Abstract: In this work, the simultaneous iterative reconstruction technique (SIRT), the total variation minimization (TVM) reconstruction technique and the discrete algebraic reconstruction technique (DART) for electron tomography are compared and the advantages and disadvantages are discussed. Furthermore, we describe how the result of a three dimensional (3D) reconstruction based on TVM can provide objective information that is needed as the input for a DART reconstruction. This approach results in a tomographic reconstruction of which the segmentation is carried out in an objective manner.

Abstract: The 3D reconstruction of a tilt series for electron tomography is mostly carried out using the weighted backprojection (WBP) algorithm or using one of the iterative algorithms such as the simultaneous iterative reconstruction technique (SIRT). However, it is known that these reconstruction algorithms cannot compensate for the missing wedge. Here, we apply a new reconstruction algorithm for electron tomography, which is based on compressive sensing. This is a field in image processing specialized in finding a sparse solution or a solution with a sparse gradient to a set of ill-posed linear equations. Therefore, it can be applied to electron tomography where the reconstructed objects often have a sparse gradient at the nanoscale. Using a combination of different simulated and experimental datasets, it is shown that missing wedge artefacts are reduced in the final reconstruction. Moreover, it seems that the reconstructed datasets have a higher fidelity and are easier to segment in comparison to reconstructions obtained by more conventional iterative algorithms.

Abstract: In electron tomography, the fidelity of the 3D reconstruction strongly depends on the employed reconstruction algorithm. In this paper, the properties of SIRT, TVM and DART reconstructions are studied with respect to having only a limited number of electrons available for imaging and applying different angular sampling schemes. A well-defined realistic model is generated, which consists of tubular domains within a matrix having slab-geometry. Subsequently, the electron tomography workflow is simulated from calculated tilt-series over experimental effects to reconstruction. In comparison with the model, the fidelity of each reconstruction method is evaluated qualitatively and quantitatively based on global and local edge profiles and resolvable distance between particles. Results show that the performance of all reconstruction methods declines with the total electron dose. Overall, SIRT algorithm is the most stable method and insensitive to changes in angular sampling. TVM algorithm yields significantly sharper edges in the reconstruction, but the edge positions are strongly influenced by the tilt scheme and the tubular objects become thinned. The DART algorithm markedly suppresses the elongation artifacts along the beam direction and moreover segments the reconstruction which can be considered a significant advantage for quantification. Finally, no advantage of TVM and DART to deal better with fewer projections was observed.

Abstract: A three-dimensional (3D) chemical characterization of nanomaterials can be obtained using tomography based on high angle annular dark field (HAADF) scanning transmission electron microscopy (STEM) or energy dispersive X-ray spectroscopy (EDS) STEM. These two complementary techniques have both advantages and disadvantages. The Z-contrast images have good image quality but lack robustness in the compositional analysis, while the elemental maps give more element-specific information, but at a low signal-to-noise ratio and a longer exposure time. Our aim is to combine these two types of complementary information in one single tomographic reconstruction process. Therefore, an imaging model is proposed combining both HAADF-STEM
and EDS-STEM. Based on this model, the elemental distributions can be reconstructed using both types of information simultaneously during the reconstruction process. The performance of the new technique is evaluated using simulated data and real experimental data. The results demonstrate that combining two imaging modalities leads to tomographic reconstructions with suppressed noise and enhanced contrast.

Abstract: Seed-mediated growth is the most efficient methodology to control the size and shape of colloidal metal nanoparticles. In this process, the final nanocrystal shape is defined by the crystalline structure of the initial seed as well as by the presence of ligands and other additives that help to stabilize certain crystallographic facets. We analyze here the growth mechanism in aqueous solution of silver shells on presynthesized gold nanoparticles displaying various well-defined crystalline structures and morphologies. A thorough three-dimensional electron microscopy characterization of the morphology and internal structure of the resulting core-shell nanocrystals indicates that {100} facets are preferred for the outer silver shell, regardless of the morphology and crystallinity of the gold cores. These results are in agreement with theoretical analysis based on the relative surface energies of the exposed facets in the presence of halide ions.

