Simulation of scanning transmission electron microscope images on desktop computers

Two independent strategies are presented for reducing the computation time of multislice simulations of scanning transmission electron microscope (STEM) images: (1) optimal probe sampling, and (2) the use of desktop graphics processing units. The first strategy is applicable to STEM images generated by elastic and/or inelastic scattering, and requires minimal effort for its implementation. Used together, these two strategies can reduce typical computation times from days to hours, allowing practical simulation of STEM images of general atomic structures on a desktop computer.     

Calculation of Bohmian quantum trajectories for STEM

We present in this work the calculation of Bohmian quantum trajectories representing the wave function propagation in a crystal for a focused electron probe in a scanning transmission electron microscope (STEM). The wave function and quantum trajectories are obtained from the calculation of time‐dependent Schrödinger equation by fast Fourier transformation multislice algorithm. In our work, the Bohmian quantum trajectories of a scanning probe penetrating a Cu crystal are studied as an example of this calculation scheme. The results help us to better understand the electron diffraction process in a microscopic imaging from a trajectory‐based point of view. This Bohmian quantum trajectory method can be used to extend the application of classical Monte Carlo method from the study of electron interaction with amorphous solid to crystalline structure.     

An efficient way of including thermal diffuse scattering in simulation of scanning transmission electron microscopic images

We propose an improved image simulation procedure for atomic-resolution annular dark-field scanning transmission electron microscopy (STEM) based on the multislice formulation, which takes thermal diffuse scattering fully into account. The improvement with regard to the classical frozen phonon approach is realized by separating the lattice configuration statistics from the dynamical scattering so as to avoid repetitive calculations. As an example, the influence of phonon scattering on the image contrast is calculated and investigated. STEM image simulation of crystals can be applied with reasonable computing times to problems involving a large number of atoms and thick or large supercells.     

Diffraction contrast STEM of dislocations: imaging and simulations

The application of scanning transmission electron microscopy (STEM) to crystalline defect analysis has been extended to dislocations. The present contribution highlights the use of STEM on two oppositely signed sets of near-screw dislocations in hcp α-Ti with 6wt% Al in solid solution. In addition to common systematic row diffraction conditions, other configurations such as zone axis and 3g imaging are explored, and appear to be very useful not only for defect analysis, but for general defect observation. It is demonstrated that conventional TEM rules for diffraction contrast such as g·b and g·R are applicable in STEM. Experimental and computational micrographs of dislocations imaged in the aforementioned modes are presented.     

Artifacts in aberration-corrected ADF-STEM imaging

The introduction of an experimental black level may introduce unintended artifactual details into high-resolution annular dark field scanning transmission electron microscopy (ADF-STEM) lattice images. This article presents the multislice simulation results of such possible situations. Three simulated scanning transmission electron microscopy (STEM) probes of sizes 0.8, 1.2 and 2.0 A are scanned on the surface of a <1;10> oriented Si/Ge crystal. The simulation results suggest that high-frequency artifact peaks will appear in the power spectra when an artificial black level clips the lowest (background) signal. The lowest signal in an ADF-STEM image decreases as the incident probe shrinks in size. Therefore, care must be taken when interpreting the resolution limit of the microscope from images taken with nonzero black level setting, especially in case of sub-A microscope. The simulation result is compared with an experimental image and they agree with each other. The analysis suggests that aberration corrected STEM provide sensitive low level detail.     

Discussions on the multiple-input maximum a-posteriori wave-function restoration method in high-resolution electron microscopy

The multiple-input maximum a-posteriori (MIMAP) wave-function restoration method in high-resolution electron microscopy proposed by Kirkland (1984) is further discussed. A modified MIMAP criterion that considers likely correlations between individual micrographs in a series of micrographs taken at different imaging conditions is presented. By performing wave-function restoration for a multislice method-simulated defocus series of MgO[110], the convergent properties of this modified MIMAP method are also described.     

Observation of dislocations and microplasma sites in semiconductors by direct correlations of STEBIC,STEM and ELS

A high voltage electron microscope, equipped with scanning transmission (STEM) attachment, electron beam induced conductivity (EBIC) facilities, and electron energy loss spectrometer (ELS), has been used to investigate semiconductor devices. The capability of STEM to produce, simultaneously or sequentially, conductive and transmission images of the same specimen region, which can also be ELS analysed, is exploited in order to establish direct and unambiguous correlations between EBIC and STEM images of defective regions (dislocations and microplasma sites) in silicon devices. The results obtained are discussed in terms of correlations, resolution, contrast, and radiation damage; in addition, a comparison is made between this method and the other correlation methods based on EBIC/SEM (scanning electron microscope) and TEM (transmission electron microscope).     

