The atomic reconstruction of a misfit dislocation (MD) core causes change in the strain distribution around the core. Several MD cores at the AlSb/GaAs (001) cubic zincblende interface, including a symmetrical glide set Lomer dislocation (LD), a left-displaced glide set LD, a glide set LD with an atomic step, a symmetrical shuffle set LD, and a 60° dislocation pair, were studied using simulated projected potential and aberration-corrected transmission electron microscope images. Image deconvolution was also used to restore structure images from nonoptimum-defocus images. The corresponding biaxial strain maps, εxx (in-plane) and εyy (out-of-plane), were obtained by geometric phase analysis using the GaAs substrate as the reference lattice. The results show that atomic structure characteristics of MD cores can be revealed by the strain maps. The strain maps should be measured from optimum-defocus images or restored structure images. Furthermore, the εxx strain map has been found more accurate than the εyy strain map for MD cores, and the specimen thickness should be below the critical thickness due to the influence of dynamical scattering.

Studies of dislocation density evolution are fundamental to improved understanding in various areas of deformation mechanics. Recent advances in cross-correlation techniques, applied to electron backscatter diffraction (EBSD) data have particularly shed light on geometrically necessary dislocation (GND) behavior. However, the framework is relatively computationally expensive—patterns are typically saved from the EBSD scan and analyzed offline. A better understanding of the impact of EBSD pattern degradation, such as binning, compression, and various forms of noise, is vital to enable optimization of rapid and low-cost GND analysis. This paper tackles the problem by setting up a set of simulated patterns that mimic real patterns corresponding to a known GND field. The patterns are subsequently degraded in terms of resolution and noise, and the GND densities calculated from the degraded patterns using cross-correlation ESBD are compared with the known values. Some confirmation of validity of the computational degradation of patterns by considering real pattern degradation is also undertaken. The results demonstrate that the EBSD technique is not particularly sensitive to lower levels of binning and image compression, but the precision is sensitive to Poisson-type noise. Some insight is also gained concerning effects of mixed patterns at a grain boundary on measured GND content.

High-quality color output from digital photocopiers and laser printers is in strong demand, motivating attempts to achieve fine dot reproducibility and stability. The resolution of a digital photocopier depends on the charge density distribution on the organic photoconductor surface; however, directly measuring the charge density distribution is impossible. In this study, we propose a new electron optical instrument that can rapidly measure the electrostatic latent image on an organic photoconductor surface, which is a dielectric surface, as well as a novel method to quantitatively estimate the charge density distribution on a dielectric surface by combining experimental data obtained from the apparatus via a computer simulation. In the computer simulation, an improved three-dimensional boundary charge density method (BCM) is used for electric field analysis in the vicinity of the dielectric material with a charge density distribution. This method enables us to estimate the profile and quantity of the charge density distribution on a dielectric surface with a resolution of the order of microns. Furthermore, the surface potential on the dielectric surface can be immediately calculated using the obtained charge density. This method enables the relation between the charge pattern on the organic photoconductor surface and toner particle behavior to be studied; an understanding regarding the same may lead to the development of a new generation of higher resolution photocopiers.

We report on the mitigation of curtaining artifacts during transmission electron microscopy (TEM) lamella preparation by means of a modified ion beam milling approach, which involves altering the incident angle of the Ga ions by rocking of the sample on a special stage. We applied this technique to TEM sample preparation of a state-of-the-art integrated circuit based on a 14-nm technology node. Site-specific lamellae with a thickness <15 nm were prepared by top-down Ga focused ion beam polishing through upper metal contacts. The lamellae were analyzed by means of high-resolution TEM, which showed a clear transistor structure and confirmed minimal curtaining artifacts. The results are compared with a standard inverted thinning preparation technique.

