-
1
-
-
84923447206
-
Alignment of direct detection device micrographs using a robust optical flow approach
-
Abrishami, V., Vargas, J., Li, X., Cheng, Y., Marabini, R., Sorzano, C., Carazo, J., Alignment of direct detection device micrographs using a robust optical flow approach. J. Struct. Biol. 189:3 (2015), 163–176.
-
(2015)
J. Struct. Biol.
, vol.189
, Issue.3
, pp. 163-176
-
-
Abrishami, V.1
Vargas, J.2
Li, X.3
Cheng, Y.4
Marabini, R.5
Sorzano, C.6
Carazo, J.7
-
2
-
-
33845302993
-
SPIRE: the SPIDER reconstruction engine
-
Baxter, W.T., Leith, A., Frank, J., SPIRE: the SPIDER reconstruction engine. J. Struct. Biol. 157:1 (2007), 56–63.
-
(2007)
J. Struct. Biol.
, vol.157
, Issue.1
, pp. 56-63
-
-
Baxter, W.T.1
Leith, A.2
Frank, J.3
-
3
-
-
84930661954
-
Low cost, high performance processing of single particle cryo-electron microscopy data in the cloud
-
Cianfrocco, M.A., Leschziner, A.E., Low cost, high performance processing of single particle cryo-electron microscopy data in the cloud. Elife, 4, 2015.
-
(2015)
Elife
, vol.4
-
-
Cianfrocco, M.A.1
Leschziner, A.E.2
-
4
-
-
84887257621
-
Xmipp 3.0: an improved software suite for image processing in electron microscopy
-
de la Rosa-Trevín, J., Otón, J., Marabini, R., Zaldívar, A., Vargas, J., Carazo, J., Sorzano, C., Xmipp 3.0: an improved software suite for image processing in electron microscopy. J. Struct. Biol. 184:2 (2013), 321–328.
-
(2013)
J. Struct. Biol.
, vol.184
, Issue.2
, pp. 321-328
-
-
de la Rosa-Trevín, J.1
Otón, J.2
Marabini, R.3
Zaldívar, A.4
Vargas, J.5
Carazo, J.6
Sorzano, C.7
-
5
-
-
84868498215
-
Simple: software for ab initio reconstruction of heterogeneous single-particles
-
Elmlund, D., Elmlund, H., Simple: software for ab initio reconstruction of heterogeneous single-particles. J. Struct. Biol. 180:3 (2012), 420–427.
-
(2012)
J. Struct. Biol.
, vol.180
, Issue.3
, pp. 420-427
-
-
Elmlund, D.1
Elmlund, H.2
-
6
-
-
0003756531
-
Three-Dimensional Electron Microscopy of Macromolecular Assemblies
-
Academic Press Burlington
-
Frank, J., Three-Dimensional Electron Microscopy of Macromolecular Assemblies. 1996, Academic Press, Burlington.
-
(1996)
-
-
Frank, J.1
-
7
-
-
0029975088
-
Spider and web: processing and visualization of images in 3d electron microscopy and related fields
-
Frank, J., Radermacher, M., Penczek, P., Zhu, J., Li, Y., Ladjadj, M., Leith, A., Spider and web: processing and visualization of images in 3d electron microscopy and related fields. J. Struct. Biol. 116:1 (1996), 190–199.
-
(1996)
J. Struct. Biol.
, vol.116
, Issue.1
, pp. 190-199
-
-
Frank, J.1
Radermacher, M.2
Penczek, P.3
Zhu, J.4
Li, Y.5
Ladjadj, M.6
Leith, A.7
-
8
-
-
33845330614
-
2DX–user-friendly image processing for 2D crystals
-
Gipson, B., Zeng, X., Zhang, Z.Y., Stahlberg, H., 2DX–user-friendly image processing for 2D crystals. J. Struct. Biol. 157:1 (2007), 64–72.
-
(2007)
J. Struct. Biol.
, vol.157
, Issue.1
, pp. 64-72
-
-
Gipson, B.1
Zeng, X.2
Zhang, Z.Y.3
Stahlberg, H.4
-
9
-
-
84930634509
-
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, 4, 2015, e06980.
-
(2015)
Elife
, vol.4
, pp. e06980
-
-
Grant, T.1
Grigorieff, N.2
-
10
-
-
33845348200
-
FREALIGN: high-resolution refinement of single particle structures
-
Grigorieff, N., FREALIGN: high-resolution refinement of single particle structures. J. Struct. Biol. 157:1 (2007), 117–125.
