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Journal of Microscopy

S M Shah, J P Crawshaw, E S Boek
In the last decade, imaging techniques capable of reconstructing three-dimensional (3-D) pore-scale model have played a pivotal role in the study of fluid flow through complex porous media. In this study, we present advances in the application of confocal laser scanning microscopy (CLSM) to image, reconstruct and characterize complex porous geological materials with hydrocarbon reservoir and CO2 storage potential. CLSM has a unique capability of producing 3-D thin optical sections of a material, with a wide field of view and submicron resolution in the lateral and axial planes...
October 25, 2016: Journal of Microscopy
C Manghani, A Gupta, V Tripathi, V Rani
Cardiomyopathy and associated heart failure continues to be one of the most severe complications that threaten a large population. Curcumin, one of the three curcuminoids of the spice turmeric, is very well known for a multitude of health benefits and functions. Norepinephrine (NE), a catecholamine and also a stress hormone may cause the cardiomyocytes to develop increased sensitivity to death with its increasing concentrations. In this study, we investigated the cardioprotective effect of curcumin in NE-induced cardiac apoptosis using several fluorescent and nonfluorescent microscopic techniques like DAPI, PI, Giemsa, PicroSirius and TUNEL...
October 25, 2016: Journal of Microscopy
Alfio Torrisi, Przemyslaw Wachulak, Łukasz Węgrzyński, Tomasz Fok, Andrzej Bartnik, Tomáš Parkman, Šárka Vondrová, Jana Turňová, Bartłomiej J Jankiewicz, Bartosz Bartosewicz, Henryk Fiedorowicz
We report on a very compact desk-top transmission extreme ultraviolet (EUV) microscope based on a laser-plasma source with a double stream gas-puff target, capable of acquiring magnified images of objects with a spatial (half-pitch) resolution of sub-50 nm. A multilayer ellipsoidal condenser is used to focus and spectrally narrow the radiation from the plasma, producing a quasi-monochromatic EUV radiation (λ = 13.8 nm) illuminating the object, whereas a Fresnel zone plate objective forms the image. Design details, development, characterization and optimization of the EUV source and the microscope are described and discussed...
October 21, 2016: Journal of Microscopy
Genene T Mola, Elhadi A A Arbab, Bidini A Taleatu, K Kaviyarasu, Ishaq Ahmad, M Maaza
Vanadium pentoxide V2 O5 thin films were grown at room temperature on ITO coated glass substrates by electrochemical deposition. The resulting films were annealed at 300, 400 and 500°C for 1 h in ambient environment. The effect of heat treatment on the films properties such as surface morphology, crystal structure, optical absorption and photoluminescence were investigated. The x-ray diffraction study showed that the films are well crystallized with temperatures. Strong reflection from plane (400) indicated the film's preferred growth orientation...
September 29, 2016: Journal of Microscopy
L Roszkowiak, A Korzynska, J Zak, D Pijanowska, Z Swiderska-Chadaj, T Markiewicz
Evaluating whole slide images of histological and cytological samples is used in pathology for diagnostics, grading and prognosis . It is often necessary to rescale whole slide images of a very large size. Image resizing is one of the most common applications of interpolation. We collect the advantages and drawbacks of nine interpolation methods, and as a result of our analysis, we try to select one interpolation method as the preferred solution. To compare the performance of interpolation methods, test images were scaled and then rescaled to the original size using the same algorithm...
September 29, 2016: Journal of Microscopy
Sergei Magonov, John Alexander, Marko Surtchev, Albert M Hung, Elham H Fini
In recent years, many researchers have investigated bitumen surface morphology, especially the so-called bee-like structures, in an attempt to relate the chemical composition and molecular conformation to bitumen micromechanics and ultimately performance properties. Even though recent studies related surface morphology and its evolution to stiffness and stress localization, the complex chemical nature of bitumen and its time- and temperature-dependent properties still engender significant questions about the nature and origin of the observed morphological features and how they evolve due to exposure to various environmental and loading conditions...