The evolution of the energy dispersive spectrometer (EDS) from the lithium-drifted silicon detector [Si(Li)] to the silicon drift detector (SDD) has created new opportunities in the field of electron probe X-ray microanalysis. The SDD permits operation at significantly higher count rates than the Si(Li) and also provides a more stable energy scale. X-ray spectra captured by EDS can now be analyzed qualitatively or quantitatively under the same beam conditions as used for wavelength dispersive spectrometry (WDS). Standards-based quantitative EDS (SB-Quant-EDS) can thus provide analyses that are accurate and precise for an ever growing number of materials measurement problems. In this study, we analyze NIST research glasses with “known” nominal concentrations of titanium (Ti) and vanadium (V) to evaluate the external reproducibility of the SB-Quant-EDS technique in the presence of severe peak overlaps. We additionally analyze several naturally occurring oxide minerals by WDS and EDS simultaneously and evaluate the outputs of these two methods when quantifying the same analytical volume within the sample.

When using bifunctional core@shell catalysts, the stability of both the shell and core–shell interface is crucial for catalytic applications. In the present study, we elucidate the stability of a CuO/ZnO/Al2O3@ZSM-5 core@shell material, used for one-stage synthesis of dimethyl ether from synthesis gas. The catalyst stability was studied in a hierarchical manner by complementary environmental transmission electron microscopy (ETEM), scanning electron microscopy (SEM) and in situ hard X-ray ptychography with a specially designed in situ cell. Both reductive activation and reoxidation were applied. The core–shell interface was found to be stable during reducing and oxidizing treatment at 250°C as observed by ETEM and in situ X-ray ptychography, although strong changes occurred in the core on a 10 nm scale due to the reduction of copper oxide to metallic copper particles. At 350°C, in situ X-ray ptychography indicated the occurrence of structural changes also on the µm scale, i.e. the core material and parts of the shell undergo restructuring. Nevertheless, the crucial core–shell interface required for full bifunctionality appeared to remain stable. This study demonstrates the potential of these correlative in situ microscopy techniques for hierarchically designed catalysts.

With the development of affordable aberration correctors, analytical scanning transmission electron microscopy (STEM) studies of complex interfaces can now be conducted at high spatial resolution at laboratories worldwide. Energy-dispersive X-ray spectroscopy (EDS) in particular has grown in popularity, as it enables elemental mapping over a wide range of ionization energies. However, the interpretation of atomically resolved data is greatly complicated by beam–sample interactions that are often overlooked by novice users. Here we describe the practical factors—namely, sample thickness and the choice of ionization edge—that affect the quantification of a model perovskite oxide interface. Our measurements of the same sample, in regions of different thickness, indicate that interface profiles can vary by as much as 2–5 unit cells, depending on the spectral feature. This finding is supported by multislice simulations, which reveal that on-axis maps of even perfectly abrupt interfaces exhibit significant delocalization. Quantification of thicker samples is further complicated by channeling to heavier sites across the interface, as well as an increased signal background. We show that extreme care must be taken to prepare samples to minimize channeling effects and argue that it may not be possible to extract atomically resolved information from many chemical maps.

Ceramic matrix composites (CMCs) are structural materials, which have useful properties that combine high strength at high temperatures with moderate toughness. Carbon fibers within a matrix of carbon and silicon carbide, called C/C–SiC, are a particular class of CMC noted for their high oxidation resistance. Here we use a combination of four-point bending and X-ray radiography, to study the mechanical failure of C/C-SiC CMCs. Correlating X-ray radiographic and load/displacement curve data reveals that the fiber bundles act to slow down crack propagation during four-point bending tests. We attribute this to the fact that strain energy is expended in breaking these fibers and in pulling fiber bundles out of the surrounding matrix material. In addition, we find that the local distribution and concentration of SiC plays an important role in reducing the toughness of the material.

The identification and accurate characterization of discrete grains of rare minerals in sulfide base-metal ores is usually a cumbersome procedure due to the small grain sizes (typically <10 μm) and complex mineral assemblages in the material. In this article, a new strategy for finding and identifying indium minerals, and quantifying their composition and abundance is presented, making use of mineral liberation analysis (MLA) and electron probe microanalysis (EPMA). The method was successfully applied to polymetallic massive sulfide ores from the Neves-Corvo deposit in Portugal. The presence of roquesite and sakuraiite could be systematically detected, their concentration quantified by MLA measurements, and their identity later confirmed by EPMA analyses. Based on these results, an almost complete indium deportment could be obtained for the studied samples. This validates the approach taken, combining automated mineralogy data with electron microprobe analysis. A similar approach could be used to find minerals of other common minor and trace elements in complex base-metal sulfide ores, for example Se, Ge, Sb, or Ag, thus permitting the targeted development of resource technologies suitable for by-product recovery.

