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Beata Turoňová

Universität des Saarlandes

FR 6.2 - Informatik
Lehrstuhl für Computergrafik
Campus E1.1, Zi. E15
66123 Saarbrücken
Germany 

Email: turonova at cs dot uni-saarland dot de 
Tel: +49 681 302 3836 
URL: http://graphics.cg.uni-saarland.de/beata-turonova/

 

 

PSRT

I am working on a novel approach to 3D tomographic reconstruction for Cryo Electron Tomography called Progressive Stochastic Reconstruction Technique (PSRT). For more information and download please visit PSRT website.

 

 

Publications

References

Articles:

10.
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.

9.
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.

8.
Turoňová, Beata, Marsalek, Lukas, Davidovic, Tomas and Slusallek, Philipp
Progressive Stochastic Reconstruction Technique (PSRT) for Cryo Electron Tomography
Journal of Structural Biology, 189(3):195-206
March 2015

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.

Conferences:

7.
Dahmen, Tim, Marsalek, Lukas, Marniok, Nico, Turoňová, Beata, Bogachev, Sviatoslav, Trampert, Patrick, Nickels, Stefan and Slusallek, Philipp
Ettention: building blocks for iterative reconstruction algorithms
Proceedings of Microscopy & Microanalysis 2015
August 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.

6.
Turoňová, Beata, Marsalek, Lukas, Davidovic, Tomas and Slusallek, Philipp
PSRT: Progressive Stochastic Reconstruction Technique for Cryo Electron Tomography
Proceedings of Microscopy & Microanalysis 2015
August 2015
accepted
5.
Turoňová, Beata, Marsalek, Lukas, Davidovic, Tomas and Slusallek, Philipp
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
July 2015
accepted

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.

Contributions to proceedings:

4.
Turonova, Beata, Marsalek, Lukas, Davidovic, Tomas and Slusallek, Philipp
Progressive stochastic reconstruction technique for cryo electron tomography
SIGGRAPH Asia 2013 Posters of SA '13 , page 11:1.
Publisher: ACM, New York, NY, USA
2013
ISBN: 978-1-4503-2634-6

Keywords: 3D reconstruction, cryo electron tomography, metropolis-hastings, stochastic reconstruction

Abstract: Cryo Electron Tomography (cryoET) plays an essential role in Structural Biology, as it is the only technique that allows to study the structure and intracellular distribution of large macromolecular complexes in their (close to) native environment. A major limitation of cryoET is the highest achievable resolution, currently at around 3 nm, which prevents its application to smaller complexes and in turn to a wider range of important biological questions.

Master theses:

3.
Turonova, Beata
Simultaneous Algebraic Reconstruction Technique for Electron Tomography using OpenCL
Universität des Saarlandes,
June 2011

Abstract: Electron tomography (ET) estimates 3D structure of an object from series of 2D transmission images taken from different perspectives. Various methods can be used to obtain the 3D reconstruction. Expansion of Graphics Processing Units (GPUs) made it possible to explore use of iterative algebraic techniques in ET. To these methods belong Algebraic Reconstruction Technique (ART), Simultaneous Iterative Reconstruction Technique (SIRT), and Simultaneous Algebraic Technique (SART). While ART and SIRT are employed in various SW packages for ET, SART seems to be neglected in this area. In this thesis we present GPU-based SART implementation modified for ET, called ET SART. After short introduction to ET, we describe mathematical principles of algebraic techniques and present previous work in this area as well as we introduce the basic concepts behind OpenCL and CUDA. We describe main features of ET SART as well as some practical aspects of its implementation. Finally, we compare ET SART with other methods and present our results. Part of this work is also implementation of wrapper providing unified API for CUDA and OpenCL.

Posters:

2.
Turoňová, Beata, Marsalek, Lukas, Davidovic, Tomas and Slusallek, Philipp
Progressive stochastic reconstruction technique (PSRT): a Monte Carlo approach to 3D reconstruction in cryo electron tomography
Microscopy Conference Gottingen 2015
September 2015
1.
Maletta, Max, Marsalek, Lukas, Turonova, Beata, Slusallek, Philipp and Peters, Peter J
Electron cryo-tomography for observation of macromolecular changes induced by test compound within a cell
March 2013
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