Biology Commons^™

Idiopathic Calcium Oxalate Nephrolithiasis: A Cellular Disease, Giovanni Gambaro, Bruno Baggio

Scanning Microscopy

Physico-chemical, metabolic and hormonal theories regarding the pathogenesis of calcium oxalate nephrolithiasis do not sufficiently explain many features of this disease. The recent findings of an abnormally faster oxalate self-exchange and higher phosphorylation of band 3 in erythrocytes of idiopathic calcium oxalate stone formers suggest the hypothesis that nephrolithiasis may be a cellular disease, characterized by a defect in the function of the anion-exchange. The cellular anomaly seems genetically controlled. Band 3 anion exchanger function seems to be biochemically regulated through modulation of band 3 phosphorylation, which depends on cyclic AMP- and phospholipid-sensitive Ca²⁺ independent protein kinases. In this …

Factors Affecting Fasting Urinary Calcium Excretion In Stone Former Patients On Different Dietary Calcium Intake, Piergiorgio Messa, Giuseppe Mioni, Rossana Franzon, Michele Messa, Aldo Cruciatti, Sandro Giannini, Angela D'Angelo

Scanning Microscopy

The effects of variable calcium content on daily and fasting urinary calcium and other lithogenic solutes excretion, on the bone turnover index (fasting hydroxyproline urinary excretion) and on the calciotropic hormones were studied in 312 stone former patients with an outpatient protocol and 15 stone former patients in an inpatient study. Furthermore in 60 of these patients, 30 while on a low calcium diet (LCD) and 30 on a free calcium home diet (FCD), the effects of an oral calcium load (OCL) on bone turnover index, calciotropic hormones and calcium excretion were evaluated. The results demonstrate that an LCD is …

Acquisition Hardware For Imaging, Peter Rez, J. K. Weiss, W. J. De Ruijter

Scanning Microscopy

In electron microscopy images can either be recorded in parallel (Transmission Electron Microscopy) or acquired as the variation in a signal as a probe is scanned over the specimen (Scanning Electron Microscopy). To extract the most information from an image requires that the best possible systems are used for acquiring image data. Ultimately, the limit to information capture is achieved when every electron from the scattering event of interest is recorded. The ideal system can be realised both for parallel recording with scientific grade CCD cameras, and for scanning microscopy with single electron counting electronics. The data rates from these …

Simulation For Scanning Electron Microscopy, G. R. Anstis, X. S. Gan

Scanning Microscopy

Simulations of images of surface steps obtained by high energy reflection electron microscopy are presented. It is shown that double images of simple steps, with no associated strain field, may occur when surface resonance conditions are established. Accurate calculation of image intensity requires large calculations and care is needed in relating the computed wave functions to those occurring for a semi-infinite incident wave. Estimates of the time to compute accurate wavefunctions are given and it is shown that they are reasonable for modem fast computers.

Atomic Resolution Electron Holography, K. Ishizuka, T. Tanji, A. Tonomura

Scanning Microscopy

It has been demonstrated that electron holography is a very powerful tool to investigate an electromagnetic potential in medium resolution, since the phase of an electron wave is approximately proportional to the potential. Now, electron holography is at the second stage of development: to establish holography at atomic resolution and further to realize Gabor's idea to improve the resolution restricted by the spherical aberration of the objective lens. We investigate the possibility of electron holography to get information at atomic resolution by computer simulations as well as by digital processing of electron holograms. We show that the phase distribution has …

Image Delocalisation And High Resolution Transmission Electron Microscopic Imaging With A Field Emission Gun, W. Coene, A. J. E. M. Jansen

Scanning Microscopy

The high spatial and temporal coherence of a field emission gun (FEG) increases the information limit of high-resolution transmission electron microscopes (HRTEM), but has also its implications on the localisation of the high resolution information in the image. In this paper, we present the results of a combined theoretical and experimental study of delocalisation in HRTEM. First, we derive a spatial frequency analysis of the delocalisation for crystal defects. Next, the delocalisation is studied from a real-space point of view, in terms of the impulse-response function, for which an instructive asymptotic mathematical analysis has been set up. Finally, we present …