September 26, 2016: Journal of Microscopy
N J R Hunter, C J L Wilson, V Luzin
Three techniques are used to measure crystallographic preferred orientations (CPO) in a naturally deformed quartz mylonite: transmitted light cross-polarized microscopy using an automated fabric analyser, electron backscatter diffraction (EBSD) and neutron diffraction. Pole figure densities attributable to crystal-plastic deformation are variably recognizable across the techniques, particularly between fabric analyser and diffraction instruments. Although fabric analyser techniques offer rapid acquisition with minimal sample preparation, difficulties may exist when gathering orientation data parallel with the incident beam...
September 22, 2016: Journal of Microscopy
G Landini, D A Randell, S Fouad, A Galton
We present an approach for automatic threshold segmentation of greyscale images. The procedure is inspired by a reinterpretation of the strategy observed in human operators when adjusting thresholds manually and interactively by means of 'slider' controls. The approach translates into two methods. The first one is suitable for single or multiple global thresholds to be applied globally to images and consists of searching for a threshold value that generates a phase whose boundary coincides with the largest gradients in the original image...
September 20, 2016: Journal of Microscopy
O Wirjadi, Y-J Kim, F Stech, L Bonfert, M Wagner
Image segmentation aims to determine structures of interest inside a digital picture in biomedical sciences. State-of-the art automatic methods however still fail to provide the segmentation quality achievable by humans who employ expert knowledge and use software to mark target structures on an image. Manual segmentation is time-consuming, tedious and suffers from interoperator variability, thus not serving the requirements of daily use well. Therefore, the approach presented here abandons the goal of full-fledged segmentation and settles for the localization of circular objects in photographs (10 training images and 20 testing images with several hundreds of nuclei each)...
September 20, 2016: Journal of Microscopy
F Moyon, D Hernandez-Maldonado, M D Robertson, A Etienne, C Castro, W Lefebvre
In this paper, we propose an algorithm to obtain a three-dimensional reconstruction of a single nanoparticle based on the method of atom counting. The location of atoms in three dimensions has been successfully performed using simulations of high-angle-annular-dark-field images from only three zone-axis projections, [110], [310] and [211], for a face-centred cubic particle. These three orientations are typically accessible by low-tilt holders often used in high-performance scanning transmission electron microscopes...
September 20, 2016: Journal of Microscopy
David S Gokhin, Velia M Fowler
The periodically arranged thin filaments within the striated myofibrils of skeletal and cardiac muscle have precisely regulated lengths, which can change in response to developmental adaptations, pathophysiological states, and genetic perturbations. We have developed a user-friendly, open-source ImageJ plugin that provides a graphical user interface (GUI) for super-resolution measurement of thin filament lengths by applying Distributed Deconvolution (DDecon) analysis to periodic line scans collected from fluorescence images...
September 19, 2016: Journal of Microscopy
L W Jiang, X F Wang, Z Y Wu, P H Lin, H P DU, S Wang, L H Li, N Fang, S M Zhuo, D Z Kang, J X Chen
Glioblastoma multiforme (GBM-WHO grade IV) is the most common and the most aggressive form of brain tumors in adults with the median survival of 10-12 months. The diagnostic detection of extracellular matrix (ECM) component in the tumour microenvironment is of prognostic value. In this paper, the fibrillar collagen deposition associated with vascular elements in GBM were investigated in the fresh specimens and unstained histological slices by using multiphoton microscopy (MPM) based on two-photon excited fluorescence (TPEF) and second harmonic generation (SHG)...
September 19, 2016: Journal of Microscopy
T Luo, H Chen, G S Kassab
A 3D reconstruction of individual fibres in vascular tissue is necessary to understand the microstructure properties of the vessel wall.  The objective of this study is to determine the 3D microstructure of elastin fibres in the adventitia of coronary arteries.  Quantification of fibre geometry is challenging due to the complex interwoven structure of the fibres.  In particular, accurate linking of gaps remains a significant challenge, and complex features such as long gaps and interwoven fibres have not been adequately addressed by current fibre reconstruction algorithms...
September 6, 2016: Journal of Microscopy
Carley Gasaway, Maria Mastalerz, Fed Krause, Chris Clarkson, Chris Debuhr
Samples of Late Devonian/Early Mississippian New Albany Shale from the Illinois Basin, having maturities ranging from early mature to postmature, were analysed using micro-Fourier transform infrared (FTIR) spectroscopy, ImageJ processing software and scanning electron microscopic X-ray spectroscopy to explore the distribution, connectivity and chemical composition of organic matter, clay minerals, carbonate minerals and quartz, and to further test the applicability of micro-FTIR mapping to study shale heterogeneity...
