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.
Shallow Embedding of DSLs via Online Partial Evaluation
Proceedings of the 14th International Conference on Generative Programming: Concepts & Experiences (GPCE) , page 11-20.
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
Ettention: building blocks for iterative reconstruction algorithms
Proceedings of Microscopy & Microanalysis 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.
Reconstruction Strategies for Combined Tilt- and Focal Series Scanning Transmission Electron Microscopy
Proceedings of Microscopy & Microanalysis 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.
PSRT: Progressive Stochastic Reconstruction Technique for Cryo Electron Tomography
Proceedings of Microscopy & Microanalysis 2015
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
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.
Plugin free remote visualization in the browser
Volume 9397 of Proc. SPIE
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.