Image-Matching As A Means Of Atomic Structure Evaluation In High Resolution Transmission Electron Microscopy, John C. Barry

Scanning Microscopy

Two of the major applications of the high resolution transmission electron microscope (HRTEM) image-matching technique are: a) to refine the structure of defects and interfaces in crystals, and b) to identify minority phases in multi-phase materials. An important advantage of the technique is that it provides spatial information at the atomic level; but an important disadvantage is that the results are often hard to quantify. There are many factors which affect the precision of the image-matching technique, and methods for measuring the pertinent experimental parameters are discussed in this paper. It is shown that if the experimental parameters are known, …

Sub-Angstrom Microscopy Through Incoherent Imaging And Image Reconstruction, S. J. Pennycook, D. E. Jesson, M. F. Chisholm, A. G. Ferridge, M. J. Seddon

Scanning Microscopy

Z-contrast scanning transmission electron microscopy (STEM) with a high-angle annular detector breaks the coherence of the imaging process, and provides an incoherent image of a crystal projection. Even in the presence of strong dynamical diffraction, the image can be accurately described as a convolution between an object function, sharply peaked at the projected atomic sites, and the probe intensity profile. Such an image can be inverted intuitively without the need for model structures, and therefore provides the important capability to reveal unanticipated interfacial arrangements. It represents a direct image of the crystal projection, revealing the location of the atomic columns …

Segmentation Of Pores In Backscattered Images Of Sediments And Soils And Their Relationship To Domain Structure, M. W. Hounslow, N. K. Tovey

Scanning Microscopy

A new technique to quantify variations in pore structure across an image is described in this paper. The method involves several stages as the original images are rarely suitable for simple segmentation by the selection of a single threshold. The processing first involves the application of a Wiener filter to remove imaging artefacts and to sharpen the edge of void/particle contacts. This image reconstruction is followed by the selection of a global threshold based on the relative contrast method, to create a binary image separating the voids from the particles. Such an image can be used to evaluate pore structure …

Cathodoluminescence Image Processing Of High Tc Superconductors, Z. Barkay, G. Deutscher, E. Grunbaum

Scanning Microscopy

Cathodoluminescence (CL) in the Scanning Electron Microscope (SEM) was performed for both ceramic pellets and thin films of YBaCuO high T_C superconductors. Image processing provided additional quantitative information. For single phase films, we demonstrated the possibility to create thickness maps in real time from the CL pictures. The gradual thickness variation within the sample was revealed by the histogram of the thickness image. The continuity of the film was observed at a few threshold thicknesses values, defined by the fraction of the occupied area. At the conduction threshold value, the location and width of the conducting paths could be …

Direct Methods In High Resolution Electron Microscopy, D. Van Dyck, M. Op De Beeck

Scanning Microscopy

New approaches are proposed to retrieve the wavefunction at the object and from this, to retrieve the projected structure of the object. The wavefunction is retrieved by capturing images at a series of closely spaced focus values and to process the whole 3D data. The structure of the object is retrieved using a formalism based on electron channelling.

Morphological Three-Dimensional Analysis, C. Gratin, F. Meyer

Scanning Microscopy

This paper presents the main results of our research on mathematical morphology for three-dimensional images. The first issue is to decide which grid must be used. The face-centred cubic grid and the centred cubic grid seem to be more suitable than the cubic grid in terms of possible rotations. For these two grids we derive the formulae for the basic Minkovski measures. Then we show through several examples that extension from 2D to 3D is straightforward for most transformations. The efficiency of direct 3D processing is illustrated by applications to filtering, overlapping particle separation and grey-scale image segmentation.

