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At least 793 records · Page 44Linked to original sources

PubMed2004

Large-scale recording of neuronal ensembles.

How does the brain orchestrate perceptions, thoughts and actions from the spiking activity of its neurons? Early single-neuron recording research treated spike pattern variability as noise that needed to be averaged out to reveal the brain's representation of invariant input. Another view is that variability of spikes is centrally coordinated and that this brain-generated ensemble pattern in cortical structures is itself a potential source of cognition. Large-scale recordings from neuronal ensembles now offer the opportunity to test these competing theoretical frameworks. Currently, wire and micro-machined silicon electrode arrays can record from large numbers of neurons and monitor local neural circuits at work. Achieving the full potential of massively parallel neuronal recordings, however, will require further development of the neuron-electrode interface, automated and efficient spike-sorting algorithms for effective isolation and identification of single neurons, and new mathematical insights for the analysis of network properties.

Action Potentials↗

PubMed1992

A conjecture of Procesi and the straightening algorithm of Rota.

Let R = Q[x1, x2,..., xn] and R* denote the quotient of R by the ideal generated by the elementary symmetric functions. R*, under the action of Sn, yields a graded version of the left regular representation. Procesi asked for a basis of R* consisting of homogeneous polynomials Gamma[S, C] indexed by pairs of tableaux, with S standard and C cocharge, that exhibits the decomposition of R* into its irreducible components. Procesi also suggested a way to construct the Gamma[S, C]. Using Rota's straightening algorithm, I show that certain polynomials [S, C] closely related to the Gamma[S, C] terms yield the desired basis. Parallel to the ring R* there is a family of Sn-modules R that have recently been studied by Garsia and Procesi. These modules have a graded character that is closely related to the q-Kostka-Foulkes polynomials Klambdamu(q). The [S, C] can be shown to yield also a basis when restricted to a given R. Through this connection the work reported here leads to an additional way of proving the charge interpretation for the polynomials Klambdamu(q).

Journal Article↗

PubMed2004

A low-order unstructured-mesh approach for computational electromagnetics in the time domain.

Maxwell's curl equations in the time domain are solved using an explicit linear finite-element approach implemented on unstructured tetrahedral meshes. For the simulation of scattering problems, a perfectly matched layer is added at the artificial far-field boundary, created by the truncation of the physical domain prior to the numerical solution. The complete solution procedure is parallelized. The computational challenges that are encountered when attempting simulations at higher frequencies suggest that the implementation of a hybrid algorithm could have certain advantages. The hybrid approach adopted uses a combination of the finite-element procedure and the well-known low operation count/low storage finite-difference time-domain method. Examples are included to demonstrate the numerical performance of the techniques that are described.

Journal Article↗

PubMed2004

Artifact analysis and reconstruction improvement in helical cardiac cone beam CT.

With the introduction of cone beam (CB) scanners, cardiac volumetric computed tomography (CT) imaging has the potential to become a noninvasive imaging tool in clinical routine for the diagnosis of various heart diseases. Heart rate adaptive reconstruction schemes enable the reconstruction of high-resolution volumetric data sets of the heart. Artifacts, caused by strong heart rate variations, high heart rates and obesity, decrease the image quality and the diagnostic value of the images. The image quality suffers from streak artifacts if suboptimal scan and reconstruction parameters are chosen, demanding improved gating techniques. In this paper, an artifact analysis is carried out which addresses the artifacts due to the gating when using a three-dimensional CB cardiac reconstruction technique. An automatic and patient specific cardiac weighting technique is presented in order to improve the image quality. Based on the properties of the reconstruction algorithm, several assessment techniques are introduced which enable the quantitative determination of the cycle-to-cycle transition smoothness and phase homogeneity of the image reconstruction. Projection data of four patients were acquired using a 16-slice CBCT system in low pitch helical mode with parallel electrocardiogram recording. For each patient, image results are presented and discussed in combination with the assessment criteria.

Algorithms↗

PubMed2000

Three-dimensional computed tomographic reconstruction using a C-arm mounted XRII: image-based correction of gantry motion nonidealities.

The image quality of 3D reconstructions produced using a C-arm mounted XRII depends on precise determination of the geometric parameters that describe the detector system in the laboratory frame of reference. We have designed a simplified calibration system that depends on images of a metal sphere, acquired during rotation of the gantry through 200 degrees. Angle-dependent shift corrections are obtained, accounting for nonideal motion in two directions: perpendicular to the axis of rotation and tangential to the circular trajectory (tau), and parallel to the axis of rotation (xi). Projection images are corrected prior to reconstruction using a simple shift-interpolation algorithm. We show that the motion of the gantry is highly reproducible during acquisitions within one day (mean standard deviation in tau and xi is 0.11 mm and 0.08 mm, respectively), and over 21 months (mean standard deviation in tau and xi is 0.10 mm and 0.06 mm, respectively). Reconstruction of a small-bead phantom demonstrates uniformity of the correction algorithm over the full volume of the reconstruction [standard deviation of full-width-half-maximum of the beads is approximately 0.25 pixels (0.13 mm) over the volume of reconstruction]. Our approach provides a simple correction technique that can be applied when trajectory deviations are significant relative to the pixel size of the detector but small relative to the detector field of view, and when the fan angle of the acquisition geometry is small (<20 degrees). A comparison with other calibration techniques in the literature is provided.

