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=== Online courses and Learning material ===
 
=== Online courses and Learning material ===
  
[http://cryo-em-course.caltech.edu Caltech] [https://www.coursera.org/learn/cryo-em (same course in Coursera)]
+
[http://cryo-em-course.caltech.edu Caltech] [https://www.coursera.org/learn/cryo-em (same course in Coursera)] [https://em-learning.com (latest version of the course in EM-learning)]
  
 
[ftp://ftp.mrc-lmb.cam.ac.uk/pub/scheres/EM-course MRC]
 
[ftp://ftp.mrc-lmb.cam.ac.uk/pub/scheres/EM-course MRC]
Line 85: Line 85:
 
[https://www.jove.com/video/52311/do-s-don-ts-cryo-electron-microscopy-primer-on-sample-preparation Do's and don'ts on sample preparation]
 
[https://www.jove.com/video/52311/do-s-don-ts-cryo-electron-microscopy-primer-on-sample-preparation Do's and don'ts on sample preparation]
  
[http://nramm.nysbc.org/2017-workshop-lectures NRAMM Workshop 2017]
+
[http://nramm.nysbc.org/2017-workshop-lectures NRAMM Workshop 2017] [https://nccat.nysbc.org/activities/courses/nccat-spa-short-course-2022 (course slides)]
  
 
[https://www.youtube.com/user/SBGridTV/videos SBGrid videos about the programs they offer]
 
[https://www.youtube.com/user/SBGridTV/videos SBGrid videos about the programs they offer]
  
 
[http://i2pc.es/coss/Docencia/ImageProcessing/imageProcessingInEM.pdf Madrid course on single particle analysis]
 
[http://i2pc.es/coss/Docencia/ImageProcessing/imageProcessingInEM.pdf Madrid course on single particle analysis]
 +
 +
[https://www.youtube.com/watch?v=F1yXJaZ2H5o&list=PLFEB3YHuxu11I4Qgj6K5jmWcghsFnE09Q CCP-EM Spring symposium 2019]
 +
 +
[https://www.youtube.com/playlist?list=PLFEB3YHuxu11Jp_pOCIEtXxSqozFHve0O CCP-EM Spring symposium 2020]
 +
 +
[https://www.youtube.com/playlist?list=PLhiuGaXlZZel2mj6S4FPjWwsvj2LPqLYL NCCAT Single Particle short course 2020]
 +
 +
[https://www.cellstructureatlas.org Cell atlas book by Grant Jensen and Catherine Oikonomou]
 +
 +
[https://va.tech.purdue.edu/cryoVR/index.php Purdue CryoEM Virtual Reality Augmented Training]
 +
 +
[https://www.youtube.com/playlist?list=PLhiuGaXlZZek9D0SZk0OVtTeFVETa1sPG NCCAT Short course on Tomography]
 +
 +
[https://www.google.com/maps/d/u/0/viewer?mid=1eQ1r8BiDYfaK7D1S9EeFJEgkLggMyoaT&ll=-3.81666561775622e-14%2C-37.83892653579875&z=1 Map with CryoEM Facilities]
 +
 +
[https://www.youtube.com/playlist?list=PLhiuGaXlZZeliWnyp_wtRqPr_QkX00um7 NCCAT Single Particle Analysis short course]
 +
 +
[https://algosb2023.loria.fr/lectures/ Algorithms for Structural Bioinformatics, AlgoSB2023, Cargese]
 +
 +
[https://cryoem.world/ One world CryoEM technical talks]
  
 
=== Image formation ===
 
=== Image formation ===
Line 114: Line 134:
 
| CTF model
 
| CTF model
 
|-  
 
|-  
 +
 +
| Paper
 +
| [[1974Taylor_Diffraction]]
 +
| Electron diffraction of crystals
 +
|-
 +
  
 
| Paper
 
| Paper
Line 368: Line 394:
 
| [[2018Hettler_Charging]]
 
| [[2018Hettler_Charging]]
 
| Charging of carbon thin films
 
| Charging of carbon thin films
|-
 
 
| Paper
 
| [[2018Koeck_PhaseShift]]
 
| Design of a phase shift device
 
 
|-  
 
|-  
  
Line 400: Line 421:
 
|-  
 
|-  
  
|}
+
| Paper
 +
| [[2020Bromberg_Aberrations]]
 +
| Estimation of strong high-order aberrations
 +
|-
  
=== Collection geometry ===
+
| Paper
 
+
| [[2020Gruza_Atomic]]
{|
+
| Detailed atomic models considering local charges and directional bonds
 
 
| Chapter
 
| [[1980Hoppe_Wedge]]
 
| Missing wedge
 
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1987Radermacher_RCT]]
+
| [[2020Naydenova_Buckling]]
| Random Conical Tilt and Single axis tilt
+
| Beam induced movement explained as ice buckling
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1988Radermacher_RCT]]
+
| [[2020Zhang_LimitsSimulated]]
| Random Conical Tilt and Single axis tilt
+
| Simulation of micrographs and 3D reconstruction for low weight proteins (14kDa)
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1995Penczek_Dual]]
+
| [[2020Tichelaar_Thick]]
| Dual axis tomography
+
| Effect of sample thickness on the CTF
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1997Mastronarde_Dual]]
+
| [[2020Yip_Atomic]]
| Dual axis tomography
+
| Atomic resolution by monochromator and a second-generation spherical aberration corrector
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2003Ludtke_FocusPairs]]
+
| [[2020Zhang_LimitsSimulated]]
| Focus pairs for single particles
+
| Simulation of micrographs and 3D reconstruction for low weight proteins (14kDa)
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2005Lanzavecchia_Conical]]
+
| [[2021Egerton_Inelastic]]
| Conical tomography
+
| PSF of inelastic scattering
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2005Zampighi_Conical]]
+
| [[2021Glaeser_Fading]]
| Conical tomography
+
| Defocus-dependent Thon-ring fading
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2006Leschziner_OT]]
+
| [[2021Wieferig_Devitrification]]
| Orthogonal Tilt
+
| Devitrification reduces beam-induced movement in cryo-EM
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2006Messaoudi_Multiple]]
+
| [[2022Heymann_PSSNR]]
| Multiple axis tomography
+
| Progressive Spectral Signal-to-Noise Ratio to assess quality and radiation damage
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2012Kudryashev_FocusPairs]]
+
| [[2022Dickerson_Inelastic]]
| Focus pairs tomography
+
| The role of inelastic scattering in thick specimens
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2014Hovden_TiltFocus]]
+
| [[2022Kulik_TAAM]]
| Combining tilt series with focus series
+
| Theoretical 3D electron diffraction electrostatic potential maps of proteins
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Sorzano_RandomConicalTilt]]
+
| [[2022Ravikumar_SideChains]]
| General formulation of Random Conical Tilt
+
| Comparison of side-chain dispersion in protein structures determined by cryo-EM and X-ray crystallography
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Hagen_DoseTomography]]
+
| [[2023Bromberg_Complex]]
| Dose optimization for subtomogram averaging
+
| CTF and Ewald sphere correction using complex-valued images
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Tan_PreferredViews]]
+
| [[2023Heymann_Ewald]]
| Solving preferred views problems through tilting
+
| The Ewald sphere/focus gradient does not limit the resolution of cryoEM reconstructions
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Donati_Compressed]]
+
| [[2023Schreiber_charge]]
| Compressed sensing for STEM
+
| Time dynamics of charge buildup
|-
 
