Abstract: In computed tomography, the reconstruction is typically obtained on a voxel grid. In this work, however, we propose a mesh-based reconstruction method. For tomographic problems, 3D meshes have mostly been studied to simulate data acquisition, but not for reconstruction, for which a 3D mesh means the inverse process of estimating shapes from projections. In this paper, we propose a differentiable forward model for 3D meshes that bridge the gap between the forward model for 3D surfaces and optimization. We view the forward projection as a rendering process, and make it differentiable by extending recent work in differentiable rendering. We use the proposed forward model to reconstruct 3D shapes directly from projections. Experimental results for single-object problems show that the proposed method outperforms traditional voxel-based methods on noisy simulated data. We also apply the proposed method on electron tomography images of nanoparticles to demonstrate the applicability of the method on real data.

Abstract: 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.

Abstract: We report a study of scattering dynamics in crystals employing momentum-resolved scanning transmission
electron microscopy under varying illumination conditions. As we perform successive changes of the probe
focus, multiple real-space signals are obtained in dependence of the shape of the incident electron wave.
With support from extensive simulations, each signal is shown to be characterised by an optimum focus for
which the contrast is maximum and which differs among different signals. For instance, a systematic focus
mismatch is found between images formed by high-angle scattering, being sensitive to thickness and chemical
composition, and the first moment in diffraction space, being sensitive to electric fields. It follows that a single
recording at one specific probe focus is usually insufficient to characterise materials comprehensively. Most
importantly, we demonstrate in experiment and simulation that the second moment (

Abstract: This paper investigates the possible benefits for counting atoms of different chemical nature when analysing multiple 2D scanning transmission electron microscopy (STEM) images resulting from independent annular dark field (ADF) detector regimes. To reach this goal, the principles of statistical detection theory are used to quantify the probability of error when determining the number of atoms in atomic columns consisting of multiple types of elements. In order to apply this theory, atom-counting is formulated as a statistical hypothesis test, where each hypothesis corresponds to a specific number of atoms of each atom type in an atomic column. The probability of error, which is limited by the unavoidable presence of electron counting noise, can then be computed from scattering-cross sections extracted from multiple ADF STEM images. Minimisation of the probability of error as a function of the inner and outer angles of a specified number of independent ADF collection regimes results in optimal experimental designs. Based on simulations of spherical Au@Ag and Au@Pt core–shell nanoparticles, we investigate how the combination of two non-overlapping detector regimes helps to improve the probability of error when unscrambling two types of atoms. In particular, the combination of a narrow low angle ADF detector with a detector formed by the remaining annular collection regime is found to be optimal. The benefit is more significant if the atomic number Z difference becomes larger. In
addition, we show the benefit of subdividing the detector regime into three collection areas for heterogeneous nanostructures based on a structure consisting of three types of elements, e.g., a mixture of Au, Ag and Al atoms. Finally, these results are compared with the probability of error resulting when one would ultimately use a pixelated 4D STEM detector and how this could help to further reduce the incident electron dose.

Abstract: Quantitative structure determination is needed in order to study and understand nanomaterials at the atomic scale. Materials characterisation resulting in precise structural information is a crucial point to understand the structure–property relation of materials. Counting the number of atoms and retrieving the 3D atomic structure of nanoparticles plays an important role here. In this paper, an overview will be given of the atom-counting methodology and its applications over the past decade. The procedure to count the number of atoms will be discussed in detail and it will be shown how the performance of the method can be further improved. Furthermore, advances toward mixed element nanostructures, 3D atomic modelling based on the atom-counting results, and quantifying the nanoparticle dynamics will be highlighted.

Abstract: Quantification of annular dark field (ADF) scanning transmission electron microscopy (STEM) images in terms
of composition or thickness often relies on probe-position integrated scattering cross sections (PPISCS). In
order to compare experimental PPISCS with theoretically predicted ones, expensive simulations are needed for
a given specimen, zone axis orientation, and a variety of microscope settings. The computation time of such
simulations can be in the order of hours using a single GPU card. ADF STEM simulations can be efficiently
parallelized using multiple GPUs, as the calculation of each pixel is independent of other pixels. However, most
research groups do not have the necessary hardware, and, in the best-case scenario, the simulation time will
only be reduced proportionally to the number of GPUs used. In this manuscript, we use a learning approach and
present a densely connected neural network that is able to perform real-time ADF STEM PPISCS predictions as
a function of atomic column thickness for most common face-centered cubic (fcc) crystals (i.e., Al, Cu, Pd, Ag,
Pt, Au and Pb) along [100] and [111] zone axis orientations, root-mean-square displacements, and microscope
parameters. The proposed architecture is parameter efficient and yields accurate predictions for the PPISCS
values for a wide range of input parameters that are commonly used for aberration-corrected transmission
electron microscopes.

