Mpfit: a robust method for fitting atomic resolution images with multiple Gaussian peaks

High-throughput image segmentation of atomic resolution electron microscopy data poses an ongoing challenge for materials characterization. In this paper, we investigate the application of the polyhedral template matching (PTM) method, a technique widely employed for visualizing three-dimensional (3D) atomistic simulations, to the analysis of two-dimensional (2D) atomic resolution electron microscopy images. This technique is complementary with other atomic resolution data reduction techniques, such as the centrosymmetry parameter, that use the measured atomic peak positions as the starting input. Furthermore, since the template matching process also gives a measure of the local rotation, the method can be used to segment images based on local orientation. We begin by presenting a 2D implementation of the PTM method, suitable for atomic resolution images. We then demonstrate the technique's application to atomic resolution scanning transmission electron microscopy images from close-packed metals, providing examples of the analysis of twins and other grain boundaries in FCC gold and martensite phases in 304 L austenitic stainless steel. Finally, we discuss factors, such as positional errors in the image peak locations, that can affect the accuracy and sensitivity of the structural determinations.

The modern aberration-corrected scanning transmission electron microscopes (AC-STEM) have successfully achieved direct visualization of atomic columns with sub-angstrom resolution. With this significant progress, advanced image quantification and analysis are still at the early stages. In this work, we present the complete pathway for the metrology of atomic resolution scanning transmission electron microscopy (STEM) images. This includes (1) tips for acquiring high-quality STEM images; (2) denoising and drift-correction for enhancing measurement accuracy; (3) obtaining initial atomic positions; (4) indexing the atoms based on unit cell vectors; (5) quantifying the atom column positions with either 2D-Gaussian single peak fitting or (6) multi-peak fitting routines for slightly overlapping atomic columns; (7) quantification of lattice distortion/strain within the crystal structures or at the defects/interfaces where the lattice periodicity is disrupted; and (8) some common methods to visualize and present the analysis. Furthermore, a simple self-developed free MATLAB app (EASY-STEM) with a graphical user interface (GUI) will be presented. The GUI can assist in the analysis of STEM images without the need for writing dedicated analysis code or software. The advanced data analysis methods presented here can be applied for the local quantification of defect relaxations, local structural distortions, local phase transformations, and non-centrosymmetry in a wide range of materials.

The modern aberration-corrected scanning transmission electron microscopes (AC-STEM) have successfully achieved direct visualization of atomic columns with sub-angstrom resolution. With this significant progress, advanced image quantification and analysis are still at the early stages. In this work, we present the complete pathway for the metrology of atomic resolution scanning transmission electron microscopy (STEM) images. This includes (1) tips for acquiring high-quality STEM images; (2) denoising and drift-correction for enhancing measurement accuracy; (3) obtaining initial atomic positions; (4) indexing the atoms based on unit cell vectors; (5) quantifying the atom column positions with either 2D-Gaussian single peak fitting or (6) multi-peak fitting routines for slightly overlapping atomic columns; (7) quantification of lattice distortion/strain within the crystal structures or at the defects/interfaces where the lattice periodicity is disrupted; and (8) some common methods to visualize and present the analysis. Furthermore, a simple self-developed free MATLAB app (EASY-STEM) with a graphical user interface (GUI) will be presented. The GUI can assist in the analysis of STEM images without the need for writing dedicated analysis code or software. The advanced data analysis methods presented here can be applied for the local quantification of defect relaxations, local structural distortions, local phase transformations, and non-centrosymmetry in a wide range of materials.

Atomic resolution scanning transmission electron microscopy at liquid helium temperatures for quantum materials

Beryl in different varieties (emerald, aquamarine, heliodor etc.) displays a wide range of colours that have fascinated humans throughout history. Beryl is a hexagonal cyclo-silicate (ring-silicate) with channels going through the crystal along the c-axis. The channels are about 0.5 nm in diameter and can be occupied by water and alkali ions. Pure beryl (Be3 Al2 Si6 O18 ) is colourless (variety goshenite). The characteristic colours are believed to be mainly generated through substitutions with metal atoms in the lattice. Which atoms that are substituted is still debated it has been proposed that metal ions may also be enclosed in the channels and that this can also contribute to the crystal colouring. So far spectroscopy studies have not been able to fully answer this. Here we present the first experiments using atomic resolution scanning transmission electron microscope imaging (STEM) to investigate the channel occupation in beryl. We present images of a natural beryl crystal (variety heliodor) from the Bin Thuan Province in Vietnam. The channel occupation can be visualized. Based on the image contrast in combination with ex situ element analysis we suggest that some or all of the atoms that are visible in the channels are Fe ions.

Ion irradiation has been observed to induce a macroscopic flattening and in-plane shrinkage of graphene sheets without a complete loss of crystallinity. Electron diffraction studies performed during simultaneous in-situ ion irradiation have allowed identification of the fluence at which the graphene sheet loses long-range order. This approach has facilitated complementary ex-situ investigations, allowing the first atomic resolution scanning transmission electron microscopy images of ion-irradiation induced graphene defect structures together with quantitative analysis of defect densities using Raman spectroscopy.

