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Volumn 197, Issue 3, 2017, Pages 279-293

Robust image alignment for cryogenic transmission electron microscopy

Author keywords

Cross correlation; Cryogenic transmission electron microscopy; Direct detection device; Dose fractionation; Image alignment; Image registration

Indexed keywords

ARTICLE; CORRELATION ANALYSIS; CRYOGENIC TRANSMISSION ELECTRON MICROSCOPY; FOURIER ANALYSIS; IMAGE ANALYSIS; IMAGE PROCESSING; IMAGING SOFTWARE; INFORMATION PROCESSING; LOW ENERGY RADIATION; RADIATION DOSE FRACTIONATION; TRANSMISSION ELECTRON MICROSCOPY; CRYOELECTRON MICROSCOPY; PROCEDURES; SOFTWARE; THEORETICAL MODEL;

EID: 85009291685     PISSN: 10478477     EISSN: 10958657     Source Type: Journal    
DOI: 10.1016/j.jsb.2016.12.006     Document Type: Article
Times cited : (23)

References (48)
  • 1
    • 84923447206 scopus 로고    scopus 로고
    • Alignment of direct detection device micrographs using a robust optical flow approach
    • Abrishami, V., Vargas, J., Li, X., Cheng, Y., Marabini, R., Sorzano, C.Ó.S., Carazo, J.M., Alignment of direct detection device micrographs using a robust optical flow approach. J. Struct. Biol. 189 (2015), 163–176, 10.1016/j.jsb.2015.02.001.
    • (2015) J. Struct. Biol. , vol.189 , pp. 163-176
    • Abrishami, V.1    Vargas, J.2    Li, X.3    Cheng, Y.4    Marabini, R.5    Sorzano, C.Ó.S.6    Carazo, J.M.7
  • 2
    • 84883459241 scopus 로고    scopus 로고
    • Fourier ring correlation as a resolution criterion for super-resolution microscopy
    • Banterle, N., Bui, K.H., Lemke, E.A., Beck, M., Fourier ring correlation as a resolution criterion for super-resolution microscopy. J. Struct. Biol. 183 (2013), 363–367, 10.1016/j.jsb.2013.05.004.
    • (2013) J. Struct. Biol. , vol.183 , pp. 363-367
    • Banterle, N.1    Bui, K.H.2    Lemke, E.A.3    Beck, M.4
  • 3
    • 84905974179 scopus 로고    scopus 로고
    • Structure of β-galactosidase at 3.2-Å resolution obtained by cryo-electron microscopy
    • Bartesaghi, A., Matthies, D., Banerjee, S., Merk, A., Subramaniam, S., Structure of β-galactosidase at 3.2-Å resolution obtained by cryo-electron microscopy. PNAS 111 (2014), 11709–11714, 10.1073/pnas.1402809111.
    • (2014) PNAS , vol.111 , pp. 11709-11714
    • Bartesaghi, A.1    Matthies, D.2    Banerjee, S.3    Merk, A.4    Subramaniam, S.5
  • 4
    • 84870426502 scopus 로고    scopus 로고
    • Nanoparticle movement: plasmonic forces and physical constraints
    • Albert Victor Crewe Memorial Issue
    • Batson, P.E., Reyes-Coronado, A., Barrera, R.G., Rivacoba, A., Echenique, P.M., Aizpurua, J., Nanoparticle movement: plasmonic forces and physical constraints. Ultramicroscopy 123 (2012), 50–58, 10.1016/j.ultramic.2012.05.004 Albert Victor Crewe Memorial Issue.
    • (2012) Ultramicroscopy , vol.123 , pp. 50-58
    • Batson, P.E.1    Reyes-Coronado, A.2    Barrera, R.G.3    Rivacoba, A.4    Echenique, P.M.5    Aizpurua, J.6
  • 7
    • 84942932604 scopus 로고    scopus 로고
    • Viscosity of deeply supercooled water and its coupling to molecular diffusion
    • Dehaoui, A., Issenmann, B., Caupin, F., Viscosity of deeply supercooled water and its coupling to molecular diffusion. PNAS 112 (2015), 12020–12025, 10.1073/pnas.1508996112.
