Steinmann J.L., Blomley E., Brosi M., Brundermann E., Caselle M., Hiller N., Kehrer B., Muller A.-S., Schedler M., Schonfeldt P., Schuh M., Schwarz M., Siegel M.

in IPAC 2016 – Proceedings of the 7th International Particle Accelerator Conference (2016) 2855-2857.

Abstract

Copyright © 2016 CC-BY-3.0 and by the respective authors. We present the effects of the filling pattern structure in multi-bunch mode on the beam spectrum. This effects can be seen by all detectors whose resolution is better than the RF frequency, ranging from stripline and Schottky measurements to high resolution synchrotron radiation measurements. Our heterodyne measurements of the emitted coherent synchrotron radiation at 270 GHz reveal discrete frequency harmonics around the 100 000th revolution harmonic of ANKA, the synchrotron radiation facility in Karlsruhe, Germany. Significant effects of bunch spacing, gaps between bunch trains and variations in individual bunch currents on the emitted CSR spectrum are described by theory and supported by observations.

Losel P., Heuveline V.

in Progress in Biomedical Optics and Imaging – Proceedings of SPIE, 9784 (2016), 97842L. DOI:10.1117/12.2216202

Abstract

© 2016 SPIE. Inspired by the diffusion of a particle, we present a novel approach for performing a semiautomatic segmentation of tomographic images in 3D, 4D or higher dimensions to meet the requirements of high-throughput measurements in a synchrotron X-ray microtomograph. Given a small number of 2D-slices with at least two manually labeled segments, one can either analytically determine the probability that an intelligently weighted random walk starting at one labeled pixel will be at a certain time at a specific position in the dataset or determine the probability approximately by performing several random walks. While the weights of a random walk take into account local information at the starting point, the random walk itself can be in any dimension. Starting a great number of random walks in each labeled pixel, a voxel in the dataset will be hit by several random walks over time. Hence, the image can be segmented by assigning each voxel to the label where the random walks most likely started from. Due to the high scalability of random walks, this approach is suitable for high throughput measurements. Additionally, we describe an interactively adjusted active contours slice by slice method considering local information, where we start with one manually labeled slice and move forward in any direction. This approach is superior with respect to accuracy towards the diffusion algorithm but inferior in the amount of tedious manual processing steps. The methods were applied on 3D and 4D datasets and evaluated by means of manually labeled images obtained in a realistic scenario with biologists.

Vogelgesang M., Rota L., Perez L.E.A., Caselle M., Chilingaryan S., Kopmann A.

in Proceedings of SPIE – The International Society for Optical Engineering, 9967 (2016), 996715. DOI:10.1117/12.2237611

Abstract

© Copyright 2016 SPIE. With ever-increasing data rates due to stronger light sources and better detectors, X-ray imaging experiments conducted at synchrotron beamlines face bandwidth and processing limitations that inhibit efficient workflows and prevent real-time operations. We propose an experiment platform comprised of programmable hardware and optimized software to lift these limitations and make beamline setups future-proof. The hardware consists of an FPGA-based data acquisition system with custom logic for data pre-processing and a PCIe data connection for transmission of currently up to 6.6 GB/s. Moreover, the accompanying firmware supports pushing data directly into GPU memory using AMD’s DirectGMA technology without crossing system memory first. The GPUs are used to pre-process projection data and reconstruct final volumetric data with OpenCL faster than possible with CPUs alone. Besides, more efficient use of resources this enables a real-time preview of a reconstruction for early quality assessment of both experiment setup and the investigated sample. The entire system is designed in a modular way and allows swapping all components, e.g. replacing our custom FPGA camera with a commercial system but keep reconstructing data with GPUs. Moreover, every component is accessible using a low-level C library or using a high-level Python interface in order to integrate these components in any legacy environment.

