Scientific motivation

X-rays and tomography provide the opportunity to visualize internal structures of optically dense materials in 3D. The invention of synchrotron-X-ray-microtomography was the onset of a new era of morphological research on microscopically small animals. Analyzing such 3D-data is time consuming and technically challenging. Especially the automation of classification processes needs close cooperation of biologists and image processing experts.



Fast synchrotron X-ray microtomography. A: Experimental setup for ultrafast X-ray microtomography showing bending magnet (1), rotation stage (2), specimen (3) and detector system (4). X-rays travelling from left to right pass through the sample mounted on a rotary stage with two translational degrees of freedom. A detector converts X-rays to visible light that is subsequently recorded by a camera. B: volume rendering of a newt larva. C: Radiograph of the same sample. D - F: Slices of the reconstructed volume.


Right now, a new high-speed-tomography setup (UFO) is built at the ANKA synchrotron in Karlsruhe (KIT) [UFO1]. This setup will enable unrivaled opportunities of high-throughput measurements and 3D/4D-tomographic imaging of dynamic systems and living organisms. However, this setup results in such large amounts of data that technical limitations will be reached regarding data acquisition, storage, organization and analyses. Therefore, users will no longer be able to process the resulting data at their home institutions, even with highly equipped computers. Hence, a strong integration of knowledge from biology, image processing and data management is needed to enable this new and fascinating high-speed-option for regular users in the future. We aim to establish and standardize measuring parameters for the UFO setup to meet the needs of a broad range of biological research. This will be achieved by optimizing data acquisition and processing, semi-automation of data analysis (reconstruction and segmentation/classification) and the creation of an online-portal providing easy access, stereoscopic visualization and semi-automatic analyses of the data using cloud technologies.



Data sets typical consist of 20-50 3D tomograms with 10-50 GB each. Metadata will be retrieved from the ANKA user management system and the beamline control system.


[UFO1]     Vogelgesang, M.; Chilingaryan, S.; Kopmann, A. & others UFO: A Scalable GPU-based Image Processing Framework for On-line Monitoring High Performance, Computing and Communication 2012, IEEE 9th International Conference on Embedded Software and Systems (HPCC-ICESS), 2012, 824-829



KIT, IPS: Thomas van de Kamp, Tomy dos Santos Rolo

KIT, IPE: Andreas Kopmann

Copyright by SWM, KIT – Universität des Landes Baden-Württemberg und nationales Forschungszentrum in der Helmholtz-Gemeinschaft
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