UFO

UFO – Ultra-fast X-ray Imaging of Scientific Processes with On-line Assessment and Data-driven Process Control

Progress in recent years concerning X-ray optics, detector technology, and the tremendous increase of processing speed of commodity computational architectures gives rise to a paradigm shift in synchrotron X-ray imaging. The UFO/UFOII projects aim to enable a new type of smart experiment using the vast computational power of massively parallel computation units: On-line assessment of sample dynamics will enable active image-based control, allow an unprecedented image quality, and will provide insight into so far inaccessible scientific processes.

A major scientific application for UFO technology is fast X-ray imaging of arthropods. In the scope of the project we developed in vivo X-ray cine-tomography, which enables real-time 4D visualization of fast-moving insect joints.

 

 

Digital reconstruction of a 30-million-year old hister beetle. (A) Photograph of the fossil ventrally embedded in a stony matrix. (B) Digital reconstruction showing fossilized beetle (green) and matrix (brown). (C) Beetle digitally isolated from the stone, revealing well-preserved morphology hidden by the matrix. (D) Perspective view of the fossil showing parts of exoskeleton, tracheal network, alimentary canal and genitals. From: Schwermann, A.H., dos Santos Rolo, T., Caterino, M.S., Bechly, G., Schmied, H., Baumbach, T. & van de Kamp, T., “Preservation of three-dimensional anatomy in phosphatized fossil arthropods enriches evolutionary inference”, eLife 5 (2016) e12129.

