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PubMed2006

Denoising and enhancing digital mammographic images for visual screening.

Dense regions in digital mammographic images are usually noisy and have low contrast, and their visual screening is difficult. This paper describes a new method for mammographic image noise suppression and enhancement, which can be effective particularly for screening image dense regions. Initially, the image is preprocessed to improve its local contrast and the discrimination of subtle details. Next, image noise suppression and edge enhancement are performed based on the wavelet transform. At each resolution, coefficients associated with noise are modelled by Gaussian random variables; coefficients associated with edges are modelled by Generalized Laplacian random variables, and a shrinkage function is assembled based on posterior probabilities. The shrinkage functions at consecutive scales are combined, and then applied to the wavelets coefficients. Given a resolution of analysis, the image denoising process is adaptive (i.e. does not require further parameter adjustments), and the selection of a gain factor provides the desired detail enhancement. The enhancement function was designed to avoid introducing artifacts in the enhancement process, which is essential in mammographic image analysis. Our preliminary results indicate that our method allows to enhance local contrast, and detect microcalcifications and other suspicious structures in situations where their detection would be difficult otherwise. Compared to other approaches, our method requires less parameter adjustments by the user.

Mammography↗

PubMed1999

Sex preselection: laboratory validation of the sperm sex ratio of flow sorted X- and Y-sperm by sort reanalysis for DNA.

Laboratory validation is essential in developing an effective method for separating X and Y sperm to preselect sex. Utilizing sexed sperm from a particular experiment to test fertility and achieve the subsequent phenotypic sex without knowing the likely outcome at conception is too costly for most applications. Further, research advances need to be built on an ongoing assessment with respect to the collection of data to continue progress towards achieving a successful outcome. The Beltsville Sperm Sexing Technology, which is based on the sorting of X- and Y-bearing sperm through the process of flow-cytometric sperm sorting, is also well suited for validation in the laboratory by "sort reanalysis" of the sperm X- and Y-bearing fractions for DNA content. Since the sexing technology is based on the use of Hoechst 33342, a permeant nuclear DNA stain for sorting X- and Y-bearing sperm, it also can be the marker for determining the proportions of X and Y populations by sort reanalysis. The process consists of using an aliquot of the sorted sperm and sonicating to obtain sperm nuclei. The uniformity of the nuclear staining is re-established through the addition of more Hoechst 33342. Separate analysis of each aliquot produces a histogram that is fitted to a double gaussian curve to determine proportions of X and Y populations. The relative breadths of the distributions of DNA of X- and Y-bearing sperm within a species affects interpretations of the histogram. Sort reanalysis is consistently repeatable with differences in X/Y DNA equal to or greater than 3.0%. This information on sex ratio of the sperm then provides the precise tool by which one can predict the outcome in terms of sex, from a particular sample of semen. Simple analysis of unsorted sperm to determine the proportions of X- and Y-bearing sperm based on DNA content is also an effective tool for validating sperm-sex ratio, whether it is in a sample assumed to be 50:50 or predicted to be something other than 50:50. This simple analysis provides for a check on the potential sex ratio of any sample of semen.

Animals↗

PubMed2005

On the theory and simulation of multiple Coulomb scattering of heavy-charged particles.

The Moliere theory of multiple Coulomb scattering is modified to take into account the difference between processes of scattering off atomic nuclei and electrons. A simple analytical expression for angular distribution of charged particles passing through a thick absorber is found. It does not assume any special form for a differential scattering cross section and has a wider range of applicability than a gaussian approximation. A well-known method to simulate multiple Coulomb scatterings is based on treating 'soft' and 'hard' collisions differently. An angular deflection in a large number of 'soft' collisions is sampled using the proposed distribution function, a small number of 'hard' collision are simulated directly. A boundary between 'hard' and 'soft' collisions is defined, providing a precise sampling of a scattering angle (1% level) and a small number of 'hard' collisions. A corresponding simulating module takes into account projectile and nucleus charged distributions and exact kinematics of a projectile-electron interaction.

Algorithms↗

PubMed2002

Detailed study of silver metallic film diffusion in a soda-lime glass substrate for optical waveguide fabrication.