Algorithms↗

PubMed1989

Standard forms of dentition and mandible for applications in rotational panoramic radiography.

Mathematical expressions describing the average form and size of the dentition and the mandible are presented. These expressions should be of value in applications of panoramic radiography when reference to an average standard jaw form is of interest. Data were collected from axial radiographs of 35 males and 35 females of three ethnic groups: Mexican-Americans, black Americans and American and Scandinavian Caucasians. Curves were traced on the axial radiographs representing the dentition and the mandible and points along these curves digitized. Mathematical expressions were established using advanced algorithms for orthogonal polynomial curve fitting, i.e. perpendicular distances to the curved dentition and mandible were minimized rather than distances parallel to the y-axis in an arbitrarily chosen coordinate system. The standard deviations around the polynomials defining the average curves are demonstrated and expressions for calculating the continuously varying standard deviations are given.

Dentition↗

PubMed2006

Noise simulation in cone beam CT imaging with parallel computing.

We developed a computer noise simulation model for cone beam computed tomography imaging using a general purpose PC cluster. This model uses a mono-energetic x-ray approximation and allows us to investigate three primary performance components, specifically quantum noise, detector blurring and additive system noise. A parallel random number generator based on the Weyl sequence was implemented in the noise simulation and a visualization technique was accordingly developed to validate the quality of the parallel random number generator. In our computer simulation model, three-dimensional (3D) phantoms were mathematically modelled and used to create 450 analytical projections, which were then sampled into digital image data. Quantum noise was simulated and added to the analytical projection image data, which were then filtered to incorporate flat panel detector blurring. Additive system noise was generated and added to form the final projection images. The Feldkamp algorithm was implemented and used to reconstruct the 3D images of the phantoms. A 24 dual-Xeon PC cluster was used to compute the projections and reconstructed images in parallel with each CPU processing 10 projection views for a total of 450 views. Based on this computer simulation system, simulated cone beam CT images were generated for various phantoms and technique settings. Noise power spectra for the flat panel x-ray detector and reconstructed images were then computed to characterize the noise properties. As an example among the potential applications of our noise simulation model, we showed that images of low contrast objects can be produced and used for image quality evaluation.

Algorithms↗

PubMed2005

Properties of star-branched and linear chains in confined space. A Monte-Carlo study.

We have studied the properties of simple models of linear and star-branched polymer chains confined in a slit formed by two parallel impenetrable walls. The polymer chains consisted of identical united atoms (homopolymers) and were restricted to a simple cubic lattice. Two macromolecular architectures of the chain: linear and regular stars with three branches of equal length, were studied. The excluded volume was the only potential introduced into the model and thus the system was athermal. Monte-Carlo simulations with the sampling algorithm based on the chain's local changes of conformation were carried out for chains with different lengths as well as for different distances between the confining surfaces. We found that the properties of model chains differ for both macromolecular architectures but a universal behavior for both kinds of chains was also found. Investigation of the frequency of chain-wall contacts shows that the ends of the chains are much more mobile than the rest of the chain, especially in the vicinity of the branching point in star polymers. [Figure: see text]. The scheme of a star-branched (left) and a linear (right) chain located between two parallel impenetrable surfaces.

Algorithms↗

PubMed1995

Conditions for electron tomographic data acquisition.

The conventional algorithms employed in electron microscope tomography require that the series of images obtained from different orientations of the specimen each represent a parallel orthographic projection under uniform magnification. Electron microscope optics can produce distortions in images that may affect the accuracy of a tomographic reconstruction. These distortions result in images with differential rotation and magnification of regions of a thick or highly tilted specimen located at different distances with respect to the plane of focus. The distortions increase in magnitude and may significantly affect the accuracy of the tomographic data when images are acquired under current center misalignment or non-eucentric positioning of the specimen. An additional source of error can be introduced if the condenser lenses are adjusted to compensate for the intensity attenuation due to the increased beam path length as the specimen is tilted. The change in beam crossover position due to adjustment of the condensers alters the beam divergence and may introduce systematic changes in magnification over the tilt series. The process of alignment of the tilt series will propagate these errors to more central regions of the image. In most cases, with proper consideration, it is possible to minimize these errors to levels where they will have negligible effects on the resolution of the tomographic reconstruction.

