Metal chalcogenides have attracted great attention because of their broad applications. It has been well acknowledged that microstructure can alter the intrinsic properties and performance of metal chalcogenides. The structure–property–performance relationships can be investigated at atomic scale with scanning transmission and transmission electron microscopy (STEM and TEM). Nevertheless, careful specimen preparation is paramount for accurate analyses and interpretations. In this work, we compare the effects of a variety of well-established TEM specimen preparation methods on the observed microstructure of an ingot stoichiometric lead telluride (PbTe). Most importantly, from aberration corrected STEM and first principles calculations, we discovered that argon (Ar) ion milling can lead to surface irradiation damage in the form of Pb vacancy clusters and self-interstitial atom (SIA) clusters. The SIA clusters appear as orthogonal nanoscale features when characterized along the <001> crystal orientation of the rock salt structured PbTe. This obfuscates the interpretation of the intrinsic microstructure of metal chalcogenides, especially lead chalcogenides. We demonstrate that with sufficiently low energy (300 eV) Ar ion cleaning or appropriate high-temperature annealing, the surface damage layer can be properly cleaned and the orthogonal nanoscale features are significantly reduced. This reveals the materials’ intrinsic structure and can be used as the standard protocol for future TEM specimen preparation of lead-based chalcogenide materials.

Binary Fe–Cu alloys are effective prototypes for investigating radiation-induced formation and growth of nanometric Cu-rich precipitates (CRPs) in nuclear reactor pressure vessels. In this report, the temporal evolution of CRPs during thermal aging of Fe–Cu binary alloys has been investigated by using complementary techniques such as atom probe tomography (APT) and small-angle neutron scattering (SANS). We report a detailed quantitative evolution of a rarely observed morphological transformation of Cu precipitates from spherical to ellipsoid with a significant change (approximately two times) in aspect ratio, an effect known to be associated with the 9R-3R structural transition of the precipitates. It is demonstrated through APT that the precipitates remain spherical up to 8 h, however, they subsequently convert to oblate ellipsoid upon further aging. SANS analysis also detected signs of this morphological transition in reciprocal space. Furthermore, SANS quantifies evolution of the precipitates and corroborates well with the APT results. Interestingly, the power-law exponent of the temporal evolution for mean size and number density agree reasonably well with the Lifshitz–Slyozov–Wagner model, in spite of the complex morphological evolution of the precipitates.

Silicon dioxide (SiO2) has been the most important insulator in the highly-developed field of silicon (Si) technology. Accurate pitch and gate linewidth measurements for SiO2/Si systems (systems with a SiO2 insulating layer and Si substrate) have become necessary. Studying one such system obviously presents different results from that of the widely researched Si/Si structure, because the edge profile of the secondary electron (SE) signal contains contributions from two materials. In this work, several scanning electron microscope (SEM) images and SE profiles of SiO2/Si pitch and trapezoidal line structures, using various geometric and experimental parameters, were simulated through the use of Monte Carlo (MC) methods. It was found that, in contrast to Si/Si systems, the height of the insulating layer cannot be ignored during the evaluation of pitch and linewidth. The thickness (i.e., height) factor does play an important role in the contrast of SEM imaging and the shape of the SE profile in these two-material systems. The mechanism of the influence of insulating layer thickness for imaging was studied in detail. In addition, the SiO2/Si pitch structure with a real rough surface was also studied. This work has significant implications for the study of various kinds of two-material systems and could help to optimize the pitch and gate linewidth measurements.

A systematic characterization of a less known Al, Fe, Mn, and Si phase in a SiC particulate-reinforced 2014Al composite (SiCp/2014Al) was performed. In addition to the expected CuAl2 phase, the Al, Fe, Mn, and Si phase was formed as either an adhesion (>1 µm) onto SiC in the as-cast composite, or as a precipitate (<100 nm) in the matrix after hot extrusion. The structure of the phase was identified as cubic by both X-ray diffraction and selected area electron diffraction (SAED). The SAED pattern also indicated that the structure belongs to the Pm$\bar{3}$ space group instead of Im$\bar{3}$. The thermodynamic phase diagram was calculated, confirming the presence of an α-AlFeMn or α-AlFeSi phase in the Al–Fe–Mn and Al–Fe–Si ternary systems, respectively, within the Fe, Mn, and Si content range corresponding to 2014Al. Wavelength-dispersive spectroscopy analysis indicated that the composition of the phase is close to Al12(Fe, Mn)3Si2, in which the Mn/Fe ratio is in the range of 0.6–1.4. The determined Mn/Fe ratio corresponds to the nominal composition of Mn and Fe in the alloy.

