Schultze, Felix

Master thesis, Faculty of Computer Science, Karlsruhe Institute of Technology, 2015.

Abstract

An ever increasing number of large tomographic images is recorded at synchrotron facilities world wide. Due to the drastic increase of data volumes, there is a recent trend to provide data analysis services at the facilities as well. The ASTOR project aims to realize a cloud-based infrastructure for remote data analysis and visualization of tomographic data. A key component is a web-based data browser to select data sets and request a virtual machine for analysis of this data. One of the challenges is to provide a fast preview of 3D volumes but also 3D sequences. Since a standard data sets exceed 10 gigabytes, standard visualization techniques are not feasible and new data reduction techniques have to be developed.

 

First assessor: Prof. Dr.-Ing. Carsten Dachsbacher
Second assessor: Dr. Suren Chilingaryan

Supervised by  Dr. Andreas Kopmann

Smith J.L., Palermo N.A., Theobald J.C., Wells J.D., Heethoff M.

in Journal of Insect Science, 15 (2015). DOI:10.1093/jisesa/iev114

Abstract

© The Author 2015. Male Chrysomya megacephala (F.) blow fly compound eyes contain an unusual area of enlarged dorsal facets believed to allow for increased light capture. This region is absent in females and has been hypothesized to aid in mate tracking in low light conditions or at greater distances. Many traits used in the attraction and capture of mates are allometric, growing at different rates relative to body size. Previous reports concerning C. megacephala eye properties did not include measurements of body size, making the relationship between the specialized eye region and body size unclear. We examined different morphological features of the eye among individuals of varying sizes. We found total eye size scaled proportionately to body size, but the number of enlarged dorsal facets increased as body size increased. This demonstrated that larger males have an eye that is morphologically different than smaller males. On the basis of external morphology, we hypothesized that since larger males have larger and a greater number of dorsally enlarged facets, and these facets are believed to allow for increased light capture, larger males would be active in lower light levels than smaller males and females of equal size. In a laboratory setting, larger males were observed to become active earlier in the morning than smaller males, although they did not remain active later in the evening. However, females followed the same pattern at similar light levels suggesting that overall body size rather than specialized male eye morphology is responsible for increased activity under low light conditions.

Heethoff M., Rall B.C.

in Chemoecology, 25 (2015) 53-61. DOI:10.1007/s00049-014-0184-z

Abstract

© 2015, Springer Basel. Morphological and chemical defences are widespread anti-predator mechanisms in most domains of life, and play an important role in understanding predator–prey interactions. Classical concepts of dynamical protection (‘inducible defence’) include the morphological changes in certain crustaceans or the production of chemicals in many plants. Permanently stored defensive secretions are, to our knowledge, ignored in food web ecology. We show that this kind of chemical defence is highly dynamic and may loose its effect over time (‘reducible defence’). Combining experimental and theoretical approaches, we show that chemical defence also changes the time budget of predators and decreases the strength of the functional response. However, this may be counteracted by increasing predator density—an effect we call ‘apparent facilitation’. The interplay of ‘reducible defence’ and ‘apparent facilitation’ may substantially contribute to stability in terrestrial ecosystems.

Schmelzle S., Norton R.A., Heethoff M.

in Zoologischer Anzeiger, 254 (2015) 27-40. DOI:10.1016/j.jcz.2014.09.002

Abstract

© 2014 Elsevier GmbH. The most complex mechanical defense of oribatid mites is ptychoidy, in which the animals can retract their legs and gnathosoma into the idiosoma and encapsulate by deflecting the prodorsum. Since Acari lack most antagonistic musculature, extension of appendages is facilitated through hemolymph pressure that in mites mostly is generated by dorso-ventral compression of the opisthosoma. The hardened notogaster of box mites requires a different system of pressure generation that is also able to accommodate huge hemolymph movement accompanying ptychoidy. We compared the functional morphology of ptychoidy in one model species from each of the two ptyctime superfamilies, Euphthiracaroidea and Phthiracaroidea, using synchrotron X-ray microtomography and high-speed videography. We show that the two groups evolved very different functional modes of hydrostatic pressure control. While euphthiracaroids employ a lateral compression of the notogaster using all muscles of the opisthosomal compressor system, phthiracaroids employ a dorsoventral compression generated by only the notogaster lateral compressor and additionally the postanal muscle; these retract the temporarily unified ventral plates into the idiosoma, revealing the poam as an integral part of the opisthosomal compressor system in this group. The primitive mode of operation for generating hemolymph pressure in the Ptyctima probably was lateral compression, as molecular studies indicate that Phthiracaroidea evolved within Euphthiracaroidea. In this hypothesis, dorsoventral compression evolved secondarily in phthiracaroid mites, but whether the immediate ancestors of Ptyctima used lateral or dorsoventral compression remains to be determined.

