Minimising damage in high resolution scanning transmission electron microscope images of nanoscale structures and processes

High-speed 4-dimensional scanning transmission electron microscopy using compressive sensing techniques

Here we show that compressive sensing allows 4-dimensional (4-D) STEM data to be obtained and accurately reconstructed with both high-speed and reduced electron fluence. The methodology needed to achieve these results compared to conventional 4-D approaches requires only that a random subset of probe locations is acquired from the typical regular scanning grid, which immediately generates both higher speed and the lower fluence experimentally. We also consider downsampling of the detector, showing that oversampling is inherent within convergent beam electron diffraction (CBED) patterns and that detector downsampling does not reduce precision but allows faster experimental data acquisition. Analysis of an experimental atomic resolution yttrium silicide dataset shows that it is possible to recover over 25 dB peak signal-to-noise ratio in the recovered phase using 0.3% of the total data. Lay abstract: Four-dimensional scanning transmission electron microscopy (4-D STEM) is a powerful technique for characterizing complex nanoscale structures. In this method, a convergent beam electron diffraction pattern (CBED) is acquired at each probe location during the scan of the sample. This means that a 2-dimensional signal is acquired at each 2-D probe location, equating to a 4-D dataset. Despite the recent development of fast direct electron detectors, some capable of 100kHz frame rates, the limiting factor for 4-D STEM is acquisition times in the majority of cases, where cameras will typically operate on the order of 2kHz. This means that a raster scan containing 256^2 probe locations can take on the order of 30s, approximately 100-1000 times longer than a conventional STEM imaging technique using monolithic radial detectors. As a result, 4-D STEM acquisitions can be subject to adverse effects such as drift, beam damage, and sample contamination. Recent advances in computational imaging techniques for STEM have allowed for faster acquisition speeds by way of acquiring only a random subset of probe locations from the field of view. By doing this, the acquisition time is significantly reduced, in some cases by a factor of 10-100 times. The acquired data is then processed to fill-in or inpaint the missing data, taking advantage of the inherently low-complex signals which can be linearly combined to recover the information. In this work, similar methods are demonstrated for the acquisition of 4-D STEM data, where only a random subset of CBED patterns are acquired over the raster scan. We simulate the compressive sensing acquisition method for 4-D STEM and present our findings for a variety of analysis techniques such as ptychography and differential phase contrast. Our results show that acquisition times can be significantly reduced on the order of 100-300 times, therefore improving existing frame rates, as well as further reducing the electron fluence beyond just using a faster camera.

Curvature-based interface restoration algorithm using phase-field equations

In this study, we propose a restoration algorithm for distorted objects using a curvature-driven flow. First, we capture the convex-hull shaped contour of the distorted object using the mean curvature flow. With the supplemented mass on the captured feature, we evolve the constraint mean curvature flow to a steady state, preserving the non-distorted region. With respect to the mass, we select a restorative shape by considering the square of the curvature derivative. The Allen-Cahn and Cahn-Hilliard equations are applied to the generated restored image from the implicit curvature motions represented by the order parameter. We impose the Dirichlet boundary condition for the order parameter and the Neumann boundary for the chemical potential to fix the feature and to inherit the mass conservation, respectively. We provided examples of the restoration of half-circle and parentheses-shaped objects to reconstruct a circle shape.

Towards real-time STEM simulations through targeted subsampling strategies

Scanning transmission electron microscopy images can be complex to interpret on the atomic scale as the contrast is sensitive to multiple factors such as sample thickness, composition, defects and aberrations. Simulations are commonly used to validate or interpret real experimental images, but they come at a cost of either long computation times or specialist hardware such as graphics processing units. Recent works in compressive sensing for experimental STEM images have shown that it is possible to significantly reduce the amount of acquired signal and still recover the full image without significant loss of image quality, and therefore it is proposed here that similar methods can be applied to STEM simulations. In this paper, we demonstrate a method that can significantly increase the efficiency of STEM simulations through a targeted sampling strategy, along with a new approach to independently subsample each frozen phonon layer. We show the effectiveness of this method by simulating a SrTiO₃ grain boundary and monolayer 2H-MoS₂ containing a sulphur vacancy using the abTEM software. We also show how this method is not limited to only traditional multislice methods, but also increases the speed of the PRISM simulation method. Furthermore, we discuss the possibility for STEM simulations to seed the acquisition of real data, to potentially lead the way to self-driving (correcting) STEM.