A technique to characterize the native passivation layer (NPL) on pure lithium metal foils in a scanning electron microscope (SEM) is described in this paper. Lithium is a very reactive metal, and consequently, observing and quantifying its properties in a SEM is often compromised by rapid oxidation. In this work, a pure lithium energy-dispersive x-ray spectrum is obtained for the first time in a high vacuum SEM using a cold stage/cold trap with liquid nitrogen reservoir outside the SEM chamber. A nanomanipulator (OmniProbe 400) inside the microscope combined with x-ray microanalysis and windowless energy dispersive spectrometer is used to fully characterize the NPL of lithium metal and some of its alloys by a mechanical removal procedure. The results show that the native films of pure lithium and its alloys are composed of a thin (25 nm) outer layer that is carbon-rich and an inner layer containing a significant amount of oxygen. Differences in thickness between laminated and extruded samples are observed and vary depending on the alloy composition.

The determination of low boron concentrations in silicate glasses by electron probe microanalysis (EPMA) remains a significant challenge. The internal interferences from the diffraction crystal, i.e. the Mo-B4C large d-spacing layered synthetic microstructure crystal, can be thoroughly diminished by using an optimized differential mode of pulse height analysis (PHA). Although potential high-order spectral interferences from Ca, Fe, and Mn on the BKα peak can be significantly reduced by using an optimized differential mode of PHA, a quantitative calibration of the interferences is required to obtain accurate boron concentrations in silicate glasses that contain these elements. Furthermore, the first-order spectral interference from ClL-lines is so strong that they hinder reliable EPMA of boron concentrations in Cl-bearing silicate glasses. Our tests also indicate that, due to the strongly curved background shape on the high-energy side of BKα, an exponential regression is better than linear regression for estimating the on-peak background intensity based on measured off-peak background intensities. We propose that an optimal analytical setting for low boron concentrations in silicate glasses (≥0.2 wt% B2O3) would best involve a proper boron-rich glass standard, a low accelerating voltage, a high beam current, a large beam size, and a differential mode of PHA.

Kinematic indicators, including certain strain fringes, represent an important group of structures related to the progressive deformation in rocks. The evolution of these fibrous textures can be explained by the combination of multiple mechanisms of deformation and fluid flow, mainly controlled by the orientation of the strain field and the morphology of the grains. In general, the observations are done with an optical microscope and compared with computational models of growth. This work proposes a combination of crystallographic and cathodoluminescence data obtained in rocks from banded iron formations of the Iron Quadrangle in Brazil to represent an example of how complementary analytical techniques can be useful to understand geological problems. The chosen sample exhibits a strain fringe structure of quartz around a clast of magnetite partially transformed into goethite and hematite. Through the crystallographic data it was possible to identify the grain boundary morphology and domains of low deformation areas. On the other hand, the cathodoluminescence signal evidenced the occurrence of grains with a higher concentration of crystalline defects.

A reliable quantitative analysis in electron tomography, which depends on the segmentation of the three-dimensional reconstruction, is challenging because of constraints during tilt-series acquisition (missing wedge) and reconstruction artifacts introduced by reconstruction algorithms such as the Simultaneous Iterative Reconstruction Technique (SIRT) and Discrete Algebraic Reconstruction Technique (DART). We have carefully evaluated the fidelity of segmented reconstructions analyzing a disordered mesoporous carbon used as support in catalysis. Using experimental scanning transmission electron microscopy (STEM) tomography data as well as realistic phantoms, we have quantitatively analyzed the effect on the morphological description as well as on diffusion properties (based on a random-walk particle-tracking simulation) to understand the role of porosity in catalysis. The morphological description of the pore structure can be obtained reliably both using SIRT and DART reconstructions even in the presence of a limited missing wedge. However, the measured pore volume is sensitive to the threshold settings, which are difficult to define globally for SIRT reconstructions. This leads to noticeable variations of the diffusion coefficients in the case of SIRT reconstructions, whereas DART reconstructions resulted in more reliable data. In addition, the anisotropy of the determined diffusion properties was evaluated, which was significant in the presence of a limited missing wedge for SIRT and strongly reduced for DART.