Steinmann J.L., Brosi M., Brundermann E., Caselle M., Hertle E., Hiller N., Kehrer B., Muller A.-S., Schonfeldt P., Schuh M., Schutze P., Schwarz M., Hesler J.

in 6th International Particle Accelerator Conference, IPAC 2015 (2015) 1509-1511.

Abstract

Copyright © 2015 CC-BY-3.0 and by the respective authors. Interferometry is the quasi-standard for spectral measurements in the THz- and IR-range. The frequency resolution, however, is limited by the travel range of the interferometer mirrors. Therefore, a resolution in the low megahertz range would require interferometer arms of about 100 m. As an alternative, heterodyne measurements provide a resolution in the Hertz range, an improvement of 6 orders of magnitude. Here we present measurements done at ANKA with a VDI WR3.4SAX, a mixer that can be tuned to frequencies from 220 GHz to 330 GHz and we show how the bunch filling pattern influences the amplitude of specific frequencies.

Yang X., Hofmann R., Dapp R., Van De Kamp T., Dos Santos Rolo T.T., Xiao X., Moosmann J., Kashef J., Stotzka R.

in Optics Express, 23 (2015) 5368-5387. DOI:10.1364/OE.23.005368

Abstract

© 2015 Optical Society of America. High-resolution, three-dimensional (3D) imaging of soft tissues requires the solution of two inverse problems: phase retrieval and the reconstruction of the 3D image from a tomographic stack of two-dimensional (2D) projections. The number of projections per stack should be small to accommodate fast tomography of rapid processes and to constrain X-ray radiation dose to optimal levels to either increase the duration of in vivo time-lapse series at a given goal for spatial resolution and/or the conservation of structure under X-ray irradiation. In pursuing the 3D reconstruction problem in the sense of compressive sampling theory, we propose to reduce the number of projections by applying an advanced algebraic technique subject to the minimisation of the total variation (TV) in the reconstructed slice. This problem is formulated in a Lagrangian multiplier fashion with the parameter value determined by appealing to a discrete L-curve in conjunction with a conjugate gradient method. The usefulness of this reconstruction modality is demonstrated for simulated and in vivo data, the latter acquired in parallel-beam imaging experiments using synchrotron radiation.

van de Kamp T., Cecilia A., dos Santos Rolo T., Vagovic P., Baumbach T., Riedel A.

in Arthropod Structure and Development, 44 (2015) 509-523. DOI:10.1016/j.asd.2015.07.004

Abstract

© 2015 Elsevier Ltd.The thorax morphology, especially the muscles and the tracheal system of three flightless species of Cryptorhynchinae is examined by digital 3D reconstructions based on synchrotron X-ray microtomography and compared to other Curculionidae. Wings, metanepisternites, and muscles functional in flight are fully reduced in the species examined: Kyklioacalles roboris (Curtis), Trigonopterus scharfi Riedel and Trigonopterus vandekampi Riedel. All three share the same set of thoracic muscles, but differences exist in the shape and size of muscles. Both Trigonopterus species examined have a conspicuous fan-shaped branch of Musculus mesosterni primus contracting pro- and mesothorax, interpreted as an adaption to their thanatosis defense strategy. Trigonopterus vandekampi furthermore shows a marked increase in the size of two metacoxal muscles, which may be functional in this species’ thanatosis blocking mechanisms. The metathoracic spiracle of all Trigonopterus species is located at the side of the metaventrite externally and not in the subelytral space as in other beetles. It is hypothesized that this translocation was triggered by the need to improve oxygen supply during thanatosis, when both the mesothoracic spiracle and the subelytral cavity are tightly sealed from the outside.

Greven H., Van De Kamp T., Dos Santos Rolo T., Baumbach T., Clemen G.

in Vertebrate Zoology, 65 (2015) 81-99.

