Journal of Microscopy

This paper reports on the development of an open-source image analysis software 'pipeline' dedicated to petrographic microscopy. Using conventional rock thin sections and images from a standard polarising microscope, the pipeline can classify minerals and subgrains into objects and obtain information about optic-axis orientation. Five metamorphic rocks were chosen to test and illustrate the method. Thin sections were imaged using reflected and cross- and plane-polarised transmitted light. Images were taken at different angles of the polariser and analyser (360° with 10° steps), both with and without the full-lambda plate...

Super sulphated cement (SSC) is a very promising substitute for traditional construction materials (i.e. Portland cement), due to its enhanced durability and particularly low environmental impact. This paper explores the microstructure and certain properties of SSC, focusing on the particular complexities of its microstructure and the difficulties of microanalysis of its hydrates. To do so, SSC paste samples were first cast to identify hydration products using X-ray diffraction, then observed at early age using confocal laser scanning microscopy (CLSM) and at early and late age using scanning electron microscopy...

Nowadays, the use of super-resolution microscopy (SRM) is increasing globally due to its potential application in several fields of life sciences. However, a detailed and comprehensive guide is necessary for understanding a single-frame image's resolution limit. This study was performed to provide information about the structural organisation of isolated cellulose fibres from garlic and agave wastes through fluorophore-based techniques and image analysis algorithms. Confocal microscopy provided overall information on the cellulose fibres' microstructure, while techniques such as total internal reflection fluorescence microscopy facilitated the study of the plant fibres' surface structures at a sub-micrometric scale...

C4 AF is considered the least reactive main clinker phase, but its reactivity may be affected by adding supplementary cementitious materials (SCMs). Pure C4 AF was synthesised in a laboratory furnace, and the role of silica fume without gypsum on its early hydration properties was monitored. Burning was carried out in four stages to achieve 99% purity of C4 AF. Heat flow development was monitored by isothermal calorimetry over 7 days of hydration at 20°C and 40°C. The role of silica fume on hydrogarnet phase katoite (Ca3 Al2 (SiO4 )3 - x (OH)4 x x = 1...

Long-term placement of facial implants requires avoiding the formation of fibrous tissue capsules around the artificial material by creating osteoconductive properties of the surface. Most promising approach is the deposition coatings made of materials very similar to bone mineral components, that is, calcium phosphates such as hydroxyapatite (HAp). As part of the research work, an innovative, cost-effective atmospheric pressure plasma deposition (APPD) system was used as a low-temperature coating technology for generating the HAp coatings deposition...

To accurately simulate the hydration process of cementitious materials, understanding the growth rate of C-S-H layers around clinker grains is crucial. Nonetheless, the thickness of the hydrate layer shows substantial variation around individual grains, depending on their surrounding. Consequently, it is not feasible to measure hydrate layers manually in a reliable and reproducible manner. To address this challenge, a software has been developed to statistically determine the C-S-H thickness, requiring minimal manual interventions for thresholding and for setting limits like particle size or circularity...

The fracture behaviour of concrete is studied in various micro- and macro-damage models. This is important for estimating serviceability and stability of concrete structures. However, a detailed understanding of the material behaviour under load is often not available. In order to better interpret the fracture behaviour and pattern, images of lightweight concrete were taken using a high-resolution computed tomography (μ-CT) scanner. The samples were loaded between the taken images and the load was kept constant during the measurement...

The accelerating pace of technological advancements necessitates specialised expertise and cutting-edge instruments to maintain competitive research in life sciences. Core facilities - collaborative laboratories equipped with state-of-the-art tools and staffed by expert personnel - are vital resources that support diverse scientific endeavours. However, their adoption in lower-income communities has been comparatively stagnant due to both financial and cultural challenges. This paper explores the perils of not supporting core facilities on national research enterprises, underscoring the need for balanced investments in discovery science and crucial infrastructure support...

Atomic electric fields in a thin GaN sample are measured with the centre-of-mass approach in 4D-scanning transmission electron microscopy (4D-STEM) using a 12-segmented STEM detector in a Spectra 300 microscope. The electric fields, charge density and potential are compared to simulations and an experimental measurement using a pixelated 4D-STEM detector. The segmented detector benefits from a high recording speed, which enables measurements at low radiation doses. However, there is measurement uncertainty due to the limited number of segments analysed in this study...

Genetically encoded, fluorescent protein (FP)-based Förster resonance energy transfer (FRET) biosensors are microscopy imaging tools tailored for the precise monitoring and detection of molecular dynamics within subcellular microenvironments. They are characterised by their ability to provide an outstanding combination of spatial and temporal resolutions in live-cell microscopy. In this review, we begin by tracing back on the historical development of genetically encoded FP labelling for detection in live cells, which lead us to the development of early biosensors and finally to the engineering of single-chain FRET-based biosensors that have become the state-of-the-art today...

Localisation microscopy of individual molecules allows one to bypass the diffraction limit, revealing cellular organisation on a nanometric scale. This method, which relies on spatial analysis of the signal emitted by molecules, is often limited to the observation of biological objects at shallow depths, or with very few aberrations. The introduction of a temporal parameter into the localisation process through a time-modulated excitation was recently proposed to address these limitations. This method, called ModLoc, is demonstrated here with an alternative flexible strategy...

An approach for the crystallographic mapping of two-phase alloys on the nanoscale using a combination of scanned precession electron diffraction and open-source python libraries is introduced in this paper. This method is demonstrated using the example of a two-phase α/β titanium alloy. The data were recorded using a direct electron detector to collect the patterns, and recently developed algorithms to perform automated indexing and analyse the crystallography from the results. Very high-quality mapping is achieved at a 3 nm step size...

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.