Farago T., Mikulik P., Ershov A., Vogelgesang M., Hanschke D., Baumbach T.
in Journal of Synchrotron Radiation, 24 (2017) 1283-1295. DOI:10.1107/S1600577517012255
© International Union of Crystallography, 2017. An open-source framework for conducting a broad range of virtual X-ray imaging experiments, syris, is presented. The simulated wavefield created by a source propagates through an arbitrary number of objects until it reaches a detector. The objects in the light path and the source are time-dependent, which enables simulations of dynamic experiments, e.g. four-dimensional time-resolved tomography and laminography. The high-level interface of syris is written in Python and its modularity makes the framework very flexible. The computationally demanding parts behind this interface are implemented in OpenCL, which enables fast calculations on modern graphics processing units. The combination of flexibility and speed opens new possibilities for studying novel imaging methods and systematic search of optimal combinations of measurement conditions and data processing parameters. This can help to increase the success rates and efficiency of valuable synchrotron beam time. To demonstrate the capabilities of the framework, various experiments have been simulated and compared with real data. To show the use case of measurement and data processing parameter optimization based on simulation, a virtual counterpart of a high-speed radiography experiment was created and the simulated data were used to select a suitable motion estimation algorithm; one of its parameters was optimized in order to achieve the best motion estimation accuracy when applied on the real data. syris was also used to simulate tomographic data sets under various imaging conditions which impact the tomographic reconstruction accuracy, and it is shown how the accuracy may guide the selection of imaging conditions for particular use cases.The flexible and efficient framework syris is presented and its capabilities for the simulation of four-dimensional X-ray imaging experiments are demonstrated by two exemplary applications.
Gasilov S., Mittone A., Dos Santos Rolo T., Polyakov S., Zholudev S., Terentyev S., Blank V., Bravin A., Baumbach T.
in Journal of Synchrotron Radiation, 24 (2017) 1137-1145. DOI:10.1107/S1600577517012772
© International Union of Crystallography, 2017. In this work a double-crystal setup is employed to study compound refractive lenses made of single-crystal diamond. The point spread function of the lens is calculated taking into account the lens transmission, the wavefront aberrations, and the ultra-small-angle broadening of the X-ray beam. It is shown that, similarly to the wavefront aberrations, the ultra-small-angle scattering effects can significantly reduce the intensity gain and increase the focal spot size. The suggested approach can be particularly useful for the characterization of refractive X-ray lenses composed of many tens of unit lenses.A double-crystal setup is used to quantify aberrations and to assess the influence of ultra-small-angle X-ray scattering on the optical properties of a single-crystal diamond compound refractive lens.
Gasilov S., Dos Santos Rolo T., Mittone A., Polyakov S., Terentyev S., Farago T., Blank V., Bravin A., Baumbach T.
in Optics Express, 25 (2017) 25090-25097. DOI:10.1364/OE.25.025090
© 2017 Optical Society of America. Quality of a refractive compound X-ray lens can be limited by imperfections in surfaces of unit lenses and stacking precision. In general case both the lens transmission and optical aberrations define properties of a beam in the lens exit plane; together they can be expressed in terms of the generalized pupil function. In this work we measure this function for a diamond single crystal compound refractive lens. Consequently, we apply the pupil function to evaluate the performance of the examined compound refractive X-ray lens. A number of practically important conclusions can be drawn from such analysis.
Karpov D., Liu Z., Rolo T.D.S., Harder R., Balachandran P.V., Xue D., Lookman T., Fohtung E.
in Nature Communications, 8 (2017), 280. DOI:10.1038/s41467-017-00318-9
© 2017 The Author(s). Topological defects of spontaneous polarization are extensively studied as templates for unique physical phenomena and in the design of reconfigurable electronic devices. Experimental investigations of the complex topologies of polarization have been limited to surface phenomena, which has restricted the probing of the dynamic volumetric domain morphology in operando. Here, we utilize Bragg coherent diffractive imaging of a single BaTiO3 nanoparticle in a composite polymer/ferroelectric capacitor to study the behavior of a three-dimensional vortex formed due to competing interactions involving ferroelectric domains. Our investigation of the structural phase transitions under the influence of an external electric field shows a mobile vortex core exhibiting a reversible hysteretic transformation path. We also study the toroidal moment of the vortex under the action of the field. Our results open avenues for the study of the structure and evolution of polar vortices and other topological structures in operando in functional materials under cross field configurations.
Onelli O.D., Kamp T.V.D., Skepper J.N., Powell J., Rolo T.D.S., Baumbach T., Vignolini S.
in Scientific Reports, 7 (2017), 1373. DOI:10.1038/s41598-017-01496-8
© 2017 The Author(s). Structural colours in living organisms have been observed and analysed in a large number of species, however the study of how the micro- A nd nano-scopic natural structures responsible of such colourations develop has been largely ignored. Understanding the interplay between chemical composition, structural morphology on multiple length scales, and mechanical constraints requires a range of investigation tools able to capture the different aspects of natural hierarchical architectures. Here, we report a developmental study of the most widespread strategy for structural colouration in nature: The cuticular multilayer. In particular, we focus on the exoskeletal growth of the dock leaf beetle Gastrophysa viridula, capturing all aspects of its formation: The macroscopic growth is tracked via synchrotron microtomography, while the submicron features are revealed by electron microscopy and light spectroscopy combined with numerical modelling. In particular, we observe that the two main factors driving the formation of the colour-producing multilayers are the polymerization of melanin during the ecdysis and the change in the layer spacing during the sclerotisation of the cuticle. Our understanding of the exoskeleton formation provides a unique insight into the different processes involved during metamorphosis.
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
© 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
© 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
© 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.
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
© 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
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.