Alignment of cryo-electron tomography datasets

Methods in Enzymology

Volumn 482, Issue C, 2010, Pages 343-367

  Amat, Fernando ^a,e   Castaño Diez, Daniel ^b   Lawrence, Albert ^c   Moussavi, Farshid ^a   Winkler, Hanspeter ^d   Horowitz, Mark ^e  

^a Stanford University   (United States)

^b UNIVERSITY OF BASEL   (Switzerland)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d FLORIDA STATE UNIVERSITY   (United States)

^e HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BOOK; COMPUTER PROGRAM; CONTRAST ENHANCEMENT; ELECTRON TOMOGRAPHY; EXPERIMENTAL MODEL; IMAGE ANALYSIS; IMAGE RECONSTRUCTION; PRIORITY JOURNAL; SIMULATION; STRUCTURE ANALYSIS; THICKNESS; THREE DIMENSIONAL IMAGING;

EID: 77957300464     PISSN: 00766879     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0076-6879(10)82014-2     Document Type: Chapter

References (36)

1. Amat F., Moussavi F., Comolli L.R., Elidan G., Downing K.H., Horowitz M. Markov random field based automatic image alignment for electron tomography. J. Struct. Biol. 2008, 161:260-275.
2. Boyd S., Vandenberghe L. Convex Optimization 2004, Cambridge University Press.
3. Brandt S.S., Ziese U. Automatic TEM image alignment by trifocal geometry. J. Microsc. 2006, 222:1-14.
4. Brandt S., Heikkonen J., Engelhardt P. Automatic alignment of transmission electron microscope tilt series without fiducial markers. J. Struct. Biol. 2001, 136:201-213.
5. Brandt S., Heikkonen J., Engelhardt P. Multiphase method for automatic alignment of transmission electron microscope images using markers. J. Struct. Biol. 2001, 133:10-22.
6. Castaño-Diez D., Seybert A., Frangakis A.S. Tilt-series and electron microscope alignment for the correction of the non-perpendicularity of beam and tilt-axis. J. Struct. Biol. 2006, 154:195-205.
7. Castaño-Diez D., Al-Amoudi A., Glynn A.M., Seybert A., Frangakis A.S. Fiducial-less alignment of cryo-sections. J. Struct. Biol. 2007, 159:413-423.
8. Castaño-Diez D., Scheffer M., Al-Amoudi A., Frangakis A.S. Alignator: A gpu powered software package for robust fiducial-less alignment of cryo tilt-series. J. Struct. Biol. 2010, 170:117-126.
9. Defrise M., Noo F.K.H. Improved 2d rebinning of helical cone-beam ct data using johns's equation. Nucl. Sci. Symp. Conf. Rec. 2002, 3:1465-1469.
10. Elidan G., McGraw I., Koller D. Residual belief propagation: Informed scheduling for asynchronous message passing. Proceedings of the Twenty-Second Conference on Uncertainty in AI (UAI). 2006, AUAI Press, Boston, MA.
11. Frank J. Electron Tomography: Methods for Three-dimensional Visualization of Structures in the Cell 2006, Springer. 2nd edn.
12. Guckenberger R. Determination of a common origin in the micrographs of tilt series in three-dimensional electron microscopy. Ultramicroscopy 1982, 9:167-173.
13. Hartley R.I., Zisserman A. Multiple View Geometry in Computer Vision. 2004, Cambridge University Press. 2nd edn.
14. Herman G.T. Fundamentals of Computerized Tomography: Image Reconstruction from Projections 2009, Springer. 2nd edition.
15. Heymann J.B., Cardone G., Winkler D.C., Steven A.C., Heymann J.B., Cardone G., Winkler D.C., Steven A.C. Computational resources for cryo-electron tomography in bsoft. J. Struct. Biol. 2008, 161:232-242.
16. Kak A.C., Slaney M. Principles of Computerized Tomographic Imaging 2001, Society of Industrial and Applied Mathematics.
