Vogelgesang M., Chilingaryan S., Rolo T.D.S., Kopmann A.
in Proceedings of the 14th IEEE International Conference on High Performance Computing and Communications, HPCC-2012 – 9th IEEE International Conference on Embedded Software and Systems, ICESS-2012 (2012) 824-829, 6332254. DOI:10.1109/HPCC.2012.116
Current synchrotron experiments require state-of-the-art scientific cameras with sensors that provide several million pixels, each at a dynamic range of up to 16 bits and the ability to acquire hundreds of frames per second. The resulting data bandwidth of such a data stream reaches several Gigabits per second. These streams have to be processed in real-time to achieve a fast process response. In this paper we present a computation framework and middleware library that provides re-usable building blocks to implement high-performance image processing algorithms without requiring profound hardware knowledge. It is based on a graph structure of computation nodes that process image transformation kernels on either CPU or GPU using the OpenCL sub-system. This system architecture allows deployment of the framework on a large range of computational hardware, from netbooks to hybrid compute clusters. We evaluated the library with standard image processing algorithms required for high quality tomographic reconstructions. The results show that speed-ups from 7x to 37x compared to traditional CPU-based solutions can be achieved with our approach, hence providing an opportunity for real-time on-line monitoring at synchrotron beam lines. © 2012 IEEE.
Balzer M., Birk M., Dapp R., Gemmeke H., Kretzek E., Menshikov S., Zapf M., Ruiter N.V.
in 2012 18th IEEE-NPSS Real Time Conference, RT 2012 (2012), 6418198. DOI:10.1109/RTC.2012.6418198
3D ultrasound computer tomography (USCT) is a new and promising method for early breast cancer diagnosis. An ultrasound computer tomograph was developed by the Karlsruhe Institute of Technology (KIT) and provides a resolution of 0.2 mm. The main components are the semi-ellipsoidal aperture with 628 ultrasound (US) emitters and 1413 US receivers and the 480 input channel data acquisition system. An additional external computing system is used for the time consuming image reconstruction. To reduce the reconstruction time different implementations on massive parallel computing architectures like multicore processor, GPUs and FPGAs were tested. One realization applies reconfiguration of the 60 FPGAs inside the DAQ system. The investigations show significant acceleration of the reconstruction time up to a factor of 15.8 for the latest FPGA generation and 17.6 for a state of the art GPU. © 2012 IEEE.
Birk M., Balzer M., Ruiter N., Becker J.
in 2012 International Conference on Reconfigurable Computing and FPGAs, ReConFig 2012 (2012), 6416735. DOI:10.1109/ReConFig.2012.6416735
With the rise of heterogeneous computing architectures, application developers are confronted with a multitude of hardware platforms and the challenge of identifying the most suitable processing platform for their application. Strong competitors for the acceleration of 3D Ultrasound Computer Tomography, a medical imaging method for early breast cancer diagnosis, are GPU and FPGA devices. In this work, we evaluate processing performance and efficiency metrics for current FPGA and GPU devices. We compare top-notch devices from the 40 nm generation as well as FPGA and GPU devices, which draw the same amount of power. For our two benchmark algorithms, the results show that if power consumption is not considered the GPU and the FPGA give both, a similar processing performance and processing efficiency per transistor. However, if the power budget is limited to a similar value, the FPGA performs between six and eight times better than the GPU. © 2012 IEEE.
Bergmann T., Bormann D., Howe M.A., Kleifges M., Kopmann A., Kunka N., Menshikov A., Tcherniakhovski D.
in 2012 18th IEEE-NPSS Real Time Conference, RT 2012 (2012), 6418197. DOI:10.1109/RTC.2012.6418197
Our group at KIT has been developing data acquisition (DAQ) systems for many years mainly for large physics experiments like the KATRIN neutrino experiment or the Pierre Auger cosmic ray observatory. The DAQ systems were continuously enhanced as new technologies became available. The core of the DAQ systems are field programmable gate arrays (FPGAs). Trigger functions running on the FPGAs select relevant events out of the permanent data stream of the ADCs and pass it over PCI bus to a embedded Linux computer for further analysis and storage. Modern experiments have raising requirements in both data rate and complexity of trigger and analysis function. To achieve a flexible and fast data link we developed a PCI to PCI Express (PCIe) adapter board which can be connected to any PC equipped with a standard PCIe plug-in adapter. We use this adapter to replace the embedded Linux system and to connect external GPU servers directly to the DAQ system. With this powerful data processing facility at the end of the data chain we can run complex third level trigger functions, reconstruction algorithms and analysis calculations. With PCIe as fast data link and GPU computing together with the well established FPGA unit we achieved a substantial enhancement of our DAQ system. © 2012 IEEE.
