GPU Ray-tracing using Irregular GridsComputer 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.
Advanced recording schemes for electron tomographyMRS Bulletin, 41(7):537-541
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.
Feature Adaptive Sampling for Scanning Electron MicroscopyScientific Reports, 6
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.
Combined Tilt- and Focal-Series Tomography for HAADF-STEMMicroscopy Today, 24(3):26-30
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.
On geometric artifacts in cryo electron tomographyUltramicroscopy, 163:48-61
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.
Building Construction Sets by Tiling Grammar SimplificationComputer 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.
The Ettention software packageUltramicroscopy, :110-118
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.
Marker Detection in Electron Tomography: A Comparative StudyMicroscopy and Microanalysis, 21(6):1591-1601
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.
Dual Motor-Cognitive Virtual Reality Training Impacts Dual-Task Performance in Freezing of GaitBiomedical and Health Informatics, IEEE Journal of, PP(99):1-1
Keywords: Accuracy;Biomedical measurement;Diseases;Foot;Legged locomotion;Time measurement;Training
An automated workflow for the biomechanical simulation of a tibia with implant using computed tomography and the finite element methodComputers and Mathematics with Applications,
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.
Progressive Stochastic Reconstruction Technique (PSRT) for Cryo Electron TomographyJournal of Structural Biology, 189(3):195-206
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.
Matched Backprojection Operator for Combined Scanning Transmission Electron Microscopy Tilt- and Focal SeriesMicroscopy & Microanalysis,
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.