Atomic-scale characterization of hydrogen and formation of niobium hydrides, using ultraviolet (wavelength=355 nm) picosecond laser-assisted local-electrode atom-probe tomography, was performed for ultrahigh purity niobium utilizing different laser pulse energies, 10 or 50 pJ/pulse or voltage pulsing. At 50 pJ/pulse, hydrogen atoms migrate onto the 110 and 111 poles as a result of stimulated surface diffusion, whereas they are immobile for <10 pJ/pulse or for voltage pulsing. Accordingly, the highest concentrations of H and NbH were obtained at 50 pJ/pulse. This is attributed to the thermal energy of the laser pulses being transferred to pure niobium specimens. Therefore, we examined the effects of the laser pulse energy being increased systematically from 1 to 20 pJ/pulse and then decreasing it from 20 to 1 pJ/pulse. The concentrations of H, H2, and NbH and the atomic concentration ratios H2/H, NbH/Nb, and Nb3+/Nb2+ were calculated with respect to the systematically changing laser pulse energies. The atomic concentration ratios H2/H and NbH/Nb are greater when decreasing the laser pulse energy than when increasing it, because the higher residual thermal energy after decreasing the laser pulse energy increases the mobility of H atoms by supplying sufficient thermal energy to form H2 or NbH.

Various practical issues affecting atom probe tomography (APT) analysis of III-nitride semiconductors have been studied as part of an investigation using a c-plane InAlN/GaN heterostructure. Specimen preparation was undertaken using a focused ion beam microscope with a mono-isotopic Ga source. This enabled the unambiguous observation of implantation damage induced by sample preparation. In the reconstructed InAlN layer Ga implantation was demonstrated for the standard “clean-up” voltage (5 kV), but this was significantly reduced by using a lower voltage (e.g., 1 kV). The characteristics of APT data from the desorption maps to the mass spectra and measured chemical compositions were examined within the GaN buffer layer underlying the InAlN layer in both pulsed laser and pulsed voltage modes. The measured Ga content increased monotonically with increasing laser pulse energy and voltage pulse fraction within the examined ranges. The best results were obtained at very low laser energy, with the Ga content close to the expected stoichiometric value for GaN and the associated desorption map showing a clear crystallographic pole structure.

A method to characterize open-cell nanoporous materials with atom probe tomography (APT) has been developed. For this, open-cell nanoporous gold with pore diameters of around 50 nm was used as a model system, and filled by electron beam-induced deposition (EBID) to obtain a compact material. Two different EBID precursors were successfully tested—dicobalt octacarbonyl [Co2(CO)8] and diiron nonacarbonyl [Fe2(CO)9]. Penetration and filling depth are sufficient for focused ion beam-based APT sample preparation. With this approach, stable APT analysis of the nanoporous material can be performed. Reconstruction reveals the composition of the deposited precursor and the nanoporous material, as well as chemical information of the interfaces between them. Thus, it is shown that, using an appropriate EBID process, local chemical information in three dimensions with sub-nanometer resolution can be obtained from nanoporous materials using APT.

We present results of cathodoluminescence (CL) investigations of high-quality zinc oxide (ZnO) nanorods obtained by an extremely fast hydrothermal method on a silicon substrate. A scanning electron microscopy (SEM) system equipped with CL allows direct comparison of SEM images and CL maps, taken from exactly the same areas of samples. Investigations are performed at a temperature of 5 K. An interlink between sample microstructure and emission properties is investigated. CL confirms a very high quality of ZnO nanorods produced by our method. In addition, the presence of super radiation effects in ZnO nanorod arrays is suggested.

Cold spray is a thermo-mechanical process where the velocity of the sprayed particles affects the deformation, bonding, and mechanical properties of the deposited material, in the form of splats or coatings. At high strain rates, the impact stresses are converted into heat, a phenomenon known as adiabatic shear, which leads to grain re-crystallization. Grain re-crystallization and growth are shown to have a direct impact on the mechanical properties of the cold-sprayed material. The present study ties the microstructural features within the cold-sprayed Ti splats and the substrate to the bonding mechanism and mechanical properties. High-resolution electron channeling contrast imaging, electron backscatter diffraction mapping, and nanoindentation were used to correlate the microstructure to the mechanical properties distribution within the titanium cold-spray splats. The formation of nanograins was observed at the titanium splat/substrate interface and contributed to metallurgical bonding. An increase in grain re-crystallization within the splat and substrate materials was observed with pre-heating of the substrate. In the substrate material, the predominant mechanism of deformation was twinning. A good relationship was found between the hardness and distribution of the twins within the substrate and the size distribution of the re-crystallized grains within the splats.

