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Electron Tomography: A Primer

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

Abstract

This chapter is an introduction to the theory and practise of electron tomography. It identifies the areas in need of most attention to maximise the efficiency of descriptive studies of morphology, and in the case of structural biology, to enable the transition from a reductionist approach to in-depth systems biology. The chapter concludes with a step-by-step guide to acquiring tomograms.

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References

  1. S. Nickell et al., A visual approach to proteomics. Nat. Rev. Mol. Cell. Biol. 7(3), 225–230 (2006)

    Article  Google Scholar 

  2. A. Hoenger, High-resolution cryo-electron microscopy on macromolecular complexes and cell organelles. Protoplasma 251(2), 417–427 (2014)

    Article  Google Scholar 

  3. Asano, S., B.D. Engel, and W. Baumeister, In Situ Cryo-Electron Tomography: A Post-Reductionist Approach to Structural Biology. J. Mol. Biol. (2016). 428(2 Pt A): p. 332–43

    Google Scholar 

  4. A. Leis et al., Visualizing cells at the nanoscale. Trends Biochem. Sci. 34(2), 60–70 (2009)

    Article  Google Scholar 

  5. U.E. Maurer, B. Sodeik, K. Grunewald, Native 3D intermediates of membrane fusion in herpes simplex virus 1 entry. Proc. Natl. Acad. Sci. U. S. A. 105(30), 10559–64 (2008)

    Article  ADS  Google Scholar 

  6. K. Iwasaki, T. Omura, Electron tomography of the supramolecular structure of virus-infected cells. Curr. Opin. Struct. Biol. 20(5), 632–9 (2010)

    Article  Google Scholar 

  7. I. Ibiricu et al., Cryo electron tomography of herpes simplex virus during axonal transport and secondary envelopment in primary neurons. PLoS Pathog. 7(12), e1002406 (2011)

    Article  Google Scholar 

  8. C. Risco et al., Three-Dimensional Imaging of Viral Infections. Annu. Rev. Virol. 1(1), 453–73 (2014)

    Article  ADS  Google Scholar 

  9. S. Padilla-Parra, M. Tramier, FRET microscopy in the living cell: different approaches, strengths and weaknesses. BioEssays. 34(5), 369–76 (2012)

    Article  Google Scholar 

  10. K. Grunewald et al., Prospects of electron cryotomography to visualize macromolecular complexes inside cellular compartments: implications of crowding. Biophys. Chem. 100(1–3), 577–91 (2003)

    Google Scholar 

  11. G. Foffi et al., Macromolecular crowding: chemistry and physics meet biology (Ascona, Switzerland, 10-14 June 2012). Phys. Biol. 10(4), 040301 (2013)

    Article  ADS  Google Scholar 

  12. V. Lucic, A. Leis, W. Baumeister, Cryo-electron tomography of cells: connecting structure and function. Histochem. Cell. Biol. 130(2), 185–96 (2008)

    Article  Google Scholar 

  13. A.V. Agronskaia et al., Integrated fluorescence and transmission electron microscopy. J. Struct. Biol. 164(2), 183–189 (2008)

    Article  Google Scholar 

  14. K. Cortese, A. Diaspro, C. Tacchetti, Advanced correlative light/electron microscopy: current methods and new developments using Tokuyasu cryosections. J. Histochem. Cytochem. 57(12), 1103–12 (2009)

    Article  Google Scholar 

  15. W. Kukulski et al., Correlated fluorescence and 3D electron microscopy with high sensitivity and spatial precision. J. Cell. Biol. 192(1), 111–9 (2011)

    Article  Google Scholar 

  16. R.I. Koning et al., Correlative cryo-fluorescence light microscopy and cryo-electron tomography of Streptomyces. Methods Cell. Biol. 124, 217–39 (2014)

    Article  Google Scholar 

  17. C. Loussert Fonta, B.M. Humbel, Correlative microscopy. Arch. Biochem. Biophys. 581, 98–110 (2015)

    Article  Google Scholar 

  18. Frank, J., ed. Electron tomography: methods for visualization of structures in the Cell. 2nd ed. (Springer: New York, 2006) p. 464

    Google Scholar 

  19. A.E. Yakushevska et al., STEM tomography in cell biology. J. Struct. Biol. 159(3), 381–91 (2007)

    Article  Google Scholar 

  20. S.G. Wolf, L. Houben, M. Elbaum, Cryo-scanning transmission electron tomography of vitrified cells. Nat. Methods 11(4), 423–8 (2014)

