Skip to main content

Alignment of Tilt Series

  • Chapter
  • First Online:
Cellular Imaging

Part of the book series: Biological and Medical Physics, Biomedical Engineering ((BIOMEDICAL))

  • 1601 Accesses

Abstract

Computing of three-dimensional reconstructions from images obtained by transmission electron tomography needs three main steps: data acquisition, projection alignment, and 3D reconstruction. In this chapter we will focus on the process of alignment moving from the justification of its need to the study of the different classical approaches (cross-correlation, use of added fiducial markers) that have been commonly used in this alignment process. We will also discuss the most recent algorithms (multiscale registration, invariant feature recognition) as they have been adapted to Electron Tomography and improved to increase the accuracy and resolution of the final tomograms.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Institutional subscriptions

References

  1. B. Turoňová, L. Marsalek, P. Slusallek, On geometric artifacts in cryo electron tomography. Ultramicroscopy 163, 48–61 (2016)

    Article  Google Scholar 

  2. J. Frank, B.F. McEwen, M. Radermacher, J.N. Turner, C.L. Rieder, Three-dimensional tomographic reconstruction in high voltage electron microscopy. J. Electron Microsc. Tech. 6, 193–205 (1987)

    Article  Google Scholar 

  3. J. Frank, B.F. McEwen, Alignment by cross-correlation. Electron Tomogr (Springer Science, 1992), pp. 205–213

    Google Scholar 

  4. R. Guckenberger, Determination of a common origin in the micrographs of titl series in three-dimensional electron microscopy. Ultramicroscopy 9, 167–174 (1982)

    Article  Google Scholar 

  5. S. Brandt, J. Heikkonen, P. Engehardt, Automatic alignment of transmission electron microscope tilt series without fiducial markers. J. Struct. Biol. 136, 201–213 (2001)

    Article  Google Scholar 

  6. M. Cao, H.-B. Zhang, Y. Lu, R. Nishi, A. Takaoka, Formation and reduction of streak artefacts in electron tomography. J. Microsc. 239(1), 66–71 (2010)

    Google Scholar 

  7. Y. Cong, J.A. Kovacs, W. Wriggers, 2D fast rotational matching for image processing of biophysical data. J. Struct. Biol. 144(1–2), 51–60 (2003)

    Article  Google Scholar 

  8. X. Li, P. Mooney, S. Zheng, C.R. Booth, M.B. Braunfeld, S. Gubbens, D.A. Agard, Y. Cheng, Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM. Nature Methods 10(6), 584–590 (2013)

    Google Scholar 

  9. M. Petrou, C. Petrou, Image processing: The Fundamentals. (John Wiley & Sons, 2010)

    Google Scholar 

  10. S. Brandt, J. Heikkonen, P. Engehardt, Multiphase method for automatic alignment of transmission electron microscope images using markers. J. Struct. Biol. 133, 10–22 (2001)

    Article  Google Scholar 

  11. H. Winkler, K.A. Taylor, Accurate marker-free alignment with simultaneous geometry determination and reconstruction of tilt series in electron tomography. Ultramicroscopy 106(3), 240–254 (2006)

    Google Scholar 

  12. S. Brandt, J. Heikkonen, Optimal method for the affine F-matrix and its uncertainty estimation in the sense of both noise and outliers. In Proc. of the 8th IEEE Intl. Conf. on Computer Vision (ICCV) (Vancouver, Canada, 2001), pp. 166–173

    Google Scholar 

  13. F. Cantele, E. Paccagnini, G. Pigino, P. Lupetti, S. Lanzavecchia, Simultaneous alignment of dual-axis tilt series. J. Struct. Biol. 169(2), 192–199 (2010)

    Article  Google Scholar 

  14. D. Castaño-Díez, A. Al-Amoudi, A.M. Glynn, A. Seybert, A.S. Frangakis, Fiducial-less alignment of cryo-sections. J. Struct. Biol. 159(3), 413–423 (2007)

    Article  Google Scholar 

  15. D. Castaño-Díez, A. Seybert, A.S. Frangakis, Tilt-series and electron microscope alignment for the correction of the non-perpendicularity of beam and tilt-axis. J. Struct. Biol. 154, 195–205 (2006)