Link to project homepage

Publications
  1. H. Anzt, A. Beglarian, S. Chilingaryan, A. Ferrone, V. Heuviline, A. Kopmann, “A unified energy foot-print for simulation software,” Comput. Sci. Res. Dev., DOI 10.1007/s00450-012-0225-1 (2012).
  2. P.-A. Douissard, A. Cecilia, X. Rochet, X. Chapel, T. van de Kamp, L. Helfen, T. Baumbach, L. Luquot, X. Xiao, J. Meinhardt, A. Rack, “A versatile indirect detector design for hard X-ray microimag-ing”, Journal of Instrumentation 7 (2012) P0901.
  3. Myagotin, A. Voropaev, L. Helfen, D. Hanschke, T. Baumbach, “Fast volume reconstruction for parallel-beam computed laminography by filtered backprojection”, International Journal of Materials Research, issue 02 (2012) 170-173.
  4. Riedel, T. dos Santos Rolo, A. Cecilia, T. van de Kamp, “Sayrevilleinae Legalov, a new subfamily of fossil weevils (Coleoptera, Curculionoidea, Attelabidae) and the use of synchrotron microtomography to examine inclusions in amber”, Zoological Journal of the Linnean Society 165 (2012) 773-794.
  5. M. Vogelgesang, S. Chilingaryan, T. dos Santos Rolo, A. Kopmann, “UFO: A Scalable GPU-based Image Processing Framework for On-line Monitoring,” Proceedings of HPCC-ICESS (2012) 824-829.
  6. D. Haas, W. Mexner, T. Spangenberg, A. Cecilia, P. Vagovic, A. Kopmann, M. Balzer, M. Vogelge-sang, H. Pasic, S. Chilingaryan, “Status of the ultra fast tomography experiments control at ANKA”, Proceedings of PCaPAC2012, Kolkata, India, December 04–07, 2012. ISBN 978-3-95450-124-3 (2012) 103-105.
  7. M. Caselle, S. Chilingaryan, A. Herth, A. Kopmann, U. Stevanovic, M. Vogelgesang, M. Balzer, M. Weber, “Ultra-fast streaming camera platform for scientific applications”, IEEE TNS Vol. 60 [5] (2013) 3669-3677.
  8. Myagotin, A. Voropaev, L. Helfen, D. Hanschke, T. Baumbach, “Efficient Volume Reconstruction for Parallel-Beam Computed Laminography by Filtered Backprojection on Multi-Core Clusters”, IEEE Transactions on Image Processing, v. 22, iss. 12 (2013) 5348-5361.
  9. T. dos Santos Rolo, A. Ershov, T. van de Kamp, T. Baumbach, “In vivo X-ray cine-tomography for tracking morphological dynamics”, PNAS 111 [11] (2014) 3921-3926.
  10. P. Vršanský, T. van de Kamp, D. Azar, A. Prokin, L. Vidličkag, P. Vagovič, “Cockroaches likely cleaned up after dinosaurs”, PLOS ONE 8 [11] (2013) e80560.
  11. T. van de Kamp, A. Ershov, T. dos Santos Rolo, A. Riedel, T. Baumbach, “Insect imaging at the ANKA Synchrotron Radiation Facility”, Entomologie heute 25, (2013) 147-160.
  12. Butcher, A. Zaldivar-Riverón, T. van de Kamp, T. dos Santos Rolo, T. Baumbach, D.L.J. Quicke, “Extension of historical range of Betylobraconinae (Hymenoptera: Braconidae) into Palaearctic Region based on a Baltic amber fossil, and description of a new species of Mesocentrus Szépligeti from Pa-pua New Guinea”, Zootaxa 3860 [5] (2014) 449-463.
  13. T. dos Santos Rolo, A. Ershov, T. van de Kamp, T. Baumbach, “In vivo X-ray cine-tomography for tracking morphological dynamics”, PNAS 111 [11] (2014) 3921-3926.
  14. T. van de Kamp, T. dos Santos Rolo, T. Baumbach, L. Krogmann, “Scanning the past – synchrotron X-ray microtomography of fossil wasps in amber”, Entomologie heute 26 (2014) 151-160.
  15. T. van de Kamp, T. dos Santos Rolo, P. Vagovič, T. Baumbach, A. Riedel, “Three-dimensional recon-structions come to life – interactive 3D PDF animations in functional morphology”, PLOS ONE 9 [7] (2014) e102355.
  16. L. Rota, M. Caselle, S. Chilingaryan, A. Kopmann, M. Weber, “A PCIe DMA Architecture for multi-Gigabyte per Second Data Transmission”, Nuclear Science, IEEE Transactions on 62 [3] (2015) 972-976.
  17. U. Stevanovic, M. Caselle, A. Cecilia, S. Chilingaryan, T. Farago, S. Gasilov, A. Herth, A. Kopmann, M. Vogelgesang, M. Balzer, T. Baumbach, M. Weber, “A control system and streaming DAQ platform with image-based trigger for X-ray imaging”, IEEE Transactions on Nuclear Science, 62 [3] (2015) art. no. 7111386, 911-918.
  18. S. Chilingaryan, A.Shkarin, R. Shkarin, M. Vogelgesang, S. Tsapko, “Benchmark for FFT Libraries”, Applied Mechanics and Materials 756 (2015) 673-677.