Three Approaches for Representing the Statistical Uncertainty on Atom-Counting Results in Quantitative ADF STEM

A decade ago, a statistics-based method was introduced to count the number of atoms from annular dark-field scanning transmission electron microscopy (ADF STEM) images. In the past years, this method was successfully applied to nanocrystals of arbitrary shape, size, and composition (and its high accuracy and precision has been demonstrated). However, the counting results obtained from this statistical framework are so far presented without a visualization of the actual uncertainty about this estimate. In this paper, we present three approaches that can be used to represent counting results together with their statistical error, and discuss which approach is most suited for further use based on simulations and an experimental ADF STEM image.

Reducing electron beam damage through alternative STEM scanning strategies, Part II: Attempt towards an empirical model describing the damage process

In this second part of a series we attempt to construct an empirical model that can mimick all experimental observations made regarding the role of an alternative interleaved scan pattern in STEM imaging on the beam damage in a specific zeolite sample. We make use of a 2D diffusion model that describes the dissipation of the deposited beam energy in the sequence of probe positions that are visited during the scan pattern. The diffusion process allows for the concept of trying to 'outrun' the beam damage by carefully tuning the dwell time and distance between consecutively visited probe positions. We add a non linear function to include a threshold effect and evaluate the accumulated damage in each part of the image as a function of scan pattern details. Together, these ingredients are able to describe qualitatively all aspects of the experimental data and provide us with a model that could guide a further optimisation towards even lower beam damage without lowering the applied electron dose. We deliberately remain vague on what is diffusing here which avoids introducing too many sample specific details. This provides hope that the model can be applied also in sample classes that were not yet studied in such great detail by adjusting higher level parameters: a sample dependent diffusion constant and damage threshold.

Research Progress of Preparation Technology of Ion-Exchange Resin Complexes

As insoluble polymer materials, ion-exchange resins (IERs) can exchange their own ions with desirable charged ions in the solution. According to the affinity of active moieties for soluble counterions, IERs could be categorized into the following four types: strongly acidic cation, weakly acidic cation, strongly basic anion, and weakly basic anion exchange resins. Due to their relative safety and high drug-loading capacity, IERs have garnered extensive attention in the pharmaceutical field since the 1950s. As numerous investigations combine drugs with IERs, this article summarizes the technologies employed in these studies from four aspects: IER screening principles, combining technologies, characterization methods, and in vitro and in vivo release of drug-resinate complexes. In addition, the advantages and disadvantages of various technologies and their scope are expounded. The article provides new insights on the preparation of ion-exchange resin complexes.

Sub-Sampled Imaging for STEM: Maximising Image Speed, Resolution and Precision Through Reconstruction Parameter Refinement

Sub-sampling during image acquisition in scanning transmission electron microscopy (STEM) has been shown to provide a means to increase the overall speed of acquisition while at the same time providing an efficient means to control the dose, dose rate and dose overlap delivered to the sample. In this paper, we discuss specifically the parameters used to reconstruct sub-sampled images and highlight their effect on inpainting using the beta-process factor analysis (BPFA) methodology. The selection of the main control parameters can have a significant effect on the resolution, precision and sensitivity of the final inpainted images, and here we demonstrate a method by which these parameters can be optimised for any image in STEM. As part of this work, we also provide a link to open source code and a tutorial on its use, whereby these parameters can be tested for any datasets. When coupled with the hardware necessary to rapidly sub-sample images in STEM, this approach can have significant implications for imaging beam sensitive materials and dynamic processes.

Event driven 4D STEM acquisition with a Timepix3 detector: Microsecond dwell time and faster scans for high precision and low dose applications

Four dimensional scanning transmission electron microscopy (4D STEM) records the scattering of electrons in a material in great detail. The benefits offered by 4D STEM are substantial, with the wealth of data it provides facilitating for instance high precision, high electron dose efficiency phase imaging via centre of mass or ptychography based analysis. However the requirement for a 2D image of the scattering to be recorded at each probe position has long placed a severe bottleneck on the speed at which 4D STEM can be performed. Recent advances in camera technology have greatly reduced this bottleneck, with the detection efficiency of direct electron detectors being especially well suited to the technique. However even the fastest frame driven pixelated detectors still significantly limit the scan speed which can be used in 4D STEM, making the resulting data susceptible to drift and hampering its use for low dose beam sensitive applications. Here we report the development of the use of an event driven Timepix3 direct electron camera that allows us to overcome this bottleneck and achieve 4D STEM dwell times down to 100 ns; orders of magnitude faster than what has been possible with frame based readout. We characterize the detector for different acceleration voltages and show that the method is especially well suited for low dose imaging and promises rich datasets without compromising dwell time when compared to conventional STEM imaging.