Stevanovic U., Caselle M., Chilingaryan S., Herth A., Kopmann A., Vogelgesang M., Balzer M., Weber M.
in Conference on Design and Architectures for Signal and Image Processing, DASIP (2012) 383-384, 6385417.
The first prototype of a high-speed camera with embedded image processing has been developed. Beside high frame rate and high through-put, the camera introduces a novel self triggering architecture to increase the frame rate and to reduce the amount of received data. The camera is intended for synchrotron ultra-fast X-ray radiography and tomography, but it’s concept is also suitable for other fields. © 2012 ECSI.
Caselle M., Chilingaryan S., Herth A., Kopmann A., Stevanovic U., Vogelgesang M., Balzer M., Weber M.
in 2012 18th IEEE-NPSS Real Time Conference, RT 2012 (2012), 6418369. DOI:10.1109/RTC.2012.6418369
X-ray computed tomography (CT) is a method for non-destructive investigation. Three-dimensional images of internal structure can be reconstructed using a two-dimensional detector. The poly-chromatic high density photon flux in the modern synchrotron light sources offers hard X-ray imaging with a spatio-temporal resolution up to the μm-μs range. Existing indirect X-ray image detectors can be adapted for fast image acquisition by employing CMOS-based digital high speed camera. In this paper, we propose a high-speed visible light camera based on commercial CMOS sensor with embedded processing implemented in FPGA. This platform has been used to develop a novel architecture for a self-event trigger. This feature is able to increase the original frame rate of the CMOS sensor and reduce the amount of the received data. Thanks to a low noise design, high frame rate (kilohertz range) and high speed data transfer, this camera can be employed in modern synchrotron ultra-fast X-ray radiography and computed tomography. The camera setup is accomplished by high-throughput Linux drivers and a seamless integration in our GPU computing framework. Selected applications from life sciences and materials research underline the high potential of this high-speed camera in a hard X-ray micro-imaging approach. © 2012 IEEE.
Alaribe L., Disch C., Fauler A., Engels R., Keller E., Cecilia A., Dos Santos Rolo T., Hamann E., Fiederle M.
in IEEE Transactions on Nuclear Science, 59 (2012) 2193-2195, 6303848. DOI:10.1109/TNS.2012.2212208
Much work is going on presently to improve the crystal growth and packaging of the Eu 2+ activated SrI 2 scintillator, thanks to its excellent scintillation properties like high light yield and good energy resolution. Larger crystals are needed for spectroscopic applications, and proper packaging is important for long-time field use and application in other areas due to its hygroscopic nature. In this paper, we report on the successful growth of a SrI 2Eu[6mol%] single crystal in silica ampoule to prevent melt hydration and oxygen contamination using the vertical Bridgman technique. The scintillation properties of a 0.314 cm 3SrI 2:Eu sample are presented, showing a light output of ∼ 80000 ph/MeV. A 360 μm sample was investigated for X-ray imaging applications; we also show how the sample was prepared for the measurement and the result of this preliminary investigation. © 2012 IEEE.
