bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of specimen thickness and carbon content on the carbon peak region in EEL spectra
Authors: DOOR R. , HÄBERLE K. D. , MARTIN R. 
Published: August 2011

SummaryAmorphous carbon films of different thicknesses and combinations of carbon films with CaF2 films of different thicknesses were used to create a standard reference library of EEL spectra. The relationship between the size and shape of the carbon peak region and the low‐loss part of the spectrum was determined. The steepness of the background of the CK edge, the size of the carbon peak and the plasmon shoulder on top of the carbon peak were investigated as a function of the thickness of the films and of the relative amount of carbon after normalization of the zero‐loss peak. The minimum at the CK edge and the maximum of the carbon peak were considered as examples for a modelling of the carbon peak region in different specimens. Methodological aspects which affect the accuracy of the measurement (characteristic lines of the detector, calculation of specimen thickness, method of t/λ measurement, mass loss, gain change correction, normalization of the spectra, energy resolution) were examined. The results indicate that modelling of the whole carbon peak region, considering its dependence on mass thickness and carbon concentration, should be possible from our standard reference spectra without use of the low‐loss region. The use of modelled standard reference spectra for background extrapolation in biological specimens with unknown calcium content is proposed.
Application of recording and processing of energy‐filtered image sequences for the elemental mapping of biological specimens: Imaging‐Spectrum
Authors: LAVERGNE J.‐L. , FOA C. , BONGRAND P. , SEUX D. , MARTIN J.‐M. 
Published: August 2011

SummaryComputerized energy‐filtered transmission electron microscope (EFTEM) permits the recording and the processing of energy‐filtered images, allowing a part of an electron energy‐loss spectrum for each picture element to be obtained. This method, called ‘Imaging‐Spectrum’, uses a Zeiss CEM902 coupled to several image analysis systems. The actual configuration records sequences of 48 images, 256 × 256 pixels, in steps of the energy loss, ΔE. Processing these sequences results in part of a core‐loss EELS‐spectrum for each pixel. This approach produces elemental maps with a short processing time. We have implemented three kinds of background calculation for the image subtraction. The influence of the irradiation dose and of the energy selecting slit width on the quality of the spectra is investigated. The method is applied to the analysis of some biological specimens (pericellular coat behaviour during adhesion between macrophages and red blood cells and location of calcite microcrystals in dental pulp cells). The Imaging‐Spectrum method appears to be suitable for the analysis of large areas.
Evaluation of lanthanide tracer methods in the study of mammalian pulmonary parenchyma and cardiac muscle by electron energy‐loss spectroscopy
Authors: FEHRENBACH H. , SCHMIEDL A. , BRASCH F. , RICHTER J. 
Published: August 2011

SummaryLanthanum (La) has widely been used as a tracer to study the integrity of plasma membranes. With conventional transmission electron microscopy (cTEM), the absence of electron scattering deposits from the cytoplasm has generally been assumed to reflect an intact cell membrane. However, the application of electron spectroscopic imaging (ESI) and electron energy‐loss spectroscopy (EELS) reveals that electron scattering deposits may be present which do not contain La. However, La could be detected in regions of pulmonary parenchyma and cardiac muscle that were devoid of electron scattering deposits. Therefore, to exclude misinterpretations based on cTEM the application of microanalytical techniques is strongly recommended for the study of the integrity of plasma membranes by means of La tracers. In addition, ESI and EELS are shown to distinguish between different tracers in simultaneous applications of La and terbium (Tb) which were used at the different faces of the pulmonary air‐blood barrier. The analysis of the distribution of both tracers which form electron scattering deposits, indistinguishable by cTEM, may help us to understand the different functional significances of cellular alterations of both cellular borders of the barrier.As was shown for La, however, strictly controlled conditions are mandatory during the fixation procedure because an increase in the incubation time to more than 1 h in samples of pulmonary parenchyma may result in the occurrence of La deposits within the cytoplasm. In the absence of electron scattering deposits, the presence of La in glycogen granules and ribosome‐containing areas of various types of alveolar septal cells even after 15 min incubation indicates that the absence of deposits does not necessarily correspond to the absence of the tracer.
Quantitative analysis of the microstructure of the human cornea and sclera using 2‐D Fourier methods
Authors: VAEZY S. , CLARK J. I. 
Published: August 2011