In Situ Observation of the Early Stages of Rapid Solid-Liquid Reaction in Closed Liquid Cell TEM Using Graphene Encapsulation

In situ liquid cell transmission electron microscopy (TEM) is a very useful tool for investigating dynamic solid–liquid reactions. However, there are challenges to observe the early stages of spontaneous solid–liquid reactions using a closed-type liquid cell system, the most popular and simple liquid cell system. We propose a graphene encapsulation method to overcome this limitation of closed-type liquid cell TEM. The solid and liquid are separated using graphene to suspend the reaction until the graphene layer is destroyed. Graphene can be decomposed by the high-energy electron beam used in TEM, allowing the reaction to proceed. Fast dissolution of graphene-capped copper nanoparticles in an FeCl3 solution was demonstrated via in situ liquid cell TEM at 300 kV using a cell with closed-type SiNx windows.

High temporal-resolution scanning transmission electron microscopy using sparse-serpentine scan pathways

Scanning transmission electron microscopy (STEM) provides structural analysis with sub-angstrom resolution. But the pixel-by-pixel scanning process is a limiting factor in acquiring high-speed data. Different strategies have been implemented to increase scanning speeds while at the same time minimizing beam damage via optimizing the scanning strategy. Here, we achieve the highest possible scanning speed by eliminating the image acquisition dead time induced by the beam flyback time combined with reducing the amount of scanning pixels via sparse imaging. A calibration procedure was developed to compensate for the hysteresis of the magnetic scan coils. A combination of sparse and serpentine scanning routines was tested for a crystalline thin film, gold nanoparticles, and in an in-situ liquid phase STEM experiment. Frame rates of 92, 23 and 5.8 s^-1 were achieved for images of a width of 128, 256, and 512 pixels, respectively. The methods described here can be applied to single-particle tracking and analysis of radiation sensitive materials.

Dynamic transformation of cubic copper catalysts during CO2 electroreduction and its impact on catalytic selectivity

To rationally design effective and stable catalysts for energy conversion applications, we need to understand how they transform under reaction conditions and reveal their underlying structure-property relationships. This is especially important for catalysts used in the electroreduction of carbon dioxide where product selectivity is sensitive to catalyst structure. Here, we present real-time electrochemical liquid cell transmission electron microscopy studies showing the restructuring of copper(I) oxide cubes during reaction. Fragmentation of the solid cubes, re-deposition of new nanoparticles, catalyst detachment and catalyst aggregation are observed as a function of the applied potential and time. Using cubes with different initial sizes and loading, we further correlate this dynamic morphology with the catalytic selectivity through time-resolved scanning electron microscopy measurements and product analysis. These comparative studies reveal the impact of nanoparticle re-deposition and detachment on the catalyst reactivity, and how the increased surface metal loading created by re-deposited nanoparticles can lead to enhanced C₂₊ selectivity and stability.

Reducing electron beam damage through alternative STEM scanning strategies, Part I: Experimental findings

The highly energetic electrons in a transmission electron microscope (TEM) can alter or even completely destroy the structure of samples before sufficient information can be obtained. This is especially problematic in the case of zeolites, organic and biological materials. As this effect depends on both the electron beam and the sample and can involve multiple damage pathways, its study remained difficult and is plagued with irreproducibility issues, circumstantial evidence, rumors, and a general lack of solid data. Here we take on the experimental challenge to investigate the role of the STEM scan pattern on the damage behavior of a commercially available zeolite sample with the clear aim to make our observations as reproducible as possible. We make use of a freely programmable scan engine that gives full control over the tempospatial distribution of the electron probe on the sample and we use its flexibility to obtain multiple repeated experiments under identical conditions comparing the difference in beam damage between a conventional raster scan pattern and a newly proposed interleaved scan pattern that provides exactly the same dose and dose rate and visits exactly the same scan points. We observe a significant difference in beam damage for both patterns with up to 11 % reduction in damage (measured from mass loss). These observations demonstrate without doubt that electron dose, dose rate and acceleration voltage are not the only parameters affecting beam damage in (S)TEM experiments and invite the community to rethink beam damage as an unavoidable consequence of applied electron dose.

