bluuebunny/crossref_metadata_2025_split huggingface dataset:
Geometric correction of digital images using orthonormal decomposition
Authors: Jeričevic ŽEljko , Benson Douglas M. , Bryan Joseph , Smith Louis C. 
Published: August 2011

SUMMARYWe have developed an algorithm which can be used to correct the geometric distortion of digital images. The method uses an orthonormal decomposition and a two‐dimensional Horner's scheme to construct and evaluate a polynomial equation of arbitrary degree in two independent variables. This numerical scheme for geometric correction combines several methods selected on the basis of their computation efficiency and numerical stability. The differences and advantages of this numerical scheme are compared with methods found in the image processing literature. The algorithm presented here has a reduced number of mathematical operations, is flexible and numerically stable. Based on the least‐squares criteria, the algorithm provides corrected pixel positions with an accuracy equal to or better than the pixel size.
Streak time‐lapse video microscopy: analysis of protoplasmic motility and cell division in Tradescantia stamen hair cells
Authors: Mineyuki Yoshinobu , Gunning Brian E. S. 
Published: August 2011

SUMMARYWe have developed a video time‐lapse analogue of a streak camera using a digital image processing technique, and have used it to analyse dynamic processes in plant cells. The same image area is selected from a succession of frames in a video tape recording. The successive images are stored in an image memory, rearranged, and displayed in a single frame according to the time course. Each image area is rectangular, with selectable length and width: the closest analogy to a streak camera is obtained when one of its sides is a single pixel. The composite image displays sequential changes in the distribution of subcellular components in the selected area. The method was shown to be useful for monitoring details of cytoplasmic streaming and organelle movement, observing the time course of chemical fixation, and also for studying kinetochore movement, shortening of chromatids and cell plate formation during mitosis and cytokinesis. Cessation and resumption of cytoplasmic movement during the cell division cycle were also clearly localized outside the nuclear region in apical cells of Tradescantia stamen hairs.
Direct measurement of the osmotic effects of buffers and fixatives in Nitella flexilis
Authors: Taylor Douglas P. 
Published: August 2011

SUMMARYThe pressure probe has been used to investigate the amount and time course of changes in turgor induced by agents used in fixation of biological material for electron microscopy. All buffers tested decreased the turgor pressure of internodal cells of the green alga Nitella flexilis in proportion to their osmotic concentration. With the exception of s‐collidine, the buffers were impermeant, as shown by the stability of the reduced turgor. The fixatives formaldehyde and glutaraldehyde caused a rapid reduction in turgor followed by recovery of turgor as the aldehyde penetrated the cell. Plasmolysis of cells can be avoided by a procedure involving stepwise increase of fixative concentration.
Classification of images of biomolecular assemblies: a study of ribosomes and ribosomal subunits of Escherichia coli
Authors: Frank Joachim , Bretaudiere Jean‐Pierre , Carazo Jose‐Maria , Verschoor Adriana , Wagenknecht Terence 
Published: August 2011

SUMMARYImages of macromolecules obtained in the electron microscope are subjected to correspondence analysis. The structure inherent in the data in the resulting low‐dimensional factor space is characterized by a mixed classification method which combines the dynamic clouds clustering technique with hierarchical ascendant classification (HAC). For our data, the rejection of marginal clusters obtained by dynamic clouds clustering appears as a crucial prerequisite for a stable performance of HAC.The method is applied to two sets of 204 and 177 images that show the 70S ribosome of Escherichia coli, in the range of overlap views as defined by A. Verschoor and co‐workers, and to two sets of 480 and 496 images of the 50S subunit of E. coli depleted of L7/L12 proteins in the well‐defined crown view. Reproducible classes are obtained, which are characterized by images reconstituted from factorial coordinates. These classes appear to be related to different orientations on the specimen grid (in the case of the 70S particle) and to different conformational states (50S subunit).
The nucleator
Authors: Gundersen H. J. G. 
Published: August 2011

