Two advanced, automated crystal orientation mapping techniques suited for nanocrystalline materials—precession electron diffraction (PED) in transmission electron microscopy (TEM) and on-axis transmission Kikuchi diffraction (TKD) in scanning electron microscopy (SEM)—are evaluated by comparing the orientation maps obtained from the identical location on a 30 nm-thick nanocrystalline tungsten (W) thin film. A side-by-side comparison of the orientation maps directly showed that the large-scale orientation features are almost identical. However, there are differences in the fine details, which arise from the fundamentally different nature of the spot pattern and Kikuchi line pattern in terms of the excitation volume and the angular resolution. While TEM-PED is more reliable to characterize grains oriented along low-index zone axes, the high angular resolution of SEM-TKD allows the detection of small misorientation between grains and thus yields better quantification and statistical analysis of grain orientation. Given that both TEM-PED and SEM-TKD orientation mapping techniques are complementary tools for nanocrystalline materials, one can be favorably selected depending on the requirements of the analysis, as they have competitive performance in terms of angular resolution and texture quantification.

This in situ transmission electron microscopy work presents a nanoscale characterization of the microstructural evolution in 3D-printed Inconel 718 (IN718) while exposed to elevated temperature and an associated change in the mechanical property under tensile loading. Here, we utilized a specially designed specimen shape that enables tensile testing of nano-sized thin films without off-plane deformations. Additionally, it allows a seamless transition from the in situ heating to tensile experiment using the same specimen, which enables a direct correlation of the microstructure and the mechanical property of the sample. The method was successfully used to observe the residual stress relaxation and the formation of incoherent γ′ precipitates when temperature was increased to 700°C. The subsequent in situ tensile test revealed that the exposure of the as-printed IN718 to a high temperature without full heat treatment (solutionizing and double aging) leads to loss of ductility.

This paper characterizes novel “star” defects in GaN films grown with metal–organic vapor phase deposition (MOVPE) on GaN substrates with electron channeling contrast imaging (ECCI) and high-resolution electron backscatter diffraction (HREBSD). These defects are hundreds of microns in size and tend to aggregate threading dislocations at their centers. They are the intersection of six nearly ideal low-angle tilt boundaries composed of $\langle a\rangle$-type pyramidal edge dislocations, each on a unique slip system.

Electron probe microanalysis is a nondestructive technique widely used to determine the elemental composition of bulk samples. This was extended to layered specimens, with the development of appropriate software. The traditional quantification method requires the use of matrix correction procedures based upon models of the ionization depth distribution, the so-called ϕ(ρz) distribution. Most of these models have led to commercial quantification programs but only few of them allow the quantification of layered specimens. Therefore, we developed BadgerFilm, a free open-source thin film program available to the general public. This program implements a documented ϕ(ρz) model as well as algorithms to calculate fluorescence in bulk and thin film samples. Part 1 of the present work aims at describing the operation of the implemented ϕ(ρz) distribution model and validating its implementation against experimental measurements and Monte Carlo simulations on bulk samples. The program has the ability to predict absolute X-ray intensities that can be directly compared to Monte Carlo simulations. We demonstrate that the implemented model works very well for bulk materials. And as will be shown in Part 2, BadgerFilm predictions for thin film specimens are also shown to be in good agreements with experimental and Monte Carlo results.

Since the 1960s, thicknesses and compositions of thin-film specimens have been determined by using the nondestructive technique of electron probe microanalysis. This approach, refined in the 1990s, is based upon models of the ionization depth distribution, the so-called ϕ(ρz) distribution, and is capable of analyzing layered specimens. Most of these quantification models have led to commercial programs. However, these programs may have possible limitations: some may not be directly compatible with modern computers, they often are “black boxes” making it difficult to assess the reliability of the results, and they are sometimes expensive enough to restrain many labs from purchasing them. We present a user-friendly, free, open-source program, BadgerFilm, implementing a documented ϕ(ρz) model and algorithms allowing the quantification of stratified samples. The program has the ability to calculate absolute X-ray intensities that can be directly compared with Monte Carlo simulations. We give a detailed explanation for the operation of the employed ϕ(ρz) model in thin films. A wide range of detailed Monte Carlo simulations and experimental data have been used to evaluate and validate the accuracy of the implemented algorithms. BadgerFilm demonstrated excellent quantification results for the films and in many cases for the substrates.