Algorithms↗

PubMed2000

3D cone-beam CT reconstruction for circular trajectories.

3D reconstruction from 2D projections obtained along a single circular source trajectory is most commonly done using an algorithm due to Feldkamp, Davis and Kress. In this paper we propose an alternative approach based on a cone-beam to parallel-beam rebinning step, a corresponding rebinning step into a rectangular virtual detector plane and a filtered backprojection. This approach yields an improved image quality reflected by a decreased low-intensity drop which is well known for 3D reconstruction from projection data obtained along circular trajectories. At the same time the computational complexity is lower than in Feldkamp's original approach. Based on this idea, a hybrid 3D cone-beam reconstruction method is formulated that enlarges the reconstruction volume in its dimension along the rotation axis of the cone-beam CT system. This enlargement is achieved by applying different reconstruction conditions for each voxel. An optimal ratio between the reconstructible and irradiated volume of the scanned object is achieved.

Algorithms↗

PubMed1999

A lattice relaxation algorithm for three-dimensional Poisson-Nernst-Planck theory with application to ion transport through the gramicidin A channel.

A lattice relaxation algorithm is developed to solve the Poisson-Nernst-Planck (PNP) equations for ion transport through arbitrary three-dimensional volumes. Calculations of systems characterized by simple parallel plate and cylindrical pore geometries are presented in order to calibrate the accuracy of the method. A study of ion transport through gramicidin A dimer is carried out within this PNP framework. Good agreement with experimental measurements is obtained. Strengths and weaknesses of the PNP approach are discussed.

Algorithms↗

PubMed1996

Real-time 3D dose calculation and display: a tool for plan optimization.

PURPOSE: Both human and computer optimization of treatment plans have advantages; humans are much better at global pattern recognition, and computers are much better at detailed calculations. A major impediment to human optimization of treatment plans by manipulation of beam parameters is the long time required for feedback to the operator on the effectiveness of a change in beam parameters. Our goal was to create a real-time dose calculation and display system that provides the planner with immediate (fraction of a second) feedback with displays of three-dimensional (3D) isodose surfaces, digitally reconstructed radiographs (DRRs), dose-volume histograms, and/or a figure of merit (FOM) (i.e., a single value plan score function). This will allow the experienced treatment planner to optimize a plan by adjusting beam parameters based on a direct indication of plan effectiveness, the FOM value, and to use 3D display of target, critical organs, DRRs, and isodose contours to guide changes aimed at improving the FOM value. METHODS AND MATERIALS: We use computer platforms that contain easily utilized parallel processors and very tight coupling between calculation and display. We ported code running on a network of two workstations and an array of transputers to a single multiprocessor workstation. Our current high-performance graphics workstation contains four 150-MHz processors that can be readily used in a shared-memory multithreaded calculation. RESULTS: When a 10 x 10-cm beam is moved, using an 8-mm dose grid, the full 3D dose matrix is recalculated using a Bentley-Milan-type dose calculation algorithm, and the 3D dose surface display is then updated, all in < 0.1s. A 64 x 64-pixel DRR calculation can be performed in < 0.1 s. Other features, such as automated aperture calculation, are still required to make real-time feedback practical for clinical use. CONCLUSION: We demonstrate that real-time plan optimization using general purpose multiprocessor workstations is a practical goal. Parallel processing technology provides this capability for 3D planning systems, and when combined with objective plan ranking algorithms should prove effective for optimizing 3D conformal radiation therapy. Compared to our earlier transputer work, multiprocessor workstations are more easily programmed, making software development costs more reasonable compared with uniprocessor development costs. How the dose calculation is partitioned into parallel tasks on a multiprocessor work station can make a significant difference in performance. Shared-memory multiprocessor workstations are our first choice for future work, because they require minimum programming effort and continue to be driven to higher performance by competition in the workstation arena.

Computer Graphics↗

PubMed2005

Vortex core identification in viscous hydrodynamics.

We describe a software package designed for the investigation of topological fluid dynamics with a novel algorithm for locating and tracking vortex cores. The package is equipped with modules for generating desired vortex knots and links and evolving them according to the Navier-Stokes equations, while tracking and visualizing them. The package is parallelized using a message passing interface for a multiprocessor environment and makes use of a computational steering library for dynamic user intervention.

Algorithms↗

PubMed2006

Automatic removal of high-amplitude artefacts from single-channel electroencephalograms.