 
 
| Paper
 
| [[2018Oveisi_Stereo]]
 
| Stereo-vision with EM
 
|-
 
 
 
| Paper
 
| [[2018Cheng_BeamShift]]
 
| Fast image acquisition through beam-shift
 
 
|-  
 
|-  
  
 
|}
 
|}
  
=== Sample preparation ===
+
=== Collection geometry ===
  
 
{|
 
{|
  
| Paper
+
| Chapter
| [[1982Dubochet_Sample]]
+
| [[1980Hoppe_Wedge]]
| Vitreous ice
+
| Missing wedge
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1986Lepault_Sample]]
+
| [[1987Radermacher_RCT]]
| Fast freezing
+
| Random Conical Tilt and Single axis tilt
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1995Dubochet_Sample]]
+
| [[1988Radermacher_RCT]]
| High-pressure freezing
+
| Random Conical Tilt and Single axis tilt
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1995VanMarle_Sample]]
+
| [[1995Penczek_Dual]]
| Sample damages in resin
+
| Dual axis tomography
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1998Adrian_Sample]]
+
| [[1997Mastronarde_Dual]]
| Cryo negative staining
+
| Dual axis tomography
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2002DeCarlo_Damage]]
+
| [[2003Ludtke_FocusPairs]]
| Radiation damage in cryonegative staining
+
| Focus pairs for single particles
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2002Hsieh_Sample]]
+
| [[2005Lanzavecchia_Conical]]
| Cryofixation
+
| Conical tomography
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2004AlAmoudi_Sample]]
+
| [[2005Zampighi_Conical]]
| CEMOVIS
+
| Conical tomography
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2008Studer_Sample]]
+
| [[2006Leschziner_OT]]
| Review on high pressure freezing
+
| Orthogonal Tilt
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2009Pierson_Sample]]
+
| [[2006Messaoudi_Multiple]]
| Review on sample preparation for electron tomography
+
| Multiple axis tomography
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2010Zhang_NegativeStaining]]
+
| [[2012Kudryashev_FocusPairs]]
| Negative staining for small protein imaging
+
| Focus pairs tomography
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2012Zhang_PositiveStaining]]
+
| [[2014Hovden_TiltFocus]]
| Positive staining
+
| Combining tilt series with focus series
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2014Rames_NegativeStaining]]
+
| [[2015Sorzano_RandomConicalTilt]]
| Optimized negative staining
+
| General formulation of Random Conical Tilt
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2014Russo_GoldGrids]]
+
| [[2017Hagen_DoseTomography]]
| Gold grids for single particles
+
| Dose optimization for subtomogram averaging
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Cabra_Sample]]
+
| [[2017Tan_PreferredViews]]
| Review on sample preparation for single particles with videos
+
| Solving preferred views problems through tilting
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Chari_ProteoPlex]]
+
| [[2017Donati_Compressed]]
| Fast evaluation of the structural stability
+
| Compressed sensing for STEM
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Passmore_Review]]
+
| [[2018Oveisi_Stereo]]
| Tutorial chapter on sample preparation
+
| Stereo-vision with EM
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Razinkov_Vitrification]]
+
| [[2018Cheng_BeamShift]]
| New vitrification method
+
| Fast image acquisition through beam-shift
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Takizawa_Sample]]
+
| [[2019Wu_BeamShiftAndTilt]]
| Review on sample preparation for EM
+
| Fast image acquisition through beam-shift and beam tilt control
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Thompson_Sample]]
+
| [[2023Seifer_RevisedSaxton]]
| Review on sample preparation for EM
+
| Revised Saxton geometry for tilt series acquisition
 
|-  
 
|-  
  
| Paper
+
|}
| [[2017Arnold_BlottingFree]]
+
 
| Blotting-free preparation
+
=== Sample preparation ===
|-
+
 
 +
{|
  
 
| Paper
 
| Paper
| [[2017Earl_review]]
+
| [[1982Dubochet_Sample]]
| Review of sample preparation
+
| Vitreous ice
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2017Feng_SprayingPlunging]]
+
| [[1986Lepault_Sample]]
| Spraying plunging
+
| Fast freezing
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2017He_FIB]]
+
| [[1995Dubochet_Sample]]
| Cryo FIB lamella for TEM
+
| High-pressure freezing
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2017Peitsch_Sample]]
+
| [[1995VanMarle_Sample]]
| iMEM: Isolation of Plasma Membrane for Cryoelectron Microscopy
+
| Sample damages in resin
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2017Scapin_Storage]]
+
| [[1998Adrian_Sample]]
| Cryo storage of samples
+
| Cryo negative staining
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2017Schaffer_FocusedIonBeam]]
+
| [[2002DeCarlo_Damage]]
| Focused Ion Beam sample preparation for membrane proteins
+
| Radiation damage in cryonegative staining
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2017Scherr_HydrogelNanomembranes]]
+
| [[2002Hsieh_Sample]]
| Sample preparation for membrane proteins
+
| Cryofixation
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2018Anderson_CLEM]]
+
| [[2004AlAmoudi_Sample]]
| Correlated light and EM
+
| CEMOVIS
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2018Arnold_Review]]
+
| [[2008Studer_Sample]]
| Review on sample preparation with special emphasis on microfluidic approaches
+
| Review on high pressure freezing
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2018Dandey_Spotiton]]
+
| [[2009Pierson_Sample]]
| Spotiton, a device for vitrification
+
| Review on sample preparation for electron tomography
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2018Gewering_Detergents]]
+
| [[2010Zhang_OpNS]]
| Detergent background in negative stain
+
| Optimized negative staining (OpNS) for small protein and lipoprotein imaging
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2018Li_CLEM]]
+
| [[2012Zhang_Cryo-PS]]
| Correlated light and EM
+
| Cryo-positive staining (Cryo-PS)
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2018Noble_Reducing]]
+
| [[2014Russo_GoldGrids]]
| Reducing particle adsorption
+
| Gold grids for single particles
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2018Rice_Ice]]
+
| [[2015Cabra_Sample]]
| Routine determination of ice thickness
+
| Review on sample preparation for single particles with videos
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2018Schmidli_Miniaturized]]
+
| [[2015Chari_ProteoPlex]]
| Protein isolation and sample preparation
+
| Fast evaluation of the structural stability
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2018Wei_Grids]]
+
| [[2016Passmore_Review]]
| "Self-wicking" nanowire grids
+
| Tutorial chapter on sample preparation
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2019DImprima_Denaturation]]
+
| [[2016Razinkov_Vitrification]]
| Protein denaturation at the air-water interface and how to prevent it
+
| New vitrification method
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2019Song_FalconIII]]
+
| [[2016Takizawa_Sample]]
| Comparison of the modes of Falcon III
+
| Review on sample preparation for EM
|-
 
 
 
|}
 
 
 
=== Automated data collection ===
 
 
 
{|
 
 
 
| Paper
 
| [[1992Dierksen_Automatic]]
 
| Automated data collection
 
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1992Koster_Automatic]]
+
| [[2016Thompson_Sample]]
| Automated data collection
+
| Review on sample preparation for EM
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1996Fung_Automatic]]
+
| [[2017Arnold_BlottingFree]]
| Automated data collection for tomography
+
| Blotting-free preparation
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2001Zhang_Automatic]]
+
| [[2017Earl_review]]
| Automated data collection: AutoEM
+
| Review of sample preparation
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2003Ziese_Automatic]]
+
| [[2017Feng_SprayingPlunging]]
| Automated autofocusing
+
| Spraying plunging
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2004Potter_Automatic]]
+
| [[2017He_FIB]]
| Automated sample loading
+
| Cryo FIB lamella for TEM
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2004Zheng_Automatic]]
+
| [[2017Peitsch_Sample]]
| Automated data collection
+
| iMEM: Isolation of Plasma Membrane for Cryoelectron Microscopy
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2005Lei_Automatic]]
+
| [[2017Scapin_Storage]]
| Automated data collection: AutoEM
+
| Cryo storage of samples
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2005Suloway_Automatic]]
+
| [[2017Schaffer_FocusedIonBeam]]
| Automated data collection: Leginon
+
| Focused Ion Beam sample preparation for membrane proteins
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2007Yoshioka_RCT]]
+
| [[2017Scherr_HydrogelNanomembranes]]
| Automated Random Conical Tilt
+
| Sample preparation for membrane proteins
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2011Korinek_TOM2]]
+
| [[2018Anderson_CLEM]]
| Automated acquisition with TOM2
+
| Correlated light and EM
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2015Li_UCSFImage]]
+
| [[2018Arnold_Review]]
| Automated acquisition with UCSFImage
+
| Review on sample preparation with special emphasis on microfluidic approaches
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2016Gil_Fuzzy]]
+
| [[2018Ashtiani_femtolitre]]
| Real time decisions during acquisition with neuro-fuzzy method
+
| Delivery of femtolitre droplets using surface acoustic wave based atomisation for cryo-EM grid preparation
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2016Liu_TiltControl]]
+
| [[2018Dandey_Spotiton]]
| Accurate control of the tilt angle for electron tomography
+
| Spotiton, a device for vitrification
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2016Vargas_FoilHole]]
+
| [[2018Gewering_Detergents]]
| Determination of image quality at low magnification
+
| Detergent background in negative stain
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2017Alewijnse_Best]]
+
| [[2018Li_CLEM]]
| Best practices for managing large CryoEM facilities
+
| Correlated light and EM
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2017Biyani_Focus]]
+
| [[2018Noble_Reducing]]
| Automatic processing of micrographs
+
| Reducing particle adsorption
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2018Gomez_Facilities]]
+
| [[2018Palovcak_Graphene]]
| Use of Scipion at facilities
+
| Preparation of graphene-oxide cryo-EM grids
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2018Sorzano_Gain]]
+
| [[2018Rice_Ice]]
| Estimation of the DDD camera gain or residual gain
+
| Routine determination of ice thickness
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2019Chreifi_TiltSeries]]
+
| [[2018Schmidli_Miniaturized]]
| Rapid tilt-series acquisition for electron cryotomography
+
| Protein isolation and sample preparation
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2019Eng_ImageCompression]]
+
| [[2018Wei_Grids]]
| 3D Reconstruction from compressed images
+
| "Self-wicking" nanowire grids
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2019Thompson_Protocol]]
+
| [[2019DImprima_Denaturation]]
| Protocol for EM acquisition
+
| Protein denaturation at the air-water interface and how to prevent it
|-  
+
|-
  