The use of in vivo X-ray microcomputed tomography (μCT) to study plant root systems has become routine, but is often hampered by poor contrast between roots, soil, soil water, and soil organic matter. In clinical radiology, imaging of poorly contrasting regions is frequently aided by the use of radio-opaque contrast media. In this study, we present evidence for the utility of iodinated contrast media (ICM) in the study of plant root systems using μCT. Different dilutions of an ionic and nonionic ICM (Gastrografin 370 and Niopam 300) were perfused into the aerial vasculature of juvenile pea plants via a leaf flap (Pisum sativum). The root systems were imaged via μCT, and a variety of image-processing approaches used to quantify and compare the magnitude of the contrast enhancement between different regions. Though the treatment did not appear to significantly aid extraction of full root system architectures from the surrounding soil, it did allow the xylem and phloem units of seminal roots and the vascular morphology within rhizobial nodules to be clearly visualized. The nonionic, low-osmolality contrast agent Niopam appeared to be well tolerated by the plant, whereas Gastrografin showed evidence of toxicity. In summary, the use of iodine-based contrast media allows usually poorly contrasting root structures to be visualized nondestructively using X-ray μCT. In particular, the vascular structures of roots and rhizobial nodules can be clearly visualized in situ.

Statoliths are the only hard structures in the gelatinous bell of most scyphozoan medusae and investigations on these structures could promote investigations of the understudied population dynamics and phylogeny of jellyfish. We examined the statoliths of Aurelia aurita jellyfish of different ages by light microscopic and microtomographic measurements supplemented by scanning electron microscopy. The morphometric analyses confirmed that statolith numbers and sizes increase during jellyfish development and revealed that newly-formed statoliths had similar shapes that may change during statolith growth. Nevertheless, most statoliths had a typical compact rod shape with an aspect ratio of 1–2.5 at all ages and we suggest that the composition of statolith shapes may be taxa specific. We developed a new approach allowing exact measurements of statolith growth for the first time. The application of calcein as a fluorescent marker resulted in clear fluorescent lines within the statoliths, allowing calculations of the statolith side face growth increments (0.1 µm/day; n=252). A single-crystal analysis revealed that the calcein incubation did not affect the statolith crystal structure. In conclusion, calcein labeling is an excellent method to follow the growth of bassanite statoliths.

Accurate and fast quantitative analysis of living cells from fluorescence microscopy images is useful for evaluating experimental outcomes and cell culture protocols. An algorithm is developed in this work to automatically segment and distinguish apoptotic cells from normal cells. The algorithm involves three steps consisting of two segmentation steps and a classification step. The segmentation steps are: (i) a coarsesegmentation, combining a range filter with a marching square method, is used as a prefiltering step to provide the approximate positions of cells within a two-dimensional matrix used to store cells’ images and the count of the number of cells for a given image; and (ii) a fine segmentation step using the Active Contours Without Edges method is applied to the boundaries of cells identified in the coarse segmentation step. Although this basic two-step approach provides accurate edges when the cells in a given image are sparsely distributed, the occurrence of clusters of cells in high cell density samples requires further processing. Hence, a novel algorithm for clusters is developed to identify the edges of cells within clusters and to approximate their morphological features. Based on the segmentation results, a support vector machine classifier that uses three morphological features: the mean value of pixel intensities in the cellular regions, the variance of pixel intensities in the vicinity of cell boundaries, and the lengths of the boundaries, is developed for distinguishing apoptotic cells from normal cells. The algorithm is shown to be efficient in terms of computational time, quantitative analysis, and differentiation accuracy, as compared with the use of the active contours method without the proposed preliminary coarse segmentation step.

