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Aberration correction is an important aspect of modern high-resolution scanning transmission electron microscopy. Most methods of aligning aberration correctors require specialized sample regions and are unsuitable for fine-tuning aberrations without interrupting on-going experiments. Here, we present an automated method of correcting first- and second-order aberrations called BEACON which uses Bayesian optimization of the normalized image variance to efficiently determine the optimal corrector settings. We demonstrate its use on gold nanoparticles and a hafnium dioxide thin film showing its versatility in nano- and atomic-scale experiments. BEACON can correct all first- and second-order aberrations simultaneously to achieve an initial alignment and first- and second-order aberrations independently for fine alignment. Ptychographic reconstructions are used to demonstrate an improvement in probe shape and a reduction in the target aberration.

Data management is a critical component of modern experimental workflows. As data generation rates increase, transferring data from acquisition servers to processing servers via conventional file-based methods is becoming increasingly impractical. The 4D Camera at the National Center for Electron Microscopy (NCEM) generates data at a nominal rate of 480 Gbit/s (87,000 frames/s) producing a 700 GB dataset in fifteen seconds. To address the challenges associated with storing and processing such quantities of data, we developed a streaming workflow that utilizes a high-speed network to connect the 4D Camera's data acquisition (DAQ) system to supercomputing nodes at the National Energy Research Scientific Computing Center (NERSC), bypassing intermediate file storage entirely. In this work, we demonstrate the effectiveness of our streaming pipeline in a production setting through an hour-long experiment that generated over 10 TB of raw data, yielding high-quality datasets suitable for advanced analyses. Additionally, we compare the efficacy of this streaming workflow against the conventional file-transfer workflow by conducting a post-mortem analysis on historical data from experiments performed by real users. Our findings show that the streaming workflow significantly improves data turnaround time, enables real-time decision-making, and minimizes the potential for human error by eliminating manual user interactions.

Diffraction is the most common method to solve for unknown or partially known crystal structures. However, it remains a challenge to determine the crystal structure of a new material that may have nanoscale size or heterogeneities. Here we train an architecture of hierarchical random forest models capable of predicting the crystal system, space group, and lattice parameters from one or more unknown 2D electron diffraction patterns. Our initial model correctly identifies the crystal system of a simulated electron diffraction pattern from a 20 nm thick specimen of arbitrary orientation 67% of the time. We achieve a topline accuracy of 79% when aggregating predictions from 10 patterns of the same material but different zone axes. The space group and lattice predictions range from 70-90% accuracy and median errors of 0.01-0.5 angstroms, respectively, for cubic, hexagonal, trigonal and tetragonal crystal systems while being less reliable on orthorhombic and monoclinic systems. We apply this architecture to a 4D-STEM scan of gold nanoparticles, where it accurately predicts the crystal structure and lattice constants. These random forest models can be used to significantly accelerate the analysis of electron diffraction patterns, particularly in the case of unknown crystal structures. Additionally, due to the speed of inference, these models could be integrated into live TEM experiments, allowing real-time labeling of a specimen.

The construction of thin film heterostructures has been a widely successful archetype for fabricating materials with emergent physical properties. This strategy is of particular importance for the design of multilayer magnetic architectures in which direct interfacial spin--spin interactions between magnetic phases in dissimilar layers lead to emergent and controllable magnetic behavior. However, crystallographic incommensurability and atomic-scale interfacial disorder can severely limit the types of materials amenable to this strategy, as well as the performance of these systems. Here, we demonstrate a method for synthesizing heterostructures comprising magnetic intercalation compounds of transition metal dichalcogenides (TMDs), through directed topotactic reaction of the TMD with a metal oxide. The mechanism of the intercalation reaction enables thermally initiated intercalation of the TMD from lithographically patterned oxide films, giving access to a new family of multi-component magnetic architectures through the combination of deterministic van der Waals assembly and directed intercalation chemistry.

Superconducting Nb thin films have recently attracted significant attention due to their utility for quantum information technologies. In the processing of Nb thin films, fluoride-based chemical etchants are commonly used to remove surface oxides that are known to affect superconducting quantum devices adversely. However, these same etchants can also introduce hydrogen to form Nb hydrides, potentially negatively impacting microwave loss performance. Here, we present comprehensive materials characterization of Nb hydrides formed in Nb thin films as a function of fluoride chemical treatments. In particular, secondary-ion mass spectrometry, X-ray scattering, and transmission electron microscopy reveal the spatial distribution and phase transformation of Nb hydrides. The rate of hydride formation is determined by the fluoride solution acidity and the etch rate of Nb2O5, which acts as a diffusion barrier for hydrogen into Nb. The resulting Nb hydrides are detrimental to Nb superconducting properties and lead to increased power-independent microwave loss in coplanar waveguide resonators. However, Nb hydrides do not correlate with two-level system loss or device aging mechanisms. Overall, this work provides insight into the formation of Nb hydrides and their role in microwave loss, thus guiding ongoing efforts to maximize coherence time in superconducting quantum devices.