|}
+
| Paper
 +
| [[2019Rubinstein_ultrasonic]]
 +
| Ultrasonic specimen preparation device
 +
|-
  
== Single particles ==
+
| Paper
 +
| [[2019Song_FalconIII]]
 +
| Comparison of the modes of Falcon III
 +
|-
  
=== Automatic particle picking ===
+
| Paper
 +
| [[2020Cianfrocco_Wrong]]
 +
| What could go wrong?
 +
|-
  
{|
+
| Paper
 +
| [[2020Egelman_Ice]]
 +
| Problems with the ice
 +
|-
  
 
| Paper
 
| Paper
| [[1982VanHeel_Detection]]
+
| [[2020Fassler_Printing]]
| Detection of particles in micrographs
+
| 3D printed cell culture grid holder
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2001Nicholson_Review]]
+
| [[2020Klebl_Deposition]]
| Review on automatic particle picking
+
| Sample deposition onto CryoEM grids: sprays and jets
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2001Zhu_Filaments]]
+
| [[2020Maeots_TimeResolved]]
| Automatic identification of filaments in micrographs
+
| Time resolved CryoEM by microfluidics
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2004Sigworth_Detection]]
+
| [[2020Tan_ThroughGrid]]
| Classical detection theory and the cryo-EM particle selection problem
+
| Through-grid wicking enables high-speed 1 cryoEM specimen preparation
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2004Volkmann_ParticlePicking]]
+
| [[2020Yoder_TimeResolved]]
| An approach to automated particle picking from electron micrographs based on reduced representation templates
+
| Time resolved CryoEM by light estimulation
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2004Wong_ParticlePicking]]
+
| [[2020Zachs_FIB]]
| Model-based particle picking for cryo-electron microscopy
+
| Automation for FIB milling
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2004Zhu_Review]]
+
| [[2021Bieber_FIBET]]
| Review on automatic particle picking
+
| Sample preparation for correlative FIB milling and CryoET
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2007Chen_Signature]]
+
| [[2021Budell_TimeResolved]]
| Automatic particle picking program: Signature
+
| Time resolved CryoEM with Spotiton
|-  
+
|-
  
 +
| Paper
 +
| [[2021Casasanta_Microchip]]
 +
| Microchip-based structure determination of low-molecular weight proteins using cryo-electron microscopy
 +
|-
  
 
| Paper
 
| Paper
| [[2007Woolford_SwarmPS]]
+
| [[2021Frechard_Preparation]]
| Automatic particle picking with several criteria, implemented in EMAN Boxer
+
| Optimization of Sample Preparation
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2009Sorzano_MachineLearning]]
+
| [[2021Engstrom_Nitrogen]]
| Automatic particle picking based on machine learning of rotational invariants
+
| Samples vitrified in boiling nitrogen
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2011Arbelaez_Comparison]]
+
| [[2021Jagota_GoldNanoparticles]]
| Evaluation of the performance of software for automated particle-boxing
+
| Gold nanoparticles to assess flexibility
 
|-
 
|-
  
 
| Paper
 
| Paper
| [[2013Abrishami_MachineLearning]]
+
| [[2021Jiang_MoAu]]
| A pattern matching approach to the automatic selection of particles from low-contrast electron micrographs
+
| Holey Gold Films on Molybdenum Grids
 
|-
 
|-
  
 
| Paper
 
| Paper
| [[2013Hauer_2013]]
+
| [[2021Jonaid_Liquid]]
| Automatic tilt pair detection in Random Conical Tilt
+
| Liquid phase EM
 
|-
 
|-
  
 
| Paper
 
| Paper
| [[2013Hoang_ParallelGPUPicking]]
+
| [[2021Ki_Conformational]]
| Parallel GPU-accelerated particle picking
+
| Conformational Distribution of a Small Protein with Nanoparticle-Aided CryoEM
 
|-
 
|-
  
 
| Paper
 
| Paper
| [[2013Shatsky_ParticlePicking]]
+
| [[2021Li_detergents]]
| Automated particle correspondence and accurate tilt-axis detection in tilted-image pairs
+
| The effect of detergents on preferential orientations
|-
+
|-
  
 
| Paper
 
| Paper
| [[2013Vargas_ParticleQuality]]
+
| [[2021Voss_Melting]]
| Automatic determination of particle quality
+
| Rapid melting and revitrification as an approach to microsecond time-resolved cryoEM
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2014Langlois_ParticlePicking]]
+
| [[2021Zhang_Pegylation]]
| Automatic particle picking
+
| Improving particle quality in cryo-EM by PEGylation
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2015Scheres_SemiAutoPicking]]
+
| [[2022Chen_Detergents]]
| Semi-automated selection of cryo-EM particles
+
| Role of detergents in the air-water interface
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2016Vilas_AutomaticTilt]]
+
| [[2022Levitz_Chameleon]]
| Automatic identification of image pairs in untilted-tilted micrograph pairs
+
| Effects of dispense-to-plunge speed on particle concentration, complex formation, and final resolution
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2016Wang_DeepPicker]]
+
| [[2022Naydenova_Grid]]
| A deep learning approach for fully automated particle picking
+
| Integrated wafer-scale manufacturing of electron cryomicroscopy specimen supports
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2017Zhu_DeepEM]]
+
| [[2022Russo_Review]]
| Deep learning approach to picking
+
| Review of sample preparation issues
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2018Huber_Helices]]
+
| [[2022Scher_FIB]]
| Automated tracing of helices
+
| Sample preparation for FIB-SEM and Correlative microscopy
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2018Heimowitz_ApplePicker]]
+
| [[2023Basanta_Graphene]]
| Automated particle picking
+
| Fabrication of Monolayer Graphene-Coated Grids
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2018Sanchez_DeepConsensus]]
+
| [[2023Han_Sample]]
| Deep learning consensus of multiple automatic pickers
+
| Challenges in making ideal cryo-EM samples
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2019Wagner_Cryolo]]
+
| [[2023Liu_AirWater]]
| Deep learning for particle picking
+
| Review on sample preparation techniques to deal with the air-water interface
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2019Wang_Biobjective]]
+
| [[2023Neselu_IceThickness]]
| Biobjective function for robust signal detection
+
| Effect of ice thickness on resolution
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2019Zhang_Pixer]]
+
| [[2023Torino_TimeResolved]]
| Deep learning for particle picking
+
| Device for the preparation of time-resolved CryoEM experiments
|-  
+
|-
  
|}
+
| Paper
 +
| [[2023Venien_Membrane]]
 +
| Review on the preparation of membrane proteins
 +
|-
  
=== 2D Preprocessing ===
+
| Paper
 +
| [[2023Zheng_Ultraflat]]
 +
| Uniform thin ice on ultraflat graphene grids
 +
|-
 +
 
