Using Your Beam Efficiently: Reducing Electron Dose in the STEM via Flyback Compensation

In the scanning transmission electron microscope, fast-scanning and frame-averaging are two widely used approaches for reducing electron-beam damage and increasing image signal noise ratio which require no additional specialized hardware. Unfortunately, for scans with short pixel dwell-times (less than 5 μs), line flyback time represents an increasingly wasteful overhead. Although beam exposure during flyback causes damage while yielding no useful information, scan coil hysteresis means that eliminating it entirely leads to unacceptably distorted images. In this work, we reduce this flyback to an absolute minimum by calibrating and correcting for this hysteresis in postprocessing. Substantial improvements in dose efficiency can be realized (up to 20%), while crystallographic and spatial fidelity is maintained for displacement/strain measurement.

In Vivo Confocal Microscopy of the Corneal Sub-Basal Nerve plexus in Medically Controlled Glaucoma

The present study investigated the corneal sub-basal nerve plexus (SNP) modifications in glaucoma. Ninety-five glaucomatous patients were enrolled and divided into Group 1 and 2, preserved and preservative-free mono-therapy (30 and 28 patients), and Group 3, multi-therapy (37). Thirty patients with dry eye disease (DED) and 32 healthy subjects (HC) served as controls. In vivo confocal microscopy evaluated the nerve fibers density (CNFD), length (CNFL), thickness (CNFT), branching density (CNBD), and dendritic cell density (DCD). CNFD, CNFL, and CNBD were reduced in Group 3 and DED compared to HC (p < 0.05). CNFL was reduced in Group 3 compared to Group 2 (p < 0.05), and in Group 1 compared to HC (p < 0.001). CNFD, CNBD, and CNFT did not differ between glaucomatous groups. DCD was higher in Group 3 and DED compared to HC and Group 2 (p < 0.01). Group 3 showed worse ocular surface disease index (OSDI) scores compared to Group 1, 2, and HC (p < 0.05). CNFL and DCD correlated with OSDI score in Group 3 (r = −0.658, p < 0.001; r = 0.699, p = 0.002). Medical therapy for glaucoma harms the corneal nerves, especially in multi-therapy regimens. Given the relations with the OSDI score, SNP changes seem features of glaucoma therapy-related OSD and negatively affects the patient's quality of life.

Ultrastructure and Morphometric Analysis of Interstitial Cells of Cajal in the Gastric Wall of the Bullfrog (Rana catesbeiana)

Interstitial cells of Cajal (ICC) play a vital role in the gastrointestinal motility. However, information on ICC in lower vertebrates is rare. Here, ICC and ICC-like features of the gastric wall in the bullfrog (Rana catesbeiana) were observed by light microscopy and transmission electron microscopy. The lengths and distances of the ICC/ICC-like features were measured by morphometric analysis. The gastric wall contained mucosa, submucosa, tunica muscularis, and serosa. The gastric glands contained mucous cells and oxynticopeptic cells. The ICC with 1–3 processes were located among smooth muscle cells (SMC) of the tunica muscularis. Moreover, the ICC-like features were observed among oxynticopeptic cells of the mucosa. The processes of ICC established direct contacts with SMC. Also, the gap junctions were observed between the processes of ICC and nerve fiber bundles in the tunica muscularis. The multivesicular bodies, including shedding exosomes, were frequently observed between ICC and SMC. In addition, ICC-like features and their processes were observed in close proximity to oxynticopeptic cells and blood vessels. Our findings illustrated that ICC are present in the gastric tunica muscularis, and ICC-like features were in the mucosal lamina propria of the gastric wall of R. catesbeiana. These histological evidences supported the notion that ICC are implicated in gastric motility.