Vogelgesang M., Farago T., Morgeneyer T.F., Helfen L., Dos Santos Rolo T., Myagotin A., Baumbach T.

in Journal of Synchrotron Radiation, 23 (2016) 1254-1263. DOI:10.1107/S1600577516010195

Abstract

© 2016 International Union of Crystallography.Real-time processing of X-ray image data acquired at synchrotron radiation facilities allows for smart high-speed experiments. This includes workflows covering parameterized and image-based feedback-driven control up to the final storage of raw and processed data. Nevertheless, there is presently no system that supports an efficient construction of such experiment workflows in a scalable way. Thus, here an architecture based on a high-level control system that manages low-level data acquisition, data processing and device changes is described. This system is suitable for routine as well as prototypical experiments, and provides specialized building blocks to conduct four-dimensional in situ, in vivo and operando tomography and laminography.

Karpov D., Dos Santos Rolo T., Rich H., Kryuchkov Y., Kiefer B., Fohtung E.

in Proceedings of SPIE – The International Society for Optical Engineering, 9931 (2016), 99312F. DOI:10.1117/12.2235865

Abstract

© 2016 SPIE. Directional dependence of the index of refraction contains a wealth of information about anisotropic optical properties in semiconducting and insulating materials. Here we present a novel high-resolution lens-less technique that uses birefringence as a contrast mechanism to map the index of refraction and dielectric permittivity in optically anisotropic materials. We applied this approach successfully to a liquid crystal polymer film using polarized light from helium neon laser. This approach is scalable to imaging with diffraction-limited resolution, a prospect rapidly becoming a reality in view of emergent brilliant X-ray sources. Applications of this novel imaging technique are in disruptive technologies, including novel electronic devices, in which both charge and spin carry information as in multiferroic materials and photonic materials such as light modulators and optical storage.

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

Abstract

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.

Rota L., Caselle M., Chilingaryan S., Kopmann A., Weber M.

in IEEE Transactions on Nuclear Science, 62 (2015) 972-976, 7111377. DOI:10.1109/TNS.2015.2426877

Abstract

© 2014 IEEE. We developed a direct memory access (DMA) engine compatible with the Xilinx PCI Express (PCIe) core to provide a high-performance and low-occupancy alternative to commercial solutions. In order to maximize the PCIe throughput while minimizing the FPGA resources utilization, the DMA engine adopts a novel strategy where the DMA address list is stored inside the FPGA and not in the central memory of the host CPU. The FPGA design package is complemented with simple register access to control the DMA engine by a Linux driver. The design is compatible with Xilinx FPGA Families 6 and 7, and operates with the Xilinx PCIe endpoint Generation 1 and 2 with all lane configurations (x1, x2, x4, x8). A multi-engine architecture is also presented, where two x8 lanes cores are used in parallel together with a PCIe bridge, to exploit fully the capabilities of a PCIe Gen2 x16 lanes link. A data throughput of 3461 MBytes/s has been achieved with a single PCIe Gen2 x8 lanes endpoint. If the dual-engine architecture is used, the throughput is increased up to 6920 MBytes/s. The presented DMA is currently used in several experiments at the ANKA synchrotron light source.

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

Abstract

© 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.

Rota L., Caselle M., Chilingaryan S., Kopmann A., Weber M.

in IEEE Transactions on Nuclear Science, 62 (2015) 972-976, 7111377. DOI:10.1109/TNS.2015.2426877

Abstract

© 2014 IEEE.We developed a direct memory access (DMA) engine compatible with the Xilinx PCI Express (PCIe) core to provide a high-performance and low-occupancy alternative to commercial solutions. In order to maximize the PCIe throughput while minimizing the FPGA resources utilization, the DMA engine adopts a novel strategy where the DMA address list is stored inside the FPGA and not in the central memory of the host CPU. The FPGA design package is complemented with simple register access to control the DMA engine by a Linux driver. The design is compatible with Xilinx FPGA Families 6 and 7, and operates with the Xilinx PCIe endpoint Generation 1 and 2 with all lane configurations (x1, x2, x4, x8). A multi-engine architecture is also presented, where two x8 lanes cores are used in parallel together with a PCIe bridge, to exploit fully the capabilities of a PCIe Gen2 x16 lanes link. A data throughput of 3461 MBytes/s has been achieved with a single PCIe Gen2 x8 lanes endpoint. If the dual-engine architecture is used, the throughput is increased up to 6920 MBytes/s. The presented DMA is currently used in several experiments at the ANKA synchrotron light source.