Tomo3dGPU
Published by fvazquez on Sunday, September 11, 2011
A package for 3D reconstruction with Matrix Implementation of tomographic algorithms on GPUs
F. Vázquez (1), E.M. Garzón (1), J.J. Fernández (1,2)
(1) Dept. Computer Architecture. Univ. Almeria. 04120 Almeria. Spain.
(2) Centro Nacional de Biotecnología (CSIC). Campus UAM. 28049 Madrid. Spain.
Description
The program TOMO3DGPU uses a matrix approach to reconstruct tomograms from aligned tilt series. This program has the most common reconstruction methods implemented, namely WBP and SIRT. The program exploits NVIDIA GPUs with compute capability 1.1 and higher. The combination of the matrix approach and GPU computing allows ultrafast 3D reconstruction. The program 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 program can be found in the following articles:
A matrix approach to tomographic reconstruction and its implementation on GPUs.
F. Vázquez, E.M. Garzón, J.J. Fernández.
Journal of Structural Biology 170:146-151, 2010.
[PDF]
Matrix Implementation of Simultaneous Iterative Reconstruction Technique (SIRT) on GPUs.
F. Vázquez, E.M. Garzón, J.J. Fernández.
The Computer Journal 54:1861-1868, 2011.
[PDF]
Please, cite these articles if you use TOMO3DGPU in your works.
Register
Please, send us an email (f.vazquez at ual.es , jjfernandez.software_at_gmail.com) with your name, affiliation and email address. We would like to know who is using the package so that we can have them updated about future versions.
Download
[Documentation]
[Documentation and Binaries for 64bits x86-based platforms under linux]
If you have problems in using the package, please contact us. Suggestions are also welcome.