47. H.T. Nguyen, M. Worring, R. van den Boomgaard, Watersnakes: Energy-driven watershed
segmentation. IEEE Trans. Pattern Anal. Mach. Intell. 25, 330–342 (2003)
48. H. Nguyen, Q. Ji, Shape-driven three-dimensional watersnake segmentation of biological
membranes in electron tomography. IEEE Trans. Med. Imaging 27, 616–628 (2008)
49. M.N. Lebbink, N. Jimenez, K. Vocking, L.H. Hekking, A.J. Verkleij, J.A. Post, Spiral
coating of the endothelial caveolar membranes as revealed by electron tomography and
template matching. Traffic 11, 138–150 (2010)
50. M.N. Lebbink, W.J. Geerts, T.P. van der Krift, M. Bouwhuis, L.O. Hertzberger,
A.J. Verkleij, A.J. Koster, Template matching as a tool for annotation of tomograms of
stained biological structures. J. Struct. Biol. 158, 327–335 (2007)
51. C. Page, D. Hanein, N. Volkmann, Accurate membrane tracing in three-dimensional
reconstructions from electron cryotomography data. Ultramicroscopy 155, 20–26 (2015)
52. A. Briegel, S. Chen, A.J. Koster, J.M. Plitzko, C.L. Schwartz, G.J. Jensen, Correlated light
and electron cryo-microscopy. Methods Enzymol. 481, 317–341 (2010)
53. P. Schellenberger, R. Kaufmann, C.A. Siebert, C. Hagen, H. Wodrich, K. Grünewald,
High-precision correlative fluorescence and electron cryo microscopy using two independent
alignment markers. Ultramicroscopy 143, 41–51 (2014)
54. M. Schorb, J.A. Briggs, Correlated cryo-fluorescence and cryo-electron microscopy with
high spatial precision and improved sensitivity. Ultramicroscopy 143, 24–32 (2014)
55. G. Wolff, C. Hagen, K. Grünewald, R. Kaufmann, Towards correlative super-resolution
fluorescence and electron cryo-microscopy. Biol. Cell 108, 245–258 (2016)
56. J. Böhm, A.S. Frangakis, R. Hegerl, S. Nickell, D. Typke, W. Baumeister, From the cover:
toward detecting and identifying macromolecules in a cellular context: template matching
applied to electron tomograms. Proc. Natl. Acad. Sci. U. S. A. 97, 14245–14250 (2000)
57. G. Turin, An introduction to matched filters. IRE Trans. Inf. Theory 3, 311–329 (1960)
58. H.L. Van Trees, Classical detection and estimation theory, Detection, Estimation, and
Modulation Theory: Detection, Estimation, and Linear Modulation Theory (Wiley, New
York, 1968), pp. 19–165
59. F.J. Sigworth, Classical detection theory and the cryo-EM particle selection problem.
J. Struct. Biol. 145, 111–122 (2004)
60. P. van der Heide, X.P. Xu, B.J. Marsh, D. Hanein, N. Volkmann, Efficient automatic noise
reduction of electron tomographic reconstructions based on iterative median filtering.
J. Struct. Biol. 158, 196–204 (2007)
61. 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, 334–
341 (2006)
62. B.K. Rath, R. Hegerl, A. Leith, T.R. Shaikh, T. Wagenknecht, J. Frank, Fast 3D motif search
of EM density maps using a locally normalized cross-correlation function. J. Struct. Biol.
144, 95–103 (2003)
63. Z. Yu, A.S. Frangakis, Classification of electron sub-tomograms with neural networks and
its application to template-matching. J Struc Biol. 174, 494–504 (2011)
64. T. Hrabe, Y. Chen, S. Pfeffer, L.K. Cuellar, A.V. Mangold, F. Förster, PyTom: a
python-based toolbox for localization of macromolecules in cryo-electron tomograms and
subtomogram analysis. J. Struct. Biol. 178, 177–188 (2012)
65. R. Danev, B. Buijsse, M. Khoshouei, J.M. Plitzko, W. Baumeister, Volta potential phase
plate for in-focus phase contrast transmission electron microscopy. Proc. Natl. Acad. Sci.