Douissard P.-A., Cecilia A., Rochet X., Chapel X., Martin T., Van De Kamp T., Helfen L., Baumbach T., Luquot L., Xiao X., Meinhardt J., Rack A.
in Journal of Instrumentation, 7 (2012), P09016. DOI:10.1088/1748-0221/7/09/P09016
Indirect X-ray detectors are of outstanding importance for high resolution imaging, especially at synchrotron light sources: while consisting mostly of components which are widely commercially available, they allow for a broad range of applications in terms of the X-ray energy employed, radiation dose to the detector, data acquisition rate and spatial resolving power. Frequently, an indirect detector consists of a thin-film single crystal scintillator and a high-resolution visible light microscope as well as a camera. In this article, a novel modular-based indirect design is introduced, which offers several advantages: it can be adapted for different cameras, i.e. different sensor sizes, and can be trimmed to work either with (quasi-)monochromatic illumination and the correspondingly lower absorbed dose or with intense white beam irradiation. In addition, it allows for a motorized quick exchange between different magnifications / spatial resolutions. Developed within the European project SCINTAX, it is now commercially available. The characteristics of the detector in its different configurations (i.e. for low dose or for high dose irradiation) as measured within the SCINTAX project will be outlined. Together with selected applications from materials research, non-destructive evaluation and life sciences they underline the potential of this design to make high resolution X-ray imaging widely available. © 2012 IOP Publishing Ltd and Sissa Medialab srl.
Riedel A., Dos Santos Rolo T., Cecilia A., Van De Kamp T.
in Zoological Journal of the Linnean Society, 165 (2012) 773-794. DOI:10.1111/j.1096-3642.2012.00825.x
Two genera of extinct weevils, Sayrevilleus Gratshev & Zherikhin from Cretaceous New Jersey amber and Baltocar Kuschel from Eocene Baltic amber, are recognized as close relatives based on similarities revealed by the use of synchrotron tomography and the availability of new amber inclusions. The subfamily Sayrevilleinae Legalov stat. nov. is characterized by possessing mandibles with an external cutting edge and an inner blunt edge. The subfamily is placed in the family Attelabidae (s.l.), although some characters also suggest a possible relationship with the ‘higher weevils’ comprising Caridae, Brentidae, and Curculionidae. Sayrevilleus is transferred from the tribe Auletini of Rhynchitinae to Sayrevilleinae, and Sayrevilleus grimaldii Gratshev & Zherikhin is redescribed. Baltocar Kuschel is transferred from Caridae to Sayrevilleinae and revised, its type species, Baltocar succinicus (Voss), is redescribed and three new species, Baltocar groehni Riedel sp. nov., Baltocar hoffeinsorum Riedel sp. nov., and Baltocar subnudus Riedel sp. nov. are described based on eight well-preserved inclusions. The genera Orapauletes Legalov and Zherichiniletes Legalov previously assigned to Sayrevilleini are regarded as Curculionoidea incertae sedis. The Sayrevilleinae were distributed over areas of North America and Europe at least since the Late Cretaceous (c.90Mya) and were probably relatively diverse until the Eocene (c.44Mya). It is speculated that they became extinct through competition with Curculionidae, which used a similar oviposition strategy. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 165, 773-794. © 2012 The Linnean Society of London.
Moosmann J., Altapova V., Hanschke D., Hofmann R., Baumbach T.
in AIP Conference Proceedings, 1437 (2012) 57-62. DOI:10.1063/1.3703343
For coherent X-ray imaging, based on phase contrast through free-space Fresnel propagation, we discuss two noniterative, nonlinear approaches to the phase-retrieval problem from a single-distance intensity map of a pure-phase object. On one hand, a perturbative set-up is proposed where nonlinear corrections to the linearized transport-of-intensity situation are expanded in powers of the object-detector distance z and are evaluated in terms of the linear estimate. On the other hand, a nonperturbative projection algorithm, which is based on the (linear and local) contrast-transfer function (CTF), works with an effective phase in Fourier space. This effective phase obeys a modified CTF relation between intensity contrast at z > 0 and phase contrast at z = 0: Unphysical singularities of the local CTF model are cut off to yield ‘quasiparticles’ in analogy to the theory of the Fermi liquid. By identifying the positions of the zeros of the Fourier transformed intensity contrast as order parameters for the dynamical breaking of scaling symmetry we investigate the phase structure of the forward-propagation problem when interpreted as a statistical system. Results justify the quasiparticle approach for a wide range of intermediary phase variations. The latter algorithm is applied to data from biological samples recorded at the beamlines TopoTomo and ID19 at ANKA and ESRF, respectively. © 2012 American Institute of Physics.