods and codes in detail and provide various simulation examples. Prismatic 2.0 is freely available both as an open-source package that can be run using a C++ or Python command line interface, or GUI, as well within a Docker container environment.

Scanning transmission electron microscopy (STEM) is an extremely versatile method for studying materials on the atomic scale. Many STEM experiments are supported or validated with electron scattering simulations. However, using the conventional multislice algorithm to perform these simulations can require extremely large calculation times, particularly for experiments with millions of probe positions as each probe position must be simulated independently. Recently, the plane-wave reciprocal-space interpolated scattering matrix (PRISM) algorithm was developed to reduce calculation times for large STEM simulations. Here, we introduce a new method for STEM simulation: partitioning of the STEM probe into “beamlets,” given by a natural neighbor interpolation of the parent beams. This idea is compatible with PRISM simulations and can lead to even larger improvements in simulation time, as well requiring significantly less computer random access memory (RAM). We have performed various simulations to demonstrate the advantages and disadvantages of partitioned PRISM STEM simulations. We find that this new algorithm is particularly useful for 4D-STEM simulations of large fields of view. We also provide a reference implementation of the multislice, PRISM, and partitioned PRISM algorithms.

Recent work has revived interest in the scattering matrix formulation of electron scattering in transmission electron microscopy as a stepping stone toward atomic-resolution structure determination in the presence of multiple scattering. We discuss ways of visualizing the scattering matrix that make its properties clear. Through a simulation-based case study incorporating shot noise, we shown how regularizing on this continuity enables the scattering matrix to be reconstructed from 4D scanning transmission electron microscopy (STEM) measurements from a single defocus value. Intriguingly, for crystalline samples, this process also yields the sample thickness to nanometer accuracy with no a priori knowledge about the sample structure. The reconstruction quality is gauged by using the reconstructed scattering matrix to simulate STEM images at defocus values different from that of the data from which it was reconstructed.

Scanning transmission electron microscopy (STEM) allows for imaging, diffraction, and spectroscopy of materials on length scales ranging from microns to atoms. By using a high-speed, direct electron detector, it is now possible to record a full two-dimensional (2D) image of the diffracted electron beam at each probe position, typically a 2D grid of probe positions. These 4D-STEM datasets are rich in information, including signatures of the local structure, orientation, deformation, electromagnetic fields, and other sample-dependent properties. However, extracting this information requires complex analysis pipelines that include data wrangling, calibration, analysis, and visualization, all while maintaining robustness against imaging distortions and artifacts. In this paper, we present py4DSTEM, an analysis toolkit for measuring material properties from 4D-STEM datasets, written in the Python language and released with an open-source license. We describe the algorithmic steps for dataset calibration and various 4D-STEM property measurements in detail and present results from several experimental datasets. We also implement a simple and universal file format appropriate for electron microscopy data in py4DSTEM, which uses the open-source HDF5 standard. We hope this tool will benefit the research community and help improve the standards for data and computational methods in electron microscopy, and we invite the community to contribute to this ongoing project.

Three-dimensional phase-contrast imaging of multiply-scattering samples in x-ray and electron microscopy is challenging due to small numerical apertures, the unavailability of wave front shaping optics, and the highly nonlinear inversion required from intensity-only measurements. In this work, we present an algorithm using the scattering matrix formalism to solve the scattering from a noncrystalline medium from scanning diffraction measurements and simultaneously recover the illumination aberrations. We demonstrate our method experimentally in a scanning transmission electron microscope, recovering the scattering matrix of a heterogeneous sample with two layers of multiwall carbon nanotubes filled with TaTe2 core-shell structures, spaced 10nm apart in the axial direction. Our work enables phase contrast imaging and materials characterization in multiply-scattering samples at high resolution for a wide range of materials.

The arrival of direct electron detectors (DED) with high frame-rates in thefield of scanning transmission electron microscopy has enabled manyexperimental techniques that require collection of a full diffraction patternat each scan position, a field which is subsumed under the name fourdimensional-scanning transmission electron microscopy (4D-STEM). DED framerates approaching 100 kHz require data transmission rates and data storagecapabilities that exceed commonly available computing infrastructure. Currentcommercial DEDs allow the user to make compromises in pixel bit depth, detectorbinning or windowing to reduce the per-frame file size and allow higher framerates. This change in detector specifications requires decisions to be madebefore data acquisition that may reduce or lose information that could havebeen advantageous during data analysis. The 4D Camera, a DED with 87 kHzframe-rate developed at Lawrence Berkeley National Laboratory, reduces the rawdata to a linear-index encoded electron event representation (EER). Here weshow with experimental data from the 4D Camera that linear-index encoded EERand its direct use in 4D-STEM phase contrast imaging methods enables real-time,interactive phase-contrast from large-area 4D-STEM datasets. We detail thecomputational complexity advantages of the EER and the necessary computationalsteps to achieve real-time interactive ptychography and center-of-massdifferential phase contrast using commonly available hardware accelerators.

Increasing interest in three-dimensional nanostructures adds impetus toelectron microscopy techniques capable of imaging at or below the nanoscale inthree dimensions. We present a reconstruction algorithm that takes as input afocal series of four-dimensional scanning transmission electron microscopy(4D-STEM) data and transcends the prevalent structure retrieval algorithmassumption of a very thin specimen homogenous along the optic axis. Wedemonstrate this approach by reconstructing the different layers of a leadiridate (Pb$_2$Ir$_2$O$_7$) and yttrium-stabilized zirconia(Y$_{0.095}$Zr$_{0.905}$O$_2$) heterostructure from data acquired with thespecimen in a single plan-view orientation, with the epitaxial layers stackedalong the beam direction.

Increasing interest in three-dimensional nanostructures adds impetus toelectron microscopy techniques capable of imaging at or below the nanoscale inthree dimensions. We present a reconstruction algorithm that takes as input afocal series of four-dimensional scanning transmission electron microscopy(4D-STEM) data. We apply the approach to a lead iridate, Pb$_2$Ir$_2$O$_7$, andyttrium-stabilized zirconia,Y$_{0.095}$Zr$_{0.905}$O$_2$ , heterostructure fromdata acquired with the specimen in a single plan-view orientation, with theepitaxial layers stacked along the beam direction. We demonstrate that Pb-Iratomic columns are visible in the uppermost layers of the reconstructed volume.We compare this approach to the alternative techniques of depth sectioningusing differential phase contrast scanning transmission electron microscopy(DPC-STEM) and multislice ptychographic reconstruction.

Four-dimensional scanning transmission electron microscopy (4D-STEM) has recently gained widespread attention for its ability to image atomic electric fields with sub-Ångstrom spatial resolution. These electric field maps represent the integrated effect of the nucleus, core electrons and valence electrons, and separating their contributions is non-trivial. In this paper, we utilized simultaneously acquired 4D-STEM center of mass (CoM) images and annular dark field (ADF) images to determine the projected electron charge density in monolayer MoS2. We evaluate the contributions of both the core electrons and the valence electrons to the derived electron charge density; however, due to blurring by the probe shape, the valence electron contribution forms a nearly featureless background while most of the spatial modulation comes from the core electrons. Our findings highlight the importance of probe shape in interpreting charge densities derived from 4D-STEM and the need for smaller electron probes. Recent electron microscopy techniques have attracted significant attention for their ability to image electric fields at the atomic level. Here, the authors investigate the possibility to separate the charge density contributions of core and valence electrons in monolayer MoS2, highlighting the limitations induced by the electron probe shape. [ABSTRACT FROM AUTHOR]