-
2
-
-
84887238690
-
A pattern matching approach to the automatic selection of particles from low-contrast electron micrographs
-
Abrishami V., Zaldívar-Peraza A., de la Rosa-Trevín J.M., Vargas J., Otón J., et al. A pattern matching approach to the automatic selection of particles from low-contrast electron micrographs. Bioinformatics 2013, 29:2460-2468.
-
(2013)
Bioinformatics
, vol.29
, pp. 2460-2468
-
-
Abrishami, V.1
Zaldívar-Peraza, A.2
de la Rosa-Trevín, J.M.3
Vargas, J.4
Otón, J.5
-
3
-
-
0029665272
-
A model-based approach for determining orientations of biological macromolecules imaged by cryoelectron microscopy
-
Baker T.S., Cheng R.H. A model-based approach for determining orientations of biological macromolecules imaged by cryoelectron microscopy. J. Struct. Biol. 1996, 116:120-130.
-
(1996)
J. Struct. Biol.
, vol.116
, pp. 120-130
-
-
Baker, T.S.1
Cheng, R.H.2
-
4
-
-
0025364361
-
Fuzzy sets-based classification of electron microscopy images of biological macromolecules with an application to ribosomal particles
-
Carazo J.M., Rivera F.F., Zapata E.L., Radermacher M., Frank J. Fuzzy sets-based classification of electron microscopy images of biological macromolecules with an application to ribosomal particles. J. Microsc. 1990, 157:187-203.
-
(1990)
J. Microsc.
, vol.157
, pp. 187-203
-
-
Carazo, J.M.1
Rivera, F.F.2
Zapata, E.L.3
Radermacher, M.4
Frank, J.5
-
5
-
-
0029878835
-
Advances in computational image processing for microscopy
-
Carragher B., Smith P.R. Advances in computational image processing for microscopy. J. Struct. Biol. 1996, 116:2-8.
-
(1996)
J. Struct. Biol.
, vol.116
, pp. 2-8
-
-
Carragher, B.1
Smith, P.R.2
-
7
-
-
11244308507
-
Qt GUI Toolkit: porting graphics to multiple platforms using a GUI toolkit
-
Article No. 2. URL:
-
Eng E. Qt GUI Toolkit: porting graphics to multiple platforms using a GUI toolkit. Linux J. 1996, 1996. Article No. 2. URL: http://dl.acm.org/citation.cfm?id=326464&CFID=250746326&CFTOKEN=69585403.
-
(1996)
Linux J.
, vol.1996
-
-
Eng, E.1
-
8
-
-
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., et al. SPIDER and WEB: processing and visualization of images in 3D electron microscopy and related fields. J. Struct. Biol. 1996, 116:190-199.
-
(1996)
J. Struct. Biol.
, vol.116
, pp. 190-199
-
-
Frank, J.1
Radermacher, M.2
Penczek, P.3
Zhu, J.4
Li, Y.5
-
9
-
-
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. 1996, 116:17-24.
-
(1996)
J. Struct. Biol.
, vol.116
, pp. 17-24
-
-
van Heel, M.1
Harauz, G.2
Orlova, E.V.3
Schmidt, R.4
Schatz, M.5
-
10
-
-
0029879294
-
The EM program package: a platform for image processing in biological electron microscopy
-
Hegerl R. The EM program package: a platform for image processing in biological electron microscopy. J. Struct. Biol. 1996, 116:30-34.
-
(1996)
J. Struct. Biol.
, vol.116
, pp. 30-34
-
-
Hegerl, R.1
-
11
-
-
33845336533
-
Bsoft: image processing and molecular modeling for electron microscopy
-
Heymann B., Belnap D. Bsoft: image processing and molecular modeling for electron microscopy. J. Struct. Biol. 2007, 157:3-18.
-
(2007)
J. Struct. Biol.
, vol.157
, pp. 3-18
-
-
Heymann, B.1
Belnap, D.2
-
12
-
-
78651295835
-
Emdatabank.org: unified data resource for cryoem
-
Lawson C.L., Baker M.L., Best C., Bi C., Dougherty M., et al. Emdatabank.org: unified data resource for cryoem. Nucleic Acids Res. 2011, 39:D456-D464.
-
(2011)
Nucleic Acids Res.
, vol.39
-
-
Lawson, C.L.1
Baker, M.L.2
Best, C.3
Bi, C.4
Dougherty, M.5
-
13
-
-
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. 1999, 128:82-97.