 +
|}
 +
 
 +
=== Automated data collection ===
  
 
{|
 
{|
  
 
| Paper
 
| Paper
| [[2003Rosenthal_DPR]]
+
| [[1992Dierksen_Automatic]]
| Contrast enhancement through DPR
+
| Automated data collection
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2004Sorzano_Normalization]]
+
| [[1992Koster_Automatic]]
| Normalization procedures and their statistical properties.
+
| Automated data collection
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2006Sorzano_Denoising]]
+
| [[1996Fung_Automatic]]
| Strong denoising in wavelet space
+
| Automated data collection for tomography
 
|-  
 
|-  
  
| Conference
+
| Paper
| [[2009Sorzano_Downsampling]]
+
| [[2001Zhang_Automatic]]
| Differences between the different downsampling schemes
+
| Automated data collection: AutoEM
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2012Brilot_Movies]]
+
| [[2003Ziese_Automatic]]
| Alignment of beam induced motion in direct detectors
+
| Automated autofocusing
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2012Campbell_Movies]]
+
| [[2004Potter_Automatic]]
| Alignment of beam induced motion in direct detectors
+
| Automated sample loading
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2012Zhao_Denoising]]
+
| [[2004Zheng_Automatic]]
| Denoising using an invariant Fourier-Bessel eigenspace
+
| Automated data collection
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Norousi_Screening]]
+
| [[2005Lei_Automatic]]
| Screening particles to identify outliers
+
| Automated data collection: AutoEM
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Bai_ElectronCounting]]
+
| [[2005Suloway_Automatic]]
| Electron counting and beam induced motion correction
+
| Automated data collection: Leginon
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Li_ElectronCounting]]
+
| [[2007Yoshioka_RCT]]
| Electron counting and beam induced motion correction
+
| Automated Random Conical Tilt
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Shigematsu_Movies]]
+
| [[2011Korinek_TOM2]]
| Drift correction for movies considering dark field
+
| Automated acquisition with TOM2
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Vargas_ParticleQuality]]
+
| [[2015Li_UCSFImage]]
| Automatic determination of particle quality
+
| Automated acquisition with UCSFImage
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2014Scheres_Movies]]
+
| [[2016Gil_Fuzzy]]
| Beam induced motion correction
+
| Real time decisions during acquisition with neuro-fuzzy method
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Abrishami_Movies]]
+
| [[2016Liu_TiltControl]]
| Alignment of direct detection device micrographs
+
| Accurate control of the tilt angle for electron tomography
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Grant_Anisotropic]]
+
| [[2016Vargas_FoilHole]]
| Automatic estimation and correction of anisotropic magnification
+
| Determination of image quality at low magnification
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Grant_OptimalExposure]]
+
| [[2017Alewijnse_Best]]
| Filter movies according to the radiation damage
+
| Best practices for managing large CryoEM facilities
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Rubinstein_Alignment]]
+
| [[2017Biyani_Focus]]
| Frame alignment at the level of particle
+
| Automatic processing of micrographs
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Spear_DoseCompensation]]
+
| [[2018Gomez_Facilities]]
| Effect of dose compensation on resolution
+
| Use of Scipion at facilities
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Zhao_AnisotropicMagnification]]
+
| [[2018Sorzano_Gain]]
| Correction of anisotropic magnification
+
| Estimation of the DDD camera gain or residual gain
 
|-  
 
|-  
  
| Conference
+
| Paper
| [[2016Bajic_Denoising]]
+
| [[2019Chreifi_TiltSeries]]
| Denoising and deconvolution of micrographs
+
| Rapid tilt-series acquisition for electron cryotomography
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Jensen_RemovalVesicles]]
+
| [[2019Eng_ImageCompression]]
| Removal of vesicles in membrane proteins
+
| 3D Reconstruction from compressed images
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Bhamre_Denoising]]
+
| [[2019Eisenstein_FISE]]
| Denoising by 2D covariance estimation
+
| Improved applicability and robustness of fast cryo-electron tomography data acquisition
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Berndsen_EMPH]]
+
| [[2019Hamaguchi_CryoARM]]
| Automated hole masking algorithm
+
| CryoARM data acquisition
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017McLeod_Zorro]]
+
| [[2019Maluenda_Scipion]]
| Movie alignment by Zorro
+
| Automated workflow processing for facilities
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Zheng_MotionCorr2]]
+
| [[2019Schorb_ET]]
| Movie alignment by MotionCorr2
+
| Automated acquisition in Electron Tomography
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Ouyang_Denoising]]
+
| [[2019Tegunov_Warp]]
| Denoising based on geodesic distance
+
| Automatic micrograph processing with Warp
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Wu_ContrastEnhancement]]
+
| [[2019Thompson_Protocol]]
| Contrast enhancement
+
| Protocol for EM acquisition
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2019Zivanov_BayesianBIM]]
+
| [[2020Baxa_Facility]]
| Bayesian correction of beam induced movement
+
| Operational workflow in a facility
 
|-  
 
|-  
  
|}
+
| Paper
 +
| [[2020Guo_EER]]
 +
| Electron event representation for acquisition
 +
|-
  
=== 2D Alignment ===
+
| Paper
 +
| [[2020Li_Workflow]]
 +
| Workflow for automatic reconstruction
 +
|-
  
{|
+
| Paper
 +
| [[2020Sader_Facility]]
 +
| Microscope installation and operation in a facility
 +
|-
  
 
| Paper
 
| Paper
| [[1981Frank_Averaging]]
+
| [[2020Schenk_CryoFlare]]
| 2D averaging and phase residual
+
| CryoFlare, automatic data acquisition
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1982Saxton_Averaging]]
+
| [[2020Stabrin_Transphire]]
| 2D averaging using correlation
+
| TranSPHIRE: Automated and feedback-optimized on-the-fly processing for cryo-EM
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1998Sigworth_ML2D]]
+
| [[2020Yokoyama_Good]]
| Maximum likelihood alignment in 2D
+
| Deep learning for determining good regions in a grid
 
|-  
 
|-  
 +
  
 
| Paper
 
| Paper
| [[2003Cong_FRM2D]]
+
| [[2020Weis_Acquisition]]
| Fast Rotational Matching in 2D
+
| Suggestions for high-quality and high-throughput acquisition
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2005Cong_FRM2D]]
+
| [[2021Feathers_Superresolution]]
| Fast Rotational Matching in 2D introduced in a 3D Alignment algorithm
+
| Effects of superresolution and magnification on final resolution
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2005Scheres_ML2D]]
+
| [[2021Bouvette_Bisect]]
| Multireference alignment and classification in 2D
+
| Beam image-shift accelerated data acquisition for near-atomic resolution single-particle cryo-electron tomography
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2010Sorzano_CL2D]]
+
| [[2021Chreifi_FISE]]
| Multireference alignment and classification in 2D
+
| Rapid tilt-series method for cryo-electron tomography: Characterizing stage behavior during FISE acquisition
 
|-  
 
|-  
  
| Conference
+
| Paper
| [[2017Anoshina_Correlation]]
+
| [[2021Efremov_ComaCorrected]]
| New correlation measure for aligning images
+
| Coma-corrected rapid single-particle cryo-EM data collection on the CRYO ARM 300
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2019Radermacher_Correlation]]
+
| [[2021Herzik_Setup]]
| On the properties of cross correlation for the alignment of images
+
| Setup for parallel illumination
 
|-  
 
|-  
  
|}
+
| Paper
 +
| [[2021Kayama_Multipurpose]]
 +
| Below 3 Å structure of apoferritin using a multipurpose TEM with a side entry cryoholder
 +
|-
  
