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Medical Imaging 2004 Conference

作者： Redmond, M Brodsky, E Hu, YH Grist, T Schulte, M Block, W Univ Wisconsin Madison WI 53792 USA

ISBN: (纸本)0819452807

It is becoming increasingly common to image time-resolved flow patterns through the vascular system in all three spatial dimensions using non-invasive methods. The capability to generate four-dimensional (4D) (x, y, z and time) vascular flow data is growing in several modalities. Vastly undersampled Isotropic PRojection (VIPR) is one such method using high-resolution, fast Magnetic Resonance Imaging (MRI) of the vasculature system during intravenous contrast injection. VIPR currently produces 4D data sets of twenty to forty frames of 256(3) voxels each, and stronger magnets will allow higher resolution time series that generate gigabytes of data. Real-time visualization and analysis of 4D data can quickly overwhelm the memory and processing capabilities of desktop workstations. 4D Cluster Visualization (4DCV) offers a straightforward, scalable approach to interactively display and manipulate 4D, reconstructed, VIPR data sets. 4DCV exploits the inherently parallel nature of 4D frame data to interactively manipulate and render individual 3D data frames simultaneously across all nodes of a visualization cluster. An interactive animation is produced in real-time by reading back the 2D rendered results, to a central animation console where the image sequence is assembled into a continuous stream for display. Basic 4DCV can be extended to allow rendering of multiple frames on one node, compression of image streams for serving remote clinical workstations, and local archival storage of 3D data frames at the cluster nodes for quick retrieval of medical exams. 4D Cluster Visualization concepts can also be extended to distributed and Grid implementations.

关键词： medical imaging 4D visualization cluster visualization parallel rendering cluster animation

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High-level design environment for massive parallel VLSI-implementations of statistical signal- and image processing models

High-level design environment for massive parallel VLSI-impl...

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IEEE International Symposium on Circuits and Systems (ISCAS)

作者： S. Stilkerich J.K. Anlauf Image and Signal Processing Groupe EADS Corporate Research Center Munich Germany Institute of Computer Science II University of Bonn Bonn Germany

In this paper we introduce and describe a generic and semiconductor-technology independent hardware development environment for a class of statistical signal- and image processing models. The statistical signal- and image processing approach under consideration formally adopts the Bayesian paradigm and uses discrete Markov random field (MRF) models for the processing models to derive the joint distribution of signal- and image processing problems by means of mathematically and computationally tractable conditional distributions. We experimentally demonstrate and prove the capabilities respectively the concepts of the proposed high-level design environment by detailed chip layouts of different neighbourhood topologies and a single processing element of a MRF-architecture, which solves the image processing problem of noise removing, restoration and intensity-level preserving.

关键词： Signal design Signal processing image processing Mathematical model Hardware Bayesian methods Markov random fields distributed computing Topology Working environment noise

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parallelization and comparison of 3D iterative reconstruction algorithms

Parallelization and comparison of 3D iterative reconstructio...

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Euromicro Conference on parallel, distributed and Network-Based processing

作者： J.-R. Bilbao-Castro J.M. Carazo J.J. Fernandez I. Garcia Biocomputing Unit Centro Nacional de Biotecnología-CSIC Madrid Spain Department Arquitectura Computadores y Electrónica Universidad de Almería Universidad de Almería Ctra. Almeria Spain

High resolution structure determination of biological macromolecules by electron microscopy is central to understand their biological function. These structural analyses involve processing thousands projection images taken from the specimen at different orientations. Regularized iterative reconstruction methods are well suited to deal with the extremely noise conditions found in those studies, but they are computationally expensive. parallel computing then emerges as a natural solution for those problems allowing huge jobs to be run in clusters of workstations. This work describes and analyzes the parallel implementations of five 3D iterative reconstruction algorithms, including simultaneous and block-iterative methods. The evaluation of the parallel approaches is carried put in terms of speedups and computation versus communication times. It is shown that there are specific iterative methods that are specially well suited for parallelization, with a great level of scalability and fast convergence rates. This work draws the conclusion that the use of those parallel reconstruction methods is going to be central to afford "grand challenge " problems currently unapproachable in structural biology, such as structure determination at close-to-atomic resolution by electron microscopy.

