We present a new analytical method, which allows the simultaneous analysis of fluorine (F), chlorine (Cl), bromine (Br), and iodine (I) in geological samples. To account for interferences of Fe on the spectral lines of F, of Al on Br-lines, and of Ca on I-lines, we prepared four new halogen-free calibration glasses. The new method is used to analyze various glass reference materials and crystal-hosted melt inclusions from the Azores. Our results show that our new method allows reliable and reproducible analyses of all four halogens in silicate glasses.

With the wide application of ultra-microtome sectioning in the preparation of transmission electron microscopy (TEM) specimens with bio- and organic materials, here, we report an ultra-microtome-based method for the preparation of TEM specimens from cathodes of Li-ion batteries. The ultra-microtome sectioning reduces the sample thickness to tens of nanometers and yields atomic resolution from the core region of particles of hundreds of nanometers. Analysis indicates that the mechanical cross-sectioning introduces no observable microstructural artifacts or structural damage, such as microcracking and nanoporosity. These results demonstrate the high efficiency of the ultra-microtome approach in preparing well-thinned specimens of particulate materials that allow for atomic-scale TEM imaging of a large number of sectioned particles in one single TEM specimen, thereby providing statistically significant results of the TEM analysis.

The phase transition in the melting of Sn–Bi eutectic solder alloy particles was observed by in situ hard X-ray ptychographic coherent diffraction imaging with a pin-point heating system. Ptychographic diffraction patterns of micrometer-sized Sn–Bi particles were collected at temperatures from room temperature to 540 K. The projection images of each particle were reconstructed at a spatial resolution of 25 nm, showing differences in the phase shifts due to two crystal phases in the Sn–Bi alloy system and the Sn/Bi oxides at the surface. By quantitatively evaluating the Bi content, it became clear that the nonuniformity of the composition of Sn and Bi at the single-particle level exists when the particles are synthesized by centrifugal atomization.

The effects of trace Ca and Sr addition on dynamic precipitates, dynamic recrystallization (DRX) behavior, and texture evolution of Mg–5Zn alloy sheets fabricated by high strain rate rolling (HSRR) were investigated by electron backscattered diffraction (EBSD), transmission electron microscopy (TEM), small-angle X-ray scattering (SAXS), and X-ray diffraction (XRD). The Zn-rich precipitates formed with plate shapes, short-rod shapes, and near-spherical shapes, indicating that the most important function of adding Ca and Sr is to promote the precipitation process. The precipitate density increases, but the precipitate size and DRX volume fraction decrease with the addition of the alloying elements. It is concluded that the effects of combined Ca/Sr addition on promoting precipitation and refining precipitate size are more effective than that of single Ca addition, and the reduction in DRX volume fraction can be attributed to the inhibition of fine precipitation on the nucleation and growth of DRX. Moreover, the macro-texture intensity is mainly related to DRX as the DRX grains are much more randomly oriented than deformed grains. In addition, the texture intensity in DRX regions is primarily associated with the precipitates, which can inhibit DRX grain rotation due to their pinning effect on the grain boundaries.

One of the limiting factors for the analysis of minor elements in multiphase materials by electron probe microanalysis is the effect of secondary fluorescence (SF), which is not accounted for by matrix corrections. Although the apparent concentration due to SF can be calculated numerically or measured experimentally, detailed investigations of this effect for fine-grained materials are scarce. In this work, we use the Monte Carlo simulation program PENEPMA to examine and correct the effect of SF affecting micron-sized mineral inclusions hosted by other minerals. A concentration profile across an olivine [(Mg,Fe)2SiO4] inclusion in chromite (Fe2+Cr2O4) is measured and used to assess the reliability of calculations, where different boundary geometries are examined. Three application examples are presented, which include the determination of Cr in olivine and serpentine [Mg3Si2O5(OH)4] inclusions hosted by chromite and of Fe in quartz (SiO2) inclusions hosted by almandine garnet (Fe3Al2Si3O12). Our results show that neglecting SF leads to concentrations that are overestimated by ~0.1–0.8 wt%, depending on inclusion size. In addition, assuming a straight boundary yields to an underestimation of SF effects by a factor of ~2–4. Because its long-range nature, SF severely compromises trace element analyses even for phases as large as 1 mm in size.