    • (2015) PNAS , vol.112 , pp. 12020-12025
    • Dehaoui, A.1    Issenmann, B.2    Caupin, F.3
  • 8
    • 11244269506 scopus 로고    scopus 로고
    • Experimental characterization and mitigation of specimen charging on thin films with one conducting layer
    • Downing, K.H., McCartney, M.R., Glaeser, R.M., Experimental characterization and mitigation of specimen charging on thin films with one conducting layer. Microsc. Microanal. 10 (2004), 783–789, 10.1017/S143192760404067X.
    • (2004) Microsc. Microanal. , vol.10 , pp. 783-789
    • Downing, K.H.1    McCartney, M.R.2    Glaeser, R.M.3
  • 10
    • 0021609521 scopus 로고
    • Noise power spectrum, MTF, and DQE of photoelectric radiographic systems
    • Society of Photo-Optical Instrumentation Engineers San Diego, CA
    • Fu, T., Roehrig, H., Noise power spectrum, MTF, and DQE of photoelectric radiographic systems. Presented at the Applications of Optical Instrumentation in Medicine XII, 1984, Society of Photo-Optical Instrumentation Engineers, San Diego, CA, 377–386.
    • (1984) Presented at the Applications of Optical Instrumentation in Medicine XII , pp. 377-386
    • Fu, T.1    Roehrig, H.2
  • 11
    • 1442263375 scopus 로고    scopus 로고
    • Specimen charging on thin films with one conducting layer: discussion of physical principles
    • Glaeser, R.M., Downing, K.H., Specimen charging on thin films with one conducting layer: discussion of physical principles. Microsc. Microanal. 10 (2004), 790–796, 10.1017/S1431927604040668.
    • (2004) Microsc. Microanal. , vol.10 , pp. 790-796
    • Glaeser, R.M.1    Downing, K.H.2
  • 12
    • 84930634509 scopus 로고    scopus 로고
    • Measuring the optimal exposure for single particle cryo-EM using a 2.6 Å reconstruction of rotavirus VP6
    • Grant, T., Grigorieff, N., Measuring the optimal exposure for single particle cryo-EM using a 2.6 Å reconstruction of rotavirus VP6. eLife Sci., 4, 2015, e06980, 10.7554/eLife.06980.
    • (2015) eLife Sci. , vol.4 , pp. e06980
    • Grant, T.1    Grigorieff, N.2
  • 13
    • 0033777020 scopus 로고    scopus 로고
    • Resolution measurement in structures derived from single particles
    • Grigorieff, N., Resolution measurement in structures derived from single particles. Acta Crystallogr. D Biol. Crystallogr. 56 (2000), 1270–1277.
    • (2000) Acta Crystallogr. D Biol. Crystallogr. , vol.56 , pp. 1270-1277
    • Grigorieff, N.1
  • 14
    • 40149088424 scopus 로고    scopus 로고
    • Efficient subpixel image registration algorithms
    • Guizar-Sicairos, M., Thurman, S.T., Fienup, J.R., Efficient subpixel image registration algorithms. Opt. Lett., 33, 2008, 156, 10.1364/OL.33.000156.
    • (2008) Opt. Lett. , vol.33 , pp. 156
    • Guizar-Sicairos, M.1    Thurman, S.T.2    Fienup, J.R.3
  • 15
    • 1942521362 scopus 로고    scopus 로고
    • Improved specimen preparation for cryo-electron microscopy using a symmetric carbon sandwich technique
    • Gyobu, N., Tani, K., Hiroaki, Y., Kamegawa, A., Mitsuoka, K., Fujiyoshi, Y., Improved specimen preparation for cryo-electron microscopy using a symmetric carbon sandwich technique. J. Struct. Biol. 146 (2004), 325–333, 10.1016/j.jsb.2004.01.012.
    • (2004) J. Struct. Biol. , vol.146 , pp. 325-333
    • Gyobu, N.1    Tani, K.2    Hiroaki, Y.3    Kamegawa, A.4    Mitsuoka, K.5    Fujiyoshi, Y.6
  • 16
    • 41449118167 scopus 로고    scopus 로고
    • Mean free path of inelastic electron scattering in elemental solids and oxides using transmission electron microscopy: atomic number dependent oscillatory behavior
    • Iakoubovskii, K., Mitsuishi, K., Nakayama, Y., Furuya, K., Mean free path of inelastic electron scattering in elemental solids and oxides using transmission electron microscopy: atomic number dependent oscillatory behavior. Phys. Rev. B, 77, 2008, 104102, 10.1103/PhysRevB.77.104102.