In this work, we present a method to extract high-amplitude artefacts from single channel electroencephalogram (EEG) signals. The method is called local singular spectrum analysis (local SSA). It is based on a principal component analysis (PCA) applied to clusters of the multidimensional signals obtained after embedding the signals in their time-delayed coordinates. The decomposition of the multidimensional signals in each cluster is achieved by relating the largest eigenvalues with the large amplitude artefact component of the embedded signal. Then by reverting the clustering and embedding processes, the high-amplitude artefact can be extracted. Subtracting it from the original signal a corrected EEG signal results. The algorithm is applied to segments of real EEG recordings containing paroxysmal epileptiform activity contaminated by large EOG artefacts. We will show that the method can be applied also in parallel to correct all channels that present high-amplitude artefacts like ocular movement interferences or high-amplitude low frequency baseline drifts. The extracted artefacts as well as the corrected EEG will be presented.

Algorithms↗

PubMed1989

Fully automated measurements by light microscopy of tissue sections using a cellular array computer.

Software was developed for the acquisition, segmentation and analysis of microscopic OD-images on a VICOM digital image processor, extended with a VISIOMORPH morphoprocessor board. The delineation algorithms for peroxisomes, lysosomes, and nuclei in liver, kidney, and adrenal gland sections start by thresholding the difference between the original image and a low pass filtered version. The resulting binary mask is then processed by morphological operations in order to produce an object overlay. The efficiency of the programs is evaluated by comparing delineated objects at different OD-levels, created by varying the stain or by multiplying the original pixel values with constant factors. Manual delineation on some images is also used as a reference. More complex algorithms are used for the delineation of muscle fibres in ATP-ase-stained sections and immunocytochemically labelled cells in monolayer preparations. Muscle images from parallel sections with different stainings are matched with a coordinate transform, enabling the transfer of the object mask from a single delineated image to the unprocessed images and thus obtain all necessary information for fibre classification. After segmentation, the OD-images and their object overlays are fed into a data extraction program, measuring for each delineated object user-selected features. Data are sent to a VAX for statistical interpretation.

Adrenal Cortex↗

PubMed2000

A multicenter validation of an active contour-based left ventricular analysis technique.

Quantitative analysis of functional cardiac magnetic resonance (MR) images has been limited by the lack of well-validated, semiautomatic, methods for rapid analysis. We describe the evaluation of a DICOM-compatible PC-based parallel-processing tool, for cardiac magnetic resonance analysis (CAMRA), which supports semiautomatic image mensuration using an active contour model-based algorithm. The CAMRA software was used to analyze data from 12 patients in a multicenter acquisition and analysis trial to compare semiautomatic contour detection with manual planimetry of the left ventricular endocardium from short-axis, breath-held, cine gradient-echo images. There was excellent agreement between the manual and semiautomatic measurements of global left ventricular function, with no significant (P = 0.32) difference in the determination of ejection fraction (-0.9 +/- 3.1% [mean difference +/- 1 standard deviation]). There was no significant interobserver difference in the semiautomatically measured ejection fraction. Additionally, a single observer completed the analysis on data from 30 patients and found no significant (P = 0.05) difference in the determination of ejection fraction (-1.3 +/- 3.5% [mean difference +/- 1 standard deviation]). The CAMRA software demonstrates the capability for the reproducible evaluation of global left ventricular function in cardiac patients, with adequate interobserver reproducibility for use in multicenter trials.

Adult↗

PubMed2006

Optimization of the Monte Carlo code for modeling of photon migration in tissue.

The Monte Carlo method is frequently used to simulate light transport in turbid media because of its simplicity and flexibility, allowing to analyze complicated geometrical structures. Monte Carlo simulations are, however, time consuming because of the necessity to track the paths of individual photons. The time consuming computation is mainly associated with the calculation of the logarithmic and trigonometric functions as well as the generation of pseudo-random numbers. In this paper, the Monte Carlo algorithm was developed and optimized, by approximation of the logarithmic and trigonometric functions. The approximations were based on polynomial and rational functions, and the errors of these approximations are less than 1% of the values of the original functions. The proposed algorithm was verified by simulations of the time-resolved reflectance at several source-detector separations. The results of the calculation using the approximated algorithm were compared with those of the Monte Carlo simulations obtained with an exact computation of the logarithm and trigonometric functions as well as with the solution of the diffusion equation. The errors of the moments of the simulated distributions of times of flight of photons (total number of photons, mean time of flight and variance) are less than 2% for a range of optical properties, typical of living tissues. The proposed approximated algorithm allows to speed up the Monte Carlo simulations by a factor of 4. The developed code can be used on parallel machines, allowing for further acceleration.

Light↗

PubMed2001

Mathematical analysis of coupled parallel simulations.

A set of parallel replicas of a single simulation can be statistically coupled to closely approximate long trajectories. In many cases, this produces nearly linear speedup over a single simulation ( M times faster with M simulations), rendering previously intractable problems within reach of large computer clusters. Interestingly, by varying the coupling of the parallel simulations, it is possible in some systems to obtain greater than linear speedup. The methods are generalizable to any search algorithm with long residence times in intermediate states.

Journal Article↗