We present the study of multimode glass waveguides fabricated by a silver-ion electromigration process followed by a diffusion process. The study is concerned mainly with the diffusion process, which occurs by variation of the diffusion time. The obtained guides are analyzed by the prism-coupling technique, which determines their effective refractive indices that are treated by the inverse WKB method,assumed to be proportional to the silver ions' concentration profiles, for which a Gaussian model is attributed. Diffusion coefficients then are determined from these Gaussian profiles experimentally by both methods. These diffusion coefficients show a concentration dependence related to the variation of the diffusion time. A mathematical model representing the best fit to this dependence is also presented. Finally, our results are compared with other research results, with which we find good agreement.

Journal Article↗

PubMed2003

Detection, identification, and estimation of biological aerosols and vapors with a Fourier-transform infrared spectrometer.

Two experiments were conducted with a Fourier-transform infrared (FTIR) spectrometer. The purpose of the first experiment was to detect and identify Bacillus subtilis subsp. niger (BG) bioaerosol spores and kaolin dust in an open-air release for which the thermal contrast between the aerosol temperature and background brightness temperature is small. The second experiment estimated the concentration of a small amount of triethyl phosphate (TEP) vapor in a closed chamber in which an external blackbody radiation source was used and where the thermal contrast was large. The deduced BG (TEP) extinction spectrum (identification) showed an excellent match to the library BG (TEP) extinction spectrum. Analysis of the time sequence of the measurements coincided well with the presence (detection) of the BG during the measurements, and the estimated concentration of time-dependent TEP vapor was excellent. The data were analyzed with hyperspectral detection, identification, and estimation algorithms. The algorithms were based on radiative transfer theory and statistical signal-processing methods. A subspace orthogonal projection operator was used to statistically subtract the large thermal background contribution to the measurements, and a robust maximum-likelihood solution was used to deduce the target (aerosol or vapor cloud) spectrum and estimate its mass-column concentration. A Gaussian-mixture probability model for the deduced mass-column concentration was computed with an expectation-maximization algorithm to produce the detection threshold, the probability of detection, and the probability of false alarm. The results of this study are encouraging, as they suggest for the first time to the authors' knowledge the feasibility of detecting biological aerosols with passive FTIR sensors.

Journal Article↗

PubMed1987

Functional properties of parietal visual neurons: mechanisms of directionality along a single axis.

The directional properties of parietal visual neurons (PVNs) were examined using the method of single-neuron analysis in waking monkeys. PVN properties were determined with passive visual stimuli as the animal executed a simple detection task. Parietal area PG was studied in 10 hemispheres of 6 male Macaca mulatta. Each class of parietal neurons was identified in PG: the fixation, projection, visual, and oculomotor neurons; 613 PVNs were identified, 323 were studied quantitatively, and 188 were studied with one or more of the protocols described. The receptive fields of PVNs are commonly large and bilateral, and at the limit some may fill the visual field; for many, the central zone of the visual field is spared when the fields are determined by stimuli that enter from the periphery and transit meridians. The receptive fields vary with the behavioral state, the angle of gaze, and the parameters of the stimuli used to determine them. PVNs are sensitive to stimulus movement but relatively insensitive to stimulus speed; many respond over a speed range of 5 degrees-500 degrees/sec. Stimulus-response relations may be incremental or decremental with increasing speed or show maxima or minima in the midrange of speed, but the response variation over the full range is rarely greater than 2:1. The directional preferences of PVNs with bilateral receptive fields are opponently organized; the preferred directions point either inward toward or outward away from the central line of gaze along the 4 meridians tested, which were equally spaced in the circular dimension of the visual field. The mechanism of the axis directionality of PVNs was studied using conditioning-test paradigms. They revealed a feed-forward inhibition preceding a stimulus, an effect that extends from the leading edge of the stimulus for 10 degrees-20 degrees in front of the moving stimulus and lasts for several hundred milliseconds. A double-Gaussian model of superimposed but unequal excitatory and inhibitory effects suffices to explain the present observations. It places demand upon the projection of functional properties from the contralateral hemisphere or from the ipsilateral prestriate areas that project upon PG over multistaged pathways and minimal demands upon intracortical processing mechanisms.

