Journal of Microscopy

DPC in Scanning Transmission Electron Microscopy (STEM) is a valuable method for mapping the electric fields in semiconductor materials. However, optimising the experimental conditions can be challenging. In this paper, we test and compare critical experimental parameters, including the convergence angle, camera length, acceleration voltage, sample configuration, and orientation using a four-quadrant segmented detector and a Si specimen containing layers of different As concentrations. The DPC measurements show a roughly linear correlation with the estimated electric fields, until the field gets close to the detection limitation, which is ∼0...

Colocalisation microscopy analysis provides an intuitive and straightforward way of determining if two biomolecules occupy the same diffraction-limited volume. A popular colocalisation coefficient, the Pearson's correlation coefficient (PCC), can be calculated using different pixel selection criteria: PCCALL includes all image pixels, PCCOR only pixels exceeding the intensity thresholds for either one of the detection channels, and PCCAND only pixels exceeding the intensity thresholds for both detection channels...

The degradation and turnover of mitochondria is fundamental to Eukaryotes and is a key homeostatic mechanism for maintaining functional mitochondrial populations. Autophagy is an important pathway by which mitochondria are degraded, involving their sequestration into membrane-bound autophagosomes and targeting to lytic endosomal compartments (the lysosome in animals, the vacuole in plants and yeast). Selective targeting of mitochondria for autophagy, also known as mitophagy, distinguishes mitochondria from other cell components for degradation and is necessary for the regulation of mitochondria-specific cell processes...

Biofilms are known to be present in tonsils, but little is known about their spatial location and size distribution throughout the tonsil. Studies of the location and distribution of biofilms in tonsil specimens have thus far been limited to either high-magnification methods such as electron microscopy, which enables high-resolution imaging but only from a tiny tissue volume, or lower magnification techniques such as light microscopy, which allow imaging of larger specimens but with poor spatial resolution...

Traditionally, automated slide scanning involves capturing a rectangular grid of field-of-view (FoV) images which can be stitched together to create whole slide images, while the autofocusing algorithm captures a focal stack of images to determine the best in-focus image. However, these methods can be time-consuming due to the need for X-, Y- and Z-axis movements of the digital microscope while capturing multiple FoV images. In this paper, we propose a solution to minimise these redundancies by presenting an optimal procedure for automated slide scanning of circular membrane filters on a glass slide...

No abstract text is available yet for this article.

Plants have been affected by water stress ever since they settled on dry land. In severe and persisting drought, plant leaves are wilting. However, a documentation at the anatomical level of the minute changes that occur before wilting is challenging. On the other hand, understanding the anatomical alteration in plant leaves with respect to water stress provides a stronger basis to study molecular and submolecular processes through which plants enhance drought tolerance. In this work, we applied an affordable method to visualise mesophyll layers of Arabidopsis thaliana cell lines without preparation steps that would alter the volume of the cells...

No abstract text is available yet for this article.

We calculate a universal shift in work function of 59.4 meV per decade of dopant concentration change that applies to all doped semiconductors and from this use Monte Carlo simulations to simulate the resulting change in secondary electron yield for doped GaAs. We then compare experimental images of doped GaAs layers from scanning electron microscopy and conductive atomic force microscopy. Kelvin probe force microscopy allows to directly measure and map local work function changes, but values measured are often smaller, typically only around half, of what theory predicts for perfectly clean surfaces...

The utility of fluorescence lifetime imaging microscopy (FLIM) for identifying bacteria in complex mineral matrices was investigated. Baseline signals from unlabelled Bacillus subtilis and Euglena gracilis, and Bacillus subtilis labelled with SYTO 9 were obtained using two-photon excitation at 730, 750 and 800 nm, identifying characteristic lifetimes of photosynthetic pigments, unpigmented cellular autofluorescence, and SYTO 9. Labelled and unlabelled B. subtilis were seeded onto marble and gypsum samples containing endolithic photosynthetic cyanobacteria and the ability to distinguish cells from mineral autofluorescence and nonspecific dye staining was examined in parallel with ordinary multichannel confocal imaging...

We present the design and performance of a novel scanning tunnelling microscope (STM) operating in a cryogen-free superconducting magnet. Our home-built STM head is compact (51.5 mm long and 20 mm in diameter) and has a single arm that provides complete openness in the scanning area between the tip and sample. The STM head consists of two piezoelectric tubes (PTs), a piezoelectric scanning tube (PST) mounted on a well-polished zirconia shaft, and a large PT housed in a sapphire tube called the motor tube...

