Kaever P., Balzer M., Kopmann A., Zimmer M., Rongen H.

in Journal of Instrumentation, 12 (2017), C04004. DOI:10.1088/1748-0221/12/04/C04004

Abstract

© 2017 IOP Publishing Ltd and Sissa Medialab srl. Various centres of the German Helmholtz Association (HGF) started in 2012 to develop a modular data acquisition (DAQ) platform, covering the entire range from detector readout to data transfer into parallel computing environments. This platform integrates generic hardware components like the multi-purpose HGF-Advanced Mezzanine Card or a smart scientific camera framework, adding user value with Linux drivers and board support packages. Technically the scope comprises the DAQ-chain from FPGA-modules to computing servers, notably frontend-electronics-interfaces, microcontrollers and GPUs with their software plus high-performance data transmission links. The core idea is a generic and component-based approach, enabling the implementation of specific experiment requirements with low effort. This so called DTS-platform will support standards like MTCA.4 in hard- and software to ensure compatibility with commercial components. Its capability to deploy on other crate standards or FPGA-boards with PCI express or Ethernet interfaces remains an essential feature. Competences of the participating centres are coordinated in order to provide a solid technological basis for both research topics in the Helmholtz Programme “Matter and Technology”: “Detector Technology and Systems” and “Accelerator Research and Development”. The DTS-platform aims at reducing costs and development time and will ensure access to latest technologies for the collaboration. Due to its flexible approach, it has the potential to be applied in other scientific programs.

Caselle M., Perez L.E.A., Balzer M., Dritschler T., Kopmann A., Mohr H., Rota L., Vogelgesang M., Weber M.

in Journal of Instrumentation, 12 (2017), C03015. DOI:10.1088/1748-0221/12/03/C03015

Abstract

© 2017 IOP Publishing Ltd and Sissa Medialab srl. Modern data acquisition and trigger systems require a throughput of several GB/s and latencies of the order of microseconds. To satisfy such requirements, a heterogeneous readout system based on FPGA readout cards and GPU-based computing nodes coupled by InfiniBand has been developed. The incoming data from the back-end electronics is delivered directly into the internal memory of GPUs through a dedicated peer-to-peer PCIe communication. High performance DMA engines have been developed for direct communication between FPGAs and GPUs using “DirectGMA (AMD)” and “GPUDirect (NVIDIA)” technologies. The proposed infrastructure is a candidate for future generations of event building clusters, high-level trigger filter farms and low-level trigger system. In this paper the heterogeneous FPGA-GPU architecture will be presented and its performance be discussed.

Reich S., Schonfeld P., Wagener P., Letzel A., Ibrahimkutty S., Gokce B., Barcikowski S., Menzel A., dos Santos Rolo T., Plech A.

in Journal of Colloid and Interface Science, 489 (2017) 106-113. DOI:10.1016/j.jcis.2016.08.030

Abstract

© 2016 Elsevier Inc. Pulsed laser ablation in liquids (PLAL) is a multiscale process, involving multiple mutually interacting phenomena. In order to synthesize nanoparticles with well-defined properties it is important to understand the dynamics of the underlying structure evolution. We use visible-light stroboscopic imaging and X-ray radiography to investigate the dynamics occurring during PLAL of silver and gold on a macroscopic scale, whilst X-ray small angle scattering is utilized to deepen the understanding on particle genesis. By comparing our results with earlier reports we can elucidate the role of the cavitation bubble. We find that symmetry breaking at the liquid-solid interface is a critical factor for bubble motion and that the bubble motion acts on the particle distribution as confinement and retraction force to create secondary agglomerates.