Action Potentials↗

PubMed2001

Accuracy and sensitivity of detection of activation foci in the brain via statistical parametric mapping: a study using a PET simulator.

Statistical parametric mapping (SPM) is currently the most widely used method for analysis of functional activation images. This paper reports a quantitative evaluation of the sensitivity and accuracy of SPM, using a realistic simulator of PET image formation, which accounted for the main physical processes involved in PET, including attenuation, scatter, randoms, Poisson noise, and limited detector resolution. Activation foci of the brain were simulated by placing spheres of specified activities in particular locations. Using these data, the sensitivity and accuracy of SPM in detecting activation foci was measured for different versions of the SPM spatial normalization method and for an elastic warping method referred to as STAR (spatial transformation algorithm for registration). The STAR method resulted in relatively better registration and hence better detection of the activation foci. A secondary goal of the paper was to evaluate the improvement in detection sensitivity obtained by applying an atlas-based adaptive smoothing method instead of the usual Gaussian filtering method. The results indicate some limitations of statistical parametric mapping, assist in the correct interpretation of the SPM maps, and point to future research directions in functional image analysis.

Adolescent↗

PubMed2003

Combinative multi-scale level set framework for echocardiographic image segmentation.

In the automatic segmentation of echocardiographic images, a priori shape knowledge has been used to compensate for poor features in ultrasound images. This shape knowledge is often learned via an off-line training process, which requires tedious human effort and is highly expertise-dependent. More importantly, a learned shape template can only be used to segment a specific class of images with similar boundary shape. In this paper, we present a multi-scale level set framework for segmentation of endocardial boundaries at each frame in a multiframe echocardiographic image sequence. We point out that the intensity distribution of an ultrasound image at a very coarse scale can be approximately modeled by Gaussian. Then we combine region homogeneity and edge features in a level set approach to extract boundaries automatically at this coarse scale. At finer scale levels, these coarse boundaries are used to both initialize boundary detection and serve as an external constraint to guide contour evolution. This constraint functions similar to a traditional shape prior. Experimental results validate this combinative framework.

Algorithms↗

PubMed1985

Spontaneous electrical activity induced by herpes virus infection in rat sensory neuron cultures.

Dissociated cultures of rat dorsal root ganglion neurons were infected with a syncytial strain of herpes simplex virus type 1. Over 90% of neurons in infected cultures were spontaneously active and fired action potentials which, on membrane potential hyperpolarization, were replaced by depolarizing events similar to excitatory postsynaptic potentials. Amplitude analysis of these events produced populations described by the sum of several unitary events with Gaussian rather than binomial or Poisson distributions. Such spontaneous activity was blocked by tetrodotoxin but not by low calcium high magnesium solutions containing cadmium. Simultaneous recording from pairs of spontaneously active neurons revealed excitatory connexions between cells. It is suggested that virus-induced fusion of nerve cell processes induces electrical coupling between sensory neurons, and that the resulting electrical network supports spontaneous activity.

Animals↗

PubMed1996

Gaussian optics for photorefractive keratectomy. Increased predictability for larger diopter corrections.

PURPOSE: To evaluate clinically a formula based on spherical Gaussian optics for enhanced predictability of excimer photorefractive keratectomy (PRK) in both high and low degrees of myopia. METHOD: Patients (24 eyes) were evaluated preoperatively with refractive measurements and corneal topography. After excimer PRK (3-24 months), postoperative remaining spectacle correction and corneal topography were measured. The attempted laser correction, calculated using algebraic equations, was compared with the achieved laser correction. RESULTS: The absolute laser correction error (mean +/- standard deviation), defined as the difference between the achieved and attempted laser corrections, was 0.37 +/- 0.31 diopter (D) for the 24 eyes. No significant difference was found in the error for attempted corrections greater than 6 D versus those less than 6 D. CONCLUSION: The use of a spherical Gaussian optics formulation results in accurate laser correction values for a wide range of myopia, even for large diopter corrections.

Adult↗

PubMed2004

Contour definition and tracking in cardiac imaging through the integration of knowledge and image evidence.