SummaryA two‐dimensional (2‐D) Fourier analysis was used to characterize the microstructure of the human cornea and sclera. The average centre‐to‐centre spacing of collagen fibrils was found to be 59 nm for the cornea and 285 nm for the sclera. These results agreed with those obtained by direct measurement using the electron micrographs, and those reported in the literature. The spatial order in the microstructure of the cornea was much greater when compared with that of the sclera. The results of the 2‐D Fourier analysis were consistent with the theory of transparency of the eye. The 2‐D Fourier analysis will be useful in quantitative characterization and analysis of the complex microstructure of biological cells and tissues in normal development and abnormal pathogenesis.
Reduced‐carrier single‐sideband microscopy: A powerful method for the observation of transparent microscopical objects
Authors: BRETSCHNEIDER F. , TEUNIS P. F. M. 
Published: August 2011

SummaryThe theoretical and practical properties of different forms of contrast formation in the microscope based on anaxial illumination are investigated: so‐called single‐sideband (SSB) techniques. The use of anaxial illumination in transmitted‐light microscopy is by itself a form of phase contrast (asymmetric illumination contrast, or AIC), but needs enhancement via a video circuit coupled to the microscope. The addition of a partially absorbing mask, known as a carrier‐attenuation filter (CAF), in a proper, conjugate plane in the microscope improves contrast substantially.The imaging properties of this reduced‐carrier, single‐sideband imaging method (RC‐SSB)were tested using the transparent parts of a compact disc (CD); the tracks may be treated as small objects with a controllable phase shift. The results were compared both theoretically and experimentally with Zernike phase contrast and with Nomarski differential interference contrast.The SSB technique has been shown to reveal transparent, submicrometre parts of living, unstained tissue, such as microvilli on sensory receptor cells of the transparent catfish, Kryptopterus. The high resolving power, together with the variable spatial‐frequency contrast enhancement, makes it a powerful technique for the imaging of in‐vivo subcellular details.
Fluorescence bleach rate imaging
Authors: BRAKENHOFF G. J. , VISSCHER K. , GIJSBERS E. J. 
Published: August 2011

SummaryBleach rate imaging on a (cooled) CCD can be easily achieved using a confocal microscope with bilateral scanning and detection coupled to a workstation; it is as easy as acquiring regular fluorescence images. Several analysis and display methods for bleach rate imaging are presented such as the bleach map (and its inverse) and a matrix‐based decomposition method for multi‐labelled specimens based on the bleach rate differences between the dyes used. With these tools, bleach‐rate‐based imaging can become a viable alternative to multiple labelling techniques for component identification in fluorescent specimens.
Calcium alginate encapsulation of small specimens for transmission electron microscopy
Authors: PAGE A. M. , LAGNADO J. R. , FORD T. W. , PLACE G. 
Published: August 2011

SummaryA technique of encapsulating small objects in calcium alginate for further processing for transmission electron microscopy is described. Five methods are outlined which enable a variety of specimens including single cells (in suspension and on agar plates), small organisms and monolayers of tissue culture cells to be processed. A method for immunolabelling alginate‐entrapped material is also outlined.
Sequential treatment by phosphotungstic acid and uranyl acetate enhances the adherence of lipid membranes and membrane proteins to hydrophobic EM grids
Authors: BARNAKOV A. N. 
Published: August 2011

