bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inherent bias in correlation averaged images
Authors: WOODWARD J. T. , KONO C. , MADSEN L. L. , ZASADZINSKI J. A. 
Published: August 2011

SummaryThe correlation averaging algorithm frequently used to enhance micrographs of repeating structures contains an inherent bias that favours images with larger pixel values or positive noise levels. This bias not only skews the composite image toward higher pixel values, but also distorts the image by increasing the value of high‐valued pixels more than that of low‐valued pixels. These errors are especially important in scanning probe microscopy images where the pixel value reflects a distinct height. A similar algorithm that uses a structure function in place of the correlation function eliminates this bias.
An image processing system for cell behaviour studies in subconfluent cultures
Authors: ZICHA D. , DUNN G. A. 
Published: August 2011

SUMMARYDRIMAPS (digitally recorded interference microscopy with automatic phase‐shifting) is a system that we have developed for quantifying the behaviour of cells in subconfluent cultures. The primary data generated by the system consist of phase‐shifted interference (PSI) images which are accurate density maps of the distribution of dry mass (non‐aqueous material) inside cells. Time‐lapse sequences of PSI images may be viewed as movie sequences or processed in various ways to reveal many different aspects of the dynamics of cell growth and motile behaviour.Here we describe the image processing routines that are an integral part of the system and are required for four main functions:1 initial calculation of the PSI images;2 compensation of these images for instrumental distortion and instability;3 identification and tracking of individual cells in a time‐lapse sequence of PSI images;4 extraction of cell behavioural data from a time‐lapse sequence of PSI images.The first function converts standard interference microscope images into an image that accurately represents the optical phase‐difference introduced by the specimen. The second function recalibrates a sequence of images by taking the cell‐free region in each image as a reference plane of zero phase‐difference. This is particularly necessary to compensate for the long‐term instability of the Horn type of double‐beam interference microscope, which has several advantages over other types of interference microscope for studying cell behaviour. The third function compares consecutive images in a sequence in order to trace the identity of individual cells throughout the sequence. Semi‐automatic tracking, which allows close interaction with a human operator, is less prone to error than fully automatic tracking. The fourth function automatically extracts dynamic data from the identified cells. These data may include the true mass centroids of cells for translocation analysis and robust morphometric parameters for cell morphology examination. The integrated intensity of a cell is an accurate measure of cell mass and allows the growth (increase in dry mass) of individual cells to be studied. These data may be entered into a relational database of cell behaviour and a rule‐based system allows efficient data access and analysis.Experiments with phase‐contrast microscopy have revealed that many of these image processing methods are generally useful for cell behaviour studies using more conventional forms of microscopy.
X‐ray microanalysis of wet biological specimens in the environmental scanning electron microscope. 1. Reduction of specimen distance under different atmospheric conditions
Authors: GILPIN C. , SIGEE D. C. 
Published: August 2011

SUMMARYX‐ray microanalysis of non‐biological and biological specimens was carried out in the environmental scanning electron microscope (ESEM) under different conditions of specimen distance (the distance travelled by the electron probe within the specimen chamber) and chamber atmosphere.Using both water vapour and argon atmospheres, it was shown that reduction in specimen distance had no effect on atmospheric gas X‐ray signal in either case. Unlike water vapour, increased levels of argon (up to 10 torr) caused a marked depression of specimen P/B ratios, with a decrease in both characteristic and background (continuum) counts. These effects in argon were not altered by reduction in specimen distance.Specimen distance was important in relation to beam skirting and elemental analysis. With an extended assembly (short specimen distance), beam skirting in a water‐vapour atmosphere was much reduced – leading to enhanced element detectability in a discrete biological specimen (Anabaena cyclindrica).
The development of coherent Foucault imaging to investigate magnetic microstructure
Authors: JOHNSTON A. B. , CHAPMAN J. N. 
Published: August 2011

