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Journal of Microscopy

S A Linge Johnsen, J Bollmann, H W Lee, Y Zhou
Here a work flow towards an accurate representation of interference colours (Michel-Lévy chart) digitally captured on a polarised light microscope using dry and oil immersion objectives is presented. The work flow includes accurate rendering of interference colours considering the colour temperature of the light source of the microscope and chromatic adaptation to white points of RGB colour spaces as well as the colour correction of the camera using readily available colour targets. The quality of different colour correction profiles was tested independently on an IT8...
September 21, 2017: Journal of Microscopy
D Kolarević, T Vujasinović, K Kanjer, J Milovanović, N Todorović-Raković, D Nikolić-Vukosavljević, M Radulovic
The purpose of this study was to improve the prognostic value of tumour histopathology image analysis methodology by image preprocessing. Key image qualities were modified including contrast, sharpness and brightness. The texture information was subsequently extracted from images of haematoxylin/eosin-stained tumour tissue sections by GLCM, monofractal and multifractal algorithms without any analytical limitation to predefined structures. Images were derived from patient groups with invasive breast carcinoma (BC, 93 patients) and inflammatory breast carcinoma (IBC, 51 patients)...
September 21, 2017: Journal of Microscopy
O Gavrilova, N Zavialova, M Tekleva, E Karasev
We have tested possibilities and limitations of confocal laser scanning microscopy to study the morphology of pollen and spores and inner structure of sporoderms. As test objects, we used pollen grains of the modern angiosperm Ribes niveum (Grossulariaceae) and Datura metel (Solanaceae), fossil angiosperm pollen grains of Pseudointegricorpus clarireticulatum and Wodehouseia spinata dated to the Late Cretaceous, fossil gymnosperm pollen grains of Cycadopites-type dated to the Middle Jurassic, and fossil megaspores Maexisporites rugulaeferus, M...
September 21, 2017: Journal of Microscopy
S Barman, D Bolin
A thresholded Gaussian random field model is developed for the microstructure of porous materials. Defining the random field as a solution to stochastic partial differential equation allows for flexible modelling of nonstationarities in the material and facilitates computationally efficient methods for simulation and model fitting. A Markov Chain Monte Carlo algorithm is developed and used to fit the model to three-dimensional confocal laser scanning microscopy images. The methods are applied to study a porous ethylcellulose/hydroxypropylcellulose polymer blend that is used as a coating to control drug release from pharmaceutical tablets...
September 8, 2017: Journal of Microscopy
P Diblíková, M Veselý, P Sysel, P Čapek
Properties of a composite material made of a continuous matrix and particles often depend on microscopic details, such as contacts between particles. Focusing on processing raw focused-ion beam scanning electron microscope (FIB-SEM) tomography data, we reconstructed three mixed-matrix membrane samples made of 6FDA-ODA polyimide and silicalite-1 particles. In the first step of image processing, backscattered electron (BSE) and secondary electron (SE) signals were mixed in a ratio that was expected to obtain a segmented 3D image with a realistic volume fraction of silicalite-1...
September 6, 2017: Journal of Microscopy
Andreas Beyer, Lennart Duschek, Jürgen Belz, Jan Oliver Oelerich, Kakhaber Jandieri, Kerstin Volz
The surfaces of thin transmission electron microscopy (TEM) specimens of strained heterostructures can relax. The resulting bending of the lattice planes significantly influences high-angle annular dark field (HAADF) measurements. We investigate the impact by evaluating the intensities measured at the atomic columns as well as their positions in high-resolution HAADF images. In addition, the consequences in the diffraction plane will be addressed by simulated position averaged convergent beam electron diffraction (PACBED) patterns...
September 1, 2017: Journal of Microscopy
M Longfils, M Röding, A Altskär, E Schuster, N Lorén, A Särkkä, M Rudemo
Recently we complemented the raster image correlation spectroscopy (RICS) method of analysing raster images via estimation of the image correlation function with the method single particle raster image analysis (SPRIA). In SPRIA, individual particles are identified and the diffusion coefficient of each particle is estimated by a maximum likelihood method. In this paper, we extend the SPRIA method to analyse mixtures of particles with a finite set of diffusion coefficients in a homogeneous medium. In examples with simulated and experimental data with two and three different diffusion coefficients, we show that SPRIA gives accurate estimates of the diffusion coefficients and their proportions...