SummaryA simple procedure for screening by electron microscopic observations of conditions for the reconstitution of membrane proteins into lipid bilayers is described. This procedure consists of a 5–10‐s treatment of electron microscopic grids, to which the sample has already been applied, with 1% phosphotungstic acid before proceeding with final staining in uranyl acetate. The method substantially enhances the adherence of lipid membranes and membrane protein particles to hydrophobic collodion/carbon grids.
Stereological analysis of the spatial Poisson–Voronoi tessellation
Authors: HAHN U. , LORZ U. 
Published: August 2011

SummaryStereological model tests and parameter estimators for the spatial Poisson–Voronoi tessellation are discussed. The tests aim to discriminate the Poisson–Voronoi tessellation from more regular or more irregular tessellations. The power of the model tests under some special parametric alternative hypotheses is investigated by simulation. Among the tests considered, the most powerful test is based on the variance of the section cell areas. Various stereological estimators for the model parameter of the spatial Poisson–Voronoi tessellation are compared with respect to their bias and variance by means of a Monte–Carlo study. Formulae are given for variance prediction. An estimator based on vertex counting is found to be the best. Robustness is investigated by applying the estimators to Voronoi tessellations generated by other point process models.
The homogeneity of phase repartition in TiB2–Fe composites using variance and covariance analysis
Authors: MISSIAEN J. M. , CHAIX J. M. 
Published: August 2011

SummaryThe microstructure of a sintered TiB2–Fe material has been studied by image analysis. The dispersion of phases, with particular attention to porosity, is investigated using chord lengths, covariance functions and variance of volume fractions. An extension of the usual point covariance analysis is made by sampling series of 10 contiguous fields, and measuring the covariance in the direction of field alignment. A model of a multiscale structure is proposed to interpret the different transitions of the variogram as composition fluctuations at different scales. Boolean models are used to give a geometrical representation of these fluctuations: the dispersion of porosity can be seen either as 20–30‐μm pore clusters or as the result of TiB2 +Fe 30–50‐μm clusters, probably formed during the elaboration process. Complementary information is obtained from the evolution of measured variance versus field size: a model is proposed to analyse the shape of the experimental curves. At small scales, ‘short’ integral ranges are determined, also obtained from the covariance. At very large scale (> 300 μm), composition fluctuations of about 2% are detected.
Shape processing and analysis using the calypter
Authors: PIRARD E. 
Published: August 2011

SummaryAfter presenting some elementary criteria that should be respected by any automatic shape analysis technique, this paper focuses on the importance of the binary image encoding method. Most image analysers simply use a raster image to represent a binary object. If, occasionally, a vectorial description is available, it is merely chosen for its performances in data compression. Data compression and shape analysis have different goals and usual methods cannot satisfy both. The calypter is a new descriptor vectorizing the shape as a set of maximal inscribed discs. It is the most efficient means of accomplishing Euclidean mathematical morphology transformations and allows for further developments in binary shape processing. A simple adaptive contour filtering technique is presented. The calypter offers local and global perception of shape characteristics. It permits complete automation of the morphometric roundness charts used in many laboratories and also generates new shape parameters. A case study of three sand populations is presented to show the pertinence of a new ‘equivalent roundness' parameter.
Optimizing the performance of confocal point scanning laser microscopes over the full field of view
Authors: ENTWISTLE A. , NOBLE M. 
Published: August 2011

SummaryTo examine many of the imaging capabilities of confocal scanning laser microscopes rapidly and reliably over the whole field of view three simple, easily prepared specimens are required: a mirror positioned on a carefully measured shallow gradient, a film of highly fluorescent material and a rectangular grid with a readily defined centre. Using these specimens the adjustment of any combination of confocal scanning laser visualization system and light microscope can be examined throughout the field of view. The effects of misalignment of the various subcomponents of a confocal scanning laser microscope on both the axial spread function of a plane and the shading pattern over the image field are described. Finally, where the design of the confocal optics permits, the three specimens can be used to facilitate the alignment of the various components to the optimal level achievable.
HREM image simulations for small particle catalysts on crystalline supports
Authors: YAO M.‐H. , SMITH D. J. 
Published: August 2011