The main contribution of this paper is the use of simple processing techniques, incorporated in a new multistage approach, to automatically delineate left ventricle contours. Another contribution is the proposal of the centerline distances for contour comparison, which promises a more accurate measurement than the common method, based on the distance to the closest point. Edges are detected by Gaussian filtering at coarse and fine scale. The region of interest is defined as a binary map where coarse edges are extracted throughout image sequence. A contour template is matched against the gradient of the first image. Candidate boundary points are instantiated by scanning the coarse edge map perpendicularly to the matched template. A candidate contour is estimated from these points by maximizing an edge likelihood function. A region growing algorithm gives another candidate contour. Both edge and region candidate contours are then integrated with the edge map computed at fine scale by maximizing another likelihood function. Evaluation was carried out on 12 echocardiographic and 4 angiocardiographic sequences (for a total of 289 frames). Distances between computer-generated contours and the contours traced by three experts were within interobserver variability, unlike the results obtained by Acoustic Quantification and by a general-purpose deformable model.

Artificial Intelligence↗

PubMed1999

Experimental comparison of data transformation procedures for analysis of principal components.

Results of principal component analysis depend on data scaling. Recently, based on theoretical considerations, several data transformation procedures have been suggested in order to improve the performance of principal component analysis of image data with respect to the optimum separation of signal and noise. The aim of this study was to test some of those suggestions, and to compare several procedures for data transformation in analysis of principal components experimentally. The experiment was performed with simulated data and the performance of individual procedures was compared using the non-parametric Friedman's test. The optimum scaling found was that which unifies the variance of noise in the observed images. In data with a Poisson distribution, the optimum scaling was the norm used in correspondence analysis. Scaling mainly affected the definition of the signal space. Once the dimension of the signal space was known, the differences in error of data and signal reproduction were small. The choice of data transformation depends on the amount of available prior knowledge (level of noise in individual images, number of components, etc), on the type of noise distribution (Gaussian, uniform, Poisson, other), and on the purpose of analysis (data compression, filtration, feature extraction).

Computer Simulation↗

PubMed2004

Developing optimal non-linear scoring function for protein design.

UNLABELLED: Motivation. Protein design aims to identify sequences compatible with a given protein fold but incompatible to any alternative folds. To select the correct sequences and to guide the search process, a design scoring function is critically important. Such a scoring function should be able to characterize the global fitness landscape of many proteins simultaneously. RESULTS: To find optimal design scoring functions, we introduce two geometric views and propose a formulation using a mixture of non-linear Gaussian kernel functions. We aim to solve a simplified protein sequence design problem. Our goal is to distinguish each native sequence for a major portion of representative protein structures from a large number of alternative decoy sequences, each a fragment from proteins of different folds. Our scoring function discriminates perfectly a set of 440 native proteins from 14 million sequence decoys. We show that no linear scoring function can succeed in this task. In a blind test of unrelated proteins, our scoring function misclassfies only 13 native proteins out of 194. This compares favorably with about three-four times more misclassifications when optimal linear functions reported in the literature are used. We also discuss how to develop protein folding scoring function.

Algorithms↗

PubMed2002

Using exact Poisson likelihood functions in Bayesian interpretation of counting measurements.

A technique for computing the exact marginalized (integrated) Poisson likelihood function for counting measurement processes involving a background subtraction is described. An empirical Bayesian method for determining the prior probability distribution of background count rates from population data is recommended and would seem to have important practical advantages. The exact marginalized Poisson likelihood function may be used instead of the commonly used Gaussian approximation. Differences occur in some cases of small numbers of measured counts, which are discussed. Optional use of exact likelihood functions in our Bayesian internal dosimetry codes has been implemented using an interpolation-table approach, which means that there is no computation time penalty except for the initial setup of the interpolation tables.

Bayes Theorem↗

PubMed2004

Fluctuation theorem for a deterministic one-particle system.