Abstract: Very uniform and well shaped Mn3O4 nano-octahedra are synthesized using a simple hydrothermal method under the help of polyethylene glycol (PEG200) as a reductant and shape-directing agent. The nano-octahedra formation mechanism is monitored. The shape and crystal orientation of the nanoparticles is reconstructed by scanning electron microscopy and electron tomography, which reveals that the nano-octahedra only selectively expose {101} facets at the external surfaces. The magnetic testing demonstrates that the Mn3O4 nano-octahedra exhibit anomalous magnetic properties: the Mn3O4 nano-octahedra around 150 nm show a similar Curie temperature and blocking temperature to Mn3O4 nanoparticles with 10 nm size because of the vertical axis of [001] plane and the exposed {101} facets. With these Mn3O4 nano-octahedra as a catalyst, the photodecomposition of rhodamine B is evaluated and it is found that the photodecomposition activity of Mn3O4 nano-octahedra is much superior to that of commercial Mn3O4 powders. The anomalous magnetic properties and high superior photodecomposition activity of well shaped Mn3O4 nano-octahedra should be related to the special shape of the nanoparticles and the abundantly exposed {101} facets at the external surfaces. Therefore, the shape preference can largely broaden the application of the Mn3O4 nano-octahedra.

Abstract: We report a method to reliably count the number of atoms from high-angle annular dark field scanning transmission electron microscopy images. A model-based analysis of the experimental images is used to measure scattering cross sections at the atomic level. The high sensitivity of these measurements in combination with a thorough statistical analysis enables us to count atoms with single-atom sensitivity. The validity of the results is confirmed by means of detailed image simulations. We will show that the method can be applied to nanocrystals of arbitrary shape, size, and atom type without the need for a priori knowledge about the atomic structure.

Abstract: It is widely accepted that the physical properties of nanostructures depend on the type of surface facets1, 2. For Au nanorods, the surface facets have a major influence on crucial effects such as reactivity and ligand adsorption and there has been controversy regarding facet indexing3, 4. Aberration-corrected electron microscopy is the ideal technique to study the atomic structure of nanomaterials5, 6. However, these images correspond to two-dimensional (2D) projections of 3D nano-objects, leading to an incomplete characterization. Recently, much progress was achieved in the field of atomic-resolution electron tomography, but it is still far from being a routinely used technique. Here we propose a methodology to measure the 3D atomic structure of free-standing nanoparticles, which we apply to characterize the surface facets of Au nanorods. This methodology is applicable to a broad range of nanocrystals, leading to unique insights concerning the connection between the structure and properties of nanostructures.

Abstract: Copper chalcogenides find applications in different domains including photonics, photothermal therapy and photovoltaics. CuTe nanocrystals have been proposed as an alternative to noble metal particles for plasmonics. Although it is known that deviations from stoichiometry are a prerequisite for plasmonic activity in the near-infrared, an accurate description of the material and its (optical) properties is hindered by an insufficient understanding of the atomic structure and the influence of defects, especially for materials in their nanocrystalline form. We demonstrate that the structure of Cu1.5±xTe nanocrystals canbe determined using electron diffraction tomography. Real-space high-resolution electron tomography directly reveals the three-dimensional distribution of vacancies in the structure. Through first-principles density functional theory, we furthermore demonstrate that the influence of these vacancies on the optical properties of the nanocrystals is determined. Since our methodology is applicable to a variety of crystalline nanostructured materials, it is expected to provide unique insights concerning structure–property correlations.

Abstract: The impact of nanoparticles (NPs) upon biological systems can be fundamentally associated with their physicochemical parameters. A further often-stated tenet is the importance of NP shape on rates of endocytosis. However, given the convoluted parameters concerning the NP-cell interaction, it is experimentally challenging to attribute any findings to shape alone. Herein we demonstrate that shape, below a certain limit, which is specific to nanomedicine, is not important for the endocytosis of spherocylinders by either epithelial or macrophage cells in vitro. Through a systematic approach, we reshaped a single batch of gold nanorods into different aspect ratios resulting in near-spheres and studied their cytotoxicity, (pro-)inflammatory status, and endocytosis/exocytosis. It was found that on a length scale of ~10-90 nm and at aspect ratios less than 5, NP shape has little impact upon their entry into either macrophages or epithelial cells. Conversely, nanorods with an aspect ratio above 5 were preferentially endocytosed by epithelial cells, whereas there was a lack of shape dependent uptake following exposure to macrophages in vitro. These findings have implications both in the understanding of nanoparticle reshaping mechanisms, as well as in the future rational design of nanomaterials for biomedical applications.

