Yearly: 2011

Acceleration of image reconstruction in 3D ultrasound computer tomography: An evaluation of CPU, GPU and FPGA computing

Birk M., Guth A., Zapf M., Balzer M., Ruiter N., Hubner M., Becker J.

in Conference on Design and Architectures for Signal and Image Processing, DASIP (2011) 67-74, 6136856. DOI:10.1109/DASIP.2011.6136856

Abstract

As today’s standard screening methods frequently fail to diagnose breast cancer before metastases have developed, earlier breast cancer diagnosis is still a major challenge. Three-dimensional ultrasound computer tomography promises high-quality images of the breast, but is currently limited by a time-consuming synthetic aperture focusing technique based image reconstruction. In this work, we investigate the acceleration of the image reconstruction by a GPU, and by the FPGAs embedded in our custom data acquisition system. We compare the obtained performance results with a recent multi-core CPU and show that both platforms are able to accelerate processing. The GPU reaches the highest performance. Furthermore, we draw conclusions in terms of applicability of the accelerated reconstructions in future clinical application and highlight general principles for speed-up on GPUs and FPGAs. © 2011 IEEE.

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A GPU-based architecture for real-time data assessment at synchrotron experiments

Chilingaryan S., Kopmann A., Mirone A., Dos Santos Rolo T., Vogelgesang M.

in SC’11 – Proceedings of the 2011 High Performance Computing Networking, Storage and Analysis Companion, Co-located with SC’11 (2011) 51-52. DOI:10.1145/2148600.2148624

Abstract

X-ray tomography has been proven to be a valuable tool for understanding internal, otherwise invisible, mechanisms in biology and other fields. Recent advances in digital detector technology enabled investigation of dynamic processes in 3D with a temporal resolution down to the milliseconds range. Unfortunately it requires computationally intensive recon- struction algorithms with long post-processing times. We have optimized the reconstruction software employed at the micro-tomography beamlines at KIT and ESRF. Using a 4 stage pipelined architecture and the computational power of modern graphic cards, we were able to reduce the processing time by a factor 75 with a single server. The time required to reconstruct a typical 3D image is reduced down to several seconds only and online visualization is possible for the first time.Copyright is held by the author/owner(s).

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Real-time X-ray diffraction imaging for semiconductor wafer metrology and high temperature in situ experiments

Danilewsky A.N., Wittge J., Hess A., Croll A., Rack A., Allen D., McNally P., Dos Santos Rolo T., Vagovic P., Baumbach T., Garagorri J., Elizalde M.R., Tanner B.K.

in Physica Status Solidi (A) Applications and Materials Science, 208 (2011) 2499-2504. DOI:10.1002/pssa.201184264

Abstract

We describe a rapid digital system for X-ray diffraction imaging and demonstrate its application to the real-time identification of edge defects in a silicon wafer that had been subjected to rapid thermal annealing. The application of the system to the in situ study of slip nucleation at the location of mechanical wafer defects, indents and a thermocouple, and the subsequent dislocation dynamics is presented. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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In-line Bragg magnifier based on V-shaped germanium crystals

Vagovic P., Korytar D., Mikulik P., Cecilia A., Ferrari C., Yang Y., Hanschke D., Hamann E., Pelliccia D., Lafford T.A., Fiederle M., Baumbach T.

in Journal of Synchrotron Radiation, 18 (2011) 753-760. DOI:10.1107/S090904951102989X

Abstract

In this work an X-ray imaging system based on a recently developed in-line two-dimensional Bragg magnifier composed of two monolithic V-shaped crystals made of dislocation-free germanium is presented. The channel-cut crystals were used in one-dimensional and in two-dimensional (crossed) configurations in imaging applications and allowed measurement of phase-contrast radiograms both in the edge-enhanced and in the holographic regimes. The measurement of the phase gradient in two orthogonal directions is demonstrated. The effective pixel size attained was 0.17 μm in the one-dimensional configuration and 0.5 μm in the two-dimensional setting, offering a twofold improvement in spatial resolution over devices based on silicon. These results show the potential for applying Bragg magnifiers to imaging soft matter at high resolution with reduced dose owing to the higher efficiency of Ge compared with Si. © 2011 International Union of Crystallography.

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LPE grown LSO:Tb scintillator films for high-resolution X-ray imaging applications at synchrotron light sources

Cecilia A., Rack A., Douissard P.-A., Martin T., Dos Santos Rolo T., Vagovic P., Hamann E., Van De Kamp T., Riedel A., Fiederle M., Baumbach T.

in Nuclear Instruments and Methods in Physics Research, Section A: Accelerators, Spectrometers, Detectors and Associated Equipment, 648 (2011). DOI:10.1016/j.nima.2010.10.150

Abstract

Within the project ScinTAX of the 6th framework program (FP6) of the European Commission (SCINTAX – STRP 033 427) we have developed a new thin single crystal scintillator for high-resolution X-ray imaging. The scintillator is based on a Tb-doped Lu2SiO5 (LSO) film epitaxially grown on an adapted substrate. The high density, effective atomic number and light yield of the scintillating LSO significantly improves the efficiency of the X-ray imaging detectors currently used in synchrotron micro-imaging applications. In this work we present the characterization of the scintillating LSO films in terms of their spatial resolution performance and we provide two examples of high spatial and high temporal resolution applications. © 2010 Elsevier B.V. All rights reserved.

