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Killane, Isabelle, Fearon, Conor, Newman, Louise, McDonnell, Conor, Waechter, Saskia, Sons, Kristian, Lynch, Tim and Reilly, Robert B.
Dual Motor-Cognitive Virtual Reality Training Impacts Dual-Task Performance in Freezing of Gait
Biomedical and Health Informatics, IEEE Journal of, PP(99):1-1
September 2015
ISSN: 2168-2194

Keywords: Accuracy;Biomedical measurement;Diseases;Foot;Legged locomotion;Time measurement;Training

Dahmen, Tim, Roland, Michael, Tjardes, Thorsten, Slusallek, Philipp and Diebels, Stefan
An automated workflow for the biomechanical simulation of a tibia with implant using computed tomography and the finite element method
Computers and Mathematics with Applications,
June 2015

Abstract: In this study, a fully automated workflow is presented for the biomechanical simulation of bone-implant systems using the example of a fractured tibia. The workflow is based on routinely acquired tomographic data and consists of an automatic segmentation and material assignment, followed by a mesh generation step and, finally, a mechanical simulation using the finite element method (FEM). Because of the high computational costs of the FEM simulations, an adaptive mesh refinement scheme was developed that limits the highest resolution to materials that can take large amounts of mechanical stress. The scheme was analyzed and it was shown that it has no relevant impact on the simulation precision. Thus, a fully automatic, reliable and computationally feasible method to simulate mechanical properties of bone-implant systems was presented, which can be used for numerous applications, ranging from the design of patient-specific implants to surgery preparation and post-surgery implant verification.

Turoňová, Beata, Marsalek, Lukas, Davidovic, Tomas and Slusallek, Philipp
Progressive Stochastic Reconstruction Technique (PSRT) for Cryo Electron Tomography
Journal of Structural Biology, 189(3):195-206
March 2015

Abstract: Cryo Electron Tomography (cryoET) plays an essential role in Structural Biology, as it is the only technique that allows to study the structure of large macromolecular complexes in their close to native environment in situ. The reconstruction methods currently in use, such as Weighted Back Projection (WBP) or Simultaneous Iterative Reconstruction Technique (SIRT), deliver noisy and low-contrast reconstructions, which complicates the application of high-resolution protocols, such as Subtomogram Averaging (SA). We propose a Progressive Stochastic Reconstruction Technique (PSRT) – a novel iterative approach to tomographic reconstruction in cryoET based on Monte Carlo random walks guided by Metropolis–Hastings sampling strategy. We design a progressive reconstruction scheme to suit the conditions present in cryoET and apply it successfully to reconstructions of macromolecular complexes from both synthetic and experimental datasets. We show how to integrate PSRT into SA, where it provides an elegant solution to the region-of-interest problem and delivers high-contrast reconstructions that significantly improve template-based localization without any loss of high-resolution structural information. Furthermore, the locality of SA is exploited to design an importance sampling scheme which significantly speeds up the otherwise slow Monte Carlo approach. Finally, we design a new memory efficient solution for the specimen-level interior problem of cryoET, removing all associated artifacts.

Dahmen, Tim, Kohr, Holger, de Jonge, Niels and Slusallek, Philipp
Matched Backprojection Operator for Combined Scanning Transmission Electron Microscopy Tilt- and Focal Series
Microscopy & Microanalysis,
January 2015

Abstract: Combined tilt- and focal series scanning transmission electron microscopy (STEM) is a recently developed method to obtain nanoscale three-dimensional (3D) information of thin specimens. In this study, we formulate the forward projection in this acquisition scheme as a linear operator and prove that it is a generalization of the Ray transform for parallel illumination. We analytically derive the corresponding backprojection operator as the adjoint of the forward projection. We further demonstrate that the matched backprojection operator drastically improves the convergence rate of iterative 3D reconstruction compared to the case where a backprojection based on heuristic weighting is used. In addition, we show that the 3D reconstruction is of better quality.


Leißa, Roland, Boesche, Klaas, Hack, Sebastian, Membarth, Richard and Slusallek, Philipp
Shallow Embedding of DSLs via Online Partial Evaluation
Proceedings of the 14th International Conference on Generative Programming: Concepts & Experiences (GPCE) , page 11-20.
October 2015

Keywords: shallow embedding; partial evaluation; domain-specific language

Abstract: This paper investigates shallow embedding of DSLs by means of online partial evaluation. To this end, we present a novel online partial evaluator for continuation-passing style languages. We argue that it has, in contrast to prior work, a predictable termination policy that works well in practice. We present our approach formally using a continuation-passing variant of PCF and prove its termination properties. We evaluate our technique experimentally in the field of visual and high-performance computing and show that our evaluator produces highly specialized and efficient code for CPUs as well as GPUs that matches the performance of hand-tuned expert code.

