bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fast Monte Carlo method for simulating electron scattering in solids
Authors: Czyżewski Zbigniew , Joy David C. 
Published: August 2011

SUMMARYA simplified Monte Carlo approach to the simulation of the scattering process of penetrating electrons in solids is presented. The Mott scattering cross‐section and simulated angular distributions for plural scattering at low energies are used to describe the angular scattering of electrons. The Mott cross‐section is more accurate than the Rutherford one and provides a longer mean free path for low electron energies. This method is particularly applicable for microcomputers.
Artefacts arising during preparation of hydrated paper pulp samples for low‐temperature SEM
Authors: Moss P. A. , Howard R. C. , Sheffield E. 
Published: August 2011

SUMMARYBeating, a pulp treatment widely used in the paper industry, causes disruption of cell wall layers and fibrillation. Previous studies of the effects of beating on fibre morphology have used conventional methods of specimen preparation, with all the attendant problems of shrinkage and distortion during dehydration. Low‐temperature scanning electron microscopy (LTSEM) therefore seemed to offer an ideal method for examining fully hydrated wood pulp fibres. Cryofixation of pulp followed by sublimation of superficial ice, however, is shown to generate artefacts indistinguishable from structures present in the samples. Fibrillar and membranous structures were generated in LTSEM‐prepared sugar solutions; their presence in pulp samples was therefore attributed to the dissolved carbohydrates inherent in pulp suspensions. Since artefact and fact are currently impossible to distinguish in LTSEM‐prepared pulp samples, it seems that the technique should be applied to wet paper or pulp samples with considerable circumspection.
Three‐dimensional imaging of neurons by confocal fluorescence microscopy
Authors: Carlsson K. , Wallén P. , Brodin L. 
Published: August 2011

SummaryThe study of neuronal architecture by means of confocal laser microscopy is described. Optical serial sectioning has been performed on whole‐mount specimens, and the resulting stacks of digitally recorded images have been processed with the help of a computer. Specimen preparation is described, as well as the instrument and its performance. It is shown that the limits in photometric quality are set by photon quantum noise. As both light absorption and scattering was low in the studied specimens, the maximum scanning depth was limited mainly by the working distance of the objectives. Compared with traditional methods, confocal microscopy in combination with digital image processing has the following advantages: (1) a truly three‐dimensional (3‐D) reconstruction is obtained, (2) the specimen remains intact, (3) a higher resolution can be obtained, (4) the process is automated and less time‐consuming and (5) various kinds of data processing are possible.
Applications of confocal microscopy in industrial solid materials: some examples and a first evaluation
Authors: Knoester A. , Brakenhoff G. J. 
Published: August 2011

SUMMARYWe report here the first results of the application of confocal scanning laser microscopy (CSLM) for the study of the microstructure of solid industrial materials. Glass‐fibre‐reinforced composites, heterogeneous and conductive polymers, homogeneous as well as heterogeneous catalyst (precursor) specimens and soils were examined. We conclude that both the fluorescence and reflection modes of CSLM can yield valuable information. In particular, the optical sectioning capability of CSLM appears to be of great value as it enables one to access the 3‐D organization of the specimen without the need for a difficult and time‐consuming specimen preparation procedure. However, local obscuration may be an important factor in confocal image formation, limiting the penetration capabilities of the technique for industrial materials.
Standards for the application of X‐ray microanalysis to biological specimens
Authors: Warley Alice 
Published: August 2011

SUMMARYA review on the subject of compounds used as standards for biological X‐ray microanalysis is presented. The general approach used for standardization has been to use standards which resemble the specimen closely in composition. Thus, standards based on proteins have been used for analysis of quench‐frozen cryosectioned specimens, whereas standards based on embedding resins have been used for resin‐embedded material. The properties of, and problems associated with, each type of standard are recognized and have been well documented. The choice and analysis of standard should not be a drawback to fully quantitative analysis of biological material. Attention is drawn to the fact that the problems associated with any quantification procedure need to be kept in mind when analysis of standards is undertaken.
Estimation of structural anisotropy based on volume orientation. A new concept
Authors: Odgaard A. , Jensen E. B. , Gundersen H. J. G. 
Published: August 2011