关键词： Reconstruction algorithms Iterative methods Electron microscopy Molecular biophysics image analysis Biology computing parallel processing Workstations Algorithm design and analysis Concurrent computing

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Scalable regularized tomography without repeated projections

Scalable regularized tomography without repeated projections

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International Symposium on parallel and distributed processing (IPDPS)

作者： J. August T. Kanade The Robotics Institute Carnegie Mellon University Pittsburgh PA USA

Summary form only given. X-ray computerized tomography (CT) and related imaging modalities (e.g., PET) are notorious for their excessive computational demands, especially when noise-resistant probabilistic methods such as regularized tomography are used. The basic idea of regularized tomography is to compute a smooth image whose simulated projections (line integrals) approximate the observed, noisy X-ray projections. The computational expense in previous methods stems from explicitly applying a large sparse projection matrix to enforce these smoothness and data fidelity constraints during each of many iterations of the algorithm. Here we review our recent work in regularized tomography in which the smoothness constraint is analytically transformed from the image to the projection domain, before any computations begin. As a result, iterations take place entirely in the projection domain, avoiding the repeated sparse matrix-vector products. A more surprising benefit is the decoupling of a large system of regularization equations into many small systems of simpler independent equations, whose solution requires an "embarassingly parallel" computation. Here, we demonstrate that this method provides linear speedup of regularized tomography for up to 20 compute nodes (Pentium 4, 1.5 GHz) on a 100 Mb/s network using a Matlab MPI implementation.

关键词： X-ray imaging Computed tomography Sparse matrices Equations Optical imaging Positron emission tomography Computational modeling image analysis Concurrent computing Computer networks

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Dynamic data access to the GT/CERCS Linux mirror site

Dynamic data access to the GT/CERCS Linux mirror site

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International Symposium on parallel and distributed processing (IPDPS)

作者： M. Mansour M. Wolf K. Schwan College of Computing Georgia Institute of Technology USA

Summary form only given. The purpose of this work is to better understand the dynamic data sharing behavior of certain classes of grid end users. Toward this end, we study a large-scale data repository and the end users' access behaviors to this repository. Interesting insights from the study include that (1) the use of parallel methods for data downloads, via download accelerators, is common, despite qualms expressed by the community about the impacts of such behavior on wide area data distribution networks, (2) high levels of burstiness exist for such data movements, as also observed for scientific or populist data repositories and Web sites (e.g., space imagery, sports events), and (3) a large number of remote data retrievals are by single clients for single files. We finally discuss the impact of our observations on grid applications in general.

关键词： Linux Mirrors Information retrieval Grid computing distributed computing Educational institutions image retrieval Large-scale systems Collaborative work Collaboration

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Triple-target microarray experiments: a novel experimental strategy

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BMC GENOMICS 2004年第1期5卷 1-16页

作者： Forster, T Costa, Y Roy, D Cooke, HJ Maratou, K Univ Edinburgh Coll Med Scottish Ctr Genom Technol & Informat Edinburgh EH16 4SB Midlothian Scotland Western Gen Hosp Dept Chromosome Biol MRC Human Genet Unit Edinburgh EH4 2XU Midlothian Scotland

Background: High-throughput, parallel gene expression analysis by means of microarray technology has become a widely used technique in recent years. There are currently two main dye-labelling strategies for microarray studies based on custom-spotted cDNA or oligonucleotides arrays: (I) Dye-labelling of a single target sample with a particular dye, followed by subsequent hybridisation to a single microarray slide, (ii) Dye-labelling of two different target samples with two different dyes, followed by subsequent co-hybridisation to a single microarray slide. The two dyes most frequently used for either method are Cy3 and Cy5. We propose and evaluate a novel experiment set-up utilising three differently labelled targets co-hybridised to one microarray slide. In addition to Cy3 and Cy5, this incorporates Alexa 594 as a third dye-label. We evaluate this approach in line with current data processing and analysis techniques for microarrays, and run separate analyses on Alexa 594 used in single-target, dual-target and the intended triple-target experiment set-ups ( a total of 18 microarray slides). We follow this by pointing out practical applications and suitable analysis methods, and conclude that triple-target microarray experiments can add value to microarray research by reducing material costs for arrays and related processes, and by increasing the number of options for pragmatic experiment design. Results: The addition of Alexa 594 as a dye-label for an additional - third - target sample works within the framework of more commonplace Cy5/Cy3 labelled target sample combinations. Standard normalisation methods are still applicable, and the resulting data can be expected to allow identification of expression differences in a biological experiment, given sufficient levels of biological replication ( as is necessary for most microarray experiments). Conclusion: The use of three dye-labelled target samples can be a valuable addition to the standard repertoire of microarray

关键词： Target Sample LoWeSS Normalisation Aminoallyl Packard BioScience image Conversion

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New grid scheduling and rescheduling methods in the GrADS project

New grid scheduling and rescheduling methods in the GrADS pr...