    • (2008) Phys. Rev. B , vol.77 , pp. 104102
    • Iakoubovskii, K.1    Mitsuishi, K.2    Nakayama, Y.3    Furuya, K.4
  • 17
    • 0004171561 scopus 로고
    • Brownian Motion and Stochastic Calculus
    • 2nd ed. Springer
    • Karatzas, I., Shreve, S.E., Brownian Motion and Stochastic Calculus. 2nd ed., 1991, Springer.
    • (1991)
    • Karatzas, I.1    Shreve, S.E.2
  • 19
    • 0002925011 scopus 로고
    • Fast normalized cross-correlation
    • Lewis, J.P., Fast normalized cross-correlation. Vision Interface 10 (1995), 120–123.
    • (1995) Vision Interface , vol.10 , pp. 120-123
    • Lewis, J.P.1
  • 20
    • 84880848354 scopus 로고    scopus 로고
    • Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM
    • Li, X., Mooney, P., Zheng, S., Booth, C.R., Braunfeld, M.B., Gubbens, S., Agard, D.A., Cheng, Y., Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM. Nat. Methods 10 (2013), 584–590, 10.1038/nmeth.2472.
    • (2013) Nat. Methods , vol.10 , pp. 584-590
    • Li, X.1    Mooney, P.2    Zheng, S.3    Booth, C.R.4    Braunfeld, M.B.5    Gubbens, S.6    Agard, D.A.7    Cheng, Y.8
  • 21
    • 84887252893 scopus 로고    scopus 로고
    • Influence of electron dose rate on electron counting images recorded with the K2 camera
    • Li, X., Zheng, S.Q., Egami, K., Agard, D.A., Cheng, Y., Influence of electron dose rate on electron counting images recorded with the K2 camera. J. Struct. Biol. 184 (2013), 251–260, 10.1016/j.jsb.2013.08.005.
    • (2013) J. Struct. Biol. , vol.184 , pp. 251-260
    • Li, X.1    Zheng, S.Q.2    Egami, K.3    Agard, D.A.4    Cheng, Y.5
  • 22
    • 0026244960 scopus 로고
    • Optimum focus for taking electron holograms
    • Lichte, H., Optimum focus for taking electron holograms. Ultramicroscopy 38 (1991), 13–22, 10.1016/0304-3991(91)90105-F.
    • (1991) Ultramicroscopy , vol.38 , pp. 13-22
    • Lichte, H.1
  • 23
    • 0033377664 scopus 로고    scopus 로고
    • EMAN: semiautomated software for high-resolution single-particle reconstructions
    • Ludtke, S.J., Baldwin, P.R., Chiu, W., EMAN: semiautomated software for high-resolution single-particle reconstructions. J. Struct. Biol. 128 (1999), 82–97, 10.1006/jsbi.1999.4174.
    • (1999) J. Struct. Biol. , vol.128 , pp. 82-97
    • Ludtke, S.J.1    Baldwin, P.R.2    Chiu, W.3
  • 24
    • 84897937344 scopus 로고    scopus 로고
    • Phase measurement error in summation of electron holography series
    • McLeod, R.A., Bergen, M., Malac, M., Phase measurement error in summation of electron holography series. Ultramicroscopy 141 (2014), 38–50, 10.1016/j.ultramic.2014.03.001.
    • (2014) Ultramicroscopy , vol.141 , pp. 38-50
    • McLeod, R.A.1    Bergen, M.2    Malac, M.3
  • 25
    • 84908056429 scopus 로고    scopus 로고
    • Comparison of optimal performance at 300 keV of three direct electron detectors for use in low dose electron microscopy
    • McMullan, G., Faruqi, A.R., Clare, D., Henderson, R., Comparison of optimal performance at 300 keV of three direct electron detectors for use in low dose electron microscopy. Ultramicroscopy 147 (2014), 156–163, 10.1016/j.ultramic.2014.08.002.
    • (2014) Ultramicroscopy , vol.147 , pp. 156-163
    • McMullan, G.1    Faruqi, A.R.2    Clare, D.3    Henderson, R.4
  • 26
    • 84934905971 scopus 로고    scopus 로고
    • Thon rings from amorphous ice and implications of beam-induced Brownian motion in single particle electron cryo-microscopy
    • McMullan, G., Vinothkumar, K.R., Henderson, R., Thon rings from amorphous ice and implications of beam-induced Brownian motion in single particle electron cryo-microscopy. Ultramicroscopy 158 (2015), 26–32, 10.1016/j.ultramic.2015.05.017.