Abstract

A study on the cranial morphology, especially on the tooth bearing (dental) systems of several preserved developmental stages (from early premetamorphic larvae, in which most skull elements were already present and ossified or ossified in part, to transformed adult) of the smooth newt Lissotriton vulgaris (Salamandridae) was undertaken. We used μCT (to visualize the ossified elements in general and their relationships to each other) and an overall Alizarinred staining (to at best visualize teeth, replacement teeth, tooth buds and, after removing the oral mucosa, the course of dental laminae). Specimens cleared and stained with Alzarinred and Alcianblue were shown to be less suitable for our questions. In one case we used histological sections to follow the course of dental laminae, and in a second case scanning electron microscopy to show the structure of teeth in detail. The general sequence, growth, and changes of the bony elements including the “dental systems”, especially around metamorphosis, known from several other salamandrids are largely confirmed. Concerning the “tooth systems”, metamorphic events include the late appearance of the maxillae, resorption of the coronoids and palatines including their tooth-patches, remodelling of the vomer, i.e. resorption of the vomerine larval tooth-patch, formation of the edentate vomerine plate, and outgrowth of the monstichously dentate vomerine bar (typical for salamandrids). We show evidence that the larval vomer is not completey resorbed and that, unlike what has been described for Salamandra salamandra, the development of the vomerine bar is probably preceded by a shift of the dental lamina towards the middle of the palate, leaving a broad area between larval vomer and dental lamina. We hypothesize that the connective tissue in this area ossifies later and extends posteriorly forming the vomerine bar. It is noteworthy that in nearly all larvae vomer and intact pterygopalatinum were very close together either on one side or on both sides leading in overwintered larvae to the fusion of the vomer and the palatinal portion of the pterygopalatinum, primarily on one side. The zone of fusion is always characterized by a buccal notch. We think that in L. vulgaris the formation of “vomeropterygopalatina” is supported by the close proximity of the two bones and that these bones may fuse due to an imbalance between differentiation- and growth rate (indirectly caused by low temperatures). Approximation and especially fusion of the two bones correspond with the extension of the vomerine dental lamina into the area of the palatine, which temporally provides the latter with teeth. Overwintered larvae show further deviations concerning growth and differentiation of the mouth roof, which can be also interpreted as signs of delayed metamorphosis. They retain, for example, a largely intact dentate palatine, but with some regression of its tooth-patch, while the larval vomer is enlarged anteriorly and posteriorly and its number of teeth has increased; and the largely intact pterygopalatinal bony bridge. Further, maxillae begin to ossify. All larvae obviously have reached a late premetamorphic larval stage before the delay has started.

Brosi M., Caselle M., Hertle E., Hiller N., Kopmann A., Muller A.-S., Schonfeldt P., Schwarz M., Steinmann J.L., Weber M.

in 6th International Particle Accelerator Conference, IPAC 2015 (2015) 882-884.

Abstract

Copyright © 2015 CC-BY-3.0 and by the respective authors. The ANKA storage ring of the Karlsruhe Institute of Technology (KIT) operates in the energy range from 0.5 to 2.5 GeV and generates brilliant coherent synchrotron radiation in the THz range with a dedicated bunch length reducing optic. The producing of radiation in the so-called THz-gap is challenging, but this intense THz radiation is very attractive for certain user experiments. The high degree of compression in this so-called low-alpha optics leads to a complex longitudinal dynamics of the electron bunches. The resulting micro-bunching instability leads to time dependent fluctuations and strong bursts in the radiated THz power. The study of these fluctuations in the emitted THz radiation provides insight into the longitudinal beam dynamics. Fast THz detectors combined with KAPTURE, the dedicated KArlsruhe Pulse Taking and Ultrafast Readout Electronics system developed at KIT, allow the simultaneous measurement of the radiated THz intensity for each bunch individually in a multibunch environment. This contribution gives an overview of the first experience gained using this setup as an online diagnostics tool.

Gehrke R., Kopmann A., Wintersberger E., Beckmann F.

in Synchrotron Radiation News, 28 (2015) 36-42. DOI:10.1080/08940886.2015.1013420

Abstract

© Taylor & Francis. The Helmholtz Association is the largest scientific organization in Germany. It operates all major German research infrastructures involved in research with photons, neutrons, and ions. These are DESY in Hamburg; the Karlsruhe Institute of Technology (KIT); the Research Centre Jülich (FZJ); the Helmholtz Centres in Geesthacht (HZG), Berlin (HZB), and Dresden-Rossendorf (HZDR); and the GSI Centre for research with heavy ions in Darmstadt. In common, all these centers are facing similar challenges related to dramatically increasing data rates and volumes generated with more and more powerful radiation sources together with larger and faster detectors. On the other hand, each center has its own specific portfolio of long-lasting technical expertise in areas like data analysis, information technology, or hardware development. Therefore, it was obvious to address the challenges by acting in concert. This was the main motivation in 2010 for the launch of a joint project among the partners called the “High Data Rate Processing and Analysis Initiative (HDRI).” The initiative is organized into three basic work packages: “Data Management,” “Real-time Data Processing,” and “Data Analysis, Modelling, and Simulation.” The aim is to carry out the development of methods, hardware components, and software for data acquisition, real-time and offline analysis, documentation and archiving, and for remote access to data. The solutions are finally meant to be integrated at the various experimental stations and thus have to be versatile and flexible to cope with the heterogeneous requirements of the different experiments. The claim to create standard solutions makes it mandatory to closely collaborate with large international activities in the field of data handling, like the European PaNdata project (see article in this issue), but also with vendors of detectors, data evaluation software, etc., as well as with corresponding standardization bodies.