Journal of Microscopy

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...

{en} Pseudomonas aeruginosa is a pathogen that forms robust biofilms which are commonly associated with chronic infections and cannot be successfully cleared by the immune system. Neutrophils, the most common white blood cells, target infections with pathogen-killing mechanisms that are rendered largely ineffective by the protective physicochemical structure of a biofilm. Visualization of the complex interactions between immune cells and biofilms will advance understanding of how biofilms evade the immune system and could aid in developing treatment methods that promote immune clearance with minimal harm to the host...

The development of inexpensive equipment adapted for the study of a specific biological object is very important for cryobiology. In the presented work, we have proposed a simple system for microscopy utilizing open-source platform Arduino. Testing this system showed that it had sufficient sensitivity to determine the physical processes occurring in a cryopreserved sample such as intra- and extracellular water crystallization, salt eutectic. Utilizing this system, we investigated the mechanisms of cryoprotection and cryodamage of testis interstitial cells (ICs) in cryoprotective media which included cryoprotective agents such as dimethyl sulfoxide (Me2 SO), as well as fetal bovine serum or polymers (dextran, hydroxyethyl starch, polyethylene glycol)...

Molecular mobility is an important measure in biological functionality, as molecules have to diffuse to meet and interact and perform actions. Measurement of mobility requires specific tools such as fluorescence correlation spectroscopy (FCS). Especially, combination with super-resolution stimulated emission depletion microscopy (STED-FCS), whether in a point- or beam-scanning mode, has proven valuable for determination of anomalous diffusion. STED-FCS however relies on an accurate calibration of the effective observation spot formed for different laser powers of the additional STED laser...

Here, we present a comprehensive holography-based system designed for detecting microparticles through microscopic holographic projections of water samples. This system is designed for researchers who may be unfamiliar with holographic technology but are engaged in microparticle research, particularly in the field of water analysis. Additionally, our innovative system can be deployed for environmental monitoring as a component of an autonomous sailboat robot. Our system's primary application is for large-scale classification of diverse microplastics that are prevalent in water bodies worldwide...

While numerical aperture of transillumination at or above 1.25 can be achieved with a substage oiled Abbe condenser, such immersion-capable condensers can be expensive limiting their use in resource poor settings. Also the measurement of numerical aperture generated by illuminators has received relatively little attention in the literature compared to methods for measuring the numerical aperture of acceptance by objectives. In this article, I show how an inexpensive paper diffuser with refractive-index coupling to the sample slide can generate illumination of a numerical aperture of over 1...

Because microstructure plays an important role in the mechanical properties of structural materials, developing the capability to quantify microstructures rapidly is important to enabling high-throughput screening of structural materials. Electron backscatter diffraction (EBSD) is a common method for studying microstructures and extracting information such as grain size distributions (GSDs), but is not particularly fast and thus could be a bottleneck in high-throughput systems. One approach to accelerating EBSD is to reduce the number of points that must be scanned...

When the first concrete was poured in 1949 for the Hungry Horse Dam (Montana, USA), pozzolan cements had already been used in several major North American dams, including Grand Coulee on the Columbia River (diatomaceous earth explored but ultimately not used), Friant on the San Joaquin River and Altus on the North Fork Red River (pumicite), and Bonneville on the Columbia River and Davis on the Colorado River (calcined clay). But Hungry Horse Dam stands out as the first dam constructed using coal combustion fly ash...

Here we outline a vignette of the Bioscience Technology Facility (BTF) at the University of York as a singular exemplar of the Full Cost Recovery model. It is fully appreciated that every facility operates slightly differently, and each are subject to various rules at the institutional, regional and national level. Understanding the regulations that need to be followed for your cost recovery model may require discussion with your administrators to ensure compliance regulations for your Institution and governing bodies are followed...

Many methods have been proposed to analyze SEM-EDS hypermaps of hydrated cementitious materials but none can fit all purposes. In this presentation, we review existing methods for phase identification, stoichiometry quantification, and microstructure quantification in cementitious materials and related materials. We first discuss the unique contribution of SEM-EDS with respect to the outstanding scientific challenges towards sustainable construction materials. We then compare the SEM-EDS and image analysis techniques which contribute to answering these challenges...

In 2015, we reported primed conversion, a novel way to convert green-to-red photoconvertible fluorescent proteins, which emerges as a powerful tool for precision optical imaging. Primed conversion uses the intercept of blue and red-to-far-red light instead of traditional violet or near-UV light illumination which offers a series of advantages. Here, we review the fundamental principles and applications of primed conversion with a focus on its use in single cell labelling and lineage tracing. We provide a historical perspective of lineage tracing techniques, thereby covering basic principles of fluorescence, photoconvertible fluorescent proteins, and eventually primed conversion...

The Cleanker (CLEAN clinKER production by Calcium Looping process) project, financed in the framework of Horizon 2020 EU funding program, has demonstrated the feasibility of the integrated CaL concept at industrial scale in a new demo system realized in the Buzzi Unicem cement plant in Vernasca (IT). The Calcium Looping (CaL) CO2 capture process exploits the reversible reaction of limestone calcination/carbonation (CaCO3 ↔ CaO + CO2 ). The Cleanker pilot plant consists of the coupling of a carbonator and an oxyfuel calciner...

Since semiconductor structures are becoming smaller and smaller, the examination methods must also take this development into account. Optical methods have long reached their limits here, but small dimensions are also a challenge for electron beam techniques. Especially when it comes to determining optical properties. In this paper, electron microscopic methods of investigating optical properties are discussed. Special attention is given to the physical limits and how to deal with them. We will cover electron energy loss spectrometry as well as cathodoluminescence spectrometry...