September 1, 2017: Journal of Microscopy
Elijah Shelton, Friedhelm Serwane, Otger Campàs
Modern fluorescence microscopy enables fast 3D imaging of biological and inert systems alike. In many studies, it is important to detect the surface of objects and quantitatively characterize its local geometry, including its mean curvature. We present a fully automated algorithm to determine the location and curvatures of an object from 3D fluorescence images, such as those obtained using confocal or light-sheet microscopy. The algorithm aims at reconstructing surface labelled objects with spherical topology and mild deformations from the spherical geometry with high accuracy, rather than reconstructing arbitrarily deformed objects with lower fidelity...
September 1, 2017: Journal of Microscopy
A P Lagrow, N M Alyami, D C Lloyd, O M Bakr, E D Boyes, P L Gai
Understanding the oxidation and reduction mechanisms of transition metals, such as nickel (Ni), is important for their use in industrial applications of catalysis. A powerful technique for investigating the redox reactive species is in situ environmental transmission electron microscopy (ETEM), where oxidation and reduction can be tracked in real time. One particular difficulty in understanding the underlying reactions is understanding the underlying morphology of the starting structure in a reaction, in particular the defects contained in the material, and the exposed surface facets...
August 29, 2017: Journal of Microscopy
P W Tinning, A J P M Franssen, S U Hridi, T J Bushell, G McConnell
We report the first demonstration of a fast wavelength-switchable 340/380 nm light-emitting diode (LED) illuminator for Fura-2 ratiometric Ca(2+) imaging of live cells. The LEDs closely match the excitation peaks of bound and free Fura-2 and enables the precise detection of cytosolic Ca(2+) concentrations, which is only limited by the Ca(2+) response of Fura-2. Using this illuminator, we have shown that Fura-2 acetoxymethyl ester (AM) concentrations as low as 250 nM can be used to detect induced Ca(2+) events in tsA-201 cells and while utilising the 150 μs switching speeds available, it was possible to image spontaneous Ca(2+) transients in hippocampal neurons at a rate of 24...
August 24, 2017: Journal of Microscopy
J Xiao, G Foray, K Masenelli-Varlot
Environmental scanning electron microscopy (ESEM) allows the observation of liquids under specific conditions of pressure and temperature. Moreover, when working in the transmission mode, that is in scanning transmission electron microscopy (STEM), nano-objects can be analysed inside a liquid. The contrast in the images is mass-thickness dependent as in STEM-in-TEM (transmission electron microscopy) using closed cells. However, in STEM-in-ESEM, as the liquid-vapour equilibrium is kept dynamically, the thickness of the water droplet remains unknown...
August 21, 2017: Journal of Microscopy
J Skibinski, J Rebis, L Kaczmarek, T Wejrzanowski, T Plocinski, K Rozniatowski
Imaging of the surface of materials by atomic force microscopy under tapping and phase imaging mode, with use of modified probes is addressed. In this study, the circularly shaped holes located in varying distance from the probe base, were cut out by focused ion beam. Such modification was a consequence of the results of the previous experiments (probe tip sharpening and cantilever thinning) where significant improvement of image quality in tapping and phase imaging mode has been revealed. The solution proposed herein gives similar results, but is much simpler from the technological point of view...
August 16, 2017: Journal of Microscopy
G Franchi, J Angulo, M Moreaud, L Sorbier
The goal of this paper is to explore the potential interest of image fusion in the context of multimodal scanning electron microscope (SEM) imaging. In particular, we aim at merging the backscattered electron images that usually have a high spatial resolution but do not provide enough discriminative information to physically classify the nature of the sample, with energy-dispersive X-ray spectroscopy (EDX) images that have discriminative information but a lower spatial resolution. The produced images are named enhanced EDX...