=== 2D Classification and clustering ===
+
| Paper
 
+
| [[2021Lane_NegativeBias]]
{|
+
| Negative potential bias for faster imaging
 +
|-
  
 
| Paper
 
| Paper
| [[1981VanHeel_MSA]]
+
| [[2021Rheinberger_IceThickness]]
| Multivariate Statistical Analysis
+
| Scripts to measure ice thickness
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1984VanHeel_MSA]]
+
| [[2021Yang_CRIM]]
| Multivariate Statistical Analysis
+
| Computer readable image markers (CRIM) for correlative microscopy
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2005Scheres_ML2D]]
+
| [[2021Weis_Strategies]]
| Multireference alignment and classification in 2D
+
| Strategies for Optimization of Cryogenic Electron Tomography Data Acquisition
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2010Sorzano_CL2D]]
+
| [[2021Wypych_gP2S]]
| Multireference alignment and classification in 2D
+
| LIMS of microscope sessions
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2011Singer_DiffusionMaps]]
+
| [[2021Yang_CLEM]]
| Classification in 2D based on graph analysis of the projections
+
| Automated correlative microscopy
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2012Yang_ISAC]]
+
| [[2021Yonekura_Hole]]
| Iterative Stable Alignment and clustering
+
| Automated hole detection using YOLO
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2014Sorzano_Outlier]]
+
| [[2022Bepler_Smart]]
| Outlier detection in 2D classifications.
+
| Smart data collection
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2014Zhao_Aspire]]
+
| [[2022Bouvette_SmartScope]]
| Fast classification based on rotational invariants and vector diffusion maps
+
| SmartScope
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Huang_Robust]]
+
| [[2022Flutty_bits]]
| Robust w-estimators of 2D classes
+
| Bit-precision for SPA and ET
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Kimanius_Accelerated]]
+
| [[2022Hagen_Screening]]
| GPU Accelerated image classification and high-resolution refinement
+
| Screening of ice thickness using energy filter-based plasmon imaging
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Reboul_Stochastic]]
+
| [[2022Hohle_Ice]]
| Stochastic Hill Climbing for calculating 2D classes
+
| Screening of ice thickness using interferometry
 
|-  
 
|-  
  
| Conference
+
| Paper
| [[2017Bhamre_Mahalanobis]]
+
| [[2022Peck_200]]
| 2D classification using Mahalanobis distance
+
| High-speed high-resolution data collection on a 200 keV cryo-TEM
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Wu_GTM]]
+
| [[2022Peck_Montage]]
| 2D classification using Generative Topographic Mapping
+
| Montage electron tomography
 
|-  
 
|-  
  
| Conference
+
| Paper
| [[2018Boumal_SinglePass]]
+
| [[2022Zhu_ElectronCounting]]
| Single pass classification
+
| New algorithm for electron counting at the microscope
 
|-  
 
|-  
  
| Conference
+
| Paper
| [[2018Shuo_Network]]
+
| [[2023Cheng_Leginon]]
| 2D Clustering by network metrics
+
| Smart data collection with Leginon
 +
|-
 +
 
 +
| Paper
 +
| [[2023Kim_Ptolemy]]
 +
| Smart data collection with Ptolemy
 +
|-
 +
 
 +
| Paper
 +
| [[2023Last_Ice]]
 +
| Measuring the ice thickness with an optical device and a neural network
 
|-  
 
|-  
  
 
|}
 
|}
  
=== 3D Alignment ===
+
== Single particles ==
 +
 
 +
=== Automatic particle picking ===
  
 
{|
 
{|
  
 
| Paper
 
| Paper
| [[1980Kam_AutoCorrelation]]
+
| [[1982VanHeel_Detection]]
| Reconstruction without angular assignment from autocorrelation function (reference free)
+
| Detection of particles in micrographs
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1986Goncharov_CommonLines]]
+
| [[2001Nicholson_Review]]
| Angular assignment using common lines (reference free)
+
| Review on automatic particle picking
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1987VanHeel_CommonLines]]
+
| [[2001Zhu_Filaments]]
| Angular assignment using common lines (reference free)
+
| Automatic identification of filaments in micrographs
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1988Provencher_Simultaneous]]
+
| [[2004Sigworth_Detection]]
| Simultaneaous alignment and reconstruction
+
| Classical detection theory and the cryo-EM particle selection problem
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1988Radermacher_RCT]]
+
| [[2004Volkmann_ParticlePicking]]
| Random Conical Tilt and Single axis tilt
+
| An approach to automated particle picking from electron micrographs based on reduced representation templates
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1988Vogel_Simultaneous]]
+
| [[2004Wong_ParticlePicking]]
| Simultaneaous alignment and reconstruction
+
| Model-based particle picking for cryo-electron microscopy
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1990Gelfand_Moments]]
+
| [[2004Zhu_Review]]
| Angular assignment using moments (reference free)
+
| Review on automatic particle picking
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1990Goncharov_Moments]]
+
| [[2007Chen_Signature]]
| Angular assignment using moments (reference free)
+
| Automatic particle picking program: Signature
 
|-  
 
|-  
  
| Paper
 
| [[1990Harauz_Quaternions]]
 
| Use of quaternions to represent rotations
 
|-
 
  
 
| Paper
 
| Paper
| [[1994Penczek_Real]]
+
| [[2007Woolford_SwarmPS]]
| Angular assignment using projection matching in real space
+
| Automatic particle picking with several criteria, implemented in EMAN Boxer
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1994Radermacher_Radon]]
+
| [[2009Sorzano_MachineLearning]]
| Angular assignment in Radon space
+
| Automatic particle picking based on machine learning of rotational invariants
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1996Penczek_CommonLines]]
+
| [[2011Arbelaez_Comparison]]
| Angular assignment using common lines (reference free)
+
| Evaluation of the performance of software for automated particle-boxing
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2003Rosenthal_DPR]]
+
| [[2013Abrishami_MachineLearning]]
| Angular assignment using DPR
+
| A pattern matching approach to the automatic selection of particles from low-contrast electron micrographs
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2004Sorzano_Wavelet]]
+
| [[2013Hauer_2013]]
| Angular assignment in the wavelet space.
+
| Automatic tilt pair detection in Random Conical Tilt
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2005Jonic_Splines]]
+
| [[2013Hoang_ParallelGPUPicking]]
| Angular assignment in Fourier space using spline interpolation.
+
| Parallel GPU-accelerated particle picking
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2005Yang_Simultaneous]]
+
| [[2013Shatsky_ParticlePicking]]
| Simultaneaous alignment and reconstruction
+
| Automated particle correspondence and accurate tilt-axis detection in tilted-image pairs
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2006Ogura_SimulatedAnnealing]]
+
| [[2013Vargas_ParticleQuality]]
| Angular asignment by simulated annealing
+
| Automatic determination of particle quality
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007Grigorieff_Continuous]]
+
| [[2014Langlois_ParticlePicking]]
| Continuous angular assignment in Fourier space
+
| Automatic particle picking
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2010Jaitly_Bayesian]]
+
| [[2015Scheres_SemiAutoPicking]]
| Angular assignment by a Bayesian method and annealing
+
| Semi-automated selection of cryo-EM particles
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2010Sanz_Random]]
+
| [[2016Vilas_AutomaticTilt]]
| Random model method
+
| Automatic identification of image pairs in untilted-tilted micrograph pairs
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2010Singer_Voting]]
+
| [[2016Wang_DeepPicker]]
| Detecting consistent common lines by voting (reference free)
+
| A deep learning approach for fully automated particle picking
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2011Singer_SDP]]
+
| [[2017Rickgauer_Detection]]
| Angular assignment by semidefinite programming and eigenvectors (reference free)
+
| Picking by correlation
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2012Giannakis_Scattering]]
+
| [[2017Zhu_DeepEM]]
| Construction of an initial volume, reference free, by graph analysis of the projections
+
| Deep learning approach to picking
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2012Shkolnisky_Sync]]
+
| [[2018Huber_Helices]]
| Angular assignment by synchronization of rotations (reference free)
+
| Automated tracing of helices
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2013Elmlund H_PRIME]]
+
| [[2018Heimowitz_ApplePicker]]
| PRIME: Probabilistic Initial 3D Model Generation for Single-Particle Cryo-Electron Microscopy
+
| Automated particle picking
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Wang_LUD]]
+
| [[2018Sanchez_DeepConsensus]]
| Angular assignment by least unsquared deviations (reference free)
+
| Deep learning consensus of multiple automatic pickers
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2014Vargas_RANSAC]]
+
| [[2019Alazzawi_Clustering]]
| Initial model using RANSAC (reference free)
+
| Use of clustering algorithms to find particles in micrographs
|-
+
|-
 +
 
 +
| Paper
 +
| [[2019Bepler_Topaz]]
 +
| Deep learning for particle picking
 +
|-
 +
 
