Publications of the computing group for ultrafast imaging
Balancing Load of GPU Subsystems to Accelerate Image Reconstruction in Parallel Beam Tomography
Chilingaryan S., Ametova E., Kopmann A., Mirone A.
in Proceedings – 2018 30th International Symposium on Computer Architecture and High Performance Computing, SBAC-PAD 2018 (2019) 158-166, 8645862. DOI:10.1109/CAHPC.2018.8645862
© 2018 IEEE.Synchrotron X-ray imaging is a powerful method to investigate internal structures down to the micro and nanoscopic scale. Fast cameras recording thousands of frames per second allow time-resolved studies with a high temporal resolution. Fast image reconstruction is essential to provide the synchrotron instrumentation with the imaging information required to track and control the process under study. Traditionally Filtered Back Projection algorithm is used for tomographic reconstruction. In this article, we discuss how to implement the algorithm on nowadays GPGPU architectures efficiently. The key is to achieve balanced utilization of available GPU subsystems. We present two highly optimized algorithms to perform back projection on parallel hardware. One is relying on the texture engine to perform reconstruction, while another one utilizes the Core computational units of the GPU. Both methods outperform current state-of-the-art techniques found in the standard reconstructions codes significantly. Finally, we propose a hybrid approach combining both algorithms to better balance load between G PU subsystems. It further boosts the performance by about 30 % on NVIDIA Pascal micro-architecture.
Reviewing GPU architectures to build efficient back projection for parallel geometries
Chilingaryan S., Ametova E., Kopmann A., Mirone A.
in Journal of Real-Time Image Processing (2019). DOI:10.1007/s11554-019-00883-w
© 2019, The Author(s).Back-Projection is the major algorithm in Computed Tomography to reconstruct images from a set of recorded projections. It is used for both fast analytical methods and high-quality iterative techniques. X-ray imaging facilities rely on Back-Projection to reconstruct internal structures in material samples and living organisms with high spatial and temporal resolution. Fast image reconstruction is also essential to track and control processes under study in real-time. In this article, we present efficient implementations of the Back-Projection algorithm for parallel hardware. We survey a range of parallel architectures presented by the major hardware vendors during the last 10 years. Similarities and differences between these architectures are analyzed and we highlight how specific features can be used to enhance the reconstruction performance. In particular, we build a performance model to find hardware hotspots and propose several optimizations to balance the load between texture engine, computational and special function units, as well as different types of memory maximizing the utilization of all GPU subsystems in parallel. We further show that targeting architecture-specific features allows one to boost the performance 2–7 times compared to the current state-of-the-art algorithms used in standard reconstructions codes. The suggested load-balancing approach is not limited to the back-projection but can be used as a general optimization strategy for implementing parallel algorithms.
Ultrafast linear array detector for real-time imaging
Caselle M., Rota L., Kopmann A., Chilingaryan S.A., Mahaveer Patil M., Wang W., Brundermann E., Funkner S., Nasse M., Niehues G., Norbert Balzer M., Weber M., Muller A.S., Bielawski S.
in Proceedings of SPIE – The International Society for Optical Engineering, 10937 (2019), 1093704. DOI:10.1117/12.2508451
© 2019 SPIE.KALYPSO is a novel detector operating at line rates above 10 Mfps. It consists of a detector board connected to FPGA based readout card for real time data processing. The detector board holds a Si or InGaAs linear array sensor, with spectral sensitivity ranging from 400 nm to 2600 nm, which is connected to a custom made front-end ASIC. A FPGA readout framework performs the real time data processing. In this contribution, we present the detector system, the readout electronics and the heterogeneous infrastructure for machine learning processing. The detector is currently in use at several synchrotron facilities for beam diagnostics as well as for single-pulse laser characterizations. Thanks to the shot-to-shot capability over long time scale, new attractive applications are open up for imaging in biological and medical research.
