Microscopy and Microanalysis

We demonstrate live-updating ptychographic reconstruction with the extended ptychographical iterative engine, an iterative ptychography method, during ongoing data acquisition. The reconstruction starts with a small subset of the total data, and as the acquisition proceeds the data used for reconstruction are extended. This creates a live-updating view of object and illumination that allows monitoring the ongoing experiment and adjusting parameters with quick turn around. This is particularly advantageous for long-running acquisitions...

Atom probe tomography requires needle-shaped specimens with a diameter typically below 100 nm, making them both very fragile and reactive, and defects (notches at grain boundaries or precipitates) are known to affect the yield and data quality. The use of a conformal coating directly on the sharpened specimen has been proposed to increase yield and reduce background. However, to date, these coatings have been applied ex situ and mostly are not uniform. Here, we report on the controlled focused-ion beam in situ deposition of a thin metal film on specimens immediately after specimen preparation...

In our pursuit of an alternative drug against Trichinella spiralis, we assessed the effectiveness of nanocurcumin in alleviating pathogenesis, parasitological factors, MMP-9 levels, and its expression in the enteral and parenteral phases of infection. The nanocurcumin particles, with a spherical shape and a size of 100 ± 20 nm, were used in the study. Eighty mice were divided into four groups: the control group, the untreated infected group, the nanocurcumin-treated group, and the albendazole-treated group...

Manipulation of host plant physiologies by leaf-galling insects is a complex, multifaceted process. Among fundamental knowledge gaps surrounding this scientifically intriguing phenomenon is the appropriation of plant mineral nutrients and moisture for galling advantage. Small, soluble mineral ions and watery cell contents in dense gall tissues are easily dislocated or lost to routine sample preparation. In this study, an X-ray microanalysis was applied to investigate gall mineral nutrition. Morphologically diverse leaf galls were sampled from three Australian rainforest tree species...

Traditional image acquisition for cryo focused ion-beam scanning electron microscopy (FIB-SEM) tomography often sees thousands of images being captured over a period of many hours, with immense data sets being produced. When imaging beam sensitive materials, these images are often compromised by additional constraints related to beam damage and the devitrification of the material during imaging, which renders data acquisition both costly and unreliable. Subsampling and inpainting are proposed as solutions for both of these aspects, allowing fast and low-dose imaging to take place in the Focused ion-beam scanning electron microscopy FIB-SEM without an appreciable loss in image quality...

A novel method for the preparation of lamellas made from porous and brittle compressed green powder using a focused ion beam (FIB) is described. One of the main purposes for the development of this methodology is to use this type of samples in micro-electromechanical systems (MEMS) chips for in situ transmission electron microscopy heating/biasing experiments, concomitant with maintaining the mechanical integrity and the absence of contamination of samples. This is accomplished through a modification of the standard FIB procedure for the preparation of lamellas, the adaptation of conventional chips, as well as the specific transfer of the lamella onto the chips...

Analysis of bone marrow aspirates (BMAs) is an essential step in the diagnosis of hematological disorders. This analysis is usually performed based on a visual examination of samples under a conventional optical microscope, which involves a labor-intensive process, limited by clinical experience and subject to high observer variability. In this work, we present a comprehensive digital microscopy system that enables BMA analysis for cell type counting and differentiation in an efficient and objective manner...

We have studied a machine learning (ML) technique for refining images acquired during in situ observation using liquid-cell transmission electron microscopy. Our model is constructed using a U-Net architecture and a ResNet encoder. For training our ML model, we prepared an original image dataset that contained pairs of images of samples acquired with and without a solution present. The former images were used as noisy images, and the latter images were used as corresponding ground truth images. The number of pairs of image sets was 1,204, and the image sets included images acquired at several different magnifications and electron doses...

Neutron irradiation (E ≥ 1 MeV) and 400 keV Kr+ ion irradiation tests were carried out and compared to study the formation and growth mechanism of dislocation loops in zirconium alloys. The results show that, as the irradiation reached 1.9 × 1025 n/m2 and 1.0 × 1020 Kr+/m2, a large number of <a>-type dislocation loops and a small amount of large-sized <c>-type dislocations hundreds of nanometers or even micrometers in size are observed in both samples...

Neural networks are promising tools for high-throughput and accurate transmission electron microscopy (TEM) analysis of nanomaterials, but are known to generalize poorly on data that is "out-of-distribution" from their training data. Given the limited set of image features typically seen in high-resolution TEM imaging, it is unclear which images are considered out-of-distribution from others. Here, we investigate how the choice of metadata features in the training dataset influences neural network performance, focusing on the example task of nanoparticle segmentation...