SUMMARYWe describe coherent Foucault (CF) imaging, a novel TEM technique which we have used successfully to investigate quantitatively micromagnetic structures in thin magnetic films. A simple analytical approach to CF imaging shows how an accurately positioned aperture in the diffraction plane leads to a magnetic interferogram forming in the image plane. Fringes follow lines of magnetic induction and there is one quantum of flux, h/e, between adjacent fringes. The aperture used can either be opaque or phase‐shifting and one‐ and two‐dimensional computer simulations have been performed to investigate how the nature and positioning of the aperture, along with the coherence of the illumination, affect the detailed form of the interferogram. Images recorded on a modified Philips CM20 FEG TEM confirm the simulations and demonstrate the power of the technique. The paper ends with a brief discussion of the broader uses of Foucault imaging.
Miniature magnetic electron lenses with permanent magnets
Authors: ADAMEC P. , DELONG A. , LENCOVÁ B. 
Published: August 2011

SUMMARYNew permanent magnet materials offer the possibility of designing lenses for applications at lower voltages. This paper briefly presents the finite‐element method (FEM) program for computation of lenses based on permanent magnets. The design of a lens unit for a low‐voltage TEM, realized in Brno, is described together with some design proposals of SEM and STEM lenses and computed results for a rotation‐free projector proposed by Le Poole in 1972.
Approximate expressions for electron lens properties*
Authors: HAWKES P. W. , LENCOVÁ B. , LENC M. 
Published: August 2011

SUMMARYNew approximate formulae for the focal length and principal aberration coefficients of electrostatic and magnetic lenses have been suggested by Crewe. These are compared with earlier approximate expressions and similarities and differences are indicated; they are also compared with calculated values for some real lenses. These comparisons confirm Crewe's findings and elucidate some unexplained features of these.
Second‐order finite element method and its practical application in charged particle optics
Authors: ZHU X. , MUNRO E. 
Published: August 2011

SUMMARYThe first‐order finite element method (FOFEM) has been widely used in computing electrostatic and magnetic fields of lenses and deflectors. With the increasing requirement of high‐accuracy field computation and the advances in the power of computers, the second‐order finite element method (SOFEM), which will be demonstrated in this paper to be more accurate than FOFEM, is becoming necessary and practical. In this paper, the concept of SOFEM will be described. Several applications of SOFEM in charged particle optics will also be illustrated, such as the simulation of electrostatic and magnetic lenses and deflectors, the modelling of electron and ion sources, and the evaluation of high‐order geometric and chromatic aberrations of charged particle columns.
Unconventional lens computation
Authors: LENCOVÁ B. 
Published: August 2011

SUMMARYProfessor Tom Mulvey has contributed significantly to the development of computer‐aided design in electron optics. Some of the problems connected with the computation of unconventional lenses and related test examples proposed by Mulvey are summarized. It is shown what boundary condition and position of boundary has to be selected for reliable results, what types and sizes of mesh should be used for required field accuracy, and which problems in the first‐order finite‐element method remain unsolved.
Double‐layer coating for high‐resolution low‐temperature scanning electron microscopy
Authors: WALTHER P. , WEHRLI E. , HERMANN R. , MÜLLER M. 
Published: August 2011

SummarySpecimen damage caused by mass loss due to electron beam irradiation is a major limitation in low‐temperature scanning electron microscopy of bulk specimens. At high primary magnifications (e.g. 100 000x) a hydrated sample is usually severely damaged after one slow scan (about 3000 e— nm—2). The consequences of this beam damage are significantly reduced by coating the frozen‐hydrated sample with a 5–10‐nm‐thick carbon layer. Since this layer covers up surface details, the sample is first unidirectionally shadowed with a thin heavy metal layer (e.g. 2 nm of platinum) that is in close contact with the biological surface (double layer coating). This heavy metal layer can be visualized in field‐emission scanning electron microscopy with the material‐dependent backscattered electron signal. The method allows for routine observation of large frozen‐hydrated samples. By use of an in‐lens field‐emission SEM and a sensitive backscattered electron detector, structural information comparable to that obtained with the transmission electron microscopy freeze‐fracture replica technique can be achieved.
Reflection conoscopy and micro‐ellipsometry of isotropic thin film structures
Authors: SHATALIN S. V. , JUŠKAITIS R. , TAN J. B. , WILSON T. 
Published: August 2011