-
(1999)
J. Struct. Biol.
, vol.128
, pp. 82-97
-
-
Ludtke, S.J.1
Baldwin, P.R.2
Chiu, W.3
-
14
-
-
0028363358
-
Pattern recognition and classification of images of biological macromolecules using artificial neural networks
-
Marabini R., Carazo J.M. Pattern recognition and classification of images of biological macromolecules using artificial neural networks. Biophys. J. 1994, 66:1804-1814.
-
(1994)
Biophys. J.
, vol.66
, pp. 1804-1814
-
-
Marabini, R.1
Carazo, J.M.2
-
15
-
-
0032053763
-
3D reconstruction in electron microscopy using ART with smooth spherically symmetric volume elements (blobs)
-
Marabini R., Herman G.T., Carazo J.M. 3D reconstruction in electron microscopy using ART with smooth spherically symmetric volume elements (blobs). Ultramicroscopy 1998, 72:53-65.
-
(1998)
Ultramicroscopy
, vol.72
, pp. 53-65
-
-
Marabini, R.1
Herman, G.T.2
Carazo, J.M.3
-
16
-
-
0029945636
-
Xmipp: an image processing package for electron microscopy
-
Marabini R., Masegosa I.M., San Martín M.C., Marco S., Fernández J.J., et al. Xmipp: an image processing package for electron microscopy. J. Struct. Biol. 1996, 116:237-240.
-
(1996)
J. Struct. Biol.
, vol.116
, pp. 237-240
-
-
Marabini, R.1
Masegosa, I.M.2
San Martín, M.C.3
Marco, S.4
Fernández, J.J.5
-
17
-
-
34548734839
-
Tomoj: software for multiple-axis tomography
-
Messaoudi C., Boudier T., Sorzano C.O.S., Marco S. Tomoj: software for multiple-axis tomography. BMC Bioinf. 2007, 8:288.
-
(2007)
BMC Bioinf.
, vol.8
, pp. 288
-
-
Messaoudi, C.1
Boudier, T.2
Sorzano, C.O.S.3
Marco, S.4
-
18
-
-
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. 2003, 142:334-347.
-
(2003)
J. Struct. Biol.
, vol.142
, pp. 334-347
-
-
Mindell, J.A.1
Grigorieff, N.2
-
19
-
-
84859428449
-
Image formation in cellular x-ray microscopy
-
Oton J., Sorzano C.O.S., Pereiro E., Cuenca-Alba J., Navarro R., et al. Image formation in cellular x-ray microscopy. J. Struct. Biol. 2012, 178:29-37.
-
(2012)
J. Struct. Biol.
, vol.178
, pp. 29-37
-
-
Oton, J.1
Sorzano, C.O.S.2
Pereiro, E.3
Cuenca-Alba, J.4
Navarro, R.5
-
20
-
-
4444221565
-
UCSF chimera - a visualization system for exploratory research and analysis
-
Pettersen E.F., Goddard T.D., Huang C.C., Couch G.S., Greenblatt D.M., et al. UCSF chimera - a visualization system for exploratory research and analysis. J. Comput. Chem. 2004, 25:1605-1612.
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 1605-1612
-
-
Pettersen, E.F.1
Goddard, T.D.2
Huang, C.C.3
Couch, G.S.4
Greenblatt, D.M.5
-
21
-
-
0344552378
-
IPLT - image processing library and toolkit for the electron microscopy community
-
Philippsen A., Schenk A.D., Stahlberg H., Engel A. IPLT - image processing library and toolkit for the electron microscopy community. J. Struct. Biol. 2003, 144:4-12.
-
(2003)
J. Struct. Biol.
, vol.144
, pp. 4-12
-
-
Philippsen, A.1
Schenk, A.D.2
Stahlberg, H.3
Engel, A.4
-
22
-
-
84985231782
-
Three-Dimensional reconstruction from a single-exposure, random conical tilt series applied to the 50s ribosomal subunit of Escherichia coli
-
Radermacher M., Wagenknecht T., Verschoor A., Frank J. Three-Dimensional reconstruction from a single-exposure, random conical tilt series applied to the 50s ribosomal subunit of Escherichia coli. J. Microsc. 1987, 146:113-136.