While application of clustering algorithms to atom probe tomography data have enabled quantification of solute clusters in terms of number density, size, and subcomposition there exist other properties (e.g., volume, surface area, and composition) that are better determined by defining an interface between the cluster and the surrounding matrix. The limitation in composition results from an ion selection step where the expected matrix ion types are omitted from the cluster search algorithm to enhance the contrast between the matrix and cluster and to reduce the complexity of the search. Previously, composition determination within solute clusters has utilized a secondary envelopment and erosion step on top of conventional methods such as maximum separation. In this work, we present a novel stochastic method that combines the particle identification fidelity of a conventional clustering algorithm with the analytical flexibility of mesh-based approaches through the generation of alpha shapes for each identified cluster. The corresponding mesh accounts for concave components of the clusters and determines the volume and surface area of the clusters; additionally, the mesh boundary is utilized to update the total composition according to the internal ions.

The characteristics of electron channeling contrast (ECC) of stacking faults in a [101] single-crystal 316L fcc (face-centered cubic) stainless steel have been evaluated. Channeling contrast was analyzed from a series of ECC images taken as a function of sample tilt at ~0.1° increments across the (111) Kikuchi band. The most relevant imaging parameters of the fault contrast, namely the number of fringes, fringe intensity, and fringe spacing, were analyzed under different channeling conditions. The present work shows that the channeling contrast of stacking faults exhibits strong dependence on the sign and magnitude of the deviation parameter, w (w = s ξg, where s is the excitation vector and ξg is the extinction distance). This effect has strong influence on channeling conditions for fault imaging and g.R analysis for determining the nature of a stacking fault. g.R analysis was evaluated by the method developed by Gevers et al. (1963) on g-reversion experiments of ECC images of a stacking fault configuration. The interplay between the stacking fault nature and ε-martensite is analyzed.

New interest in microscopic studies of ferroelectric materials with low piezoelectric coefficient, $d_{33}^\ast$, has emerged after the discovery of ferroelectric properties in HfO2 thin films, which are the main candidate for the next generation of nonvolatile ferroelectric memory. The study of the microscopic structure of ferroelectric HfO2 capacitors is crucial to get insights into the device behavior and performance. However, a small $d_{33}^\ast$ of ferroelectric HfO2 films leads to a low piezoresponse, especially in band excitation piezoresponse force microscopy (BE-PFM). In this work, we have implemented the BE-PFM technique with an increased scanning rate, thus improving this versatile tool for weak ferroelectrics. The acceleration of measurement was achieved by focusing excitation into a narrow frequency band and tuning the central frequency on-the-fly using an online real-time model estimation by fitting a complex BE response. The tracking of the contact resonance frequency was implemented using a pure mechanical cantilever response acquired in BE atomic force acoustic microscopy. To obtain optimal excitation parameters, we perform statistical analysis by minimizing estimator variance. The measurement precision of several PFM techniques was compared both by the simulation and experimentally using a Hf0.5Zr0.5O2-based ferroelectric capacitor.

A simple and fast method for thickness measurements using electron probe microanalysis (EPMA) is described. The method is applicable on samples with a thickness smaller than the electron depth range and does not require any knowledge of instrumental parameters. The thickness is determined by means of the distance that electrons travel inside the sample before crossing through it. Samples are first deposited on a substrate that, when reached by the transmitted electrons, produces an X-ray signal. The measured characteristic X-ray line intensity of the substrate is later used to determine the energy of transmitted electrons, which is proportional to the distance that electrons travel inside the sample. The study was performed on spherical K411 glass particles and cylindrical particles of U–Ce oxide with a size ranging from 0.2 to 4 μm. The measured thicknesses of all the studied particles showed good agreements with the real values. Although the method is only validated on particles with usual shapes, it can be applied to determine a local thickness of thin samples with irregular morphologies. This can help solving multiple issues in analysis with EPMA of non-bulk samples exhibiting complex geometries. Three dimensional microscopic imaging could also find a good utility in the described method.

