Weier, Martin, Stengel, Michael, Roth, Thorsten, Didyk, Piotr, Eisemann, Elmar, Eisemann, Martin, Grogorick, Steve, Hinkenjann, André, Krujiff, Ernst, Magnor, Marcus, Myszkowski, Karol and Slusallek, Philipp
Perception-driven Accelerated Rendering
Computer Graphics Forum (Proceedings of Eurographics), 36

Abstract: Advances in computer graphics enable us to create digital images of astonishing complexity and realism. However, processing resources are still a limiting factor. Hence, many costly but desirable aspects of realism are often not accounted for, including global illumination, accurate depth of field and motion blur, spectral effects, etc. especially in real-time rendering. At the same time, there is a strong trend towards more pixels per display due to larger displays, higher pixel densities or larger fields of view. Further observable trends in current display technology include more bits per pixel (high dynamic range, wider color gamut/fidelity), increasing refresh rates (better motion depiction), and an increasing number of displayed views per pixel (stereo, multi-view, all the way to holographic or lightfield displays). These developments cause significant unsolved technical challenges due to aspects such as limited compute power and bandwidth. Fortunately, the human visual system has certain limitations, which mean that providing the highest possible visual quality is not always necessary. In this report, we present the key research and models that exploit the limitations of perception to tackle visual quality and workload alike. Moreover, we present the open problems and promising future research targeting the question of how we can minimize the effort to compute and display only the necessary pixels while still offering a user full visual experience.

Pérard-Gayot, Arsène, Kalojanov, Javor and Slusallek, Philipp
GPU Ray-tracing using Irregular Grids
Computer Graphics Forum,

Abstract: We present a spatial index structure to accelerate ray tracing on GPUs. It is a flat, non-hierarchical spatial subdivision of the scene into axis aligned cells of varying size. In order to construct it, we first nest an octree into each cell of a uniform grid. We then apply two optimization passes to increase ray traversal performance: First, we reduce the expected cost for ray traversal by merging cells together. This adapts the structure to complex primitive distributions, solving the "teapot in a stadium" problem. Second, we decouple the cell boundaries used during traversal for rays entering and exiting a given cell. This allows us to extend the exiting boundaries over adjacent cells that are either empty or do not contain additional primitives. Now, exiting rays can skip empty space and avoid repeating intersection tests. Finally, we demonstrate that in addition to the fast ray traversal performance, the structure can be rebuilt efficiently in parallel, allowing for ray tracing dynamic scenes.


Dahmen, Tim, Trampert, Patrick, de Jonge, Niels and Slusallek, Philipp
Advanced recording schemes for electron tomography
MRS Bulletin, 41(7):537-541
July 2016

Abstract: Three-dimensional (3D) scanning transmission electron microscopy (STEM) has become one of the primary tools for analytical characterization in materials science, and also finds increasing use in the life sciences. A number of different recording schemes exist for the acquisition of 3D data using STEM, each capturing different spatial frequencies and, thus, different information about the shape of a specimen. In this article, we present and compare different sampling approaches based on images with both large and small depth of field. We highlight the latest contribution to 3D data acquisition, the combined tilt and focal series. This recording scheme combines the advantages of tilt series-based tomography with 3D data acquisition using a focal series and is particularly beneficial for imaging specimens with thickness of 1 µm or greater.

Dahmen, Tim, Engstler, Michael, Pauly, Christoph, Trampert, Patrick, de Jonge, Niels, Mücklich, Frank and Slusallek, Philipp
Feature Adaptive Sampling for Scanning Electron Microscopy
Scientific Reports, 6
May 2016

Abstract: A new method for the image acquisition in scanning electron microscopy (SEM) was introduced. The method used adaptively increased pixel-dwell times to improve the signal-to-noise ratio (SNR) in areas of high detail. In areas of low detail, the electron dose was reduced on a per pixel basis, and a-posteriori image processing techniques were applied to remove the resulting noise. The technique was realized by scanning the sample twice. The first, quick scan used small pixel-dwell times to generate a first, noisy image using a low electron dose. This image was analyzed automatically, and a software algorithm generated a sparse pattern of regions of the image that require additional sampling. A second scan generated a sparse image of only these regions, but using a highly increased electron dose. By applying a selective low-pass filter and combining both datasets, a single image was generated. The resulting image exhibited a factor of ≈3 better SNR than an image acquired with uniform sampling on a Cartesian grid and the same total acquisition time. This result implies that the required electron dose (or acquisition time) for the adaptive scanning method is a factor of ten lower than for uniform scanning.

Dahmen, Tim, Kohr, Holger, Lupini, Andrew, Beaudoin, Jean-Pierre, Kübel, Christian, Trampert, Patrick, Slusallek, Philipp and de Jonge, Niels
Combined Tilt- and Focal-Series Tomography for HAADF-STEM
Microscopy Today, 24(3):26-30
May 2016

Abstract: A new aid to tomography in the scanning transmission electron microscope (STEM) is called combined tilt- and focal-series (CTFS). This software controls the recording of a tilt series where for each specimen tilt an entire focal series is recorded. This approach is particularly useful for thick specimens where the tilt range may be limited. Use of CTFS leads to a significant reduction of the missing wedge effect and a better representation of the 3D shapes of features in the specimen.

