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.

Losel P., Heuveline V.

in Progress in Biomedical Optics and Imaging – Proceedings of SPIE, 9784 (2016), 97842L. DOI:10.1117/12.2216202

Abstract

© 2016 SPIE. Inspired by the diffusion of a particle, we present a novel approach for performing a semiautomatic segmentation of tomographic images in 3D, 4D or higher dimensions to meet the requirements of high-throughput measurements in a synchrotron X-ray microtomograph. Given a small number of 2D-slices with at least two manually labeled segments, one can either analytically determine the probability that an intelligently weighted random walk starting at one labeled pixel will be at a certain time at a specific position in the dataset or determine the probability approximately by performing several random walks. While the weights of a random walk take into account local information at the starting point, the random walk itself can be in any dimension. Starting a great number of random walks in each labeled pixel, a voxel in the dataset will be hit by several random walks over time. Hence, the image can be segmented by assigning each voxel to the label where the random walks most likely started from. Due to the high scalability of random walks, this approach is suitable for high throughput measurements. Additionally, we describe an interactively adjusted active contours slice by slice method considering local information, where we start with one manually labeled slice and move forward in any direction. This approach is superior with respect to accuracy towards the diffusion algorithm but inferior in the amount of tedious manual processing steps. The methods were applied on 3D and 4D datasets and evaluated by means of manually labeled images obtained in a realistic scenario with biologists.

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

in IPAC 2016 – Proceedings of the 7th International Particle Accelerator Conference (2016) 2855-2857.

Abstract

Copyright © 2016 CC-BY-3.0 and by the respective authors. We present the effects of the filling pattern structure in multi-bunch mode on the beam spectrum. This effects can be seen by all detectors whose resolution is better than the RF frequency, ranging from stripline and Schottky measurements to high resolution synchrotron radiation measurements. Our heterodyne measurements of the emitted coherent synchrotron radiation at 270 GHz reveal discrete frequency harmonics around the 100 000th revolution harmonic of ANKA, the synchrotron radiation facility in Karlsruhe, Germany. Significant effects of bunch spacing, gaps between bunch trains and variations in individual bunch currents on the emitted CSR spectrum are described by theory and supported by observations.

Bruckner A., Wehner K., Neis M., Heethoff M.

in Acarologia, 56 (2016).

Abstract

© Brückner A. et al. Oribatid mites represent a diverse group of soil micro-arthropods. They have evolved a broad range of defensive chemical and morphological traits (e.g. sclerotization, ptychoidy, biomineralization). Chemical defense, rather than sclerotization, can provide protection against large predators (staphylinid beetles) and many oribatid mite species are also well protected against gamasid soil mites using morphological traits (“enemy-free-space hypothesis”). However, since predatory mites and staphylinid beetles have different types of attacking and feeding, the adaptive values of chemical and morphological traits might differ accordingly. We used the oribatid model species Archegozetes longisetosus Aoki and the common gamasid mite Stratiolaelaps miles Berlese in a predator-prey experiment. We tested for effects of chemical defense (treatments with and without oil gland secretions) and sclerotization (treatments with unsclerotized tritonymphs and sclerotized adults) in an orthogonal design. In contrast to attacks by large predators, chemical defense was mostly ineffective against gamasid mites. Sclerotization, however, had a positive effect. Hence, in a natural environment with diverse types of predators, the “enemy-free space” seems only realizable by combinations of chemical and morphological protective traits.