The most crucial task of petroleum geology is to explore oil and gas reservoirs in the deep underground. As one of the analysis techniques in petroleum geological research, rock thin section identification method includes particle segmentation, which is one of the key steps. A conventional sandstone thin section image typically contains hundreds of mineral particles with blurred boundaries and complex microstructures inside the particles. Moreover, the complex lithology and low porosity of tight sandstone make traditional image segmentation methods unsuitable for solving the complex thin section segmentation problems...

Quantitative phase imaging (QPI) is a powerful tool for label-free visualisation of living cells. Here, we compare two QPI microscopes - the Telight Q-Phase microscope and the Nanolive 3D Cell Explorer-fluo microscope. Both systems provide unbiased information about cell morphology, such as individual cell dry mass, perimeter and area. The Q-Phase microscope uses artefact-free, coherence-controlled holographic imaging technology to visualise cells in real time with minimal phototoxicity. The 3D Cell Explorer-fluo employs laser-based holotomography to reconstruct 3D images of living cells, visualising their internal structures and dynamics...

In this study, transmission electron microscopy (TEM) and cryo-scanning electron microscopy (cryo-SEM) were evaluated for their ability to detect lipid bodies in microalgae. To do so, Phaeodactylum tricornutum and Nannochloropsis oculata cells were harvested in both the mid-exponential and early stationary growth phase. Two different cryo-SEM cutting methods were compared: cryo-planing and freeze-fracturing. The results showed that, despite the longer preparation time, TEM visualisation preceded by cryo-immobilisation allows a clear detection of lipid bodies, and is preferable to cryo-SEM...

Correlative superresolution microscopy has the potential to accurately visualize and validate new biological structures past the diffraction limit. However, combining different superresolution modalities, such as deterministic stimulated emission depletion (STED) and stochastic single-molecule localization microscopy (SMLM), is a challenging endeavor. For correlative STED and SMLM, the following poses a significant challenge: (1) the photobleaching of the fluorophores in STED; (2) the subsequent reactivation of the fluorophores for SMLM; and (3) finding the right fluorochrome and imaging buffer for both imaging modalities...

Reliable and consistent preparation of atom probe tomography (APT) specimens from aqueous and hydrated biological specimens remains a significant challenge. One particularly difficult process step is the use of a focused ion beam (FIB) instrument for preparing the required needle-shaped specimen, typically involving a "lift-out" procedure of a small sample of material. Here, two alternative substrate designs are introduced that enable using FIB only for sharpening, along with example APT datasets. The first design is a laser-cut FIB-style half-grid close to those used for transmission-electron microscopy, that can be used in a grid holder compatible with APT pucks...

FIB-SEM tomography is a serial sectioning technique where a Focused Ion Beam (FIB) mills off slices from the material sample that is being analyzed. After every slicing, a Scanning Electron Microscopy (SEM) image is taken showing the newly exposed layer of the sample. By combining all slices in a stack, a 3D image of the material is generated. However, specific artifacts caused by the imaging technique distort the images, hampering the morphological analysis of the structure. Typical quality problems in microscopy imaging are noise and lack of contrast or focus...

Gallium ion (Ga+ ) beam damage induced indium (In) precipitation in indium gallium arsenide (InGaAs) / indium aluminium arsenide (InAlAs) multiple quantum wells and its corresponding evolution under electron beam irradiation was investigated by valence electron energy loss spectroscopy (VEELS) and high-angle annular dark field imaging (HAADF) in scanning transmission electron microscopy (STEM). Compared with argon ion milling for sample preparation, the heavier projectiles of Ga+ ions pose a risk to trigger In formation in the form of tiny metallic In clusters...

In this paper, we present an enhanced method for automatically capturing a large number of consecutive paraffin sections using a microscope. Leveraging these microstructural images, we employed three-dimensional visualization and reconstruction techniques to investigate the dispersal growth process of pollen tube bundles upon entering the ovary of Solanum nigrum. Additionally, we explored their behavior within different ovules and examined the relationship between the germination rate of seeds and the fertilization process...

Sample preparation is of utmost importance for any microscopy and microstructural analysis. Correct preparation will allow accurate interpretation of microstructural features. A well-polished section is essential when Scanning Electron Microscopy (SEM) is used in Backscattering Electron (BSE) mode and characteristic X-rays are to be quantified using an Energy Dispersive Spectroscopy (EDS) detector. However, obtaining a well-polished section, especially for cementitious materials containing aggregates, is considered to be challenging and requires experience...