Vectorization with SIMD extensions speeds up reconstruction in electron tomography
- PMID: 20085820
- DOI: 10.1016/j.jsb.2010.01.008
Vectorization with SIMD extensions speeds up reconstruction in electron tomography
Abstract
Electron tomography allows structural studies of cellular structures at molecular detail. Large 3D reconstructions are needed to meet the resolution requirements. The processing time to compute these large volumes may be considerable and so, high performance computing techniques have been used traditionally. This work presents a vector approach to tomographic reconstruction that relies on the exploitation of the SIMD extensions available in modern processors in combination to other single processor optimization techniques. This approach succeeds in producing full resolution tomograms with an important reduction in processing time, as evaluated with the most common reconstruction algorithms, namely WBP and SIRT. The main advantage stems from the fact that this approach is to be run on standard computers without the need of specialized hardware, which facilitates the development, use and management of programs. Future trends in processor design open excellent opportunities for vector processing with processor's SIMD extensions in the field of 3D electron microscopy.
Similar articles
-
A matrix approach to tomographic reconstruction and its implementation on GPUs.J Struct Biol. 2010 Apr;170(1):146-51. doi: 10.1016/j.jsb.2010.01.021. Epub 2010 Feb 2. J Struct Biol. 2010. PMID: 20132889
-
Tomo3D 2.0--exploitation of advanced vector extensions (AVX) for 3D reconstruction.J Struct Biol. 2015 Feb;189(2):147-52. doi: 10.1016/j.jsb.2014.11.009. Epub 2014 Dec 17. J Struct Biol. 2015. PMID: 25528570
-
4D electron tomography.Science. 2010 Jun 25;328(5986):1668-73. doi: 10.1126/science.1190470. Science. 2010. PMID: 20576886
-
Methods for segmentation and interpretation of electron tomographic reconstructions.Methods Enzymol. 2010;483:31-46. doi: 10.1016/S0076-6879(10)83002-2. Methods Enzymol. 2010. PMID: 20888468 Review.
-
Self-organizing neural networks bridge the biomolecular resolution gap.J Mol Biol. 1998 Dec 18;284(5):1247-54. doi: 10.1006/jmbi.1998.2232. J Mol Biol. 1998. PMID: 9878345 Review.
Cited by
-
A Survey of the Use of Iterative Reconstruction Algorithms in Electron Microscopy.Biomed Res Int. 2017;2017:6482567. doi: 10.1155/2017/6482567. Epub 2017 Sep 17. Biomed Res Int. 2017. PMID: 29312997 Free PMC article. Review.
-
Adaptive multiresolution method for MAP reconstruction in electron tomography.Ultramicroscopy. 2016 Nov;170:24-34. doi: 10.1016/j.ultramic.2016.08.002. Epub 2016 Aug 6. Ultramicroscopy. 2016. PMID: 27522477 Free PMC article.
-
The magnetosome membrane protein, MmsF, is a major regulator of magnetite biomineralization in Magnetospirillum magneticum AMB-1.Mol Microbiol. 2012 Aug;85(4):684-99. doi: 10.1111/j.1365-2958.2012.08132.x. Epub 2012 Jul 10. Mol Microbiol. 2012. PMID: 22716969 Free PMC article.
-
The stack: a new bacterial structure analyzed in the Antarctic bacterium Pseudomonas deceptionensis M1(T) by transmission electron microscopy and tomography.PLoS One. 2013 Sep 9;8(9):e73297. doi: 10.1371/journal.pone.0073297. eCollection 2013. PLoS One. 2013. PMID: 24039905 Free PMC article.
-
A distributed multi-GPU system for high speed electron microscopic tomographic reconstruction.Ultramicroscopy. 2011 Jul;111(8):1137-43. doi: 10.1016/j.ultramic.2011.03.015. Epub 2011 Apr 1. Ultramicroscopy. 2011. PMID: 21741915 Free PMC article.
Publication types
MeSH terms
LinkOut - more resources
Full Text Sources