-
(2007)
J. Struct. Biol.
, vol.157
, Issue.1
, pp. 117-125
-
-
Grigorieff, N.1
-
11
-
-
33845336533
-
Bsoft: image processing and molecular modeling for electron microscopy
-
Heymann, J.B., Belnap, D.M., Bsoft: image processing and molecular modeling for electron microscopy. J. Struct. Biol. 157:1 (2007), 3–18.
-
(2007)
J. Struct. Biol.
, vol.157
, Issue.1
, pp. 3-18
-
-
Heymann, J.B.1
Belnap, D.M.2
-
12
-
-
84895921737
-
gEMpicker: a highly parallel gpu-accelerated particle picking tool for cryo-electron microscopy
-
Hoang, T.V., Cavin, X., Schultz, P., Ritchie, D.W., gEMpicker: a highly parallel gpu-accelerated particle picking tool for cryo-electron microscopy. BMC Struct. Biol. 13:1 (2013), 1–10.
-
(2013)
BMC Struct. Biol.
, vol.13
, Issue.1
, pp. 1-10
-
-
Hoang, T.V.1
Cavin, X.2
Schultz, P.3
Ritchie, D.W.4
-
13
-
-
33845296470
-
Sparx, a new environment for Cryo-EM image processing
-
Hohn, M., Tang, G., Goodyear, G., Baldwin, P.R., Huang, Z., Penczek, P.A., Yang, C., Glaeser, R.M., Adams, P.D., Ludtke, S.J., Sparx, a new environment for Cryo-EM image processing. J. Struc. Biol. 157:1 (2007), 47–55.
-
(2007)
J. Struc. Biol.
, vol.157
, Issue.1
, pp. 47-55
-
-
Hohn, M.1
Tang, G.2
Goodyear, G.3
Baldwin, P.R.4
Huang, Z.5
Penczek, P.A.6
Yang, C.7
Glaeser, R.M.8
Adams, P.D.9
Ludtke, S.J.10
-
14
-
-
84894623755
-
Quantifying the local resolution of cryo-em density maps
-
Kucukelbir, A., Sigworth, F.J., Tagare, H.D., Quantifying the local resolution of cryo-em density maps. Nat. Meth. 11 (2014), 63–65.
-
(2014)
Nat. Meth.
, vol.11
, pp. 63-65
-
-
Kucukelbir, A.1
Sigworth, F.J.2
Tagare, H.D.3
-
15
-
-
84897000286
-
Biochemistry. The resolution revolution
-
Kuhlbrandt, W., Biochemistry. The resolution revolution. Science 343:6178 (2014), 1443–1444.
-
(2014)
Science
, vol.343
, Issue.6178
, pp. 1443-1444
-
-
Kuhlbrandt, W.1
-
16
-
-
60649103238
-
Appion: an integrated, database-driven pipeline to facilitate EM image processing
-
Lander, G.C., Stagg, S.M., Voss, N.R., Cheng, A., Fellmann, D., Pulokas, J., Yoshioka, C., Irving, C., Mulder, A., Lau, P.W., Lyumkis, D., Potter, C.S., Carragher, B., Appion: an integrated, database-driven pipeline to facilitate EM image processing. J. Struct. Biol. 166:1 (2009), 95–102.
-
(2009)
J. Struct. Biol.
, vol.166
, Issue.1
, pp. 95-102
-
-
Lander, G.C.1
Stagg, S.M.2
Voss, N.R.3
Cheng, A.4
Fellmann, D.5
Pulokas, J.6
Yoshioka, C.7
Irving, C.8
Mulder, A.9
Lau, P.W.10
Lyumkis, D.11
Potter, C.S.12
Carragher, B.13
-
17
-
-
84880848354
-
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. Meth. 10:6 (2013), 584–590.
-
(2013)
Nat. Meth.
, vol.10
, Issue.6
, 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
-
18
-
-
0033377664
-
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. 128:1 (1999), 82–97.
-
(1999)
J. Struct. Biol.
, vol.128
, Issue.1
, pp. 82-97
-
-
Ludtke, S.J.1
Baldwin, P.R.2
Chiu, W.3
-
19
-
-
84960473601
-
The electron microscopy exchange (EMX) initiative
-
Marabini, R., Ludtke, S.J., Murray, S.C., Chiu, W., de la Rosa-Trevin, J.M., Patwardhan, A., Bernard Heymann, J., Carazo, J.M., The electron microscopy exchange (EMX) initiative. J. Struct. Biol., 2016.
