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At least 739 records · Page 41Linked to original sources
PubMed2005

Method of generalized projections algorithm for image-based reduction of artifacts in radial imaging.

This work describes the method of generalized projections (MGP) as an image-based, postprocessing method to correct for phase inconsistencies caused by echo misalignments in radial imaging. Computer simulations show that MGP can correct for echo shifts, constant phase, and amplitude errors, but the accuracy of the correction is limited, and this accuracy is reduced by the addition of more degrees of freedom. In phantom experiments, MGP performed better than magnitude filtered backprojection and anti-parallel projections correction.

Algorithms↗
PubMed2006

Single particle tracking across sequences of microscopical images: application to platelet adhesion under flow.

A versatile and automated image processing technique and data extraction procedure from videomicroscopic data is presented. The motivation is a detailed quantification of blood platelet adhesion from laminar flow onto a surface. The characteristics of the system under observation (type of cells, their speed of movement, and the quality of the optical image to analyze) provided the criteria for developing a new procedure enabling tracking for long image sequences. Specific features of the novel method include: automatic segmentation methodology which removes operator bias; platelet recognition across the series of images based on a probability density function (two-dimensional, Gaussian-like) tailored to the physics of platelet motion on the surface; options to automatically tune the procedure parameters to explore different applications; integrated analysis of the results (platelet trajectories) to obtain relevant information, such as deposition and removal rates, displacement distributions, pause times and rolling velocities. Synthetic images, providing known reference conditions, are used to test the method. The algorithm operation is illustrated by application to images obtained by fluorescence microscopy of the interaction between platelets and von Willebrand factor-coated surfaces in parallel-plate flow chambers. Potentials and limits are discussed, together with evaluation of errors resulting from an inaccurate tracking.

Algorithms↗
PubMed1992

Deblurring of 3-dimensional patterns of evoked rat cerebellar cortical activity: a study using voltage-sensitive dyes and optical sectioning.

One of the benefits of imaging neuronal activity is the capability of resolving spatial patterns in the x-y plane. With optical sectioning microscopy, the 3-dimensional (3-D) structure may also be studied without physical deformation by serially moving the focal plane of the microscope through the volume of interest along the focal axis. However, each image is blurred by contributions from neighboring planes. This degradation is most severe for low numerical aperture lenses and large amounts of defocus. In this study, an image restoration method using the optical properties of an aberration-free, defocused optical system has been developed for improving optical signals from voltage-sensitive dyes. Deblurring based on the optical transfer function (OTF) of the system was applied on two test sets of serially sectioned images: (1) fluorescent beads and (2) in vivo rat cerebellar cortex stained with the voltage-sensitive dye RH795. This method was shown to reduce significantly the out-of-focus contribution to the images, improving the spatial resolution not only in the x-y plane, but also the z axis. The algorithms were then applied to optical signals obtained by stimulation of the cerebellar surface. Optical signals having a distinct beam-like pattern were evoked and recorded over depths ranging from 0 to 300 microns prior to deblurring. Application of the deblurring algorithm reduced the depth of cerebellar cortex over which the optical signals were observed. In agreement, field potential recordings of the evoked parallel fiber volley and post-synaptic components were restricted to a narrow range of depths similar to the deblurred optical images. Removal of out-of-focus information is an essential step in the serial sectioning of central nervous system structures for neuronal imaging and 3-D reconstruction.

Algorithms↗
PubMed2005

Diffractive electron imaging of nanoparticles on a substrate.

The observation of the detailed atomic arrangement within nanostructures has previously required the use of an electron microscope for imaging. The development of diffractive (lensless) imaging in X-ray science and electron microscopy using ab initio phase retrieval provides a promising tool for nanostructural characterization. We show that it is possible experimentally to reconstruct the atomic-resolution complex image (exit-face wavefunction) of a small particle lying on a thin carbon substrate from its electron microdiffraction pattern alone. We use a modified iterative charge-flipping algorithm and an estimate of the complex substrate image is subtracted at each iteration. The diffraction pattern is recorded using a parallel beam with a diameter of approximately 50 nm, illuminating a gold nanoparticle of approximately 13.6 nm diameter. Prior knowledge of the boundary of the object is not required. The method has the advantage that the reconstructed exit-face wavefunction is free of the aberrations of the objective lens normally used in the microscope, whereas resolution is limited only by thermal vibration and noise.

Algorithms↗
PubMed2000

The impact of electron transport on the accuracy of computed dose.

