Yearly Archives: 2014

A comprehensive comparison of GPU- and FPGA-based acceleration of reflection image reconstruction for 3D ultrasound computer tomography

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Birk M., Zapf M., Balzer M., Ruiter N., Becker J.

in Journal of Real-Time Image Processing, 9 (2014) 159-170. DOI:10.1007/s11554-012-0267-4

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 image reconstruction. In this work, we investigate the acceleration of the image reconstruction by GPUs and FPGAs. We compare the obtained performance results with a recent multi-core CPU. We show that both architectures are able to accelerate processing, whereas 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. © 2012 Springer-Verlag.

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An ultrafast linear array detector for single-shot electro-optical bunch profile measurements

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Rota L., Caselle M., Hiller N., Muller A.-S., Weber M.

in International Beam Instrumentation Conference, IBIC 2014 (2014).

Abstract

A new spectrometer system has been developed at ANKA for near-field single-shot Electro-Optical (EO) bunch profile measurements with a frame rate of 5 Mfps. The frame rate of commercial line detectors is limited to several tens of kHz, unsuitable for measuring fast dynamic changes of the bunch conditions. The new system aims to realize continuous data acquisition and over long observation periods without dead time. InGaAs or Si linear array pixel sensors are used to detect the near IR and visible spectrum radiation. The detector signals are fed via wire-bonding connections to the GOTTHARD ASIC, a charge-sensitive amplifier with analog outputs. The front-end board is also equipped with an array of fast ADCs. The digital samples are then acquired by an FPGA-based readout card and transmitted to an external DAQ system via a high-speed PCI-Express data link. The DAQ system uses high-end Graphics Processors Units (GPUs) to perform a real-time analysis of the beam conditions. In this paper we present the concept, the first prototype and the low-noise layout techniques used for fast linear detectors.

Extension of historical range of Betylobraconinae (Hymenoptera: Braconidae) into Palaearctic Region based on a Baltic amber fossil, and description of a new species of Mesocentrus Szépligeti from Papua New Guinea

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Butcher B.A., Zaldivar-Riveron A., Van De Kamp T., Rolo T.D.S., Baumbach T., Quicke D.L.J.

in Zootaxa, 3860 (2014) 449-463. DOI:10.11646/zootaxa.3860.5.4

Abstract

Copyright © 2014 Magnolia Press. Two new species of the parasitic wasp genus Mesocentrus Szépligeti (Betylobraconinae) are described. One based on a new species from Papua New Guinea, the other the first Palaearctic member of the subfamily based on a 30+ mya, species from Baltic amber. The second species is illustrated using synchrotron X-ray microtomography. Whereas the extant Betylobraconinae are restricted to Australia, New Guinea and New Caledonia, their ancestral distribution is now known to have extended considerably further. A key to the four species of Mesocentrus known from Papua New Guinea is provided. Both species possess some putatively plesiomorphic characters absent in other extant Mesocentrus spp. The new extant species differs in having a considerably larger number of antennal segments and a less laterally depressed frons, while the extinct one has the clypeus separated from the face dorsally and strongly developed hypoclypeal depression. Availability of sequence data for this species enabled further analysis of the relationships of the subfamily, which we present in a phylogenetic analysis additionally including the release of a number of new sequences of related taxa.

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Synchrotron radiation microtomography of Taylor bubbles in capillary two-phase flow

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Boden S., Dos Santos Rolo T., Baumbach T., Hampel U.

in Experiments in Fluids, 55 (2014), 1768. DOI:10.1007/s00348-014-1768-7

Abstract

We report on a study to measure the three-dimensional shape of Taylor bubbles in capillaries using synchrotron radiation in conjunction with ultrafast radiographic imaging. Moving Taylor bubbles in 2-mm round and square capillaries were radiographically scanned with an ultrahigh frame rate of up to 36,000 fps and 5.6-μm pixel separation. Consecutive images were properly processed to yield 2D transmission radiographs of high contrast-to-noise ratio. Application of 3D tomographic image reconstruction disclosed the 3D bubble shape. The results provide a reference data base for development of sophisticated interface resolving CFD computations. © 2014 Springer-Verlag Berlin Heidelberg.

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Studies of bursting CSR in multi-bunch operation at the ANKA storage ring

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Judin V., Brosi M., Caselle M., Hertle E., Hiller N., Kopmann A., Muller A.-S., Schuh M., Smale N.J., Steinmann J.L., Weber M.

in IPAC 2014: Proceedings of the 5th International Particle Accelerator Conference (2014) 225-227.

Abstract

Copyright © 2014 CC-BY-3.0 and by the respective authors.The ANKA storage ring can generate brilliant coherent synchrotron radiation (CSR) in the THz range due to a dedicated low-α<inf>c</inf>-optics with reduced bunch lengths. At higher electron currents the radiation is not stable, but occurs in powerful bursts caused by micro-bunching instabilities. This intense THz radiation is very attractive for users. However, the reproducibility of the experimental conditions is very low due to those power fluctuations. Systematic studies of bursting CSR in multi-bunch operation were performed with fast THz detectors at ANKA using a dedicated, ultra-fast DAQ-FPGA board. The technique and preliminary results of these studies are presented in this paper.

