Publications of UFO life science applications, mainly morphology of small insects
Kopmann A., Chilingaryan S., Vogelgesang M., Dritschler T., Shkarin A., Shkarin R., Dos Santos Rolo T., Farago T., Van De Kamp T., Balzer M., Caselle M., Weber M., Baumbach T.
in 2016 IEEE Nuclear Science Symposium, Medical Imaging Conference and Room-Temperature Semiconductor Detector Workshop, NSS/MIC/RTSD 2016, 2017-January (2017), 8069895. DOI:10.1109/NSSMIC.2016.8069895
© 2016 IEEE. New imaging stations aim for high spatial and temporal resolution and are characterized by ever increasing sampling rates and demanding data processing workflows. Key to successful imaging experiments is to open up high-performance computing resources. This includes carefully selected components for computing hardware and development of advanced imaging algorithms optimized for efficient use of parallel processor architectures. We present the novel UFO computing platform for online data processing for imaging experiments and image-based feedback. The platform handles the full data life cycle from the X-ray detector to long-term data archives. Core components of this system are an FPGA platform for ultra-fast data acquisition, the GPU-based UFO image processing framework, and the fast control system “Concert”. Reconstruction algorithms implemented in the UFO framework are optimized for the latest GPU architectures and provide a reconstruction throughput in the GB/s-range. The control system “Concert” integrates high-speed computing nodes and fast beamline devices and thus enables image-based control loops and advanced workflow automation for efficient beam time usage. Low latencies are ensured by direct communication between FPGA and GPUs using AMDs DirectGMA technology. Time resolved tomography is supported by cutting edge regularization methods for high quality reconstructions with a reduced number of projections. The new infrastructure at ANKA has dramatically accelerated tomography from hours to second and resulted in new application fields, like high-throughput tomography, pump-probe radiography and stroboscopic tomography. Ultra-fast X-ray cine-tomography for the first time allows one to observe internal dynamics of moving millimeter-sized objects in real-time.
Schmelzle S., Heethoff M., Heuveline V., Losel P., Becker J., Beckmann F., Schluenzen F., Hammel J.U., Kopmann A., Mexner W., Vogelgesang M., Jerome N.T., Betz O., Beutel R., Wipfler B., Blanke A., Harzsch S., Hornig M., Baumbach T., Van De Kamp T.
in Proceedings of SPIE – The International Society for Optical Engineering, 10391 (2017), 103910P. DOI:10.1117/12.2275959
© 2017 SPIE. Beamtime and resulting SRμCT data are a valuable resource for researchers of a broad scientific community in life sciences. Most research groups, however, are only interested in a specific organ and use only a fraction of their data. The rest of the data usually remains untapped. By using a new collaborative approach, the NOVA project (Network for Online Visualization and synergistic Analysis of tomographic data) aims to demonstrate, that more efficient use of the valuable beam time is possible by coordinated research on different organ systems. The biological partners in the project cover different scientific aspects and thus serve as model community for the collaborative approach. As proof of principle, different aspects of insect head morphology will be investigated (e.g., biomechanics of the mouthparts, and neurobiology with the topology of sensory areas). This effort is accomplished by development of advanced analysis tools for the ever-increasing quantity of tomographic datasets. In the preceding project ASTOR, we already successfully demonstrated considerable progress in semi-automatic segmentation and classification of internal structures. Further improvement of these methods is essential for an efficient use of beam time and will be refined in the current NOVAproject. Significant enhancements are also planned at PETRA III beamline p05 to provide all possible contrast modalities in x-ray imaging optimized to biological samples, on the reconstruction algorithms, and the tools for subsequent analyses and management of the data. All improvements made on key technologies within this project will in the long-term be equally beneficial for all users of tomography instrumentations.
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
© 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.
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
© 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.
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.
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.
Hahn S., Muller Y., Hofmann R., Moosmann J., Oktem O., Helfen L., Guigay J.-P., Van De Kamp T., Baumbach T.
in Physical Review A – Atomic, Molecular, and Optical Physics, 93 (2016), 053834. DOI:10.1103/PhysRevA.93.053834
© 2016 American Physical Society. ©2016 American Physical Society. We analyze theoretically and investigate experimentally the transfer of phase to intensity power spectra of spatial frequencies through free-space Fresnel diffraction. Depending on λz (where λ is the wavelength and z is the free-space propagation distance) and the phase-modulation strength S, we demonstrate that for multiscale and broad phase spectra critical behavior transmutes a quasilinear to a nonlinear diffractogram except for low frequencies. On the contrary, a single-scale and broad phase spectrum induces a critical transition in the diffractogram at low frequencies. In both cases, identifying critical behavior encoded in the intensity power spectra is of fundamental interest because it exhibits the limits of perturbative power counting but also guides resolution and contrast optimization in propagation-based, single-distance, phase-contrast imaging, given certain dose and coherence constraints.
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
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.
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
© 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.
Kuhsel S., Bruckner A., Schmelzle S., Heethoff M., Bluthgen N.
in Insect Science (2016). DOI:10.1111/1744-7917.12362
© 2016 Institute of Zoology, Chinese Academy of Sciences. Body mass, volume and surface area are important for many aspects of the physiology and performance of species. Whereas body mass scaling received a lot of attention in the literature, surface areas of animals have not been measured explicitly in this context. We quantified surface area-volume (SA/V) ratios for the first time using 3D surface models based on a structured light scanning method for 126 species of pollinating insects from 4 orders (Diptera, Hymenoptera, Lepidoptera, and Coleoptera). Water loss of 67 species was measured gravimetrically at very dry conditions for 2 h at 15 and 30 °C to demonstrate the applicability of the new 3D surface measurements and relevance for predicting the performance of insects. Quantified SA/V ratios significantly explained the variation in water loss across species, both directly or after accounting for isometric scaling (residuals of the SA/V ∼ mass2/3 relationship). Small insects with a proportionally larger surface area had the highest water loss rates. Surface scans of insects to quantify allometric SA/V ratios thus provide a promising method to predict physiological responses, improving the potential of body mass isometry alone that assume geometric similarity.
Mangold S., Van De Kamp T., Steininger R.
in Journal of Physics: Conference Series, 712 (2016), 012141. DOI:10.1088/1742-6596/712/1/012141
The usefulness of full field transmission spectroscopy is shown using the example of mandible of the stick insect Peruphasma schultei. An advanced data evaluation tool chain with an energy drift correction and highly reproducible automatic background correction is presented. The results show significant difference between the top and the bottom of the mandible of an adult stick insect.