In this study, the effect of simple shearing on microstructure evolution and mechanical properties of 316L austenitic stainless steel were investigated. Two different shear strain routes were obtained by twisting cylindrical specimens in the forward and backward directions. The strain-induced martensite phase was effectively obtained by alteration of the routes. Formation of the martensite phase clearly resulted in significant hardening of the steel. Grain-size reduction and strain-induced martensitic transformation within the deformed structures of the strained specimens were characterized by scanning electron microscopy – electron back-scattered diffraction, X-ray diffraction, and the TEM-ASTAR (transmission electron microscopy – analytical scanning transmission atomic resolution, automatic crystal orientation/phase mapping for TEM) system. Significant numbers of twin networks were formed by alteration of the shear strain routes, and the martensite phases were nucleated at the twin interfaces.

Nanobelt-like precipitates in an Al–Si–Mg–Hf alloy were studied using electron backscattered diffraction (EBSD) and focused ion beam (FIB) scanning electron microscopy techniques. One grain of the Al matrix with a near [111] normal direction was identified by EBSD and the three-dimensional (3D) microstructure of nanobelt-like precipitates in this grain was studied using 3D-FIB. Ten growth directions of the nanobelt-like precipitates in the grain were identified.

The effect of carbon contamination on the analysis of carbon-coated silicate minerals at 5 kV for X-ray energies 0.7–4 keV is examined. For individual spot analyses, carbon is found to deposit adjacent to the beam spot forming ring-shaped deposits with no impact on the analysis. Carbon contamination becomes important for closely spaced analyses such as multipoint transects, where each subsequent analysis overlaps the carbon ring of the previous analysis. X-ray intensity loss due to contamination is most severe for low-overvoltage elements such as Ca K consistent with carbon deposition effectively reducing beam energy. Rates of contamination are calculated and the use of a liquid nitrogen cold trap is shown to greatly reduce the amount of carbon deposited. A complimentary empirical correction is developed to correct for X-ray intensity loss from measured carbon, assuming the carbon is a film, and is compared with corrections derived from thin film calculations. PENELOPE electron probe microanalysis (PENEPMA) calculations confirm that asymmetry of the carbon deposition can be ignored for X-ray energies where intensity loss is predominantly through energy loss of beam electrons. Using a cold trap and/or an empirical correction high spatial resolution analysis (ca. 400 nm between points) is achievable with analytical errors of ca. 1–3%.

The present study characterizes the main deterioration mechanisms affecting the early 17th frescoes of Casa de Fresco, the only known example in Portugal of a semi-underground leisure room richly decorated with a balcony over a water well. Frescoes from the vault are at risk due to salt weathering and biodeterioration. The aim of the research was identification of the deterioration materials, determination of their origin, and their effect on the frescoes before future intervention. Scanning electron microscopy with an energy-dispersive X-ray detector (SEM-EDS) was used to determine salt morphology and microanalysis. The mineralogical characterization was performed by X-ray powder diffraction, complemented with µ-Raman and µ-Fourier transform infrared spectroscopy. Biological assessment was evaluated with optical microscopy and SEM-EDS. Bacterial and fungal isolation and identification were performed using standard culture media and methods according to Bergey’s Manual of Systematic Bacteriology and from the Compendium of Soil Fungi. The results show that Ca and Ca-Mg carbonates from the paint renderings are the predominant salt species affecting the site. Bacterial strains from the genera Bacillus and Pseudomonas and fungal strains from the Cladosporium spp. and Penicillium spp. were isolated in the salt formations, within and between the mortar layers. Azurite, malachite, and smalt paint layers are the most affected by the weathering conditions.

In order to achieve reliable structural characterization by transmission electron microscopy, beam-induced structural changes should be clarified for any target material system. As an example, the movement of heavy adatoms on a thin carbon support has been repeatedly reported under the electron beam while the underlying reason for such motion is still in debate. By applying statistical analysis to the group behavior of gold adatoms, we investigated their motion under different beam conditions and detected features corresponding to beam-induced motion, under typical scanning transmission electron microscopy observation conditions. Our results are consistent with the theoretical prediction proposed by Egerton (2013).

Until recently, the analysis of polymer laminates using infrared microspectroscopy involved the painstaking separation of individual layers by dissection or by obtaining micrometer thin cross-sections. The latter usually requires the expertise of an individual trained in microtomy and even then, the very structure of the laminate could affect the outcome of the spectral results. The recent development of attenuated total internal reflection (ATR) infrared microspectroscopy imaging has provided a new avenue for the analysis of these multilayer structures. This report compares ATR infrared microspectroscopy imaging with conventional transmission infrared microspectroscopy imaging. The results demonstrate that the ATR method offers improved spatial resolution, eliminates a variety of competing optical processes, and requires minimal sample preparation relative to transmission measurements. These advantages were illustrated using a polymer laminate consisting of 11 different layers whose thickness ranged in size from 4–20 μm. The spatial resolution achieved by using an ATR-FTIR (Fourier transform infrared spectroscopy) imaging technique was diffraction limited. Contrast in the ATR images was enhanced by principal component analysis.

