bluuebunny/crossref_metadata_2025_split huggingface dataset:
Three‐dimensional distribution of damaged cells in cryopreserved pancreatic islets as determined by laser scanning confocal microscopy
Authors: MERCHANT F. A. , AGGARWAL S. J. , DILLER K. R. , BARTELS K. A. , BOVIK A. C. 
Published: August 2011

SUMMARYThe technique of serial optical sectioning by confocal microscopy, in conjunction with off‐line digital image analysis, was used to quantify the radial distribution of damaged cells in rat pancreatic islets following cryopreservation. The process consists of imaging frozen‐thawed islets of Langerhans using laser scanning confocal microscopy (LSCM). The three‐dimensional (3‐D) distribution and analysis of the two populations of viable and damaged cells was visualized via acridine orange/propidium iodide (AO/PI) fluorescent staining. In preparation for cryopreservation, isolated and cultured rat pancreatic islets were brought to a 2 m concentration of dimethyl sulphoxide (DMSO) by serial addition at decreasing temperatures. Ice was nucleated in the islet suspension at −10°C, and individual specimens were frozen to −70°C at cooling rates of 1, 3, 10 and 30°C/min in a programmable bulk freezer and subsequently stored in liquid nitrogen. After rapid thawing and serial dilution to remove DMSO, individual islets were prepared with AO/PI stains for imaging on the LSCM. Serial sections of the islets, 2–7 μm in thickness, were obtained and processed to obtain high‐contrast images. Analysis algorithms consisted of template masking, grey‐level thresholding, median filtering and 3‐D blob colouring. The radial distribution of damaged cells in the islets was determined by isolating the cell and computing its distance from the centroid of the 3‐D islet volume. An increase in the number of blobs corresponding to single and/or aggregates of damaged cells was observed progressively with distance from the centre towards the periphery of the islet. This pattern of freeze‐induced killing of cells within the islet was found to occur consistently in the numerous individual specimens processed.
Iterative, constrained 3‐D image reconstruction of transmitted light bright‐field micrographs based on maximum likelihood estimation
Authors: WILLIS B. , ROYSAM B. , TURNER J. N. , HOLMES T. J. 
Published: August 2011

SUMMARYWe present several image reconstruction algorithms for generating three‐dimensional (3‐D) renderings of bright‐field micrographs that are founded on maximum likelihood estimation (MLE) theory. The basic principle of the algorithms is in estimating the values of the optical densities of the specimen. A computer simulation and initial experimental testing of a steepest ascent version of the algorithm is presented. The computer simulation demonstrates that the MLE algorithm has an advantage over previously used inverse filtering techniques in that it partially restores the zeroed Fourier components in the well‐known missing‐cone region. We present 3‐D reconstructions from real biological data to show the potential of the algorithm in practical applications.
Measurement of co‐localization of objects in dual‐colour confocal images
Authors: MANDERS E. M. M. , VERBEEK F. J. , ATEN J. A. 
Published: August 2011

SUMMARYA method to measure the degree of co‐localization of objects in confocal dual‐colour images has been developed. This image analysis produced two coefficients that represent the fraction of co‐localizing objects in each component of a dual‐channel image. The generation of test objects with a Gaussian intensity distribution, at well‐defined positions in both components of dual‐channel images, allowed an accurate investigation of the reliability of the procedure. To do that, the co‐localization coefficients were determined before degrading the image with background, cross‐talk and Poisson noise. These synthesized sources of image deterioration represent sources of deterioration that must be dealt with in practical confocal imaging, namely dark current, non‐specific binding and cross‐reactivity of fluorescent probes, optical cross‐talk and photon noise. The degraded images were restored by filtering and cross‐talk correction. The co‐localization coefficients of the restored images were not significantly different from those of the original undegraded images. Finally, we tested the procedure on images of real biological specimens. The results of these tests correspond with data found in the literature. We conclude that the co‐localization coefficients can provide relevant quantitative information about the positional relation between biological objects or processes.
Unbiased volume estimation with coaxial sections: an application to the human bladder
Authors: CRUZ‐ORIVE L. M. , ROBERTS N. 
Published: August 2011

