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) Spanish National Research Council (CSIC). Oviedo. Spain.
Contact: jjfernandez.software @ gmail.com
Description
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.
Version 2.2 contains implementations of the well-known WBP and SIRT methods, and WBP using a SIRT-like filter (also known as 'Fake SIRT') as well as CTF deconvolution using D. Tegunov's filter.
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.
Bioinformatics 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.
Description of the CTF deconvolution implementation in Tomo3D:
EJ Cohen et al. Developmental Cell 59:1-16, 2024. doi: https://doi.org/10.1016/j.devcel.2024.09.008
Please, cite any of these articles if you use Tomo3D in your works.
Request the package
Current version: 2.2 (January 2023)
Available material:
Documentation in PDF: tomo3d.pdf
Binaries for x86-based platforms under Linux (64 bits) and Windows WSL.
Binaries for Macs based on Intel and Apple Silicon processors under OSX/macOS.
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.