    • (2015) Ultramicroscopy , vol.158 , pp. 26-32
    • McMullan, G.1    Vinothkumar, K.R.2    Henderson, R.3
  • 28
    • 0004255908 scopus 로고    scopus 로고
    • Machine Learning
    • 1st ed. McGraw-Hill Education
    • Mitchell, T.M., Machine Learning. 1st ed., 1997, McGraw-Hill Education http://www.cs.cmu.edu/~tom/mlbook.html.
    • (1997)
    • Mitchell, T.M.1
  • 29
    • 0038441501 scopus 로고    scopus 로고
    • Accurate determination of local defocus and specimen tilt in electron microscopy
    • Mindell, J.A., Grigorieff, N., Accurate determination of local defocus and specimen tilt in electron microscopy. J. Struct. Biol. 142 (2003), 334–347, 10.1016/S1047-8477(03)00069-8.
    • (2003) J. Struct. Biol. , vol.142 , pp. 334-347
    • Mindell, J.A.1    Grigorieff, N.2
  • 30
    • 33847192758 scopus 로고    scopus 로고
    • Optimization of image collection for cellular electron microscopy
    • Academic Press
    • Mooney, P., McIntosh, J.R., Optimization of image collection for cellular electron microscopy. Methods Cell Biol, 2007, 661–719 Academic Press.
    • (2007) Methods Cell Biol , pp. 661-719
    • Mooney, P.1    McIntosh, J.R.2
  • 31
    • 84886635386 scopus 로고    scopus 로고
    • Performance evaluation metrics and statistics for positional tracker evaluation
    • J.L. Crowley J.H. Piater M. Vincze L. Paletta Springer Berlin Heidelberg
    • Needham, C.J., Boyle, R.D., Performance evaluation metrics and statistics for positional tracker evaluation. Crowley, J.L., Piater, J.H., Vincze, M., Paletta, L., (eds.) Computer Vision Systems Lecture Notes in Computer Science, 2003, Springer, Berlin Heidelberg, 278–289.
    • (2003) Computer Vision Systems, Lecture Notes in Computer Science , pp. 278-289
    • Needham, C.J.1    Boyle, R.D.2
  • 33
    • 84860145732 scopus 로고    scopus 로고
    • Masked object registration in the Fourier domain
    • Padfield, D., Masked object registration in the Fourier domain. IEEE Trans. Image Process. 21 (2012), 2706–2718, 10.1109/TIP.2011.2181402.
    • (2012) IEEE Trans. Image Process. , vol.21 , pp. 2706-2718
    • Padfield, D.1
  • 35
    • 0037375602 scopus 로고    scopus 로고
    • Particle finding in electron micrographs using a fast local correlation algorithm
    • Roseman, A.M., Particle finding in electron micrographs using a fast local correlation algorithm. Ultramicroscopy 94 (2003), 225–236, 10.1016/S0304-3991(02)00333-9.
    • (2003) Ultramicroscopy , vol.94 , pp. 225-236
    • Roseman, A.M.1
  • 36
    • 84928390823 scopus 로고    scopus 로고
    • Alignment of cryo-EM movies of individual particles by optimization of image translations
    • arXiv:1409.6789 [physics, q-bio].
    • Rubinstein, J.L., Brubaker, M.A., 2014. Alignment of cryo-EM movies of individual particles by optimization of image translations. arXiv:1409.6789 [physics, q-bio].
    • (2014)
    • Rubinstein, J.L.1    Brubaker, M.A.2
  • 37
    • 84888064039 scopus 로고    scopus 로고
    • Quantitative characterization of electron detectors for transmission electron microscopy
    • Ruskin, R.S., Yu, Z., Grigorieff, N., Quantitative characterization of electron detectors for transmission electron microscopy. J. Struct. Biol. 184 (2013), 385–393, 10.1016/j.jsb.2013.10.016.
    • (2013) J. Struct. Biol. , vol.184 , pp. 385-393
    • Ruskin, R.S.1    Yu, Z.2    Grigorieff, N.3
  • 38
    • 0019987933 scopus 로고
    • The correlation averaging of a regularly arranged bacterial cell envelope protein
    • Saxton, W.O., Baumeister, W., The correlation averaging of a regularly arranged bacterial cell envelope protein. J. Microsc. 127 (1982), 127–138, 10.1111/j.1365-2818.1982.tb00405.x.