-
(1987)
J. Microsc.
, vol.146
, pp. 113-136
-
-
Radermacher, M.1
Wagenknecht, T.2
Verschoor, A.3
Frank, J.4
-
23
-
-
35148891312
-
Modeling experimental image formation for likelihood-based classification of electron microscopy data
-
Scheres S., Núñez-Ramírez R., Gómez-Llorente Y., San Martín C., Eggermont P.P.B., et al. Modeling experimental image formation for likelihood-based classification of electron microscopy data. Structure 2007, 15:1167-1177.
-
(2007)
Structure
, vol.15
, pp. 1167-1177
-
-
Scheres, S.1
Núñez-Ramírez, R.2
Gómez-Llorente, Y.3
San Martín, C.4
Eggermont, P.P.B.5
-
24
-
-
71049139404
-
Averaging of electron subtomograms and random conical tilt reconstructions through likelihood optimization
-
Scheres S.H., Melero R., Valle M., Carazo J.M. Averaging of electron subtomograms and random conical tilt reconstructions through likelihood optimization. Structure 2009, 17:1563-1572.
-
(2009)
Structure
, vol.17
, pp. 1563-1572
-
-
Scheres, S.H.1
Melero, R.2
Valle, M.3
Carazo, J.M.4
-
25
-
-
77957322190
-
Classification of structural heterogeneity by maximum-likelihood methods
-
Scheres S.H.W. Classification of structural heterogeneity by maximum-likelihood methods. Methods Enzymol. 2010, 482:295-320.
-
(2010)
Methods Enzymol.
, vol.482
, pp. 295-320
-
-
Scheres, S.H.W.1
-
26
-
-
33845939047
-
Disentangling conformational states of macromolecules in 3D-EM through likelihood optimization
-
Scheres S.H.W., Gao H., Valle M., Herman G.T., Eggermont P.P.B., et al. Disentangling conformational states of macromolecules in 3D-EM through likelihood optimization. Nat. Methods 2007, 4:27-29.
-
(2007)
Nat. Methods
, vol.4
, pp. 27-29
-
-
Scheres, S.H.W.1
Gao, H.2
Valle, M.3
Herman, G.T.4
Eggermont, P.P.B.5
-
27
-
-
44949165726
-
Image processing for electron microscopy single-particle analysis using Xmipp
-
Scheres S.H.W., Núñez-Ramírez R., Sorzano C.O.S., Carazo J.M., Marabini R. Image processing for electron microscopy single-particle analysis using Xmipp. Nat. Protoc. 2008, 3:977-990.
-
(2008)
Nat. Protoc.
, vol.3
, pp. 977-990
-
-
Scheres, S.H.W.1
Núñez-Ramírez, R.2
Sorzano, C.O.S.3
Carazo, J.M.4
Marabini, R.5
-
28
-
-
16244396466
-
Maximum-likelihood multi-reference refinement for electron microscopy images
-
Scheres S.H.W., Valle M., Núñez R., Sorzano C.O.S., Marabini R., et al. Maximum-likelihood multi-reference refinement for electron microscopy images. J. Mol. Biol. 2005, 348:139-149.
-
(2005)
J. Mol. Biol.
, vol.348
, pp. 139-149
-
-
Scheres, S.H.W.1
Valle, M.2
Núñez, R.3
Sorzano, C.O.S.4
Marabini, R.5
-
29
-
-
0029928871
-
Suprim: easily modified image processing software
-
Schroeter J.P., Bretaudiere J.P. Suprim: easily modified image processing software. J. Struct. Biol. 1996, 116:131-137.
-
(1996)
J. Struct. Biol.
, vol.116
, pp. 131-137
-
-
Schroeter, J.P.1
Bretaudiere, J.P.2
-
30
-
-
0029916486
-
The micrograph data processing program
-
doi:10.1006/jsbi.1996.0007
-
Smith P.R., Gottesman S.M. The micrograph data processing program. J. Struct. Biol. 1996, 116:35-40. URL: http://dx.doi.org/10.1006/jsbi.1996.0007, doi:10.1006/jsbi.1996.0007.
-
(1996)
J. Struct. Biol.
, vol.116
, pp. 35-40
-
-
Smith, P.R.1
Gottesman, S.M.2
-
31
-
-
51349087192
-
Software tools for molecular microscopy
-
Smith R., Carragher B. Software tools for molecular microscopy. J. Struct. Biol. 2008, 163:224-228.