SUMMARYA new, fundamental stereological principle is described which allows unbiased estimates of absolute structural quantities in arbitrarily shaped structures to be made from observations sampled in arbitrary points on independently isotropic probes. As an introduction to the principle, method(s) are described which lead to assumption‐free estimates of mean volume from the usual number‐distribution of particle sizes. Specifically, the estimation is unbiased when arbitrarily shaped particles are sampled with uniform probability using the disector or one of its many modifications. A special case, of interest when observations are restricted to sections, occurs when the particles are associated with some recognizable unit, like eukaryotic cells in biology. The estimation may then be carried out on a few sections of unknown thickness, or—under verifiable assumptions—on just one random section.
Quick sampling and perpendicular cryosectioning of cell monolayers for the X‐ray microanalysis of diffusible elements
Authors: Tvedt K. E. , Halgunset J. , Haugen O. A. 
Published: August 2011

SUMMARYA quick sampling and preparation method for freezing of cell monolayers is described. The cells are grown on a large Formvar film supported by a frame of polystyrene. A polyvinylpyrrolidone (PVP) solution is applied to one side of the film forming a flat disc when frozen with a pair of pliers precooled in liquid nitrogen. The PVP solution provides the specimen with sufficient strength and may be used as an elemental standard for absolute quantification if salts of known concentrations are added. Manipulation of the cells prior to freezing is thus restricted to a minimum, which eliminates possible harmful treatments like scraping and centrifugation. The procedure is quickly performed, the freezing being completed within 30 s of the cells having been removed from the culture well. The analytical results reveal low and stable Na: K ratios. Our results confirm that cells in vitro are comparable to cells in vivo with respect to elemental composition.
Quantitative high resolution transmission electron microscopy: the need for energy filtering and the advantages of energy‐loss imaging
Authors: Stobbs W. M. , Saxton W. O. 
Published: August 2011

SUMMARYEvidence is presented that inelastically scattered electrons contribute significant detail at the atomic level to high resolution images, particularly in high voltage instruments. The implications for quantitative image interpretation are shown to be serious and a case is made for incorporating facilities for energy‐filtered imaging in future high resolution electron microscopes.
Freeze‐fracture of 3T3 cells for high‐resolution scanning electron microscopy
Authors: Haggis G. H. , Pawley J. B. 
Published: August 2011

SUMMARYTriton‐extracted, freeze‐fractured 3T3 cells have been examined in the Hitachi S‐900 field‐emission SEM, after light platinum coating, at low beam voltage to evaluate the performance of the microscope under these conditions. For unstained material fixed in glutaraldehyde alone, high‐resolution images can be obtained, at accelerating voltages of 1.5‐5kV, after rotary deposition of platinum to an average thickness of 1.5‐3nm. Comparisons are made between these results and those of studies by TEM of deep‐etch replicas of similar material previously published.
An interesting pair of identically distributed random tessellations, with vertices of Y‐type, which always cross orthogonally
Authors: MILES R. E. 
Published: August 2011

SUMMARYIt is shown that the skeletons of the polygons determined by a line process in the plane form two identically distributed tessellations I′, I″ with all vertices of Y‐type, such that wherever I′, I″ cross, they do so at a right angle. The characteristics N̄, B̄, Ā for I′ or I″ are derived, along with the joint distribution of the random angles, at a random vertex. The space‐filling three‐dimensional versions are also considered.
An extremal property of random flats
Authors: Mecke J. 
Published: August 2011

SUMMARYThis paper deals with anisotropic random two‐dimensional flats meeting a ball B in the four‐dimensional Euclidean space. The probability p that two independent, identically distributed random flats have a common point in B depends on the direction distribution of the random flats. The direction distributions maximizing p are determined. If the random flats are isotropic, p is not maximal, in contrast to the case of random hyperplanes (three‐dimensional flats). Related results for flat processes are explained.
Random packing and random tessellation in relation to the dimension of space
Authors: Tanemura Masaharu 
Published: August 2011