September 6, 2016: Journal of Microscopy
S Ray, T El Khassawna, U Sommer, U Thormann, N D Wijekoon, K Lips, C Heiss, V Alt
Wnt/β-catenin signalling components was shown to affect bone cells function including chondrocytes.Secreted Dkk1, a potent osteogenesis inhibiting factor mediates bone loss in diseased bones by suppressing the biological actions of Wnt proteins. In addition, increased Dkk1 signalling inhibits chondrogenesis in new bone formation. Recent findings also show there exists a cross-talk between the chondrocytes and the cells of the osteoblast lineage, which are the most affected cell types in muskuloskeletal disorders...
August 31, 2016: Journal of Microscopy
Qiaoling Jin, Tatjana Paunesku, Barry Lai, Sophie-Charlotte Gleber, S I Chen, Lydia Finney, David Vine, Stefan Vogt, Gayle Woloschak, Chris Jacobsen
Trace metals play important roles in biological function, and x-ray fluorescence microscopy (XFM) provides a way to quantitatively image their distribution within cells. The faithfulness of these measurements is dependent on proper sample preparation. Using mouse embryonic fibroblast NIH/3T3 cells as an example, we compare various approaches to the preparation of adherent mammalian cells for XFM imaging under ambient temperature. Direct side-by-side comparison shows that plunge-freezing-based cryoimmobilization provides more faithful preservation than conventional chemical fixation for most biologically important elements including P, S, Cl, K, Fe, Cu, Zn and possibly Ca in adherent mammalian cells...
August 31, 2016: Journal of Microscopy
V Chandrashekar, A Tarigopula, P Govindasami
Karyotype, bone marrow blast percentage and cytopenia influence the prognosis of myelodysplastic syndrome. We studied the abnormalities detected by fluorescence in situ hybridization (FISH) in myelodysplastic syndrome and associated haematological profile with abnormalities detected by FISH. Complete blood counts, peripheral blood and bone marrow of patients were evaluated for cytopenia, dysplasia and blasts. FISH probes were used to detect del(5q), gain of chromosome 8, de (7q/-7) and del(20 q). Multiple regression analysis was used to study the association of FISH abnormalities, age and sex with haematological profile...
August 31, 2016: Journal of Microscopy
Katarzyna Odziomek, Daniela Ushizima, Przemyslaw Oberbek, Krzysztof Jan Kurzydłowski, Tomasz Puzyn, Maciej Haranczyk
A sample of a nanomaterial contains a distribution of nanoparticles of various shapes and/or sizes. A scanning electron microscopy image of such a sample often captures only a fragment of the morphological variety present in the sample. In order to quantitatively analyse the sample using scanning electron microscope digital images, and, in particular, to derive numerical representations of the sample morphology, image content has to be assessed. In this work, we present a framework for extracting morphological information contained in scanning electron microscopy images using computer vision algorithms, and for converting them into numerical particle descriptors...
August 29, 2016: Journal of Microscopy
M Khanmohammadi, S Darkner, J Sporring, N Nava, J R Nyengaard, G Wegener, M Popoli
Behavioural stress has shown to strongly affect neurotransmission within the neocortex. In this study, we analysed the effect of an acute stress model on density and distribution of neurotransmitter-containing vesicles within medial prefrontal cortex. Serial section transmission electron microscopy was employed to compare two groups of male rats: (1) rats subjected to foot-shock stress and (2) rats with sham stress as control group. Two-dimensional (2D) density measures are common in microscopic images and are estimated by following a 2D path in-section...
August 22, 2016: Journal of Microscopy
Ivan Gutierrez-Urrutia
We have investigated the Ga(+) ion-damage effect induced by focused ion beam (FIB) milling in a [001] single crystal of a 316 L stainless steel by the electron channelling contrast imaging (ECCI) technique. The influence of FIB milling on the characteristic electron channelling contrast of surface dislocations was analysed. The ECCI approach provides sound estimation of the damage depth produced by FIB milling. For comparison purposes, we have also studied the same milled surface by a conventional electron backscatter diffraction (EBSD) approach...
August 22, 2016: Journal of Microscopy
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