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International Symposium on parallel and distributed processing (IPDPS)

作者： K. Cooper A. Dasgupta K. Kennedy C. Koelbel A. Mandal G. Marin M. Mazina J. Mellor-Crummey F. Berman H. Casanova A. Chien H. Dail X. Liu A. Olugbile O. Sievert H. Xia L. Johnsson B. Liu M. Patel D. Reed W. Deng C. Mendes Z. Shi A. YarKhan J. Dongarra Computer Science Department Rice University USA Department of Computer Science University of California San Diego USA Department of Computer Science University of Houston USA Department of Computer Science University of Illinois USA ICL University of Tennessee Knoxville USA

Summary form only given. The goal of the Grid Application Development Software (GrADS) project is to provide programming tools and an execution environment to ease program development for the grid. We present recent extensions to the GrADS software framework: 1. A new approach to scheduling workflow computations, applied to a 3D image reconstruction application; 2. A simple stop/migrate/restart approach to rescheduling grid applications, applied to a QR 3. A process-swapping approach to rescheduling, applied to an N-body simulation. Experiments validating these methods were carried out on both the GrADS MacroGrid (a small but functional grid) and the MicroGrid (a controlled emulation of the grid) and the results were demonstrated at the SC2003 conference.

关键词： Grid computing Application software Computer science distributed computing Contracts Processor scheduling Software tools Instruments Usability Runtime

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Design of DCS duplexer using SAW ladder filter

Design of DCS duplexer using SAW ladder filter

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IEEE International Symposium on Intelligent Signal processing and Communication Systems (ISPACS)

作者： Ru-Yue Lee Hung-Yu Lee Ruyen Ro Hsin-Yuan Tung Department of Electrical Engineering I-Shou University Kaohsiung Taiwan

ISBN: (纸本)0780386396

The frequency responses of SAW ladder filters, which consist of a one-port resonator in a parallel arm and one in a series arm, are investigated and their applications in designing a duplexer are also illustrated. The one-port resonators with apodized interdigital transducers and width-controlled reflection gratings are employed to increase the operating bandwidth as well as to suppress the effects of spurious modes. The transmission matrix method along with the image parameter method is applied to design the duplexer, which consists of two SAW ladder filters connected in parallel. Simulation results indicate that with a proper design of transmission line for impedance matching, a switchless duplexer with very low loss can be tailored using SAW devices.

关键词： distributed control Surface acoustic waves Resonator filters Transmission line matrix methods Frequency Transducers Reflection Gratings Bandwidth Impedance matching

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Real-time 3D cone beam reconstruction

Real-time 3D cone beam reconstruction

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IEEE Symposium on Nuclear Science (NSS/MIC)

作者： D. Stsepankou K. Kommesser J. Hesser R. Manner Institute for Computational Medicine Universities Mannheim and Heidelberg Mannheim Germany

The paper presents a comparison of filtered back-projection and iterative approaches (modified SIRT and OSEM) where backprojection is performed on FPGA hardware and forward projection is realized by a graphics card. The FPGA-architecture allows scaling parallel processing of the backprojection with a constant memory bandwidth and it performs its task about a factor of 6 faster than conventional graphics card architectures (using a Xilinx Virtex ii 6000 compared to a floating-point implementation on a graphics hardware). For the forward projection a graphics card (with NVIDIA GeForce FX 5900) is used. The system reconstructs a volume of 256/sup 3/ voxels and 60 projections (5122) within 6 seconds for each backprojection step and 12.5 s for the forward projection. As assumed filtered backprojection is the fastest method but shows most artifacts. SIRT and OSEM generate results with suppressed artifacts and require between 4 (SIRT) and 3 (OSEM) minutes for reconstruction. The limited precision of on the FPGA does not lead to any degradation in the reconstructed image quality.

关键词： image reconstruction Field programmable gate arrays Graphics Hardware Bandwidth Reconstruction algorithms Subspace constraints Iterative methods parallel processing Degradation

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Reducing memory bottlenecks in embedded, parallel image processors

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ELECTRONICS LETTERS 2003年第1期39卷 33-35页

作者： McBader, S Lee, P NeuriCam SpA Res & Dev I-38100 Trent Italy Univ Kent Elect Engn Lab Canterbury CT2 7NT Kent England

Owing to the sequential nature of memory interfaces, as well as the growing processor-memory performance gap, the design of parallel image processors is often faced with a challenge in deciding memory organisation and distribution. This work addresses the problem of memory access bottlenecks in parallel digital image processors and presents one solution which demonstrates up to 93.4% reduction over standard sequential methods.

关键词： image processing parallel memories DMA channel distributed memory systems Computer vision and image processing techniques parallel image processor design Xilinx XCV200E FPGA embedded systems memory distribution Storage system design memory organisation parallel architecture embedded parallel image processors Multiprocessing systems sequential memory interfaces memory access bottleneck reduction processor-memory performance gap

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