Chemical vapor deposition (CVD) has been established as a versatile route for the large-scale synthesis of transition metal dichalcogenides, such as tungsten disulfide (WS2). Yet, the precursor composition's role on the CVD process remains largely unknown and remains to be explored. Here, we employ Pulsed Laser Deposition (PLD) in a two-stage approach to tune the oxygen content in the tungsten oxide (WO3-x) precursors and demonstrate the presence of oxygen vacancies in the oxide films leads to a more facile conversion from WO3-x to WS2. Using a joint study based on ab initio density functional theory (DFT) calculations and experimental observations, we unravel that the oxygen vacancies in WO3-x can serve as niches through which sulfur atoms enter the lattice and facilitate an efficient conversion into WS2 crystals. By solely modulating the precursor stoichiometry, the photoluminescence emission of WS2 crystals can be significantly enhanced. Atomic resolution scanning transmission electron microscopy imaging (STEM) reveals that tungsten vacancies are the dominant intrinsic defects in mono- and bilayers WS2. Moreover, bi- and multilayer WS2 crystals derived from oxides with a high V0 content exhibit dominant AA'/AB or AA(A…) stacking orientations. The atomic resolution images reveal local strain buildup in bilayer WS2 due to competing effects of complex grain boundaries. Our study provides means to tune the precursor composition to control the lateral growth of TMDs while revealing insights into the different pathways for forming grain boundaries in bilayer WS2.

SIM-STEM Lab: Incorporating Compressed Sensing Theory for Fast STEM Simulation

The Noise2Void technique is demonstrated for successful denoising of atomic resolution scanning transmission electron microscopy (STEM) images. The technique is applied to denoising atomic resolution images and videos of gold adatoms on a graphene surface within a graphene liquid-cell, with the denoised experimental data qualitatively demonstrating improved visibility of both the Au adatoms and the graphene lattice. The denoising performance is quantified by comparison to similar simulated data and the approach is found to significantly outperform both total variation and simple Gaussian blurring. Compared to other denoising methods, the Noise2Void technique has the combined advantages that it requires no manual intervention during training or denoising, no prior knowledge of the sample and is compatible with real-time data acquisition rates of at least 45 frames per second.

Atomically resolved images of monolayer organic crystals have only been obtained with scanning probe methods so far. On the one hand, they are usually prepared on surfaces of bulk materials, which are not accessible by (scanning) transmission electron microscopy. On the other hand, the critical electron dose of a monolayer organic crystal is orders of magnitudes lower than the one for bulk crystals, making (scanning) transmission electron microscopy characterization very challenging. In this work we present an atomically resolved study on the dynamics of a monolayer CuPcCl16 crystal under the electron beam as well as an image of the undamaged molecules obtained by low-dose electron microscopy. The results show the dynamics and the radiation damage mechanisms in the 2D layer of this material, complementing what has been found for bulk crystals in earlier studies. Furthermore, being able to image the undamaged molecular crystal allows the characterization of new composites consisting of 2D materials and organic molecules.

Position averaged convergent beam electron diffraction: Theory and applications

SnGe4N4O4 was synthesized at high pressure (16 and 20 GPa) and high temperature (1200 and 1500°C) in a large-volume press. Powder X-ray diffraction experiments using synchrotron radiation indicate that the derived samples are mixtures of known and unknown phases. However, the powder X-ray diffraction patterns are not sufficient for structural characterization. Transmission electron microscopy studies reveal crystals of several hundreds of nanometres in size with different chemical composition. Among them, crystals of a previously unknown phase with stoichiometry SnGe4N4O4 were detected and investigated using automated diffraction tomography (ADT), a three-dimensional electron diffraction method. Via ADT, the crystal structure could be determined from single nanocrystals in space group P63mc, exhibiting a nolanite-type structure. This was confirmed by density functional theory calculations and atomic resolution scanning transmission electron microscopy images. In one of the syntheses runs a rhombohedral 6R polytype of SnGe4N4O4 could be found together with the nolanite-type SnGe4N4O4. The structure of this polymorph was solved as well using ADT.

This paper investigated the growth of (AlxGa1−x)2O3 thin films on semi-insulating (010) Ga2O3 substrates over the entire Al composition range (0% < x ≤ 100%) via metalorganic chemical vapor deposition (MOCVD). For the Al composition x < 27%, high quality single phase β-(AlxGa1−x)2O3 was achieved. A mixture of β and γ phases existed in (AlxGa1−x)2O3 when Al composition ranged between 27% and 40%, whereas a single γ-phase was observed for the films with Al composition x > 40%. The transition from the β to γ phase in AlGaO alloys was observed from x-ray diffraction spectra. The growth of γ-phase AlGaO with higher Al content was further confirmed via atomic resolution scanning transmission electron microscopy imaging and nanodiffraction. Compositional and statistical analyses performed on data acquired from atom probe tomography provided insight on the local compositional homogeneity in AlGaO films with different Al compositions. For AlGaO with pure β or γ phases, the Al composition distribution showed homogeneity with similar Al composition values as extracted from the x-ray diffraction peak positions. For AlGaO films with mixed β and γ phases, inhomogeneity in the Al composition distribution became more obvious in the nm scale. A mechanism was proposed for the observed phase transformation between β and γ phases in MOCVD growth of AlGaO films.

Role of dislocation climb on twin boundary and antiphase boundary formations in inverse-spinel MnAl2O4

Incorporating heteroatoms into the graphene lattice may be used to tailor its electronic, mechanical and chemical properties, although directly observed substitutions have thus far been limited to incidental Si impurities and P, N and B dopants introduced using low-energy ion implantation. We present here the heaviest impurity to date, namely 74Ge+ ions implanted into monolayer graphene. Although sample contamination remains an issue, atomic resolution scanning transmission electron microscopy imaging and quantitative image simulations show that Ge can either directly substitute single atoms, bonding to three carbon neighbors in a buckled out-of-plane configuration, or occupy an in-plane position in a divacancy. First-principles molecular dynamics provides further atomistic insight into the implantation process, revealing a strong chemical effect that enables implantation below the graphene displacement threshold energy. Our results demonstrate that heavy atoms can be implanted into the graphene lattice, pointing a way toward advanced applications such as single-atom catalysis with graphene as the template.