-
(2016)
J. Struct. Biol.
-
-
Marabini, R.1
Ludtke, S.J.2
Murray, S.C.3
Chiu, W.4
de la Rosa-Trevin, J.M.5
Patwardhan, A.6
Bernard Heymann, J.7
Carazo, J.M.8
-
20
-
-
0038441501
-
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. 142:3 (2003), 334–347.
-
(2003)
J. Struct. Biol.
, vol.142
, Issue.3
, pp. 334-347
-
-
Mindell, J.A.1
Grigorieff, N.2
-
21
-
-
33845382411
-
Collaborative EM image processing with the IPLT image processing library and toolbox
-
Philippsen, A., Schenk, A.D., Signorell, G.A., Mariani, V., Berneche, S., Engel, A., Collaborative EM image processing with the IPLT image processing library and toolbox. J. Struct. Biol. 157:1 (2007), 28–37.
-
(2007)
J. Struct. Biol.
, vol.157
, Issue.1
, pp. 28-37
-
-
Philippsen, A.1
Schenk, A.D.2
Signorell, G.A.3
Mariani, V.4
Berneche, S.5
Engel, A.6
-
22
-
-
84946488108
-
CTFFIND4: fast and accurate defocus estimation from electron micrographs
-
Rohou, A., Grigorieff, N., CTFFIND4: fast and accurate defocus estimation from electron micrographs. J. Struct. Biol. 192:2 (2015), 216–221.
-
(2015)
J. Struct. Biol.
, vol.192
, Issue.2
, pp. 216-221
-
-
Rohou, A.1
Grigorieff, N.2
-
23
-
-
84868444740
-
Relion: implementation of a bayesian approach to cryo-em structure determination
-
Scheres, S.H., Relion: implementation of a bayesian approach to cryo-em structure determination. J. Struct. Biol. 180:3 (2012), 519–530.
-
(2012)
J. Struct. Biol.
, vol.180
, Issue.3
, pp. 519-530
-
-
Scheres, S.H.1
-
24
-
-
84922727036
-
Semi-automated selection of cryo-EM particles in RELION-1.3
-
Scheres, S.H., Semi-automated selection of cryo-EM particles in RELION-1.3. J. Struct. Biol. 189:2 (2015), 114–122.
-
(2015)
J. Struct. Biol.
, vol.189
, Issue.2
, pp. 114-122
-
-
Scheres, S.H.1
-
25
-
-
68149169697
-
Parallel, distributed and GPU computing technologies in single-particle electron microscopy
-
Schmeisser, M., Heisen, B.C., Luettich, M., Busche, B., Hauer, F., Koske, T., Knauber, K.H., Stark, H., Parallel, distributed and GPU computing technologies in single-particle electron microscopy. Acta Crystallogr. D Biol. Crystallogr. 65:Pt 7 (2009), 659–671.
-
(2009)
Acta Crystallogr. D Biol. Crystallogr.
, vol.65
, pp. 659-671
-
-
Schmeisser, M.1
Heisen, B.C.2
Luettich, M.3
Busche, B.4
Hauer, F.5
Koske, T.6
Knauber, K.H.7
Stark, H.8
-
26
-
-
5144235316
-
XMIPP: a new generation of an open-source image processing package for electron microscopy
-
Sorzano, C.O.S., Marabini, R., Velázquez-Muriel, J., Bilbao-Castro, J.R., Scheres, S.H.W., et al. XMIPP: a new generation of an open-source image processing package for electron microscopy. J. Struct. Biol. 148 (2004), 194–204.
-
(2004)
J. Struct. Biol.
, vol.148
, pp. 194-204
-
-
Sorzano, C.O.S.1
Marabini, R.2
Velázquez-Muriel, J.3
Bilbao-Castro, J.R.4
Scheres, S.H.W.5
-
27
-
-
35048832803
-
Fast, robust, and accurate determination of transmission electron microscopy contrast transfer function
-
Sorzano, C.O., Jonic, S., Núñez Ramírez, R., Boisset, N., Carazo, J.M., Fast, robust, and accurate determination of transmission electron microscopy contrast transfer function. J. Struct. Biol. 160:2 (2007), 249–262.
-
(2007)
J. Struct. Biol.
, vol.160
, Issue.2
, pp. 249-262
-
-
Sorzano, C.O.1
Jonic, S.2
Núñez Ramírez, R.3
Boisset, N.4
Carazo, J.M.5
-
28
-
-
84923525032
-
A statistical approach to the initial volume problem in single particle analysis by electron microscopy
-
Sorzano, C., Vargas, J., de la Rosa-Trevin, J., Oton, J., Alvarez-Cabrera, A., Abrishami, V., Sesmero, E., Marabini, R., Carazo, J., A statistical approach to the initial volume problem in single particle analysis by electron microscopy. J. Struct. Biol. 189:3 (2015), 213–219.