Improving Quantitative EDS Chemical Analysis of Alloy Nanoparticles by PCA Denoising: Part I, Reducing Reconstruction Bias

Scanning transmission electron microscopy is a crucial tool for nanoscience, achieving sub-nanometric spatial resolution in both image and spectroscopic studies. This generates large datasets that cannot be analyzed without computational assistance. The so-called machine learning procedures can exploit redundancies and find hidden correlations. Principal component analysis (PCA) is the most popular approach to denoise data by reducing data dimensionality and extracting meaningful information; however, there are many open questions on the accuracy of reconstructions. We have used experiments and simulations to analyze the effect of PCA on quantitative chemical analysis of binary alloy (AuAg) nanoparticles using energy-dispersive X-ray spectroscopy. Our results demonstrate that it is possible to obtain very good fidelity of chemical composition distribution when the signal-to-noise ratio exceeds a certain minimal level. Accurate denoising derives from a complex interplay between redundancy (data matrix size), counting noise, and noiseless data intensity variance (associated with sample chemical composition dispersion). We have suggested several quantitative bias estimators and noise evaluation procedures to help in the analysis and design of experiments. This work demonstrates the high potential of PCA denoising, but it also highlights the limitations and pitfalls that need to be avoided to minimize artifacts and perform reliable quantification.

Pulmonary Guardians and Special Regulatory Devices in the Lung of Nile Monitor Lizard (Varanus niloticus) with Special Attention to the Communication Between Telocyte, Pericyte, and Immune Cells

Monitor lizards are acclimatized to a variety of environments. Most of the monitor species are terrestrial, although there are arboreal and semiaquatic monitors. Such accommodation requires unique cellular structure and regulatory devices in various organs, particularly their lungs. This study aimed to report the pulmonary guardians and special regulatory devices that may guard and promote the function of the lungs of the Nile monitor lizards (Varanus niloticus). Specially structured vessels were recorded in the pulmonary tissue involving atypical glomus vessels, vessels with variable wall thickness, and a venule with specialized internal elastic membrane. Moreover, numerous lung resident guardians could be identified including both alveolar and interstitial macrophages, dendritic cells, mast cells, and B- and T-lymphocytes. Pericytes were demonstrated surrounding the capillary endothelium with a characteristic direct hetero-cellular junction with telocytes. Telocytes established a microenvironment through an indirect hetero-cellular junction with the interstitial macrophage, dendritic cells, and pneumocyte type II. Collectively, these data indicate a significant role played by the specially structured vessels and the resident immune cells in guarding the pulmonary tissue of the Nile monitor lizards and promoting its function. Telocytes are suggested to play a key role in angiogenesis and cellular communication to promote the function of the immune cells.

Automated SEM Image Analysis of the Sphere Diameter, Sphere-Sphere Separation, and Opening Size Distributions of Nanosphere Lithography Masks

Colloidal nanosphere monolayers—used as a lithography mask for site-controlled material deposition or removal—offer the possibility of cost-effective patterning of large surface areas. In the present study, an automated analysis of scanning electron microscopy (SEM) images is described, which enables the recognition of the individual nanospheres in densely packed monolayers in order to perform a statistical quantification of the sphere size, mask opening size, and sphere-sphere separation distributions. Search algorithms based on Fourier transformation, cross-correlation, multiple-angle intensity profiling, and sphere edge point detection techniques allow for a sphere detection efficiency of at least 99.8%, even in the case of considerable sphere size variations. While the sphere positions and diameters are determined by fitting circles to the spheres edge points, the openings between sphere triples are detected by intensity thresholding. For the analyzed polystyrene sphere monolayers with sphere sizes between 220 and 600 nm and a diameter spread of around 3% coefficients of variation of 6.8–8.1% for the opening size are found. By correlating the mentioned size distributions, it is shown that, in this case, the dominant contribution to the opening size variation stems from nanometer-scale positional variations of the spheres.