Advances and Applications of Atomic-Resolution Scanning Transmission Electron Microscopy

Although scanning transmission electron microscopy (STEM) images of individual heavy atoms were reported 50 years ago, the applications of atomic-resolution STEM imaging became wide spread only after the practical realization of aberration correctors on field-emission STEM/TEM instruments to form sub-Ångstrom electron probes. The innovative designs and advances of electron optical systems, the fundamental understanding of electron–specimen interaction processes, and the advances in detector technology all played a major role in achieving the goal of atomic-resolution STEM imaging of practical materials. It is clear that tremendous advances in computer technology and electronics, image acquisition and processing algorithms, image simulations, and precision machining synergistically made atomic-resolution STEM imaging routinely accessible. It is anticipated that further hardware/software development is needed to achieve three-dimensional atomic-resolution STEM imaging with single-atom chemical sensitivity, even for electron-beam-sensitive materials. Artificial intelligence, machine learning, and big-data science are expected to significantly enhance the impact of STEM and associated techniques on many research fields such as materials science and engineering, quantum and nanoscale science, physics and chemistry, and biology and medicine. This review focuses on advances of STEM imaging from the invention of the field-emission electron gun to the realization of aberration-corrected and monochromated atomic-resolution STEM and its broad applications.

Dose measurement in the TEM and STEM

Practical aspects of dosimetry are considered, including the measurement of electron-beam current and current density. Complications that arise in the case of a focused probe or a STEM image are discussed and solutions proposed. Advantages of expressing the radiation dose in Grays are listed and a simple formula given for converting electron fluence to Gray units, based on a near constancy of the stopping power per atomic electron. Comparisons with stopping-power calculations and EELS measurements suggest that this formula is accurate to within 5%. Based on the stopping power formula, a new way of measuring the local mass-thickness of light-element specimens is proposed. The average energy loss per inelastic collision is shown to be higher than previous expectations.

Mechanistic Understanding of Water Oxidation in the Presence of a Copper Complex by In Situ Electrochemical Liquid Transmission Electron Microscopy

The design of molecular oxygen-evolution reaction (OER) catalysts requires fundamental mechanistic studies on their widely unknown mechanisms of action. To this end, copper complexes keep attracting interest as good catalysts for the OER, and metal complexes with TMC (TMC = 1,4,8,11-tetramethyl-1,4,8,11-tetraazacyclotetradecane) stand out as active OER catalysts. A mononuclear copper complex, [Cu(TMC)(H₂O)](NO₃)₂ (TMC = 1,4,8,11-tetramethyl-1,4,8,11-tetraazacyclotetradecane), combined both key features and was previously reported to be one of the most active copper-complex-based catalysts for electrocatalytic OER in neutral aqueous solutions. However, the functionalities and mechanisms of the catalyst are still not fully understood and need to be clarified with advanced analytical studies to enable further informed molecular catalyst design on a larger scale. Herein, the role of nanosized Cu oxide particles, ions, or clusters in the electrochemical OER with a mononuclear copper(II) complex with TMC was investigated by operando methods, including in situ vis-spectroelectrochemistry, in situ electrochemical liquid transmission electron microscopy (EC-LTEM), and extended X-ray absorption fine structure (EXAFS) analysis. These combined experiments showed that Cu oxide-based nanoparticles, rather than a molecular structure, are formed at a significantly lower potential than required for OER and are candidates for being the true OER catalysts. Our results indicate that for the OER in the presence of a homogeneous metal complex-based (pre)catalyst, careful analyses and new in situ protocols for ruling out the participation of metal oxides or clusters are critical for catalyst development. This approach could be a roadmap for progress in the field of sustainable catalysis via informed molecular catalyst design. Our combined approach of in situ TEM monitoring and a wide range of complementary spectroscopic techniques will open up new perspectives to track the transformation pathways and true active species for a wide range of molecular catalysts.

Controlling radiolysis chemistry on the nanoscale in liquid cell scanning transmission electron microscopy

When high-energy electrons from a scanning transmission electron microscope (STEM) are incident on a liquid, the vast majority of the chemical reactions that are observed are induced by the radiolysis breakdown of the liquid molecules. In the study of liquids, the radiolysis products of pure water are well known, and their rate of formation for a given flux of high-energy electrons has been studied intensively over the last few years for uniform TEM illumination. In this paper, we demonstrate that the temporal and spatial distribution of the electron illumination can significantly affect the final density of radiolysis products in water and even change the type of reaction taking place. We simulate the complex array of possible spatial/temporal distributions of electrons that are accessible experimentally by controlling the size, the scan rate and the hopping distance of the electron probe in STEM mode and then compare the results to the uniformly illuminated TEM mode of imaging. By distributing the electron dose both spatially and temporally in the STEM through a randomised "spot-scan" mode of imaging, the diffusion overlap of the radiolysis products can be reduced, and the resulting reactions can be more readily controlled. This control allows the resolution of the images to be separated from the speed of the induced reaction (which is based on beam current alone) and this facet of the experiment will allow a wide range of chemical reactions to be uniquely tailored and observed in all liquid cell STEM experiments.