In photon upconverting core-shell nanoparticles, structure strongly dictates performance. Conventional imaging in scanning transmission electron microscopy has sufficient resolution to probe the atomic structure of these nanoparticles, but contrast, dose, and projection limitations make conventional imaging modes insufficient for fully characterizing these structures. Phase retrieval methods provide a promising alternative imaging mode, and in particular, multislice electron ptychography can recover depth-dependent information. Here, we study beam-sensitive photon upconverting core-shell nanoparticles with a multislice ptychography approach using a low electron dose to avoid damage. Large strain fields arise in these heterostructures due to the mismatch in lattice parameter between the core and the shell. We reconstruct both a nanoparticle that appears defect-free and one that has a large break in the side and map the distribution of strain in 3D by computing distortion fields from high-resolution potential images of each slice. In the defect-free nanoparticle, we observe twisting of the shell, while in the broken nanoparticle we measure the 3D position of the crack, the core, and dislocations. These results highlight the advantage of multislice electron ptychography to recover 3D information from a single scan, even under strict electron dose requirements from beam-sensitive samples., Comment: 6 pages, 4 figures

Scanning transmission electron microscopy (STEM) has been extensively used for imaging complex materials down to atomic resolution. The most commonly employed STEM modality, annular dark-field imaging, produces easily-interpretable contrast, but is dose-inefficient and produces little to no discernible contrast for light elements and weakly-scattering samples. An alternative is to use STEM phase retrieval imaging, enabled by high speed detectors able to record full images of a diffracted STEM probe over a grid of scan positions. Phase retrieval imaging in STEM is highly dose-efficient, enabling the measurement of the structure of beam-sensitive materials such as biological samples. Here, we comprehensively describe the theoretical background, algorithmic implementation details, and perform both simulated and experimental tests for three iterative phase retrieval STEM methods: focused-probe differential phase contrast, defocused-probe parallax imaging, and a generalized ptychographic gradient descent method implemented in two and three dimensions. We discuss the strengths and weaknesses of each of these approaches by comparing the transfer of information using analytical expressions and numerical results for a white-noise model. This presentation of STEM phase retrieval methods aims to make these methods more approachable, reproducible, and more readily adoptable for many classes of samples., Comment: 25 pages, 14 figures, 1 table

In a scanning transmission electron microscope (STEM), producing a high-resolution image generally requires an electron beam focused to the smallest point possible. However, the magnetic lenses used to focus the beam are unavoidably imperfect, introducing aberrations that limit resolution. Modern STEMs overcome this by using hardware aberration correctors comprised of many multipole lenses, but these devices are complex, expensive, and can be difficult to tune. We demonstrate a design for an electrostatic phase plate that can act as an aberration corrector. The corrector is comprised of annular segments, each of which is an independent two-terminal device that can apply a constant or ramped phase shift to a portion of the electron beam. We show the improvement in image resolution using an electrostatic corrector. Engineering criteria impose that much of the beam within the probe-forming aperture be blocked by support bars, leading to large probe tails for the corrected probe that sample the specimen beyond the central lobe. We also show how this device can be used to create other STEM beam profiles such as vortex beams and beams with a high degree of phase diversity, which improve information transfer in ptychographic reconstructions., Comment: 12 pages, 10 figures

Material properties strongly depend on the nature and concentration of defects. Characterizing these features may require nano- to atomic-scale resolution to establish structure-property relationships. 4D-STEM, a technique where diffraction patterns are acquired at a grid of points on the sample, provides a versatile method for highlighting defects. Computational analysis of the diffraction patterns with virtual detectors produces images that can map material properties. Here, using multislice simulations, we explore different virtual detectors that can be applied to the diffraction patterns that go beyond the binary response functions that are possible using ordinary STEM detectors. Using graphene and lead titanate as model systems, we investigate the application of virtual detectors to study local order and in particular defects. We find that using a small convergence angle with a rotationally varying detector most efficiently highlights defect signals. With experimental graphene data, we demonstrate the effectiveness of these detectors in characterizing atomic features, including vacancies, as suggested in simulations. Phase and amplitude modification of the electron beam provides another process handle to change image contrast in a 4D-STEM experiment. We demonstrate how tailored electron beams can enhance signals from short-range order and how a vortex beam can be used to characterize local symmetry., Comment: 16 pages, 14 figures

Superconducting thin films of niobium have been extensively employed in transmon qubit architectures. Although these architectures have demonstrated remarkable improvements in recent years, further improvements in performance through materials engineering will aid in large-scale deployment. Here, we use information retrieved from secondary ion mass spectrometry and electron microscopy to conduct a detailed assessment of the surface oxide that forms in ambient conditions for transmon test qubit devices patterned from a niobium film. We observe that this oxide exhibits a varying stoichiometry with NbO and NbO$_2$ found closer to the niobium film and Nb$_2$O$_5$ found closer to the surface. In terms of structural analysis, we find that the Nb$_2$O$_5$ region is semicrystalline in nature and exhibits randomly oriented grains on the order of 1-2 nm corresponding to monoclinic N-Nb$_2$O$_5$ that are dispersed throughout an amorphous matrix. Using fluctuation electron microscopy, we are able to map the relative crystallinity in the Nb$_2$O$_5$ region with nanometer spatial resolution. Through this correlative method, we observe that amorphous regions are more likely to contain oxygen vacancies and exhibit weaker bonds between the niobium and oxygen atoms. Based on these findings, we expect that oxygen vacancies likely serve as a decoherence mechanism in quantum systems., Comment: 13 pages, 4 figures

In situ electron microscopy is a key tool for understanding the mechanisms driving novel phenomena in 2D structures. Unfortunately, due to various practical challenges, technologically relevant 2D heterostructures prove challenging to address with electron microscopy. Here, we use the differential phase contrast imaging technique to build a methodology for probing local electrostatic fields during electrical operation with nanoscale precision in such materials. We find that by combining a traditional DPC setup with a high pass filter, we can largely eliminate electric fluctuations emanating from short-range atomic potentials. With this method, a priori electric field expectations can be directly compared with experimentally derived values to readily identify inhomogeneities and potentially problematic regions. We use this platform to analyze the electric field and charge density distribution across layers of hBN and MoS2., Comment: 13 pages, 4 figures