4. J. Bohm, A.S. Frangakis, R. Hegerl, S. Nickell, D. Typke, W. Baumeister, Toward detecting
and identifying macromolecules in a cellular context: template matching applied to electron
tomograms. Proc. Natl. Acad. Sci. U.S.A. 97(26), 14245–14250 (2000). doi:10.1073/pnas.
230282097
5. M. Xu, F. Alber, Automated target segmentation and real space fast alignment methods for
high-throughput classification and averaging of crowded cryo-electron subtomograms.
Bioinformatics 29(13), i274–282 (2013). doi:10.1093/bioinformatics/btt225
6. X. Chen, Y. Chen, J.M. Schuller, N. Navab, F. Förster, Automatic particle picking and
multi-class classification in cryo-electron tomograms. Paper presented at the IEEE 11th
International Symposium on Biomedical Imaging, Beijing (2014)
7. F. Forster, B.G. Han, M. Beck, Visual proteomics. Methods Enzymol. 483, 215–243 (2010).
doi:10.1016/S0076-6879(10)83011-3
8. A.S. Frangakis, J. Bohm, F. Forster, S. Nickell, D. Nicastro, D. Typke, R. Hegerl,
W. Baumeister, Identification of macromolecular complexes in cryoelectron tomograms of
phantom cells. Proc. Natl. Acad. Sci. U.S.A. 99(22), 14153–14158 (2002). doi:10.1073/pnas.
172520299
9. F. Forster, O. Medalia, N. Zauberman, W. Baumeister, D. Fass, Retrovirus envelope protein
complex structure in situ studied by cryo-electron tomography. Proc. Natl. Acad. Sci. U.S.A.
102(13), 4729–4734 (2005). doi:10.1073/pnas.0409178102
10. J.O. Ortiz, F. Forster, J. Kurner, A.A. Linaroudis, W. Baumeister, Mapping 70S ribosomes in
intact cells by cryoelectron tomography and pattern recognition. J. Struct. Biol. 156(2),
334–341 (2006). doi:10.1016/j.jsb.2006.04.014
11. M. Beck, J.A. Malmstrom, V. Lange, A. Schmidt, E.W. Deutsch, R. Aebersold, Visual
proteomics of the human pathogen Leptospira interrogans. Nat. Methods 6(11), 817–823
(2009). doi:10.1038/nmeth.1390
12. J. Walz, D. Typke, M. Nitsch, A.J. Koster, R. Hegerl, W. Baumeister, Electron Tomography
of single ice-embedded macromolecules: three-dimensional alignment and classification.
J. Struct. Biol. 120(3), 387–395 (1997)
13. S.H. Scheres, R. Melero, M. Valle, J.M. Carazo, Averaging of electron subtomograms and
random conical tilt reconstructions through likelihood optimization. Structure 17(12),
1563–1572 (2009). doi:10.1016/j.str.2009.10.009
14. M. Stolken, F. Beck, T. Haller, R. Hegerl, I. Gutsche, J.M. Carazo, W. Baumeister, S.H.
Scheres, S. Nickell, Maximum likelihood based classification of electron tomographic data.
J. Struct. Biol. 173(1), 77–85 (2011). doi:10.1016/j.jsb.2010.08.005
15. T.A. Bharat, C.J. Russo, J. Lowe, L.A. Passmore, S.H. Scheres, Advances in single-particle
electron cryomicroscopy structure determination applied to sub-tomogram averaging.
Structure 23(9), 1743–1753 (2015). doi:10.1016/j.str.2015.06.026
16. S.H. Scheres, RELION: implementation of a Bayesian approach to cryo-EM structure
determination. J. Struct. Biol. 180(3), 519–530 (2012). doi:10.1016/j.jsb.2012.09.006
17. T. Hrabe, Y. Chen, S. Pfeffer, L.K. Cuellar, A.V. Mangold, F. Forster, PyTom: a
python-based toolbox for localization of macromolecules in cryo-electron tomograms and
subtomogram analysis. J. Struct. Biol. 178(2), 177–188 (2012). doi:10.1016/j.jsb.2011.12.003
18. N. Grigorieff, Resolution measurement in structures derived from single particles. Acta
Crystallogr. D Biol. Crystallogr. 56(Pt 10), 1270–1277 (2000)
19. Y. Chen, S. Pfeffer, T. Hrabe, J.M. Schuller, F. Forster, Fast and accurate reference-free
alignment of subtomograms. J. Struct. Biol. (2013). doi:10.1016/j.jsb.2013.03.002
20. A. Bartesaghi, P. Sprechmann, J. Liu, G. Randall, G. Sapiro, S. Subramaniam, Classification
and 3D averaging with missing wedge correction in biological electron tomography. J. Struct.
Biol. 162(3), 436–450 (2008). doi:10.1016/j.jsb.2008.02.008
21. F. Forster, S. Pruggnaller, A. Seybert, A.S. Frangakis, Classification of cryo-electron
sub-tomograms using constrained correlation. J. Struct. Biol. 161(3), 276–286 (2008). doi:10.