    Article  Google Scholar 

  21. W. Denk, H. Horstmann, Serial block-face scanning electron microscopy to reconstruct three-dimensional tissue nanostructure. PLoS Biol. 2(11), e329 (2004)

    Article  Google Scholar 

  22. M. Ballerini et al., Life science applications of focused ion beams (FIB). Eur. J. Histochem. 41(Suppl 2), 89–90 (1997)

    Google Scholar 

  23. J.A. Heymann et al., Site-specific 3D imaging of cells and tissues with a dual beam microscope. J. Struct. Biol. 155(1), 63–73 (2006)

    Article  Google Scholar 

  24. G. Knott et al., Serial section scanning electron microscopy of adult brain tissue using focused ion beam milling. J. Neurosci. 28(12), 2959–64 (2008)

    Article  Google Scholar 

  25. G. Knott, S. Rosset, M. Cantoni, Focussed ion beam milling and scanning electron microscopy of brain tissue. J. Vis. Exp. 53, e2588 (2011)

    Google Scholar 

  26. C. Kizilyaprak, J. Daraspe, B.M. Humbel, Focused ion beam scanning electron microscopy in biology. J. Microsc. 254(3), 109–14 (2014)

    Article  Google Scholar 

  27. W. Chiu et al., Electron cryomicroscopy of biological machines at subnanometer resolution. Structure 13(3), 363–72 (2005)

    Article  Google Scholar 

  28. J. Frank, Single-particle reconstruction of biological macromolecules in electron microscopy–30 years. Q. Rev. Biophys. 42(3), 139–58 (2009)

    Article  Google Scholar 

  29. C.F. Hryc, D.H. Chen, W. Chiu, Near-atomic-resolution cryo-EM for molecular virology. Curr. Opin. Virol. 1(2), 110–7 (2011)

    Article  Google Scholar 

  30. J. Chang et al., Reconstructing virus structures from nanometer to near-atomic resolutions with cryo-electron microscopy and tomography. Adv. Exp. Med. Biol. 726, 49–90 (2012)

    Article  Google Scholar 

  31. X.C. Bai, G. McMullan, S.H. Scheres, How cryo-EM is revolutionizing structural biology. Trends Biochem. Sci. 40(1), 49–57 (2015)

    Article  Google Scholar 

  32. E. Binshtein, M.D. Ohi, Cryo-electron microscopy and the amazing race to atomic resolution. Biochemistry 54(20), 3133–41 (2015)

    Article  Google Scholar 

  33. D. Elmlund, H. Elmlund, Cryogenic electron microscopy and single-particle analysis. Annu. Rev. Biochem. 84, 499–517 (2015)

    Article  Google Scholar 

  34. A.C. Steven, W. Baumeister, The future is hybrid. J. Struct. Biol. 163(3), 186–195 (2008)

    Article  Google Scholar 

  35. Plitzko, J.M. W. Baumeister, in Cryoelectron Tomography (CET), in Science of Microscopy, ed. by P.W. Hawkes, J.C.H. Spence (Springer: New York, 2007)

    Google Scholar 

  36. M.G. Rossmann, Structure of viruses: a short history. Q. Rev. Biophys. 46(2), 133–80 (2013)

    Article  Google Scholar 

  37. C.M. Oikonomou, G.J. Jensen, A new view into prokaryotic cell biology from electron cryotomography. Nat. Rev. Microbiol. 14(4), 205–20 (2016)

    Article  Google Scholar 

  38. S. Asano et al., Proteasomes. A molecular census of 26S proteasomes in intact neurons. Science 347(6220), 439–42 (2015)

    Article  ADS  Google Scholar 

  39. B.D. Engel et al., In situ structural analysis of Golgi intracisternal protein arrays. Proc. Natl. Acad. Sci. U. S. A. 112(36), 11264–9 (2015)

    Article  ADS  Google Scholar 

  40. Engel, B.D., et al., Native architecture of theChlamydomonaschloroplast revealed by in situ cryo-electron tomography. Elife 4 (2015)

    Google Scholar 

  41. J. Mahamid et al., Visualizing the molecular sociology at the HeLa cell nuclear periphery. Science 351(6276), 969–72 (2016)

