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Journal of Microscopy

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https://www.readbyqxmd.com/read/28806482/automated-segmentation-and-quantification-of-actin-stress-fibres-undergoing-experimentally-induced-changes
#1
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
https://www.readbyqxmd.com/read/28795400/application-of-micro-ftir-mapping-and-sem-to-study-compositional-heterogeneity-of-siltstones-example-from-the-late-devonian-early-mississippian-middle-bakken-member
#2
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
https://www.readbyqxmd.com/read/28795398/robust-fluorescent-labelling-of-micropipettes-for-use-in-fluorescence-microscopy-application-to-the-observation-of-a-mosquito-borne-parasite-infection
#3
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
https://www.readbyqxmd.com/read/28768053/textural-pattern-classification-for-oral-squamous-cell-carcinoma
#4
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
https://www.readbyqxmd.com/read/28758683/effects-of-donor-and-acceptor-s-fluorescence-lifetimes-on-the-method-of-applying-f%C3%A3-rster-resonance-energy-transfer-in-sted-microscopy
#5
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
https://www.readbyqxmd.com/read/28758682/ten-implementations-of-ptychography
#6
Peng Li, Andrew M Maiden
Ptychography is an increasingly popular phase retrieval imaging technique, able to routinely deliver quantitative phase images with extended field of view at diffraction limited resolution. Different variants of this technique, like Bragg ptychography and Fourier ptychography, have also been developed and applied to various fields. Here we experimentally demonstrate 10 ways to implement the conventional real space transmission ptychography, and compare their properties to provide a guide to choosing the optimal setup for a specific application...
July 31, 2017: Journal of Microscopy
https://www.readbyqxmd.com/read/28758212/multichannel-wide-field-microscopic-fret-imaging-based-on-simultaneous-spectral-unmixing-of-excitation-and-emission-spectra
#7
M DU, Z Mai, F Yang, F Lin, L Wei, T Chen
Simultaneous spectral unmixing of excitation and emission spectra (ExEm unmixing) has inherent ability resolving spectral crosstalks, two key issues of quantitative fluorescence resonance energy transfer (FRET) measurement, of both the excitation and emission spectra between donor and acceptor without additional corrections. We here set up a filter-based multichannel wide-field microscope for ExEm unmixing-based FRET imaging (m-ExEm-spFRET) containing a constant system correction factor (fsc ) for a stable system...
July 31, 2017: Journal of Microscopy
https://www.readbyqxmd.com/read/28745429/exploring-the-interior-of-cuticles-and-compressions-of-fossil-plants-by-fib-sem-milling-and-image-microscopy
#8
L M Sender, I Escapa, A Benedetti, R Cúneo, J B Diez
We present the first study of cuticles and compressions of fossil leaves by Focused Ion Beam Scanning Electron Microscopy (FIB-SEM). Cavities preserved inside fossil leaf compressions corresponding to substomatal chambers have been observed for the first time and several new features were identified in the cross-section cuts. These results open a new way in the investigation of the three-dimensional structures of both micro- and nanostructural features of fossil plants. Moreover, the application of the FIB-SEM technique to both fossils and extant plant remains represent a new source of taxonomical, palaeoenvironmental and palaeoclimatic information...
July 26, 2017: Journal of Microscopy
https://www.readbyqxmd.com/read/28722767/plastic-deformation-mechanisms-in-a-new-ni-base-single-crystal-superalloy-at-room-temperature
#9
P Zhang, Y Yuan, Z Gao, B Li, G Yang, X Song
The evolution of dislocation configurations in a new Ni-base single crystal superalloy, M4706, during tensile deformation at room temperature is characterised by transmission electron microscopy. Experimental results show that contrary to previous reports, numerous isolated superlattice stacking faults and extended stacking faults are formed in the slightly deformed specimens with and without tertiary γ' precipitates. Meanwhile, it is also found that as the plastic deformation proceeds, the dominant deformation mechanism changes from stacking fault shearing to antiphase boundary shearing...
July 19, 2017: Journal of Microscopy
https://www.readbyqxmd.com/read/28703278/reconstruction-of-3d-grain-boundaries-from-rock-thin-sections-using-an-advanced-polarised-light-microscopy-method
#10
D M Hammes, M Peternell
Grain boundaries play a significant role in materials by initiating reactions and collecting impurities. Here we present FAGO (Fabric Analyser Grain boundary recOnstruction), a first step towards the automatic determination of three-dimensional (3D) grain boundary geometry using polarised light. The trace of the grain boundaries from 2D rock thin sections are determined primarily from data acquired using an automatic fabric analyser microscope and the FAME software (fabric analyser-based microstructure evaluation; Peternell and colleagues and Hammes and Peternell)...