    Article  Google Scholar 

  16. M.C. Lawrence, Least-squares method of alignment using markers. Electron tomogr. (Springer, 1992), pp. 197–204

    Google Scholar 

  17. P. Penczek, M. Marko, K. Buttle, J. Frank, Double-tilt electron tomography. Ultramicroscopy 60(3), 393–410 (1995)

    Article  Google Scholar 

  18. C.O.S. Sorzano, C. Messaoudi, M. Eibauer, J.R. Bilbao-Castro, R. Hegerl, S. Nickell, S. Marco, J.M. Carazo, Marker-free image registration of electron tomography tilt-series. Bmc Bioinf. 10(1), 1 (2009)

    Google Scholar 

  19. P.J. Burt, E.H. Adelson, The Laplacian pyramid as a compact image code. Commun. IEEE Trans. 31(4), 532–540 (1983)

    Google Scholar 

  20. E. Tadmor, S. Nezzar, L. Vese, A multiscale image representation using hierarchical (BV, L 2) decompositions. Multiscale Model. Simul. 2(4), 554–579 (2004)

    Article  MathSciNet  MATH  Google Scholar 

  21. S. Klein, M. Staring, J.P.W. Pluim, Evaluation of optimization methods for nonrigid medical image registration using mutual information and B-splines. Image Process. IEEE Trans. 16(12), 2879–2890 (2007)

    Google Scholar 

  22. V.R.S. Mani, S. Arivazhagan, J.J. Braino, Multimodal image fusion using multiresolution techniques. Elixir Adv. Engg. Info. A. 55, 13160–13163 (2013)

    Google Scholar 

  23. D.C. Paquin, D. Levy, E. Schreibmann, L. Xing, Multiscale image registration. Mathematics 5 (2006)

    Google Scholar 

  24. P.J. Slomka, R.P. Baum, Multimodality image registration with software: state-of-the-art. Eur. J. Nucl. Med. Mol. Imaging 36(1), 44–55 (2009)

    Google Scholar 

  25. A. Collignon, F. Maes, D. Delaere, D. Vandermeulen, P. Suetens, G. Marchal, Automated multi-modality image registration based on information theory. Inf. Process. Med. Imaging 263–274 (1995)

    Google Scholar 

  26. W.M. Wells, P. Viola, H. Atsumi, S. Nakajima, R. Kikinis, Multi-modal volume registration by maximization of mutual information. Med. Image Anal. 1(1), 35–51 (1996)

    Google Scholar 

  27. D.G. Lowe, Distinctive image features from scale-invariant keypoints. Int. J. Comput. Vis. 60(2), 91–110 (2004)

    Google Scholar 

  28. R. Han, F. Zhang, X. Wan, J.-J. Fernández, F. Sun, Z. Liu, A marker-free automatic alignment method based on scale-invariant features. J. Struct. Biol. 186(1), 167–180 (2014)

    Article  Google Scholar 

  29. E. Rosten, T. Drummond, Machine learning for high-speed corner detection. Comput. Vision–ECCV 2006 (Springer, 2006), pp. 430–443

    Google Scholar 

  30. H. Bay, T. Tuytelaars, L. Van Gool, Surf: speeded up robust features. Proc. Computer Vision-ECCV (2006)

    Google Scholar 

  31. E. Rublee, V. Rabaud, K. Konolige, G. Bradski, ORB: an efficient alternative to SIFT or SURF. In Computer Vision (ICCV), 2011 IEEE International Conference on, pp. 2564–2571 (IEEE) (2011)

    Google Scholar 

  32. M. Calonder, V. Lepetit, M. Ozuysal, T. Trzcinski, C. Strecha, Pascal Fua, BRIEF: computing a local binary descriptor very fast. IEEE Trans. Pattern Anal. Mach. Intell. 34, 1281–1298 (2012)

    Article  Google Scholar 

  33. Engin Tola, Vincent Lepetit, Pascal Fua, Daisy: an efficient dense descriptor applied to wide-baseline stereo. Pattern Anal. Mach. Intell. IEEE Trans. 32(5), 815–830 (2010)

    Article  Google Scholar 

  34. S. Leutenegger, M. Chli, R.Y. Siegwart, BRISK: binary robust invariant scalable keypoints. In Computer Vision (ICCV), 2011 IEEE International Conference on, pp. 2548–2555 (IEEE) (2011)

