Abstract: High angle annular dark field scanning transmission electron microscopy (HAADF STEM) images provide sample information which is sensitive to the chemical composition. The image intensities indeed scale with the mean atomic number Z. To some extent, chemically different atomic column types can therefore be visually distinguished. However, in order to quantify the atomic column composition with high accuracy and precision, model-based methods are necessary. Therefore, an empirical incoherent parametric imaging model can be used of which the unknown parameters are determined using statistical parameter estimation theory (Van Aert et al., 2009, [1]). In this paper, it will be shown how this method can be combined with frozen lattice multislice simulations in order to evolve from a relative toward an absolute quantification of the composition of single atomic columns with mixed atom types. Furthermore, the validity of the model assumptions are explored and discussed.

Abstract: Annular dark-field (ADF) scanning transmission electron microscopy (STEM) has become widely used in quantitative studies based on the opportunity to directly compare experimental and simulated images. This comparison merely requires the experimental data to be normalised and expressed in units of fractional beam-current. However, inhomogeneities in the response of electron detectors can complicate this normalisation. The quantification procedure becomes both experiment and instrument specific, requiring new simulations for the particular response of each instrument's detector, and for every camera-length used. This not only impedes the comparison between different instruments and research groups, but can also be computationally very time consuming. Furthermore, not all image simulation methods allow for the inclusion of an inhomogeneous detector response. In this work, we propose an alternative method for normalising experimental data in order to compare these with simulations that consider a homogeneous detector response. To achieve this, we determine the electron flux distribution reaching the detector by means of a camera-length series or a so-called atomic column cross-section averaged convergent beam electron diffraction (XSACBED) pattern. The result is then used to determine the relative weighting of the detector response. Here we show that the results obtained by this new electron flux weighted (EFW) method are comparable to the currently used method, while considerably simplifying the needed simulation libraries. The proposed method also allows one to obtain a metric that describes the quality of the detector response in comparison with the ideal detector response.

Abstract: The recently discovered EMCD technique (energy loss magnetic chiral dichroism) can detect atom specific magnetic moments with nanometer resolution, exploiting the spin selectivity of electronic transitions in energy loss spectroscopy. Yet, direct imaging of magnetic moments on the atomic scale is not possible. In this paper we present an extension of EMCD that can overcome this limit. As a model system we chose bcc Fe. We present image simulations of the L3 white line signal, based on the kinetic equation for the density matrix of the 200 kV probe electron. With actual progress in instrumentation (high brightness sources, aberration corrected lenses) this technique should allow direct imaging of spin moments on the atomic scale.

Abstract: Principal component analysis (PCA) noise filtering is a popular method to remove noise from experimental electron energy loss (EELS) spectrum images. Here, we investigate the statistical behaviour of this method by applying it on a simulated data set with realistic noise levels. This phantom data set provides access to the true values contained in the data set as well as to many different realizations of the noise. Using least squares fitting and parameter estimation theory, we demonstrate that even though the precision on the estimated parameters can be better as the CramérRao lower bound, a significant bias is introduced which can alter the conclusions drawn from experimental data sets. The origin of this bias is in the incorrect retrieval of the principal loadings for noisy data. Using an expression for the bias and precision of the singular values from literature, we present an evaluation criterion for these singular values based on the noise level and the amount of information present in the data set. This criterion can help to judge when to avoid PCA noise filtering in practical situations. Further we show that constructing elemental maps of PCA noise filtered data using the background subtraction method, does not guarantee an increase in the signal to noise ratio due to correlation of the spectral data as a result of the filtering process.

Abstract: The holographic mask technique is used to create freely moving electrons with quantized angular momentum. With electron optical elements they can be focused to vortices with diameters below the nanometer range. The understanding of these vortex beams is important for many applications. Here, we produce electron vortex beams and compare them to a theory of electrons with topological charge. The experimental results show excellent agreement with simulations. As an immediate application, fundamental experimental parameters like spherical aberration and partial coherence are determined. (C) 2012 Elsevier B.V. All rights reserved.