17. Kang K., Tarel J.P., Fishman R., Coope D. A linear dual-space approach to 3d surface reconstruction from occluding contours using algebraic surfaces. International Conference on Computer Vision. 2001, 198-204.
18. Kremer J.R., Mastronarde D.N., McIntosh J.R. Computer visualization of three-dimensional image data using imod. J. Struct. Biol. 1996, 116:71-76.
19. Lanzavecchia S., Cantele F., Bellon P., Zampighi L., Kreman M., Wright E., Zampighi G. Conical tomography of freeze-fracture replicas: a method for the study of integral membrane proteins inserted in phospholipid bilayers. J. Struct. Biol. 2005, 149:87-98.
20. Lawrence A., Bouwer J.C., Perkins G., Ellisman M.H. Transform-based backprojection for volume reconstruction of large format electron microscope tilt series. J. Struct. Biol. 2006, 154:144-167.
21. Lawrence A., Phan S., Moussavi F. 3d reconstruction from electron microscope images with txbr 2009, ISBI.
22. Liu J., Wu S., Reedy M.C., Winkler H., Lucaveche C., Cheng Y., Reedy M.K., Taylor K.A. Electron tomography of swollen rigor fibers of insect flight muscle reveals a short and variably angled s2 domain. J. Mol. Biol. 2006, 362:844-860.
23. Ma Y., Soatto S., Kosecka J., Sastry S.S. An Invitation to 3-D Vision: From Images to Geometric Models 2003, Springer.
24. Mastronarde D.N. Dual-axis tomography: An approach with alignment methods that preserve resolution. J. Struct. Biol. 1997, 120:343-352.
25. Nickell S., Frster F., Linaroudis A., Net W.D., Beck F., Hegerl R., Baumeister W., Plitzko J.M. Tom software toolbox: acquisition and analysis for electron tomography. J. Struct. Biol. 2005, 149:227-234.
26. Patch S.K. Consistency conditions upon 3d ct data and the wave equation. Phys. Med. Biol. 2002, 47:2637-2650.
27. Penczek P., Marko M., Buttle K., Frank J. Double-tilt electron tomography. Ultramicroscopy 1995, 60:393-410.
28. Phan S., Bouwer J., Lanman J., Terada M., Lawrence A. Non-linear bundle adjustment for electron tomography. World Congress on Computer Science and Information Engineering 2009.
29. Sorzano C., Messaoudi C., Eibauer M., Bilbao-Castro J., Hegerl R., Nickell S., Marco S., Carazo J. Marker-free image registration of electron tomography tilt-series. BMC Bioinform. 2009, 10:124.
30. Taylor K.A., Tang J., Cheng Y., Winkler H. The use of electron tomography for structural analysis of disordered protein arrays. J. Struct. Biol. 1997, 120:372-386.
31. Torresani L., Kolmogorov V., Rother C. Feature correspondence via graph matching: Models and global optimization 2008, Computer Vision ECCV 2008, pp. 596-609.
32. Trucco E., Verri A. Introductory Techniques for 3-D Computer Vision. 1998, Prentice Hall.
33. Winkler H. 3d reconstruction and processing of volumetric data in cryo-electron tomography. J. Struct. Biol. 2007, 157:126-137.
34. Winkler H., Taylor K.A. Accurate marker-free alignment with simultaneous geometry determination and reconstruction of tilt series in electron tomography. Ultramicroscopy 2006, 106:240-254.
35. Yedidia J.S., Freeman W.T., Weiss Y. Constructing free energy approximations and generalized belief propagation algorithms. IEEE Trans. Inf. Theory 2005, 51:2282-2313.
36. Zhu P., Liu J., Bess J., Chertova E., Lifson J.D., Gris H., Ofek G.A., Taylor K.A., Roux K.H. Distribution and three-dimensional structure of aids virus envelope spikes. Nature 2006, 441:847-852.