SUMMARYA problem of current medical interest is how to estimate the volume of an object from coaxial sections. Such images can be produced in ultrasound scanning, when the planar scan sections all emanate from a common axis. Two unbiased volume estimators for this sampling regime, previously published without derivation, are derived and presented here in some detail. The estimators are based on an ancient theorem of Pappus of Alexandria (c. ad 320). One of the estimators was used to estimate the volume of urine in the bladder of six human volunteers. The case example was attractive because the corresponding volumes could be voided and directly measured after the scanning session, thus confirming the unbiasedness of the estimator used. Sample size guidelines are also given.
Computerized characterization of the geometry of real porous media: their discretization, analysis and interpretation
Authors: THOVERT J. F. , SALLES J. , ADLER P. M. 
Published: August 2011

SUMMARYReal or reconstructed porous media can be discretized as a series of elementary cubes, which are filled either with a solid or a fluid phase. Various algorithms, based on pseudo‐diffusion processes, are proposed to determine the connected and percolating components of the pore space. The graph of the pore space is obtained by two different methods; the most efficient is based upon homotopic thinning. Topological characteristics, such as the number of loops, are derived. Systematic applications of these algorithms are illustrated on computer reconstructions of various sandstones.
Characterization of materials using surface and thin‐film analysis techniques
Authors: FITZGERALD A. G. 
Published: August 2011

SummaryThe application of X‐ray microanalysis, electron energy‐loss spectroscopy (EELS) and the surface analysis techniques of Auger electron spectroscopy (AES) and X‐ray photoelectron spectroscopy (XPS) to the characterization of materials is discussed. Examples of the application of these techniques to the characterization of amorphous films of silicon nitride, silicon carbide, hydrogenated carbon films and synthetic diamond films are described. Compositions obtained by each of these analytical techniques have been found to be in good agreement. The use of AES, XPS and EELS to investigate bonding and electronic structure in thin films and surfaces is discussed. Computer programs that have been developed to improve quantification in AES and XPS are described. These programs allow a comparison of matrix factor and final surface compositions obtained using different electron attenuation length corrections, back‐scatter corrections and photo‐ionization cross‐sections. Computer programs involving Monte Carlo simulations of X‐ray emission, which have been developed to enable quantification of the composition of thin films on thick substrates, are also described.
Infra‐red microspectroscopy as a complementary technique to electron‐probe microanalysis for the investigation of natural corrosion on potash glasses
Authors: COOPER G. I. , COX G. A. , PERUTZ R. N. 
Published: August 2011

SummaryNatural corrosion crusts on potash—lime—silica glasses, that have been buried in soil for very long periods, were examined using infra‐red reflectance microspectroscopy and electron‐probe techniques. Individually these techniques are useful: infra‐red provides information on which functional groups are present, but is not good at distinguishing between cations; electron‐probe microanalysis reveals the composition of a sample, but cannot explain how the elements are combined. By using both techniques on the same sample areas the corrosion was shown to be composed of layers of amorphous silica gel with precipitates such as carbonate‐substituted calcium phosphate, calcium sulphate and manganese dioxide.
Theoretical calculation of probe size of low‐voltage scanning electron microscopes
Authors: XIMEN J. , SHAO Z. , LIN P. S. D. 
Published: August 2011

SummaryDetailed investigating into the effects of spherical and chromatic aberrations, diffraction and the probe current allows the more general formulae for the optimized aperture and the minimum probe radius in low‐voltage scanning electron microscopes (LVSEMs) to be derived using both wave optics and geometric optics. The probe sizes for a diversity of electron sources in LVSEMs have been estimated, which may be useful for practical applications. The computed results indicate the possibility of achieving 1·5–2·0‐nm resolution at low voltages.
Electron microprobe study of the effect of long‐term vacuum storage of freeze‐dried cryosections on distribution of elements in cells
Authors: PELC R. , ŽIŽKA Z. 
Published: August 2011