Hydrocarbon contamination plagues high-resolution and analytical electron microscopy by depositing carbonaceous layers onto surfaces during electron irradiation, which can render carefully prepared specimens useless. Increased specimen thickness degrades resolution with beam broadening alongside loss of contrast. The large inelastic cross-section of carbon hampers accurate atomic species detection. Oxygen and water molecules pose problems of lattice damage by chemically etching the specimen during imaging. These constraints on high-resolution and spectroscopic imaging demand clean, high-vacuum microscopes with dry pumps. Here, we present an open-hardware design of a high-vacuum manifold for transmission electron microscopy (TEM) holders to mitigate hydrocarbon and residual species exposure. We quantitatively show that TEM holders are inherently dirty and introduce a range of unwanted chemical species. Overnight storage in our manifold reduces contaminants by one to two orders of magnitude and promotes two to four times faster vacuum recovery. A built-in bakeout system further reduces contaminants partial pressure to below 10−10 hPa (Torr) (approximately four orders of magnitude down from ambient storage) and alleviates monolayer adsorption during a typical TEM experiment. We determine that bakeout of TEM holder with specimen held therein is the optimal cleaning method. Our high-vacuum manifold design is published with open-source blueprints, parts, and cost list.

In this work, a new method to determine and correct the linear drift for any crystalline orientation in a single-column-resolved high-resolution scanning transmission electron microscopy (HR-STEM) image, which is based on angle measurements in the Fourier space, is presented. This proposal supposes a generalization and the improvement of a previous work that needs the presence of two symmetrical planes in the crystalline orientation to be applicable. Now, a mathematical derivation of the drift effect on two families of asymmetric planes in the reciprocal space is inferred. However, though it was not possible to find an analytical solution for all conditions, a simple formula was derived to calculate the drift effect that is exact for three specific rotation angles. Taking this into account, an iterative algorithm based on successive rotation/drift correction steps is devised to remove drift distortions in HR-STEM images. The procedure has been evaluated using a simulated micrograph of a monoclinic material in an orientation where all the reciprocal lattice vectors are different. The algorithm only needs four iterations to resolve a 15° drift angle in the image.

The selection of the correct convergence angle is essential for achieving the highest resolution imaging in scanning transmission electron microscopy (STEM). The use of poor heuristics, such as Rayleigh's quarter-phase rule, to assess probe quality and uncertainties in the measurement of the aberration function results in the incorrect selection of convergence angles and lower resolution. Here, we show that the Strehl ratio provides an accurate and efficient way to calculate criteria for evaluating the probe size for STEM. A convolutional neural network trained on the Strehl ratio is shown to outperform experienced microscopists at selecting a convergence angle from a single electron Ronchigram using simulated datasets. Generating tens of thousands of simulated Ronchigram examples, the network is trained to select convergence angles yielding probes on average 85% nearer to optimal size at millisecond speeds (0.02% of human assessment time). Qualitative assessment on experimental Ronchigrams with intentionally introduced aberrations suggests that trends in the optimal convergence angle size are well modeled but high accuracy requires a high number of training datasets. This near-immediate assessment of Ronchigrams using the Strehl ratio and machine learning highlights a viable path toward the rapid, automated alignment of aberration-corrected electron microscopes.

This study aimed to develop and evaluate a blind-deconvolution framework using the alternating direction method of multipliers (ADMMs) incorporated with weighted L1-norm regularization for light microscopy (LM) images. A presimulation study was performed using the Siemens star phantom prior to conducting the actual experiments. Subsequently, the proposed algorithm and a total generalized variation-based (TGV-based) method were applied to cross-sectional images of a mouse molar captured at 40× and 400× on-microscope magnifications and the results compared, and the resulting images were compared. Both simulation and experimental results confirmed that the proposed deblurring algorithm effectively restored the LM images, as evidenced by the quantitative evaluation metrics. In conclusion, this study demonstrated that the proposed deblurring algorithm can efficiently improve the quality of LM images.

We report an approach to expand the effective number of pixels available to small, two-dimensional electron detectors. To do so, we acquire subsections of a diffraction pattern that are then accurately stitched together in post-processing. Using an electron microscopy pixel array detector (EMPAD) that has only 128 × 128 pixels, we show that the field of view can be expanded while achieving high reciprocal-space sampling. Further, we highlight the need to properly account for the detector position (rotation) and the non-orthonormal diffraction shift axes to achieve an accurate reconstruction. Applying the method, we provide examples of spot and convergent beam diffraction patterns acquired with a pixelated detector.

