Koenig T., Zuber M., Trimborn B., Farago T., Meyer P., Kunka D., Albrecht F., Kreuer S., Volk T., Fiederle M., Baumbach T.

in Physics in Medicine and Biology, 61 (2016) 3427-3442, 3427. DOI:10.1088/0031-9155/61/9/3427

Abstract

© 2016 Institute of Physics and Engineering in Medicine. The x-ray dark-field contrast accessible via grating interferometry is sensitive to features at length scales well below what is resolvable by a detector system. It is commonly explained as arising from small-angle x-ray scattering (SAXS), and can be implemented both at synchrotron beamlines and with low-brilliance sources such as x-ray tubes. Here, we demonstrate that for tube based setups the underlying process of image formation can be fundamentally different. For focal spots or detector pixels that comprise multiple grating periods, we show that dark-field images contain a strong artificial and system-specific component not arising from SAXS. Based on experiments carried out with a nanofocus x-ray tube and the example of an excised rat lung, we demonstrate that the dark-field contrast observed for porous media transforms into a differential phase contrast for large geometric magnifications. Using a photon counting detector with an adjustable point spread function, we confirm that a dark-field image can indeed be formed by an intra-pixel differential phase contrast that cannot be resolved as such due to a dephasing between the periodicities of the absorption grating and the Talbot carpet. Our findings are further corroborated by a link between the strength of this pseudo-dark-field contrast and our x-ray tube’s focal spot size in a three-grating setup. These results must not be ignored when measurements are intended to be reproducible across systems.

Huang D.-Y., Bechly G., Nel P., Engel M.S., Prokop J., Azar D., Cai C.-Y., Van De Kamp T., Staniczek A.H., Garrouste R., Krogmann L., Dos Santos Rolo T., Baumbach T., Ohlhoff R., Shmakov A.S., Bourgoin T., Nel A.

in Scientific Reports, 6 (2016), 23004. DOI:10.1038/srep23004

Abstract

With nearly 100,000 species, the Acercaria (lice, plant lices, thrips, bugs) including number of economically important species is one of the most successful insect lineages. However, its phylogeny and evolution of mouthparts among other issues remain debatable. Here new methods of preparation permitted the comprehensive anatomical description of insect inclusions from mid-Cretaceous Burmese amber in astonishing detail. These “missing links” fossils, attributed to a new order Permopsocida, provide crucial evidence for reconstructing the phylogenetic relationships in the Acercaria, supporting its monophyly, and questioning the position of Psocodea as sister group of holometabolans in the most recent phylogenomic study. Permopsocida resolves as sister group of Thripida + Hemiptera and represents an evolutionary link documenting the transition from chewing to piercing mouthparts in relation to suction feeding. Identification of gut contents as angiosperm pollen documents an ecological role of Permopsocida as early pollen feeders with relatively unspecialized mouthparts. This group existed for 185 million years, but has never been diverse and was superseded by new pollenivorous pollinators during the Cretaceous co-evolution of insects and flowers. The key innovation of suction feeding with piercing mouthparts is identified as main event that triggered the huge post-Carboniferous radiation of hemipterans, and facilitated the spreading of pathogenic vectors.

Hofmann R., Schober A., Hahn S., Moosmann J., Kashef J., Hertel M., Weinhardt V., Hanschke D., Helfen L., Salazar I.A.S., Guigay J.-P., Xiao X., Baumbach T.

in Optics Express, 24 (2016) 4331-4348. DOI:10.1364/OE.24.004331

Abstract

© 2016 Optical Society of America.The interactions of a beam of hard and spatio-temporally coherent X-rays with a soft-matter sample primarily induce a transverse distribution of exit phase variations δφ (retardations or advancements in pieces of the wave front exiting the object compared to the incoming wave front) whose free-space propagation over a distance z gives rise to intensity contrast gz. For single-distance image detection and |δφ|<1 all-order-in-z phase-intensity contrast transfer is linear in df. Here we show that ideal coherence implies a decay of the (shot-)noise-to-signal ratio in gz and of the associated phase noise as z-1-2 and z-1, respectively. Limits on X-ray dose thus favor large values of z. We discuss how a phase-scaling symmetry, exact in the limit δφ → 0 and dynamically unbroken up to |δφ| 1, suggests a filtering of gz in Fourier space, preserving non-iterative quasi-linear phase retrieval for phase variations up to order unity if induced by multi-scale objects inducing phase variations δφ of a broad spatial frequency spectrum. Such an approach continues to be applicable under an assumed phase-attenuation duality. Using synchrotron radiation, ex and in vivo microtomography on frog embryos exemplifies improved resolution compared to a conventional single-distance phase-retrieval algorithm.