Lithotripsy methods show relatively low efficiency in the fragmentation of sialoliths compared with the success rates achieved in the destruction of renal calculi. However, the information available on the mechanical behavior of sialoliths is limited and their apparently tougher response is not fully understood. This work evaluates the hardness and Young’s modulus of sialoliths at different scales and analyzes specific damage patterns induced in these calcified structures by ultrasonic vibrations, pneumoballistic impacts, shock waves, and laser ablation. A clear correlation between local mechanical properties and ultrastructure/chemistry has been established: sialoliths are composite materials consisting of hard and soft components of mineralized and organic nature, respectively. Ultrasonic and pneumoballistic reverberations damage preferentially highly mineralized regions, leaving relatively unaffected the surrounding organic matter. In contrast, shock waves leach the organic component and lead to erosion of the overall structure. Laser ablation destroys homogeneously the irradiated zones regardless of the mineralized/organic nature of the underlying ultrastructure; however, damage is less extensive than with mechanical methods. Overall, the present results show that composition and internal structure are key features behind sialoliths’ comminution behavior and that the organic matter contributes to reduce the therapeutic efficiency of lithotripsy methods.

As erythrocyte and estrogens interact so closely and erythrocytes can indicate the healthiness of an individual, it is essential to investigate the effects of natural estrogens as well as synthetic estrogens on these cells. Whole blood samples were used for thromboelastography (TEG), light microscopy (LM), and scanning electron microscopy (SEM) investigation. Viscoelastic investigation with TEG revealed that estrogens affected the rate of clot formation without any significant effect on the strength or stability of the clot. Axial ratio analysis with LM showed a statistically significant increase in number of erythrocytes with decreased roundness. Morphological analysis with SEM confirmed the change in erythrocyte shape and revealed both ultrastructural membrane changes and erythrocyte interactions. As erythrocyte shape and membrane flexibility correlates to physiological functioning of these cells in circulation, these changes, indicative of possible eryptosis brought on by estrogens, when experienced by individuals with an underlying inflammatory or hematological illness, could impair erythrocyte functioning and even result in obstructions in circulation. In conclusion, we suggest that whole blood analysis with viscoelastic and morphological techniques could be used as assessment of the hematological healthiness of individuals using estrogens.

Combined oral contraceptive (COC) use is a risk factor for venous thrombosis (VT) and related to the specific type of progestin used. VT is accompanied by inflammation and pathophysiological clot formation, that includes aberrant erythrocytes and fibrin(ogen) interactions. In this paper, we aim to determine the influence of progesterone and different synthetic progestins found in COCs on the viscoelasticity of whole blood clots, as well as erythrocyte morphology and membrane ultrastructure, in an in vitro laboratory study. Thromboelastography (TEG), light microscopy, and scanning electron microscopy were our chosen methods. Our results point out that progestins influence the rate of whole blood clot formation. Alterations to erythrocyte morphology and membrane ultrastructure suggest the presence of eryptosis. We also note increased rouleaux formation, erythrocyte aggregation, and spontaneous fibrin formation in whole blood which may explain the increased risk of VT associated with COC use. Although not all COC users will experience a thrombotic event, individuals with a thrombotic predisposition, due to inflammatory or hematological illness, should be closely monitored to prevent pathological thrombosis.

Secondary fluorescence, the final term in the familiar matrix correction triumvirate Z·A·F, is the most challenging for Monte Carlo models to simulate. In fact, only two implementations of Monte Carlo models commonly used to simulate electron probe X-ray spectra can calculate secondary fluorescence—PENEPMA and NIST DTSA-IIa (DTSA-II is discussed herein). These two models share many physical models but there are some important differences in the way each implements X-ray emission including secondary fluorescence. PENEPMA is based on PENELOPE, a general purpose software package for simulation of both relativistic and subrelativistic electron/positron interactions with matter. On the other hand, NIST DTSA-II was designed exclusively for simulation of X-ray spectra generated by subrelativistic electrons. NIST DTSA-II uses variance reduction techniques unsuited to general purpose code. These optimizations help NIST DTSA-II to be orders of magnitude more computationally efficient while retaining detector position sensitivity. Simulations execute in minutes rather than hours and can model differences that result from detector position. Both PENEPMA and NIST DTSA-II are capable of handling complex sample geometries and we will demonstrate that both are of similar accuracy when modeling experimental secondary fluorescence data from the literature.