Abstract: Radiation-induced modifications of nanostructures are of fundamental interest and constitute a viable out-of-equilibrium approach to the development of novel nanomaterials. Herein, we investigated the structural transformation of silica-coated CdSe/CdS nanorods (NRs) under femtosecond (fs) illumination. By comparing the same nanorods before and after illumination with different fluences we found that the silica-shell did not only enhance the stability of the NRs but that the confinement of the NRs also led to novel morphological and chemical transformations. Whereas uncoated CdSe/CdS nanorods were found to sublimate under such excitations the silica-coated nanorods broke into fragments which deformed towards a more spherical shape. Furthermore, CdS decomposed which led to the formation of metallic Cd, confirmed by high-resolution electron microscopy and energy dispersive X-ray spectrometry (EDX), whereby an epitaxial interface with the remaining CdS lattice was formed. Under electron beam exposure similar transformations were found to take place which we followed in situ.

Abstract: Currently, ultrathin colloidal CdSe semiconductor nanoplatelets (NPLs) with a uniform thickness that is controllable up to the atomic scale can be prepared. The optical properties of these 2D semiconductor systems are the subject of extensive research. Here, we reveal their natural morphology and atomic arrangement. Using cryo-TEM (cryo-transmission electron microscopy), we show that the shape of rectangular NPLs in solution resembles a helix. Fast incorporation of these NPLs in silica preserves and immobilizes their helical shape, which allowed us to perform an in-depth study by high angle annular dark field scanning transmission electron microscopy (HAADF-STEM). Electron tomography measurements confirm and detail the helical shape of these systems. Additionally, high-resolution HAADF-STEM shows the thickness of the NPLs on the atomic scale and furthermore that these are consistently folded along a ?110? direction. The presence of a silica shell on both the top and bottom surfaces shows that Cd atoms must be accessible for silica precursor (and ligand) molecules on both sides.

Abstract: The three-dimensional (3D) atomic structure of nanomaterials, including strain, is crucial to understand their properties. Here, we investigate lattice strain in Au nanodecahedra using electron tomography. Although different electron tomography techniques enabled 3D characterizations of nanostructures at the atomic level, a reliable determination of lattice strain is not straightforward. We therefore propose a novel model-based approach from which atomic coordinates are measured. Our findings demonstrate the importance of investigating lattice strain in 3D.

Abstract: A thorough understanding of the three-dimensional (3D) atomic structure and composition of coreshell nanostructures is indispensable to obtain a deeper insight on their physical behavior. Such 3D information can be reconstructed from two-dimensional (2D) projection images using electron tomography. Recently, different electron tomography techniques have enabled the 3D characterization of a variety of nanostructures down to the atomic level. However, these methods have all focused on the investigation of nanomaterials containing only one type of chemical element. Here, we combine statistical parameter estimation theory with compressive sensing based tomography to determine the positions and atom type of each atom in heteronanostructures. The approach is applied here to investigate the interface in coreshell Au@Ag nanorods but it is of great interest in the investigation of a broad range of nanostructures.

Abstract: Over the last two decades, three-dimensional (3D) imaging by transmission electron microscopy or “electron tomography” has evolved into a powerful tool to investigate a variety of nanomaterials in different fields, such as life sciences, chemistry, solid-state physics, and materials science. Most of these results were obtained with nanometer-scale resolution, but different approaches have recently pushed the resolution to the atomic level. Such information is a prerequisite to understand the specific relationship between the atomic structure and the physicochemical properties of (nano) materials. We provide an overview of the latest progress in the field of atomic-resolution electron tomography. Different imaging and reconstruction approaches are presented, and state-of-the-art results are discussed. This article demonstrates the power and importance of electron tomography with atomic-scale resolution.