Rota L., Vogelgesang M., Perez L.E.A., Caselle M., Chilingaryan S., Dritschler T., Zilio N., Kopmann A., Balzer M., Weber M.

in Journal of Instrumentation, 11 (2016), P02007. DOI:10.1088/1748-0221/11/02/P02007

Abstract

© 2016 IOP Publishing Ltd and Sissa Medialab srl.Modern physics experiments produce multi-GB/s data rates. Fast data links and high performance computing stages are required for continuous data acquisition and processing. Because of their intrinsic parallelism and computational power, GPUs emerged as an ideal solution to process this data in high performance computing applications. In this paper we present a high-throughput platform based on direct FPGA-GPU communication. The architecture consists of a Direct Memory Access (DMA) engine compatible with the Xilinx PCI-Express core, a Linux driver for register access, and high- level software to manage direct memory transfers using AMD’s DirectGMA technology. Measurements with a Gen3 x8 link show a throughput of 6.4 GB/s for transfers to GPU memory and 6.6 GB/s to system memory. We also assess the possibility of using the architecture in low latency systems: preliminary measurements show a round-trip latency as low as 1 μs for data transfers to system memory, while the additional latency introduced by OpenCL scheduling is the current limitation for GPU based systems. Our implementation is suitable for real-time DAQ system applications ranging from photon science and medical imaging to High Energy Physics (HEP) systems.

Schwermann A.H., dos Santos Rolo T., Caterino M.S., Bechly G., Schmied H., Baumbach T., van de Kamp T.

in eLife, 5 (2016), e12129. DOI:10.7554/eLife.12129

Abstract

© Schwermann et al. External and internal morphological characters of extant and fossil organisms are crucial to establishing their systematic position, ecological role and evolutionary trends. The lack of internal characters and soft-tissue preservation in many arthropod fossils, however, impedes comprehensive phylogenetic analyses and species descriptions according to taxonomic standards for Recent organisms. We found well-preserved three-dimensional anatomy in mineralized arthropods from Paleogene fissure fillings and demonstrate the value of these fossils by utilizing digitally reconstructed anatomical structure of a hister beetle. The new anatomical data facilitate a refinement of the species diagnosis and allowed us to reject a previous hypothesis of close phylogenetic relationship to an extant congeneric species. Our findings suggest that mineralized fossils, even those of macroscopically poor preservation, constitute a rich but yet largely unexploited source of anatomical data for fossil arthropods.

Caselle M., Blank T., Colombo F., Dierlamm A., Husemann U., Kudella S., Weber M.

in Journal of Instrumentation, 11 (2016), C01050. DOI:10.1088/1748-0221/11/01/C01050

Abstract

© 2016 IOP Publishing Ltd and Sissa Medialab srl.In the next generation of collider experiments detectors will be challenged by unprecedented particle fluxes. Thus large detector arrays of highly pixelated detectors with minimal dead area will be required at reasonable costs. Bump-bonding of pixel detectors has been shown to be a major cost-driver. KIT is one of five production centers of the CMS barrel pixel detector for the Phase I Upgrade. In this contribution the SnPb bump-bonding process and the production yield is reported. In parallel to the production of the new CMS pixel detector, several alternatives to the expensive photolithography electroplating/electroless metal deposition technologies are developing. Recent progress and challenges faced in the development of bump-bonding technology based on gold-stud bonding by thin (15 μm) gold wire is presented. This technique allows producing metal bumps with diameters down to 30 μm without using photolithography processes, which are typically required to provide suitable under bump metallization. The short setup time for the bumping process makes gold-stud bump-bonding highly attractive (and affordable) for the flip-chipping of single prototype ICs, which is the main limitation of the current photolithography processes.