Scanning electron microscopy (SEM) is one of the most common inspection methods in the semiconductor industry and in research labs. To extract the height of structures using SEM images, various techniques have been used, such as tilting a sample, or modifying the SEM tool with extra sources and/or detectors. However, none of these techniques focused on extraction of height information directly from top-down images. In this work, using Monte Carlo simulations, we studied the relation between step height and the emission of secondary electrons (SEs) resulting from exposure with primary electrons at different energies. It is found that part of the SE signal, when scanning over a step edge, is determined by the step height rather than the geometry of the step edge. We present a way to quantify this, arriving at a method to determine the height of structures from top-down SEM images. The method is demonstrated on three different samples using two different SEM tools, and atomic force microscopy is used to measure the step height of the samples. The results obtained are in qualitative agreement with the results from the Monte Carlo simulations.

An automated approach to fully reconstruct spherical Kikuchi maps from experimentally collected electron backscatter diffraction patterns and overlay each pattern onto its corresponding position on a simulated Kikuchi sphere is presented in this study. This work demonstrates the feasibility of warping any Kikuchi pattern onto its corresponding location of a simulated Kikuchi sphere and reconstructing a spherical Kikuchi map of a known phase based on any set of experimental patterns. This method consists of the following steps after pattern collection: (1) pattern selection based on multiple threshold values; (2) extraction of multiple scan parameters and phase information; (3) generation of a kinematically simulated Kikuchi sphere as the “skeleton” of the spherical Kikuchi map; and (4) overlaying the inverse gnomonic projection of multiple selected patterns after appropriate pattern center calibration and refinement. The proposed method is the first automated approach to reconstructing spherical Kikuchi maps from experimental Kikuchi patterns. It potentially enables more accurate orientation calculation, new pattern center refinement methods, improved dictionary-based pattern matching, and phase identification in the future.

Problems involving image segmentation, atomic cluster identification, segmentation of microstructure constituents in images and austenite reconstruction have seen various approaches attempt to solve them with mixed results. No single computational technique has been able to effectively tackle these problems due to the vast differences between them. We propose the application of graph cutting as a versatile technique that can provide solutions to numerous materials data analysis problems. This can be attributed to its configuration flexibility coupled with the ability to handle noisy experimental data. Implementation of a Bayesian statistical approach allows for the prior information, based on experimental results and already ingrained within nodes, to drive the expected solutions. This way, nodes within the graph can be grouped together with similar, neighboring nodes that are then assigned to a specific system with respect to calculated likelihoods. Associating probabilities with potential solutions and states of the system allows for quantitative, stochastic analysis. The promising, robust results for each problem indicate the potential usefulness of the technique so long as a network of nodes can be effectively established within the model system.

Correlated light and electron microscopy (CLEM) has become a popular technique for combining the protein-specific labeling of fluorescence with electron microscopy, both at room and cryogenic temperatures. Fluorescence applications at cryo-temperatures have typically been limited to localization of tagged protein oligomers due to known issues of extended triplet state duration, spectral shifts, and reduced photon capture through cryo-CLEM objectives. Here, we consider fluorophore characteristics and behaviors that could enable more extended applications. We describe how dialkylcarbocanine DiD, and its autoquenching by resonant energy transfer (RET), can be used to distinguish the fusion state of a lipid bilayer at cryo-temperatures. By adapting an established fusion assay to work under cryo-CLEM conditions, we identified areas of fusion between influenza virus-like particles and fluorescently labeled lipid vesicles on a cryo-EM grid. This result demonstrates that cryo-CLEM can be used to localize functions in addition to tagged proteins, and that fluorescence autoquenching by RET can be incorporated successfully into cryo-CLEM approaches. In the case of membrane fusion applications, this method provides both an orthogonal confirmation of functional state independent of the morphological description from cryo-EM and a way to bridge room-temperature kinetic assays and the cryo-EM images.

