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Use of High-Performance Computing Algorithms in Combination With Parallel Computing for Tomography

Published online by Cambridge University Press:  02 July 2020

G.A. Perkins ,
C.W. Renken ,
S.J. Young ,
S. Lindsey ,
M.H. Ellisman  and
T.G. Frey
G.A. Perkins
Affiliation:
Department of Biology, San Diego State University, San Diego, CA92182-4614
C.W. Renken
Affiliation:
Department of Biology, San Diego State University, San Diego, CA92182-4614
S.J. Young
Affiliation:
National Center for Microscopy and Imaging Research, University of California, San Diego, LaJolla, CA92093-0608
S. Lindsey
Affiliation:
San Diego Supercomputer Center, La Jolla, CA92093
M.H. Ellisman
Affiliation:
National Center for Microscopy and Imaging Research, University of California, San Diego, LaJolla, CA92093-0608
T.G. Frey
Affiliation:
Department of Biology, San Diego State University, San Diego, CA92182-4614
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Extract

The electron microscope is essential for resolving complex biological structures, such as mitochondria, which are too small to be viewed in detail with the light microscope. In contrast to a conventional instrument, the High-Voltage Electron Microscope (HVEM) located at the National Center for Microscopy and Imaging Research (NCMIR) can obtain images from relatively thick specimens that contain substantial three-dimensional structure. Though a single image acquired with the HVEM represents a projection through the specimen, tomographic methods can be applied to a set of images acquired from different orientations to derive a three-dimensional representation of its biological structure. Tomography requires extensive computation and considerable processing time on conventional workstations in order to reconstruct the typically large HVEM volumes from the tilt series.

In order to expedite tomographic processing, we have implemented both the commonly used singleaxis tilt, R-weighted backprojection algorithm and two iterative reconstruction methods, algebraic reconstruction (ART) and simultaneous iterative reconstruction (SIRT) on the massively parallel Intel Paragon at the San Diego Supercompter Center.

Type
Computational Advances and Enabling Technologies for 3D Microscopies in Biology
Information
Microscopy and Microanalysis , Volume 3 , Issue S2: Proceedings: Microscopy & Microanalysis '97, Microscopy Society of America 55th Annual Meeting, Microbeam Analysis Society 31st Annual Meeting, Histochemical Society 48th Annual Meeting, Cleveland, Ohio, August 10-14, 1997 , August 1997 , pp. 1123 - 1124
Copyright
Copyright © Microscopy Society of America 1997

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References

1.Young, S.J.et al., Int. J. Supercomputing Applications, 10(1996)170.Google Scholar
2. We are grateful for the help provided by Steve Lamont of the NCMIR. This work was funded by American Heart Association, CA Affiliate grant #95-301 to TGF and NIH grants RR04050 and NS14718toMHE.Google Scholar