    Article  ADS  Google Scholar 

  42. W. Hoppe et al., Three-dimensional reconstruction of individual negatively stained yeast fatty-acid synthetase molecules from tilt series in the electron microscope. Hoppe Seylers Z. Physiol. Chem. 355(11), 1483–7 (1974)

    Google Scholar 

  43. B.J. Marsh, M. Pavelka, Viewing Golgi structure and function from a different perspective–insights from electron tomography. Methods Cell. Biol. 118, 259–79 (2013)

    Article  Google Scholar 

  44. C. Suarez et al., Open membranes are the precursors for assembly of large DNA viruses. Cell. Microbiol. 15(11), 1883–95 (2013)

    Google Scholar 

  45. C. Suarez et al., African swine fever virus assembles a single membrane derived from rupture of the endoplasmic reticulum. Cell. Microbiol. 17(11), 1683–98 (2015)

    Article  Google Scholar 

  46. R.L. Felts et al., 3D visualization of HIV transfer at the virological synapse between dendritic cells and T cells. Proc. Natl. Acad. Sc.i U. S. A. 107(30), 13336–41 (2010)

    Article  ADS  Google Scholar 

  47. A.A. Linaroudis, Interpretation of electron tomograms of biological specimens by means of the Scaling Index Method, in Faculty of Chemistry. Technische Universität München (2006)

    Google Scholar 

  48. Y. Cheng et al., A primer to single-particle cryo-electron microscopy. Cell 161(3), 438–49 (2015)

    Article  Google Scholar 

  49. A. Leschziner, The orthogonal tilt reconstruction method. Methods Enzymol. 482, 237–62 (2010)

    Article  Google Scholar 

  50. J.O. Ortiz et al., Mapping 70S ribosomes in intact cells by cryoelectron tomography and pattern recognition. J. Struct. Biol. 156(2), 334–41 (2006)

    Article  Google Scholar 

  51. M. Beck et al., Visual proteomics of the human pathogenLeptospira interrogans. Nat. Methods 6(11), 817–U55 (2009)

    Article  Google Scholar 

  52. F. Forster, B.G. Han, M. Beck, Visual proteomics. Methods Enzymol. 483, 215–43 (2010)

    Article  Google Scholar 

  53. M. Beck et al., Exploring the spatial and temporal organization of a cell’s proteome. J. Struct. Biol. 173(3), 483–96 (2011)

    Article  Google Scholar 

  54. J.A. Briggs, Structural biology in situ–the potential of subtomogram averaging. Curr. Opin. Struct. Biol. 23(2), 261–7 (2013)

    Article  MathSciNet  Google Scholar 

  55. K. Grunewald et al., Three-dimensional structure of herpes simplex virus from cryo-electron tomography. Science 302(5649), 1396–8 (2003)

    Article  ADS  Google Scholar 

  56. N. Grigorieff, S.C. Harrison, Near-atomic resolution reconstructions of icosahedral viruses from electron cryo-microscopy. Curr. Opin. Struct. Biol. 21(2), 265–73 (2011)

    Article  Google Scholar 

  57. Baker, T.S., N.H. Olson, S.D. Fuller, Adding the third dimension to virus life cycles: three-dimensional reconstruction of icosahedral viruses from cryo-electron micrographs. Microbiol. Mol. Biol. Rev. 63(4), 862–922 (1999) table of contents

    Google Scholar 

  58. B.A. Afzelius, A.B. Maunsbach, Biological ultrastructure research; the first 50 years. Tissue Cell 36(2), 83–94 (2004)

    Article  Google Scholar 

  59. K.L. McDonald, R.I. Webb, Freeze substitution in 3 hours or less. J. Microsc. 243(3), 227–233 (2011)

    Article  Google Scholar 

  60. J.J. Wolosewick, K.R. Porter, Microtrabecular lattice of the cytoplasmic ground substance. Artifact or reality. J. Cell. Biol. 82(1), 114–39 (1979)

    Article  Google Scholar 

  61. J. Heuser, Whatever happened to the ‘microtrabecular concept’? Biol. Cell 94(9), 561–96 (2002)

    Article  Google Scholar 

  62. M.H. Ellisman, K.R. Porter, Microtrabecular structure of the axoplasmic matrix: visualization of cross-linking structures and their distribution. J. Cell. Biol. 87(2 Pt 1), 464–79 (1980)

