Evaluation of a Multicore-Optimized Implementation for Tomographic Reconstruction

Tomography allows elucidation of the three-dimensional structure of an object from a set of projection images. In life sciences, electron microscope tomography is providing invaluable information about the cell structure at a resolution of a few nanometres. Here, large images are required to combine wide fields of view with high resolution requirements. The computational complexity of the algorithms along with the large image size then turns tomographic reconstruction into a computationally demanding problem. Traditionally, high-performance computing techniques have been applied to cope with such demands on supercomputers, distributed systems and computer clusters. In the last few years, the trend has turned towards graphics processing units (GPUs). Here we present a detailed description and a thorough evaluation of an alternative approach that relies on exploitation of the power available in modern multicore computers. The combination of single-core code optimization, vector processing, multithreading and efficient disk I/O operations succeeds in providing fast tomographic reconstructions on standard computers. The approach turns out to be competitive with the fastest GPU-based solutions thus far.

[1]  J R Kremer,et al.  Computer visualization of three-dimensional image data using IMOD. , 1996, Journal of structural biology.

[2]  John W Sedat,et al.  A distributed multi-GPU system for high speed electron microscopic tomographic reconstruction. , 2011, Ultramicroscopy.

[3]  José-Jesús Fernández,et al.  Fast tomographic reconstruction on multicore computers , 2011, Bioinform..

[4]  Friedrich Förster,et al.  Snapshots of nuclear pore complexes in action captured by cryo-electron tomography , 2007, Nature.

[5]  G A Perkins,et al.  Electron tomography of large, multicomponent biological structures. , 1997, Journal of structural biology.

[6]  D. Agard,et al.  Three-dimensional structure of basal body triplet revealed by electron cryo-tomography , 2011, The EMBO journal.

[7]  Julio O. Ortiz,et al.  The Native 3D Organization of Bacterial Polysomes , 2009, Cell.

[8]  K. Downing,et al.  The magnetosome membrane protein, MmsF, is a major regulator of magnetite biomineralization in Magnetospirillum magneticum AMB‐1 , 2012, Molecular microbiology.

[9]  John W Sedat,et al.  UCSF tomography: an integrated software suite for real-time electron microscopic tomographic data collection, alignment, and reconstruction. , 2007, Journal of structural biology.

[10]  K J Batenburg,et al.  Performance improvements for iterative electron tomography reconstruction using graphics processing units (GPUs). , 2011, Journal of structural biology.

[11]  N. Abrescia,et al.  Three-dimensional visualization of forming Hepatitis C virus-like particles by electron-tomography. , 2012, Virology.

[12]  J I Agulleiro,et al.  Vectorization with SIMD extensions speeds up reconstruction in electron tomography. , 2010, Journal of structural biology.

[13]  Jie Cheng,et al.  Programming Massively Parallel Processors. A Hands-on Approach , 2010, Scalable Comput. Pract. Exp..

[14]  Wolfgang Baumeister,et al.  Three-Dimensional Structure of Herpes Simplex Virus from Cryo-Electron Tomography , 2003, Science.

[15]  Zhiyong Liu,et al.  High-Performance Blob-Based Iterative Reconstruction of Electron Tomography on Multi-GPUs , 2011, ISBRA.

[16]  E M Garzón,et al.  A matrix approach to tomographic reconstruction and its implementation on GPUs. , 2010, Journal of structural biology.

[17]  Gabor T. Herman,et al.  Fundamentals of Computerized Tomography: Image Reconstruction from Projections , 2009, Advances in Pattern Recognition.

[18]  Wolfgang Baumeister,et al.  Cryo-electron tomography of vaccinia virus. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[19]  V. Lučić,et al.  Structural studies by electron tomography: from cells to molecules. , 2005, Annual review of biochemistry.

[20]  J I Agulleiro,et al.  Hybrid computing: CPU+GPU co-processing and its application to tomographic reconstruction. , 2012, Ultramicroscopy.

[21]  Sabine Pruggnaller,et al.  Performance evaluation of image processing algorithms on the GPU. , 2008, Journal of structural biology.