SummaryThe conoscopic image of isotropic thin film structures is discussed, and it is shown that, although the specimens may be optically isotropic, the conoscopic images are generally not angularly symmetric. Theoretical expressions for these patterns are derived and from which full ellipsometric data about the specimen are extracted. In addition, a variety of spatial filters which may be inserted into the optical system in order to enhance specific image contrast are recommended.
Vitrification of articular cartilage by high‐pressure freezing
Authors: STUDER D. , MICHEL M. , WOHLWEND M. , HUNZIKER E. B. , BUSCHMANN M. D. 
Published: August 2011

SummaryFor more than 20 years, high‐pressure freezing has been used to cryofix bulk biological specimens and reports are available in which the potential and limits of this method have been evaluated mostly based on morphological criteria. By evaluating the presence or absence of segregation patterns, it was postulated that biological samples of up to 600 μm in thickness could be vitrified by high‐pressure freezing. The cooling rates necessary to achieve this result under high‐pressure conditions were estimated to be of the order of several hundred degrees kelvin per second. Recent results suggest that the thickness of biological samples which can be vitrified may be much less than previously believed.It was the aim of this study to explore the potential and limits of high‐pressure freezing using theoretical and experimental methods. A new high‐pressure freezing apparatus (Leiċa EM HPF), which can generate higher cooling rates at the sample surface than previously possible, was used. Using bovine articular cartilage as a model tissue system, we were able to vitrify 150‐μm‐thick tissue samples. Vitrification was proven by subjecting frozen‐hydrated cryosections to electron diffraction analysis and was found to be dependent on the proteoglycan concentration and water content of the cartilage. Only the lower radical zone (with a high proteoglycan concentration and a low water content compared to the other zones) could be fully vitrified. Our theoretical calculations indicated that applied surface cooling rates in excess of 5000 K/s can be propagated into specimen centres only if samples are relatively thin (<200 μm). These calculations, taken together with our zone‐dependent attainment of vitrification in 150‐μm‐thick cartilage samples, suggest that the critical cooling rates necessary to achieve vitrification of biological samples under high‐pressure freezing conditions are significantly higher (1000–100 000 K/s) than previously proposed, but are reduced by about a factor of 100 when compared to cooling rates necessary to vitrify biological samples at ambient pressure.
Electron energy‐loss near‐edge structure of internal interfaces by spatial difference spectroscopy
Authors: MÜLLEJANS H. , BRULEY J. 
Published: August 2011

SUMMARYInternal interfaces determine the macroscopic mechanical and electronic properties of materials. Their investigation is therefore essential for an understanding of the relationship between microstructure and the materials properties. Besides the atomic structure, the bonding and electronic structure on an atomic scale are of interest. This information is contained in the interface‐sensitive component of the electron energy‐loss near‐edge structure (ELNES). It can be extracted by the spatial difference method. Such spectra have already been interpreted with respect to the bonding and the local atomic environment of the atoms at the interface. Here we assess critically the application of the spatial difference for the investigation of internal interfaces. The method is subjective because a suitable scaling factor has to be chosen. As a guideline we propose to minimize the number of turning points in the difference spectrum. With this hypothesis we successfully determine the ELNES arising from atoms at two internal interfaces between a metal and a ceramic. This reveals qualitatively which type of bonding is present at the interface and quantitatively how many atoms are involved in it.
Quantitative near‐edge structure analysis of diamond‐like carbon in the electron microscope using a two‐window method
Authors: BRULEY J. , WILLIAMS D. B. , CUOMO J. J. , PAPPAS D. P. 
Published: August 2011