An Optical Moiré Technique For The Analysis Of Displacements In Lattice Images, C. J. D. Hetherington, U. Dahmen

Scanning Microscopy

High resolution electron microscopy is a means for imaging not only the local structure at a defect or interface but also the displacement field in the surrounding lattice. However, in general it is difficult or tedious to analyse this field which can extend across the entire micrograph. The optical moiré technique, which is based on interference effects between the experimental lattice image and an artificial reference lattice, allows a rapid and accurate measurement of the displacements. Small violations of translation, rotation or mirror symmetries give rise to large changes in the periodicity or orientation of the moiré pattern.

The spacing …

Application Of Slow-Scan Charge-Coupled Device (Ccd) Cameras To On-Line Microscope Control, O. L. Krivanek, G. Y. Fan

Scanning Microscopy

Autotuning methods for transmission electron microscopy are reviewed, and a distinction is drawn between predictive and non-predictive methods. The predictive methods make better use of the input data and therefore need fewer images to carry out complete autotuning. They typically require high quality of input data, which can be best provided by cooled slow-scan charge-coupled device (CCD) cameras. Two predictive methods are considered in more detail. These are the tilt-induced image shift (TIS) method of Koster, van der Mast and de Ruijter, and a new automated diffractogram analysis (ADA) method, which is introduced in this paper. The ADA method is …

Measurement Of Electron-Optical Parameters For High-Resolution Electron Microscopy Image Interpretation, A. F. De Jong, A. J. Koster

Scanning Microscopy

A method is presented to measure various electron-optical parameters needed for high-resolution electron microscopy image interpretation with high accuracy. The method is based on the measurement of a series of beam-tilt induced image displacements. The displacements are calculated via cross-correlation of the images, and subsequently fitted to a third-order polynomal in the beam tilt. From two series of images (using the x and y beam tilt coils), the spherical aberration constant of the microscope can be measured, as well as the current values of defocus, beam tilt and astigmatism. The spherical aberration constant of three Philips microscopes is measured with …

Imaging Deformed Proteins: Characterising The State Fully, W. O. Saxton

Scanning Microscopy

By analysing the positions of individual unit cells in the image of a distorted macromolecular crystal, it is possible to achieve considerably more than is achieved by the correlation averaging or unbending now widely practised. It is possible partly to compensate for individual molecular distortion; and it is possible to identify molecules in equivalent environments (which can be expected to be in equivalent states of strain), selective averaging of which yields images that show how strain is accommodated at the sub-molecular level. The possible presence of surface forces applied to the crystal by its support film complicates the analysis and …

The Watershed Transformation Applied To Image Segmentation, Serge Beucher

Scanning Microscopy

Image segmentation by mathematical morphology is a methodology based upon the notions of watershed and homotopy modification.This paper aims at introducing this methodology through various examples of segmentation in materials sciences, electron microscopy and scene analysis.

First, we defined our basic tool, the watershed transform. We showed that this transformation can be built by implementing a flooding process on a greytone image. This flooding process can be performed by using elementary morphological operations such as geodesic skeleton and reconstruction. Other algorithms are also briefly presented (arrows representation).

Then, the use of this transformation for image segmentation purposes is discussed. The …

Phase Space Methods In Image Formation Theory, Victor Castaño, Gustavo Vásquez-Polo, Ramón Gutiérrez-Castrejón

Scanning Microscopy

A review of the basic mathematical principles and properties of some phase space functions (Wigner and Ambiguity functions) is first presented in a more general mathematical context. Then, we deal in detail with three applications : image formation in optical systems (specifically cascading systems of lenses), image formation in Transmission Electron Microscopy, by taking advantage of some formal similarities with the previous examples and, finally, contrast transfer functions in Electron Microscopy in order to obtain 2-dimensional plots which provide information on the behavior of a transmission electron microscope. Also, the relations of these functions with other mathematical tools utilized in …

Random Image Models For Microstructure Analysis And Simulation, Dominique Jeulin

Scanning Microscopy

A wide spectrum of Random Function models, based on the theory of Random sets, are introduced to simulate single or multivariate signals as encountered in the common practice of electron probe microscopy.

