References
1. A. Leis, B. Rockel, L. Andrees, W. Baumeister, Visualizing cells at the nanoscale. Trends
Biochem. Sci. 34, 60–70 (2009)
2. E.I. Tocheva, Z. Li, G.J. Jensen, Electron cryotomography. Cold Spring Harb. Perspect.
Biol. 2, a003442 (2010)
3. C.V. Robinson, A. Sali, W. Baumeister, The molecular sociology of the cell. Nature 450,
973–982 (2007)
4. S. Nickell, C. Kofler, A.P. Leis, W. Baumeister, A visual approach to proteomics. Nat. Rev.
Mol. Cell Biol. 7, 225–230 (2006)
5. S. Asano, B.D. Engel, W. Baumeister, In situ cryo-electron tomography: a post-reductionist
approach to structural biology. J. Mol. Biol. 428, 332–343 (2015)
6. W.T. Baxter, R.A. Grassucci, H. Gao, J. Frank, Determination of signal-to-noise ratios and
spectral SNRs in cryo-EM low-dose imaging of molecules. J. Struct. Biol. 166, 126–132
(2009)
7. S.H. Scheres, H. Gao, M. Valle, G.T. Herman, P.P. Eggermont, J. Frank, J.M. Carazo,
Disentangling conformational states of macromolecules in 3D-EM through likelihood
optimization. Nat. Methods 4, 27–29 (2007)
8. P. Penczek, M. Marko, K. Buttle, J. Frank, Double-tilt electron tomography.
Ultramicroscopy 60, 393–410 (1995)
9. D.N. Mastronarde, Dual-axis tomography: an approach with alignment methods that
preserve resolution. J. Struct. Biol. 120, 343–352 (1997)
10. S. Nickell, R. Hegerl, W. Baumeister, R. Rachel, Pyrodictium cannulae enter the periplasmic
space but do not enter the cytoplasm, as revealed by cryo-electron tomography. J. Struct.
Biol. 141, 34–42 (2003)
11. J. Dubochet, M. Adrian, J.-J. Chang, J.-C. Homo, J. Lepault, A.W. McDowall, P. Schultz,
Cryo-electron microscopy of vitrified specimens. Q. Rev. Biophys. 21, 129–228 (1988)
12. C.V. Iancu, E.R. Wright, J.B. Heymann, G.J. Jensen, A comparison of liquid nitrogen and
liquid helium as cryogens for electron cryotomography. J. Struct. Biol. 153, 231–240 (2006)
13. B.F. McEwen, K.H. Downing, R.M. Glaeser, The relevance of dose-fractionation in
tomography of radiation-sensitive specimens. Ultramicroscopy 60, 357–373 (1995)
14. N. Grigorieff, Direct detection pays off for electron cryo-microscopy. Elife 2, e00573 (2013)
15. Y. Fukuda, U. Laugks, V. Lučić, W. Baumeister, R. Danev, Electron cryotomography of
vitrified cells with a Volta phase plate. J. Struct. Biol. 190, 143–154 (2015)
16. A. Al-Amoudi, L.P. Norlen, J. Dubochet, Cryo-electron microscopy of vitreous sections of
native biological cells and tissues. J. Struct. Biol. 148, 131–135 (2004)
17. A. Rigort, F.J. Bäuerlein, E. Villa, M. Eibauer, T. Laugks, W. Baumeister, J.M. Plitzko,
Focused ion beam micromachining of eukaryotic cells for cryoelectron tomography. Proc.
Natl. Acad. Sci. U. S. A. 109, 4449–4454 (2012)
18. B.F. McEwen, M. Marko, The emergence of electron tomography as an important tool for
investigating cellular ultrastructure. J. Histochem. Cytochem. 49, 553–564 (2001)
19. K. Grünewald, O. Medalia, A. Gross, A.C. Steven, W. Baumeister, Prospects of electron
cryotomography to visualize macromolecular complexes inside cellular compartments:
implications of crowding. Biophys. Chem. 100, 577–591 (2003)
20. B.J. Marsh, Lessons from tomographic studies of the mammalian Golgi. Biochim. Biophys.
Acta 1744, 273–292 (2005)
21. T.G. Frey, G.A. Perkins, M.H. Ellisman, Electron tomography of membrane-bound cellular
organelles. Annu. Rev. Biophys. Biomol. Struct. 35, 199–224 (2006)
22. R.I. Koning, A.J. Koster, Cryo-electron tomography in biology and medicine. Ann Anat.
191, 427–445 (2009)
23. K. Ben-Harush, T. Maimon, I. Patla, E. Villa, O. Medalia, Visualizing cellular processes at
the molecular level by cryo-electron tomography. J. Cell Sci. 123, 7–12 (2010)
12 Segmentation of Features in Electron Tomographic Reconstructions
313
1. A. Leis, B. Rockel, L. Andrees, W. Baumeister, Visualizing cells at the nanoscale. Trends
Biochem. Sci. 34, 60–70 (2009)