SUMMARYTo extract quantitative electronic structure information from electron energy‐loss near‐edge structure typically necessitates the separation of spectra into linearly independent components. For this to be accomplished, certain conditions need to be met concerning the localization of chemical bonding and the linear scaling of fine structure with density of states. The dependence of the processing parameters, such as window widths and positions, of the commonly used ‘two‐window intensity‐ratio’ method to determine the distribution of π and σ bonding of diamond‐like carbon films is investigated. It is shown that, although the selection of the integration windows can lead to very large variations in the resultant bonding fractions, the placement of two small windows centred on the edge structures of interest does permit a robust and reliable estimate of bonding. It is demonstrated that the sp3 variations can be reproducibly monitored with a relative accuracy of about ± 5%, and an absolute concentration given with an accuracy of ± 13% for foils of thickness at least up to twice the inelastic mean free path.
A software package for the processing and reconstruction of electron holograms
Authors: VÖLKL E. , ALLARD L. F. , FROST B. 
Published: August 2011

SUMMARYElectron holography is leaving its state of infancy and is rapidly becoming a tool for everyday use. This is due to the increasing availability of field‐emission electron microscopes as well as the increasing use of slow‐scan CCD cameras, which provide the linear image recording so essential to electron holography. At the same time, the continuing boost in performance of desktop computers both in hardware and in software has facilitated the handling of many of the complex reconstruction and processing tasks of electron holography. We describe here the software package ‘HoloWorks©’, recently developed at Oak Ridge National Laboratories. This package is designed for the processing of electron holograms stressing easy‐to‐use functions and is a plug‐in module for Gatan's software DigitalMicrograph®.
Analysis of bonding state in pure and gold‐implanted amorphous SiC by a combination of UHVEM and AES
Authors: YASUDA H. , MORI H. 
Published: August 2011

SUMMARYSingle crystalline α‐SiC films and Au(target metal)/α‐SiC(substrate) bilayer films were irradiated with 2‐MeV electrons in an ultrahigh‐voltage electron microscope (UHVEM) to form, in situ, pure amorphous SiC (a‐SiC) and gold‐implanted a‐SiC. respectively. In the latter case, sample films were set so that the electron beam was incident on the gold layer. Differences in the bonding state between pure a‐SiC and gold‐implanted a‐SiC were studied by Auger valence electron spectroscopy (AES). In pure a‐SiC. the carbon valence state was markedly different from that of α‐SiC but the silicon valence state was similar to that of α‐SiC. In gold‐implanted α‐SiC. both the carbon and the silicon valence states were different from those of α‐SiC. It is suggested that a high density of molecularized carbon clusters are formed in the amorphous matrix in gold‐enriched a‐SiC.
The effects of total internal reflection on the spread function along the axis in confocal microscopy
Authors: ENTWISTLE A. 
Published: August 2011

SummaryA broadening and splitting of the axial spread function is observed when high‐numerical‐aperture (NA) oil‐immersion objectives are used on a confocal microscope to examine dielectric interfaces when the refractive index below the boundary is lower than the NA of the objective. The phenomena is due to total internal reflection probably as a consequence of the Goos‐Hänchen shift. If total internal reflection occurs when undertaking confocal microscopy, this shift creates obvious problems when the optical sectioning capabilities must be optimal in reflectance mode and more subtle difficulties can arise when examining fluorescent emission. Alternatively, deliberately inducing total internal reflection can be used to estimate the refractive index in component parts within foams, emulsions and aerated specimens where such measurements can be relatively difficult to make by other means. Furthermore, the examination of total internal reflection with a confocal microscope permits the phenomena of total internal reflection itself to be probed with very high illumination intensities without disturbing the boundary conditions with an external probe. Finally, other changes in the apparent position of the focus were noted to occur when high‐NA oil‐immersion objectives are used to examine specimens such as metal mirrors.
Edge effect in Auger electron microscopy: Quantification of the effect
Authors: FRANK L. , MATÊJKA F. 
Published: August 2011