In shape-from-focus (SFF) methods, a single focus measure is used to compute the focus volume. However, it seems that a single focus measure operator is not capable of computing accurate focus values for the images of diverse types of object shapes. Furthermore, most of the SFF methods try to improve the depth map without considering any additional structural or prior information. Consequently, the extracted shape of the object might lack important details. In this work, we address these problems and suggest a method in which depth hypotheses are combined for a more accurate 3D shape through 3D weighted least squares. First, depth hypotheses are obtained by applying a number of focus operators. Then, structural prior or guidance volume is extracted from the focus measure volumes. Finally, a 3D weighted least squares optimization technique is applied to the depth hypothesis volume, where weights are computed from the guidance volume. Thus, by inducing structural prior, an improved resultant depth map is obtained. The proposed method was tested using various image sequences of synthetic and microscopic real objects. Experimental results and comparative analysis demonstrated the effectiveness of the proposed method.

A method is presented to determine the feature resolution of physically relevant metrics of data obtained from segmented image sets. The presented method determines the best-fit distribution curve of a dataset by analyzing a truncated portion of the data. An effective resolvable size for the metric of interest is established when including parts of the truncated dataset results in exceeding a specified error tolerance. As such, this method allows for the determination of the feature resolution regardless of the processing parameters or imaging instrumentation. Additionally, the number of missing objects that exist below the resolution of the instrumentation may be estimated. The application of the developed method was demonstrated on data obtained via 2D scanning electron microscopy of a pressed explosive material and from 3D micro X-ray computed tomography of a polymer-bonded explosive material. It was shown that the minimum number of pixels/voxels required for the accurate determination of a physically relevant metric is dependent on the metric of interest. This proposed method, utilizing the prior knowledge of the distribution of metrics of interest, was found to be well suited to determine the feature resolution in applications where large datasets can be achieved.

This article presents a fast and highly efficient algorithm developed to reconstruct a three-dimensional (3D) volume with a high spatial precision from a set of field ion microscopy (FIM) images, and specific tools developed to characterize crystallographic lattice and defects. A set of FIM digital images and image processing algorithms allow the construction of a 3D reconstruction of the sample at the atomic scale. The capability of the 3D FIM to resolve the crystallographic lattice and the finest defects in metals opens a new way to analyze materials. This spatial precision was quantified on tungsten, analyzed at different analyzing conditions. A specific data mining tool, based on Fourier transforms, was also developed to characterize lattice distortions in the reconstructed volumes. This tool has been used in simulated and experimental volumes to successfully locate and characterize defects such as dislocations and grain boundaries.

In this research, atomic force microscopy (AFM) with a flat tip cantilever is utilized to measure Young's modulus of a whole yeast cell (Saccharomyces cerevisiae BY4741). The results acquired from AFM are similar to those obtained using a microfluidic chip compression system. The mechanical properties of single yeast cells are important parameters which can be examined using AFM. Conventional studies apply AFM with a sharp cantilever tip to indent the cell and measure the force-indentation curve, from which Young's modulus can be calculated. However, sharp tips introduce problems because the shape variation can lead to a different result and cannot represent the stiffness of the whole cell. It can lead to a lack of broader meaning when evaluating Young's modulus of yeast cells. In this report, we confirm the differences in results obtained when measuring the compression of a poly(dimethylsiloxane) bead using a commercial sharp tip versus a unique flat tip. The flat tip effectively avoids tip-derived errors, so we use this method to compress whole yeast cells and generate a force–deformation curve. We believe our proposed method is effective for evaluating Young's modulus of whole yeast cells.

GBF1 [Golgi brefeldin A (BFA) resistance factor 1] is a member of the guanine nucleotide exchange factors Arf family. GBF1 localizes at the cis-Golgi and endoplasmic reticulum (ER)-Golgi intermediate compartment where it participates in ER-Golgi traffic by assisting in the recruitment of the coat protein COPI. However, the roles of GBF1 in oocyte meiotic maturation are still unknown. In the present study, we investigated the regulatory functions of GBF1 in mouse oocyte organelle dynamics. In our results, GBF1 was stably expressed during oocyte maturation, and GBF1 localized at the spindle periphery during metaphase I. Inhibiting GBF1 activity led to aberrant accumulation of the Golgi apparatus around the spindle. This may be due to the effects of GBF1 on the localization of GM130, as GBF1 co-localized with GM130 and inhibiting GBF1 induced condensation of GM130. Moreover, the loss of GBF1 activity affected the ER distribution and induced ER stress, as shown by increased GRP78 expression. Mitochondrial localization and functions were affected, as the mitochondrial membrane potential was altered. Taken together, these results suggest that GBF1 has wide-ranging effects on the distribution and functions of Golgi apparatus, ER, and mitochondria as well as normal polar body formation in mouse oocytes.