Abstract: Electron ptychography provides highly sensitive, dose efficient phase images which can be corrected for aberrations after the data has been acquired. This is crucial when very precise quantification is required, such as with sensitivity to charge transfer due to bonding. Drift can now be essentially eliminated as a major impediment to focused probe ptychography, which benefits from the availability of easily interpretable simultaneous Z-contrast imaging. However challenges have remained when quantifying the ptychographic phases of atomic sites. The phase response of a single atom has a negative halo which can cause atoms to reduce in phase when brought closer together. When unaccounted for, as in integrating methods of quantification, this effect can completely obscure the effects of charge transfer. Here we provide a new method of quantification that overcomes this challenge, at least for 2D materials, and is robust to experimental parameters such as noise, sample tilt.

Abstract: To understand the structure–property relationship of nanostructures, reliably quantifying parameters, such as the number of atoms along the projection direction, is important. Advanced statistical methodologies have made it possible to count the number of atoms for monotype crystalline nanoparticles from a single ADF STEM image. Recent developments enable one to simultaneously acquire multiple ADF STEM images. Here, we present an extended statistics-based method for atom counting from a combination of multiple statistically independent ADF STEM images reconstructed from non-overlapping annular detector collection regions which improves the accuracy and allows one to retrieve precise atom-counts, especially for images acquired with low electron doses and multiple element structures.

Abstract: We compare the magnetic properties of pure and oxidized Co nanoparticles embedded in an amorphous Al2O3 matrix. Nanoparticles with diameters of 2 or 3 nm were prepared by alternate pulsed laser deposition in high vacuum conditions, and some of them were exposed to O-2 after production and before being embedded. The nanoparticles are organized in layers, the effective edge-to-edge in-depth separation being 5 or 10 nm. The lower saturation magnetizations per Co atom for the samples containing oxidized nanoparticles provide evidence for the formation of antiferromagnetic CoO shells in the nanoparticles. None of the samples with Co/CoO nanoparticles show exchange bias, while vertical hysteresis loop shifts and enhanced coercivities (as compared to samples with pure Co nanoparticles) are observed. This constitutes evidence for the nanoparticles size being in all cases smaller than the critical size for exchange bias. The difference in coercivity versus temperature dependences for the samples with pure and oxidized Co nanoparticles shows that the exchange anisotropy in Co/CoO nanoparticles appears at temperatures lower than 50 K. (c) 2007 American Institute of Physics.

Abstract: In this paper, a methodology is presented to count the number of atoms in heterogeneous nanoparticles based on the combination of multiple annular dark field scanning transmission electron microscopy (ADF STEM) images. The different non-overlapping annular detector collection regions are selected based on the principles of optimal statistical experiment design for the atom-counting problem. To count the number of atoms, the total intensities of scattered electrons for each atomic column, the so-called scattering cross-sections, are simultaneously compared with simulated library values for the different detector regions by minimising the squared differences. The performance of the method is evaluated for simulated Ni@Pt and Au@Ag core-shell nanoparticles. Our approach turns out to be a dose efficient alternative for the investigation of beam-sensitive heterogeneous materials as compared to the combination of ADF STEM and energy dispersive X-ray spectroscopy.

Abstract: In this work, we report an anomalous phenomenon on superelastic cycling of NiTi shape memory alloys when deforming at the temperature close to the border of superelastic window. New unexpected effects are found-(i) critical stress for inducing martensite transformation during the second loading cycle is higher than that of the first cycle; ( ii ) the plateau stress of the second cycle decreases to the original level when the strain overcomes the limit of the first cycle; ( iii ) transition from good superelasticity in the first cycle to fully irreversible strain in the second. We propose that defects generated during the first superelastic cycle close to the border of superelastic window impede following stress-induced martensitic transformations, leading to the increase of critical stress beyond yield stress of the B2 matrix, and thus functional fatigue of NiTi alloys. (c) 2021 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Abstract: We present a first-principles computational study of cation–Se 3 (112) grain boundaries in CuGaSe. We discuss the structure of these grain boundaries, as well as the effect of native defects and Na impurities on their electronic properties. The formation energies show that the defects will tend to form preferentially at the grain boundaries, rather than in the grain interiors. We find that in Ga-rich growth conditions Cu vacancies as well as Ga at Cu and Cu at Ga antisites are mainly responsible for having the equilibrium Fermi level pinned toward the middle of the gap, resulting in carrier depletion. The Na at Cu impurity in its +1 charge state contributes to this. In Ga-poor growth conditions, on the other hand, the formation energies of Cu vacancies and Ga at Cu antisites are comparatively too high for any significant influence on carrier density or on the equilibrium Fermi level position. Thus, under these conditions, the Cu at Ga antisites give rise to a -type grain boundary. Also, their formation energy is lower than the formation energy of Na at Cu impurities. Thus, the latter will fail to act as a hole barrier preventing recombination at the grain boundary, in contrast to what occurs in CuInSe grain boundaries. We also discuss the effect of the defects on the electronic properties of bulk CuGaSe, which we assume reflect the properties of the grain interiors.