July 13, 2017: Journal of Microscopy
https://www.readbyqxmd.com/read/28700079/study-of-the-surfactant-role-in-latex-aerogel-systems-by-scanning-transmission-electron-microscopy-on-aqueous-suspensions
#11
A Perret, G Foray, K Masenelli-Varlot, E Maire, B Yrieix
For insulation applications, boards thinner than 2 cm are under design with specific thermal conductivities lower than 15 mW m(-1)  K(-1) . This requires binding slightly hydrophobic aerogels which are highly nanoporous granular materials. To reach this step and ensure insulation board durability at the building scale, it is compulsory to design, characterise and analyse the microstructure at the nanoscale. It is indeed necessary to understand how the solid material is formed from a liquid suspension. This issue is addressed in this paper through wet-STEM experiments carried out in an Environmental Scanning Electron Microscope (ESEM)...
July 12, 2017: Journal of Microscopy
https://www.readbyqxmd.com/read/28686305/nanoscopic-analysis-of-oxygen-segregation-at-tilt-boundaries-in-silicon-ingots-using-atom-probe-tomography-combined-with-tem-and-ab-initio-calculations
#12
Y Ohno, K Inoue, K Fujiwara, K Kutsukake, M Deura, I Yonenaga, N Ebisawa, Y Shimizu, K Inoue, Y Nagai, H Yoshida, S Takeda, S Tanaka, M Kohyama
We have developed an analytical method to determine the segregation levels on the same tilt boundaries (TBs) at the same nanoscopic location by a joint use of atom probe tomography and scanning transmission electron microscopy, and discussed the mechanism of oxygen segregation at TBs in silicon ingots in terms of bond distortions around the TBs. The three-dimensional distribution of oxygen atoms was determined at the typical small- and large-angle TBs by atom probe tomography with a low impurity detection limit (0...
July 7, 2017: Journal of Microscopy
https://www.readbyqxmd.com/read/28686286/3-d-microstructure-of-olivine-in-complex-geological-materials-reconstructed-by-correlative-x-ray-%C3%AE-ct-and-ebsd-analyses
#13
W-A Kahl, N Dilissen, K Hidas, C J Garrido, V López-Sánchez-Vizcaíno, M J Román-Alpiste
We reconstruct the 3-D microstructure of centimetre-sized olivine crystals in rocks from the Almirez ultramafic massif (SE Spain) using combined X-ray micro computed tomography (μ-CT) and electron backscatter diffraction (EBSD). The semidestructive sample treatment involves geographically oriented drill pressing of rocks and preparation of oriented thin sections for EBSD from the μ-CT scanned cores. The μ-CT results show that the mean intercept length (MIL) analyses provide reliable information on the shape preferred orientation (SPO) of texturally different olivine groups...
July 7, 2017: Journal of Microscopy
https://www.readbyqxmd.com/read/28686283/a-reliable-approach-to-prepare-brittle-semiconducting-materials-for-cross-sectional-transmission-electron-microscopy
#14
J H Dycus, J M Lebeau
Here, we present a sample preparation approach that simplifies the thinning of very brittle wide bandgap semiconducting materials in cross-section geometry for (scanning) transmission electron microscopy. Using AlN thin films grown on sapphire and AlN substrates as case studies, we demonstrate that high-quality samples can be routinely prepared while greatly reducing the preparation time and consumables cost. The approach removes the sample preparation barrier to studying a wide variety of materials by electron microscopy...
July 7, 2017: Journal of Microscopy
https://www.readbyqxmd.com/read/28682468/direct-observations-of-dynamic-ptco-interactions-in-fuel-cell-catalyst-precursors-at-the-atomic-level-using-e-s-tem
#15
M R Ward, B Theobald, J Sharman, E D Boyes, P L Gai
Reduction reactions in practical bimetallic platinum-cobalt electrode catalyst precursors containing platinum, cobalt and cobalt oxides in hydrogen at 200, 450 and 700 °C for 6 h have been studied in situ using an aberration corrected environmental (scanning) transmission electron microscope (AC E(S)TEM). Little difference was observed in reduction at 200 °C but during and after reduction at 450 °C, small nanoparticles less than 3 nm in diameter with tetragonal PtCo structures were observed and limited Pt3 Co ordering could be seen on the surfaces of larger nanoparticles...