These models are built in three steps, combining the choice of a family of primary random functions and of Poisson varieties in the n-dimensional space for their implantation. For electron microscopy images, they can describe the following situations:

- topography (as obtained from stereo pair images in fractography) simulated by Boolean and by alternate sequential random functions;

- thick slices (as in the case of Transmission Electron Microscope …

Some Applications Of Image Analysis To Materials Science, François Grillon

Scanning Microscopy

We have presented four applications of Image Analysis to material science. The first one is on a yarn composite SiC where we want to know the relative proportion of matrix, fibers, porosity and the size of the fibers. The results are used to estimate mechanical properties of the composite.

The second one is to measure the residual porosity after a laser shock on powder metallurgy steel. The knowledge of the depth of the affected zone is necessary to optimise the laser treatment.

The third one uses Fourier transformation to analyse plastic deformation on grains. Values are obtained from Fourier transform …

Diffraction And Imaging Theory Of Inelastically Scattered Electrons - A New Approach, Z. L. Wang, J. Bentley

Scanning Microscopy

A new dynamical theory is developed for describing inelastic electron scattering in thin crystals. Compared to existing theories, the first advantage of this new theory is that the incoherent summation of the diffracted intensities contributed by electrons after exciting vast numbers of degenerate excited states has been evaluated before any numerical calculation. The second advantage is that only the modulus squared of the transition matrix elements are needed in the final computation. This greatly reduces the effort in searching for "phase shifts" in inelastic scattering matrix calculations. By iterative operation of this single-inelastic scattering theory, multiple-inelastic electron scattering of phonons, …

The Application Of Multispectral Techniques To Analytical Electron Microscopy, P. G. Kenny, M. Prutton, R. H. Roberts, I. R. Barkshire, J. C. Greenwood, M. J. Hadley, S. P. Tear

Scanning Microscopy

The York multispectral analytical electron microscope (MULSAM) was the first instrument specifically designed to acquire and process multiple Auger, X-ray, backscattered electron, elastically scattered electron, scanning electron microscopy (SEM) and specimen absorption current images simultaneously. Analyzing combinations of these signals with multispectral correlation techniques yields more information than would normally be obtained by treating each image separately. This paper reports some of the multispectral methods we have investigated at York which may be of use to other workers. Included are (1) a method that corrects for beam current fluctuations during long acquisition runs which is based on the anti-correlation between …

A Brief Introduction To Aims And Methods For Image Processing Of Electron Micrographs Of Biological Specimens, Murray Stewart

Scanning Microscopy

A common problem with electron micrographs of biological objects is that fine details are usually faint and, moreover, tend to be obscured by background noise from stain and support film. Filtering is a useful way to improve the signal-to-noise ratio and is particularly important when trying to detect small changes (conformational or due to labelling) or when examining frozen hydrated objects, where the statistical definition of the image has been reduced because of the low-dose conditions needed to prevent radiation damage. Filtering can also be used to address the superposition effects that result from the large depth of focus of …

Three-Dimensional Crystallographic Reconstruction For Atomic Resolution, Kenneth H. Downing

Scanning Microscopy

Three-dimensional structures have recently been determined by electron crystallography at a resolution high enough to determine atomic arrangements in both protein and mineral specimens. The different nature of these two types of specimens produces some very significant differences in the way data is obtained and processed, although the principles are the same. The sensitivity of proteins to damage by the electron beam limits the signal-to-noise ratio in the image and the resolution to which data can be extracted from the image. A number of constraints, such as the amino acid sequence and the connectivity of atoms within amino acids, can …

Alignment, Classification, And Three-Dimensional Reconstruction Of Single Particles Embedded In Ice, Joachim Frank, Pawel Penczek, Weiping Liu