 +
| Paper
 +
| [[2019Carrasco_IP]]
 +
| Use of standard image processing for particle picking
 +
|-
 +
 
 +
| Conference
 +
| [[2019Li_Deep]]
 +
| Deep learning for particle picking without box size
 +
|-  
  
 
| Paper
 
| Paper
| [[2015Joubert_Pseudoatoms]]
+
| [[2019Wagner_Cryolo]]
| Initial model based on pseudo-atoms
+
| Deep learning for particle picking
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Singer_Kam]]
+
| [[2019Wang_Biobjective]]
| Reconstruction without angular assignment from autocorrelation function (reference free)
+
| Biobjective function for robust signal detection
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Sorzano_Significant]]
+
| [[2019Zhang_Pixer]]
| Statistical approach to the initial volume estimation (reconstruct significant)
+
| Deep learning for particle picking
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Cossio_BayesianGPU]]
+
| [[2020Sanchez_Cleaner]]
| GPU implementation of the Bayesian 3D reconstruction approach
+
| Deep learning for removing particles from the carbon edges, aggregations, contaminations, ...
 
|-  
 
|-  
  
 
| Conference
 
| Conference
| [[2016Michels_Heterogeneous]]
+
| [[2021Li_PickerOptimizers]]
| Initial volume in the presence of heterogeneity
+
| Removal of badly picked particles with Deep Learning
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Pragier_Graph]]
+
| [[2021Ohashi_GRIPS]]
| Graph partitioning approach to angular reconstitution
+
| Two-pass picking with GRIPS
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Greenberg_CommonLines]]
+
| [[2022Eldar_ASOCEM]]
| Common lines for reference free ab-initio reconstruction
+
| Automatic segmentation of contaminations
 +
|-  
 +
 
 +
| Conference
 +
| [[2022Huang_DenoisingAndPicking]]
 +
| Simultaneous denoising and picking with deep learning
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Sorzano_Highres]]
+
| [[2022Olek_Icebreaker]]
| New algorithm for 3D Reconstruction and alignment with emphasis on significance
+
| Ice thickness detection and its use for particle picking
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Sorzano_Swarm]]
+
| [[2022Zhang_EPicker]]
| Consensus of several initial volumes by swarm optimization
+
| Particle picking based on continual learning
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2019Zehni_Joint]]
+
| [[2023Dhakal_CryoPPP]]
| Continuous angular refinement and reconstruction
+
| A public database for particle picking
 
|-  
 
|-  
  
 
|}
 
|}
  
=== 3D Reconstruction ===
+
=== 2D Preprocessing ===
 +
 
 
{|
 
{|
  
 
| Paper
 
| Paper
| [[1972Gilbert_SIRT]]
+
| [[1978Carrascosa_matching]]
| Simultaneous Iterative Reconstruction Technique (SIRT)
+
| Gray values matching by linear transformations
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1973Herman_ART]]
+
| [[2003Rosenthal_DPR]]
| Algebraic Reconstruction Technique (ART)
+
| Contrast enhancement through DPR
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1980Kam_SphericalHarmonics]]
+
| [[2004Sorzano_Normalization]]
| 3D Reconstruction using spherical harmonics
+
| Normalization procedures and their statistical properties.
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1984Andersen_SART]]
+
| [[2006Sorzano_Denoising]]
| Simultaneous Algebraic Reconstruction Technique (SART)
+
| Strong denoising in wavelet space
 
|-  
 
|-  
  
| Paper
+
| Conference
| [[1986Harauz_FBP]]
+
| [[2009Sorzano_Downsampling]]
| Exact filters for Filtered Back Projection
+
| Differences between the different downsampling schemes
 
|-  
 
|-  
  
| Chapter
+
| Paper
| [[1992Radermacher_WBP]]
+
| [[2012Brilot_Movies]]
| Exact filters for Weighted Back Projection
+
| Alignment of beam induced motion in direct detectors
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1997Zhu_RecCTF]]
+
| [[2012Campbell_Movies]]
| 3D Reconstruction (SIRT like) and simultaneous CTF correction
+
| Alignment of beam induced motion in direct detectors
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1998Boisset_Uneven]]
+
| [[2012Zhao_Denoising]]
| Artifacts in SIRT and WBP under uneven angular distributions
+
| Denoising using an invariant Fourier-Bessel eigenspace
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1998Marabini_ART]]
+
| [[2013Norousi_Screening]]
| Algebraic Reconstruction Technique with blobs (Xmipp)
+
| Screening particles to identify outliers
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2001Sorzano_Uneven]]
+
| [[2013Bai_ElectronCounting]]
| Free parameter selection under uneven angular distributions
+
| Electron counting and beam induced motion correction
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2005Sorzano_Parameters]]
+
| [[2013Li_ElectronCounting]]
| Free parameter selection for optimizing multiple tasks
+
| Electron counting and beam induced motion correction
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2008Sorzano_Constraints]]
+
| [[2013Shigematsu_Movies]]
| Mass, surface, positivity and symmetry constraints for real-space algorithms
+
| Drift correction for movies considering dark field
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2009Bilbao_ParallelART]]
+
| [[2013Vargas_ParticleQuality]]
| Efficient parallelization of ART
+
| Automatic determination of particle quality
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2011Li_GradientFlow]]
+
| [[2014Scheres_Movies]]
| Regularized 3D Reconstruction by Gradient Flow
+
| Beam induced motion correction
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2011Vonesch_Wavelets]]
+
| [[2015Abrishami_Movies]]
| Fast wavelet-based 3D reconstruction
+
| Alignment of direct detection device micrographs
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2012Gopinath_ShapeRegularization]]
+
| [[2015Grant_Anisotropic]]
| Regularized 3D Reconstruction by Shape information
+
| Automatic estimation and correction of anisotropic magnification
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2012Kucukelbir_adaptiveBasis]]
+
| [[2015Grant_OptimalExposure]]
| 3D reconstruction in an adaptive basis promoting sparsity
+
| Filter movies according to the radiation damage
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2012Sindelar_NoiseReduction]]
+
| [[2015Rubinstein_Alignment]]
| Optimal noise reduction in 3D reconstructions
+
| Frame alignment at the level of particle
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Elmlund H_PRIME]]
+
| [[2015Spear_DoseCompensation]]
| PRIME: Probabilistic Initial 3D Model Generation for Single-Particle Cryo-Electron Microscopy
+
| Effect of dose compensation on resolution
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Lyumkis_Optimod]]
+
| [[2015Zhao_AnisotropicMagnification]]
| Construction of initial volumes with Optimod
+
| Correction of anisotropic magnification
 
|-  
 
|-  
  
| Paper
+
| Conference
| [[2013Wang FIRM]]
+
| [[2016Bajic_Denoising]]
| Fast 3D reconstruction in Fourier domain
+
| Denoising and deconvolution of micrographs
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2014Kunz_SART_OS]]
+
| [[2016Jensen_RemovalVesicles]]
| Simultaneous ART with OS
+
| Removal of vesicles in membrane proteins
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Abrishami_Fourier]]
+
| [[2016Bhamre_Denoising]]
| 3D Reconstruction in Fourier space
+
| Denoising by 2D covariance estimation
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Dvornek_SubspaceEM]]
+
| [[2017Berndsen_EMPH]]
| Fast Maximum a posteriori
+
| Automated hole masking algorithm
 
|-  
 
|-  
  
| Conference
+
| Paper
| [[2018Michels_RBF]]
+
| [[2017McLeod_Zorro]]
| Ab-initio reconstruction with radial basis functions
+
| Movie alignment by Zorro
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Moriya_Bayesian]]
+
| [[2017Zheng_MotionCorr2]]
| Bayesian approach to suppress limited angular artifacts
+
| Movie alignment by MotionCorr2
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Xu_GeometricFlow]]
+
| [[2018Ouyang_Denoising]]
| Multi-scale geometric flow
+
| Denoising based on geodesic distance
|-
 
