Automated tilt series alignment and tomographic reconstruction in IMOD

Journal of Structural Biology

Volumn 197, Issue 2, 2017, Pages 102-113

  Mastronarde, David N ^a   Held, Susannah R ^a  

^a UNIVERSITY OF COLORADO   (United States)

Author keywords

Automated processing; Electron tomography; Tilt series alignment; Tomographic reconstruction

Indexed keywords

ACCURACY; ARTICLE; AUTOANALYSIS; BUDDING YEAST; CONTROLLED STUDY; HISTOGRAM; MITOSIS; NONHUMAN; PAPILLOMAVIRIDAE; PARTICLE SIZE; RELIABILITY; SOFTWARE; STRUCTURE ANALYSIS; SURFACE PROPERTY; VIRUS PARTICLE; ALGORITHM; AUTOMATION; CRYOELECTRON MICROSCOPY; DEVICES; ELECTRON TOMOGRAPHY; IMAGE PROCESSING; PROCEDURES;

ALGORITHMS; AUTOMATION; CRYOELECTRON MICROSCOPY; ELECTRON MICROSCOPE TOMOGRAPHY; IMAGE PROCESSING, COMPUTER-ASSISTED; SOFTWARE;

EID: 84994002598     PISSN: 10478477     EISSN: 10958657     Source Type: Journal    
DOI: 10.1016/j.jsb.2016.07.011     Document Type: Article

References (41)