Lysosomes are integration hubs for several signaling pathways, such as autophagy and endocytosis, and also crucial stores of ions, including Zn2+. Lysosomal dysfunction caused by changes in their morphology by fusion and fission processes can result in several pathological disorders. However, the role of Zn2+ in modulating the morphology of lysosomes is unclear. The resolution of conventional epifluorescence microscopy restricts accurate observation of morphological changes of subcellular fluorescence punctum. In this study, we used a modified epifluorescence microscopy to identify the center of a punctum from a series of z-stack images and calculate the morphological changes. We stained primary cultured rat embryonic cortical neurons with FluoZin3, a Zn2+-sensitive fluorescent dye, and Lysotracker, a lysosome-specific marker, to visualize the distribution of Zn2+-enriched vesicles and lysosomes, respectively. Our results revealed that treating neurons with N,N,N′,N′-tetrakis(2-pyridylmethyl)ethylenediamine, a cell-permeable Zn2+ chelator, shrank Zn2+-enriched vesicles and lysosomes by up to 25% in an hour. Pretreating the neurons with YM201636, a blocker of lysosome fission, could suppress this shrinkage. These results demonstrate the usefulness of the modified epifluorescence microscopy for investigating the homeostasis of intracellular organelles and related disorders.

The aim of the present study was to determine and elaborate on all changes in old-aged (OA) versus young-aged (YA) rat thyroids by using stereological, ultrastructural, hormonal, and gene expression analyses. We used 4- and 24-month-old male Wistar rats in our evaluation, presenting all changes in comparison with YA rats. Results showed that the thyroid parenchyma was characterized by higher absolute volumes of the gland, colloid, epithelium, and interstitium by 135, 135, 140, and 142% (p < 0.05) respectively, while the relative volumes of colloid and glands were unchanged. Ultrastructural analysis revealed less active glands, with smaller amounts of lysosomes, thyroglobulin (Tg) granules, and microvilli in the luminal colloid. Optical density values for thyroid peroxidase (TPO), Tg, and vascular-endothelial growth factor immunostaining remained unchanged; however, TPO and Tg exhibited visually stronger expression in small active follicles. Thyroxine (T4)-Tg, the relative intensity of fluorescence (RIF), serum T4, and the sodium-iodide symporter immunohistochemical and gene expressions decreased by 20, 40, 29, and 31% (p < 0.05), respectively, in OA thyroids. Pituitary thyroid-stimulating hormone (TSH) RIF increased by 44% (p < 0.05), but the TSH serum concentration remained unchanged. In conclusion, the obtained results indicate depression of the thyroid gland synthetic and secretory capacity with advanced age.

The present study aims to investigate the efficacy of intravenously injected mesenchymal stem cells (MSCs) in treating neuropathic pain either before or after its induction by a chronic constriction injury (CCI) model. Rats were divided into four groups: control group, neuropathic group, and treated groups (pre and postinduction) with i.v. mononuclear cells (106 cell/mL). For these rats, experimental testing for both thermal and mechanical hyperalgesia was evaluated. The cerebral cortex of the rats was dissected, and immunohistochemical analysis using anti-proliferating cell nuclear antigen (PCNA), CD117, nestin, and glial fibrillary acidic protein was performed. Our results showed that a single injection of MSCs (either preemptive/or post-CCI) produced equipotent effects on allodynia, mechanical hyperalgesia, and thermal response. Immunohistochemical analysis showed that the stem cells have reached the cerebral cortex. The injected group with MSCs before CCI showing few stem cells expressed PCNA, CD117, and nestin in the cerebral cortex. The group injected with MSCs after CCI, showing numerous recently proliferated CD117-, nestin-, PCNA-positive stem cells in the cerebral cortex. In conclusion, our findings demonstrate that the most probable effect of i.v. stem cells is the central anti-inflammatory effect, which opens concerns about how stem cells circulating in systemic administration to reach the site of injury.