Abstract: The discovery of a two-dimensional electron system (2DES) at the interfaces of perovskite oxides such as LaAlO3 and SrTiO3 has motivated enormous efforts in engineering interfacial functionalities with this type of oxide heterostructures. However, the fundamental origins of the 2DES are still not understood, e.g., the microscopic mechanisms of coexisting interface conductivity and magnetism. Here we report a comprehensive spectroscopic investigation on the depth profile of 2DES-relevant Ti 3d interface carriers using depthand element-specific techniques like standing-wave excited photoemission and resonant inelastic scattering. We found that one type of Ti 3d interface carriers, which give rise to the 2DES are located within three unit cells from the n-type interface in the SrTiO3 layer. Unexpectedly, another type of interface carriers, which are polarity-induced Ti-on-Al antisite defects, reside in the first three unit cells of the opposing LaAlO3 layer (similar to 10 angstrom). Our findings provide a microscopic picture of how the localized and mobile Ti 3d interface carriers distribute across the interface and suggest that the 2DES and 2D magnetism at the LaAlO3/SrTiO3 interface have disparate explanations as originating from different types of interface carriers.

Abstract: For the first time, the local structure and physical properties of Ru1222 based compounds (RuSr(2)Gd(1.4)Ce(0.6)Cu(2)O(10-delta) and RuSr(2)Gd(1.8-x)Y(0.2)CexCu(2)O(10) (x = 0.90-0.55)) have been investigated and analyzed together on the very same compounds. The Ru1222 superstructure was confirmed by TEM at a local scale and was suggested to have an orthorhombic symmetry with space group Aba2 and lattice parameters a(s) similar or equal to root 2a, b(s) similar or equal to root 2a and c(s) = c. This new Ru1222 superstructure distortion from tetragonal symmetry is proposed to have a positive correlation with the superconductivity variation of these compounds. The more the distortion towards orthorhombic symmetry, the higher the critical superconducting temperature these compounds can achieve. The T(c)(0) of RuSr(2)Gd(1.8-x)Y(0.2)Ce(x)Cu(2)O(10-delta) (x = 0.85-0.55) increases monotonically from 4 to 16 K when x decreases from 0.85 to 0.70, then RuSr(2)Gd(2)Cu(2)O(8) defects emerge and the T(c) decreases with decreasing x. Ru1212 defects are observed to intergrow epitaxially with the Ru1222 structure as lamellas along the c-axis in RuSr(2)Gd(1.4)Ce(0.6)Cu(2)O(10-delta). Although Ru1212 is a superconductor, the intergrowth severely restrains its superconductivity.

Abstract: Si nanowires with a ⟨111⟩ orientation, synthesized by vapor-liquid-solid process with low silane partial pressure reactant and gold as the catalyst, are known to exhibit sawtooth facets containing gold adsorbates. We report herein the study of the nanowire morphology by means of transmission electron microscopy and scanning tunneling microscopy. The nanowires consist of faceted sidewalls. The number of the sidewalls changes from 12 to 6 along the growth axis, giving rise to nanowires with an irregular hexagonal cross section at their base. The sidewalls are covered with Au-rich clusters. Their facets also exhibit atomic structures that reveal the presence of gold, resulting from the diffusion of gold during the growth. Based on these observations, the tapering of the nanowire is found to be related to two contributions: the reduction in the catalyst particle size during the growth and lateral overgrowth from the direct incorporation of Si species onto the nanowire sidewalls. Because the rearrangement of atoms at surfaces and interfaces might affect the growth kinetics, the trigonal symmetry as well as the higher lateral growth rate on the widest sidewalls are explained from the existence of an interfacial atomic structure with two inequivalent parts in the unit cell. Finally, spectroscopic measurements were performed on the major facets and revealed a metallic behavior at 77 K.