    Article  Google Scholar 

  63. H. Kondo, On the real structure of the cytoplasmic matrix: learning from the embedment-free electron microscopy. Arch. Histol. Cytol. 58(4), 397–415 (1995)

    Article  Google Scholar 

  64. M. Gruska et al., Electron tomography of vitreous sections from cultured mammalian cells. J. Struct. Biol. 161(3), 384–392 (2008)

    Article  Google Scholar 

  65. T. Wagenknecht, C. Hsieh, M. Marko, Skeletal muscle triad junction ultrastructure by focused-ion-beam milling of muscle and cryo-electron tomography. Eur. J. Transl. Myol. 25(1), 4823 (2015)

    Article  Google Scholar 

  66. Y. Fukuda, A. Leis, A. Rigort, Preparation of vitrified cells for TEM by Cryo-FIB Microscopy, in Biological Field Emission Scanning Electron Microscopy, ed. by B. Humbel, R. Fleck (2016)

    Google Scholar 

  67. M. Marko et al., Focused-ion-beam thinning of frozen-hydrated biological specimens for cryo-electron microscopy. Nat. Methods 4(3), 215–217 (2007)

    Article  Google Scholar 

  68. A. Schertel et al., Cryo FIB-SEM: volume imaging of cellular ultrastructure in native frozen specimens. J. Struct. Biol. 184(2), 355–360 (2013)

    Article  Google Scholar 

  69. B.D. Engel, et al., Native architecture of the Chlamydomonas chloroplast revealed by in situ cryo-electron tomography. Elife 4 (2015)

    Google Scholar 

  70. C. Hoffmann et al., Disclosure of the mycobacterial outer membrane: Cryo-electron tomography and vitreous sections reveal the lipid bilayer structure. Proc. Natl. Acad. Sci. U.S.A. 105(10), 3963–3967 (2008)

    Article  ADS  Google Scholar 

  71. B. Zuber et al., Direct visualization of the outer membrane of mycobacteria and corynebacteria in their native state. J. Bacteriol. 190(16), 5672–5680 (2008)

    Article  Google Scholar 

  72. P.K. Luther, Sample shrinkage and radiation damage of plastic sections, in Electron Tomography: Methods for Three-Dimensional Visualization of Structures in the Cell, ed. by J. Frank (Springer, 2006)

    Google Scholar 

  73. Gordon, R., G.T. Herman, S.A. Johnson, Image reconstruction from projections. Sci. Am. 233(4), 56–61, 64–8 (1975)

    Google Scholar 

  74. R. Hegerl, W. Hoppe, Influence of electron noise on three-dimensional image reconstruction. Zeitschrift Naturforsch. A 314(12), 1717–1721 (1976)

    ADS  Google Scholar 

  75. B.F. McEwen, K.H. Downing, R.M. Glaeser, The relevance of dose-fractionation in tomography of radiation-sensitive specimens. Ultramicroscopy 60(3), 357–73 (1995)

    Article  Google Scholar 

  76. R. Grimm et al., Zero-loss energy filtering under low-dose conditions using a post-column energy filter. J. Microsc. 183(1), 60–68 (1996)

    Article  Google Scholar 

  77. D.N. Mastronarde, Dual-axis tomography: an approach with alignment methods that preserve resolution. J. Struct. Biol. 120(3), 343–52 (1997)

    Article  Google Scholar 

  78. S. Nickell et al., Pyrodictium cannulae enter the periplasmic space but do not enter the cytoplasm, as revealed by cryo-electron tomography. J. Struct. Biol. 141(1), 34–42 (2003)

    Article  Google Scholar 

  79. V. Lucic, F. Forster, W. Baumeister, Structural studies by electron tomography: from cells to molecules. Annu. Rev. Biochem. 74, 833–65 (2005)

    Article  Google Scholar 

  80. M.B. Braunfeld et al., Cryo automated electron tomography: towards high-resolution reconstructions of plastic-embedded structures. J. Microsc. 174(Pt 2), 75–84 (1994)

    Article  Google Scholar 

  81. M.L. Harlow et al., The architecture of active zone material at the frog’s neuromuscular junction. Nature 409, 479–484 (2001)