 
 
| Arxiv
 
| [[2016Ye_Cohomology]]
 
| Cohomology properties of 3D reconstruction
 
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Punjani_CryoSPARC]]
+
| [[2018Wu_ContrastEnhancement]]
| CryoSPARC
+
| Contrast enhancement
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Punjani_CryoSPARCTheory]]
+
| [[2019Zivanov_BayesianBIM]]
| Theory related to CryoSPARC
+
| Bayesian correction of beam induced movement
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Sorzano_SurveyIterative]]
+
| [[2020Bepler_TopazDenoise]]
| Survey of iterative reconstruction methods for EM
+
| Preprocessing of micrographs for better picking
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Bartesaghi_Refinement]]
+
| [[2020Chung_2SDR]]
| Refinement of CTF, frame weight and alignment for high resolution reconstruction
+
| PCA to denoise particles
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Hu_ParticleFilter]]
+
| [[2020Chung_Prepro]]
| A particle filter framework for 3D reconstruction
+
| Preprocessing of particles for better alignment
 
|-  
 
|-  
  
 
| Conference
 
| Conference
| [[2018Levin_Kam]]
+
| [[2020Huang_SuperResolution]]
| Ab initio reconstruction by autocorrelation analysis
+
| Deep learning superresolution combination of frames
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Reboul_Simple]]
+
| [[2020Palovcak_noise2noise]]
| Ab initio reconstruction with Simple
+
| Noise2noise denoising of micrographs
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Sorzano_Highres]]
+
| [[2020Strelak_FlexAlign]]
| New algorithm for 3D Reconstruction and alignment with emphasis on significance
+
| Continuous deformation model for aligning movie frames
 +
|-
 +
 
 +
| Conference
 +
| [[2021Fan_Denoising]]
 +
| Particle denoising using vector diffusion maps
 +
|-
 +
 
 +
| Paper
 +
| [[2022Heymann_ProgressiveSSNR]]
 +
| Progressive SSNR to assess quality and radiation damage
 +
|-
 +
 
 +
| Paper
 +
| [[2022Shi_Denoising]]
 +
| Contrast estimation and denoising in SPA
 +
|-
 +
 
 +
| Paper
 +
| [[2023Huang_ZSSR]]
 +
| Multiple image super-resolution, upsampling with deep learning
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Sorzano_Swarm]]
+
| [[2023Marshall_PCA]]
| Consensus of several initial volumes by swarm optimization
+
| Fast PCA on single particle images
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Zhu_Ewald]]
+
| [[2023Sharon_Enhancement]]
| 3D Reconstruction with Ewald sphere correction
+
| Signal enhancement of SPA particles
 
|-  
 
|-  
  
| Master
+
| Paper
| [[2019Havelkova_Regularization]]
+
| [[2023Strelak_MovieAlignment]]
| Regularization methods in 3D reconstruction
+
| Comparison of movie alignment programs
 
|-  
 
|-  
  
 
|}
 
|}
  
=== 3D Heterogeneity ===
+
=== 2D Alignment ===
  
 
{|
 
{|
  
 
| Paper
 
| Paper
| [[2004White_Size]]
+
| [[1981Frank_Averaging]]
| Heterogeneity classification of differently sized images
+
| 2D averaging and phase residual
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2006Penczek_Bootstrap]]
+
| [[1982Saxton_Averaging]]
| 3D heterogeneity through bootstrap
+
| 2D averaging using correlation
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007Leschziner_Review]]
+
| [[1998Sigworth_ML2D]]
| Review of 3D heterogeneity handling algorithms
+
| Maximum likelihood alignment in 2D
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007Scheres_ML3D]]
+
| [[2003Cong_FRM2D]]
| Maximum Likelihood alignment and classification in 3D
+
| Fast Rotational Matching in 2D
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2008Herman_Graph]]
+
| [[2005Cong_FRM2D]]
| Classification by graph partitioning
+
| Fast Rotational Matching in 2D introduced in a 3D Alignment algorithm
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2009Spahn_Bootstrap]]
+
| [[2005Scheres_ML2D]]
| 3D heterogeneity through bootstrap
+
| Multireference alignment and classification in 2D
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2010Elmlund_AbInitio]]
+
| [[2016Aguerrebere_Limits]]
| Solving the initial volume problem with multiple conformations
+
| Fundamental limits of 2D translational alignment
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2010Shatsky_MultiVariate]]
+
| [[2010Sorzano_CL2D]]
| Multivariate Statistical Analysis
+
| Multireference alignment and classification in 2D
 
|-  
 
|-  
  
| Paper
+
| Conference
| [[2012Scheres_Bayesian]]
+
| [[2017Anoshina_Correlation]]
| A Bayesian view on cryo-EM structure determination
+
| New correlation measure for aligning images
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2012Zheng_Covariance]]
+
| [[2019Radermacher_Correlation]]
| Estimation of the volume covariance
+
| On the properties of cross correlation for the alignment of images
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Wang_MLVariance]]
+
| [[2020Lederman_representation]]
| Maximum Likelihood estimate of the map variance
+
| A representation theory perspective of alignment and classification
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Lyumkis D_FREALIGN]]
+
| [[2020Marshall_Invariants]]
| Likelihood-based classification of cryo-EM images using FREALIGN.
+
| Recovery of an image from its invariants
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2014Jin_NMA]]
+
| [[2021Chen_Fast]]
| Continuous heterogeneity through Normal Mode Analysis
+
| Fast alignment through Power Spectrum
 
|-  
 
|-  
  
| Paper
+
| Conference
| [[2014Dashti_Brownian]]
+
| [[2021Chung_CryoRALIB]]
| Continuous heterogeneity through Brownian trajectories
+
| Image alignment acceleration
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2014Chen_Migration]]
+
| [[2021Heimowitz_Centering]]
| Particle migration analysis in 3D classification
+
| Centering noisy images
 
|-  
 
|-  
 +
 +
|}
 +
 +
=== 2D Classification and clustering ===
 +
 +
{|
  
 
| Paper
 
| Paper
| [[2015Anden_Covariance]]
+
| [[1981VanHeel_MSA]]
| 3D Covariance matrix estimation for heterogeneity
+
| Multivariate Statistical Analysis
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Bai_Focused]]
+
| [[1984VanHeel_MSA]]
| Focused classification
+
| Multivariate Statistical Analysis
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Katsevich_Covariance]]
+
| [[2005Scheres_ML2D]]
| 3D Covariance matrix estimation for heterogeneity
+
| Multireference alignment and classification in 2D
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Klaholz_MRA]]
+
| [[2010Sorzano_CL2D]]
| Multivariate Statistical Analysis of Jackknife and Bootstrapping on random subsets
+
| Multireference alignment and classification in 2D
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Liao_Covariance]]
+
| [[2011Singer_DiffusionMaps]]
| Estimation of the 3D covariance from 2D projections
+
| Classification in 2D based on graph analysis of the projections
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Tagare_Direct]]
+
| [[2012Yang_ISAC]]
| Direct reconstruction of PCA components
+
| Iterative Stable Alignment and clustering
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Gong_Mechanical]]
+
| [[2014Sorzano_Outlier]]
| Mechanical model for macromolecules
+
| Outlier detection in 2D classifications.
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Rawson_Movement]]
+
| [[2014Zhao_Aspire]]
| Movement and flexibility
+
| Fast classification based on rotational invariants and vector diffusion maps
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Shan_Multibody]]
+
| [[2015Huang_Robust]]
| Multibody refinement
+
| Robust w-estimators of 2D classes
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Sorzano_StructMap]]
+
| [[2016Kimanius_Accelerated]]
| Sorting a discrete set of conformational states
+
| GPU Accelerated image classification and high-resolution refinement
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Sorzano_Strain]]
+
| [[2016Reboul_Stochastic]]
| Calculate local stretches, strains and rotations from two conformational states
+
| Stochastic Hill Climbing for calculating 2D classes
 
|-  
 
|-  
  
| Paper
+
| Conference
| [[2017Punjani_CryoSPARC]]
+
| [[2017Bhamre_Mahalanobis]]
| CryoSPARC
+
| 2D classification using Mahalanobis distance
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Schillbach_Warpcraft]]
+
| [[2017Wu_GTM]]
| Warpcraft: 3D Reconstruction in the presence of continuous heterogeneity
+
| 2D classification using Generative Topographic Mapping
 
|-  
 
|-  
  
| Paper
+
| Conference
| [[2018Anden_Covariance]]
+
| [[2018Boumal_SinglePass]]
| Structural Variability from Noisy Tomographic Projections
+
| Single pass classification
 