By transmission electron microscopy with extended Burgers vector analyses, we demonstrate the edge and screw character of vertical dislocations (VDs) in novel SiGe heterostructures. The investigated pillar-shaped Ge epilayers on prepatterned Si(001) substrates are an attempt to avoid the high defect densities of lattice mismatched heteroepitaxy. The Ge pillars are almost completely strain-relaxed and essentially defect-free, except for the rather unexpected VDs. We investigated both pillar-shaped and unstructured Ge epilayers grown either by molecular beam epitaxy or by chemical vapor deposition to derive a general picture of the underlying dislocation mechanisms. For the Burgers vector analysis we used a combination of dark field imaging and large-angle convergent beam electron diffraction (LACBED). With LACBED simulations we identify ideally suited zeroth and second order Laue zone Bragg lines for an unambiguous determination of the three-dimensional Burgers vectors. By analyzing dislocation reactions we confirm the origin of the observed types of VDs, which can be efficiently distinguished by LACBED. The screw type VDs are formed by a reaction of perfect 60° dislocations, whereas the edge types are sessile dislocations that can be formed by cross-slips and climbing processes. The understanding of these origins allows us to suggest strategies to avoid VDs.

Owing to exceptional heterogeneity in the outcome of invasive breast cancer it is essential to develop highly accurate prognostic tools for effective therapeutic management. Based on this pressing need, we aimed to improve breast cancer prognosis by exploring the prognostic value of tumor histology image analysis. Patient group (n=78) selection was based on invasive breast cancer diagnosis without systemic treatment with a median follow-up of 147 months. Gray-level co-occurrence matrix texture analysis was performed retrospectively on primary tumor tissue section digital images stained either nonspecifically with hematoxylin and eosin or specifically with a pan-cytokeratin antibody cocktail for epithelial malignant cells. Univariate analysis revealed stronger association with metastasis risk by texture analysis when compared with clinicopathological parameters. The combination of individual clinicopathological and texture variables into composite scores resulted in further powerful enhancement of prognostic performance, with an accuracy of up to 90%, discrimination efficiency by the area under the curve [95% confidence interval (CI)] of 0.94 (0.87–0.99) and hazard ratio (95% CI) of 20.1 (7.5–109.4). Internal validation was successfully performed by bootstrap and split-sample cross-validation, suggesting that the models are generalizable. Whereas further validation is needed on an external set of patients, this preliminary study indicates the potential use of primary breast tumor histology texture as a highly accurate, simple, and cost-effective prognostic indicator of distant metastasis risk.

For many cancers, liver metastasis is common and usually indicates poor prognosis. Gastro-enteropancreatic neuroendocrine tumors (GEPNETs) of the midgut are a heterogeneous group of cancers that typically remain asymptomatic until they metastasize to the liver. However, the mechanisms by which these usually indolent cancers establish distal metastasis remain unclear.

To begin to elucidate this process, we performed standard in vitro assays to assess cell motility, transendothelial migration, and invasion using BON cells, a widely used model GEPNET cell line. In addition, transmission electron microscopy was used in combination with a novel ex vivo organ slice xenograft model to reveal ultrastructural details of the initial events of BON cell extravasation and re-distribution within the liver. The ultrastructural resolution of the extravasation process revealed the route, sequence, and time course by which tumor cells migrated from the sinusoidal lumen into the hepatic parenchyma in this organ slice model. Both standard in vitro assays and our organ slice model indicated that tumor cells migrated through the discontinuous sinusoidal endothelium to invade the liver parenchyma.

We report the ultrastructure and 3D transmission electron tomography of collagen fibrils (CFs), proteoglycans (PGs), and microfibrils within the CF of corneas of patients with macular corneal dystrophy (MCD). Three normal corneas and three MCD corneas from three Saudi patients (aged 25, 31, and 49 years, respectively) were used for this study. The corneas were processed for light and electron microscopy studies. 3D images were composed from a set of 120 ultrastructural images using the program “Composer” and visualized using the program “Visuliser Kai”. 3D image analysis of MCD cornea showed a clear organization of PGs around the CF at very high magnification and degeneration of the microfibrils within the CF. Within the MCD cornea, the PG area in the anterior stroma was significantly larger than in the middle and posterior stroma. The PG area in the MCD cornea was significantly larger compared with the PG area in the normal cornea. The CF diameter and inter-fibrillar spacing of the MCD cornea were significantly smaller compared with those of the normal cornea. Ultrastructural 3D imaging showed that the production of unsulfated keratin sulfate (KS) may lead to the degeneration of micro-CFs within the CFs. The effect of the unsulfated KS was higher in the anterior stroma compared with the posterior stroma.