Ultra-fast detector for wide range spectral measurements
Caselle M., Brundermann E., Dusterer S., Funkner S., Gerth C., Haack D., Kopmann A., Patil M.M., Makowski D., Mielczarek A., Nasse M., Niehues G., Rota L., Steffen B., Wang W., Balzer M.N., Weber M., Muller A.S., Bielawski S.
in Proceedings of SPIE – The International Society for Optical Engineering, 10903 (2019), 1090306. DOI:10.1117/12.2511341
© COPYRIGHT SPIE. Downloading of the abstract is permitted for personal use only.KALYPSO is a novel detector operating at line rates above 10 Mfps. The detector board holds a silicon or InGaAs linear array sensor with spectral sensitivity ranging from 400 nm to 2600 nm. The sensor is connected to a cutting-edge, custom designed, ASIC readout chip, which is responsible for the remarkable frame rate. The FPGA readout architecture enables continuous data acquisition and processing in real time. This detector is currently employed in many synchrotron facilities for beam diagnostics and for the characterization of self-built Ytterbium-doped fiber laser emitting around 1050 nm with a bandwidth of 40 nm.
Parasitoid biology preserved in mineralized fossils
van de Kamp T., Schwermann A.H., dos Santos Rolo T., Losel P.D., Engler T., Etter W., Farago T., Gottlicher J., Heuveline V., Kopmann A., Mahler B., Mors T., Odar J., Rust J., Tan Jerome N., Vogelgesang M., Baumbach T., Krogmann L.
in Nature Communications, 9 (2018), 3325. DOI:10.1038/s41467-018-05654-y
© 2018, The Author(s). About 50% of all animal species are considered parasites. The linkage of species diversity to a parasitic lifestyle is especially evident in the insect order Hymenoptera. However, fossil evidence for host–parasitoid interactions is extremely rare, rendering hypotheses on the evolution of parasitism assumptive. Here, using high-throughput synchrotron X-ray microtomography, we examine 1510 phosphatized fly pupae from the Paleogene of France and identify 55 parasitation events by four wasp species, providing morphological and ecological data. All species developed as solitary endoparasitoids inside their hosts and exhibit different morphological adaptations for exploiting the same hosts in one habitat. Our results allow systematic and ecological placement of four distinct endoparasitoids in the Paleogene and highlight the need to investigate ecological data preserved in the fossil record.
Laboratory Microtomographs: Design and Data Processing Algorithms
Buzmakov A.V., Asadchikov V.E., Zolotov D.A., Roshchin B.S., Dymshits Y.M., Shishkov V.A., Chukalina M.V., Ingacheva A.S., Ichalova D.E., Krivonosov Y.S., Dyachkova I.G., Balzer M., Castele M., Chilingaryan S., Kopmann A.
in Crystallography Reports, 63 (2018) 1057-1061. DOI:10.1134/S106377451806007X
© 2018, Pleiades Publishing, Inc. Abstract: The design of a new automatic X-ray microtomograph is described. The parameters of optical schemes and X-ray detectors in use are presented. Methods for automating experiments, processing tomographic data, and getting access to them are reported.
A computationally inexpensive model for estimating dimensional measurement uncertainty due to x-ray computed tomography instrument misalignments
Ametova E., Ferrucci M., Chilingaryan S., Dewulf W.
in Measurement Science and Technology, 29 (2018), 065007. DOI:10.1088/1361-6501/aab1a1
© 2018 IOP Publishing Ltd. The recent emergence of advanced manufacturing techniques such as additive manufacturing and an increased demand on the integrity of components have motivated research on the application of x-ray computed tomography (CT) for dimensional quality control. While CT has shown significant empirical potential for this purpose, there is a need for metrological research to accelerate the acceptance of CT as a measuring instrument. The accuracy in CT-based measurements is vulnerable to the instrument geometrical configuration during data acquisition, namely the relative position and orientation of x-ray source, rotation stage, and detector. Consistency between the actual instrument geometry and the corresponding parameters used in the reconstruction algorithm is critical. Currently available procedures provide users with only estimates of geometrical parameters. Quantification and propagation of uncertainty in the measured geometrical parameters must be considered to provide a complete uncertainty analysis and to establish confidence intervals for CT dimensional measurements. In this paper, we propose a computationally inexpensive model to approximate the influence of errors in CT geometrical parameters on dimensional measurement results. We use surface points extracted from a computer-aided design (CAD) model to model discrepancies in the radiographic image coordinates assigned to the projected edges between an aligned system and a system with misalignments. The efficacy of the proposed method was confirmed on simulated and experimental data in the presence of various geometrical uncertainty contributors.