    Article  ADS  Google Scholar 

  82. P.K. Luther, Sample shrinkage and radiation damage of plastic sections, in Electron Tomography: Methods for Three-Dimensional Visualization of Structuresin the Cell, ed. by J. Frank (Springer, 2006)

    Google Scholar 

  83. P. Walther, M. Muller, Biological ultrastructure as revealed by high resolution cryo-SEM of block faces after cryo-sectioning. J. Microsc. 196(Pt 3), 279–87 (1999)

    Article  Google Scholar 

  84. A. Kreshuk et al., Automated detection and segmentation of synaptic contacts in nearly isotropic serial electron microscopy images. PLoS ONE 6(10), e24899 (2011)

    Article  ADS  Google Scholar 

  85. M. Marko et al., Focused ion beam milling of vitreous water: prospects for an alternative to cryo-ultramicrotomy of frozen-hydrated biological samples. Journal of Microscopy-Oxford 222, 42–47 (2006)

    Article  MathSciNet  Google Scholar 

  86. S. Masich et al., A procedure to deposit fiducial markers on vitreous cryo-sections for cellular tomography. J. Struct. Biol. 156(3), 461–8 (2006)

    Article  Google Scholar 

  87. D. Castano-Diez et al., Fiducial-less alignment of cryo-sections. J. Struct. Biol. 159(3), 413–423 (2007)

    Article  Google Scholar 

  88. C.O. Sorzano et al., Marker-free image registration of electron tomography tilt-series. BMC Bioinformatics 10, 124 (2009)

    Article  Google Scholar 

  89. F. Amat et al., Alignment of cryo-electron tomography datasets. Methods Enzymol. 482, 343–67 (2010)

    Article  Google Scholar 

  90. P.F.C. Gilbert, Reconstruction of a 3-dimensional structure from projections and its application to electron-microscopy. 2. Direct methods. Proc. Roy. Soc. London B, 182(1066), 89–102 (1972)

    Google Scholar 

  91. J. Radon, Über die Bestimmung von Funktionen durch ihre Integralwerte längs gewisser Mannigfaltigkeiten. Berichte über die Verhandlungen der Königlich Sächsischen Gesellschaft der Wissenschaften zu Leipzig. Math. Phys. Klasse. 69, 262–277 (1917)

    Google Scholar 

  92. R.N. Bracewell, A.C. Riddle, Inversion of fan-beam scans in radio astronomy. Astrophys. J. 150, 427–434 (1967)

    Article  ADS  Google Scholar 

  93. R. Gordon, G.T. Herman, Reconstruction of pictures from their projections. Graph. Image Proc. 14(12), 759–768 (1971)

    MATH  Google Scholar 

  94. G. Harauz, M. van Heel, Exact filters for general three-dimensional reconstruction. Optik 73, 146–156 (1986)

    Google Scholar 

  95. A.P. Leis et al., Cryo- electron tomography of biological specimens: the essential role of digital signal processing. IEEE Signal Process. Mag. 23(3), 95–103 (2006)

    Article  ADS  Google Scholar 

  96. G.T. Herman, S. Rowland, Resolution in ART. An experimental investigation of the resolving power of an algebraic picture reconstruction technique. J. Theor. Biol. 33(1), 213–23 (1971)

    Article  Google Scholar 

  97. G.T. Herman, A. Lent, S.W. Rowland, ART: mathematics and applications. A report on the mathematical foundations and on the applicability to real data of the algebraic reconstruction techniques. J. Theor. Biol. 42(1), 1–32 (1973)

    Article  Google Scholar 

  98. P. Gilbert, Iterative methods for 3-dimensional reconstruction of an object from projections. J. Theoret. Biol. 36(1), 105–117 (1972)

    Article  Google Scholar 

  99. R. Danev et al., Volta potential phase plate for in-focus phase contrast transmission electron microscopy. Proc. Natl. Acad. Sci. U. S. A. 111(44), 15635–40 (2014)

    Article  ADS  Google Scholar 

  100. G. Cardone, K. Grunewald, A.C. Steven, A resolution criterion for electron tomography based on cross-validation. J. Struct. Biol. 151(2), 117–29 (2005)

    Article  Google Scholar 

  101. P.A. Penczek, Resolution measures in molecular electron microscopy. Methods Enzymol. 482, 73–100 (2010)

    Article  Google Scholar 

  102. D. Derosier, 3D reconstruction from electron micrographs a personal account of its development. Methods Enzymol. 481, 1–24 (2010)