SUMMARYThe quantification of anisotropy—its main direction and the degree of dispersion around it—is desirable in numerous research fields dealing with physical structures. Conventional methods are based on the orientation of interface elements. The results of these methods do not always agree with perceived anisotropy, and anisotropic structures do not necessarily turn out to be ‘anisotropic’ using these methods. In the present paper, we propose an alternative to curve and surface orientation, namely volume orientation. Using trabecular bone as an example of a two‐phase anisotropic structure, the new concept is studied in some detail. In particular, a parametric method of estimating volume orientation from sections is presented and discussed.
Fluorescence discrimination in a reflecting environment
Authors: Galassi L. 
Published: August 2011

SUMMARYA method to discriminate fluorescence from reflected or scattered light in epifluorescence microscopy is described. The method is based on the fact that the intensity of fluorescence measured with a long pass (LP) filter placed along the emerging beam (i.e. as a barrier filter) is higher than that measured with the same filter placed ahead of the objective (i.e. along the incident beam). On the other hand, when specific precautions are taken, the intensity of reflected or scattered light is identical to within a small difference. Within the margins of error of this small difference, it can be concluded that when the light intensity I measured with an LP filter along the emerging beam is higher than the intensity I' measured with the same filter along the incident beam, a fluorescent emission is present and the fraction of fluorescent light in the emerging beam is at least (I — I')/I.
Fuzzy sets‐based classification of electron microscopy images of biological macromolecules with an application to ribosomal particles
Authors: Carazo J. M. , Rivera F. F. , Zapata E. L. , Radermacher M. , Frank J. 
Published: August 2011

SUMMARYPattern recognition methods based on the theory of fuzzy sets are tested for their ability to classify electron microscopy images of biological specimens. The concept of fuzzy sets was chosen for its ability to represent classes of objects that are vaguely described from the measured data. A number of partitional clustering algorithms and an extensive set of cluster‐validity functionals (some already reported and some newly developed) have been applied to a test‐data set and to two real‐data sets of images. One of the real‐data sets corresponded to images of the Escherichia coli 50S ribosomal subunits depleted of proteins L7/L12 and the other set to images of the E. coli 70S monosome in the range of overlap views. These two latter sets had been previously studied by another clustering methodology. The new results obtained by the application of fuzzy clustering techniques will be compared to those previously obtained and some conclusions about the consistency of these classifications will be drawn from this comparison.
A quantitative interference light microscope study of human first trimester chorionic villi
Authors: Ockleford C. D. 
Published: August 2011

SUMMARYUsing a Jamin‐Lebedeff‐type interference microscope an analysis of frozen sections of human first trimester chorionic villi reveals regional differences down to subcellular resolution. The evidence indicates compositional differences between villus cell types and shows that the syncytiotrophoblast is differentiated into at least three layers, one of which corresponds positionally to the previously described syncytioskeletal layer.Quantitative measurements have been made of specimen thickness, refractive index and dry mass of regions in the tissue.Local differences in syncytiotrophoblast have been noted with respect to the content of a population of organelles with distinctive optical properties. These may correspond to stored forms of steroid hormone or their precursors.
Theoretical prediction of the electron backscattering coefficient for multilayer structures
Authors: August Hans‐Jürgen , Wernisch Johann 
Published: August 2011

SUMMARYBased on existing formulae for the backscattering coefficient for coated samples, i.e. for samples consisting of one film on a massive homogeneous substrate, a theory for the backscattering coefficient for multilayer structures is derived in a clear mathematical way without using approximations. The resulting expression is simple and ready to be applied in scanning electron microscopy or other related analytical techniques.
The total number of neurons in the human neocortex unbiasedly estimated using optical disectors
Authors: Braendgaard H. , Evans S. M. , Howard C. V. , Gundersen H. J. G. 
Published: August 2011

