Biology Commons^™

A Robust Solution To The Super-Resolution Phase Problem In Scanning Transmission Electron Microscopy, J. M. Rodenburg, B. C. Mccallum

Scanning Microscopy

From a set of images, each of poor resolution, recorded in a transmission microscope under many different incident angles of coherent illumination, it is possible to obtain wavelength-limited resolution even if there is a narrow aperture lying in the back-focal plane of the imaging lens. This is achieved by a deconvolution algorithm which retrieves the phase of the Fourier transform of the specimen. The method accounts for complex components in the transfer function of the lens, is not very sensitive to defocus and is remarkably resilient to noise. It may have important applications in overcoming the resolution limit in the …

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 …

Multi-Dimensional Data Analysis And Processing In Electron-Induced Microanalysis, N. Bonnet, P. Trebbia

Scanning Microscopy

The new facilities offered by computer controlled data capturing devices allow one to open the field of data acquisition from one or two-dimensional spaces to multi-dimensional ones. The methods used for analysing and processing such data sets have to move in parallel towards multi-dimensionality. Multivariate Statistical Analysis is one of the tools which appear to be promising in : data analysis, data reduction, data processing (multivariate noise filtering), data interpolation and extrapolation. Illustrations of these different possibilities are given in the fields of spatially resolved spectroscopy, time-dependent spectroscopy and elemental mapping from Electron Energy Loss Spectroscopy.

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 …

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 …

Random Access Direct Parallel Detection Of Electron Energy Loss Spectra With A New Photodiode Array, Stephan La Barré, Eckhard Quandt, Heinz Niedrig

Scanning Microscopy

A new type of photodiode array (PDA) which allows the individual access of single diodes is used to record energy loss electrons directly without electron photon conversion.

The detector is part of an electron energy loss parallel detection system which consists of a sector field spectrometer and a quadrupole lens system to magnify the spectra electron-optically.

The parallel detector is a new random access PDA (RAPDA) which allows the individual access of single diodes. Therefore, different parts of the spectrum with dramatically different electron rates (zero loss peak, plasmon loss, ionization edges) can be recorded, each with optimum acquisition time …

On-Line Processing And Computer Control In High Resolution Transmission Electron Microscopy, F. A. Ponce, H. Hikashi

Scanning Microscopy

Recent advances in hardware and software make it possible to perform real-time image processing, and to do simultaneous analysis of the image characteristics in the transmission electron microscope (TEM). We have used a commercially available image processor and a suitable computer/TEM interface to build a automated computer-control system for a JEOL 4000EX TEM. We report here the characteristics of the system, which has direct access to all electronic controls of a JEOL 4000EX. The various microscope parameters are set by changing one parameter at a time while the image processor measures a specific image variable such as the variance. From …

Quantification Of High-Resolution Lattice Images And Electron Holograms, W. J. De Ruijter, M. Gajdardziska-Josifovska, M. R. Mccartney, R. Sharma, David J. Smith, J. K. Weiss

Scanning Microscopy

Progress towards the quantification of high-resolution electron microscopy and electron holograms has been achieved using digital acquisition with a slow-scan charge-coupled device (CCD) camera. Two applications are described: the precise measurement of lattice-fringe spacings and the determination of the mean inner potential. Lattice images can be characterized by a finite sum of two-dimensional sinusoids. A new method for measurement of the frequency, amplitude and phase of each sinusoid, based on an interpolation technique in reciprocal space, is presented. The method offers considerably higher precision for measurement of lattice fringes than the optical bench and is applicable to images recorded with …

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, …

Nonlinear Statistical Filtering And Applications To Segregation In Steels From Microprobe Images, C. Daly, D. Jeulin, D. Benoît

Scanning Microscopy

Microprobe images of solidification studies are well known to be subject to a Poisson noise. That is, the radiation count at a pixel x for a certain element may be considered to be an observation of a Poisson random variable whose parameter is equal to the true chemical concentration of the element at x. By modeling the image as a random function, we are able to use geostatistical techniques to perform various filtering operations. This filtering of the image itself may be done using linear kriging. For explicitely nonlinear problems such as the estimation of the underlying histogram of the …

Holography - Just Another Method Of Image Processing?, Hannes Lichte

Scanning Microscopy

The advantage of all different kinds of electron holography lies in the fact that in addition to the image intensity they make use of the phase in real space and in Fourier space. Therefore, they are in principle superior to conventional imaging techniques, even if these are supported by highly sophisticated methods of image processing. The technique of electron off-axis holography, under development in Tübingen for more than 20 years, now enters atomic resolution domain. After correction of aberrations, amplitudes and phases can be determined quantitatively, both in real space and Fourier space, opening up novel facilities for the analysis …

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 …

Individualistic Perspectives On Plant Competition, Nancy J. Huntly

Biology Faculty Publications

No abstract provided.

