Life Sciences Commons^™

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 …

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.

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 …

Processing Multi-Spectral Scanning Electron Microscopy Images For Quantitative Microfabric Analysis, N. K. Tovey, D. L. Dent, W. M. Corbett, D. H. Krinsley

Scanning Microscopy

Multi-spectral image analysis is a powerful method to characterise quantitatively the mineralogy and microfabric of soils, sediments, and other particulate materials. Backscattered scanning electron microscope (SEM) images of polished, resin-impregnated samples are grouped with the corresponding X-ray elemental maps using classification methods commonly used in remote sensing. However, the resulting mineral-segmented images require processing to render them suitable for quantification. In the past, this has been done subjectively and interactively, but the new objective methods described in this paper largely eliminate this subjectivity. An intensity gradient magnitude image of the original backscattered electron image is used as the basis of …

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 …

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 …

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.

Automatic Orientation Analysis Of Microfabric, N. K. Tovey, P. Smart, M. W. Hounslow, J. P. Desty

Scanning Microscopy

The orientation of features in digitized scanning electron micrographs may be estimated using a technique which examines the changes in intensity in two orthogonal directions about each pixel. Typically, over 250, 000 estimates of orientation may be made generating an output image where the pixel value relates to the orientation direction of the feature at the corresponding pixel in the original image. At the same time, a rosette histogram may be generated to give a visual impression of any preferred alignment. These data may be reduced to two parameters specifying the direction and degree of orientation.

A new algorithm involving …

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.

Image Segmentation Applied To Scanning Electron Microscopy Multi-Images Of Weathered Stones Of Monuments, M. Rautureau, R. Harba, G. Jacquet

Scanning Microscopy

This paper describes a three complementary images processing method. The three images are coming from a scanning electron microscope (SEM) during the analysis of a particular stone: the Tuffeau used in most monuments of the Loire valley (France). The goal is to separate two classes of particles (calcareous and siliceous) from the porosity to give more information to experts who evaluate the damage of weathering on monuments. A specific process is developed: a first threshold on the good quality image allows separation of particles from porosity. Then, the complementarity of the three images gives the two other thresholds. Granulometry, percentages …

The Detection And Quantification Of Straight-Lined Irregularities On Surfaces, J. Alan Swift

Scanning Microscopy

Under the microscope, scratches or abrasions on hard otherwise flat surfaces are usually revealed as straight-lined irregularities. At a more macroscopic level creases in thin sheets such as of paper and textile fabrics are also observed to be straight-lined. A computer-aided image analytical method is described here not only for identifying such features but also for counting them, measuring their lengths and evaluating their contrast. Further measures are derived that are in accord with the qualitative visual impact of each line within the milleau of lines in the original image. The method makes use of a parametric transformation from two …

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 …

Digital Image Processing Of Electron Micrographs: The Pic System Ii, Benes L. Trus, Michael Unser, Thierry Pun, Alasdair C. Steven

Scanning Microscopy

The PIC system, an integrated package of Fortran programs and subroutines designed to run on the Digital Equipment Corporation VAX family of computers, has been developed for analysis of electron micrographs with emphasis on the particular requirements for structural analysis of biological macromolecules. The substantially improved VAX version of PIC reported here has been developed from an earlier PDP-11 version which was, in turn, developed from a set of IBM 370 programs called MDPP. PIC now encompasses over 150 commands or processing operations that afford a comprehensive range of image processing operations including image restoration, enhancement, Fourier analysis, correlation averaging, …

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 …

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 …

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 …