    Article  Google Scholar 

  103. A.B. Maunsbach, B.A. Afzelius, Biomedical Electron Microscopy: Illustrated Methods and Interpretations (San Diego: Academic Press, 1999), p. 548

    Google Scholar 

  104. S.W. Watson et al., A lobular, ammonia-oxidizing bacterium, Nitrosolobus multiformis nov.gen.nov.sp. Arch. Mikrobiol. 76(3), 183–203 (1971)

    Article  Google Scholar 

  105. A. Rigort et al., Automated segmentation of electron tomograms for a quantitative description of actin filament networks. J. Struct. Biol. 177(1), 135–44 (2012)

    Article  Google Scholar 

  106. M. Rusu et al., Automated tracing of filaments in 3D electron tomography reconstructions using Sculptor and Situs. J. Struct. Biol. 178(2), 121–8 (2012)

    Article  Google Scholar 

  107. O. Medalia et al., Macromolecular architecture in eukaryotic cells visualized by cryoelectron tomography. Science 298(5596), 1209–13 (2002)

    Article  ADS  Google Scholar 

  108. A.S. Frangakis, R. Hegerl, Noise reduction in electron tomographic reconstructions using nonlinear anisotropic diffusion. J. Struct. Biol. 135(3), 239–50 (2001)

    Article  Google Scholar 

  109. R. Henderson, Realizing the potential of electron cryo-microscopy. Q. Rev. Biophys. 37(1), 3–13 (2004)

    Article  Google Scholar 

  110. Y. Fukuda et al., Electron cryotomography of vitrified cells with a Volta phase plate. J. Struct. Biol. 190(2), 143–54 (2015)

    Article  Google Scholar 

  111. G. McMullan et al., Enhanced imaging in low dose electron microscopy using electron counting. Ultramicroscopy 109, 1411–1416 (2009)

    Article  Google Scholar 

  112. F. Forster et al., Retrovirus envelope protein complex structure in situ studied by cryo-electron tomography. Proc. Natl. Acad.Sci. U. S. A. 102(13), 4729–34 (2005)

    Article  ADS  Google Scholar 

  113. F.K. Schur et al., Structure of the immature HIV-1 capsid in intact virus particles at 8.8 A resolution. Nature 517(7535), 505–8 (2015)

    Article  ADS  Google Scholar 

  114. K. Murata et al., Zernike phase contrast cryo-electron microscopy and tomography for structure determination at nanometer and subnanometer resolutions. Structure 18(8), 903–12 (2010)

    Article  Google Scholar 

  115. K. Nagayama, Biological applications of phase-contrast electron microscopy. Methods Mol. Biol. 1117, 385–99 (2014)

    Article  Google Scholar 

  116. G.P. Kishchenko et al., Effect of fringe-artifact correction on sub-tomogram averaging from Zernike phase-plate cryo-TEM. J. Struct. Biol. 191(3), 299–305 (2015)

    Article  Google Scholar 

  117. T.H. Sharp, A.J. Koster, P. Gros, Heterogeneous MAC Initiator and Pore Structures in a Lipid Bilayer by Phase-Plate Cryo-electron Tomography. Cell. Rep. 15(1), 1–8 (2016)

    Article  Google Scholar 

  118. J. Dubochet, et al., CEMOVIS: Cryo-electron microscopy of vitreous sections, in Handbook of Cryo-Preparation Methods for Electron Microscopy, ed. by B. Humbel D. Spehner (CRC Press: Boca Raton, 2009) pp. 259–289

    Google Scholar 

  119. R. Danev, W. Baumeister, Cryo-EM single particle analysis with the Volta phase plate. Elife 5 (2016)

    Google Scholar 

  120. M.F. Schmid, C.R. Booth, Methods for aligning and for averaging 3D volumes with missing data. J. Struct. Biol. 161(3), 243–8 (2008)

    Article  Google Scholar 

  121. L. Kovacik et al., A simple Fourier filter for suppression of the missing wedge ray artefacts in single-axis electron tomographic reconstructions. J. Struct. Biol. 186(1), 141–52 (2014)