SummaryThe distribution of elements in yeast cells was measured on freshly prepared, freeze‐dried cryosections and compared with the distribution obtained on the same sections after storage for 20 months in a vacuum below 2·6 kPa. The average concentration of phosphorus remained unchanged but was equalized throughout the cells, i.e. it migrated from vacuoles into the cytoplasm and mitochondria. Zinc remained preferentially localized in the vacuoles, but the ratio between vacuolar and cytoplasmic zinc concentrations decreased about three‐fold. Cytoplasmic and mitochondrial concentrations of potassium remained unchanged while partial release from the vacuoles and subsequently from the cells was observed. This resulted in a homogeneous distribution of potassium in the cells after 20 months and some of the vacuolar potassium appeared in spectra of formvar film measured several micrometres from the cells. A large increase in the sodium (from 160 to 360% more than in fresh sections), magnesium (from 110 to 200% more) and sulphur (from 70 to 350% more) contents was observed in all cellular compartments (except for vacuoles, where only a 20% increase in the magnesium content was observed), while chlorine was almost completely released from the cells. The limitations of the use of long‐term vacuum‐stored cryosections for electron micro‐probe analysis of cells are discussed.yeast.
The study of fission track and other crystalline defects using confocal scanning laser microscopy
Authors: PETFORD N. , MILLER J. A. 
Published: August 2011

SummaryConfocal scanning laser microscopy (SLM) is a technique that offers geologists a new way of studying structures in minerals at the submicrometre level. As an example we show how the non‐destructive nature of confocal SLM can be used to measure and count fission tracks (line defects formed by the spontaneous fission of238U) in the uranium‐bearing mineral apatite, and to provide information about the geometry and crystallographic orientation of fluid inclusions trapped inside apatite grains during crystallization. The technique also provides a means of studying the internal geometry of chemical zonation in minerals. The digitized nature of the SLM images makes them amenable to a variety of image analysis techniques, and we show how image analysis can be used to measure fission tracks in mica sheets and provide crude estimates of track dip. Finally, using a chemically etched mica sheet we show how confocal SLM can be used to provide a detailed near‐surface (1–5 μm) analysis of geological materials.
Evaluation of several common standards for the X‐ray microanalysis of thin biological specimens
Authors: PATAK A. , WRIGHT A. , MARSHALL A. T. 
Published: August 2011

SummaryThe question of the best type of standard to use for X‐ray microanalysis of thin biological specimens remains unanswered. Standards embedded in an organic matrix have the advantage that they resemble biological specimens, but their composition is generally not known exactly. We compared several standards and, surprisingly, inorganic binary salts sprayed onto a supporting film were the most suitable: they corresponded closely with several other methods using organic matrices; they were easily produced; and their composition is known. Glutaraldehydeurea aminoplastic resin thin sections and thin films containing dissolved salts were problematic. The composition of the polymer appears to be variable, and the thin films did not correspond with any other standard tested. Chelex100 bio‐standard beads and flakes loaded with accurately determined concentrations of ions, embedded in epoxy resin and thin sectioned, tended to correspond to the results obtained with the binary salts. However, the results from some bio‐standards were inexplicably aberrant. An epoxy resin standard was used for bromine, and was found to agree closely with the binary standards.
Computed three‐dimensional reconstruction of median‐eminence capillary modules: Image alignment and correlation
Authors: HIBBARD L. S. , GROTHE R. A. , ARNICAR‐SULZE T. L. , DOVEY‐HARTMAN B. J. , PAGE R. B. 
Published: August 2011

SummaryImage alignment is an absolute requirement for three‐dimensional (3‐D) reconstruction from serial sections, and Fourier correlation is the most powerful way to compute alignments. The rotational and translational components of misalignment can be corrected by an iterative correlation procedure, but for images having significant differences, alignment can fail with a likelihood proportional to the extent of the differences. We found that translational correction was determined much more reliably when low‐pass filters were applied to the product transforms from which the correlations were calculated. Rotational corrections based on polar analyses of the auto‐correlations of the images instead of on the images directly contributed to more accurate alignments. These methods were used to generate 3‐D reconstructions of brain capillary modules from serial‐section mosaics of digitized transmission electron micrographs.
Applied stereology in materials science and engineering
Authors: LIU G. 
Published: August 2011

