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Publications

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

Articles:

7.
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.

6.
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.

5.
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.

4.
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.

Contributions to proceedings:

3.
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.

2.
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

1.
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.

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