Metabolite Production By Entomopathogenic Fungi, Donald W. Roberts, Raymond J. St. Leger, Sandeep Gupta

Biology Faculty Publications

The entomopathogenic fungi produce a wide assortment of metabolites, some of which are important to the host-specialization of this group of fungi. Very few entomopathogenic fungi have been examined in detail for their metabolites in the disease process. Nevertheless, it is clear that certain proteases and lipases are crucial to the invasion of insect cuticle by the fungus. These fungi have the unusual ability to hydrolyze branched alkanes. Also, they normally produce very active, broad-spectrum proteases. These are needed for penetration of the hydrophobic epicuticle and the highly proteinaceous cuticle of insects. Chitinases also are involved, but usually have only …

The Effect Of Colcemid On The Heat Survival Of Mitotic V79 Chinese Hamster Cells, J. G. Szekely, G. P. Raaphorst, A. U. Lobreau, S. Delaney, E. I. Azzam

Scanning Microscopy

V79 Chinese hamster cells were collected by colcemid addition to study the effect of heat on mitosis. When they were heated at 42°C and 45°C in the presence of 0.06 μg/mL colcemid, cell survival increased over the control samples, which were heated in ordinary medium. Scanning electron microscopy showed that cells heated to 45°C in the presence or absence of colcemid had fewer microvilli on the surface, but they did not have increased bleb formation. Transmission electron microscopy showed that the chromatin was diffuse in the heated cells and the kinetochores were indistinct. The mitochondria in the heated cells were …

Microbeam Studies Of The Sensitivity Of Structures Within Living Cells, L. A. Braby

Scanning Microscopy

Determining the biological effects of low doses of radiation with high linear energy transfer (LET) is complicated by the stochastic nature of charged-particle interactions. Populations of cells exposed to very low radiation doses contain a few cells which have been hit by a charged particle, while the majority of the cells receive no radiation damage. At somewhat higher doses, a few cells receive two or more events. Because the effects of damage produced by separate events can interact in the cell, we have had to make assumptions about the nature of these interactions in order to interpret the results of …

A Review Of Scanning Tunneling Microscope And Atomic Force Microscope Imaging Of Large Biological Structures: Problems And Prospects, B. L. Blackford, M. H. Jericho, P. J. Mulhern

Scanning Microscopy

The application of the scanning tunneling microscope (STM) and the atomic force microscope (AFM) to the study of small biological molecules, such as DNA and smaller molecules, has received considerable attention in the literature. This paper reviews STM and AFM studies of larger biological structures such as bacterial membranes, bacteriophages, viruses, antibodies, etc. The problems encountered in these applications are emphasized, with particular reference to the unknown conduction mechanism, tip-sample interaction forces, and tip-sample convolution artifacts in the images. The latter problem is illustrated by new results from IgG antibody complexes attached to a bacterial sheath layer. A new conduction …

The Microvasculature Of Human Oral Mucosa Using Vascular Corrosion Casts And India Ink Injection I. Tongue Papillae, Q. X. Yu, W. Ran, K. M. Pang, H. P. Philipsen, J. Theilade, X. H. Chen, Y. C. Mok

Scanning Microscopy

The microvasculature of human tongue papillae originating from 9 males and 6 females, aged 0.5 to 2 years was studied by scanning electron microscopy (SEM) of vascular corrosion casts and by light microscopy (LM) of India ink injected specimens. All papillae showed a microvasculature characterized by primary, secondary and tertiary capillary loops. In the filiform papillae the loops were generally arranged in a corolla-like pattern with the tertiary loops demonstrating a hair-pin shape. The fungiform papillae showed basically a similar architectural pattern although the loops were somewhat more compact and complex in structure. A small, shallow depression of the tertiary …

Increasing Resolution And Versatility In Low Temperature Conventional And Field Emission Scanning Electron Microscopy, William P. Wergin, Eric F. Erbe