Annexin A2 (ANXA2) is reported to be associated with cancer development. To investigate the roles ANXA2 plays during the development of cancer, the RNAi method was used to inhibit the ANXA2 expression in caco2 (human colorectal cancer cell line) and SMMC7721 (human hepatocarcinoma cell line) cells. The results showed that when the expression of ANXA2 was efficiently inhibited, the growth and motility of both cell lines were significantly decreased, and the development of the motility relevant microstructures, such as pseudopodia, filopodia, and the polymerization of microfilaments and microtubules were obviously inhibited. The cancer cell apoptosis was enhanced without obvious significance. The possible regulating pathway in the process was also predicted and discussed. Our results suggested that ANXA2 plays important roles in maintaining the malignancy of colorectal and hepatic cancer by enhancing the cell proliferation, motility, and development of the motility associated microstructures of cancer cells based on a possible complicated signal pathway.

Vasodilation occurs as a result of the relaxation of the smooth muscle cells present in the walls of blood vessels. Various suitable models are available for the analysis of the vasoactive properties of drugs with therapeutic applications. But all these models have limitations, such as ethical issues and high cost. The purpose of this study is to develop an alternative model for studying the vasoactive properties of drugs using an in-ovo chicken embryo model. In the preliminary experiment, we used a well-known vasoconstrictor (adrenaline) and a vasodilator (spermine NoNoate) in the chick embryo area vasculosa and evaluated their concentration-response curve. Adrenaline (10 µM) and spermine NoNoate (10 µM) were administered in different arteries and veins and different positions of the right vitelline artery of the chick embryo. Results showed the middle of the vessel bed of the right vitelline artery having the best vasoactive effect compared to others. Finally, anti-hypertensive drugs, calcium channel blockers, and NOS agonists were administered in the chick embryo area vasculosa to validate the model. Results demonstrate that the chick embryo area vasculosa can be an alternative, robust, and unique in-ovo model for screening of anti-hypertensive drugs in real time.

Collagen microstructure is closely related to the mechanical properties of tissues and affects cell migration through the extracellular matrix. To study these structures, three-dimensional (3D) in vitro collagen-based gels are often used, attempting to mimic the natural environment of cells. Some key parameters of the microstructure of these gels are fiber orientation, fiber length, or pore size, which define the mechanical properties of the network and therefore condition cell behavior. In the present study, an automated tool to reconstruct 3D collagen networks is used to extract the aforementioned parameters of gels of different collagen concentration and determine how their microstructure is affected by the presence of cells. Two different experiments are presented to test the functionality of the method: first, collagen gels are embedded within a microfluidic device and collagen fibers are imaged by using confocal fluorescence microscopy; second, collagen gels are directly polymerized in a cell culture dish and collagen fibers are imaged by confocal reflection microscopy. Finally, we investigate and compare the collagen microstructure far from and in the vicinities of MDA-MB 23 cells, finding that cell activity during migration was able to strongly modify the orientation of the collagen fibers and the porosity-related values.

The gray level co-occurrence matrix (GLCM) algorithm is a contemporary computational biology method which, today, is frequently used to detect small changes in texture that are not visible using conventional techniques. We demonstrate that the toxic compound 6-hydroxydopamine (6-OHDA) and iron oxide nanoparticles (IONPS) have opposite effects on GLCM features of cell nuclei. Saccharomyces cerevisiae yeast cells were treated with 6-OHDA and IONPs, and imaging with GLCM analysis was performed at three different time points: 30 min, 60 min, and 120 min after the treatment. A total of 200 cell nuclei were analyzed, and for each nucleus, 5 GLCM parameters were calculated: Angular second moment (ASM), Inverse difference moment (IDM), Contrast (CON), Correlation (COR) and Sum Variance (SVAR). Exposure to IONPs was associated with the increase of ASM and IDM while the values of SVAR and COR were reduced. Treatment with 6-OHDA was associated with the increase of SVAR and CON, while the values of nuclear ASM and IDM were reduced. This is the first study to indicate that IONPs and 6-OHDA have opposite effects on nuclear texture. Also, to the best of our knowledge, this is the first study to apply the GLCM algorithm in Saccharomyces cerevisiae yeast cells in this experimental setting.