The aim of this work was to investigate the accuracy of dose predicted by a Batho power law correction, and two models which account for electron range: A superposition/convolution algorithm and a Monte Carlo algorithm. The results of these models were compared in phantoms with cavities and low-density inhomogeneities. An idealized geometry was considered with inhomogeneities represented by regions of air and lung equivalent material. Measurements were performed with a parallel plate ionization chamber, thin TLDs (thermoluminescent dosimeters) and film. Dose calculations were done with a generalized Batho model, the Pinnacle collapsed cone convolution model (CCC), and the Peregrine Monte Carlo dose calculation algorithm. Absolute central axis and off axis dose data at various depths relative to interfaces of inhomogeneities were compared. Our results confirm that for a Batho correction, dose errors in the calculated depth dose arise from the neglect of electron transport. This effect increases as the field size decreases, as the density of the inhomogeneity decreases, and with the energy of incident photons. The CCC calculations were closer to measurements than the Batho model, but significant discrepancies remain. Monte Carlo results agree with measurements within the measurement and computational uncertainties.

Air↗
PubMed2004

Automatic phase determination for retrospectively gated cardiac CT.

The recent improvements in CT detector and gantry technology in combination with new heart rate adaptive cone beam reconstruction algorithms enable the visualization of the heart in three dimensions at high spatial resolution. However, the finite temporal resolution still impedes the artifact-free reconstruction of the heart at any arbitrary phase of the cardiac cycle. Cardiac phases must be found during which the heart is quasistationary to obtain outmost image quality. It is challenging to find these phases due to intercycle and patient-to-patient variability. Electrocardiogram (ECG) information does not always represent the heart motion with an adequate accuracy. In this publication, a simple and efficient image-based technique is introduced which is able to deliver stable cardiac phases in an automatic and patient-specific way. From low-resolution four-dimensional data sets, the most stable phases are derived by calculating the object similarity between subsequent phases in the cardiac cycle. Patient-specific information about the object motion can be determined and resolved spatially. This information is used to perform optimized high-resolution reconstructions at phases of little motion. Results based on a simulation study and three real patient data sets are presented. The projection data were generated using a 16-slice cone beam CT system in low-pitch helical mode with parallel ECG recording.

Algorithms↗
PubMed2000

Quantitative gated myocardial SPECT: effect of collimation on left-ventricular ejection fraction.

OBJECTIVE: Left-ventricular ejection fraction (LVEF) can be computed from gated myocardial perfusion SPECT studies using quantitative algorithms. The purpose of this study was to compare the LVEF obtained using the conventional high-resolution parallel-hole collimator (HRC) to the Cardiofocal collimator (CFC) (Siemens Medical Systems, Hoffman Estates, IL) using a quantitative LVEF program. METHODS: Thirty-four patients (15 men, 19 women; mean age = 62 y) had either treadmill or pharmacological stress testing with 25-30 mCi 99mTc sestamibi injected at peak stress. Conventional gated SPECT imaging was performed approximately 30 min poststress, first with the HRC collimator, then with the CFC, using the same acquisition parameters on a single-head gamma camera. Traditional (TRAD) determination of LVEF using planar gated blood pool and/or cardiac catherization also was obtained for each patient. RESULTS: The correlation in LVEF between the CFC and HRC acquisitions was excellent, r = 0.99. The correlation between CFC and TRAD LVEF was good, r = 0.95, as was the HRC and TRAD correlation, r = 0.97. The mean LVEF value for HRC was slightly less than TRAD (54% vs. 55.4%), while the CFC mean LVEF was higher (62% vs. 55.4%). Although CFC LVEF correlated well with HRC, mean LVEF value using CFC was higher than HRC. CONCLUSION: The choice of collimator may alter the LVEF obtained from gated SPECT perfusion studies.

Algorithms↗
PubMed2000

On the parallelization of linkmap from the LINKAGE/FASTLINK package.

Genetic linkage calculations can be time consuming, even on a fast computer. The ability to collect large family pedigrees has increased the magnitude of linkage computations. Sequential genetic algorithms have many successful applications in very different domains, but they have a main drawback in their utilization. Evaluations are very time-consuming, e.g., a pedigree consisting of 55 nodes takes about 70 min on a DEC-Alpha processor and about 270 min on a 166 MHz Pentium for certain likelihood calculations. This time increases exponentially with the increase in the size of the pedigree. In order to solve these shortcomings and to study new models of higher efficiency and efficacy, parallel platforms are being used for genetic programs. LINKAGE is a software package for performing genetic likelihood calculations; FASTLINK is an improved, faster version of it. This paper provides a parallel implementation of the "Linkmap" program (one of the four programs in LINKAGE/FASTLINK) for a heterogeneous environment, using a static and a dynamic strategy for task allocation. It was found that the increased performance by the dynamic strategy was close to the estimated maximum speed up.