SummaryA general view of the role of stereology in materials science and engineering (MSE), is followed by a discussion of applied stereology for one‐, two‐ and multi‐phase structures, and by examples of stereology applications to MSE, such as the impact of stereology on the creation and evolution of modern high–strength, low‐alloy steels. The present state and prospects of applied stereology in MSE are informally discussed. It is demonstrated that, without stereology, materials science cannot evolve into a truly quantitative science, and that the needs of both materials scientists and materials engineers should be met by the continuing cooperation of those who develop stereological methods and those who apply them.To solve such problems as quantifying the interaction between features of similar and different dimensions in two‐ or multi‐phase structures, a general parameter for volumetrical contiguity of second‐phase particles, a contiguity parameter for second‐phase particle profiles in grain‐boundary surfaces, and techniques termed ‘reversed stereology’ are proposed and discussed.
Contribution to microscopic analysis of birefringence in polarization‐maintaining optical fibres
Authors: SOVA M. , BERKA L. , ŜPUNDA J. 
Published: August 2011

SummaryA direct microscopic method for determination of birefringence in polarization‐maintaining optoelectronic fibres has been developed. The fibre, approximately 0·15 mm in diameter, is embedded in a suitable resin (epoxy). A thin section (approximately 3 mm in thickness) is then cut perpendicular to the fibre axis, ground and polished. Birefringent patterns (isochromatic fringes) can be seen and photographed using a light‐polarizing microscope with appropriate magnification. A method for performing a quantitative analysis of birefringence in real optoelectronic fibres using a macroscopic model is indicated.
Viruses accumulate spontaneously near droplet surfaces: A method to concentrate viruses for electron microscopy
Authors: JOHNSON R. P. C. , GREGORY D. W. 
Published: August 2011

SummaryVirus particles suspended in a drop of water tend to concentrate at or near its surface with the air. The concentrated, and probably more purified, particles may then be collected on a film‐coated grid for negative staining and electron microscopy. This is a useful method, simpler than others (e.g. high‐speed centrifugation, Lyphogel, or precipitation by (NH4)2SO4) which are used to process clinical specimens for diagnosis where virus particles may be too dilute in the original sample. It is shown, by freeze‐fracturing for electron microscopy, that Orf virus particles do accumulate at and just below the surfaces of drops. Various physical effects which may cause the particles to accumulate are considered. Results from a computer model suggest that Brownian motion alone could be adequate to transport a useful quantity of the particles in the body of a 2‐mm‐diameter hemispherical drop to its surface if the particles do not clump and if they remain trapped at the surface when they reach it. In practice, transport by Brownian motion is likely to be augmented by swirling, convection and other effects within drops.
New infiltration method permits use of freeze substitution for preparation of wood tissues for transmission electron microscopy
Authors: RISTIC Z. , ASHWORTH E. N. 
Published: August 2011

SummaryA new infiltration method was developed for preparation of wood tissues for transmission electron microscopy (TEM) using freeze substitution. The method included treatment of freeze‐substituted samples with sodium phosphate buffer before infiltration with epoxy resin. Samples from red osier (Cornus sericea L.) and flowering dogwood (C. florida L.) were studied to assess the quality of the infiltration method. The method produced well‐embedded samples with good trimming and cutting qualities. To our knowledge, this is the first report on preparation of wood tissues for TEM using freeze substitution.
Thermal oxidation stages of copper studied by STM in flowing argon
Authors: GARCÍA‐CANTÚ R. , ALVARADO J. J. , SOLORZA O. 
Published: August 2011

SummaryScanning tunnelling microscopy (STM) images under flowing argon are reported for successive stages of thermal oxidation of copper at room temperature. These STM images show zones with high tunnelling current peaks, more directly related to oxide growth than to the roughness of the topography.
Unbiased estimation of human body composition by the Cavalieri method using magnetic resonance imaging
Authors: ROBERTS N. , CRUZ‐ORIVE L. M. , REID N. M. K. , BRODIE D. A. , BOURNE M. , EDWARDS R. H. T. 
Published: August 2011