Here, different tissue surfaces of tomato root were characterized employing atomic force microscopy on day 7 and day 21 of growth through Young's modulus and plasticity index. These parameters provide quantitative information regarding the mechanical behavior of the tomato root under fresh conditions in different locations of the cross-section of root [cell surface of the epidermis, parenchyma (Pa), and vascular bundles (Vb)]. The results show that the mechanical parameters depend on the indented region, tissue type, and growth time. Thereby, the stiffness increases in the cell surface of epidermal tissue with increasing growth time (from 9.19 ± 0.68 to 13.90 ± 1.68 MPa) and the cell surface of Pa tissue displays the opposite behavior (from 1.74 ± 0.49 to 0.48 ± 0.55); the stiffness of cell surfaces of Vb tissue changes from 10.60 ± 0.58 to 6.37 ± 0.53 MPa, all cases showed a statistical difference (p < 0.05). Viscoelastic behavior dominates the mechanical forces in the tomato root. The current study is a contribution to a better understanding of the cell mechanics behavior of different tomato root tissues during growth.

Phototrophic microorganisms are the dominant populations in microbial mats, which play an important role in stabilizing sediments, such as happens in the Ebro Delta. These microorganisms are exposed to low metal concentrations over a long period of time. Distinct methods have been used to evaluate their toxic effect on the preservation of these ecosystems. Nevertheless, most of these techniques are difficult to apply in isolated phototrophs because (i) they usually form consortia with heterotrophic bacteria, (ii) are difficult to obtain in axenic cultures, and (iii) do not grow on solid media.

In this study, and for the first time, a combination of fast, non-invasive, and in vivo Confocal Laser Scanning Microscopy (CLSM) techniques were applied in a consortium of Scenedesmus sp. DE2009 to analyze its physiological state and viability under metal stress conditions. Microalga was more resistant to Pb followed by Cr and Cu. However, in multimetal combinations, the presence of Cu negatively affected microalga growth. Additionally, the inhibitory concentration (IC) values were also calculated by CLSM pigment analysis. The result determines a higher degree of toxicity for Cu and Cr in comparison to Pb. The high sensitivity of these CLSM-methods to detect low concentrations allows consideration of Scenedesmus sp. DE2009 as a good bioindicator of metal pollution in natural environments.

The process of autophagy has been detected in the midgut epithelium of four millipede species: Julus scandinavius, Polyxenus lagurus, Archispirostreptus gigas, and Telodeinopus aoutii. It has been examined using transmission electron microscopy (TEM), which enabled differentiation of cells in the midgut epithelium, and some histochemical methods (light microscope and fluorescence microscope). While autophagy appeared in the cytoplasm of digestive, secretory, and regenerative cells in J. scandinavius and A. gigas, in the two other species, T. aoutii and P. lagurus, it was only detected in the digestive cells. Both types of macroautophagy, the selective and nonselective processes, are described using TEM. Phagophore formation appeared as the first step of autophagy. After its blind ends fusion, the autophagosomes were formed. The autophagosomes fused with lysosomes and were transformed into autolysosomes. As the final step of autophagy, the residual bodies were detected. Autophagic structures can be removed from the midgut epithelium via, e.g., atypical exocytosis. Additionally, in P. lagurus and J. scandinavius, it was observed as the neutralization of pathogens such as Rickettsia-like microorganisms. Autophagy and apoptosis ca be analyzed using TEM, while specific histochemical methods may confirm it.

The current investigation was carried out to record the final stages of the development of both middle and distal parts of quail ceca, Coturnix coturnix japonica to understand the role of ceca in digestion, immune system, and absorption. The cellular and subcellular structures, including epithelial cell height, microvillus surface area, the proportion of goblet cells, the thickness of muscle layer, and cecum diameter showed great variations during the development. An undeveloped smooth muscularis mucosa was observed for the first time on the ED5. Primordia of glands were observed on the ED7. On the ED15, the middle part exhibited two shapes of mucosal villi: tongue-shaped villi and U-shaped. The plicae and crypts of Lieberkühn were demonstrated on the hatching day. The lymphatic tissues appeared in the wall of both parts of the ceca at the 4 weeks of age. Scanning electron microscopy revealed a great difference in the mucosal surface between different regions. Telocytes were observed in-between the muscle fibers and formed a network during the post-hatching period. Because of fermentation and other bacterial or chemical processes that have been shown to occur in the ceca, this study supports two hypotheses: the cecal development is related to diet and the cecal epithelium act as a site for primary absorption of nutrients or for re-absorption of electrolytes or amino acids derived from the urine.