SUMMARYAn efficient method is presented for obtaining, in under 4h, an unbiased estimate of the total number of neurons in the human neocortex, with a coefficient of error on the estimate of ∼ 5%. The novel sampling scheme used in this study is unbiased and was designed so that only a small amount of neocortical grey matter had to be removed. Hence, the majority of the cerebral grey matter and all the internal grey matter was left intact for further resampling and analysis. Each cerebral hemisphere was subdivided into the four major neocortical regions, sliced coronally at 7‐mm intervals and the volume of the neocortex determined using Cavalieri's principle. Uniform sampling of neocortex was performed in the hemisphere followed by regional subsampling with a varying sampling fraction being taken from each region. Neuronal density estimates were made in thick plastic sections using optical disectors. Shrinkage estimates were made in parallel with the number estimates and found to be negligible. The total number of neocortical neurons in the right hemisphere of five normal 80‐year‐old men was found to be 13·7 × 109 with an inter‐individual coefficient of variation of 12%.
Estimating mean particle volume and number from random sections by sampling profile boundaries
Authors: Gittes Frederick 
Published: August 2011

SUMMARYWe describe some new shape‐independent stereological estimates of particle mean volume and surface area. Finding volumes or surface areas of cell nuclei, from electron micrographs of random thin sections, is a central problem of biological stereology. The well‐known point‐sampled intercept (PSI) method samples profile interiors to find the volume‐weighted mean volume. This can be used in place of the true mean volume, but to do so introduces bias when volumes vary a great deal, as they do in fixed specimens. Jensen and Gundersen quite recently extended the PSI estimator to provide particle surface area, with no bias in the case of uniform surface areas. Here we extend the PSI volume estimator in a different way, sampling profile boundaries rather than their interiors. We obtain a boundary‐sampled intercept (BSI) volume estimator, simpler than the PSI surface area estimator, but also unbiased for uniform surface areas. Both of these estimators are attractive, for example, in measuring and counting cell nuclei, where membrane surface area varies less than volume. Furthermore, they have no shape bias whatsoever. This paper also examines the general relationship between boundary‐ and area‐sampled estimates, and we clarify the formal connection between our volume estimator and the PSI surface area estimator. We also calculate and compare their theoretical efficiencies.
Estimating the total number of lymphatic valves in infant lungs with the fractionator
Authors: Ogbuihi Sylvester , Cruz‐Orive Luis M. 
Published: August 2011

SUMMARYThe fractionator is illustrated by means of a biomedical example involving the estimation of the number of lymphatic valves in lungs of infants who had died from sudden infant death syndrome (SIDS) and other known causes.The method is unbiased irrespective of tissue deformations and it does not require external information such as section thickness. An upper bound of the coefficient of error of the estimate of the number of valves within one lung was 6.5%, despite the fact that the number of valves counted per lung at the last stage ranged between 11 and 37 only. The upper bound includes the biological variation of the number of valves among infant lungs.Some theoretical remarks are also made on the efficiency of the fractionator. It is suggested, for instance, that the initial sampling stages cause more impact on the precision of the final estimator than the subsequent stages, and that an optimal arrangement of fragments submitted to systematic sampling should have the smallest fragments at the ends, with fragment contents increasing smoothly toward the middle of the series.
Curvature measurement with reflected‐light microscopy and its application to fly facet lenses
Authors: Stavenga D. G. , Leertouwer H. L. 
Published: August 2011

SUMMARYTwo methods for microscopically measuring the curvature of strongly curved surfaces are compared: one using a Michelson interferometer‐type microscope and one using a novel reflectometrical method implemented in an epi‐illumination microscope. The curvature values obtained with the two methods were very similar, but the latter proved to be by far the simplest.Curvature measurements on the front surface of the facet lenses of various dipteran flies revealed that facet lens diameter and radius of curvature are linearly related over a wide range of facet lens sizes.
Scanning tunnelling microscopy of tobacco mosaic virus on evaporated and sputter‐coated palladium/gold substrates
Authors: Mantovani J. G. , Allison D. P. , Warmack R. J. , Ferrell T. L. , Ford J. R. , Manos R. E. , Thompson J. R. , Reddick B. B. , Jacobson K. Bruce 
Published: August 2011

