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.
Progressive Light Transport Simulation on the GPU: Survey and ImprovementsCM Trans. Graph, 33(3):29:1-29:19
Keywords: GPU; Global illumination; bidirectional path tracing; high performance; vertex connection and merging
Abstract: Graphics Processing Units (GPUs) recently became general enough to enable implementation of a variety of light transport algorithms. However, the efficiency of these GPU implementations has received relatively little attention in the research literature and no systematic study on the topic exists to date. The goal of our work is to fill this gap. Our main contribution is a comprehensive and in-depth investigation of the efficiency of the GPU implementation of a number of classic as well as more recent progressive light transport simulation algorithms. We present several improvements over the state-of-the-art. In particular, our Light Vertex Cache, a new approach to mapping connections of sub-path vertices in Bidirectional Path Tracing on the GPU, outperforms the existing implementations by 30-60%. We also describe a first GPU implementation of the recently introduced Vertex Connection and Merging algorithm [Georgiev et al. 2012], showing that even relatively complex light transport algorithms can be efficiently mapped on the GPU. With the implementation of many of the state-of-the-art algorithms within a single system at our disposal, we present a unique direct comparison and analysis of their relative performance.
3D Rasterization: A Bridge between Rasterization and Ray CastingProceedings of the 2012 Graphics Interace Conference, :201 - 208
Progressive Lightcuts for GPUACM SIGGRAPH 2012 Talks,
Light Transport Simulation with Vertex Connection and MergingACM Trans. Graph., 31:XXX:1--XXX:10
Note: SIGGRAPH Asia 2012
Combining global and local virtual lights for detailed glossy illuminationACM Trans. Graph., 29:143:1--143:8
Keywords: global illumination, glossy interreflection, many lights
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.
Contributions to proceedings:
Progressive stochastic reconstruction technique for cryo electron tomography
SIGGRAPH Asia 2013 Posters of SA '13 , page 11:1.
Publisher: ACM, New York, NY, USA
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.
Performance Considerations When Using a Dedicated Ray Traversal Engine
19th International Conference on Computer Graphics, Visualization and Computer Vision 2011 (WSCG 2011) Pilsen , page 65--72.
Efficient Stack-less BVH Traversal for Ray Tracing
Proceedings 27th Spring Conference on Computer Graphics (SCCG) 2011 , page 29-34.
Czech Technical University in Prague,