SummaryThe imaging conditions for electron microscope studies of supported ultrafine particle catalysts have been investigated by multislice simulations. Images of Pt and ReO4 particles ranging from 0·4 to 2·3 nm in size were simulated in both plan view and profile view with a rutile (TiO2) support. It was shown that particle visibility varied greatly with the objective lens defocus. Optimum defocus was not favourable for supported particles in plan view since the ultrafine supported particles were least visible at this defocus. Underfocusing, especially at defoci corresponding to half‐spacing fringes in the TiO2 support, led to improved visibility and resolution of the supported particles. Although the structure and shape of supported ultrafine particles should be resolved better with a 400‐kV high‐resolution electron microscope, their detectability is poorer than with a 200‐kV instrument. An ReO4 cluster should be detectable at 200 kV on TiO2 supports up to 5 nm in thickness, whereas it is only likely to be detectable at 400 kV on supports up to 3 nm in thickness. The simulations confirmed that optimum defocus is most favourable for imaging supported particles in profile view. Atomic information for particles as small as a 13‐atom Pt cuboctahedral cluster should be resolvable with a 400‐kV instrument. The crystalline Ti monolayer observed on surfaces of Pt particles, which could explain the mechanism known as SMSI, was simulated as an example of profile imaging.
Scanning microphotolysis: A new photobleaching technique based on fast intensity modulation of a scanned laser beam and confocal imaging
Authors: WEDEKIND P. , KUBITSCHECK U. , PETERS R. 
Published: August 2011

SummaryThe fluorescence photobleaching method has been widely used to study molecular transport in single living cells and other microsystems while confocal microscopy has opened new avenues to high‐resolution, three‐dimensional imaging. A new technique, scanning microphotolysis (Scamp), combines the potential of photobleaching, beam scanning and confocal imaging. A confocal scanning laser microscope was equipped with a sufficiently powerful laser and a novel device, the ‘Scamper’. This consisted essentially of a filter changer, an acousto‐optical modulator (AOM) and a computer. The computer was programmed to activate the AOM during scanning according to a freely defined image mask. As a result almost any desired pattern could be bleached (‘written’) into fluorescent samples at high definition and then imaged (‘read’) at non‐bleaching conditions, employing full confocal resolution. Furthermore, molecular transport could be followed by imaging the dissipation of bleach patterns. Experiments with living cells concerning dynamic processes in cytoskeletal filaments and the lateral mobility of membrane lipids suggest a wide range of potential biological applications. Thus, Scamp offers new possibilities for the optical manipulation and analysis of both technical and biological microsystems.
Light microscopical evaluation of pyrite oxidation of heap leached samples from a Pittsburgh seam coal
Authors: IRDI G. A. , BOOHER H. B. 
Published: August 2011

SummaryThe U.S. Department of Energy and the U.S. Bureau of Mines conducted experiments to determine the feasibility of reducing the pyritic sulphur content of a conventionally cleaned Pittsburgh seam coal by heap leaching. Two identical heaps, one indoor and one outdoor, were constructed, and sprayed with recycled rainwater/leachate for approximately 200 days. Lump samples were selected prior to initiation of heap leaching activities and from both heaps after 5‐ and 11‐month intervals for microscopic (petrographic) examination. These examinations revealed no significant differences in the occurrence of pyrite oxidation between the two heaps. These observations were consistent with the results from the chemical analyses that showed no significant differences in pyritic sulphur removal between the indoor and outdoor heaps. Samples from the starting coal were also selected and examined to see how different pyrite morphologies behaved during artificial weathering. Dendritic and framboidal pyrite forms appeared to be the more reactive forms.
An atomic force microscope for cytological and histological investigations
Authors: MARIANI T. , MUSIO A. , FREDIANI C. , SBRANA I. , ASCOLI C. 
Published: August 2011