SUMMARYWe present scanning tunnelling microscope (STM) images of untreated tobacco mosaic virus (TMV) deposited on thermally evaporated and on sputter‐coated palladium/gold 40:60 (Pd/Au) substrates, and imaged under ordinary atmospheric conditions. The TMV imaged on both evaporated and sputter‐coated substrates was consistently several times wider than the known diameter of the virus. TMV on evaporated Pd/Au became overcoated with Pd/Au material during sample preparation and appeared elevated in STM images, whereas TMV on sputter‐coated Pd/Au appeared as depressions. When naked TMV were intentionally overcoated with Pd/Au, the STM images were found to be similar to those for TMV on evaporated Pd/Au.
Quantitative fluorescence in confocal microscopy
Authors: Van Oostveldt P. , Bauwens S. 
Published: August 2011

SUMMARYThe relationship between integrated fluorescence intensity and integrated absorbance was measured in Feulgen‐stained pigeon erythrocyte nuclei hydrolysed for different periods of time and stained at different dye concentrations.In conventional as well as confocal quantitative fluorescence microscopy the relationship between the integrated fluorescence intensity and the integrated absorbance shows a maximum. This is due to inner filtering and re‐absorption of the excitation light and emission light respectively.In conventional quantitative fluorescence microscopy the relationship is influenced by the numerical aperture of the objective lens.Under confocal observation, as measured with the BIO‐RAD MRC‐500 Confocal Imaging System, no influence of the numerical aperture of the objective lens on the relationship between the integrated fluorescence intensity and the integrated absorbance could be observed.
The role of detector geometry in confocal imaging
Authors: Wilson T. 
Published: August 2011

SUMMARYThe key property of confocal microscopes is their ability to produce three‐dimensional images. This arises simply by the use of a point detector. We discuss the use of point detectors, slit detectors, detector arrays and finite‐sized detectors on the strength of the optical sectioning when the systems are operated in both fluorescence and non‐fluorescence modes. We find that the sectioning is sharper in the non‐fluorescence case. We also discuss methods of obtaining differential phase contrast information and show that it is not possible to obtain pure differential phase contrast from a simple confocal microscope. However, a scheme consisting of two, suitably configured, confocal microscopes can give differential phase contrast with optical sectioning.
Optical sectioning with a fluorescence confocal SLM: procedures for determination of the 2‐D digital modulation transfer function and for 3‐D reconstruction by tessellation
Authors: Schormann Thorsten , Jovin Thomas M. 
Published: August 2011

SUMMARYWe have determined the operational parameters of a confocal scanning laser microscope (CSLM) used for fluorescence imaging. The system performance was characterized by the modulation transfer function (MTF), calculated from an edge response function (ERF) corresponding to a standard test pattern overlaying fluorescence solutions on a microscopic slide. Signal truncation error was avoided by making the ERF continuous at its limits through superposition of a suitable linear curve. We determined an appropriate scanning step density by defining a compromise between the requirements of the sampling theorem with respect to aliasing and the need for minimal suppression of higher spatial frequencies. These procedures for choosing the sampling density of the total digital CSLM permit a systematic optimization of the image acquisition parameters.A reproducible digital image was obtained, an important prerequisite for subsequent 3‐D image reconstruction. The latter was accomplished by first developing and applying a maximally automated algorithm for finding closed and distinct contours (corresponding to objects in the 2‐D optical sections). The missing information between contour loops was then interpolated by tessellation (triangulation) using a minimal polygon edge length criterion capable of describing closed surfaces even for adjacent contours with highly dissimilar geometries. In this procedure, we define an average shift length which compensates for the inherent disadvantage of run length encoding algorithms applied to different starting points in successive planes. The surface segments were used to calculate 3‐D representations by applying a shading model, in the present applications specifically to chromosome I and the nucleolus of polytenized Chironomus thummi salivary gland nuclei.
Three‐dimensional optical microscopy using tilted views
Authors: Shaw P. J. 
Published: August 2011