Borrelia burgdorferi sensu lato, the causative agent of Lyme disease, is transmitted to humans through the bite of infected Ixodes spp. ticks. Successful infection of vertebrate hosts necessitates sophisticated means of the pathogen to escape the vertebrates’ immune system. One strategy employed by Lyme disease spirochetes to evade adaptive immunity involves a highly coordinated regulation of the expression of outer surface proteins that is vital for infection, dissemination, and persistence. Here we characterized the expression pattern of bacterial surface antigens using different microscopy techniques, from fluorescent wide field to super-resolution and immunogold-scanning electron microscopy. A fluorescent strain of B. burgdorferi spirochetes was labeled with monoclonal antibodies directed against various bacterial surface antigens. Our results indicate that OspA is more evenly distributed over the surface than OspB and OspC that were present as punctate areas.

This study evaluated the structural and morphological differences between human and bovine primary root canals. Primary human maxillary central incisors (H) (n=9) and primary bovine incisors (B) (n=9) were selected. The roots were sectioned in the vestibular-lingual direction, planed and delimited in cervical, middle, and apical thirds. Tubule density (number of tubules per mm2) and diameter were analyzed by scanning electron microscopy (1,000 and 5,000×) using Image J 1.47 software. Data were submitted to two-way repeated measures ANOVA and Tukey tests (α=0.05). The highest tubule density was observed for B (28.527±1.717 mm2) compared with H (15.931±0.170 mm2) (p<0.01). Regarding root thirds, the cervical third presented a greater tubule density (26.417±11.654 mm2) than the apical third (17.999±5.873 mm2). The diameter of the dentin tubules was not different for cervical (3.50±0.08 µm), middle (3.45±0.30 µm) and apical thirds (3.42±0.33 µm) and substrate (H—3.29±0.14 µm; B—3.63±0.06 µm). It could be concluded that: (1) the radicular dentin structure of human and bovine primary teeth and root thirds differ in terms of the tubule density; (2) the radicular dentin morphology of human and bovine primary teeth and root thirds are similar in terms of the diameter of the dentin tubules.

X-ray fluorescence (XRF) was used to image 40 histological cross-sections of bovine ovaries (n=19), focusing on structures including: antral follicles at different stages of growth or atresia, corpora lutea at three stages of development (II–IV), and capillaries, arterioles, and other blood vessels. This method identified three key trace elements [iron (Fe), zinc (Zn), and selenium (Se)] within the ovarian tissue which appeared to be localized to specific structures. Owing to minimal preprocessing of the ovaries, important high-resolution information regarding the spatial distribution of these elements was obtained with elemental trends and colocalizations of Fe and Zn apparent, as well as the infrequent appearance of Se surrounding the antrum of large follicles, as previously reported. The ability to use synchrotron radiation to measure trace element distributions in bovine ovaries at such high resolution and over such large areas could have a significant impact on understanding the mechanisms of ovarian development. This research is intended to form a baseline study of healthy ovaries which can later be extended to disease states, thereby improving our current understanding of infertility and endocrine diseases involving the ovary.

When will a small or low-contrast feature, such as an embedded second-phase particle, be visible in a scanning transmission electron microscopy (STEM) X-ray map? This work illustrates a computationally inexpensive method to simulate X-ray maps and spectrum images (SIs), based upon the equations of X-ray generation and detection. To particularize the general procedure, an example of nanostructured ferritic alloy (NFA) containing nm-sized Y2Ti2O7 embedded precipitates in ferritic stainless steel matrix is chosen. The proposed model produces physically appearing simulated SI data sets, which can either be reduced to X-ray dot maps or analyzed via multivariate statistical analysis. Comparison to NFA X-ray maps acquired using three different STEM instruments match the generated simulations quite well, despite the large number of simplifying assumptions used. A figure of merit of electron dose multiplied by X-ray collection solid angle is proposed to compare feature detectability from one data set (simulated or experimental) to another. The proposed method can scope experiments that are feasible under specific analysis conditions on a given microscope. Future applications, such as spallation proton–neutron irradiations, core-shell nanoparticles, or dopants in polycrystalline photovoltaic solar cells, are proposed.

Combined tilt- and focal series scanning transmission electron microscopy is a recently developed method to obtain nanoscale three-dimensional (3D) information of thin specimens. In this study, we formulate the forward projection in this acquisition scheme as a linear operator and prove that it is a generalization of the Ray transform for parallel illumination. We analytically derive the corresponding backprojection operator as the adjoint of the forward projection. We further demonstrate that the matched backprojection operator drastically improves the convergence rate of iterative 3D reconstruction compared to the case where a backprojection based on heuristic weighting is used. In addition, we show that the 3D reconstruction is of better quality.