Projection-based volume alignment

Journal of Structural Biology

Volumn 182, Issue 2, 2013, Pages 93-105

  Yu, Lingbo ^a,b   Snapp, Robert R ^a   Ruiz, Teresa ^b   Radermacher, Michael ^a,b  

^a University of Vermont   (United States)

^b UNIVERSITY OF VERMONT   (United States)

Author keywords

3D electron microscopy; 3D reconstruction; Image processing; Missing data; Volume alignment; Volume averaging

Indexed keywords

RADON; REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE;

ALGORITHM; ARTICLE; ELECTRON MICROSCOPY; NONHUMAN; PRIORITY JOURNAL; SIGNAL NOISE RATIO; YARROWIA; YEAST;

ALGORITHMS; ELECTRON TRANSPORT COMPLEX I; IMAGING, THREE-DIMENSIONAL; MACROMOLECULAR SUBSTANCES; MICROSCOPY, ELECTRON; MODELS, CHEMICAL; SIGNAL-TO-NOISE RATIO; YARROWIA;

YARROWIA LIPOLYTICA;

EID: 84876733961     PISSN: 10478477     EISSN: 10958657     Source Type: Journal    
DOI: 10.1016/j.jsb.2013.01.011     Document Type: Article

References (37)

1. Bartesaghi A., Sprechmann P., Liu J., Randall G., Sapiro G., Subramaniam S. Classification and 3D averaging with missing wedge correction in biological electron tomography. J. Struct. Biol. 2008, 162:436-450.
2. Clason T., Zickermann V., Ruiz T., Brandt U., Radermacher M. Direct localization of the 51 and 24kDa subunits of mitochondrial complex I by three-dimensional difference imaging. J. Struct. Biol. 2007, 159:433-442.
3. Crowther R.A., DeRosier D.J., Klug A. The reconstruction of a three-dimensional structure from its projections and its applications to electron microscopy. Proc. R. Soc. Lond. 1970, A317:319-340.
4. Deans S.R. The Radon Transform and Some of Its Applications 1983, John Wiley & Sons, New York.
5. Dröse S., Krack S., Sokolova L., Zwicker K., Barth H.-D., Morgner N., Heide H., Steger M., Nübel E., Zickermann V., Kerscher S., Brutschy B., Radermacher M., Brandt U. Functional dissection of the proton pumping modules of mitochondrial complex I. PLoS Biol. 2011, 9(8):e1001128.
6. Euler L. Formulae generales pro translatione quacunque corporum rigidorum. Novi Commentarii academiae scientiarum Petropolitanae 1776, 20:189-207.
7. Förster F., Pruggnaller S., Seybert A., Frangakis A.S. Classification of cryo-electron sub-tomograms using constrained correlation. J. Struct. Biol. 2008, 161:276-286.
8. Frangakis A.S., Bohm J., Förster F., Nickell S., Nicastro D., Typke D., Hegerl R., Baumeister W. Identification of macromolecular complexes in cryoelectron tomograms of phantom cells. Proc. Natl. Acad. Sci. USA 2002, 99:14153-14158.
9. Frank J. Electron Tomography 1992, Plenum Press, New York.
10. Frank J. Three-Dimensional Electron Microscopy of Macromolecular Assemblies: Visualization of Biological Molecules in Their Native State 2006, Oxford University Press, USA.
11. Frank J., Shimkin B., Dowse H. Spider - a modular software system for electron image-processing. Ultramicroscopy 1981, 6:343-357.
12. Hegerl R., Altbauer A. The " EM" program system. Ultramicroscopy 1982, 9:109-116.
13. Hoppe W., Schramm H.J., Sturm M., Hunsmann N., Gassmann J. 3-Dimensional electron-microscopy of individual biological objects. III. Experimental results on yeast fatty-acid synthetase. Z. Naturforsch. a 1976, 31a:1380-1390.
14. Hoppe W., Schramm H.J., Sturm M., Hunsmann N., Gassmann J. 3-Dimensional electron-microscopy of individual biological objects. II. Test calculations. Z. Naturforsch. a 1976, 31a:1370-1379.
15. Hoppe W., Schramm H.J., Sturm M., Hunsmann N., Gassmann J. 3-Dimensional electron-microscopy of individual biological objects. I. Methods. Z. Naturforsch. a 1976, 31a:645-655.