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X-ray phase-contrast radiography using a filtered white beam with a grating interferometer

Altapova V., Butzer J., Rolo T.D.S., Vagovic P., Cecilia A., Moosmann J., Kenntner J., Mohr J., Pelliccia D., Pichugin V.F., Baumbach T.

in Nuclear Instruments and Methods in Physics Research, Section A: Accelerators, Spectrometers, Detectors and Associated Equipment, 648 (2011). DOI:10.1016/j.nima.2010.12.218

Abstract

One of the most promising methods of phase-contrast imaging is the Talbot grating interferometry. We report about the optimization of the method for fast imaging, requiring reduced exposure times by keeping sufficient imaging contrast. To do this a new Talbot interferometer working with a broad energy bandwidth beam has been installed at the TopoTomo beamline at ANKA. We demonstrate the method with a filtered white beam and without the need of a source grating that is commonly used at moderate-emittance synchrotron sources. Taking advantage of a higher photon flux, the exposure time is significantly reduced. At the same time, images obtained with this setup show a sufficient visibility contrast of 25% on average, which opens the way for new applications in real-time measurements. © 2010 Elsevier B.V. All rights reserved.

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FPGA-based embedded signal processing for 3-D ultrasound computer tomography

Birk M., Koehler S., Balzer M., Huebner M., Ruiter N.V., Becker J.

in IEEE Transactions on Nuclear Science, 58 (2011) 1647-1651, 5942184. DOI:10.1109/TNS.2011.2159017

Abstract

A three-dimensional ultrasound computer tomography (3-D USCT) system for early breast cancer diagnosis is currently being developed at Institute for Data Processing and Electronics (IPE) at Karlsruhe Institute of Technology, Karlsruhe, Germany. A field-programmable gate array (FPGA)-based data acquisition (DAQ) system is used to acquire the measurement data. Over 3.5 million data sets are recorded for each breast, resulting in 20 GB of raw data. The data is subsequently transferred to a PC for time-consuming image reconstruction, which is in the order of days. A promising approach in reducing reconstruction time is mapping further computation to the FPGAs in the DAQ system. This paper covers the investigation of FPGA-based processing for a set of signal processing algorithms. In the best suited approach, processing time per data set is approximately 50 μs, occupying less than 30% of device resources. © 2006 IEEE.

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A GPU-based architecture for real-time data assessment at synchrotron experiments

Chilingaryan S., Mirone A., Hammersley A., Ferrero C., Helfen L., Kopmann A., Dos Santos Rolo T., Vagovic P.

in IEEE Transactions on Nuclear Science, 58 (2011) 1447-1455, 5766797. DOI:10.1109/TNS.2011.2141686

Abstract

Advances in digital detector technology leads presently to rapidly increasing data rates in imaging experiments. Using fast two-dimensional detectors in computed tomography, the data acquisition can be much faster than the reconstruction if no adequate measures are taken, especially when a high photon flux at synchrotron sources is used. We have optimized the reconstruction software employed at the micro-tomography beamlines of our synchrotron facilities to use the computational power of modern graphic cards. The main paradigm of our approach is the full utilization of all system resources. We use a pipelined architecture, where the GPUs are used as compute coprocessors to reconstruct slices, while the CPUs are preparing the next ones. Special attention is devoted to minimize data transfers between the host and GPU memory and to execute memory transfers in parallel with the computations. We were able to reduce the reconstruction time by a factor 30 and process a typical data set of 20 GB in 40 seconds. The time needed for the first evaluation of the reconstructed sample is reduced significantly and quasi real-time visualization is now possible. © 2006 IEEE.

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A biological screw in a beetle’s leg

Van De Kamp T., Vagovic P., Baumbach T., Riedel A.

in Science, 333 (2011). DOI:10.1126/science.1204245

Abstract

The coxa-trochanteral joints on the legs of the weevil Trigonopterus oblongus (Pascoe) work as a biological screw-and-nut system. The apical portions of the coxae closely resemble nuts with well-defined inner threads covering 345°. The corresponding trochanters have perfectly compatible external spiral threads of 410°.

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Evaluation of the reconfiguration of the data acquisition system for 3D USCT

Birk M., Hagner C., Balzer M., Ruiter N.V., Hubner M., Becker J.

in International Journal of Reconfigurable Computing, 2011 (2011), 952937. DOI:10.1155/2011/952937

Abstract

As today’s standard screening methods often fail to diagnose breast cancer before metastases have developed, an earlier breast cancer diagnosis is still a major challenge. To improve this situation, we are currently developing a fully three-dimensional ultrasound computer tomography (3D USCT) system, promising high-quality volume images of the breast. For obtaining these images, a time-consuming reconstruction has to be performed. As this is currently done on a PC, parallel processing in reconfigurable hardware could accelerate both signal and image processing. In this work, we investigated the suitability of an existing data acquisition (DAQ) system for further computation tasks. The reconfiguration features of the embedded FPGAs have been exploited to enhance the systems functionality. We have adapted the DAQ system to allow for bidirectional communication and to provide an overall process control. Our results show that the studied system can be applied for data processing. Copyright © 2011 Matthias Birk et al.

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