July 6, 2017: Journal of Microscopy
https://www.readbyqxmd.com/read/28675472/retrieving-overlapping-crystals-information-from-tem-nano-beam-electron-diffraction-patterns
#16
A Valery, E F Rauch, L Clément, F Lorut
The diffraction patterns acquired with a transmission electron microscope (TEM) contain Bragg reflections related to all the crystals superimposed in the thin foil and crossed by the electron beam. Regarding TEM-based orientation and phase characterisation techniques, the nondissociation of these signals is usually considered as the main limitation for the indexation of diffraction patterns. A new method to identify the information related to the distinct but overlapped grains is presented. It consists in subtracting the signature of the dominant crystal before reindexing the diffraction pattern...
July 4, 2017: Journal of Microscopy
https://www.readbyqxmd.com/read/28654222/imprint-cytology-based-breast-malignancy-screening-an-efficient-nuclei-segmentation-technique
#17
M Saha, I Arun, S Agarwal, R Ahmed, S Chatterjee, C Chakraborty
Imprint cytology (IC) refers to one of the most reliable, rapid and affordable techniques for breast malignancy screening; where shape variation of H&E stained nucleus is examined by the pathologists. This work aims at developing an automated and efficient segmentation algorithm by integrating Lagrange's interpolation and superpixels in order to delineate overlapped nuclei of breast cells (normal and malignant). Subsequently, a computer assisted IC tool has been designed for breast cancer (BC) screening. The proposed methodology consists of mainly three subsections: gamma correction for preprocessing, single nuclei segmentation and segmentation of overlapping nuclei...
June 27, 2017: Journal of Microscopy
https://www.readbyqxmd.com/read/28654160/pontamine-fast-scarlet-4b-bifluorescence-and-measurements-of-cellulose-microfibril-angles
#18
J Thomas, N A Idris, D A Collings
Pontamine fast scarlet 4B is a red paper and textiles dye that has recently been introduced as a fluorescent probe for plant cell walls. Pontamine exhibits bifluorescence, or fluorescence dependent on the polarization of the excitation light: Because cellulose is aligned within the cell wall, pontamine-labelled cell walls exhibit variable fluorescence as the excitation polarization is modulated. Thus, bifluorescence measurements require polarized excitation that can be directly or indirectly modulated. In our confocal microscopy observations of various cellulose samples labelled with pontamine, we modulated excitation polarization either through sample rotation or by the confocal's scanfield rotation function...
June 27, 2017: Journal of Microscopy
https://www.readbyqxmd.com/read/28613400/wear-mechanisms-of-the-biotribological-nanocomposite-a-c-h-coatings-implanted-by-metallic-nanoparticles
#19
L Major, M Janusz, J M Lackner, M Kot, M Dyner, B Major
Recently, to reduce the residual stress and increase the mechanical properties of a-C:H coatings, metallic nanoparticles have been implanted into their structure. In the present work, to improve the properties of the coating, metallic nanoparticles, including Cu, Nb, Ta, Zr, AgPt and Ag, were inserted into the a-C:H structure. The applied biological and mechanical analysis allowed the optimal biotribological parameters to be indicated for the potential application as protective coatings for metallic medical tools...
June 14, 2017: Journal of Microscopy
https://www.readbyqxmd.com/read/28613391/evaluation-of-five-diffeomorphic-image-registration-algorithms-for-mouse-brain-magnetic-resonance-microscopy
#20
Zhenrong Fu, Lan Lin, Miao Tian, Jingxuan Wang, Baiwen Zhang, Pingping Chu, Shaowu Li, Muhammad Mohsin Pathan, Yulin Deng, Shuicai Wu
The development of genetically engineered mouse models for neuronal diseases and behavioural disorders have generated a growing need for small animal imaging. High-resolution magnetic resonance microscopy (MRM) provides powerful capabilities for noninvasive studies of mouse brains, while avoiding some limits associated with the histological procedures. Quantitative comparison of structural images is a critical step in brain imaging analysis, which highly relies on the performance of image registration techniques...
June 14, 2017: Journal of Microscopy
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