Fast pixelated detectors incorporating direct electron detection (DED) technology are increasingly being regarded as universal detectors for scanning transmission electron microscopy (STEM), capable of imaging under multiple modes of operation. However, several issues remain around the post-acquisition processing and visualization of the often very large multidimensional STEM datasets produced by them. We discuss these issues and present open source software libraries to enable efficient processing and visualization of such datasets. Throughout, we provide examples of the analysis methodologies presented, utilizing data from a 256 × 256 pixel Medipix3 hybrid DED detector, with a particular focus on the STEM characterization of the structural properties of materials. These include the techniques of virtual detector imaging; higher-order Laue zone analysis; nanobeam electron diffraction; and scanning precession electron diffraction. In the latter, we demonstrate a nanoscale lattice parameter mapping with a fractional precision ≤6 × 10−4 (0.06%).

We describe a method to estimate background noise in atom probe tomography (APT) mass spectra and to use this information to enhance both background correction and quantification. Our approach is mathematically general in form for any detector exhibiting Poisson noise with a fixed data acquisition time window, at voltages varying through the experiment. We show that this accurately estimates the background observed in real experiments. The method requires, as a minimum, the z-coordinate and mass-to-charge-state data as input and can be applied retrospectively. Further improvements are obtained with additional information such as acquisition voltage. Using this method allows for improved estimation of variance in the background, and more robust quantification, with quantified count limits at parts-per-million concentrations. To demonstrate applications, we show a simple peak detection implementation, which quantitatively suppresses false positives arising from random noise sources. We additionally quantify the detectability of 121-Sb in a standardized-doped Si microtip as (1.5 × 10−5, 3.8 × 10−5) atomic fraction, α = 0.95. This technique is applicable to all modes of APT data acquisition and is highly general in nature, ultimately allowing for improvements in analyzing low ionic count species in datasets.

Symmetry is omnipresent in nature and we encounter symmetry routinely in our everyday life. It is also common on the microscopic level, where symmetry is often key to the proper function of core biological processes. The human brain is exquisitely well suited to recognize such symmetrical features with ease. In contrast, computational recognition of such patterns in images is still surprisingly challenging. In this paper we describe a mathematical approach to identifying smaller local symmetrical structures within larger images. Our algorithm attributes a local symmetry score to each image pixel, which subsequently allows the identification of the symmetrical centers of an object. Though there are already many methods available to detect symmetry in images, to the best of our knowledge, our algorithm is the first that is easily applicable in ImageJ/FIJI. We have created an interactive plugin in FIJI that allows the detection and thresholding of local symmetry values. The plugin combines the different reflection symmetry axis of a square to get a good coverage of reflection symmetry in all directions. To demonstrate the plugins potential, we analyzed images of bacterial chemoreceptor arrays and intracellular vesicle trafficking events, which are two prominent examples of biological systems with symmetrical patterns.

Combined oral contraceptives (COCs) are commonly prescribed and increase the risk of venous thromboembolism (VTE). We have previously found that two COCs, both containing drospirenone (DRSP) and ethinyl estradiol (EE), cause spontaneous fibrin formation in whole blood. The aim of this study was, therefore, to use platelet-poor plasma (PPP) from the same cohort of DRSP/EE users to determine the impact of these COCs on the fibrin component, specifically the fibrin clot viscoelasticity, turbidimetry, and biophysical traits. PPP from 25 females per test group and a control group (n = 25) were analyzed using thromboelastography (TEG), turbidimetry, and scanning electron microscopy. The results highlight abnormal fibrin clot formation, lysis, and architecture; DRSP/20EE showed the greatest effect. DRSP/EE use increased the fibrin fiber diameter and showed dense matted clots. Only when the influence of COCs on the structural properties and behavior of fibrin fibers during thrombus formation and lysis is better understood are we able to predict and prevent coagulopathies associated with these synthetic hormones. Clinical practitioners should take this into consideration for female patients that either have comorbidities, which could burden the coagulation system, or may be exposed to external factors that could increase their risk for VTE.