A suite of natural, synthetic, and mixed synthetic-natural woven fabrics, along with nonwoven filtration layers from a surgical mask and an N95 respirator, was examined using visible light microscopy, scanning electron microscopy, and micro-X-ray computed tomography (µXCT) to determine the fiber diameter distribution, fabric thickness, and the volume of solid space of the fabrics. Nonwoven materials exhibit a positively skewed distribution of fiber diameters with a mean value of ≈3 μm, whereas woven fabrics exhibit a normal distribution of diameters with mean values roughly five times larger (>15 μm)...

This study aimed to investigate sexual dimorphism in stillborn hawksbill sea turtles (Eretmochelys imbricata) through gonadal morphological characterizations. Macroscopic, light microscopy, and transmission electron analyses were performed for 30 gonad-mesonephros complexes. Female gonads were spindle-shaped and present a translucent whitish appearance with a grainy texture. Male gonads were approximately ovoid with a smooth opaque white surface. A primary sexual difference concerns different marrow structures, with females presenting organized cellularity featuring oocytes, lacunae, and blood vessels, while males presented a distinct organizational medulla pattern marked by testicular cords extending throughout the gonad length...

In this paper, the capability for quantifying the composition of Ba-doped SrTiO layers from an atom probe measurement was explored. Rutherford backscattering spectrometry and time-of-flight/energy elastic recoil detection were used to benchmark the composition where the amount of titanium was intentionally varied between samples. The atom probe results showed a significant divergence from the benchmarked composition. The cause was shown to be a significant oxygen underestimation (≳14 at%). The ratio between oxygen and titanium for the samples varied between 2...

In this study, a novel application of synchrotron X-ray nanotomography based on high-resolution full-field transmission X-ray microscopy for characterizing the structure and morphology of micrometric hollow polymeric fibers is presented. By employing postimage analysis using an open-source software such as Tomviz and ImageJ, various key parameters in fiber morphology, including diameter, wall thickness, wall thickness distribution, pore size, porosity, and surface roughness, were assessed. Electrospun polycaprolactone fibers with micrometric diameters and submicrometric features with induced porosity via gas dissolution foaming were used to this aim...

In this study, a conjugate radiation/conduction multimode heat transfer analysis of cryogenic focused ion beam (FIB) milling steps necessary for producing ex situ lift out specimens under cryogenic conditions (cryo-EXLO) is performed. Using finite volume for transient heat conduction and enclosure theory for radiation heat transfer, the analysis shows that as long as the specimen is attached or touching the FIB side wall trenches, the specimen will remain vitreous indefinitely, while actively cooled at liquid nitrogen (LN2) temperatures...

Automated quantification of human epidermal growth factor receptor 2 (HER2) immunohistochemistry (IHC) using whole slide imaging (WSI) is expected to eliminate subjectivity in visual assessment. However, the color intensity in WSI varies depending on the staining process and scanner device. Such variations affect the image analysis results. This paper presents methods to diminish the influence of color variation produced in the staining process using a calibrator slide consisting of peptide-coated microbeads...

Triphenyltin chloride (TPT-Cl) is an organometallic organotin. This study aimed to investigate the role of trigonelline (TG) along with the impact of TPT withdrawal on the testicular toxicity induced by TPT-Cl. Thirty-six adult male albino rats were divided into control, TG (40 mg/kg/day), TPT-Cl (0.5 mg/kg/day), TG + TPT-Cl, and recovery groups. Animals were daily gavaged for 12 weeks. Both TG and TPT-Cl withdrawal improved TPT-Cl-induced testicular toxicity features involving testis and relative testis weight reduction, luteinizing hormone, follicular stimulating hormone, and sex hormone-binding globulin elevation, reduction of inhibin B, free testosterone levels, and sperm count reduction with increased abnormal sperm forms...

Early-stage clustering in two Al-Mg-Zn(-Cu) alloys has been investigated using atom probe tomography and transmission electron microscopy. Cluster identification by the isoposition method and a statistical approach based on the pair correlation function have both been applied to estimate the cluster size, composition, and volume fraction from atom probe data sets. To assess the accuracy of the quantification of clusters of different mean sizes, synthesized virtual data sets were used, accounting for a simulated degraded spatial resolution...

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Morphological study of the tongue is an interesting way of understanding evolutionary processes associated with feeding habits. Therefore, the aim of the present study was to describe the tongue morphology of the Antillean manatee and to understand possible morphological relationships with its way of capturing food. Macroscopic dissections and light and scanning electron microscopy analyses of seven manatee tongues were performed. The tongue in Antillean manatees is a muscular and robust organ, divided into apex, body, and root...