SUMMARYThe random packing of non‐overlapping objects and the random tessellation of space by objects are discussed with relation to the dimension of space. The random packing discussed here is random ‘sequential’ packing and random tessellation is defined in this paper as the Voronoi tessellation of Poisson point processes. The conjecture by Palásti is examined for homothetic packing of cubes by using the existing data up to four dimensions; the generalized Palásti conjecture for spheres is also examined from the results of Monte Carlo simulations for two‐ and three‐dimensional space. As for the random tessellation, Kiang's conjecture is examined using the data for two‐ and three‐dimensional space. The results of the study indicate that all of the conjectures are false. Some details are given of the simulation methods.
Some stereological and statistical consequences derived from Cartier's formula
Authors: Lantuéjoul Ch. 
Published: August 2011

SUMMARYLet X and Y be two random variables with distribution functions Fx and FY, respectively. If Cartier's formula E[Y|X]=X holds, then Fx is necessarily less dispersed than FY. In this paper, the main consequences of Cartier's formula are derived. Some examples where such a formula holds are also given, namely in stereology (comparison of various estimators of Minkowsky's functionals) and in geostatistics (the change of support problem).
The effect of aberrations on the axial response of confocal imaging systems
Authors: Wilson T. , Carlini A. R. 
Published: August 2011

SUMMARYA confocal scanning microscope permits three‐dimensional imaging of a volume specimen. The role of lens aberrations on the axial response of the system is considered both experimentally and theoretically. It is found that primary coma, for example, plays no part in the axial response from a perfect reflector. The role of detector size is also considered and compared with theory. In general, the effect of aberrations is increased as the size of the detector is increased.
Freeze‐substitution of plant tissues with a new medium containing dimethoxypropane*
Authors: Kaeser Wulf 
Published: August 2011

SUMMARYMeristematic cells from root tips of Dahlia variabilis (L.) and highly vacuolated storage parenchyma cells of Helianthus tuberosus (L.) were fixed by the high‐pressure freezing technique and freeze‐substituted. A new water‐free medium for freeze‐substitution was developed to obtain better preservation of the ultrastructure of plant tissues. Adding dimethoxypropane (DMP) to the substitution medium gave two positive results: (1) water could be withdrawn from the samples without an exchange of the medium and without adding drying agents or working in a nitrogen atmosphere, and (2) the ultrastructural preservation of the substituted tissues was better than in a methanol medium and at least as good as in tissues fixed chemically at room temperature.
Energy filtered STEM imaging of thick biological sections
Authors: Colliex C. , Mory C. , Olins A. L. , Olins D. E. , Tencé M. 
Published: August 2011

Energy filtered imaging of thick biological specimens was analysed using a dedicated STEM fitted with an energy loss spectrometer and interfaced with a sophisticated data collection setup. All images were digital, thus permitting a quantitative analysis of the data. We also present a mathematical explanation of the data, which is useful in pradicting the quality of thick specimen images formed with energy filtered electrons.It is known that increasing specimen thickness leads to a decrease of the zero energy loss intensity and an increase in higher (multiply scattered) energy loss electrons. We show that contrast decreases gradually with increased energy loss but, most important, the signal to noise ratio is maximal at an energy loss position slightly below the intensity maximum. This is the optimal position for imaging thick specimens. Moreover our studies confirm that the following parameters have similar effects on the energy loss spectra: (1) increased thickness (t); (2) higher average Z number elements (or lower mean free path Ai); and (3) lower primary voltage (V0).
Examination of mucosal surfaces by scanning electron microscopy before and after removal of debris
Authors: Dickson G. R. , Mckenna S. , Mccoll K. , Carr K. E. 
Published: August 2011

SUMMARYA rapid method is described whereby gastrointestinal biopsy specimen surfaces can be examined by scanning electron microscopy with overlying tract contents (debris) intact, and also re‐examined after cleaning to determine the structure of the underlying mucosal surface. The conductive coating of gold is removed using mercury, a non‐wetting agent. The specimen surface is suitably cleaned of debris after a brief ultrasonication in absolute ethanol which mixes with the transitional fluid (CO2) used for critical point drying.
Phospholipid, Nature's own slide and cover slip for cryo‐electron microscopy
Authors: Frederik P. M. , Stuart M. C. A. , Bomans P. H. H. , Busing W. M. 
Published: August 2011