SummaryAn atomic force microscope (AFM) specifically designed for cytological and histological studies and able to operate on the same scale of the highest optical magnification is described. The AFM is a non‐invasive instrument; it operates on samples which do not require any kind of treatment and it can produce information that supplements and completes the information given by traditional microscopical methods. The apparatus has been used to image fixed human chromosomes and to investigate the action of trypsin during the staining for banding. First results showed that banding patterns very similar to G‐banding pre‐exist to staining and to trypsin treatment in human metaphase chromosomes, and that the trypsin treatment induces a structural collapse in the chromatin. The instrument was also used on thin sections of plant tissue and gave promising results. Experience confirmed that AFM is a suitable tool for this kind of investigation, and proved the importance of developing AFM microscopes specifically designed for routine use in cytology and histology, conceived for non‐specialized users.
Unstained and in vivo fluorescently stained bacterial nucleoids and plasmolysis observed by a new specimen preparation method for high‐power light microscopy of metabolically active cells
Authors: KELLENBERGER E. , VAN DER KAMP C. KELLENBERGER 
Published: August 2011

SummaryMicroscope slides were coated with a layer of gelatin, the thickness of the gelatin increasing linearly along the long axis. The bacterial suspension is applied to the dried gelatin and covered by a coverslip. The medium is absorbed by the gelatin and thus the cells applied against the coverslip. By this method, cultures of concentrations below 108 cells/ml provide statistically relevant numbers for observation without prior concentration steps. It is easier to apply than the existing methods for the observation of bacterial nucleoids by phase contrast imaging. Because the cells are maintained in growing conditions the method is useful for the vital fluorescence DAPI‐staining of various bacterial species and for observations of plasmolysis and its reversal at different physiological conditions and extracellular osmolalities. The previously generally assumed view that the plasmolytic changes of the cell morphology are immediate upon the hyperosmotic shock and are rapidly repaired when the cell is able to metabolize actively was confirmed; this is in contrast to some recent claims.
Fibre optic scrambling in light microscopy: A computer simulation and analysis
Authors: REITZ F. B. , PAGLIARO L. 
Published: August 2011

SummaryOptical fibres bent in two mutually perpendicular planes have proven useful for randomizing illumination in light microscopes. These optical scramblers can increase the resolution and/or contrast obtained with several modes of light microscopy. Here, computer simulations are used to investigate several parameters affecting light randomization in curved optical fibres in order to further the theoretical basis for scrambler design. Light passing through 90° bends of optical fibre of varying radii of curvature was modelled by ray tracing in two dimensions, and scrambling mechanisms were observed. The effects of varying the position and angle of entry of light on the phase and direction of propagation of the emergent light were determined. It was found that (a) thorough scrambling does not necessarily require high numerical aperture (NA) entry of light into the fibre, (b) considerable order persists after a single 90° bend of an idealized fibre and (c) a higher degree of scrambling (at the cost of transmission efficiency) is achieved in more tightly curved fibres. The pathlength variations introduced by scrambling proved smaller than typical laser coherence lengths, requiring temporal scrambling (vibrating the fibre).
Edge detection, three‐dimensional cell boundary reconstruction and volume and surface area estimation from differential interference contrast images
Authors: KENYON C. M. , YANAI M. , MACKLEM P. T. 
Published: August 2011

SummaryThree‐dimensional (3‐D) cell morphology is important for the understanding of cell function and can by quantified in terms of volume and surface area. Differential interference contrast (DIC, or Nomarski) imaging can enable cell edges to be clearly visualized in unstained tissue due to the slight difference in refractive index between aqueous media and cytoplasm. DIC is affected in only one direction ‐ the direction of the optical shear. A 1‐D edge detector was used in that direction with a scale length equal to that of an in‐focus edge to highlight cell boundaries. By comparison with the signal from the edge detector on an out‐of‐focus slice, the in‐focus slices could be segmented and, after noise suppression, cell outlines obtained. A voxel paradigm was used to calculate cell volume and differential geometry was used for surface area estimation. We applied this approach to obtain 3‐D dimensional information by optical sectioning of motile Amoeba proteus.