Ibrahimkutty S., Wagener P., Rolo T.D.S., Karpov D., Menzel A., Baumbach T., Barcikowski S., Plech A.

in Scientific Reports, 5 (2015), 16313. DOI:10.1038/srep16313


Pulsed-laser assisted nanoparticle synthesis in liquids (PLAL) is a versatile tool for nanoparticle synthesis. However, fundamental aspects of structure formation during PLAL are presently poorly understood. We analyse the spatio-temporal kinetics during PLAL by means of fast X-ray radiography (XR) and scanning small-angle X-ray scattering (SAXS), which permits us to probe the process on length scales from nanometers to millimeters with microsecond temporal resolution. We find that the global structural evolution, such as the dynamics of the vapor bubble can be correlated to the locus and evolution of silver nanoparticles. The bubble plays an important role in particle formation, as it confines the primary particles and redeposits them to the substrate. Agglomeration takes place for the confined particles in the second bubble. Additionally, upon the collapse of the second bubble a jet of confined material is ejected perpendicularly to the surface. We hypothesize that these kinetics influence the final particle size distribution and determine the quality of the resulting colloids, such as polydispersity and modality through the interplay between particle cloud compression and particle release into the liquid.

Stevanovic U., Caselle M., Cecilia A., Chilingaryan S., Farago T., Gasilov S., Herth A., Kopmann A., Vogelgesang M., Balzer M., Baumbach T., Weber M.

in IEEE Transactions on Nuclear Science, 62 (2015) 911-918, 7111386. DOI:10.1109/TNS.2015.2425911


© 1963-2012 IEEE.High-speed X-ray imaging applications play a crucial role for non-destructive investigations of the dynamics in material science and biology. On-line data analysis is necessary for quality assurance and data-driven feedback, leading to a more efficent use of a beam time and increased data quality. In this article we present a smart camera platform with embedded Field Programmable Gate Array (FPGA) processing that is able to stream and process data continuously in real-time. The setup consists of a Complementary Metal-Oxide-Semiconductor (CMOS) sensor, an FPGA readout card, and a readout computer. It is seamlessly integrated in a new custom experiment control system called Concert that provides a more efficient way of operating a beamline by integrating device control, experiment process control, and data analysis. The potential of the embedded processing is demonstrated by implementing an image-based trigger. It records the temporal evolution of physical events with increased speed while maintaining the full field of view. The complete data acquisition system, with Concert and the smart camera platform was successfully integrated and used for fast X-ray imaging experiments at KIT’s synchrotron radiation facility ANKA.

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

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


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.

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


© 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.

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


© 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., Dos Santos Rolo T., Vagovic P., Baumbach T., Riedel A.

in PLoS ONE, 9 (2014), e102355. DOI:10.1371/journal.pone.0102355


Digital surface mesh models based on segmented datasets have become an integral part of studies on animal anatomy and functional morphology; usually, they are published as static images, movies or as interactive PDF files. We demonstrate the use of animated 3D models embedded in PDF documents, which combine the advantages of both movie and interactivity, based on the example of preserved Trigonopterus weevils. The method is particularly suitable to simulate joints with largely deterministic movements due to precise form closure. We illustrate the function of an individual screw-and-nut type hip joint and proceed to the complex movements of the entire insect attaining a defence position. This posture is achieved by a specific cascade of movements: Head and legs interlock mutually and with specific features of thorax and the first abdominal ventrite, presumably to increase the mechanical stability of the beetle and to maintain the defence position with minimal muscle activity. The deterministic interaction of accurately fitting body parts follows a defined sequence, which resembles a piece of engineering. © 2014 van de Kamp et al.

Rolo T.D.S., Ershov A., Van De Kamp T., Baumbach T.

in Proceedings of the National Academy of Sciences of the United States of America, 111 (2014) 3921-3926. DOI:10.1073/pnas.1308650111


Scientific cinematography using ultrafast optical imaging is a common tool to study motion. In opaque organisms or structures, X-ray radiography captures sequences of 2D projections to visualize morphological dynamics, but for many applications full fourdimensional (4D) spatiotemporal information is highly desirable. We introduce in vivo X-ray cine-tomography as a 4D imaging technique developed to study real-time dynamics in small living organisms with micrometer spatial resolution and subsecond time resolution. The method enables insights into the physiology of small animals by tracking the 4D morphological dynamics of minute anatomical features as demonstrated in this work by the analysis of fast-moving screw-and-nut-type weevil hip joints. The presented method can be applied to a broad range of biological specimens and biotechnological processes.