    • (1982) J. Microsc. , vol.127 , pp. 127-138
    • Saxton, W.O.1    Baumeister, W.2
  • 39
    • 84866078359 scopus 로고    scopus 로고
    • Prevention of overfitting in cryo-EM structure determination
    • Scheres, S.H.W., Chen, S., Prevention of overfitting in cryo-EM structure determination. Nat. Methods 9 (2012), 853–854, 10.1038/nmeth.2115.
    • (2012) Nat. Methods , vol.9 , pp. 853-854
    • Scheres, S.H.W.1    Chen, S.2
  • 40
    • 84920942671 scopus 로고    scopus 로고
    • Beam-induced motion correction for sub-megadalton cryo-EM particles
    • Scheres, S.H., Beam-induced motion correction for sub-megadalton cryo-EM particles. eLife, 3, 2014, 03665, 10.7554/eLife.03665.
    • (2014) eLife , vol.3 , pp. 03665
    • Scheres, S.H.1
  • 41
    • 0001262105 scopus 로고
    • A note on the heavy-atom method
    • Sim, G.A., A note on the heavy-atom method. Acta Crystallogr. A, 13, 1960, 511.
    • (1960) Acta Crystallogr. A , vol.13 , pp. 511
    • Sim, G.A.1
  • 43
    • 8844219659 scopus 로고    scopus 로고
    • Noise bias in the refinement of structures derived from single particles
    • Stewart, A., Grigorieff, N., Noise bias in the refinement of structures derived from single particles. Ultramicroscopy 102 (2004), 67–84, 10.1016/j.ultramic.2004.08.008.
    • (2004) Ultramicroscopy , vol.102 , pp. 67-84
    • Stewart, A.1    Grigorieff, N.2
  • 44
    • 0002573122 scopus 로고
    • Anthropod hemocyanin structures studied by image analysis
    • In: The Structure and Function of Invertebrate Respiratory Proteins. Presented at the EMBO Workshop, Leeds.
    • van Heel, M., Keegstra, W., Schutter, W., van Bruggen, E.F.J., 1982. Anthropod hemocyanin structures studied by image analysis. In: The Structure and Function of Invertebrate Respiratory Proteins. Presented at the EMBO Workshop, Leeds.
    • (1982)
    • van Heel, M.1    Keegstra, W.2    Schutter, W.3    van Bruggen, E.F.J.4
  • 45
    • 25144494651 scopus 로고    scopus 로고
    • Fourier shell correlation threshold criteria
    • van Heel, M., Schatz, M., Fourier shell correlation threshold criteria. J. Struct. Biol. 151 (2005), 250–262, 10.1016/j.jsb.2005.05.009.
    • (2005) J. Struct. Biol. , vol.151 , pp. 250-262
    • van Heel, M.1    Schatz, M.2
  • 46
    • 0000560869 scopus 로고    scopus 로고
    • Global optimization by basin-hopping and the lowest energy structures of Lennard-Jones clusters containing up to 110 atoms
    • Wales, D.J., Doye, J.P.K., Global optimization by basin-hopping and the lowest energy structures of Lennard-Jones clusters containing up to 110 atoms. J. Phys. Chem. A 101 (1997), 5111–5116, 10.1021/jp970984n.
    • (1997) J. Phys. Chem. A , vol.101 , pp. 5111-5116
    • Wales, D.J.1    Doye, J.P.K.2
  • 47
    • 84955216953 scopus 로고    scopus 로고
    • Gctf: real-time CTF determination and correction
    • Zhang, K., Gctf: real-time CTF determination and correction. J. Struct. Biol. 193 (2016), 1–12, 10.1016/j.jsb.2015.11.003.
    • (2016) J. Struct. Biol. , vol.193 , pp. 1-12
    • Zhang, K.1
  • 48
    • 0031345518 scopus 로고    scopus 로고
    • Algorithm 778: L-BFGS-B: Fortran subroutines for large-scale bound-constrained optimization
    • Zhu, C., Byrd, R.H., Lu, P., Nocedal, J., Algorithm 778: L-BFGS-B: Fortran subroutines for large-scale bound-constrained optimization. ACM Trans. Math. Softw. 23 (1997), 550–560, 10.1145/279232.279236.
    • (1997) ACM Trans. Math. Softw. , vol.23 , pp. 550-560
    • Zhu, C.1    Byrd, R.H.2    Lu, P.3    Nocedal, J.4


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