A Duffing oscillator is driven by a sum of N chaotic time series. These time series are solutions of the undriven Duffing equation. It is shown that N=1 is sufficient to render the fluctuation theorem [Phys. Rev. Lett. 74, 2694 (1995)]; J. Math. Phys. 41, 4061 (2000)]; Adv. Phys. 51, 1529 (2002)]] for the power J(tau) averaged within intervals of length tau . In particular, the probabilities p( J(tau) ) follow a nearly Gaussian distribution. Also, ln[p( J(tau) )/p(- J(tau) )] versus J(tau) can be fitted by strikingly linear functions, the slopes being proportional to tau for large tau . These results indicate that validity of the fluctuation theorem requires neither a many-particle system nor a stochastic process, which are requirements used in previous works.

Journal Article↗

PubMedDate not supplied

Transfer function measurement and analysis for a magnetic resonance imager.

The transfer function characteristics of a 1.5T imager have been determined. An edge response function (ERF) was obtained from a water/Plexiglas interface at various pixel widths ranging from 0.312 to 1.0 mm. An SE pulse sequence was used with a 5-mm transaxial slice. The ERF was smoothed, differentiated, and Fourier transformed to obtain MTF curves. The LSF was analyzed for skewness and kurtosis. The area under the MTF amplitude curves and the equivalent bandpass were calculated. All ERFs, LSFs, and MTFs were well behaved. The resulting LSF was Gaussian. All calculated MTFs had cutoff frequencies slightly less than the theoretical Nyquist limit. The MTF calculated from the theoretical Gaussian LSF is slightly superior to that calculated from experimental data and provides an upper limit to the MTF. Spatial resolution in our MR imager is dominated by the pixel size via the Nyquist sampling theorem. System performance is slightly less than theoretically predicted, possibly due to image processing algorithms during the reconstruction process.

Humans↗

PubMed1999

Mixtures of probabilistic principal component analyzers.

Principal component analysis (PCA) is one of the most popular techniques for processing, compressing, and visualizing data, although its effectiveness is limited by its global linearity. While nonlinear variants of PCA have been proposed, an alternative paradigm is to capture data complexity by a combination of local linear PCA projections. However, conventional PCA does not correspond to a probability density, and so there is no unique way to combine PCA models. Therefore, previous attempts to formulate mixture models for PCA have been ad hoc to some extent. In this article, PCA is formulated within a maximum likelihood framework, based on a specific form of gaussian latent variable model. This leads to a well-defined mixture model for probabilistic principal component analyzers, whose parameters can be determined using an expectation-maximization algorithm. We discuss the advantages of this model in the context of clustering, density modeling, and local dimensionality reduction, and we demonstrate its application to image compression and handwritten digit recognition.

Algorithms↗

PubMed1999

Comparison of matched BOLD and FAIR 4.0T-fMRI with [15O]water PET brain volumes.

Valid comparisons of functional activation volumes from fMRI and PET require accurate registration, matched spatial resolution, and if possible matched noise. We coregistered 4.0T-fMRI and PET volumes, using a series of linear and nonlinear transformations applied to the PET volumes. Because of the limited number of fMRI slices that were available, PET volumes were transformed to the fMRI space. Since 4.0T-fMRI and 4.0T-MRI volumes have significant spatial distortion due to magnet inhomogeneities, high resolution 1.5T-MRI volumes were nonlinearly transformed to 4.0T-MRI volumes as part of the transformation chain. The smoothing effects of these registration transformations were measured, in order to match the spatial resolution of the coregistered fMRI and PET volumes. Spatial resolution of the transformed PET volumes in the fMRI space was degraded by up to 60% due to the transformation process. Due to both the image acquisition characteristics and the coregistration process, the transformed PET volumes had a spatial resolution that was lower than that of tMRI. Therefore, significant smoothing of fMRI volumes was necessary to match their spatial resolution with that of the transformed PET volumes. Matching the spatial resolution of the fMRI volumes to those of the transformed PET volumes was achieved by matching the shape of their point spread functions. In order to do this, Gaussian kernels were employed to smooth the fMRI volumes. We were unable to simultaneously match the resolution and noise of fMRI and PET signals in the motor cortex. Activation maps derived from transformed PET and smoothed fMRI volumes were compared. Contralateral motor cortex was active in all modalities but there were large variations in the size of the activated region and its signal to noise ratio across BOLD, FAIR, and PET images within each subject. Nevertheless, the relative CBF changes measured by FAIR were consistent with those determined by PET.

Biophysical Phenomena↗