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Publications

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All :: 1990, ... , 2013, 2014, 2015, 2016
References

Articles:

12.
Dahmen, Tim, Trampert, Patrick, de Jonge, Niels; 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.

11.
Dahmen, Tim, Engstler, Michael, Pauly, Christoph, Trampert, Patrick, de Jonge, Niels, Mücklich, Frank; 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.

10.
Dahmen, Tim, Kohr, Holger, Lupini, Andrew, Beaudoin, Jean-Pierre, Kübel, Christian, Trampert, Patrick, Slusallek, Philipp; 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.

9.
Turoňová, Beata, Marsalek, Lukas; 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.

8.
Kalojanov, Javor, Wand, Michael; Slusallek, Philipp
Building Construction Sets by Tiling Grammar Simplification
Computer Graphics Forum}, 35(2):013--025
2016

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.

Conferences:

7.
Weier, Martin, Roth, Thorsten, Krujiff, Ernst, Hinkenjann, André, Pérard-Gayot, Arsène, Slusallek, Philipp; Li, Yongmin
Foveated Real-Time Ray Tracing for Head-Mounted Displays
Computer Graphics Forum
October 2016

Abstract: Head-mounted displays with dense pixel arrays used for virtual reality applications require high frame rates and low latency rendering. This forms a challenging use case for any rendering approach. In addition to its ability of generating realistic images, ray tracing offers a number of distinct advantages, but has been held back mainly by its performance. In this paper, we present an approach that significantly improves image generation performance of ray tracing. This is done by combining foveated rendering based on eye tracking with reprojection rendering using previous frames in order to drastically reduce the number of new image samples per frame. To reproject samples a coarse geometry is reconstructed from a G-Buffer. Possible errors introduced by this reprojection as well as parts that are critical to the perception are scheduled for resampling. Additionally, a coarse color buffer is used to provide an initial image, refined smoothly by more samples were needed. Evaluations and user tests show that our method achieves real-time frame rates, while visual differences compared to fully rendered images are hardly perceivable. As a result, we can ray trace non-trivial static scenes for the Oculus DK2 HMD at 1182 * 1464 per eye within the the VSync limits without perceived visual differences.

Contributions to proceedings:

6.
Einabadi, Farshad; Grau, Oliver
Light Harmonisation for Virtual Production
Proceedings of the 13th European Conference on Visual Media Production (CVMP 2016)
December 2016
accepted

Note: Short Paper

5.
Dahmen, Tim, Jonge, Niels De, Trampert, Patrick, Engstler, Michael; Pauly, Christoph
Smart Microscopy: Feature Based Adaptive Sampling for Focused Ion Beam Scanning Electron Microscopy
Volume 22 , page 632--633.
July 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.

4.
Trampert, Patrick, Bogachev, Sviatoslav, Marniok, Nico, Dahmen, Tim; Slusallek, Philipp
A Comparative Study of Three Marker Detection Algorithms in Electron Tomography.
Volume 22 , page 0.
July 2016

Keywords: electron tomography,marker detection,particle detection,tomographic reconstruction

Abstract: We conducted a comparative study of three widely used algorithms for the detection of fiducial\backslashnmarkers in electron microscopy images. The algorithms were applied to four datasets from different sources. For\backslashnthe purpose of obtaining comparable results, we introduced figures of merit and implemented all three algorithms\backslashnin a unified code base to exclude software-specific differences. The application of the algorithms revealed that\backslashnnone of the three algorithms is superior to the others in all cases. This leads to the conclusion that the choice of a\backslashnmarker detection algorithm highly depends on the properties of the dataset to be analyzed, even within the\backslashnnarrowed domain of electron tomography

3.
Trampert, Patrick, Chen, Delei, Bogachev, Sviatoslav, Dahmen, Tim; Slusallek, Philipp
Dictionary-based Filling of the Missing Wedge in Electron Tomography .
Volume 22 , page 554--555.
July 2016

Abstract: A new method for dealing with electron tomography data from incomplete projection sets is proposed. The approach is inspired by exemplar-based inpainting techniques in image processing [1] and heuristically generates data for missing projection directions. The method has also been extended to work on three dimensional data. In general, electron tomography reconstructions suffer from elongation artifacts along the beam direction at 0° tilt. These artifacts can be seen in the corresponding Fourier domain as a missing wedge. The new method synthetically generates projections for these missing directions with the help of a dictionary-based approach that is able to convey both structure and texture at the same time. It constitutes a preprocessing step that can be combined with any tomographic reconstruction algorithm. The new algorithm was applied to the well-known Shepp-Logan phantom. Visually, the synthetic projections, reconstructions, and corresponding Fourier power spectra showed a decrease of the typical missing wedge artifacts. Quantitatively, the inpainting method is capable to reduce missing wedge artifacts and improves tomogram quality with respect to several figures-of-merit.

2.
Lemme, Stefan, Sutter, Jan, Schlinkmann, Christian; Slusallek, Philipp
The Basic Building Blocks of Declarative 3D on the Web
Proceedings of the 21st International Conference on Web3D Technology of Web3D '16 , page 17-25.
Publisher: ACM, New York, NY, USA
July 2016

Keywords: Dec3D, HTML, X3DOM, XML3D, web components

Abstract: WebGL enabled real-time 3D graphics on the Web. With the objective to integrate 3D graphics into the rest of the Web technology stack, and to make it easier for Web developers to develop interactive 3D graphics, Declarative 3D approaches were developed: X3DOM and XML3D. While the former focuses on backward-compatibility to X3D and a large set of convenience elements, the latter attempts to define a minimal set of flexible elements as an extension to HTML5. It has now been more than 6 years since Declarative 3D was first proposed for the Web. However, despite their different philosophies neither X3DOM nor XML3D has yet been able to achieve the same momentum and adoption rate as imperative frameworks like three.js. In the meantime, the underlying Web technology stack has made significant advances. In this paper we revisit both approaches in light of new Web technologies, such as Web Components, to define a small set of core elements that can provide the convenience of X3DOM while remaining as flexible and customizable as XML3D. Further, we present a strategy for building upon these core elements to enable user-defined elements, with the ability to cover domain-specific needs in Declarative 3D. Lastly, we show how these concepts can be used to simplify existing approaches (i.e. X3DOM and XML3D) and provide the basic building blocks of Declarative 3D on the Web.

1.
Limberger, Daniel, Scheibel, Willy, Lemme, Stefan; Döllner, Jürgen
Dynamic 2.5D Treemaps Using Declarative 3D on the Web
Proceedings of the 21st International Conference on Web3D Technology of Web3D '16 , page 33-36.
Publisher: ACM, New York, NY, USA
July 2016

Keywords: 2.5D treemap, Dec3D, X3DOM, XML3D, glTF

Abstract: The 2.5D treemap represents a general purpose visualization technique to map multi-variate hierarchical data in a scalable, interactive, and consistent way used in a number of application fields. In this paper, we explore the capabilities of Declarative 3D for the web-based implementation of 2.5D treemap clients. Particularly, we investigate how X3DOM and XML3D can be used to implement clients with equivalent features that interactively display 2.5D treemaps with dynamic mapping of attributes. We also show a first step towards a glTF-based implementation. These approaches are benchmarked focusing on their interaction capabilities with respect to rendering and speed of dynamic data mapping. We discuss the results for our representative example of a complex 3D interactive visualization technique and summerize recommendations for improvements towards operational web clients.

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