Wulff N.C., Van De Kamp T., Dos Santos Rolo T., Baumbach T., Lehmann G.U.C.

in Scientific Reports, 7 (2017), 42345. DOI:10.1038/srep42345

Abstract

© The Author(s) 2017. Male genital organs are among the fastest evolving morphological structures. However, large parts of the male’s genitalia are often hidden inside the female during mating. In several bushcricket species, males bear a pair of sclerotized genital appendices called titillators. By employing synchrotron-based in vivo X-ray cineradiography on mating couples, we were able to visualize titillator movement and spermatophore attachment inside the female. Titillators are inserted and retracted rhythmically. During insertion the titillator processes tap the soft and sensillae-covered dorsal side of the female’s flap-like genital fold, which covers the opening of the female’s genitalia, without tissue penetration. Titillators thus appear to be initially used for stimulation; later they may apply pressure that forces the female’s genital fold to stay open, thereby aiding mechanically in spermatophore transfer.

Cecilia A., Baecker A., Hamann E., Rack A., van de Kamp T., Gruhl F.J., Hofmann R., Moosmann J., Hahn S., Kashef J., Bauer S., Farago T., Helfen L., Baumbach T.

in Materials Science and Engineering C, 71 (2017) 465-472. DOI:10.1016/j.msec.2016.10.038

Abstract

© 2016 Prostate cancer (PCa) currently is the second most diagnosed cancer in men and the second most cause of cancer death after lung cancer in Western societies. This sets the necessity of modelling prostatic disorders to optimize a therapy against them. The conventional approach to investigating prostatic diseases is based on two-dimensional (2D) cell culturing. This method, however, does not provide a three-dimensional (3D) environment, therefore impeding a satisfying simulation of the prostate gland in which the PCa cells proliferate. Cryogel scaffolds represent a valid alternative to 2D culturing systems for studying the normal and pathological behavior of the prostate cells thanks to their 3D pore architecture that reflects more closely the physiological environment in which PCa cells develop. In this work the 3D morphology of three potential scaffolds for PCa cell culturing was investigated by means of synchrotron X-ray computed micro tomography (SXCμT) fitting the according requirements of high spatial resolution, 3D imaging capability and low dose requirements very well. In combination with mechanical tests, the results allowed identifying an optimal cryogel architecture, meeting the needs for a well-suited scaffold to be used for 3D PCa cell culture applications. The selected cryogel was then used for culturing prostatic lymph node metastasis (LNCaP) cells and subsequently, the presence of multi-cellular tumor spheroids inside the matrix was demonstrated again by using SXCμT.

Zuber M., Laass M., Hamann E., Kretschmer S., Hauschke N., Van De Kamp T., Baumbach T., Koenig T.

in Scientific Reports, 7 (2017), 41413. DOI:10.1038/srep41413

Abstract

© 2017 The Author(s). Non-destructive imaging techniques can be extremely useful tools for the investigation and the assessment of palaeontological objects, as mechanical preparation of rare and valuable fossils is precluded in most cases. However, palaeontologists are often faced with the problem of choosing a method among a wide range of available techniques. In this case study, we employ X-ray computed tomography (CT) and computed laminography (CL) to study the first fossil xiphosuran from the Muschelkalk (Middle Triassic) of the Netherlands. The fossil is embedded in micritic limestone, with the taxonomically important dorsal shield invisible, and only the outline of its ventral part traceable. We demonstrate the complementarity of CT and CL which offers an excellent option to visualize characteristic diagnostic features. We introduce augmented laminography to correlate complementary information of the two methods in Fourier space, allowing to combine their advantages and finally providing increased anatomical information about the fossil. This method of augmented laminography enabled us to identify the xiphosuran as a representative of the genus Limulitella.

Caselle M., Perez L.E.A., Balzer M., Kopmann A., Rota L., Weber M., Brosi M., Steinmann J., Brundermann E., Muller A.-S.

in Journal of Instrumentation, 12 (2017), C01040. DOI:10.1088/1748-0221/12/01/C01040

Abstract

© 2017 IOP Publishing Ltd and Sissa Medialab srl. This paper presents a novel data acquisition system for continuous sampling of ultra-short pulses generated by terahertz (THz) detectors. Karlsruhe Pulse Taking Ultra-fast Readout Electronics (KAPTURE) is able to digitize pulse shapes with a sampling time down to 3 ps and pulse repetition rates up to 500 MHz. KAPTURE has been integrated as a permanent diagnostic device at ANKA and is used for investigating the emitted coherent synchrotron radiation in the THz range. A second version of KAPTURE has been developed to improve the performance and flexibility. The new version offers a better sampling accuracy for a pulse repetition rate up to 2 GHz. The higher data rate produced by the sampling system is processed in real-time by a heterogeneous FPGA and GPU architecture operating up to 6.5 GB/s continuously. Results in accelerator physics will be reported and the new design of KAPTURE be discussed.