Algorithms↗
PubMed1994

Protein design by optimization of a sequence-structure quality function.

An automated procedure for protein design by optimization of a sequence-structure quality has been developed. The method selects a statistically optimal sequence for a particular structure, on the assumption that such a protein will adopt the desired structure. We present two optimization algorithms: one provides an exact optimization while the other uses a combinatorial technique for comparatively rapid results. Both are suitable for massively parallel computers. A prototype system was used to design sequences which should adopt the four-helix bundle conformation of myohemerythrin. These appear satisfactory to secondary structure and profile analysis. Detailed inspection reveals that the sequences are generally plausible but, as expected, lack some specific structural features. The design parameters provide some insight into the general determinants of protein structure.

Algorithms↗
PubMed2003

Corrim-based alignment for improved speed in single-particle image processing.

The technique of single-particle electron cryomicroscopy is currently making possible the 3D structure determination of large macromolecular complexes at constantly increasing levels of resolution. Work at resolution now attainable requires many thousands of individual images to be processed computationally. The most time-consuming step of the image-processing procedure is usually the iterative alignment of individual particle images against a set of reference images derived from a preliminary 3-D structure. We have developed an improved multireference alignment procedure based on interpolated cross-correlation images (corrims) that results in an approximately 8-fold acceleration of the iterative alignment steps. These corrims can be used to restrict the number of image-alignment calculations by narrowing down the set of reference images. Another improvement in alignment speed has been achieved by optimising the software and its implementation on many parallel processors. This new corrim-based refinement has been found to work well with two different alignment algorithms, the commonly used "fast alignment by separate translational/rotational searches" and "exhaustive alignment by polar coordinates."

Algorithms↗
PubMed2006

Guest-host colloid crystals: experimental study and simulations.

Disorder in colloid crystals was induced by doping them with a different number of large or small guest particles, which had a different deviation in size from the host colloids. The change in optical properties of the guest-host colloid crystals was assessed by using optical transmission spectroscopy while the variation in crystal structure was examined using scanning electron microscopy (SEM). The disruption in the crystalline lattices depended on the relative deviation in sizes of the guest and host particles and the concentration of the guest colloids. In parallel with experiments, the packing of spheres in guest-host crystals was modeled with a simulated annealing algorithm. A good correlation was found between the changes in crystal structure observed by SEM imaging and the simulated sphere packing. The experimental and simulated changes in the transmission spectra of guest-host colloid crystals were in good agreement.

Journal Article↗
PubMed2006

Experimental phantom lesion detectability study using a digital breast tomosynthesis prototype system.

PURPOSE: To compare the sensitivity of conventional two-dimensional (2D) projection imaging with tomosynthesis with respect to the detectability of mammographic phantom lesions. MATERIALS AND METHODS: Using a breast tomosynthesis prototype based on a commercial FFDM system (Siemens MAMMOMAT Novation), but modified for a wide angle tube motion and equipped with a fast read-out amorphous selenium detector, we acquired standard 2D images and tomosynthesis series of projection views. We used the Wisconsin mammographic random phantom, model RMI 152A. The anode filter combinations Mo/Mo and W/Rh at two different doses were used as typical radiographic techniques. Slice images through the phantom parallel to the detector were reconstructed with a distance of 1 mm employing a filtered back-projection algorithm. The image data sets were read by five radiologists and evaluated with respect to the detectability of the phantom details. RESULTS: For all studied radiographic techniques, the detection rate in the tomosynthesis mode was 100 %, i. e. 75 true positive findings out of 75 possible hits. In contrast, the conventional projection mode yielded a detection rate between 80 and 93 % (corresponding to 60 and 70 detected details) depending on the dose and X-ray spectrum. CONCLUSION: Tomosynthesis has the potential to increase the sensitivity of digital mammography. Overlapping structures from out-of-plane tissue can be removed in the tomosynthesis reconstruction process, thereby enhancing the diagnostic accuracy.

Algorithms↗
PubMed1999

Attenuation correction in SPECT using consistency conditions for the exponential ray transform.

Using data consistency conditions for the exponential ray transform, a method is derived to correct SPECT data for attenuation effects. No transmission measurements are required, and no operator-defined contours are needed. Furthermore, any 3D parallel-ray geometry can be considered for SPECT data acquisition, even unconventional geometries which do not lead to a set of 2D parallel-beam sinograms. The method is presented for both the 2D parallel-beam geometry and a particular 3D case, called the rotating slant hole geometry. Full details of the algorithms are given. Implementation has been carried out and results are presented in 2D and in 3D using simulated data.