Automatic selection of molecular images from dark field electron micrographs

A method is described which can be used objectively to select putative molecular images from dark field electron micrographs of unstained molecules. The only characteristic of the molecule required for automatic selection is an estimate of molecular weight. Structures are selected from micrographs by a series of steps including: low pass filtering, edge detection and mass determination. The procedure is shown to be reliable for images with signal-to-noise ratios of at least 4.0. Moreover, the method is insensitive to both the shape and the number of molecules in the image. Five different molecules with molecular weights between MW 330,000 and MW 4000 are successfully selected from low dose STEM and high dose tilt beam dark field electron micrographs.     

Use of sputter coating to prepare whole mounts of cytoskeletons for transmission and high-resolution scanning and scanning transmission electron microscopy

This paper describes the use of sputter coating to prepare detergent-extracted cytoskeletons for observation by scanning (SEM), scanning transmission (STEM), inverted contrast STEM, and transmission (TEM) electron microscopy. Sputtered coats of 1–2 nm of platinum or tungsten provide both an adequate secondary electron signal for SEM and good contrast for STEM and TEM. At the same time, the grain size of the coating is sufficiently fine to be just at (platinum) or below (tungsten) the limit of resolution for SEM and STEM. In TEM, the granular structure of platinum coats is resolved, and platinum decoration artifacts are observed on the surface of structures. The platinum is deposited as small islands with a periodic distribution that may reveal information about the underlying molecular structure. This method produces samples that are similar in appearance to replicas prepared by low-angle rotary shadowing with platinum and carbon. However, the sputter-coating method is easier to use; more widely available to investigators; and compatible with SEM, STEM, and TEM. It may also be combined with immunogold and other labeling methods. While TEM provides the highest resolution images of sputter-coated cytoskeletons, it also damages the specimens owing to heating in the beam. In SEM and STEM cytoskeletons are stable and the resolution is adequate to resolve individual microfilaments. The best single method for visualizing cytoskeletons is inverted contrast STEM, which images both the metal-coated cytoskeletal structures and electron-dense material within the nucleus and cytoplasm as white against a dark background. STEM and TEM were both suitable for visualizing colloidal gold particles in immunolabeled samples.     

An expanded approach to noise reduction from high-resolution STEM images based on the maximum entropy method

An expanded use of the maximum entropy method (MEM) is suggested to reduce noise from an experimental high-angle annular dark-field (HAADF) scanning transmission electron microscope (STEM) image. The MEM is combined with an estimate of the standard deviation of noise from an experimental HAADF STEM image and low-pass filtering using the information limit for an incoherent STEM image. Consequently, the present method has just one parameter of a Lagrange multiplier. It is demonstrated that the present method can reduce noise efficiently in high-resolution HAADF STEM images.     

Z-衬度像成像原理及其特点

扫描透射电子显微术（STEM）的原子序数衬度（Z-contrast）像具有分辨率高、对化学组成敏感以及图像直观可直接解释等优点。Z-衬度像成像方法是近年来在国外兴起的一种新型的高分辨成像方法，本文主要介绍了扫描透射电子显微术（STEM）的原子序数衬度像（Z-衬度像）的成像原理及方法，并指出了在材料科学研究中Z-衬度像的突出特点及应用前景。     

Quantitative atomic resolution mapping using high-angle annular dark field scanning transmission electron microscopy

A model-based method is proposed to relatively quantify the chemical composition of atomic columns using high angle annular dark field (HAADF) scanning transmission electron microscopy (STEM) images. The method is based on a quantification of the total intensity of the scattered electrons for the individual atomic columns using statistical parameter estimation theory. In order to apply this theory, a model is required describing the image contrast of the HAADF STEM images. Therefore, a simple, effective incoherent model has been assumed which takes the probe intensity profile into account. The scattered intensities can then be estimated by fitting this model to an experimental HAADF STEM image. These estimates are used as a performance measure to distinguish between different atomic column types and to identify the nature of unknown columns with good accuracy and precision using statistical hypothesis testing. The reliability of the method is supported by means of simulated HAADF STEM images as well as a combination of experimental images and electron energy-loss spectra. It is experimentally shown that statistically meaningful information on the composition of individual columns can be obtained even if the difference in averaged atomic number Z is only 3. Using this method, quantitative mapping at atomic resolution using HAADF STEM images only has become possible without the need of simultaneously recorded electron energy loss spectra.     

