35. Suloway C, Pulokas J, Fellmann D, Cheng A, Guerra F, Quispe J, Stagg S, Potter CS,
Carragher B (2005) Automated molecular microscopy: the new Leginon system. J Struct
Biol 151:41–60
36. Mastronarde DN (2005) Automated electron microscope tomography using robust prediction
of specimen movements. J Struct Biol 152:36–51
37. Li X, Zheng S, Agard DA, Cheng Y (2015) Asynchronous data acquisition and on-the-fly
analysis of dose fractionated cryoEM images by UCSFImage. J Struct Biol 192:174–178
38. Zhang J, Nakamura N, Shimizu Y, Liang N, Liu X, Jakana J, Marsh MP, Booth CR,
Shinkawa T, Nakata M, Chiu W (2009) JADAS: a customizable automated data acquisition
system and its application to ice-embedded single particles. J Struct Biol 165:1–9
39. Lander GC, Stagg SM, Voss NR, Cheng A, Fellmann D, Pulokas J, Yoshioka C, Irving C,
Mulder A, Lau PW, Lyumkis D, Potter CS, Carragher B (2009) Appion: an integrated,
database-driven pipeline to facilitate EM image processing. J Struct Biol 166:95–102
40. Hoppe W (1983) Electron-diffraction with the transmission electron-microscope as a
phase-determining diffractometer—from spatial-frequency filtering to the 3-Dimensional
structure-analysis of ribosomes. Angew Chem Int Edit 22:456–485
41. Orlova EV, Saibil HR (2011) Structural analysis of macromolecular assemblies by electron
microscopy. Chem Rev 111:7710–7748
42. Erickson HP, Klug A (1971) Measurement and compensation of defocusing and aberrations
by fourier processing of electron micrographs. Philos T Roy Soc B. 261:105–118
43. Wade RH (1992) A brief look at imaging and contrast transfer. Ultramicroscopy 46:145–156
44. Bell JM, Chen M, Baldwin PR, Ludtke SJ (2016) High resolution single particle refinement
in EMAN2.1. Methods 100:25–34
45. Rohou A, Grigorieff N (2015) CTFFIND4: fast and accurate defocus estimation from
electron micrographs. J Struct Biol 192:216–221
46. Zhang K (2016) Gctf: real-time CTF determination and correction. J Struct Biol 193:1–12
47. Mallick SP, Carragher B, Potter CS, Kriegman DJ (2005) ACE: automated CTF estimation.
Ultramicroscopy 104:8–29
48. Roseman AM (2004) FindEM–a fast, efficient program for automatic selection of particles
from electron micrographs. J Struct Biol 145:91–99
49. Tang G, Peng L, Baldwin PR, Mann DS, Jiang W, Rees I, Ludtke SJ (2007) EMAN2: an
extensible image processing suite for electron microscopy. J Struct Biol 157:38–46
50. Ludtke SJ, Bell JM, Chen M, Baldwin PR, Ludtke SJ (2016) Single-particle refinement and
variability analysis in EMAN2.1, high resolution single particle refinement in EMAN2.1.
Methods Enzymol 579:159–189
51. van Heel M, Harauz G, Orlova EV, Schmidt R, Schatz M (1996) A new generation of the
IMAGIC image processing system. J Struct Biol 116:17–24
52. Smith JM (1999) Ximdisp–a visualization tool to aid structure determination from electron
microscope images. J Struct Biol 125:223–228
53. Wood C, Burnley T, Patwardhan A, Scheres S, Topf M, Roseman A, Winn M (2015)
Collaborative computational project for electron cryo-microscopy. Acta Crystallogr D Biol