Moosmann J., Ershov A., Weinhardt V., Baumbach T., Prasad M.S., Labonne C., Xiao X., Kashef J., Hofmann R.

in Nature Protocols, 9 (2014) 294-304. DOI:10.1038/nprot.2014.033


X-ray phase-contrast microtomography (XPCμT) is a label-free, high-resolution imaging modality for analyzing early development of vertebrate embryos in vivo by using time-lapse sequences of 3D volumes. Here we provide a detailed protocol for applying this technique to study gastrulation in Xenopus laevis (African clawed frog) embryos. In contrast to μMRI, XPCμT images optically opaque embryos with subminute temporal and micrometer-range spatial resolution. We describe sample preparation, culture and suspension of embryos, tomographic imaging with a typical duration of 2 h (gastrulation and neurulation stages), intricacies of image pre-processing, phase retrieval, tomographic reconstruction, segmentation and motion analysis. Moreover, we briefly discuss our present understanding of X-ray dose effects (heat load and radiolysis), and we outline how to optimize the experimental configuration with respect to X-ray energy, photon flux density, sample-detector distance, exposure time per tomographic projection, numbers of projections and time-lapse intervals. The protocol requires an interdisciplinary effort of developmental biologists for sample preparation and data interpretation, X-ray physicists for planning and performing the experiment and applied mathematicians/computer scientists/physicists for data processing and analysis. Sample preparation requires 9-48 h, depending on the stage of development to be studied. Data acquisition takes 2-3 h per tomographic time-lapse sequence. Data processing and analysis requires a further 2 weeks, depending on the availability of computing power and the amount of detail required to address a given scientific problem. © 2014 Nature America, Inc. All rights reserved.

Boden S., Dos Santos Rolo T., Baumbach T., Hampel U.

in Experiments in Fluids, 55 (2014), 1768. DOI:10.1007/s00348-014-1768-7


We report on a study to measure the three-dimensional shape of Taylor bubbles in capillaries using synchrotron radiation in conjunction with ultrafast radiographic imaging. Moving Taylor bubbles in 2-mm round and square capillaries were radiographically scanned with an ultrahigh frame rate of up to 36,000 fps and 5.6-μm pixel separation. Consecutive images were properly processed to yield 2D transmission radiographs of high contrast-to-noise ratio. Application of 3D tomographic image reconstruction disclosed the 3D bubble shape. The results provide a reference data base for development of sophisticated interface resolving CFD computations. © 2014 Springer-Verlag Berlin Heidelberg.

Butcher B.A., Zaldivar-Riveron A., Van De Kamp T., Rolo T.D.S., Baumbach T., Quicke D.L.J.

in Zootaxa, 3860 (2014) 449-463. DOI:10.11646/zootaxa.3860.5.4


Copyright © 2014 Magnolia Press. Two new species of the parasitic wasp genus Mesocentrus Szépligeti (Betylobraconinae) are described. One based on a new species from Papua New Guinea, the other the first Palaearctic member of the subfamily based on a 30+ mya, species from Baltic amber. The second species is illustrated using synchrotron X-ray microtomography. Whereas the extant Betylobraconinae are restricted to Australia, New Guinea and New Caledonia, their ancestral distribution is now known to have extended considerably further. A key to the four species of Mesocentrus known from Papua New Guinea is provided. Both species possess some putatively plesiomorphic characters absent in other extant Mesocentrus spp. The new extant species differs in having a considerably larger number of antennal segments and a less laterally depressed frons, while the extinct one has the clypeus separated from the face dorsally and strongly developed hypoclypeal depression. Availability of sequence data for this species enabled further analysis of the relationships of the subfamily, which we present in a phylogenetic analysis additionally including the release of a number of new sequences of related taxa.