IMAGE-WARP: a real-space restoration method for high-resolution STEM images using quantitative HRTEM analysis

We have developed a new method for processing distorted high-resolution scanning transmission electron microscopy (STEM) images. The method is based on finding the displaced vertices in the experimental STEM image and warping to geometrically correct reference grid of the object. As a reference grid for warping a structural model obtained using a high-resolution transmission electron microscopy (HRTEM) analysis of the area of interest is utilised. Combined with quantitative HRTEM analysis the IMAGE-WARP method provides a real-space restoration of high-resolution high-angle annular dark-field (HAADF) STEM images without affecting the original Z-contrast information. The method can be applied to extract valuable compositional atomic-column data from any HAADF-STEM image of any kind of bulk crystals with local occupancy or chemistry fluctuations, stacking faults, special grain boundaries or interfaces, for which we have an available structural model. After the warping, distortion-corrected images can be further enhanced using conventional image-filtering techniques, and finally quantified with HAADF-STEM image simulations. The applicability of the IMAGE-WARP method was illustrated using experimental HAADF-STEM images of a strontium titanate crystal disrupted with a Ruddlesden-Popper-type antiphase boundary.     

Semianalytical treatment of beam broadening in crystals

Contrast and specimen resolution in electron micrographs of point defects, voids, aggregates, and precipitates in crystalline material are diminished by multiple scattering of the incident electrons within the crystalline top layer. For the scanning transmission electron microscope (STEM) the current density distribution inside the crystal has been calculated by employing the k · p perturbation expansion used in solid state physics. Neglecting inelastic scattering the solution of the electron wave function within the crystal can be expressed as a sum of Bloch waves. The excited Bloch waves are expanded in a power series of the angle of incidence, and only terms up to the second order inclusively are taken into account. This procedure permits the analytical integration over the illumination angles in STEM or the aperture angles in the case of a fixed-beam electron microscope (FBEM). Considering only the two strongest Bloch waves an approximate formula is obtained for the current density distribution within the crystal which is valid for light atoms and resolution limits larger than twice the lattice constant. In the case of heavy atoms the approximation for the current density is only valid in the region near the atoms. As the incident electrons channel along the atom rows beam broadening within the crystal is largely suppressed up to depths of about 1000 Å. The image contrast of an embedded scatterer resting on an atom row is strongly enhanced, whereas it is diminished when the scatterer is located midway among the atom rows. The proposed method makes possible a fast calculation of the electron wave propagating in crystalline material.     

Study of atomic resolved plasmon-loss image by spherical aberration-corrected STEM-EELS method

To gain an understanding of a plasmon-loss image obtained with an atomic resolution scanning transmission electron microscope (STEM)-electron energy loss spectroscopy (EELS) method, the detailed analysis is experimentally and theoretically performed. In order to theoretically explain a plasmon-loss image, a dynamical simulation method of the plasmon-loss image combined with a first-principle calculation is firstly proposed. By making comparisons between simulated and experimental plasmon-loss images, we find that the experimental plasmon-loss images closely resemble the high-angle bright-field STEM images, which show the reverse contrast of the corresponding high-angle annular dark-field STEM image.     

Identification of the three-dimensional gel microstructure from transmission electron micrographs

Mass transport in gels depends crucially on local properties of the gel network. We propose a method for identifying the three‐dimensional (3D) gel microstructure from statistical information in transmission electron micrographs. The gel strand network is modelled as a random graph with nodes and edges (branches). The distribution of edge length, the number of edges at nodes and the angles between edges at a node are estimated from transmission electron micrographs by image analysis methods. The 3D network is simulated by Markov chain Monte Carlo, with a probability function based on the statistical information found from the micrographs. The micrographs are projections of stained gel strands in slices, and we derive a formula for estimating the thickness of the stained gel slice based on the total projected gel strand length and the number of times that gel strands enter or exit the slice.     

Optimization of STEM tomography acquisition — A comparison of convergent beam and parallel beam STEM tomography

In this paper two imaging modes in a state-of-the-art scanning transmission electron microscope (STEM) are compared: conventional STEM with a convergent beam (referred to as nanoprobe) and STEM with a parallel beam (referred to as microprobe). The effect and influence of both modes with respect to their depth of field are investigated. Tomograms of a human white blood cell (hemophagocytes) are acquired, aligned, and evaluated. It is shown that STEM using a parallel beam produces tomograms with fewer distortions and artifacts that allows resolving finer features. Microprobe STEM tomography is advantageous especially in life science, when semi-thin sections (approximately 0.5 μm thick) of biological samples are imaged at relatively low magnification with a large field of view.     

A high-voltage scanning transmission electron microscope at Nagoya University

A high-voltage scanning transmission electron microscope (STEM) H-1250ST of the maximum accelerating voltage of 1.25 MV was constructed at Nagoya University in 1983. The microscope, equipped with a field-emission gun, is designed with high-level STEM performance as well as conventional transmission microscopy mode operation. The aim of developing the microscope, basic design schemes, principal instrumentation, and techniques developed are described.