Briceno R.D., Eberhard W.G., Chinea-Cano E., Wegrzynek D., Dos Santos Rolo T.

in Ethology Ecology and Evolution, 28 (2016) 53-76. DOI:10.1080/03949370.2014.1002114

Abstract

© 2015 Dipartimento di Biologia, Università di Firenze, Italia. A long-standing question in morphological evolution is why male genitalia tend to diverge more rapidly than other structures. One possible explanation is that male genitalia are under sexual selection to function as internal courtship devices. Males of closely related species may provide divergent stimulation using different genital morphologies and behaviors. Testing this hypothesis has been difficult, however, because the presumed genital courtship behavior is often hidden from view inside the female, and because studies of how the males genitalia interact with those of the female are nearly always limited to a single species in a given group, thus restricting opportunities for comparison of closely related species. We present new morphological and behavioral data for portions of the male genitalia that are hidden in the female during copulation in five species in the tsetse fly genus Glossina using data from dissections of pairs frozen in copula, artificially stimulated males, and from copulating pairs viewed with a new X-ray technique that allows events inside the female to be recorded in real time. These data almost certainly give only an incomplete view of this complex, previously hidden world. But even so they clearly reveal that, as predicted by sexual selection theory, the male genitalia of Glossina flies perform dramatic, stereotyped, rhythmic movements deep within the females reproductive tract and in inward folds of her external surface, and that many of these movements probably differ among closely related species. Most of the movements are not explicable as means by which the male anchors himself more securely to the female; all are likely to result in stimulation of the female. A female Glossina can be stimulated tactilely at a given moment during copulation at up to 8-10 or more different sites on her body.

Vogelgesang M., Farago T., Morgeneyer T.F., Helfen L., Dos Santos Rolo T., Myagotin A., Baumbach T.

in Journal of Synchrotron Radiation, 23 (2016) 1254-1263. DOI:10.1107/S1600577516010195

Abstract

© 2016 International Union of Crystallography.Real-time processing of X-ray image data acquired at synchrotron radiation facilities allows for smart high-speed experiments. This includes workflows covering parameterized and image-based feedback-driven control up to the final storage of raw and processed data. Nevertheless, there is presently no system that supports an efficient construction of such experiment workflows in a scalable way. Thus, here an architecture based on a high-level control system that manages low-level data acquisition, data processing and device changes is described. This system is suitable for routine as well as prototypical experiments, and provides specialized building blocks to conduct four-dimensional in situ, in vivo and operando tomography and laminography.

Karpov D., Dos Santos Rolo T., Rich H., Kryuchkov Y., Kiefer B., Fohtung E.

in Proceedings of SPIE – The International Society for Optical Engineering, 9931 (2016), 99312F. DOI:10.1117/12.2235865

Abstract

© 2016 SPIE. Directional dependence of the index of refraction contains a wealth of information about anisotropic optical properties in semiconducting and insulating materials. Here we present a novel high-resolution lens-less technique that uses birefringence as a contrast mechanism to map the index of refraction and dielectric permittivity in optically anisotropic materials. We applied this approach successfully to a liquid crystal polymer film using polarized light from helium neon laser. This approach is scalable to imaging with diffraction-limited resolution, a prospect rapidly becoming a reality in view of emergent brilliant X-ray sources. Applications of this novel imaging technique are in disruptive technologies, including novel electronic devices, in which both charge and spin carry information as in multiferroic materials and photonic materials such as light modulators and optical storage.

Brosi M., Steinmann J.L., Blomley E., Brundermann E., Caselle M., Hiller N., Kehrer B., Mathis Y.-L., Nasse M.J., Rota L., Schedler M., Schonfeldt P., Schuh M., Schwarz M., Weber M., Muller A.-S.

in Physical Review Special Topics – Accelerators and Beams, 19 (2016), 110701. DOI:10.1103/PhysRevAccelBeams.19.110701

Abstract

© 2016, American Physical Society. All rights reserved. Dedicated optics with extremely short electron bunches enable synchrotron light sources to generate intense coherent THz radiation. The high degree of spatial compression in this so-called low-αc optics entails a complex longitudinal dynamics of the electron bunches, which can be probed studying the fluctuations in the emitted terahertz radiation caused by the microbunching instability (“bursting”). This article presents a “quasi-instantaneous” method for measuring the bursting characteristics by simultaneously collecting and evaluating the information from all bunches in a multibunch fill, reducing the measurement time from hours to seconds. This speed-up allows systematic studies of the bursting characteristics for various accelerator settings within a single fill of the machine, enabling a comprehensive comparison of the measured bursting thresholds with theoretical predictions by the bunched-beam theory. This paper introduces the method and presents first results obtained at the ANKA synchrotron radiation facility.