Scanning Microscopy

Studies were undertaken to expand the versatility and the resolution of low temperature conventional and field emission scanning electron microscopy (SEM). The results indicated that simple modified specimen holders, which could be used in conjunction with the commercial cryosystems, allowed one to store specimens for several weeks in liquid nitrogen, either before or after observation in a conventional SEM, without incurring degradation of the surface features. Other modified holders permitted one to move the specimen closer to the final lens or to use the upper secondary electron detector, which is available with some SEMs. Both of these procedures increased the …

New Directions In Scanning Electron Microscopy Cathodoluminescence Microcharacterization, D. B. Holt

Scanning Microscopy

The general principles of the low-temperature spectroscopic cathodoluminescence (LTSCL) technique in the scanning electron microscope (SEM) are outlined. CL microscopy and spectroscopy are now being extended in new directions. Analysis of the intrinsic CL from quantum well materials by LTSCL is proving valuable for microcharacterization and such work can be expected to expand rapidly. The main, early CL results in this exciting field are summarized here. In geology, CL microscopy, without spectroscopy, is widely used via electron-beam attachments to light microscopes and the addition of spectral analysis to these studies is overdue. Much CL from minerals and ceramics comes from …

Tooth Tissues Of Certain Sharks And Lungfishes, Yasutomo Iwai-Liao, Yoshikage Higashi, Yoshitaka Tamada

Scanning Microscopy

A comparative odontologic study was conducted on teeth and their supporting tissues from extant sharks, fossil sharks, and living lungfishes using scanning electron microscopy (SEM) and energy dispersive spectroscopy (EDS) X-ray microprobe to investigate evolutionary changes in tooth structure of the fishes.

No histological differences between the extant and fossil teeth of lamnoid sharks were observed. The weight percent of calcium in osteodentin of the fossil shark was higher than that in the extant shark. The weight percents of both P and Ca of tooth tissues in the giant extinct shark showed comparatively low values.

Both the upper and lower …

Calcium Oxalate Crystal Growth In The Presence Of Mucin, Mostafa Akbarieh, Rashad Tawashi

Scanning Microscopy

Using interfacially-controlled crystallization and gel diffusion crystallization methods, calcium oxalate monohydrate (COM), dihydrate (COD) and trihydrate (COT) crystals were grown by the slow diffusion of reacting ions in the presence of mucin. It was demonstrated that mucin in the growth media dramatically affected the size, habit, surface structure, thermodynamic stability and phase transition kinetics of hydrated calcium oxalate crystals. The results obtained revealed that mucin as a glycoprotein model controlled the growth of COT and COD single crystals as well as cluster formation. Growth inhibition of specific crystal faces and phase transition retardation occurred in its presence. The data confirmed …

Panchromatic And Spectral Characterization Of Cu Contaminated Semi-Insulating Gaas, Thomas E. Zirkle, Stephan Myhajlenko, Nam Soo Kang, Ronald J. Roedel, Dieter K. Schroder

Scanning Microscopy

Panchromatic (integral) and spectrally resolved cathodoluminescence characterization was used to investigate the near surface gettering properties of Cu in liquid-encapsulated, Czochralski-grown, undoped semi-insulating (SI) GaAs. Samples from two sources were investigated to determine if gettering treatments applied to GaAs result in improvements in uniformity similar to those observed in gettered Si. Before Cu contamination, typical cellular structure is observed for all samples. Experimentally, it is found that the panchromatic CL images change significantly after Cu doping and subsequent gettering processing for all samples. A contrast reversal is generally observed after Cu contamination. After gettering, the image of the samples from …

Epistomatal Wax Injury To Red Spruce Needles (Picea Rubens Sarg.) Grown In Elevated Levels Of Ozone And Acidified Rain, C. R. Krause, W. N. Cannon Jr.