Thin films of surface‐active compounds, with or without particulate material, can be obtained by immersing and withdrawing a bare specimen grid from a solution/suspension of the compound. Immediately after withdrawing the grid, thinning of the film starts. Thinning is initially powered by gravity and capillary forces and will proceed in thin films (< 100 nm) driven by intermolecular forces until the London‐van der Waals attractive forces come to an equilibrium with electrostatic repulsion of similarly charged surfaces of the film. With small unilamellar vesicles prepared from the phospholipid dimyristoyl phosphatidyl choline (DMPC) the draining behaviour of these films was studied by cryo‐electron microscopy. Small unilamellar vesicles were observed within the film as well as the coalescence of these vesicles into sheets (‘leaky’ membrane fusion). Sheets dominate the images when films are allowed to drain for longer periods (>3min).Thin films were formed on grids from catalase crystals suspended in a DMPC suspension and vitrified by cooling. High‐resolution information was obtained by electron diffraction at low temperature and under low‐dose conditions from catalase crystals surrounded by small vesicles as well as from catalase crystals surrounded by sheets of DMPC. In the latter case the water content drops from 99% (DMPC in small vesicles) to less than 30% (DMPC in sheets) during draining. Ferritin was added to a DMPC suspension and thin films were prepared and vitrified. After prolonged draining ferritin molecules were deposited in layers with a stepwise increase in thickness. Draining of thin films has thus a dehydrating effect as well as a sorting and ordering effect. These effects must be considered when using surface‐active compounds at air‐water interfaces as a slide and cover slip for electron microscopy.
Analysis of heterogeneous fluorescence photobleaching by video kinetics imaging: The method of cumulants
Authors: Koppel Dennis E. , Carlson Curt , Smilowitz Henry 
Published: August 2011

SUMMARYThe method of cumulants has been applied to digital video fluorescence microscopy. The method is used to reconstruct the distribution of fluorescent molecules before the initiation of fluorescence photobleaching, and to characterize heterogeneous photobleaching by imaging one or more of the cumulants of the bleaching decay rate. Using the pipelined pixel processor of the image analysis system for the bulk of the calculations, rather than the general‐purpose host‐computer CPU, the video kinetics imaging can be performed in near real‐time. The method is applied to chick embryo myotubes labelled with fluorescein‐conjugated α‐bungarotoxin. The pre‐bleach fluorescence distribution is derived, and the image of fluorescein fluorescence is separated from glutaraldehyde‐induced autofluorescence on the basis of the spatially resolved average photobleaching decay rate.
Aluminium binding to chromatin DNA as revealed by formation of fluorescent complexes with 8‐hydroxyquinoline and other ligands
Authors: Llorente A. R. , Castillo P. Del , Stockert J. C. 
Published: August 2011

SUMMARYAfter aluminium mordanting of chicken blood smears, several chelating dyes and reagents were tested in order to detect the metal binding to chromatin DNA by fluorescence microscopy. 8‐Hydroxyquinoline induced the most selective fluorescence reaction, which was abolished after DNase or trichloroacetic acid treatment. Morin, purpurin and nuclear fast red showed an intense nuclear fluorescence, but lower selectivity. Fluorescence was also observed in chromatin treated with morin or cur‐cumin without mordanting. The simplicity and microscopical characteristics of the Al/8‐hydroxyquinoline fluorescence reaction make it very suitable for cytological studies of chromatin.
The development of biological preparative techniques for light microscopy, 1839–1989
Authors: Bracegirdle Brian 
Published: August 2011

SUMMARYThe development of techniques of preparing biological material for microscopical observation is summarized, with much greater emphasis being given to the introduction and establishment of the various techniques, largely in the nineteenth century, than to their perfection and extremely widespread use in the twentieth century. The development of the microtome as an instrument of the greatest importance is summarized and an assessment is made of the impact of preparative techniques on the development of the medical sciences.
TEM in materials science—past, present and future
Authors: Hirsch P. B. 
Published: August 2011