    Article  Google Scholar 

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

    Article  Google Scholar 

  123. C.M. Palmer, J. Lowe, A cylindrical specimen holder for electron cryo-tomography. Ultramicroscopy 137, 20–9 (2014)

    Article  Google Scholar 

  124. W. Kukulski et al., Precise, correlated fluorescence microscopy and electron tomography of lowicryl sections using fluorescent fiducial markers. Methods Cell. Biol. 111, 235–57 (2012)

    Article  Google Scholar 

  125. J. Arnold et al., Site-specific cryo-focused ion beam sample preparation guided by 3d correlative microscopy. Biophys. J. 110(4), 860–9 (2016)

    Article  ADS  Google Scholar 

  126. R. Henderson, Avoiding the pitfalls of single particle cryo-electron microscopy: einstein from noise. Proc. Natl. Acad. Sci. U.S.A. 110(45), 18037–18041 (2013)

    Article  ADS  Google Scholar 

  127. G.P. Henderson, L. Gan, G.J. Jensen, 3-D ultrastructure of O. tauri: electron cryotomography of an entire eukaryotic cell. PLoS ONE 2(8), e749 (2007)

    Article  ADS  Google Scholar 

  128. M.M. Farley et al., Minicells. Back in Fashion. J. Bacteriol. 198(8), 1186–95 (2016)

    Google Scholar 

  129. A. Rigort et al., Focused ion beam micromachining of eukaryotic cells for cryoelectron tomography. Proc. Natl. Acad. Sci. U.S.A. 109(12), 4449–4454 (2012)

    Article  ADS  Google Scholar 

  130. W.E. Moerner, M. Orrit, Illuminating single molecules in condensed matter. Science 283(5408), 1670–6 (1999)

    Article  ADS  Google Scholar 

  131. C.L. Schwartz et al., Cryo-fluorescence microscopy facilitates correlations between light and cryo-electron microscopy and reduces the rate of photobleaching. J. Microsc. 227(Pt 2), 98–109 (2007)

    Article  MathSciNet  Google Scholar 

  132. E. Betzig et al., Imaging intracellular fluorescent proteins at nanometer resolution. Science 313(5793), 1642–1645 (2006)

    Article  ADS  Google Scholar 

  133. Y.W. Chang et al., Correlated cryogenic photoactivated localization microscopy and cryo-electron tomography. Nat. Methods 11(7), 737–9 (2014)

    Article  Google Scholar 

  134. R. Kaufmann, C. Hagen, K. Grunewald, Fluorescence cryo-microscopy: current challenges and prospects. Curr. Opin. Chem. Biol. 20, 86–91 (2014)

    Article  Google Scholar 

  135. R. Kaufmann et al., Super-resolution microscopy using standard fluorescent proteins in intact cells under cryo-conditions. Nano. Lett. 14(7), 4171–5 (2014)

    Article  ADS  Google Scholar 

  136. G. Wolff, et al., Towards correlative super-resolution fluorescence and electron cryo-microscopy. Biol. Cell. (2016)

    Google Scholar 

  137. W. Kukulski et al., Plasma membrane reshaping during endocytosis is revealed by time-resolved electron tomography. Cell 150(3), 508–20 (2012)

    Article  Google Scholar 

  138. J. Sun, H. Li, How to operate a cryo-electron microscope. Methods Enzymol. 481, 231–49 (2010)

    Article  Google Scholar 

  139. C.V. Iancu et al., Electron cryotomography sample preparation using the Vitrobot. Nat. Protoc. 1(6), 2813–2819 (2006)

    Article  Google Scholar 

  140. R.A. Grassucci, D.J. Taylor, J. Frank, Preparation of macromolecular complexes for cryo-electron microscopy. Nat. Protoc. 2(12), 3239–3246 (2007)

    Article  Google Scholar 

  141. G.P. Resch et al., Immersion freezing of cell monolayers for cryo-electron tomography. Cold. Spring. Harb. Protoc. 2011(7), 815–23 (2011)

    Google Scholar 

  142. J.R. Kremer, D.N. Mastronarde, J.R. McIntosh, Computer visualization of three-dimensional image data using IMOD. J. Struct. Biol. 116(1), 71–6 (1996)

    Article  Google Scholar 

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Leis, A. (2018). Electron Tomography: A Primer. In: Hanssen, E. (eds) Cellular Imaging. Biological and Medical Physics, Biomedical Engineering. Springer, Cham. https://doi.org/10.1007/978-3-319-68997-5_1

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