Fast tomographic reconstruction on multicore computers

J.I. Agulleiro (1), J.J. Fernández (2)

(1) Associated unit CSIC+UAL. Univ. Almeria. 04120 Almeria. Spain.
(2) Centro Nacional de Biotecnologia - CSIC. 28049 Madrid. Spain.

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Tomo3D implements a multithreaded vectorized approach to tomographic reconstruction that takes full advantage of the power in modern multicore computers. Full resolution tomograms are generated at high speed on standard computers with no special system requirements. Tomo3D has the most common reconstruction methods implemented, namely WBP and SIRT. It proves to be competitive with current GPU solutions in terms of processing time, in the order of a few seconds with WBP or minutes with SIRT. Tomo3D reads input tilt-series and writes output tomograms in MRC format. The program is compatible with standard packages, which allows easy integration in the electron tomography workflow.

 A detailed description of the procedure implemented in the package can be found in the following articles:

Primary publications to cite:

Fast tomographic reconstruction on multicore computers.
J.I. Agulleiro, J.J. Fernandez.
27:582-583, 2011.

Tomo3D 2.0 - Exploitation of Advanced Vector eXtensions (AVX) for 3D reconstruction.
J.I. Agulleiro, J.J. Fernandez.
Journal of Structural Biology 189:147-152, 2015.

Additional references:

Vectorization with SIMD extensions speeds up reconstruction in electron tomography.
JI Agulleiro, EM Garzon, I Garcia, JJ Fernandez.
Journal of Structural Biology 170:570-575, 2010.

Evaluation of a multicore-optimized implementation for tomographic reconstruction.
JI Agulleiro, JJ Fernandez.
PLoS ONE  7(11):e48261, 2012.

Please, cite these articles if you use Tomo3D in your works.

Current version: January 2015

Available material:
  • Documentation in PDF:  tomo3d.pdf

  • Binaries for x86-based platforms under Linux (64 and 32 bits)

  • Binaries for Intel-based Macs under OSX (built on OSX 10.6.8 - Snow Leopard)
  • Binaries for Windows (XP and onwards; 32 and 64 bits)

The development of Tomo3D has been supported by the Spanish MEC and MCI, J.Andalucia and CSIC.

Copyright by the authors.