Crystallogr 71:123–126
54. Burnley T, Palmer CM, Winn M (2017) Recent developments in the CCP-EM software
suite. Acta Crystallogr Sect D Struct Biol 73:469–477
55. Scheres SH (2012) RELION: implementation of a Bayesian approach to cryo-EM structure
determination. J Struct Biol 180:519–530
56. Punjani A, Rubinstein JL, Fleet DJ, Brubaker MA (2017) cryoSPARC: algorithms for rapid
unsupervised cryo-EM structure determination. Nat Methods 14:290–296
57. Heimowitz A, Andén J, Singer A (2018) APPLE picker: automatic particle picking, a
low-effort Cryo-EM framework. J Struct Biol 204(2):215–227
58. Singer A et al. (2010) Algorithms for Single Particle Reconstruction (ASPIRE), http://spr.
math.princeton.edu/
Single-Particle cryo-EM as a Pipeline for Obtaining Atomic …
397
Carragher B (2005) Automated molecular microscopy: the new Leginon system. J Struct
Biol 151:41–60
36. Mastronarde DN (2005) Automated electron microscope tomography using robust prediction
of specimen movements. J Struct Biol 152:36–51
37. Li X, Zheng S, Agard DA, Cheng Y (2015) Asynchronous data acquisition and on-the-fly
analysis of dose fractionated cryoEM images by UCSFImage. J Struct Biol 192:174–178
38. Zhang J, Nakamura N, Shimizu Y, Liang N, Liu X, Jakana J, Marsh MP, Booth CR,
Shinkawa T, Nakata M, Chiu W (2009) JADAS: a customizable automated data acquisition
system and its application to ice-embedded single particles. J Struct Biol 165:1–9
39. Lander GC, Stagg SM, Voss NR, Cheng A, Fellmann D, Pulokas J, Yoshioka C, Irving C,
Mulder A, Lau PW, Lyumkis D, Potter CS, Carragher B (2009) Appion: an integrated,
database-driven pipeline to facilitate EM image processing. J Struct Biol 166:95–102
40. Hoppe W (1983) Electron-diffraction with the transmission electron-microscope as a
phase-determining diffractometer—from spatial-frequency filtering to the 3-Dimensional
structure-analysis of ribosomes. Angew Chem Int Edit 22:456–485
41. Orlova EV, Saibil HR (2011) Structural analysis of macromolecular assemblies by electron
microscopy. Chem Rev 111:7710–7748
42. Erickson HP, Klug A (1971) Measurement and compensation of defocusing and aberrations
by fourier processing of electron micrographs. Philos T Roy Soc B. 261:105–118
43. Wade RH (1992) A brief look at imaging and contrast transfer. Ultramicroscopy 46:145–156
44. Bell JM, Chen M, Baldwin PR, Ludtke SJ (2016) High resolution single particle refinement
in EMAN2.1. Methods 100:25–34
45. Rohou A, Grigorieff N (2015) CTFFIND4: fast and accurate defocus estimation from
electron micrographs. J Struct Biol 192:216–221
46. Zhang K (2016) Gctf: real-time CTF determination and correction. J Struct Biol 193:1–12
47. Mallick SP, Carragher B, Potter CS, Kriegman DJ (2005) ACE: automated CTF estimation.
Ultramicroscopy 104:8–29
48. Roseman AM (2004) FindEM–a fast, efficient program for automatic selection of particles
from electron micrographs. J Struct Biol 145:91–99
49. Tang G, Peng L, Baldwin PR, Mann DS, Jiang W, Rees I, Ludtke SJ (2007) EMAN2: an
extensible image processing suite for electron microscopy. J Struct Biol 157:38–46
50. Ludtke SJ, Bell JM, Chen M, Baldwin PR, Ludtke SJ (2016) Single-particle refinement and
variability analysis in EMAN2.1, high resolution single particle refinement in EMAN2.1.
Methods Enzymol 579:159–189
51. van Heel M, Harauz G, Orlova EV, Schmidt R, Schatz M (1996) A new generation of the
IMAGIC image processing system. J Struct Biol 116:17–24
52. Smith JM (1999) Ximdisp–a visualization tool to aid structure determination from electron
microscope images. J Struct Biol 125:223–228
53. Wood C, Burnley T, Patwardhan A, Scheres S, Topf M, Roseman A, Winn M (2015)
Collaborative computational project for electron cryo-microscopy. Acta Crystallogr D Biol
Crystallogr 71:123–126
54. Burnley T, Palmer CM, Winn M (2017) Recent developments in the CCP-EM software
suite. Acta Crystallogr Sect D Struct Biol 73:469–477
55. Scheres SH (2012) RELION: implementation of a Bayesian approach to cryo-EM structure
determination. J Struct Biol 180:519–530
56. Punjani A, Rubinstein JL, Fleet DJ, Brubaker MA (2017) cryoSPARC: algorithms for rapid
unsupervised cryo-EM structure determination. Nat Methods 14:290–296
57. Heimowitz A, Andén J, Singer A (2018) APPLE picker: automatic particle picking, a
low-effort Cryo-EM framework. J Struct Biol 204(2):215–227
58. Singer A et al. (2010) Algorithms for Single Particle Reconstruction (ASPIRE), http://spr.
math.princeton.edu/
Single-Particle cryo-EM as a Pipeline for Obtaining Atomic …
397