  19. Shkarin, E. Ametova, A. Kopmann, S. Chilingaryan, R. Shkarin, S. Tsapko, T. Dritschler, M. Vo-gelgesang, “An Open Source GPU Accelerated Framework for Flexible Algebraic Reconstruction at Synchrotron Light Sources”, Fundamenta Informaticae 141 [2-3] (2015) 259-274.
  20. R. Shkarin, E. Ametova, S. Chilingaryan, T. Dritschler, A. Kopmann, A. Mirone, A. Shkarin, S. Tsapko, M. Vogelgesang, “GPU-optimized direct fourier method for on-line tomography”, Fundamenta Infor-maticae 141 [2-3] (2015) 245–258
  21. T. van de Kamp, A. Cecilia, T. dos Santos Rolo, P. Vagovič, T. Baumbach, A. Riedel, “Comparative thorax morphology of death-feigning flightless cryptorhynchine weevils (Coleoptera: Curculionidae) based on 3D reconstructions”, Arthropod Structure & Development 44 (2015) 509-523.
  22. T. van de Kamp, T. dos Santos Rolo, T. Baumbach, H. Greven, “X-ray radiography of a spraying stick insect (Phasmatodea)”, Entomologie heute 27 (2015) 37-44.
  23. T. van de Kamp, M. Dörstelmann, T. dos Santos Rolo, T. Baumbach, A. Menges, J. Knippers, “Beetle elytra as role models for lightweight building construction”, Entomologie heute 27 (2015) 149-158.
  24. H. Greven, T. van de Kamp, T. dos Santos Rolo, T. Baumbach, G. Clemen, “The “tooth systems” of Lissotriton vulgaris (Amphibia: Urodela) with special regard to delayed metamorphosis”, Vertebrate Zoology 65 (2015) 81-99
  25. X. Yang, R. Hofmann, R. Dapp, T. van de Kamp, T. dos Santos Rolo, X. Xiao, J. Moosmann, J. Ka-shef, T. Baumbach, R. Stotzka, “TV-based conjugate gradient method and discrete L-curve for few-view CT reconstruction of X-ray in vivo data”, Optics Express 23 [5] (2015) 5368-5387.
  26. S. Hahn, Y. Müller, R. Hofmann, J. Moosmann, O. Öktem, L. Helfen, J.-P. Guigay, T. van de Kamp, T. Baumbach, “Spectral transfer from phase to intensity in Fresnel diffraction”, Physical Review A 93 (2016) 053834.
  27. D.-Y. Huang, G. Bechly, P. Nel, M.S. Engel, J. Prokop, D. Azar, C.-Y. Cai, T. van de Kamp, A.H. Stan-iczek, R. Garrouste, L. Krogmann, T. dos Santos Rolo, T. Baumbach, R. Ohlhoff, A.S. Shmakov, T. Bourgoin, A. Nel, “New fossil insect order Permopsocida elucidates major radiation and evolution of suction feeding in hemimetabolous insects (Hexapoda: Acercaria)”, Scientific Reports 6 (2016) 23004.
  28. S. Mangold, T. van de Kamp, R. Steininger, “New data evaluation procedure including advanced background subtraction for radiography using the example of insect mandibles”, Journal of Physics: Conference Series 712 [1] (2016) 012141.
  29. L. Rota, M. Vogelgesang, L.E. Ardila Perez, M. Caselle, S. Chilingaryan, T. Dritschler, N. Zilio, A. Kopmann, M. Balzer, M. Weber, “A high-throughput readout architecture based on PCI-Express Gen3 and DirectGMA technology”, Journal of Instrumentation 11.02 (2016) P02007.
  30. A.H. Schwermann, T. dos Santos Rolo, M.S. Caterino, G. Bechly, H. Schmied, T. Baumbach, T. van de Kamp, “Preservation of three-dimensional anatomy in phosphatized fossil arthropods enriches evo-lutionary inference”, eLife 5 (2016) e12129.
  31. A.H. Schwermann, M. Wuttke, T. dos Santos Rolo, M.S. Caterino, G. Bechly, H. Schmied, T. Baumbach, T. van de Kamp, “The fossil insects of the Quercy region: a historical review”, Entomologie heute 28 T. (2016) 127-142.
  32. M. Vogelgesang, T. Farago, T.F. Morgeneyer, L. Helfen, T. Dos Santos Rolo, A. Myagotin, T. Baumbach, “Real-time image-content-based beamline control for smart 4D X-ray imaging”, Journal of Synchrotron Radiation 23 (2016) 1254-1263.
  33. M. Vogelgesang, L. Rota, L.E. Ardila Perez, M. Caselle, S. Chilingaryan, A. Kopmann, “High-throughput data acquisition and processing for real-time x-ray imaging”, Proc. of SPIE Vol. 9967 (2016) 996715-8.
  34. T. Bergmann, M. Balzer, T. Hopp, T. van de Kamp, A. Kopmann, N. Tan Jerome, M. Zapf, “Inspiration from VR gaming technology: deep immersion and realistic interaction for scientific visualization”, Proc. of the 12th Int. Joint Conf. on Computer Vision, Imaging and Computer Graphics Theory and Applica-tions, VISIGRAPP 2017 (2017) 330-334.
  35. H. Greven, T. van de Kamp, T. dos Santos Rolo, T. Baumbach, G. Clemen, „Vomeropterygopalatina in larval Ichthyosaura alpestris apuanus (Amphibia: Urodela) and comments on the formation of the definite vomer in the Salamandridae”, Vertebr Zool 67 (2017) 179-196.
