Microscopy and Microanalysis

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We have developed a methodology for the systematic generation of a large image dataset of macerated wood references, which we used to generate image data for nine hardwood genera. This is the basis for a substantial approach to automate, for the first time, the identification of hardwood species in microscopic images of fibrous materials by deep learning. Our methodology includes a flexible pipeline for easy annotation of vessel elements. We compare the performance of different neural network architectures and hyperparameters...

Leishmaniasis is a neglected tropical disease (endemic in 99 countries) caused by parasitic protozoa of the genus Leishmania. As treatment options are limited, there is an unmet need for new drugs. The hydroxynaphthoquinone class of compounds demonstrates broad-spectrum activity against protozoan parasites. Buparvaquone (BPQ), a member of this class, is the only drug licensed for the treatment of theileriosis. BPQ has shown promising antileishmanial activity but its mode of action is largely unknown. The aim of this study was to evaluate the ultrastructural and physiological effects of BPQ for elucidating the mechanisms underlying the in vitro antiproliferative activity in Leishmania donovani...

Accurately controlling trace additives in dielectric barium titanate (BaTiO3) layers is important for optimizing the performance of multilayer ceramic capacitors (MLCCs). However, characterizing the spatial distribution and local concentration of the additives, which strongly influence the MLCC performance, poses a significant challenge. Atom probe tomography (APT) is an ideal technique for obtaining this information, but the extremely low electrical conductivity and piezoelectricity of BaTiO3 render its analysis with existing sample preparation approaches difficult...

Texture stands as a fundamental descriptor in the realms of geology and earth and planetary science. Beyond offering insights into the geological processes underlying mineral formation, its characterization plays a pivotal role in advancing engineering applications, notably in mining, mineral processing, and metal extraction, by providing quantitative data for predictive modeling. Laboratory diffraction contrast tomography (LabDCT), a recently developed 3D characterization technique, offers nondestructive measurement of grain phases including their morphology, distribution, and crystal orientation...

Scanning electron microscopy (SEM) can reveal the ultrastructure of bacterial spores, including morphology, surface features, texture, spore damage, germination, and appendages. Understanding these features can provide a basis for adherence, how physical and environmental stressors affect spore viability, integrity, and functionality, as well as the distribution and function of surface appendages. However, the spore sample preparation method can significantly impact the SEM images' appearance, resolution, and overall quality...

Automated image acquisition can significantly improve the throughput of serial section scanning electron microscopy (ssSEM). However, image quality can vary from image to image depending on autofocusing and beam stigmation. Automatically evaluating the quality of images is, therefore, important for efficiently generating high-quality serial section scanning electron microscopy (ssSEM) datasets. We tested several convolutional neural networks for their ability to reproduce user-generated evaluations of ssSEM image quality...

In this article, porous GaN distributed Bragg reflectors (DBRs) were fabricated by epitaxy of undoped/doped multilayers followed by electrochemical etching. We present backscattered electron scanning electron microscopy (BSE-SEM) for sub-surface plan-view imaging, enabling efficient, non-destructive pore morphology characterization. In mesoporous GaN DBRs, BSE-SEM images the same branching pores and Voronoi-like domains as scanning transmission electron microscopy. In microporous GaN DBRs, micrographs were dominated by first porous layer features (45 nm to 108 nm sub-surface) with diffuse second layer (153 nm to 216 nm sub-surface) contributions...

The purpose of this study was to analyze the pigments used in the wooden paintings of Zarir Mosque, dating back to the Safavid era in Maragheh, Iran. These paintings, known as "Pardu," were commonly used for decorative false ceilings in various regions of Iran, particularly the northwest, during the Safavid and Qajar periods. Raman spectroscopy, scanning electron microscopy-energy-dispersive X-ray spectroscopy, multiband imaging, and optical microscopy were employed to examine the pigments. Fourier-transform infrared spectroscopy was also used to investigate the binder...

Spatial distribution of water-soluble molecules and ions in living organisms is still challenging to assess. Energy-dispersive X-ray spectroscopy (EDS) via cryogenic scanning electron microscopy (cryo-SEM) is one of the promising methods to study them without loss of dissolved contents. High-resolution cryo-SEM-EDS has challenges in sample preparation, including cross-section exposure and sample drift/charging due to insulative surrounding water. The former becomes problematic for large and inseparable organisms, such as benthic foraminifera, a unicellular eukaryote playing significant roles in marine ecosystems, which often exceed the size limit for the most reliable high-pressure freezing...