1016/j.jsb.2007.07.006
256
S. Pfeffer and F. Förster
and identifying macromolecules in a cellular context: template matching applied to electron
tomograms. Proc. Natl. Acad. Sci. U.S.A. 97(26), 14245–14250 (2000). doi:10.1073/pnas.
230282097
5. M. Xu, F. Alber, Automated target segmentation and real space fast alignment methods for
high-throughput classification and averaging of crowded cryo-electron subtomograms.
Bioinformatics 29(13), i274–282 (2013). doi:10.1093/bioinformatics/btt225
6. X. Chen, Y. Chen, J.M. Schuller, N. Navab, F. Förster, Automatic particle picking and
multi-class classification in cryo-electron tomograms. Paper presented at the IEEE 11th
International Symposium on Biomedical Imaging, Beijing (2014)
7. F. Forster, B.G. Han, M. Beck, Visual proteomics. Methods Enzymol. 483, 215–243 (2010).
doi:10.1016/S0076-6879(10)83011-3
8. A.S. Frangakis, J. Bohm, F. Forster, S. Nickell, D. Nicastro, D. Typke, R. Hegerl,
W. Baumeister, Identification of macromolecular complexes in cryoelectron tomograms of
phantom cells. Proc. Natl. Acad. Sci. U.S.A. 99(22), 14153–14158 (2002). doi:10.1073/pnas.
172520299
9. F. Forster, O. Medalia, N. Zauberman, W. Baumeister, D. Fass, Retrovirus envelope protein
complex structure in situ studied by cryo-electron tomography. Proc. Natl. Acad. Sci. U.S.A.
102(13), 4729–4734 (2005). doi:10.1073/pnas.0409178102
10. J.O. Ortiz, F. Forster, J. Kurner, A.A. Linaroudis, W. Baumeister, Mapping 70S ribosomes in
intact cells by cryoelectron tomography and pattern recognition. J. Struct. Biol. 156(2),
334–341 (2006). doi:10.1016/j.jsb.2006.04.014
11. M. Beck, J.A. Malmstrom, V. Lange, A. Schmidt, E.W. Deutsch, R. Aebersold, Visual
proteomics of the human pathogen Leptospira interrogans. Nat. Methods 6(11), 817–823
(2009). doi:10.1038/nmeth.1390
12. J. Walz, D. Typke, M. Nitsch, A.J. Koster, R. Hegerl, W. Baumeister, Electron Tomography
of single ice-embedded macromolecules: three-dimensional alignment and classification.
J. Struct. Biol. 120(3), 387–395 (1997)
13. S.H. Scheres, R. Melero, M. Valle, J.M. Carazo, Averaging of electron subtomograms and
random conical tilt reconstructions through likelihood optimization. Structure 17(12),
1563–1572 (2009). doi:10.1016/j.str.2009.10.009
14. M. Stolken, F. Beck, T. Haller, R. Hegerl, I. Gutsche, J.M. Carazo, W. Baumeister, S.H.
Scheres, S. Nickell, Maximum likelihood based classification of electron tomographic data.
J. Struct. Biol. 173(1), 77–85 (2011). doi:10.1016/j.jsb.2010.08.005
15. T.A. Bharat, C.J. Russo, J. Lowe, L.A. Passmore, S.H. Scheres, Advances in single-particle
electron cryomicroscopy structure determination applied to sub-tomogram averaging.
Structure 23(9), 1743–1753 (2015). doi:10.1016/j.str.2015.06.026
16. S.H. Scheres, RELION: implementation of a Bayesian approach to cryo-EM structure
determination. J. Struct. Biol. 180(3), 519–530 (2012). doi:10.1016/j.jsb.2012.09.006
17. T. Hrabe, Y. Chen, S. Pfeffer, L.K. Cuellar, A.V. Mangold, F. Forster, PyTom: a
python-based toolbox for localization of macromolecules in cryo-electron tomograms and
subtomogram analysis. J. Struct. Biol. 178(2), 177–188 (2012). doi:10.1016/j.jsb.2011.12.003
18. N. Grigorieff, Resolution measurement in structures derived from single particles. Acta
Crystallogr. D Biol. Crystallogr. 56(Pt 10), 1270–1277 (2000)
19. Y. Chen, S. Pfeffer, T. Hrabe, J.M. Schuller, F. Forster, Fast and accurate reference-free
alignment of subtomograms. J. Struct. Biol. (2013). doi:10.1016/j.jsb.2013.03.002
20. A. Bartesaghi, P. Sprechmann, J. Liu, G. Randall, G. Sapiro, S. Subramaniam, Classification
and 3D averaging with missing wedge correction in biological electron tomography. J. Struct.
Biol. 162(3), 436–450 (2008). doi:10.1016/j.jsb.2008.02.008
21. F. Forster, S. Pruggnaller, A. Seybert, A.S. Frangakis, Classification of cryo-electron
sub-tomograms using constrained correlation. J. Struct. Biol. 161(3), 276–286 (2008). doi:10.
1016/j.jsb.2007.07.006
256
S. Pfeffer and F. Förster