SUMMARYThe progress in transmission electron microscopy as applied in materials science is reviewed briefly, from the era of replica techniques in the 1940s and 1950s, through the development of the diffraction contrast technique in the late 1950s and 1960s, to the present day when instrumental resolution is sufficient to obtain structure images of a wide variety of crystalline solids. One of the most important advances has been the development of combined imaging and microanalytical techniques in a single instrument. The versatility of the TEM technique with atomic resolution and microanalytical facilities, the variety of signals and contrast effects available, and its universal application, establishes it as an essential tool in materials science for the foreseeable future.
Does light microscopy have a future?
Authors: Tanke Hans J. 
Published: August 2011

SUMMARYThe application of light microscopy in medicine and cell biology has been significantly influenced by both the availability of specific biological reagents such as monoclonal antibodies and nucleic acid probes, as well as by the enormous progress in microelectronics and computer technology. It is likely that specific reagents for a variety of cellular macromolecules will become available on a large scale in the coming years. Moreover, methods using both sensitive detection devices such as charge‐coupled device (CCD) cameras and sophisticated image processing exist to quantify this information at the single molecule level in morphologically intact cells.This paper describes the impact of these two factors on the light microscope of the future, with special emphasis on fluorescence. It defines the improvements that still are required to solve some of the challenging problems such as the quantification of unique genes and their products in intact cells, the quantification of DNA adducts and the detection of rare mutant cells or circulating tumour cells.
Mathematical morphology and convolutions
Authors: Mazille J. E. 
Published: August 2011

SUMMARYThe transforms of mathematical morphology may be generated by convolutions followed by thresholdings. Furthermore, the convolution‐thresholding pair may generalize mathematical morphology in three directions thanks to adjustments of the thresholding level, weighting of the coefficients of the convolution matrix and iterations. This leads to a wide set of non‐linear operators and structuring elements, including powerful directional transforms and an accurate iterative approach of a circular structuring element of any size and thus to a good approximation of the Euclidean distance.
Shape characterization of particles via generalized Fourier analysis
Authors: Réti Tamás , Czinege Imre 
Published: August 2011

SUMMARYA general method for shape characterization of two‐dimensional (2‐D) microscopical particles is presented. The proposed procedure based on Fourier analysis techniques can be regarded as a generalization and further development of methods described in the literature. The geometry of the particles is characterized by a set of shape functions which is invariant under translation, rotation and dilation. Shape descriptors generated from the Fourier coefficients are used for shape evaluation. Similarity between particles has been evaluated using an appropriately defined distance measure. The method is demonstrated by an application using a collection of 2‐D objects.
Boolean random functions
Authors: Serra J. 
Published: August 2011

SUMMARYA Boolean function f in Rn is the supremum of upper semi‐continuous random functions f'i which are almost surely positive, bounded with compact support and centred at the Poisson points (i). They generalize to functions of classical Boolean model for sets. The Boolean function f may be studied via its subgraph, i.e. as a random set in Rn x R. The key notion is then the functional Q(Bt), i.e. the probability that a compact set Bt centred at altitude t misses the subgraph of f. The general expression of Q(Bt) is given, and followed by a series of important derivations (volumes, gradients, numbers of summits, etc). Theorems of structure are given: they concern the properties of infinite divisibility for the sup, and domains of attraction for Boolean functions. The last sections are devoted to the study of two particular Boolean functions; emphasis is put on the stereological implications of the approach. A critical example illustrates the theory.
An interactive image analysis system for mean particle volume estimation using stereological principles
Authors: Moss M. C. , Browne M. A. , Howard C. V. , Joyner D. J. 
Published: August 2011

SUMMARYA semi‐automatic image analysis system based on the stereological approach of point‐sampled intercepts for mean volume estimation is described. The method used requires no assumptions about particle geometries and is thus general in its application. To ease implementation in this application, the assumption of particle convexity is made, making the measurement of intercepts easier for the user.The system was tested with computer‐generated sample sections to determine the accuracy and precision of the estimates obtained. The results were found to be within 10% of expected values in all cases. When tested with ‘real’ samples a typical result gave a coefficient of variation of 9% from eight independent estimates of one sample.