Abstract: We present energy filtered holography experiments on a thin foil of Al. By propagating the reduced density matrix of the probe electron through the microscope, we quantitatively predict the fringe contrast as a function of energy loss. Fringe contrast simulations include the effect of Fresnel fringes created at the edges of the defocused biprism, the effect of partial coherence in combination with inelastic scattering, and the effect of a finite energy distribution of the incoming beam. (c) 2007 Elsevier B.V. All rights reserved.

Abstract: In thispaperweinvestigatewhichprobesizemaximizesthethroughputwhenmeasuringtheradiusof nanoparticlesinhighangleannulardarkfieldscanningtransmissionelectronmicroscopy(HAADFSTEM). The sizeandthecorrespondingcurrentoftheelectronprobedeterminetheprecisionoftheestimateofa particlesradius.Maximizingthroughputmeansthatamaximumnumberofparticlesshouldbeimaged withinagiventimeframe,sothataprespecifiedprecisionisattained.WeshowthatBayesianstatistical experimentaldesignisaveryusefulapproachtodeterminetheoptimalprobesizeusingacertainamount of priorknowledgeaboutthesample.Thedependenceoftheoptimalprobesizeonthedetectorgeometry and thediameter,variabilityandatomicnumberoftheparticlesisinvestigated.Anexpressionforthe optimalprobesizeintheabsenceofanykindofpriorknowledgeaboutthespecimenisderivedaswell.

Abstract: We present the ASTRA Toolbox as an open platform for 3D image reconstruction in tomography. Most of the software tools that are currently used in electron tomography offer limited flexibility with respect to the geometrical parameters of the acquisition model and the algorithms used for reconstruction. The ASTRA Toolbox provides an extensive set of fast and flexible building blocks that can be used to develop advanced reconstruction algorithms, effectively removing these limitations. We demonstrate this flexibility, the resulting reconstruction quality, and the computational efficiency of this toolbox by a series of experiments, based on experimental dual-axis tilt series.

Abstract: A new version of the open source program MULTEM is presented here. It includes a graphical user interface, tapering truncation of the atomic potential, CPU multithreading functionality, single/double precision calculations, scanning transmission electron microscopy (STEM) simulations using experimental detector sensitivities, imaging STEM (ISTEM) simulations, energy filtered transmission electron microscopy (EFTEM) simulations, STEM electron energy loss spectroscopy (EELS) simulations along with other improvements in the algorithms. We also present a mixed channeling approach for the calculation of inelastic excitations, which allows one to considerably speed up time consuming EFTEM/STEM-EELS calculations.

Abstract: This study sheds light on the prerequisites, possibilities, limitations and interpretation of high-resolution differential phase contrast (DPC) imaging in scanning transmission electron microscopy (STEM). We draw particular attention to the well-established DPC technique based on segmented annular detectors and its relation to recent developments based on pixelated detectors. These employ the expectation value of the momentum transfer as a reliable measure of the angular deflection of the STEM beam induced by an electric field in the specimen. The influence of scattering and propagation of electrons within the specimen is initially discussed separately and then treated in terms of a two-state channeling theory. A detailed simulation study of GaN is presented as a function of specimen thickness and bonding. It is found that bonding effects are rather detectable implicitly, e.g., by characteristics of the momentum flux in areas between the atoms than by directly mapping electric fields and charge densities. For strontium titanate, experimental charge densities are compared with simulations and discussed with respect to experimental artifacts such as scan noise. Finally, we consider practical issues such as figures of merit for spatial and momentum resolution, minimum electron dose, and the mapping of larger-scale, built-in electric fields by virtue of data averaged over a crystal unit cell. We find that the latter is possible for crystals with an inversion center. Concerning the optimal detector design, this study indicates that a sampling of 5mrad per pixel is sufficient in typical applications, corresponding to approximately 10x10 available pixels.