SummaryThe classical methods for estimating the volume of human body compartments in vivo (e.g. skin‐fold thickness for fat, radioisotope counting for different compartments, etc.) are generally indirect and rely on essentially empirical relationships — hence they are biased to unknown degrees. The advent of modern non‐invasive scanning techniques, such as X‐ray computed tomography (CT) and magnetic resonance imaging (MRI) is now widening the scope of volume quantification, especially in combination with stereological methods. Apart from its superior soft tissue contrast, MRI enjoys the distinct advantage of not using ionizing radiations.By a proper landmarking and control of the scanner couch, an adult male volunteer was scanned exhaustively into parallel systematic MR ‘sections’. Four compartments were defined, namely bone, muscle, organs and fat (which included the skin), and their corresponding volumes were easily and efficiently estimated by the Cavalieri method: the total section area of a compartment times the section interval estimates the volume of the compartment without bias. Formulae and nomograms are given to predict the errors and to optimize the design. To estimate an individual's muscle volume with a 5% coefficient of error, 10 sections and less than 10min point counting (to estimate the relevant section areas) are required. Bone and fat require about twice as much work. To estimate the mean muscle volume of a population with the same error contribution, from a random sample of six subjects, the workload per subject can be divided by √6, namely 4 min per subject. For a given number of sections planimetry would be as accurate but far more time consuming than point counting.
SPARK, a kernel of software programs for spatial reconstruction in electron microscopy
Authors: LANZAVECCHIA S. , BELLON P. L. , SCATTURIN V. 
Published: August 2011

SummarySPARK, an acronym for ‘SPAtial Reconstruction Kernel’, is the nucleus of a software library being developed for the three‐dimensional (3‐D) reconstruction of objects observed by the electron microscope. A unifying concept is used: the Fourier transform, known in several central sections, is resampled to obtain a 3‐D Cartesian grid, which is inverted by a fast Fourier transform. This technique is used for both single‐axis tilting (of 2‐D periodic layers or of isolated objects) and for the random conical‐tilt technique. The principles that make it possible to recover Cartesian grids in the two different geometries are illustrated and some preliminary results are reported. SPARK resamples the Cartesian grids with the use of a fast and efficient algorithm of Shannon interpolation developed by the authors.Compared to back‐projection techniques the method shows a considerable improvement in execution time with no sacrifice in accuracy; it therefore allows the effects of a variety of parameters in a given reconstruction to be scrutinized in a reasonable time. Some new possibilities and future extensions of the library are briefly outlined.
Quantitative acoustic microscopy of individual living human cells
Authors: BRIGGS G. A. D. , WANG J. , GUNDLE R. 
Published: August 2011

SummaryThe elastic properties of cells can be measured with microscopic resolution by acoustic microscopy. By measuring the waveform of very short pulses, the thickness, and the acoustic velocity, impedance and attenuation can be determined from the two separate signals reflected from the top and the bottom of the cell.
Spatial distribution of curve length: Concept and estimation
Authors: ROBERTS N. , CRUZ‐ORIVE L. M. 
Published: August 2011

SummaryThe length of a curvilinear feature, such as a dendrite tree of a neuron, can, in principle, be estimated by the recent, non‐invasive method of total vertical projections (TVPs). Curve length is a measure of size, but it reports nothing about curve shape. The shape of a tree‐like structure can be described to some extent by the distribution of branch length in properly defined regions of three‐dimensional (3‐D) space. A definition of curve length distribution in three dimensions is proposed and implemented here on a human neuron. The relevant 3‐D regions overlap after projection, and therefore the TVPs method cannot be used directly to estimate the corresponding feature lengths. However, using the ANALYZETM software system running on a SUN®SPARC workstation, dendrite subsets sitting in predefined regions of space were rendered in different colours and measured separately by the TVPs method using a cycloid test system. In combination with non‐invasive image acquisition and processing techniques, the length distribution concept is likely to be useful in the metrical analysis of either microscopic or macroscopic arborizations in a wide variety of contexts, including living cells and organisms.