Gray-Level Co-occurrence Matrix Analysis for the Detection of Discrete, Ethanol-Induced, Structural Changes in Cell Nuclei: An Artificial Intelligence Approach

Gray-level co-occurrence matrix (GLCM) analysis is a contemporary and innovative computational method for the assessment of textural patterns, applicable in almost any area of microscopy. The aim of our research was to perform the GLCM analysis of cell nuclei in Saccharomyces cerevisiae yeast cells after the induction of sublethal cell damage with ethyl alcohol, and to evaluate the performance of various machine learning (ML) models regarding their ability to separate damaged from intact cells. For each cell nucleus, five GLCM parameters were calculated: angular second moment, inverse difference moment, GLCM contrast, GLCM correlation, and textural variance. Based on the obtained GLCM data, we applied three ML approaches: neural network, random trees, and binomial logistic regression. Statistically significant differences in GLCM features were observed between treated and untreated cells. The multilayer perceptron neural network had the highest classification accuracy. The model also showed a relatively high level of sensitivity and specificity, as well as an excellent discriminatory power in the separation of treated from untreated cells. To the best of our knowledge, this is the first study to demonstrate that it is possible to create a relatively sensitive GLCM-based ML model for the detection of alcohol-induced damage in Saccharomyces cerevisiae cell nuclei.

ESEM Methodology for the Study of Ice Samples at Environmentally Relevant Subzero Temperatures: “Subzero ESEM”

Frozen aqueous solutions are an important subject of study in numerous scientific branches including the pharmaceutical and food industry, atmospheric chemistry, biology, and medicine. Here, we present an advanced environmental scanning electron microscope methodology for research of ice samples at environmentally relevant subzero temperatures, thus under conditions in which it is extremely challenging to maintain the thermodynamic equilibrium of the specimen. The methodology opens possibilities to observe intact ice samples at close to natural conditions. Based on the results of ANSYS software simulations of the surface temperature of a frozen sample, and knowledge of the partial pressure of water vapor in the gas mixture near the sample, we monitored static ice samples over several minutes. We also discuss possible artifacts that can arise from unwanted surface ice formation on, or ice sublimation from, the sample, as a consequence of shifting conditions away from thermodynamic equilibrium in the specimen chamber. To demonstrate the applicability of the methodology, we characterized how the true morphology of ice spheres containing salt changed upon aging and the morphology of ice spheres containing bovine serum albumin. After combining static observations with the dynamic process of ice sublimation from the sample, we can attain images with nanometer resolution.

Design and Development of an Automated Dual-Mode Microscopic System Using Electrically Tunable Lenses

Maintaining telecentricity and zooming in microscopic systems with prolonged depths of focus is a difficult challenge because these properties degrade while moving to different axial planes in the extended focal depth. In this paper, we propose the proof of concept for an automated dual-mode microscopic system that combines two electrically tunable lenses (ETLs) with a variable numerical aperture controller placed. It acts as a viable solution to allow both multiplane microscopic zooming and telecentricity with consistent image resolution throughout the objective's extended focal depth. The image plane remains fixed for both the modes of operation, namely telecentricity and multiplane zooming. To validate the performance of the proposed idea, both simulations and experiments are carried out at various ETL curvature ranges. Over the whole zoom distance range, the experimental zoom ratio is determined to range from −2.723X to −34.42X. The experimental and simulation findings are compared and found to be quite similar, with magnification error percentages of 2.26% for zoom mode and 1.27% for telecentric mode. The comprehensive explanation of simulation and experimental results demonstrate the feasibility of the proposed method for both multiplane zoom and telecentric operations on a single platform in microscopic applications.

An Atom Probe with Ultra-Low Hydrogen Background

Atom probe tomography (APT) is a single-ion sensitive time-of-flight mass spectrometry method with near-atomic spatial resolution. In principle, it can be used to detect any chemical element, but so far hydrogen in the form of protium (1H) had to be largely excluded. This is owing to the residual H emitted from the stainless-steel chambers and in-vacuum parts commonly used in atom probe instrumentation. This residual H is then picked up in the APT experiment. In this paper, we show that by replacing the stainless-steel chamber and in-vacuum parts with titanium parts, this residual H can largely be removed, thus enabling the direct imaging of H using APT. We show that besides the drastic reduction of H, also other contaminants such as O, OH, and H2O are reduced by employing this instrument. In the current set-up, the instrument is equipped with high-voltage pulsing limiting the application to conductive materials.