Scanning Microscopy

Red spruce seedlings (Picea rubens Sarg.) were exposed to charcoal-filtered air, at 0.07 ppm or 0.15 ppm ozone (O₃), alone or in combination with pH 4.2 or pH 3.0 acidified rain, and examined with scanning electron microscopy (SEM) to determine if epistomatal wax fine structure was affected. Acidified rain in combination with 0.15 ppm O₃ produced changes in wax tubule morphology. Changes were moderate at pH 4.2 and severe at pH 3.0. Needles collected from Whiteface Mountain, New York, displayed injured epistomatal wax structure similar to that observed on needles exposed in the laboratory to 0.15 …

Correlation Of Cochlear Pathology With Auditory Brainstem And Cortical Responses In Cats With High Frequency Hearing Loss, R. J. Mount, R. V. Harrison, S. G. Stanton, A. Nagasawa

Scanning Microscopy

Newborn kittens were treated with the aminoglycoside amikacin to produce a bilateral high frequency cochlear hearing loss. The degree and stability of hearing loss were confirmed by recording auditory brainstem evoked potentials (ABR audiograms). After maturation, cochleotopic frequency representation within primary auditory cortex (Al) was mapped using standard microelectrode recording techniques. The cochlear sensory epithelium was assessed with SEM and the pattern of damage compared with the ABR audiograms and cortical frequency maps.

Amikacin treatment resulted in various patterns of haircell damage towards the base of the cochlea. A relatively abrupt transition between damaged and undamaged haircell regions resulted in …

Optimization Design For The Electron Emission System Using Improved Powell Method, Chang-Xin Gu, Li-Ying Shan, Zhi-Rong Chen

Scanning Microscopy

The electron emission system, which may mostly decide the main properties of the whole electron optical system, is a crucial element for an electron gun. The design of the electron emission system is more important compared with other electron lenses in the electron gun. In this paper, an optimization design method for the electron emission system is presented by using an Improved Powell Method with linear search for the one dimensional search. The optimal structure parameters with a criterion of minimum objective function value for this system are provided. The computed results may show that this direct search optimization method …

An Integrated Study Of The Morphological And Gross-Elemental Consequences Of Methyl Mercury Intoxication In Rats, With Particular Attention On The Cerebellum, K. Leyshon, A. J. Morgan

Scanning Microscopy

Methylmercury accumulates in the kidney and liver of rats, but fairly selectively damages the cerebellum, resulting in the clinical symptoms of neurological ataxia after prolonged exposures. Within the cerebellum, morphological examination indicated that the small granule cells beneath the Purkinje layer are especially susceptible to the toxin, showing signs of pyknosis during the phase of locomotory disability, whilst the large Purkinje cells are relatively resistant to cytotoxic injury. Flame photometric and electron probe X-ray microanalysis (EPXMA) of digested samples of the major organs failed to detect any significant changes in the Na, K, Ca, Mg, S and P concentrations of …

Application Of The Nuclear Microprobe To The Imaging Of Single Event Upsets In Integrated Circuits, K. M. Horn, B. L. Doyle, D. S. Walsh, F. W. Sexton

Scanning Microscopy

A new form of microscopy has been developed which produces micron-resolution maps of where single event upsets occur during ion irradiation of integrated circuits. Utilizing a nuclear microprobe, this imaging technique can irradiate, in isolation, individual components of an integrated circuit (e.g. transistor drains, gates, feedback resistors) and measure immediately the effect of a high energy ion strike on circuit performance. This detailed circuit characterization technique provides a precision diagnostic with which to evaluate the design of integrated circuits that are to be used in space or other radiation environments.

Seed Testa Morphology Of 18 Species Of Rafnia Thunb. (Fam. Fabaceae, Sub-Family Papilionoideae), G. R. Richardson, R. Cross

Scanning Microscopy

Scanning electron microscopy was used to conduct a micromorphological study of testae of the seeds of 18 species of Rafnia Thunb. (Fam. Fabaceae, Sub-family Papilionoideae). The testa patterns revealed diagnostic taxonomic features which proved useful in the construction of a key for the identification of the various Rafnia species. Comparisons between air-dried freshly collected, and long-term stored herbarium specimens revealed that testa patterns remained consistent and valid for taxonomic purposes.

Microscopy Of Mixed Surfaces On Layered Semiconductors, L. Margulis, D. Mahalu, B. Parkinson, R. Tenne

Scanning Microscopy

A large number of well-defined hexagonal etch pits is produced on the WSe₂ surface by controlled anisotropic corrosion. As a result a mixed surface (combining both ⊥c and ||c components) is created. This surface exhibits photovoltaic properties even better than the atomically smooth van der Waals surface. Measurements of electron beam induced current performed at low temperatures give direct evidence for enhanced current collection of ||c facets. Observations made by transmission electron microscopy and scanning tunneling microscopy show the presence of very low ||c steps on the van der Waals surface.