[22]  J. McIntosh,et al.  FcRn-mediated antibody transport across epithelial cells revealed by electron tomography , 2008, Nature.

[23]  Jose-Jesus Fernandez,et al.  Computational methods for electron tomography. , 2012, Micron.

[24]  Wei Xu,et al.  High-performance iterative electron tomography reconstruction with long-object compensation using graphics processing units (GPUs). , 2010, Journal of structural biology.

[25]  José-Jesús Fernández,et al.  Efficient parallel implementation of iterative reconstruction algorithms for electron tomography , 2008, J. Parallel Distributed Comput..

[26]  J J Fernández,et al.  High performance computing in structural determination by electron cryomicroscopy. , 2008, Journal of structural biology.

[27]  Isom L. Crawford,et al.  Software Optimization for High Performance Computers , 2000 .

[28]  G. Jensen,et al.  Bacterial chemoreceptor arrays are hexagonally packed trimers of receptor dimers networked by rings of kinase and coupling proteins , 2012, Proceedings of the National Academy of Sciences.

[29]  W. Baumeister,et al.  Macromolecular Architecture in Eukaryotic Cells Visualized by Cryoelectron Tomography , 2002, Science.

[30]  Pradeep Dubey,et al.  Debunking the 100X GPU vs. CPU myth: an evaluation of throughput computing on CPU and GPU , 2010, ISCA.

[31]  Steven G. Johnson,et al.  The Design and Implementation of FFTW3 , 2005, Proceedings of the IEEE.

[32]  Emilio Luque,et al.  Analytical Performance Prediction for Iterative Reconstruction Techniques in Electron Tomography of Biological Structures , 2010, Int. J. High Perform. Comput. Appl..

[33]  David A. Patterson,et al.  Computer Architecture: A Quantitative Approach , 1969 .

[34]  P. Gilbert Iterative methods for the three-dimensional reconstruction of an object from projections. , 1972, Journal of theoretical biology.

[35]  David Lee,et al.  The Telescience Portal for advanced tomography applications , 2003, J. Parallel Distributed Comput..

[36]  Inmaculada García,et al.  Electron tomography of complex biological specimens on the Grid , 2007, Future Gener. Comput. Syst..

[37]  Shinji Shimojo,et al.  Global Telescience featuring IPv6 at iGrid2002 , 2003, Future Gener. Comput. Syst..

[38]  Zhiyong Liu,et al.  High-performance blob-based iterative three-dimensional reconstruction in electron tomography using multi-GPUs , 2012, BMC Bioinformatics.

[39]  R. Marabini,et al.  Image processing and 3-D reconstruction in electron microscopy , 2006, IEEE Signal Processing Magazine.

[40]  J. Frank Electron tomography : methods for three-dimensional visualization of structures in the cell , 2005 .

[41]  Inmaculada García,et al.  High-performance electron tomography of complex biological specimens. , 2002, Journal of structural biology.

[42]  Dennis C Winkler,et al.  The Role of Capsid Maturation on Adenovirus Priming for Sequential Uncoating* , 2012, The Journal of Biological Chemistry.

[43]  Inmaculada García,et al.  Three-dimensional reconstruction of cellular structures by electron microscope tomography and parallel computing , 2004, J. Parallel Distributed Comput..

[44]  M. Radermacher Weighted Back-Projection Methods , 2007 .

[45]  Francisco Vázquez,et al.  Matrix Implementation of Simultaneous Iterative Reconstruction Technique (SIRT) on GPUs , 2011, Comput. J..

[46]  Achilleas S Frangakis,et al.  Implementation and performance evaluation of reconstruction algorithms on graphics processors. , 2007, Journal of structural biology.

[47]  Zhiyong Liu,et al.  Modified Simultaneous Algebraic Reconstruction Technique and its Parallelization in Cryo-electron Tomography , 2009, 2009 15th International Conference on Parallel and Distributed Systems.

[48]  G. Jensen,et al.  Growth and Localization of Polyhydroxybutyrate Granules in Ralstonia eutropha , 2011, Journal of bacteriology.