Annotation: Best Paper Award

Dahmen, Tim, Marsalek, Lukas, Marniok, Nico, Turoňová, Beata, Bogachev, Sviatoslav, Trampert, Patrick, Nickels, Stefan and Slusallek, Philipp
Ettention: building blocks for iterative reconstruction algorithms
Proceedings of Microscopy & Microanalysis 2015
August 2015

Abstract: We present a novel software package for tomographic reconstruction in electron microscopy, named Ettention. The software consists of a set of modular building-blocks for iterative reconstruction algorithms. Ettention simultaneously features (1) a modular, object-oriented software design, (2) optimized access to high-performance computing (HPC) platforms such as graphic processing units (GPU) or many-core architectures like Xeon Phi, and (3) accessibility to microscopy end-users via integration in the IMOD package and user interface. We provide developers with a clean application programming interface (API) that allows for extending the software easily and thus makes it an ideal platform for algorithmic research while hiding most of the technical details of high-performance computing. Several case studies are provided to demonstrate the feasibility of the concept.

Dahmen, Tim, Kohr, Holger, de Jonge, Niels and Slusallek, Philipp
Reconstruction Strategies for Combined Tilt- and Focal Series Scanning Transmission Electron Microscopy
Proceedings of Microscopy & Microanalysis 2015
August 2015

Abstract: The STEM transform was thus formulated as a mathematical model applicable to STEM imaging with a convergent electron beam. It was shown that it is (1) a linear convolution, (2) a generalization of the Ray transform that contains the latter as the special case where the beam convergence semi-angle α→0, and (3) self-adjoint, a result that facilitated a new iterative reconstruction algorithm for TFS based on a matched backprojection, which drastically improved the convergence rate, resulting in 60 times less iterations compared to previous methods. It also solved theoretical concerns about the convergence of the method, which was not guaranteed in the case of an unmatched projection/backprojection pair. This brings the combined tilt- and focal series one more step towards broad applicability by allowing the reconstruction of high resolution tomograms in feasible computation time.

Turoňová, Beata, Marsalek, Lukas, Davidovic, Tomas and Slusallek, Philipp
PSRT: Progressive Stochastic Reconstruction Technique for Cryo Electron Tomography
Proceedings of Microscopy & Microanalysis 2015
August 2015
Turoňová, Beata, Marsalek, Lukas, Davidovic, Tomas and Slusallek, Philipp
On a novel approach to 3D reconstruction in Cryo Electron Tomography: Progressive Stochastic Reconstruction Technique (PSRT)
14. French Microscopy Congress, Nice, France, 30.6. - 3.7.2015
July 2015

Abstract: Cryo Electron Tomography (cryoET) plays an essential role in Structural Biology, as it is the only technique that allows us to study structure of macromolecular complexes in their close to native environment in-situ. The reconstruction process faces many challenges as the input projections suffer from very low signal-to-noise ratio and limited tilt angle. Moreover, the scanned specimen is larger than the detector, which introduces the interior problem into the reconstruction process. High-resolution protocols such as Subtomogram Averaging (SA) can alleviate some of these limitations; however, in order to be fully automatic they require reconstructions of high quality. Current state-of-the-art methods, such as Weighted Back Projection (WBP) or Simultaneous Iterative Reconstruction Technique (SIRT), deliver reconstructions that often require manual intervention during SA. We present a novel iterative approach to the tomographic reconstruction problem called Progressive Stochastic Reconstruction Technique (PSRT). The method is based on Monte Carlo random walks guided by a sampling strategy similar to the Metropolis-Hastings strategy. PSRT is designed to suit the specific conditions in cryoET - it delivers high-contrast reconstructions without any loss of high-resolution structural information and it implements memory efficient solution to the interior problem. Finally, it can be easily incorporated into a typical SA pipeline, where it significantly improves template-based localization and provides an elegant solution to the region-of-interest reconstruction.

Tamm, Georg and Slusallek, Philipp
Plugin free remote visualization in the browser
Volume 9397 of Proc. SPIE
February 2015

Keywords: Visualization, Video, Computing systems, Internet, Mobile devices, Personal digital assistants, Tablets

Abstract: Today, users access information and rich media from anywhere using the web browser on their desktop computers, tablets or smartphones. But the web evolves beyond media delivery. Interactive graphics applications like visualization or gaming become feasible as browsers advance in the functionality they provide. However, to deliver large-scale visualization to thin clients like mobile devices, a dedicated server component is necessary. Ideally, the client runs directly within the browser the user is accustomed to, requiring no installation of a plugin or native application. In this paper, we present the state-of-the-art of technologies which enable plugin free remote rendering in the browser. Further, we describe a remote visualization system unifying these technologies. The system transfers rendering results to the client as images or as a video stream. We utilize the upcoming World Wide Web Consortium (W3C) conform Web Real-Time Communication (WebRTC) standard, and the Native Client (NaCl) technology built into Chrome, to deliver video with low latency.

Contributions to proceedings:

Trottnow, Jonas, Götz, Kai, Seibert, Stefan, Spielmann, Simon, Helzle, Volker, Einabadi, Farshad, Sielaff, Clemens K. H. and Grau, Oliver
Intuitive Virtual Production Tools for Set and Light Editing
Proceedings of the 12th European Conference on Visual Media Production (CVMP 2015)
Publisher: ACM,
November 2015
ISBN: 978-1-4503-3560-7/15/11
Einabadi, Farshad and Grau, Oliver
Discrete Light Source Estimation from Light Probes for Photorealistic Rendering
In Xianghua Xie, Mark W. Jones, and Gary K. L. Tam, editor, Proceedings of the British Machine Vision Conference (BMVC) , page 43.1-43.10.
Publisher: BMVA Press,
September 2015
ISBN: 1-901725-53-7
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