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.
Cheng Y., Altapova V., Helfen L., Xu F., Dos Santos Rolo T., Vagovi P., Fiederle M., Baumbach T.
in Journal of Physics: Conference Series, 463 (2013), 012038. DOI:10.1088/1742-6596/463/1/012038
X-ray computed laminography has been developed as a non-destructive imaging technique for inspecting laterally extended objects. Benefiting from a parallel-beam geometry, high photon flux of synchrotron sources and modern high-resolution detector systems, synchrotron radiation computed laminography (SRCL) results in a powerful three-dimensional microscopy technique. SRCL can be combined with different contrast modes, such as absorption, phase and dark-field contrasts, in order to provide complementary information for the same specimen. Here we show the development of SRCL at the TopoTomo beamline of the ANKA light source. A novel instrumentation design is reported and compared to the existing one. For this design, experimental results from different contrast modalities are shown. © Published under licence by IOP Publishing Ltd.
Yang X., Jejkal T., Pasic H., Stotzka R., Streit A., Van Wezel J., Rolo T.D.S.
in Proceedings of the 2013 21st Euromicro International Conference on Parallel, Distributed, and Network-Based Processing, PDP 2013 (2013) 86-93, 6498537. DOI:10.1109/PDP.2013.21
In this paper, the method of data intensive computing is studied for large amounts of data in computed tomography (CT). An automatic workflow is built up to connect the tomography beamline of ANKA with the large scale data facility (LSDF), able to enhance the data storage and analysis efficiency. In this workflow, this paper focuses on the parallel computing of 3D computed tomography reconstruction. Different from the existing reconstruction system with filtered back-projection method, an algebraic reconstruction technique based on compressive sampling theory is presented to reconstruct the data from ultrafast computed tomography with fewer projections. Then the connected computing resources at the LSDF are used to implement the 3D CT reconstruction by distributing the whole job into multiple tasks executed in parallel. Promising reconstruction images and high computing performance are reported. For the 3D X-ray CT reconstruction, less than six minutes are actually required. LSDF is not only able to organize data efficiently, but also can provide reconstructed results to users in nearly instantaneous time. After integration into the workflow, this data intensive computing method will largely improve the data processing for ultrafast computed tomography at ANKA. © 2013 IEEE.
Mangold S., Steininger R., Rolo T.D.S., Gottlicher J.
in Journal of Physics: Conference Series, 430 (2013), 012130. DOI:10.1088/1742-6596/430/1/012130
Full field transmission spectroscopic imaging is a powerful method for screening complex and large systems to map the distribution of valence state and electronic configuration of elements. Here, we describe an optimized hardware set-up and data evaluation tool chain for spectroscopic X-ray imaging. We tested this system successful on a ferruginous quartz (SiO2) sample.
Zabler S., Ershov A., Rack A., Garcia-Moreno F., Baumbach T., Banhart J.
in Acta Materialia, 61 (2013) 1244-1253. DOI:10.1016/j.actamat.2012.10.047
Semi-solid melts exhibit a very unpredictable rheology and filling dynamics, when injected into thin-walled components. Optimization of the process requires an insight into the casting process during injection. For this purpose we injected semi-solid an Al-Ge alloy into two different thin channel geometries while recording high resolution radiographs at fast frame rates (up to 1000 images per s). Comparison of a bottleneck channel, which has previously been used for slower experiments, with a right-angle turn geometry reveals a significant influence of the channel shape on the flow behaviour of the particle-liquid mixture. While the bottleneck is quickly sealed with densified solid, turbulences in the right-angle turn apparently permit solid particles and clusters to move conjointly with the liquid and thus achieve a more complete filling. Single particle trajectories and rapid break-up of solid skeletons in such a system have been observed for the first time in situ. © 2012 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.
Alaribe L., Fauler A., Cecilia A., Santos Rolo T.D., Fiederle M., Burger A.
in Materials Research Society Symposium Proceedings, 1576 (2013). DOI:10.1557/opl.2013.1143
Much has been reported on the excellent performance of the Eu2+ activated SrI2-scintillator in spectroscopic applications, like the high light yield (97 660 ph/MeV) and good energy resolution (2.7% FWHM at 662 keV). The exploitation of these properties for other application fields is limited by the hygroscopic nature of the SrI2. Single crystal scintillating screens exhibit high spatial resolution, this combined with the high density, high effective atomic number, and the high light yield of the SrI2 could be used for high resolution X-ray imaging. Some of the questions we tried to answer in this work are the following: owing to the excellent performance of the SrI2-scintillator in spectroscopic applications, how would it perform in X-ray imaging applications. X-ray images are described based on their (spatial) resolution and contrast, how would they look like when recorded using the SrI2-scintillator detector. First a packaging technique was developed that protected the hygroscopic screens during the measurements. Our results show a high resolution of the images obtained with thin SrI2-scintillator screens both in 2D radiography and 3D tomography measurements. With these results, we think that the SrI2-scinitillator is not only a candidate for spectroscopic applications, but also for high resolution X-ray imaging purposes. Copyright © Materials Research Society 2013A.
Alaribe L., Fauler A., Cecilia A., Santos Rolo T.D., Fiederle M., Burger A.
in International Journal of Microwave and Wireless Technologies, 1576 (2013). DOI:10.1557/opl.2013.1143
© Materials Research Society 2013. Much has been reported on the excellent performance of the Eu2+ activated SrI2-scintillator in spectroscopic applications, like the high light yield (97 660 ph/MeV) and good energy resolution (2.7% FWHM at 662 keV). The exploitation of these properties for other application fields is limited by the hygroscopic nature of the SrI2. Single crystal scintillating screens exhibit high spatial resolution, this combined with the high density, high effective atomic number, and the high light yield of the SrI2 could be used for high resolution X-ray imaging. Some of the questions we tried to answer in this work are the following: owing to the excellent performance of the SrI2-scintillator in spectroscopic applications, how would it perform in X-ray imaging applications. X-ray images are described based on their (spatial) resolution and contrast, how would they look like when recorded using the SrI2-scintillator detector. First a packaging technique was developed that protected the hygroscopic screens during the measurements. Our results show a high resolution of the images obtained with thin SrI2-scintillator screens both in 2D radiography and 3D tomography measurements. With these results, we think that the SrI2-scinitillator is not only a candidate for spectroscopic applications, but also for high resolution X-ray imaging purposes.
Vogelgesang M., Chilingaryan S., Rolo T.D.S., Kopmann A.
in Proceedings of the 14th IEEE International Conference on High Performance Computing and Communications, HPCC-2012 – 9th IEEE International Conference on Embedded Software and Systems, ICESS-2012 (2012) 824-829, 6332254. DOI:10.1109/HPCC.2012.116
Current synchrotron experiments require state-of-the-art scientific cameras with sensors that provide several million pixels, each at a dynamic range of up to 16 bits and the ability to acquire hundreds of frames per second. The resulting data bandwidth of such a data stream reaches several Gigabits per second. These streams have to be processed in real-time to achieve a fast process response. In this paper we present a computation framework and middleware library that provides re-usable building blocks to implement high-performance image processing algorithms without requiring profound hardware knowledge. It is based on a graph structure of computation nodes that process image transformation kernels on either CPU or GPU using the OpenCL sub-system. This system architecture allows deployment of the framework on a large range of computational hardware, from netbooks to hybrid compute clusters. We evaluated the library with standard image processing algorithms required for high quality tomographic reconstructions. The results show that speed-ups from 7x to 37x compared to traditional CPU-based solutions can be achieved with our approach, hence providing an opportunity for real-time on-line monitoring at synchrotron beam lines. © 2012 IEEE.