-
(2015)
J. Struct. Biol.
, vol.189
, Issue.3
, pp. 213-219
-
-
Sorzano, C.1
Vargas, J.2
de la Rosa-Trevin, J.3
Oton, J.4
Alvarez-Cabrera, A.5
Abrishami, V.6
Sesmero, E.7
Marabini, R.8
Carazo, J.9
-
29
-
-
20544468931
-
Automated molecular microscopy: the new Leginon system
-
Suloway, C., Pulokas, J., Fellmann, D., Cheng, A., Guerra, F., Quispe, J., Stagg, S., Potter, C.S., Carragher, B., Automated molecular microscopy: the new Leginon system. J. Struct. Biol. 151:1 (2005), 41–60.
-
(2005)
J. Struct. Biol.
, vol.151
, Issue.1
, pp. 41-60
-
-
Suloway, C.1
Pulokas, J.2
Fellmann, D.3
Cheng, A.4
Guerra, F.5
Quispe, J.6
Stagg, S.7
Potter, C.S.8
Carragher, B.9
-
30
-
-
33845332754
-
EMAN2: an extensible image processing suite for electron microscopy
-
Tang, G., Peng, L., Baldwin, P.R., Mann, D.S., Jiang, W., Rees, I., Ludtke, S.J., EMAN2: an extensible image processing suite for electron microscopy. J. Struct. Biol. 157:1 (2007), 38–46.
-
(2007)
J. Struct. Biol.
, vol.157
, Issue.1
, pp. 38-46
-
-
Tang, G.1
Peng, L.2
Baldwin, P.R.3
Mann, D.S.4
Jiang, W.5
Rees, I.6
Ludtke, S.J.7
-
31
-
-
0029916485
-
A new generation of the IMAGIC image processing system
-
van Heel, M., Harauz, G., Orlova, E.V., Schmidt, R., Schatz, M., A new generation of the IMAGIC image processing system. J. Struct. Biol. 116:1 (1996), 17–24.
-
(1996)
J. Struct. Biol.
, vol.116
, Issue.1
, pp. 17-24
-
-
van Heel, M.1
Harauz, G.2
Orlova, E.V.3
Schmidt, R.4
Schatz, M.5
-
32
-
-
84873143158
-
Fastdef: fast defocus and astigmatism estimation for high-throughput transmission electron microscopy
-
Vargas, J., Otón, J., Marabini, R., Jonic, S., de la Rosa-Trevín, J., Carazo, J., Sorzano, C., Fastdef: fast defocus and astigmatism estimation for high-throughput transmission electron microscopy. J. Struct. Biol. 181:2 (2013), 136–148.
-
(2013)
J. Struct. Biol.
, vol.181
, Issue.2
, pp. 136-148
-
-
Vargas, J.1
Otón, J.2
Marabini, R.3
Jonic, S.4
de la Rosa-Trevín, J.5
Carazo, J.6
Sorzano, C.7
-
33
-
-
84921716413
-
Efficient initial volume determination from electron microscopy images of single particles
-
btu404
-
Vargas, J., Álvarez-Cabrera, A.-L., Marabini, R., Carazo, J.M., Sorzano, C.O.S., Efficient initial volume determination from electron microscopy images of single particles. Bioinformatics, 2014 btu404.
-
(2014)
Bioinformatics
-
-
Vargas, J.1
Álvarez-Cabrera, A.-L.2
Marabini, R.3
Carazo, J.M.4
Sorzano, C.O.S.5
-
34
-
-
63649113687
-
Dog picker and tiltpicker: software tools to facilitate particle selection in single particle electron microscopy
-
Voss, N.R., Yoshioka, C.K., Radermacher, M., Potter, C.S., Carragher, B., Dog picker and tiltpicker: software tools to facilitate particle selection in single particle electron microscopy. J. Struct. Biol. 166:2 (2009), 205–213.
-
(2009)
J. Struct. Biol.
, vol.166
, Issue.2
, pp. 205-213
-
-
Voss, N.R.1
Yoshioka, C.K.2
Radermacher, M.3
Potter, C.S.4
Carragher, B.5
-
35
-
-
84955216953
-
Gctf: real-time CTF determination and correction
-
Zhang, K., Gctf: real-time CTF determination and correction. J. Struct. Biol. 193:1 (2016), 1–12.
-
(2016)
J. Struct. Biol.
, vol.193
, Issue.1
, pp. 1-12
-
-
Zhang, K.1
|