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. 161 (2008), 260–275.
2. Asano, S., Engel, B.D., Baumeister, W., In situ cryo-electron tomography: a post-reductionist approach to structural biology. J. Mol. Biol. 428 (2016), 332–343.
3. Beaton, A.E., Tukey, J.W., The fitting of power series, meaning polynomials, illustrated on band-spectroscopic data. Technometrics 16 (1974), 147–185.
4. Bharat, T.A., Russo, C.J., Lowe, J., Passmore, L.A., Scheres, S.H., Advances in single-particle electron cryomicroscopy structure determination applied to sub-tomogram averaging. Structure 23 (2015), 1743–1753.
5. Brandt, S., Heikkonen, J., Engelhardt, P., Automatic alignment of transmission electron microscope tilt series without fiducial markers. J. Struct. Biol. 136 (2001), 201–213.
6. Briggs, J.A., Structural biology in situ – the potential of subtomogram averaging. Curr. Opin. Struct. Biol. 23 (2013), 261–267.
7. Brilot, A.F., Chen, J.Z., Cheng, A., Pan, J., Harrison, S.C., Potter, C.S., Carragher, B., Henderson, R., Grigorieff, N., Beam-induced motion of vitrified specimen on holey carbon film. J. Struct. Biol. 177 (2012), 630–637.
8. Castano-Diez, D., Al-Amoudi, A., Glynn, A.M., Seybert, A., Frangakis, A.S., Fiducial-less alignment of cryo-sections. J. Struct. Biol. 159 (2007), 413–423.
9. Castano-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. 170 (2010), 117–126.
10. Ding, H.J., Oikonomou, C.M., Jensen, G.J., The Caltech tomography database and automatic processing pipeline. J. Struct. Biol. 192 (2015), 279–286.
11. Engel, B.D., Schaffer, M., Albert, S., Asano, S., Plitzko, J.M., Baumeister, W., In situ structural analysis of Golgi intracisternal protein arrays. Proc. Natl. Acad. Sci. U.S.A. 112 (2015), 11264–11269.
12. Frangakis, A.S., Hegerl, R., Noise reduction in electron tomographic reconstructions using nonlinear anisotropic diffusion. J. Struct. Biol. 135 (2001), 239–250.
13. Fung, J.C., Liu, W., de Ruijter, W.J., Chen, H., Abbey, C.K., Sedat, J.W., Agard, D.A., Toward fully automated high-resolution electron tomography. J. Struct. Biol. 116 (1996), 181–189.
14. Gilbert, P., Iterative methods for the three-dimensional reconstruction of an object from projections. J. Theor. Biol. 36 (1972), 105–117.
15. Gross, A.M., Confidence intervals for bisquare regression estimates. J. Am. Stat. Assoc. 72 (1977), 341–354.
16. Han, R., Zhang, F., Wan, X., Fernandez, J.J., Sun, F., Liu, Z., A marker-free automatic alignment method based on scale-invariant features. J. Struct. Biol. 186 (2014), 167–180.
17. Han, R., Wang, L., Liu, Z., Sun, F., Zhang, F., A novel fully automatic scheme for fiducial marker-based alignment in electron tomography. J. Struct. Biol. 192 (2015), 403–417.
18. Holland, P.W., Welsch, R.E., Robust regression using iteratively reweighted least-squares. Commun. Stat. – Theory Methods 6 (1977), 813–827.
19. Hoog, J.L., Schwartz, C., Noon, A.T., O'Toole, E.T., Mastronarde, D.N., McIntosh, J.R., Antony, C., Organization of interphase microtubules in fission yeast analyzed by electron tomography. Dev. Cell 12 (2007), 349–361.
20. Koster, A.J., Chen, H., Sedat, J.W., Agard, D.A., Automated microscopy for electron tomography. Ultramicroscopy 46 (1992), 207–227.
21. Kremer, J.R., Mastronarde, D.N., McIntosh, J.R., Computer visualization of three-dimensional image data using IMOD. J. Struct. Biol. 116 (1996), 71–76.
22. Lander, G.C., Stagg, S.M., Voss, N.R., Cheng, A., Fellmann, D., Pulokas, J., Yoshioka, C., Irving, C., Mulder, A., Lau, P.W., Lyumkis, D., Potter, C.S., Carragher, B., Appion: an integrated, database-driven pipeline to facilitate EM image processing. J. Struct. Biol. 166 (2009), 95–102.
23. Mastronarde, D.N., Dual-axis tomography: an approach with alignment methods that preserve resolution. J. Struct. Biol. 120 (1997), 343–352.
24. Mastronarde, D.N., Automated electron microscope tomography using robust prediction of specimen movements. J. Struct. Biol. 152 (2005), 36–51.
25. Mastronarde, D.N., Fiducial marker and hybrid alignment methods for single- and double-axis tomography. Frank, J., (eds.) Electron Tomography, 2007, Springer, New York, 163–185.
26. Mastronarde, D.N., Automated tomographic reconstruction in the IMOD software package. Microsc. Microanal. 19:Suppl. 2 (2013), 544–545.
27. Nannas, N.J., O'Toole, E.T., Winey, M., Murray, A.W., Chromosomal attachments set length and microtubule number in the Saccharomyces cerevisiae mitotic spindle. Mol. Biol. Cell 25 (2014), 4034–4048.
28. Noble, A.J., Stagg, S.M., Automated batch fiducial-less tilt-series alignment in Appion using Protomo. J. Struct. Biol. 192 (2015), 270–278.
29. Noske, A.B., Costin, A.J., Morgan, G.P., Marsh, B.J., Expedited approaches to whole cell electron tomography and organelle mark-up in situ in high-pressure frozen pancreatic islets. J. Struct. Biol. 161 (2008), 298–313.
30. Owen, C.H., Landis, W.J., Alignment of electron tomographic series by correlation without the use of gold particles. Ultramicroscopy 63 (1996), 27–38.
31. Penczek, P., Marko, M., Buttle, K., Frank, J., Double-tilt electron tomography. Ultramicroscopy 60 (1995), 393–410.
32. Pfeffer, S., Burbaum, L., Unverdorben, P., Pech, M., Chen, Y., Zimmermann, R., Beckmann, R., Forster, F., Structure of the native Sec61 protein-conducting channel. Nat. Commun., 6, 2015, 8403.
33. Redemann, S., Muller-Reichert, T., Correlative light and electron microscopy for the analysis of cell division. J. Microsc. 251 (2013), 109–112.
34. Rousseeuw, P.J., Leroy, A.M., Robust Regression and Outlier Detection. 2003, John Wiley and Sons, Hoboken, New Jersey.
35. Schur, F.K.M., Hagen, W.J.H., de Marco, A., Briggs, J.A.G., Determination of protein structure at 8.5 Å resolution using cryo-electron tomography and sub-tomogram averaging. J. Struct. Biol. 184 (2013), 394–400.
36. Sorzano, C.O., Messaoudi, C., Eibauer, M., Bilbao-Castro, J.R., Hegerl, R., Nickell, S., Marco, S., Carazo, J.M., Marker-free image registration of electron tomography tilt-series. BMC Bioinformatics, 10, 2009, 124.
37. Suloway, C., Shi, J., Cheng, A., Pulokas, J., Carragher, B., Potter, C.S., Zheng, S.Q., Agard, D.A., Jensen, G.J., Fully automated, sequential tilt-series acquisition with Leginon. J. Struct. Biol. 167 (2009), 11–18.
38. Wilcox, R.R., Introduction to Robust Estimation and Hypothesis Testing. 2nd ed., 2005, Elsevier/Academic Press, Amsterdam.
39. Winkler, H., Taylor, K.A., Accurate marker-free alignment with simultaneous geometry determination and reconstruction of tilt series in electron tomography. Ultramicroscopy 106 (2006), 240–254.
40. Xiong, Q., Morphew, M.K., Schwartz, C.L., Hoenger, A.H., Mastronarde, D.N., CTF determination and correction for low dose tomographic tilt series. J. Struct. Biol. 168 (2009), 378–387.
41. Zheng, Q.S., Braunfeld, M.B., Sedat, J.W., Agard, D.A., An improved strategy for automated electron microscopic tomography. J. Struct. Biol. 147 (2004), 91–101.