2. E.I. Tocheva, Z. Li, G.J. Jensen, Electron cryotomography. Cold Spring Harb. Perspect.
Biol. 2, a003442 (2010)
3. C.V. Robinson, A. Sali, W. Baumeister, The molecular sociology of the cell. Nature 450,
973–982 (2007)
4. S. Nickell, C. Kofler, A.P. Leis, W. Baumeister, A visual approach to proteomics. Nat. Rev.
Mol. Cell Biol. 7, 225–230 (2006)
5. S. Asano, B.D. Engel, W. Baumeister, In situ cryo-electron tomography: a post-reductionist
approach to structural biology. J. Mol. Biol. 428, 332–343 (2015)
6. W.T. Baxter, R.A. Grassucci, H. Gao, J. Frank, Determination of signal-to-noise ratios and
spectral SNRs in cryo-EM low-dose imaging of molecules. J. Struct. Biol. 166, 126–132
(2009)
7. S.H. Scheres, H. Gao, M. Valle, G.T. Herman, P.P. Eggermont, J. Frank, J.M. Carazo,
Disentangling conformational states of macromolecules in 3D-EM through likelihood
optimization. Nat. Methods 4, 27–29 (2007)
8. P. Penczek, M. Marko, K. Buttle, J. Frank, Double-tilt electron tomography.
Ultramicroscopy 60, 393–410 (1995)
9. D.N. Mastronarde, Dual-axis tomography: an approach with alignment methods that
preserve resolution. J. Struct. Biol. 120, 343–352 (1997)
10. S. Nickell, R. Hegerl, W. Baumeister, R. Rachel, Pyrodictium cannulae enter the periplasmic
space but do not enter the cytoplasm, as revealed by cryo-electron tomography. J. Struct.
Biol. 141, 34–42 (2003)
11. J. Dubochet, M. Adrian, J.-J. Chang, J.-C. Homo, J. Lepault, A.W. McDowall, P. Schultz,
Cryo-electron microscopy of vitrified specimens. Q. Rev. Biophys. 21, 129–228 (1988)
12. C.V. Iancu, E.R. Wright, J.B. Heymann, G.J. Jensen, A comparison of liquid nitrogen and
liquid helium as cryogens for electron cryotomography. J. Struct. Biol. 153, 231–240 (2006)
13. B.F. McEwen, K.H. Downing, R.M. Glaeser, The relevance of dose-fractionation in
tomography of radiation-sensitive specimens. Ultramicroscopy 60, 357–373 (1995)
14. N. Grigorieff, Direct detection pays off for electron cryo-microscopy. Elife 2, e00573 (2013)
15. Y. Fukuda, U. Laugks, V. Lučić, W. Baumeister, R. Danev, Electron cryotomography of
vitrified cells with a Volta phase plate. J. Struct. Biol. 190, 143–154 (2015)
16. A. Al-Amoudi, L.P. Norlen, J. Dubochet, Cryo-electron microscopy of vitreous sections of
native biological cells and tissues. J. Struct. Biol. 148, 131–135 (2004)
17. A. Rigort, F.J. Bäuerlein, E. Villa, M. Eibauer, T. Laugks, W. Baumeister, J.M. Plitzko,
Focused ion beam micromachining of eukaryotic cells for cryoelectron tomography. Proc.
Natl. Acad. Sci. U. S. A. 109, 4449–4454 (2012)
18. B.F. McEwen, M. Marko, The emergence of electron tomography as an important tool for
investigating cellular ultrastructure. J. Histochem. Cytochem. 49, 553–564 (2001)
19. K. Grünewald, O. Medalia, A. Gross, A.C. Steven, W. Baumeister, Prospects of electron
cryotomography to visualize macromolecular complexes inside cellular compartments:
implications of crowding. Biophys. Chem. 100, 577–591 (2003)
20. B.J. Marsh, Lessons from tomographic studies of the mammalian Golgi. Biochim. Biophys.
Acta 1744, 273–292 (2005)
21. T.G. Frey, G.A. Perkins, M.H. Ellisman, Electron tomography of membrane-bound cellular
organelles. Annu. Rev. Biophys. Biomol. Struct. 35, 199–224 (2006)
22. R.I. Koning, A.J. Koster, Cryo-electron tomography in biology and medicine. Ann Anat.
191, 427–445 (2009)
23. K. Ben-Harush, T. Maimon, I. Patla, E. Villa, O. Medalia, Visualizing cellular processes at
the molecular level by cryo-electron tomography. J. Cell Sci. 123, 7–12 (2010)
12 Segmentation of Features in Electron Tomographic Reconstructions
313