Turoňová, Beata, Marsalek, Lukas and Slusallek, Philipp
On geometric artifacts in cryo electron tomography
Ultramicroscopy, 163:48-61
April 2016

Abstract: Single-tilt scheme is nowadays the prevalent acquisition geometry in electron tomography and subtomogram averaging experiments. Being an incomplete scheme that induces ill-posedness in the sense of the X-ray or Radon transform inverse problem, it introduces a number of artifacts that directly influence the quality of tomographic reconstructions. Though individually described by different authors before, a systematic study of these acquisition geometry-related artifacts in one place and across representative set of reconstruction methods has not been, to our knowledge, performed before. Moreover, the effects of these artifacts on the reconstructed density are sometimes misinterpreted, attributing them to the wrong cause, especially if their effects accumulate. In this work, we systematically study the major artifacts of single-tilt geometry known as the missing wedge (incomplete projection set problem), the missing information and the specimen-level interior problem (long-object problem). First, we illustratively describe, using a unified terminology, how and why these artifacts arise and when they can be avoided. Next, we describe the effects of these artifacts on the reconstructions across all major classes of reconstruction methods, including newly-appeared methods like the Iterative Nonuniform fast Fourier transform based Reconstruction method (INFR) and the Progressive Stochastic Reconstruction Technique (PSRT). Finally, we draw conclusions and recommendations on numerous points, especially regarding the mutual influence of the geometric artifacts, ability of different reconstruction methods to suppress them as well as implications to the interpretation of both electron tomography and subtomogram averaging experiments.

Kalojanov, Javor, Wand, Michael and Slusallek, Philipp
Building Construction Sets by Tiling Grammar Simplification
Computer Graphics Forum}, 35(2):013--025

Abstract: This paper poses the problem of fabricating physical construction sets from example geometry: A construction set provides a small number of different types of building blocks from which the example model as well as many similar variants can be reassembled. This process is formalized by tiling grammars. Our core contribution is an approach for simplifying tiling grammarssuchthatweobtainphysicallymanufacturablebuildingblocksofcontrollablegranularitywhileretainingvariability, i.e., the ability to construct many different, related shapes. Simplification is performed by sequences of two types of elementary operations: non-local joint edge collapses in the tile graphs reduce the granularity of the decomposition and approximate replacement operations reduce redundancy. We evaluate our method on abstract graph grammars in addition to computing several physical construction sets, which are manufactured using a commodity 3D printer.

Roth, Thorsten, Weier, Martin, Hinkenjann, André, Li, Yongmin and Slusallek, Philipp
An Analysis of Eye-Tracking Data in Foveated Ray Tracing
Proceedings of the 2016 Workshop on Eye Tracking and Visualization,

Abstract: We present an analysis of eye tracking data produced during a quality-focused user study of our own foveated ray tracing method. Generally, foveated rendering serves the purpose of adapting actual rendering methods to a user’s gaze. This leads to performance improvements which also allow for the use of methods like ray tracing, which would be computationally too expensive otherwise, in fields like virtual reality (VR), where high rendering performance is important to achieve immersion, or fields like scientific and information visualization, where large amounts of data may hinder real-time rendering capabilities. We provide an overview of our rendering system itself as well as information about the data we collected during the user study, based on fixation tasks to be fulfilled during flights through virtual scenes displayed on a head-mounted display (HMD). We analyze the tracking data regarding its precision and take a closer look at the accuracy achieved by participants when focusing the fixation targets. This information is then put into context with the quality ratings given by the users, leading to a surprising relation between fixation accuracy and quality ratings.


Dahmen, Tim, Marsalek, Lukas, Marniok, Nico, Turoňová, Beata, Bogachev, Sviatoslav, Trampert, Patrick, Nickels, Stefan and Slusallek, Philipp
The Ettention software package
Ultramicroscopy, :110-118
December 2015

Keywords: Electron tomography Tomographic reconstruction Software architecture GPU OpenCL Block iterative methods High performance computing

Abstract: We present a novel software package for the problem “reconstruction from projections” in electron microscopy. The Ettention framework consists of a set of modular building-blocks for tomographic reconstruction algorithms. The well-known block iterative reconstruction method based on Kaczmarz algorithm is implemented using these building-blocks, including adaptations specific to electron tomography. 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 manycore architectures like Xeon Phi, and (3) accessibility to microscopy end-users via integration in the IMOD package and eTomo user interface. We also provide developers with a clean and well-structured 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.

Trampert, Patrick, Bogachev, Sviatoslav, Marniok, Nico, Dahmen, Tim and Slusallek, Philipp
Marker Detection in Electron Tomography: A Comparative Study
Microscopy and Microanalysis, 21(6):1591-1601
November 2015

Keywords: marker detection particle detection electron tomography tomographic reconstruction

Abstract: We conducted a comparative study of three widely used algorithms for the detection of fiducial markers in electron microscopy images. The algorithms were applied to four datasets from different sources. For the purpose of obtaining comparable results, we introduced figures of merit and implemented all three algorithms in a unified code base to exclude software-specific differences. The application of the algorithms revealed that none of the three algorithms is superior to the others in all cases. This leads to the conclusion that the choice of a marker detection algorithm highly depends on the properties of the dataset to be analyzed, even within the narrowed domain of electron tomography.

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.

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