Bergmann T., Balzer M., Hopp T., Van De Kamp T., Kopmann A., Jerome N.T., Zapf M.

in VISIGRAPP 2017 – Proceedings of the 12th International Joint Conference on Computer Vision, Imaging and Computer Graphics Theory and Applications, 3 (2017) 330-334.

Abstract

Copyright © 2017 by SCITEPRESS – Science and Technology Publications, Lda. All rights reserved. The computer gaming industry is traditionally the moving power and spirit in the development of computer visualization hardware and software. This year, affordable and high quality virtual reality headsets became available and the science community is eager to get benefit from it. This paper describes first experiences in adapting the new hardware for three different visualization use cases. In all three examples existing visualization pipelines were extended by virtual reality technology. We describe our approach, based on the HTC Vive VR headset, the open source software Blender and the Unreal Engine 4 game engine. The use cases are from three different fields: large-scale particle physics research, X-ray-imaging for entomology research and medical imaging with ultrasound computer tomography. Finally we discuss benefits and limits of the current virtual reality technology and present an outlook to future developments.

Losel P., Heuveline V.

in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 10129 LNCS (2017) 121-128. DOI:10.1007/978-3-319-52280-7_12

Abstract

© Springer International Publishing AG 2017. Segmenting the blood pool and myocardium from a 3D cardiovascular magnetic resonance (CMR) image allows to create a patient-specific heart model for surgical planning in children with complex congenital heart disease (CHD). Implementation of semi-automatic or automatic segmentation algorithms is challenging because of a high anatomical variability of the heart defects, low contrast, and intensity variations in the images. Therefore, manual segmentation is the gold standard but it is labor-intensive. In this paper we report the set-up and results of a highly scalable semi-automatic diffusion algorithm for image segmentation. The method extrapolates the information from a small number of expert manually labeled reference slices to the remaining volume. While results of most semi-automatic algorithms strongly depend on well-chosen but usually unknown parameters this approach is parameter-free. Validation is performed on twenty 3D CMR images.

Lautner S., Lenz C., Hammel J., Moosmann J., Kuhn M., Caselle M., Vogelgesang M., Kopmann A., Beckmann F.

in Proceedings of SPIE – The International Society for Optical Engineering, 10391 (2017), 1039118. DOI:10.1117/12.2287221

Abstract

© 2017 SPIE. Water transport from roots to shoots is a vital necessity in trees in order to sustain their photosynthetic activity and, hence, their physiological activity. The vascular tissue in charge is the woody body of root, stem and branches. In gymnosperm trees, like spruce trees (Picea abies (L.) Karst.), vascular tissue consists of tracheids: elongated, protoplast- free cells with a rigid cell wall that allow for axial water transport via their lumina. In order to analyze the over-all water transport capacity within one growth ring, time-consuming light microscopy analysis of the woody sample still is the conventional approach for calculating tracheid lumen area. In our investigations at the Imaging Beamline (IBL) operated by the Helmholtz-Zentrum Geesthacht (HZG) at PETRA III storage ring of the Deutsches Elektronen-Synchrotron DESY, Hamburg, we applied SRμCT on small wood samples of spruce trees in order to visualize and analyze size and formation of xylem elements and their respective lumina. The selected high-resolution phase-contrast technique makes full use of the novel 20 MPixel CMOS area detector developed within the cooperation of HZG and the Karlsruhe data by light microscopy analysis and, hence, prove, that μCT is a most appropriate method to gain valid information on xylem cell structure and tree water transport capacity.