    Google Scholar 

  35. F. Von Hundelshausen, R. Sukthankar, D-nets: beyond patch-based image descriptors. In Computer Vision and Pattern Recognition (CVPR), 2012 IEEE Conference on, pp. 2941–2948 (IEEE) (2012)

    Google Scholar 

  36. S. Lanzavecchia, F. Cantele, P.L. Bellon, L. Zampighi, M. Kreman, E. Wright, G.A. Zampighi, Conical tomography of freeze-fracture replicas: a method for the study of integral membrane proteins inserted in phospholipid bilayers. J. Struct. Biol. 149(1), 87–98 (2005)

    Article  Google Scholar 

  37. D.N. Mastronarde, Dual-axis tomography: an approach with alignment methods that preserve resolution. J Struct. Biol. 120(3), 343–352 (1997)

    Google Scholar 

  38. S. Hata, H. Miyazaki, S. Miyazaki, M. Mitsuhara, M. Tanaka, K. Kaneko, K. Higashida, K. Ikeda, H. Nakashima, S. Matsumura, and others, High-angle triple-axis specimen holder for three-dimensional diffraction contrast imaging in transmission electron microscopy. Ultramicroscopy. 111(8), 1168–1175 (2011)

    Google Scholar 

  39. C. Messaoudi, N.Garreau Loubresse, T. Boudier, P. Dupuis-Williams, S. Marco, Multiple-axis tomography: applications to basal bodies from Paramecium tetraurelia. Biol. Cell 98(7), 415–425 (2006)

    Article  Google Scholar 

  40. J.R. Kremer, D.N. Mastronarde, J.R. McIntosh, Computer visualization of three-dimensional image data using IMOD. J. Struct. Biol. 71–76 (1996)

    Google Scholar 

  41. J.A.G. Briggs, Structural biology in situ–the potential of subtomogram averaging. Curr. Opin. Struct. Biol. 23(2), 261–267 (2013)

    Google Scholar 

  42. J. Frank, Three-Dimensional Electron Microscopy of Macromolecular Assemblies: Visualization of Biological Molecules in Their Native State (Oxford Univ. Press, New York, USA, 2006)

    Book  Google Scholar 

  43. D. Castaño-Dez, M. Kudryashev, M. Arheit, H. Stahlberg, Dynamo: a flexible, user-friendly development tool for subtomogram averaging of cryo-EM data in high-performance computing environments. J. Struct. Biol. 178(2), 139–151 (2012)

    Article  Google Scholar 

  44. A.M.B. Tanmay, J.R. Christophe, L. Jan, A.P. Lori, H.W.S. Sjors, Advances in single-particle electron cryomicroscopy structure determination applied to sub-tomogram averaging. Structure 23(9), 1743–1753 (2015)

    Google Scholar 

  45. I. Arganda-Carreras, C.O.S. Sorzano, J. Kybic, C. Ortiz de Solórzano, bUnwarpJ: consistent and Elastic Registration in ImageJ. Methods and Applications. Proc. Conference Image J Users-Developers, Luxembourg (2008)

    Google Scholar 

  46. C.O.S. Sorzano, P. Thévenaz, M. Unser, Elastic registration of biological images using vector-spline regularization. IEEE Trans. Biomed. Eng. 52(4), 652–663 (2005)

    Google Scholar 

  47. C.-W. Wang, E.B. Gosno, Y.-S. Li, Fully automatic and robust 3D registration of serial-section microscopic images. Sci. R. 5 (2015)

    Google Scholar 

  48. S. Saalfeld, R. Fetter, A. Cardona, P. Tomancak, Elastic volume reconstruction from series of ultra-thin microscopy sections. Nat. Methods 9(7), 717–720 (2012)

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to S. Marco .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2018 Springer International Publishing AG

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Verguet, A., Messaoudi, C., Sorzano, C.O.S., Marco, S. (2018). Alignment of Tilt Series. In: Hanssen, E. (eds) Cellular Imaging. Biological and Medical Physics, Biomedical Engineering. Springer, Cham. https://doi.org/10.1007/978-3-319-68997-5_7

Download citation

Publish with us

Policies and ethics