U. S. A. 111, 15635–15640 (2014)
66. S. Asano, Y. Fukuda, F. Beck, A. Aufderheide, F. Förster, R. Danev, W. Baumeister,
Proteasomes. A molecular census of 26S proteasomes in intact neurons. Science 347, 439–
442 (2015)
67. J. Mahamid, S. Pfeffer, M. Schaffer, E. Villa, R. Danev, L.K. Cuellar, F. Förster,
A.A. Hyman, J.M. Plitzko, W. Baumeister, Visualizing the molecular sociology at the HeLa
cell nuclear periphery. Science 351, 969–972 (2016)
12 Segmentation of Features in Electron Tomographic Reconstructions
315
segmentation. IEEE Trans. Pattern Anal. Mach. Intell. 25, 330–342 (2003)
48. H. Nguyen, Q. Ji, Shape-driven three-dimensional watersnake segmentation of biological
membranes in electron tomography. IEEE Trans. Med. Imaging 27, 616–628 (2008)
49. M.N. Lebbink, N. Jimenez, K. Vocking, L.H. Hekking, A.J. Verkleij, J.A. Post, Spiral
coating of the endothelial caveolar membranes as revealed by electron tomography and
template matching. Traffic 11, 138–150 (2010)
50. M.N. Lebbink, W.J. Geerts, T.P. van der Krift, M. Bouwhuis, L.O. Hertzberger,
A.J. Verkleij, A.J. Koster, Template matching as a tool for annotation of tomograms of
stained biological structures. J. Struct. Biol. 158, 327–335 (2007)
51. C. Page, D. Hanein, N. Volkmann, Accurate membrane tracing in three-dimensional
reconstructions from electron cryotomography data. Ultramicroscopy 155, 20–26 (2015)
52. A. Briegel, S. Chen, A.J. Koster, J.M. Plitzko, C.L. Schwartz, G.J. Jensen, Correlated light
and electron cryo-microscopy. Methods Enzymol. 481, 317–341 (2010)
53. P. Schellenberger, R. Kaufmann, C.A. Siebert, C. Hagen, H. Wodrich, K. Grünewald,
High-precision correlative fluorescence and electron cryo microscopy using two independent
alignment markers. Ultramicroscopy 143, 41–51 (2014)
54. M. Schorb, J.A. Briggs, Correlated cryo-fluorescence and cryo-electron microscopy with
high spatial precision and improved sensitivity. Ultramicroscopy 143, 24–32 (2014)
55. G. Wolff, C. Hagen, K. Grünewald, R. Kaufmann, Towards correlative super-resolution
fluorescence and electron cryo-microscopy. Biol. Cell 108, 245–258 (2016)
56. J. Böhm, A.S. Frangakis, R. Hegerl, S. Nickell, D. Typke, W. Baumeister, From the cover:
toward detecting and identifying macromolecules in a cellular context: template matching
applied to electron tomograms. Proc. Natl. Acad. Sci. U. S. A. 97, 14245–14250 (2000)
57. G. Turin, An introduction to matched filters. IRE Trans. Inf. Theory 3, 311–329 (1960)
58. H.L. Van Trees, Classical detection and estimation theory, Detection, Estimation, and
Modulation Theory: Detection, Estimation, and Linear Modulation Theory (Wiley, New
York, 1968), pp. 19–165
59. F.J. Sigworth, Classical detection theory and the cryo-EM particle selection problem.
J. Struct. Biol. 145, 111–122 (2004)
60. P. van der Heide, X.P. Xu, B.J. Marsh, D. Hanein, N. Volkmann, Efficient automatic noise
reduction of electron tomographic reconstructions based on iterative median filtering.
J. Struct. Biol. 158, 196–204 (2007)
61. 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, 334–
341 (2006)
62. B.K. Rath, R. Hegerl, A. Leith, T.R. Shaikh, T. Wagenknecht, J. Frank, Fast 3D motif search
of EM density maps using a locally normalized cross-correlation function. J. Struct. Biol.
144, 95–103 (2003)
63. Z. Yu, A.S. Frangakis, Classification of electron sub-tomograms with neural networks and
its application to template-matching. J Struc Biol. 174, 494–504 (2011)
64. T. Hrabe, Y. Chen, S. Pfeffer, L.K. Cuellar, A.V. Mangold, F. Förster, PyTom: a
python-based toolbox for localization of macromolecules in cryo-electron tomograms and
subtomogram analysis. J. Struct. Biol. 178, 177–188 (2012)
65. R. Danev, B. Buijsse, M. Khoshouei, J.M. Plitzko, W. Baumeister, Volta potential phase
plate for in-focus phase contrast transmission electron microscopy. Proc. Natl. Acad. Sci.
U. S. A. 111, 15635–15640 (2014)
66. S. Asano, Y. Fukuda, F. Beck, A. Aufderheide, F. Förster, R. Danev, W. Baumeister,
Proteasomes. A molecular census of 26S proteasomes in intact neurons. Science 347, 439–
442 (2015)
67. J. Mahamid, S. Pfeffer, M. Schaffer, E. Villa, R. Danev, L.K. Cuellar, F. Förster,
A.A. Hyman, J.M. Plitzko, W. Baumeister, Visualizing the molecular sociology at the HeLa
cell nuclear periphery. Science 351, 969–972 (2016)
12 Segmentation of Features in Electron Tomographic Reconstructions
315