Down syndrome (DS) is a genetically based disease caused by triplication of chromosome 21. DS is characterized by severe muscle weakness associated with motor deficits; however, understanding the DS-associated skeletal muscle condition is limited. In this study, we used a combined methodological approach involving light and electron microscopy, as well as nuclear magnetic resonance spectroscopy metabolomics, to investigate morphology and composition of the quadriceps muscles in the Ts65Dn mouse, a model of DS, to identify structural and/or functional trisomy-associated alterations. Morphometric analysis demonstrated a larger size of myofibers in trisomic versus euploid mice; however, myofibrils were thinner and contained higher amounts of mitochondria and lipid droplets. In trisomic mice, magnetic resonance spectroscopy showed a tendency to an overall increase in muscle metabolites involved in protein synthesis. These data strongly suggest that in DS, a sarcoplasmic hypertrophy associated with myofibril loss characterizes quadriceps myofibers. In addition, large-sized mitochondria suggestive of impaired fission/fusion events, as well as metabolites modifications suggestive of decreased mitochondrial function, were found in the trisomic muscle. Albeit preliminary, the results provided by this novel approach consistently indicate structural and compositional alterations of the DS skeletal muscle, which are typical of early aging.

The vascular and perivascular cells, including telocytes (TCs) and immune cells, play an important role in male fertility. The current study intended to describe in detail the microvascular structures harboring special regulatory devices in addition to the interstitial cellular components of the one-humped camel epididymis. The samples were collected from 10 clinically healthy mature camels (Camelus dromedarius). The distribution and characteristics of TCs, peripheral blood vessels of the epididymis, and immune cells were investigated using the light, immunohistochemistry, immunofluorescence, and transmission electron microscopy analyses. Frequent occlusive or throttle arterioles were demonstrated in the epididymal interstitium and their tunica media consisted of glomus cells. In addition, some vein walls consisted of one or two layers of glomus cells. TCs, fibroblasts, muscle cells, and tunica media of the blood vessels, that present in the loose connective tissue surrounding the intertubular interstitium of camel epididymis, showed a positive reaction with vimentin. The endothelium of blood vessels and veins showed positive immunoreactivity for CD34 and vascular endothelial growth factor (VEGF). Furthermore, VEGF, CD34, and S100 proteins were expressed in dendritic cells (DCs) as well as TCs. The current data suggest the involvement of DCs and TCs in angiogenesis and a possible role for the interstitial components in creating an appropriate milieu for the full maturation of sperms.

The current study aimed to characterize different stages of rodlet cells using light microscopy, immunohistochemistry, and transmission electron microscopy. Granular rodlet cells have a distinct granular cytoplasm. Transitional rodlet cells had distinct capsules, and immature granules. Mature rodlet cells were pear-shaped and had elongated granules. Ruptured rodlet cells had a granular cytoplasm. The affinity of rodlet cells for different histochemical techniques was detected. Immunohistochemical analysis of rodlet cells for stem cell markers such as CD117, CD34, proliferation marker, proliferating cell nuclear antigen (PCNA), endopeptidase activity; matrix metalloproteinase-9 (MPP-9) and the angiogenic factor; vascular endothelial growth factor (VEGF) was investigated. All stages of rodlet cells were expressed CD117. However, the ruptured stage was CD117-negative. The granular, transitional, and mature stages had strong CD34 immunoaffinity, while the ruptured rodlet cells were CD34-negative. The most potent immunoreactivity for PCNA was the granular rodlet cells. The transitional cells exhibited less immunoreactivity, while mature rodlet cells had no immunoaffinity for PCNA. All stages of rodlet cells had high enzyme activity as indicated by Acridine orange and exhibited strong MPP-9 immunoaffinity. VEGF is mostly expressed by granular, transitional, and mature rodlet cells. In conclusion, rodlet cells relatively had stemness properties, endopeptidase activity, express a proliferation marker, and angiogenic factors. We suggest a potential role of rodlet cells in immune defense.

The aim of this in vitro study was to present a method using confocal laser scanning microscopy for three-dimensional analysis of human dental enamel subjected to ceramic bracket debonding. The labial enamel surfaces of three upper central incisors were prepared and mounted in the form of standardized specimens. A sample repositioning protocol was established to enable surface measurement and analysis before and after bracket debonding. Observations were made of representative areas measuring 1,280 × 1,280 μm2, in the center of the enamel samples, as well as of the total topography (2,500 × 3,500 μm) of the bonding areas provided by the equipment software. Noncontact three-dimensional high-resolution image analyses revealed the capabilities of the employed technique and methodology to permit the examination of specific characteristics and alterations on the surfaces, before and after the debonding and finishing procedures. The new protocol was effective to provide qualitative and quantitative assessments of changes on the same dental surfaces at different trial times. The methodology constitutes a feasible tool for revealing the effects of debonding of ceramic brackets on sound and previously injured dental enamel surfaces.