August 16, 2017: Journal of Microscopy
L Weber, A Hänsch, U Wolfram, A Pacureanu, P Cloetens, F Peyrin, S Rit, M Langer
X-ray phase tomography aims at reconstructing the 3D electron density distribution of an object. It offers enhanced sensitivity compared to attenuation-based X-ray absorption tomography. In propagation-based methods, phase contrast is achieved by letting the beam propagate after interaction with the object. The phase shift is then retrieved at each projection angle, and subsequently used in tomographic reconstruction to obtain the refractive index decrement distribution, which is proportional to the electron density...
August 16, 2017: Journal of Microscopy
M Liu
Differential interference contrast-photothermal microscopy (DIC-PTM), as a promising tool for trace analysis of nonfluorescent compounds, suffered low sensitivity in nanospace especially for aqueous samples, due to the poor thermophysical property of water and the unoptimised configuration. To improve its performance, a five-layer DIC-PTM model is built and influences of different parameters on the photothermal signal are investigated. The initial phase shift φ0 between two branches of the probe beam is found to be a key factor determining the detection sensitivity and response linearity: at a large φ0 (≤π/2) both a high sensitivity and a good linearity can be achieved, while a high signal-to-noise ratio occurs at a small φ0 ...
August 16, 2017: Journal of Microscopy
H Rogge, N Artelt, N Endlich, K Endlich
The actin cytoskeleton is a main component of cells and it is crucially involved in many physiological processes, e.g. cell motility. Changes in the actin organization can be effected by diseases or vice versa. Due to the nonuniform pattern, it is difficult to quantify reasonable features of the actin cytoskeleton for a significantly high cell number. Here, we present an approach capable to fully segment and analyse the actin cytoskeleton of 2D fluorescence microscopic images with a special focus on stress fibres...
August 14, 2017: Journal of Microscopy
C Gasaway, M Mastalerz, F Krause, C Clarkson, C Debuhr
This paper explores the applicability of micro-FTIR mapping to study heterogeneity of organic matter-lean siltstones. Closely spaced samples of Late Devonian dolomitic siltstones of the Middle Bakken Member were analysed with micro-FTIR, powder X-ray diffraction, and scanning electron microscopy (SEM) to explore the distribution and chemical properties of organic matter (OM), muscovite/feldspar/clay group, carbonates, and quartz, and their influence on porosity and permeability of these rocks. Our results show that quartz is the dominant component of the samples, and the main mineralogical differences between the samples are reflected in the abundance of carbonate minerals...
August 10, 2017: Journal of Microscopy
Amanda E Balaban, Keir Neuman, Photini Sinnis, Robert S Balaban
The ability to monitor micropipette injections with a high-resolution fluorescent microscope has utility for a variety of applications. Herein, different approaches were tested for creating broad-band fluorescently labelled glass micropipettes including: UV cured glass glues, baked glass enamel containing fluorescent dyes as well as nanodiamonds attached during pipette formation in the microforge. The most robust and simplest approach was to use labelled baked enamel on the exterior of the pipette. This approach was tested using pipettes designed to mimic a mosquito proboscis for the injection of the malaria parasite, Plasmodium spp...
August 10, 2017: Journal of Microscopy
T Y Rahman, L B Mahanta, C Chakraborty, A K DAS, J D Sarma
Despite being an area of cancer with highest worldwide incidence, oral cancer yet remains to be widely researched. Studies on computer-aided analysis of pathological slides of oral cancer contribute a lot to the diagnosis and treatment of the disease. Some researches in this direction have been carried out on oral submucous fibrosis. In this work an approach for analysing abnormality based on textural features present in squamous cell carcinoma histological slides have been considered. Histogram and grey-level co-occurrence matrix approaches for extraction of textural features from biopsy images with normal and malignant cells are used here...
August 2, 2017: Journal of Microscopy
Suhui Deng, Jianfang Chen, Zhaoshuai Gao, Chunhai Fan, Qiurong Yan, Yuhao Wang
Förster resonance energy transfer (FRET) probes being used to improve the resolution of stimulated emission depletion (STED) microscopy are numerically discussed. Besides the FRET efficiency and the excitation intensity, the fluorescence lifetimes of donor and acceptor are found to be another key parameter for the resolution enhancement. Using samples of FRET pairs with shorter donor lifetime and longer acceptor lifetime enhances the nonlinearity of the donor fluorescence, which leads to an increased resolution...
July 31, 2017: Journal of Microscopy
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