Scanning Microscopy

Cryo-electron microscopy of single biological particles poses new challenges to digital image processing due to the low signal-to-noise ratio of the data. New tools have been devised to deal with important aspects of 3-D reconstruction following the random-conical data collection scheme: (a) a new shift-invariant function has been derived, which promises to facilitate alignment and classification of single particle projections; (b) a new method of orientation search is proposed, which makes it possible to relate random-conical data sets to one another prior to reconstruction; and (c) the foundation is laid for a 3-D variance estimation which utilizes the oversampling of …

Confocal Microscopy And Three-Dimensional Reconstruction Of Thick, Transparent, Vital Tissue, Barry R. Masters

Scanning Microscopy

The three-dimensional visualization of the 400 micron thick, transparent, in situ cornea is described to demonstrate the use of confocal light microscopy for noninvasive imaging of living cells and thick tissues in their normal, vital conditions. Specimen preparation and physiological stability, as well as light attenuation corrections are critical to data acquisition. The technique to provide mechanical stability of the specimen during the duration of the image acquisition is explained. A laser scanning confocal light microscope (LSCM) was used to obtain optical serial sections from rabbit eyes that were freshly removed and placed in a physiological Ringer's solution. This study …

Structure Analysis Of Ice-Embedded Single Particles, M. Van Heel, H. Winkler, E. Orlova, M. Schatz

Scanning Microscopy

The conventional negative-stain preparation method for electron microscopy, in which biological macromolecules are contrasted using heavy metal salts (such as uranyl-acetate), is a simple and fast technique which has helped visualize hundreds of different molecular structures. Computer analysis of such negatively stained images of individual (i.e., non-crystalline) macromolecules using statistical pattern-recognition techniques has revealed considerable new structural information. Negative staining, however, has some disadvantages: the specimens are often severely flattened (as much as 25%-75%), they often exhibit strong preferential attachment of the molecules to the supporting carbon foil, and the molecular images may be difficult to interpret due to the …

Morphological Filtering And Granulometric Analysis On Scanning Electron Micrographs: Applications In Materials Science, Murielle Prod'homme, Michel Coster, Liliane Chermant, Jean-Louis Chermant

Scanning Microscopy

For many applications, scanning electron microscopy (SEM) images reflect the granular texture of analysed objects. So it is important to characterise the morphology of this texture and also to filter these images. Because the size of the texture is the main criterion to be studied, we have focused our paper on granulometric analysis.

We present basic parameters, morphological filtering and granulometry for Rⁿ•R functions and their properties with local knowledge and anamorphosis.

Some applications in the domain of materials science illustrate these methods and present their suitable possibilities.

Application Of The Wavelet Transform To The Digital Image Processing Of Electron Micrographs And Of Backreflection Electron Diffraction Patterns, A. Gómez, L. Beltrán Del Río, D. Romeu, M. Jose Yacamán

Scanning Microscopy

In this work we explore the use of the so-called wavelet transform in the digital image processing of micrographs. The wavelet transform of an image f(x,y) is defined as:

Wf(s,u,v)

= f(x,y) s Ψ(s(x-u),s(y-v)) dxdy

where Ψ is an analyzing function called "wavelet" and which is in our examples always taken to be the "Mexican hat" given by

Ψ(x)=(2-(x²+y²))exp(-(x²+y²)/2)

Some synthetic images are shown in which it can be clearly seen how the wavelet transform can be useful to reveal edges and to emphasize the boundaries of the clusters.

The technique is …

Image Algebra And Restoration, P. W. Hawkes

Scanning Microscopy

The arrival of image algebras has made it possible to express a vast amount of the heterogeneous material in the image processing literature in a convenient and consistent manner. Furthermore, this type of formulation has proved very fertile and many new ideas have emerged. Image restoration has, however, been studied very much less than enhancement and analysis. We explain briefly the use of one such algebra in this field and show that such tasks as reconstruction from focal series and three-dimensional reconstruction can easily be incorporated.