-
(2008)
J. Struct. Biol.
, vol.163
, pp. 224-228
-
-
Smith, R.1
Carragher, B.2
-
32
-
-
77953710827
-
A clustering approach to multireference alignment of single-particle projections in electron microscopy
-
Sorzano C.O.S., Bilbao-Castro J.R., Shkolnisky Y., Alcorlo M., Melero R., et al. A clustering approach to multireference alignment of single-particle projections in electron microscopy. J. Struct. Biol. 2010, 171:197-206.
-
(2010)
J. Struct. Biol.
, vol.171
, pp. 197-206
-
-
Sorzano, C.O.S.1
Bilbao-Castro, J.R.2
Shkolnisky, Y.3
Alcorlo, M.4
Melero, R.5
-
33
-
-
84870493241
-
Semiautomatic, high-throughput, high-resolution protocol for three-dimensional reconstruction of single particles in electron microscopy
-
Sorzano C.O.S., de la Rosa Trevín J.M., Otón J., Vega J.J., Cuenca J., et al. Semiautomatic, high-throughput, high-resolution protocol for three-dimensional reconstruction of single particles in electron microscopy. Methods Mol. Biol. 2013, 950:171-193.
-
(2013)
Methods Mol. Biol.
, vol.950
, pp. 171-193
-
-
Sorzano, C.O.S.1
de la Rosa Trevín, J.M.2
Otón, J.3
Vega, J.J.4
Cuenca, J.5
-
34
-
-
35048832803
-
Fast, robust and accurate determination of transmission electron microscopy contrast transfer function
-
Sorzano C.O.S., 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. 2007, 160:249-262.
-
(2007)
J. Struct. Biol.
, vol.160
, pp. 249-262
-
-
Sorzano, C.O.S.1
Jonic, S.2
Núñez-Ramírez, R.3
Boisset, N.4
Carazo, J.M.5
-
35
-
-
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. 2004, 148:194-204.
-
(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
-
36
-
-
67650908133
-
Marker-free image registration of electron tomography tilt-series
-
Sorzano C.O.S., Messaoudi C., Eibauer M., Bilbao-Castro J.R., Hegerl R., Nickell S., Marco S., Carazo J.M. Marker-free image registration of electron tomography tilt-series. BMC Bioinf. 2009, 10:124.
-
(2009)
BMC Bioinf.
, vol.10
, pp. 124
-
-
Sorzano, C.O.S.1
Messaoudi, C.2
Eibauer, M.3
Bilbao-Castro, J.R.4
Hegerl, R.5
Nickell, S.6
Marco, S.7
Carazo, J.M.8
-
37
-
-
67651054955
-
Automatic particle selection from electron micrographs using machine learning techniques
-
Sorzano C.O.S., Recarte E., Alcorlo M., Bilbao-Castro J.R., San-Martín C., et al. Automatic particle selection from electron micrographs using machine learning techniques. J. Struct. Biol. 2009, 167:252-260.
-
(2009)
J. Struct. Biol.
, vol.167
, pp. 252-260
-
-
Sorzano, C.O.S.1
Recarte, E.2
Alcorlo, M.3
Bilbao-Castro, J.R.4
San-Martín, C.5
-
38
-
-
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. 2007, 157:38-46. URL: http://dx.doi.org/10.1016/j.jsb.2006.05.009.
-
(2007)
J. Struct. Biol.
, vol.157
, 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
-
39
-
-
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.M., et al. FASTDEF: fast defocus and astigmatism estimation for high-throughput transmission electron microscopy. J. Struct. Biol. 2013, 181:136-148.
-
(2013)
J. Struct. Biol.
, vol.181
, pp. 136-148
-
-
Vargas, J.1
Otón, J.2
Marabini, R.3
Jonic, S.4
de la Rosa-Trevín, J.M.5
-
40
-
-
0345701398
-
A method for estimating the CTF in electron microscopy based on ARMA models and parameter adjusting
-
Velázquez-Muriel J.A., Sorzano C.O.S., Fernández J.J., Carazo J.M. A method for estimating the CTF in electron microscopy based on ARMA models and parameter adjusting. Ultramicroscopy 2003, 96:17-35.
-
(2003)
Ultramicroscopy
, vol.96
, pp. 17-35
-
-
Velázquez-Muriel, J.A.1
Sorzano, C.O.S.2
Fernández, J.J.3
Carazo, J.M.4
|