Modern aberration correctors in the scanning transmission electron microscope (STEM) have dramatically improved the attainable spatial resolution and enabled atomical structure and spectroscopic analysis even at low acceleration voltages (≤80 kV). For a large-angle illumination, achieving successful aberration correction to high angles is challenging with an aberration corrector, which limits further improvements in applications such as super-resolution, three-dimensional atomic depth resolution, or atomic surface morphology analyses...

The integration of microelectromechanical systems (MEMS)-based chips for in situ transmission electron microscopy (TEM) has emerged as a highly promising technique in the study of nanoelectronic devices within their operational parameters. This innovative approach facilitates the comprehensive exploration of electrical properties resulting from the simultaneous exposure of these devices to a diverse range of stimuli. However, the control of each individual stimulus within the confined environment of an electron microscope is challenging...

Nanoparticles are utilized in a multitude of applications due to their unique properties. Consequently, characterization of nanoparticles is crucial, and various methods have been employed in these pursuits. One such method is Atom Probe Tomography (APT). However, existing sample preparation techniques for APT generally involve embedding of the nanoparticles in a matrix different from their environment in solutions or at solid-liquid interfaces. In this work, we demonstrate a methodology based on silica embedding and explore how it can be utilized to form a matrix for nanoparticles suitable for APT analysis...

Correlative light and electron microscopy (CLEM) methods are powerful methods that combine molecular organization (from light microscopy) with ultrastructure (from electron microscopy). However, CLEM methods pose high cost/difficulty barriers to entry and have very low experimental throughput. Therefore, we have developed an indirect correlative light and electron microscopy (iCLEM) pipeline to sidestep the rate-limiting steps of CLEM (i.e., preparing and imaging the same samples on multiple microscopes) and correlate multiscale structural data gleaned from separate samples imaged using different modalities by exploiting biological structures identifiable by both light and electron microscopy as intrinsic fiducials...

Deviation of blood flow from an optimal range is known to be associated with the initiation and progression of vascular pathologies. Important open questions remain about how the abnormal flow drives specific wall changes in pathologies such as cerebral aneurysms where the flow is highly heterogeneous and complex. This knowledge gap precludes the clinical use of readily available flow data to predict outcomes and improve treatment of these diseases. As both flow and the pathological wall changes are spatially heterogeneous, a crucial requirement for progress in this area is a methodology for acquiring and comapping local vascular wall biology data with local hemodynamic data...

Vacuum diffusion-bonded printed circuit heat exchangers are an attractive choice for the high-temperature, high-pressure demands of next-generation energy applications. However, early reports show that the high-temperature materials desired for these applications suffer from poor bond strengths due to precipitation at the bond line, preventing grain boundary migration. In this study, a diffusion bond of the high-temperature stainless steel grade 321H is investigated, and poor mechanical properties are found to be caused by Ti(C, N) precipitation at the bond line...

We present an efficient approach for electron ptychography based on a mathematical relationship that differs from that underlying the established algorithms of the ptychography iterative engine or the noniterative algorithms like the Wigner-distribution-deconvolution or the single-side-band method. Three variables are handled in this method-the transfer function of the objective lens, the object spectrum, and the diffraction wave whose phase is unknown. In the case of an aberration-corrected electron microscope, one is able to obtain a well-estimated transfer function of the lens...

Biomineralization of brain tissues occurs both in normal and pathological conditions. Dura mater biomineralization is widespread and occurs in 1-72% of cases, depending on the patient's age and research method. The amount of biomineral deposits under the conditions of tumor growth in the meninges only increases, reaching 100% in the case of psammomatous meningiomas. Since calcifications are often found in the meninges, the problem of differential diagnosis with calcified meningiomas arises. A total of 30 samples of meningiomas with signs of biomineralization-dense structure, characteristic crunch, psammoma bodies (group I) and 30 samples of meningiomas without any signs of biomineralization were examined as controls (group II)...

The quantitative description of biological structures is a valuable yet difficult task in the life sciences. This is commonly accomplished by imaging samples using fluorescence microscopy and analyzing resulting images using Pearson's correlation or Manders' co-occurrence intensity-based colocalization paradigms. Though conceptually and computationally simple, these approaches are critically flawed due to their reliance on signal overlap, sensitivity to cursory signal qualities, and inability to differentiate true and incidental colocalization...

Dry particle coating processes are of key importance for creating functionalized materials. By a change in surface structure, initiated during coating, a surface property change and thus functionalization can be achieved. This study introduces an innovative approach employing 3D X-ray micro-computed tomography (micro-CT) to characterize coated particles, consisting of spherical alumina particles (d50 = 45.64 μm), called hosts, surrounded by spherical polystyrene particles (d50 = 3.5 μm), called guests...