16. Leschziner A.E., Nogales E. The orthogonal tilt reconstruction method: an approach to generating single-class volumes with no missing cone for ab initio reconstruction of asymmetric particles. J. Struct. Biol. 2006, 153:284-299.
17. Penczek P.A. Fundamentals of three-dimensional reconstruction from projections. Methods Enzymol. 2010, 482:1-33.
18. Radermacher M. Three-dimensional reconstruction from random projections: orientational alignment via Radon transforms. Ultramicroscopy 1994, 53:121-136.
19. Radermacher M. Radon transform techniques for alignment and three-dimensional reconstruction from random projections. Scanning Microsc. 1997, 11:171-177.
20. Radermacher M., Frank J. Use of nonlinear mapping in multivariate image analysis of molecule projections. Ultramicroscopy 1985, 17:117-126.
21. Radermacher M., Wagenknecht T., Verschoor A., Frank J. A new 3-dimensional reconstruction scheme applied to the 50s ribosomal subunit of E. coli. J. Microsc. 1986, 141:Rp1-Rp2.
22. Radermacher M., Wagenknecht T., Verschoor A., Frank J. Three-dimensional reconstruction from a single-exposure, random conical tilt series applied to the 50S ribosomal subunit of Escherichia coli. J. Microsc. 1987, 146:113-136.
23. Radermacher M., Ruiz T., Wieczorek H., Gruber G. The structure of the V(1)-ATPase determined by three-dimensional electron microscopy of single particles. J. Struct. Biol. 2001, 135:26-37.
24. Radermacher M., Ruiz T., Clason T., Benjamin S., Brandt U., Zickermann V. The three-dimensional structure of complex I from Yarrowia lipolytica: a highly dynamic enzyme. J. Struct. Biol. 2006, 154:269-279.
25. Rath B.K., Frank J. Fast automatic particle picking from cryo-electron micrographs using a locally normalized cross-correlation function: a case study. J. Struct. Biol. 2004, 145:84-90.
26. Rath B.K., Hegerl R., Leith A., Shaikh T.R., Wagenknecht T., Frank J. Fast 3D motif search of EM density maps using a locally normalized cross-correlation function. J. Struct. Biol. 2003, 144:95-103.
27. Rosenthal P.B., Henderson R. Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. J. Mol. Biol. 2003, 333:721-745.
28. Ruiz T., Kopperschläger G., Radermacher M. The first three-dimensional structure of phosphofructokinase from Saccharomyces cerevisiae determined by electron microscopy of single particles. J. Struct. Biol. 2001, 136:167-180.
29. Sachs L. Applied Statistics. A Handbook of Techniques 1984, Springer, New York, p. 77. second ed.
30. Sammon J.W. A nonlinear mapping for data structure analysis. IEEE Trans. Comput. 1969, 18:401-409.
31. Schmid M.F., Booth C.R. Methods for aligning and for averaging 3D volumes with missing data. J. Struct. Biol. 2008, 161:243-248.
32. Stölken M., Beck F., Haller T., Hegerl R., Gutsche I., Carazo J.-M., Baumeister W., Scheres S.H.W., Nickell S. Maximum likelihood based classification of electron tomographic data. J. Struct. Biol. 2011, 173:77-85.
33. Welling J.S., Eddy W.F., Young T.K. Rotation of 3D volumes by Fourier-interpolated shears. Graph Models 2006, 68:356-370.
34. Winkler H. 3D reconstruction and processing of volumetric data in cryo-electron tomography. J. Struct. Biol. 2007, 157:126-137.
35. Winkler H., Zhu P., Liu J., Ye F., Roux K.H., Taylor K.A. Tomographic subvolume alignment and subvolume classification applied to myosin V and SIV envelope spikes. J. Struct. Biol. 2009, 165:64-77.
36. Yoo J.C., Han T. Fast normalized cross-correlation. Circ. Syst. Signal Process. 2009, 28:819-843.
37. Yu L., Snapp R.R., Ruiz T., Radermacher M. Probabilistic principal component analysis with expectation maximization (PPCA-EM) facilitates volume classification and estimates the missing data. J. Struct. Biol. 2010, 171:18-30.