SummaryThe edge effect in electron microscopical images is proposed to be measured in length units by using a ratio of the edge or near‐to‐edge signal enhancement or depletion integrated over all this feature along a line‐scan across an edge, to the mean signal away from the edge, giving the result in length units. This approach is applied to quantification of the edge effect in Auger electron images, which is examined by using specimens with sharp edge terminated overlayer terraces, both chemically homogeneous and heterogeneous. The following combinations of overlayer/substrate materials were used: Si/Si of three different overlayer thicknesses, W/W and W/Si, and line‐scans across the edges were recorded in both the low‐ and the high‐energy Auger electrons mode, i.e. Si LMM and Si KLL or W NOO and W MNN. The experimental results are presented for the 3‐, 10‐ and 20‐keV primary electron energies. Owing to a low signal‐to‐noise ratio in the measured data, basic relations between the effect appearance and the experimental conditions were revealed only: on both Si and W homogeneous specimens with a surface step, the edge enhancement is the dominating subphenomenon while at the W terrace edge on the Si substrate, the ‘penetration’ of the radiation characteristic to both areas separated by the step, to the neighbouring feature, is observed as the most significant effect. The quantification has shown that the effect is, first of all, proportional to the step height, amounting to one‐third to up to the full height, while the material dependence was weak, equally to the dependence on the Auger electron energy. The primary electron energy dependence is increasing in accordance with expectation. The results indicate that the effect cannot be modelled simply by the interaction volume cut by the surface step but phenomena such as subsurface electron channelling along the sidewall have to be taken into account.
Imaging and nano‐dissection of tobacco mosaic virus by atomic force microscopy
Authors: BUSHELL G. R. , WATSON G. S. , HOLT S. A. , MYHRA S. 
Published: August 2011

SummaryTobacco mosaic virus (TMV) has been deposited on freshly cleaved mica substrates. The topography was investigated by contact, non‐contact and lateral‐force microscopy under ambient conditions in air. The results were in accord with known dimensions of TMV (i.e. 18 nm in diameter and 300 nm in length). However, convolution of tip shape with TMV morphology resulted in an apparent width of 80–140 nm in the lateral plane, a factor of 4–7 greater than the known diameter. Other artefacts ‐ broadening and double images ‐ were observed and ascribed to tip anomalies.High force loadings and slow repetitive scanning resulted in controlled removal of parts of the TMV structure. Accordingly, it was possible to reveal and image the central core channel of the TMV. The precision and resolution of dissection induced by AFM is currently limited by the shape of the tip, having a 40‐nm radius of curvature for standard Si3N4 tips. It is estimated that sharper tips, with a radius of curvature of less than 10 nm, should be able to resolve, non‐destructively, the protein subunits in the non‐contact mode, and selectively remove single subunits in the contact mode.
Preparation of metal multilayer TEM cross‐sections using ultramicrotomy
Authors: HOWELL D. A. , JR J. W. HECKMAN , CRIMP M. A. 
Published: August 2011

SummaryUltramicrotomy is an effective method of sample preparation for TEM of metal multilayer thin‐films. Large, thin, cross‐sectional areas can be obtained for TEM observations from a small amount of thin‐film which has been mechanically removed from its substrate. An example of a TEM cross‐section made from an AuFe0.03/a‐silicon multilayer used in the study of metallic spin‐glass properties illustrates the usefulness of ultramicrotomy in preparing samples that are largely free of the deleterious effects associated with ion‐milling such as irradiation damage, differential thinning and variable thickness.
Recent developments in secondary electron imaging
Authors: HOWIE A. 
Published: August 2011

SUMMARYSome recent experimental and theoretical developments in secondary electron (SE) imaging are reviewed. Coincidence experiments identify inner‐shell excitations and single electron valence excitations often as more significant initial events in SE production than the more delocalized process of plasmon generation. Quantitative measurement and interpretation of escape depths in different materials are now becoming possible. Local variations in surface barrier height or work function can be imaged, e.g. at p‐n junctions in semiconductors, especially if the effects of external patch fields are overcome.
Changes in the iron white‐line ratio in the electron energy‐loss spectrum of iron‐copper multilayers
Authors: LLOYD S. J. , BOTTON G. A. , STOBBS W. M. 
Published: August 2011

SUMMARYWe report changes in the iron L3/L2 white‐line ratio of the electron energy‐loss spectrum of a series of iron‐copper multilayers which we discuss in terms of the lattice plane spacings present in the multilayer system. Momentum‐resolved data from one multilayer is also considered.