  36. S. Lautner, C. Lenz, J. Hammel, J. Moosmann, M. Kühn, M. Caselle, M. Vogelgesang, A. Kopmann, F. Beckmann, “Using SRμCT to define water transport capacity in Picea abies”, Proc. SPIE 10391, Developments in X-Ray Tomography XI (2017) 1039118.
  37. W. Mexner, M. Bonn, A. Kopmann, V. Mauch, D. Ressmann, S. Chilingaryan, N. Tan Jerome, T. van de Kamp, V. Heuveline, P. Lösel, S. Schmelzle, M. Heethoff, “OpenGL API based analysis of large datasets in a cloud environment”, In: Das K, Deka GC (Eds.), “Design and Use of Virtualization Tech-nology in Cloud Computing”, IGI Global, Hershey (2017) 161-181.
  38. O.D. Onelli, T. van de Kamp, J.N. Skepper, J. Powell, T. dos Santos Rolo, T. Baumbach, S. Vignolini, „Development of structural colour in leaf beetles”, Sci Rep 7 (2017) 1373.
  39. S. Schmelzle, M. Heethoff, V. Heuveline, P. Lösel, J. Becker, F. Beckmann, F. Schluenzen, J.U. Hammel, A. Kopmann, W. Mexner, M. Vogelgesang, N. Tan Jerome, O. Betz, R. Beutel, B. Wipfler, A. Blanke, S. Harzsch, M. Hörnig, T. Baumbach, T. van de Kamp, “The NOVA project – maximizing beam time efficiency through synergistic analyses of SRμCT data”, Proc. SPIE 10391, Developments in X-Ray Tomography XI (2017) 103910P
  40. N. Tan Jerome, Chilingaryan S, Kopmann A, Shkarin A, Zapf M, Lizin A, Bergmann T (2017). “WAVE: A 3D Online Previewing Framework for Big Data Archives”, Proc. of the 12th Int. Joint Conf. on Com-puter Vision, Imaging and Computer Graphics Theory and Applications, VISIGRAPP 2017 (2017) 152-163.
  41. N.C. Wulff, T. van de Kamp, T. dos Santos Rolo, T. Baumbach, G.U.C. Lehmann, “Copulatory court-ship by internal genitalia in bushcrickets”, Sci Rep 7 (2017) 42345.
  42. T. Faragó, P. Mikulik, A. Ershov, M. Vogelgesang, D. Haenschke, T. Baumbach, “syris: a flexible and efficient framework for X-ray imaging experiments simulation”, Journal of synchrotron radiation, 24 [6] (2017) 1283-1295
  43. Kopmann, S. Chilingaryan, M. Vogelgesang, T. Dritschler, A. Shkarin, R. Shkarin, T. Dos Santos Rolo, T. Farago, T. van de Kamp, M. Balzer, M. Caselle, M. Weber, T. Baumbach, „UFO – A scalable platform for high-speed synchrotron X-ray imaging”, 2016 IEEE Nucl. Sci. Symp., MIC/RTSD (2017) January, 8069895.
  44. P. Kaever, M. Balzer, A. Kopmann, H. Rongen, M. Zimmer, „The Common Data Acquisition Platform in the Helmholtz Association”, Journal of Instrumentation 12 (2017) C04004
  45. T. van de Kamp, A. H. Schwermann, T. dos Santos Rolo, P. D. Lösel, T. Engler, W. Etter, T. Faragó, J. Göttlicher, V. Heuveline, A. Kopmann, B. Mähler, T. Mörs, J. Odar, J. Rust, N. Tan Jerome, M. Vo-gelgesang, T. Baumbach, L. Krogmann, „Parasitoid biology preserved in mineralized fossils“, Nature communications 9 [1] (2018) 3325
  46. N. Tan Jerome, Z. Ateyev, S. Schmelzle, S. Chilingaryan, A. Kopmann, “Real-time Local Noise Filter in 3D Visualization of CT Data”, arXiv preprint arXiv:1807.03119 (2018)
  47. Mikó, T. van de Kamp, C. Trietsch, J. Ulmer, M. Zuber, T. Baumbach, A. D. Deans, “A new megaspilid wasp from Eocene Baltic amber (Hymenoptera: Ceraphronoidea), with notes on two non-ceraphronoid families: Radiophronidae and Stigmaphronidae”. PeerJ 6 (2018) e5174.
  48. Mikó, C. Trietsch, T. van de Kamp, L. Masner, J. Ulmer, M. Zuber, E. L. Sandall, T. Baumbach, A. R. Deans, “Revision of Trassedia (Hymenoptera: Ceraphronidae), an evolutionary relict with an unusual distribution”. Insect Systematics and Diversity 2 (2018) 1-29.
  49. A.V. Buzmakov, V.E. Asadchikov, D.A. Zolotov, B.S. Roshchin, Y.M. Dymshits, V.A. Shishkov, M.V. Chukalina, A.S. Ingacheva, D.E. Ichalova, Y.S. Krivonosov, I.G. Dyachkova, M. Balzer, M. Caselle, S. Chilingaryan, A. Kopmann, “Laboratory Microtomographs: Design and Data Processing Algorithms”, Crystallography Reports 63 [6] (2018) 1057-1061
  50. Mikó, S. R. Rahman, S. Anzaldo, T. van de Kamp, B. A. Parslow, M. T. Wetherington, J. Anderson, R.J. Schilder, J. M. Ulmer, A. R. Deans, H. M. Hines, “Fat in the leg: function of the expanded hind leg in gasteruptiid wasps”, Insect Systematics and Diversity, Volume 3, Issue 1, 2019