Investigation of the flow structure in thin polymer films using 3D µPTV enhanced by GPU
Cavadini P., Weinhold H., Tonsmann M., Chilingaryan S., Kopmann A., Lewkowicz A., Miao C., Scharfer P., Schabel W.
in Experiments in Fluids, 59 (2018), 61. DOI:10.1007/s00348-017-2482-z
© 2018, Springer-Verlag GmbH Germany, part of Springer Nature. To understand the effects of inhomogeneous drying on the quality of polymer coatings, an experimental setup to resolve the occurring flow field throughout the drying film has been developed. Deconvolution microscopy is used to analyze the flow field in 3D and time. Since the dimension of the spatial component in the direction of the line-of-sight is limited compared to the lateral components, a multi-focal approach is used. Here, the beam of light is equally distributed on up to five cameras using cubic beam splitters. Adding a meniscus lens between each pair of camera and beam splitter and setting different distances between each camera and its meniscus lens creates multi-focality and allows one to increase the depth of the observed volume. Resolving the spatial component in the line-of-sight direction is based on analyzing the point spread function. The analysis of the PSF is computational expensive and introduces a high complexity compared to traditional particle image velocimetry approaches. A new algorithm tailored to the parallel computing architecture of recent graphics processing units has been developed. The algorithm is able to process typical images in less than a second and has further potential to realize online analysis in the future. As a prove of principle, the flow fields occurring in thin polymer solutions drying at ambient conditions and at boundary conditions that force inhomogeneous drying are presented.
Digital visual exploration library
Jerome N.T., Kopmann A.
in VISIGRAPP 2018 – Proceedings of the 13th International Joint Conference on Computer Vision, Imaging and Computer Graphics Theory and Applications, 3 (2018) 341-348.
© 2018 by SCITEPRESS – Science and Technology Publications, Lda. All rights reserved. With the advancement of instrument precision, research facilities are generating data at an unprecedented rate. These experimental results are stored in a digital library platform which the contents are later accessible from within the facility or the public. However, the sheer volume of collected data is overwhelming the capacity of researchers and impedes the process of browsing for the desired data. In this paper, we present a concept of Digital Visual Exploration Library (DVEL) based on the confluence of two major research domains-digital library and visualisation-that enables efficient browsing of the growing data within a digital library. We complement the current state-of-the-art textual metadata description by integrating visual exploration to address big complex data, i.e., data of large size, multimodal data and multivariate data. We describe our concept based on use cases from three unique domains: climate research with Doppler wind lidar, X-ray-imaging for entomology research, and medical imaging with ultrasound computer tomography.
Software-based compensation of instrument misalignments for X-ray computed tomography dimensional metrology
Ametova E., Ferrucci M., Chilingaryan S., Dewulf W.
in Precision Engineering (2018). DOI:10.1016/j.precisioneng.2018.05.016
© 2018 Elsevier Inc. X-ray computed tomography (CT) is an imaging technique that allows the reconstruction of an imaged part in the form of a three-dimensional attenuation map. The CT data acquisition process consists of acquiring X-ray transmission images from multiple perspectives. Analysis of the reconstructed attenuation map can provide dimensional and material information about the measured part(s). Therefore, CT is recognized as a solution for quality control tasks, for example dimensional inspection of complex objects with intricate inner geometries. CT measurements can suffer from various sources of error in the measurement procedure. One such influence is the geometrical alignment of the CT instrument components. Typical tomographic reconstruction algorithms impose strict requirements on the relative position and orientation of the three main components: X-ray source, rotation axis of the sample stage, and X-ray detector. Any discrepancy in the actual CT geometry from the geometry assumed by the reconstruction algorithm will contribute to errors in measurements performed on the reconstructed data. There is currently no standardized or easily implementable method for users to compensate geometrical misalignments of the CT instrument. In many cases, the procedure of mechanical adjustment of CT instrument is time consuming and impractical. In this paper, we show that software-based compensation of deviations in CT instrument geometry is an effective alternative to mechanical adjustment of CT instrument. Through computer simulations, we compare qualitatively and quantitatively two methods to compensate CT instrument misalignment: radiographic re-binning (interpolation) and a modified conventional reconstruction algorithm with embedded misalignment compensation.