Algorithms↗
PubMed2003

FAIR: a hardware architecture for real-time 3-D image registration.

Mutual information-based image registration, shown to be effective in registering a range of medical images, is a computationally expensive process, with a typical execution time on the order of minutes on a modern single-processor computer. Accelerated execution of this process promises to enhance efficiency and therefore promote routine use of image registration clinically. This paper presents details of a hardware architecture for real-time three-dimensional (3-D) image registration. Real-time performance can be achieved by setting up a network of processing units, each with three independent memory buses: one each for the two image memories and one for the mutual histogram memory. Memory access parallelization and pipelining, by design, allow each processing unit to be 25 times faster than a processor with the same bus speed, when calculating mutual information using partial volume interpolation. Our architecture provides superior per-processor performance at a lower cost compared to a parallel supercomputer.

Algorithms↗
PubMed2007

The impact of aberration on high frame rate cardiac B-mode imaging.

In echocardiography, especially in 3D echocardiography, achieving high frame rates is a major challenge. A suggested solution is parallel receive beamforming. Without any compensation, this approach is known to produce block-like artifacts, where each block corresponds to one parallel receive group. In this work, in vitro imaging, in vivo imaging, and simulations were used to investigate the artifacts. In vitro, imaging a tissue phantom, the artifacts were successfully compensated for. However, in vivo, imaging the heart, the compensation techniques no longer sufficed and the artifacts persisted. With in vivo imaging, aberrating tissue layers are present between the heart and the probe. To investigate the effects of aberration on a parallel receive system, an in vitro experiment was performed with and without a silicon phase aberrator in front of the probe. The aberrator caused the artifacts to appear even when compensation techniques were applied. Simulations confirmed the measured results and indicated that distorted beam profiles and decorrelation between parallel receive groups caused the artifacts. To quantify the magnitude of the artifacts, a correlation-based indicator was developed. The indicator separated images with and without artifacts and confirmed that the artifacts appeared from the combination of parallel receive beams and aberration.

Algorithms↗
PubMed1990

PR interval behavior during exercise: implications for physiological pacemakers.

The relationship between heart rate response and the dynamic changes in the PR interval was assessed in 631 patients undergoing routine cardiac exercise tests for a variety of clinical indications. Patients were stratified into four subsets: nonmedicated normals (n = 437), patients on beta-antagonist agents (n = 118), those on antiarrhythmic agents alone (n = 61) and those with a clinical diagnosis of advanced (New York Heart Association [NYHA] Class III or IV) congestive heart failure. All patients were in stable sinus rhythm throughout the test. PR intervals were measured at rest, at mid-exercise and at peak exercise. Mean PR intervals shortened to a statistically significant degree in most subgroups. This effect was predominantly observed in the earlier stages of exercise. In patients with advanced heart failure, there was no statistically significant shortening of exercise PR intervals later in exercise, demonstrating a parallel with their relatively blunted heart rate response. These changes in exercise PR intervals suggest that implanted pacemaker algorithms may be constructed to maximize hemodynamic benefit in patients requiring physiological pacemakers.

Adolescent↗
PubMed2002

Quantifying uncertainty in geoacoustic inversion. I. A fast Gibbs sampler approach.

This paper develops a new approach to estimating seabed geoacoustic properties and their uncertainties based on a Bayesian formulation of matched-field inversion. In Bayesian inversion, the solution is characterized by its posterior probability density (PPD), which combines prior information about the model with information from an observed data set. To interpret the multi-dimensional PPD requires calculation of its moments, such as the mean, covariance, and marginal distributions, which provide parameter estimates and uncertainties. Computation of these moments involves estimating multi-dimensional integrals of the PPD, which is typically carried out using a sampling procedure. Important goals for an effective Bayesian algorithm are to obtain efficient, unbiased sampling of these moments, and to verify convergence of the sample. This is accomplished here using a Gibbs sampler (GS) approach based on the Metropolis algorithm, which also forms the basis for simulated annealing (SA). Although GS can be computationally slow in its basic form, just as modifications to SA have produced much faster optimization algorithms, the GS is modified here to produce an efficient algorithm referred to as the fast Gibbs sampler (FGS). An automated convergence criterion is employed based on monitoring the difference between two independent FGS samples collected in parallel. Comparison of FGS, GS, and Monte Carlo integration for noisy synthetic benchmark test cases indicates that FGS provides rigorous estimates of PPD moments while requiring orders of magnitude less computation time.

Acoustics↗