Abstract: Nanocorrugation of 2D crystals is an important phenomenon since it affects their electronic and mechanical properties. The corrugation may have various sources; one of them is flexural phonons that, in particular, are responsible for the thermal conductivity of graphene. A study of corrugation of just the suspended graphene can reveal much of valuable information on the physics of this complicated phenomenon. At the same time, the suspended crystal nanorelief can hardly be measured directly because of high flexibility of the 2D crystal. Moreover, the relief portion related to rapid out-of-plane oscillations (flexural phonons) is also inaccessible by such measurements. Here we present a technique for measuring the Fourier components of the height-height correlation function H(q) of suspended graphene which includes the effect of flexural phonons. The technique is based on the analysis of electron diffraction patterns. The H(q) is measured in the range of wavevectors q approximately 0.4-4.5nm(-1). At the upper limit of this range H(q) does follow the T/kappaq(4) law. So, we measured the value of suspended graphene bending rigidity kappa=1.2+/-0.4eV at ambient temperature T approximately 300K. At intermediate wave vectors, H(q) follows a slightly weaker exponent than theoretically predicted q(-3.15) but is closer to the results of the molecular dynamics simulation. At low wave vectors, the dependence becomes even weaker, which may be a sign of influence of charge carriers on the dynamics of undulations longer than 10nm. The technique presented can be used for studying physics of flexural phonons in other 2D materials.

Abstract: An efficient model-based estimation algorithm is introduced to quantify the atomic column positions and intensities from atomic resolution (scanning) transmission electron microscopy ((S)TEM) images. This algorithm uses the least squares estimator on image segments containing individual columns fully accounting for overlap between neighbouring columns, enabling the analysis of a large field of view. For this algorithm, the accuracy and precision with which measurements for the atomic column positions and scattering cross-sections from annular dark field (ADF) STEM images can be estimated, has been investigated. The highest attainable precision is reached even for low dose images. Furthermore, the advantages of the model-based approach taking into account overlap between neighbouring columns are highlighted. This is done for the estimation of the distance between two neighbouring columns as a function of their distance and for the estimation of the scattering cross-section which is compared to the integrated intensity from a Voronoi cell. To provide end-users this well-established quantification method, a user friendly program, StatSTEM, is developed which is freely available under a GNU public license.

Abstract: In quantitative scanning transmission electron microscopy (STEM), scattering cross-sections have been shown to be very sensitive to the number of atoms in a column and its composition. They correspond to the integrated intensity over the atomic column and they outperform other measures. As compared to atomic column peak intensities, which saturate at a given thickness, scattering cross-sections increase monotonically. A study of the electron wave propagation is presented to explain the sensitivity of the scattering cross-sections. Based on the multislice algorithm, we analyse the wave propagation inside the crystal and its link to the scattered signal for the different probe positions contained in the scattering cross-section for detector collection in the low-, middle- and high-angle regimes. The influence to the signal from scattering of neighbouring columns is also discussed.

Abstract: Recently, imaging scanning transmission electron microscopy (ISTEM) has been proposed as a promising new technique combining the advantages of conventional TEM (CTEM) and STEM [1]. The ability to visualize light and heavy elements together makes it a particularly interesting new, spatially incoherent imaging mode. Here, we evaluate this technique in term of precision with which atomic column locations can be measured. By using statistical parameter estimation theory, we will show that these locations can be accurately measured with a precision in the picometer range. Furthermore, a quantitative comparison is made with HAADF STEM imaging to investigate the advantages of ISTEM.

Abstract: Aberration correction in scanning transmission electron microscopy (STEM) has greatly improved the lateral and depth resolution. When using depth sectioning, a technique during which a series of images is recorded at different defocus values, single impurity atoms can be visualised in three dimensions. In this paper, we investigate new possibilities emerging when combining depth sectioning and precise atom-counting in order to reconstruct nanosized particles in three dimensions. Although the depth resolution does not allow one to precisely locate each atom within an atomic column, it will be shown that the depth location of an atomic column as a whole can be measured precisely. In this manner, the morphology of a nanoparticle can be reconstructed in three dimensions. This will be demonstrated using simulations and experimental data of a gold nanorod.