An ultra-fast data acquisition system for coherent synchrotron radiation with terahertz detectors

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Caselle M., Balzer M., Chilingaryan S., Hofherr M., Judin V., Kopmann A., Smale N.J., Thoma P., Wuensch S., Muller A.-S., Siegel M., Weber M.

in Journal of Instrumentation, 9 (2014), C01024. DOI:10.1088/1748-0221/9/01/C01024

Abstract

The recording of coherent synchrotron radiation requires data acquisition systems with a temporal resolution of tens of picosecond. This paper describes a new real-time and high-accuracy data acquisition system suitable for recording individual ultra-short pulses generated by a fast terahertz (THz) detector (e.g. YBCO, NbN, Zero Biased Schottky Diode). The system consists of a fast sampling board combined with a high data throughput readout. The first board is designed for sampling the fast pulse signals with a full width half maximum (FWHM) between a few tens to one hundred picoseconds with a minimum sampling time of 3 ps. The high data throughput board consists of a PCIe-Bus Master DMA architecture used for fast data transfer up to 3 GByte/s. The full readout chain with fast THz detectors and the acquisition system has been successfully tested at the synchrotron ANKA. An overview of the electronics system and preliminary results with multi-bunch filling pattern will be presented. © 2014 IOP Publishing Ltd and Sissa Medialab srl.

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Integrated control system environment for high-throughput tomography

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Khokhriakov I., Lottermoser L., Gehrke R., Kracht T., Wintersberger E., Kopmann A., Vogelgesang M., Beckmann F.

in Proceedings of SPIE – The International Society for Optical Engineering, 9212 (2014), 921217. DOI:10.1117/12.2060975

Abstract

© 2014 SPIE. A new control system for high-throughput experiments (X-Ray, Neutrons) is introduced in this article. The system consists of several software components which are required to make optimized use of the beamtime and to fulfill the demand to implement the new standardized data format established within the Helmholtz Association in Germany. The main components are: PreExperiment Data Collector; Status server; Data Format Server. Especially for tomography a concept for an online reconstruction based on GPU computing is presented. One of the main goals of the system is to collect data that extends standard experimental data, e.g. instrument’s hardware state, preinvestigation data, experiment description data etc. The collected data is stored together with the experiment data in the permanent storage of the user. The stored data is then used for post processing and analysis of the experiment.

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A unified energy footprint for simulation software

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Anzt H., Beglarian A., Chilingaryan S., Ferrone A., Heuveline V., Kopmann A.

in Computer Science – Research and Development, 29 (2014) 131-138. DOI:10.1007/s00450-012-0225-1

Abstract

The focus in High-Performance Computing increasingly turns to energy efficiency. Therefore the pure concentration on floating point operations and runtime performance is no longer sufficient. In terms of hardware, this change of paradigm has already taken place: The GREEN500 list as counterpart to the runtime performance oriented TOP500 list has been established. The new metrics take runtime and energy consumption into account. Nevertheless, all these developments consider hardware only – still an inadequate situation to face the challenges of Energy-Efficient Exascale Computing. The necessity of optimizing simulation software with respect to power and energy draft demands for detailed profiling of the power consumption during the calculations and a norm quantifying the respective efficiency. In this paper we propose a unified energy footprint for simulation software that enables a fast comparison between different models, implementations and hardware configurations, respectively. By way of example we provide the footprints for the tomographic reconstruction code PyHST optimized for CPU and GPU operation as well as the operational numerical weather prediction model COSMO. We then discuss the power and energy profiles and investigate the effects of scaling with respect to hardware resources and simulation parameters. © 2012 Springer-Verlag.

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Characterization of the CCD and CMOS cameras for grating-based phase-contrast tomography

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Lytaev P., Hipp A., Lottermoser L., Herzen J., Greving I., Khokhriakov I., Meyer-Loges S., Plewka J., Burmester J., Caselle M., Vogelgesang M., Chilingaryan S., Kopmann A., Balzer M., Schreyer A., Beckmann F.

in Proceedings of SPIE – The International Society for Optical Engineering, 9212 (2014), 921218. DOI:10.1117/12.2061389

Abstract

© 2014 SPIE. In this article we present the quantitative characterization of CCD and CMOS sensors which are used at the experiments for microtomography operated by HZG at PETRA III at DESY in Hamburg, Germany. A standard commercial CCD camera is compared to a camera based on a CMOS sensor. This CMOS camera is modified for grating-based differential phase-contrast tomography. The main goal of the project is to quantify and to optimize the statistical parameters of this camera system. These key performance parameters such as readout noise, conversion gain and full-well capacity are used to define an optimized measurement for grating-based phase-contrast. First results will be shown.

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Control system and smart camera with image based trigger for fast synchrotron applications

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Stevanovic U., Caselle M., Balzer M., Cecilia A., Chilingaryan S., Farago T., Gasilov S., Herth A., Kopmann A., Vogelgesang M., Weber M.

in 2014 19th IEEE-NPSS Real Time Conference, RT 2014 – Conference Records (2014), 7097495. DOI:10.1109/RTC.2014.7097495

Abstract

© 2014 IEEE. High-speed X-ray imaging applications such as radiography and tomography play a crucial role for non-destructive investigations in material and biology sciences. For data-intensive applications, on-line analysis of the data is necessary for initial quality assurance and data-driven feedback. In this article we will present a new smart camera platform, with embedded FPGA processing that is able to stream and process data continuously in real-time. It is used in the new imaging beamline IMAGE, in ANKA. The new smart camera platform consists of a CMOS sensor, an FPGA readout card connected with a high speed PCIe interface to the GPU-based readout computer. It is tightly coupled to a newly implemented control system, called Concert. Concert enables efficient operation of the beamline by integrating devices and experiment process control, as well as data analysis. A key feature of smart cameras is embedded image processing. In this article we will demonstrate the potential of this approach with the implementation of an image-based self-event trigger. The algorithm automatically restricts the readout to selected regions with changed content. Application dependent trigger parameters are hidden by our control system which sets them automatically according to experiment requirements and conditions.

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