The Monte Carlo program PENEPMA performs simulations of X-ray emission from samples bombarded with both electron and photon beams. It is based on the general-purpose Monte Carlo simulation package PENELOPE, an elaborate system for the simulation of coupled electron-photon transport in arbitrary materials, and on the geometry subroutine package PENGEOM, which tracks particles through complex material structures defined by quadric surfaces. After a brief description of the interaction models implemented in the simulation subroutines and of the structure and operation of PENEPMA, we provide an overview of the capabilities of the program along with several examples of its application to the modeling of electron probe microanalysis measurements.

Diffuse rings from amorphous materials sit on a steep background resulting in a monotonically decreasing intensity over scattering vector length, frequently with no clear local maximum that could be used to determine the center of the ring. The novelty of the method reported here is that it successful processes such weak patterns. It is based on separating the angular dependence of the positions of the maxima on the azimuthal angle in the measured two-dimensional pattern for a manually preselected peak. Both pattern center and elliptical distortion are simultaneously refined from this angular dependence. Both steps are based on nonlinear least square fitting, using the Levenberg–Marquardt method. It can be successfully applied to any amorphous patterns provided they were recorded with experimental conditions that facilitate dividing them into sectors with acceptable statistics. Patterns with the center shifted to the camera corner (recording a quadrant of a ring) can also be reliably evaluated, keeping precalibrated values of the elliptical distortion fixed during the fit. Finally, the limited number of counts in any pattern is overcome by cumulating many patterns (from equivalent areas) into a single pattern. Eliminating false effects is facilitated by masking out unwanted parts of any recorded pattern from processing.

Essentially all biological processes are highly dependent on the nanoscale architecture of the cellular components where these processes take place. Statistical measures, such as the autocorrelation function (ACF) of the three-dimensional (3D) mass–density distribution, are widely used to characterize cellular nanostructure. However, conventional methods of reconstruction of the deterministic 3D mass–density distribution, from which these statistical measures can be calculated, have been inadequate for thick biological structures, such as whole cells, due to the conflict between the need for nanoscale resolution and its inverse relationship with thickness after conventional tomographic reconstruction. To tackle the problem, we have developed a robust method to calculate the ACF of the 3D mass–density distribution without tomography. Assuming the biological mass distribution is isotropic, our method allows for accurate statistical characterization of the 3D mass–density distribution by ACF with two data sets: a single projection image by scanning transmission electron microscopy and a thickness map by atomic force microscopy. Here we present validation of the ACF reconstruction algorithm, as well as its application to calculate the statistics of the 3D distribution of mass–density in a region containing the nucleus of an entire mammalian cell. This method may provide important insights into architectural changes that accompany cellular processes.

Cytological responses in different organs of sentinel organisms have proven to be useful tools for characterizing the health status of those organisms and assessing the impact of environmental contaminants. Our study shows that nickel (II) accumulated in both germ cells (oogonia and developing oocytes) and somatic cells (muscle cells, follicle cells) in the Astacus leptodactylus ovary. Muscle cells from ovarian wall show disorganization and the disruption of cytoplasmic microtubules and pyknosis of the cell nucleus. Follicle cells, both those that surround the developing oocytes and also those that are not associated with the oocytes contained within the cytoplasm vacuoles of different sizes, degenerated mitochondria, myelin bodies, disorganized microtubules, and pyknotic nuclei. The most evident pathological phenomenon was the alteration and disorganization of the basal matrix, which separates the ovarian interstitium from ovarian follicles compartment. Exposure to nickel induces cytoplasmic vacuolation in oogonia and developing oocytes, structural alteration of the developing yolk granules and condensation of the nucleoli. Ultrastructural autometallography has shown grains of silver-enhanced nickel inside the cytoplasm of the muscle cells with altered morphology, including the cytoplasm, nucleus, and basal matrix of the follicle cells, and in intracisternal granules and developing yolk granules of the oocytes.