SUMMARYThe resolution of an optical microscope is considerably less in the direction of the optical axis (z) than in the x–y plane. This is true of conventional or confocal microscopes. To alleviate this problem we used multiple tilted views to supply the ‘missing data’ and thus increase the resolution in z. A special tilting stage was constructed which allowed specimens to be rotated through large angles. The relative, translation, rotation and z‐spacing between data sets were determined by a novel Wiener/phase cross‐correlation function. Once brought to a common coordinate system the data sets can be combined by Fourier space techniques similar to those used in X‐ray crystallography. We applied this technique to metaphase chromosomes from intact embryos of Drosophila melanogaster. As determined from significant intensity in the Fourier transform, the resolution of the final reconstruction was about 0ċ25 μm in x and y, and 0ċ4 μm in z.
Measurement of osteoclastic resorption pits with a tandem scanning microscope
Authors: Boyde A. , Dillon C. E. , Jones S. J. 
Published: August 2011

SUMMARYThe functional capacity of isolated osteoclasts is measured by determining the volume of bone or dentine which they can resorb in vitro when cultured on flat tissue slices. Previous SEM stereophotogrammetric evaluations showed that the measurement of total resorptive area per sample, number of pits per sample, area per pit, etc., may be insufficient and that the volume to area ratio may be of utmost importance. A new procedure for the 3‐D description and measurement of resorption pits using confocal microscopy has been established. Osteoclasts were cultured on slices of dentine which were prepared as for SEM. They were imaged with a Tracor Northern TSM equipped with piezo‐electric translators for the objective lens focusing motion, interfaced to a TN8500 computer, using a TV camera for image transfer. The procedure consisted of generating a z map image of the focus depth at which maximum brightness was found at each pixel. Constructing binary masks corresponding to (i) the edge of the resorption pit to define the area beneath which the volume is to be calculated, and (ii) a uniform width at a small distance outside the edge of the pit, enabled the average height of the original surface to be measured and the slice above the pit to be subtracted. After subtraction of the volume element which lay above the top of the original specimen surface, the z map is a measure of both the area and volume of the pit.
Study of Golgi‐impregnated material using the confocal tandem scanning reflected light microscope
Authors: Freire M. , Boyde A. 
Published: August 2011

SUMMARYThe tandem scanning reflected‐light microscope (TSM) is a real‐time, direct‐view confocal microscope. Only those points in the specimen situated in the focal plane contribute information to the image. A Tracor Northern TMS with piezo‐electric control of the objective lens was used to generate 3‐D images from Golgi‐impregnated hamster cerebral cortex. Stereoscopic pairs of images were recorded as 35‐mm colour film transparencies by photographing while automatically through‐focusing along inclined axes. Transferring the image via a TV camera to the computer, stereo‐pairs were obtained by oblique through‐focusing and summing, displaying maximum intensity data in each line of sight. Pseudocolour topographic displays were generated by assigning the pixel value in a z map image as the focal depth at which the back‐scattered light signal was maximal. The TSM was also modified so that a conventional transmitted‐light image with a large depth of field could be obtained simultaneously as the very shallow depth of field confocal back‐scattered‐light image seen at any focus level. The conventional image is a silhouette of the impregnated neurons: the top surface of the cell is not visible and the relationships of processes that cross over cell bodies cannot be discerned. TSM gives a high‐contrast image. The Golgi precipitate over the neuronal surface is resolved as globular or ovoid, coloured particles. The smaller particles also cover the dendritic spines. All the confocal range (extended focus) image display methods satisfactorily demonstrated the 3‐D arrangement of cell bodies and processes in the chosen volume.