|-  
 
|-  
  
| Paper
+
| Conference
| [[2018Haselbach_FreeEnergy]]
+
| [[2018Shuo_Network]]
| Analysis of the free energy landscape through PCA
+
| 2D Clustering by network metrics
 
|-  
 
|-  
  
| Paper
+
| Conference
| [[2018Nakane_MultiBody]]
+
| [[2020Miolane_VAEGAN]]
| Structural Variability through multi-body refinement
+
| 2D Analysis by deep learning
 
|-  
 
|-  
  
| Paper
+
| Conference
| [[2019Serna_Review]]
+
| [[2021Rao_Wasserstein]]
| Review of classification tools
+
| Wasserstein K-Means for Clustering Tomographic Projections
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Solernou_FFEA]]
+
| [[2022Wang_Spectral]]
| Fluctuating Finite Element Analysis, continuum approach to Molecular Dynamics
+
| 2D classification with spectral clustering
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2019Sorzano_Review]]
+
| [[2022Zhang_DRVAE]]
| Review of continuous heterogeneity biophysics
+
| 2D classification with deep learning and K-means++
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2019Zhang_Local]]
+
| [[2023Chen_Joint]]
| Local variability and covariance
+
| 2D classification with deep learning and joint unsupervised difference learning
 
|-  
 
|-  
  
 
|}
 
|}
  
=== Validation ===
+
=== 3D Alignment ===
  
 
{|
 
{|
  
 
| Paper
 
| Paper
| [[2008Stagg_TestBed]]
+
| [[1980Kam_AutoCorrelation]]
| Effect of voltage, dosis, number of particles and Euler jumps on resolution
+
| Reconstruction without angular assignment from autocorrelation function (reference free)
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2011Henderson]]
+
| [[1986Goncharov_CommonLines]]
| Tilt Validation
+
| Angular assignment using common lines (reference free)
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2011Read]]
+
| [[1987VanHeel_CommonLines]]
| Validation of PDBs
+
| Angular assignment using common lines (reference free)
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2012Henderson]]
+
| [[1988Provencher_Simultaneous]]
| EM Map Validation
+
| Simultaneaous alignment and reconstruction
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Cossio_Bayesian]]
+
| [[1988Radermacher_RCT]]
| EM Map Validation in a probabilistic setting
+
| Random Conical Tilt and Single axis tilt
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Chen_NoiseSubstitution]]
+
| [[1988Vogel_Simultaneous]]
| Noise substitution at high resolution for measuring overfitting
+
| Simultaneaous alignment and reconstruction
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Ludtke_Validation]]
+
| [[1990Gelfand_Moments]]
| Structural validation, example of the Calcium release channel
+
| Angular assignment using moments (reference free)
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Murray_Validation]]
+
| [[1990Goncharov_Moments]]
| Validation of a 3DEM structure through a particular example
+
| Angular assignment using moments (reference free)
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2014Russo_StatisticalSignificance]]
+
| [[1990Harauz_Quaternions]]
| EM Map Validation through the statistical significance of the tilt-pair angular assignment
+
| Use of quaternions to represent rotations
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2014Stagg_Reslog]]
+
| [[1994Penczek_Real]]
| EM Map Validation through the resolution evolution with the number of particles
+
| Angular assignment using projection matching in real space
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2014Wasilewski_Tilt]]
+
| [[1994Radermacher_Radon]]
| Web implementation of the tilt pair validation
+
| Angular assignment in Radon space
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Heymann_Alignability]]
+
| [[1996Penczek_CommonLines]]
| EM Map Validation through the resolution of reconstructions from particles and noise
+
| Angular assignment using common lines (reference free)
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Oliveira_FreqLimited]]
+
| [[2003Rosenthal_DPR]]
| Comparison of gold standard and frequency limited optimization
+
| Angular assignment using DPR
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Rosenthal_Review]]
+
| [[2004Sorzano_Wavelet]]
| Review of validation methods
+
| Angular assignment in the wavelet space.
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Wriggers_Secondary]]
+
| [[2005Jonic_Splines]]
| Validation by secondary structure
+
| Angular assignment in Fourier space using spline interpolation.
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Degiacomi_IM]]
+
| [[2005Yang_Simultaneous]]
| Comparison of Ion Mobility data and EM volumes
+
| Simultaneaous alignment and reconstruction
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Kim_SAXS]]
+
| [[2006Ogura_SimulatedAnnealing]]
| Comparison of SAXS data and EM projections
+
| Angular asignment by simulated annealing
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Rosenthal_Review]]
+
| [[2007Grigorieff_Continuous]]
| Review of validation methods
+
| Continuous angular assignment in Fourier space
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Vargas_Alignability]]
+
| [[2010Jaitly_Bayesian]]
| Validation by studying the tendency of an angular assignment to cluster in the projection space
+
| Angular assignment by a Bayesian method and annealing
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2017Monroe_PDBRefinement]]
+
| [[2010Sanz_Random]]
| Validation by comparison to a refined PDB
+
| Random model method
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2018Afonine_Phenix]]
+
| [[2010Singer_Voting]]
| Tools in Phenix for the validation of EM maps
+
| Detecting consistent common lines by voting (reference free)
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2018Heymann_Bsoft]]
+
| [[2011Singer_SDP]]
| Map validation using Bsoft
+
| Angular assignment by semidefinite programming and eigenvectors (reference free)
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2018Heymann_Challenge]]
+
| [[2012Giannakis_Scattering]]
| A summary of the assessments of the 3D Map Challenge
+
| Construction of an initial volume, reference free, by graph analysis of the projections
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2018Jonic_Gaussian]]
+
| [[2012Shkolnisky_Sync]]
| Assessment of sets of volumes by pseudoatomic structures
+
| Angular assignment by synchronization of rotations (reference free)
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2018Naydenova_AngularDistribution]]
+
| [[2013Elmlund H_PRIME]]
| Evaluating the angular distribution of a 3D reconstruction
+
| PRIME: Probabilistic Initial 3D Model Generation for Single-Particle Cryo-Electron Microscopy
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Pages_Symmetry]]
+
| [[2013Wang_LUD]]
| Looking for a symmetry axis in a PDB
+
| Angular assignment by least unsquared deviations (reference free)
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2018Pintilie_SSE]]
+
| [[2014Vargas_RANSAC]]
| Evaluating the quality of SSE and side chains
+
| Initial model using RANSAC (reference free)
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2019Herzik_Multimodel]]
+
| [[2015Joubert_Pseudoatoms]]
| Local and global quality by multi-model fitting
+
| Initial model based on pseudo-atoms
 
|-  
 
|-  
 
|}
 
 
=== Resolution ===
 
 
{|
 
  
 
| Paper
 
| Paper
| [[1986Harauz_FBP]]
+
| [[2015Singer_Kam]]
| Fourier Shell Correlation
+
| Reconstruction without angular assignment from autocorrelation function (reference free)
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1987Unser_SSNR]]
+
| [[2015Sorzano_Significant]]
| 2D Spectral Signal to Noise Ratio
+
| Statistical approach to the initial volume estimation (reconstruct significant)
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2002Penczek_SSNR]]
+
| [[2016Cossio_BayesianGPU]]
| 3D Spectral Signal to Noise Ratio for Fourier based algorithms
+
| GPU implementation of the Bayesian 3D reconstruction approach
 
|-  
 
|-  
  
| Paper
+
| Conference
| [[2003Rosenthal_DPR]]
+
| [[2016Michels_Heterogeneous]]
| Review of the FSC and establishment of a new threshold
+
| Initial volume in the presence of heterogeneity
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2005Unser_SSNR]]
+
| [[2016Pragier_Graph]]
| 3D Spectral Signal to Noise Ratio for any kind of algorithms
+
| Graph partitioning approach to angular reconstitution
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2005VanHeel_FSC]]
+
| [[2017Greenberg_CommonLines]]
| Establishment of a new threshold for FSC
+
| Common lines for reference free ab-initio reconstruction
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007Sousa_AbInitio]]
+
| [[2018Sorzano_Highres]]
| Resolution measurement on neighbour Fourier voxels
+
| New algorithm for 3D Reconstruction and alignment with emphasis on significance
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2014Kucukelbir_Local]]
+
| [[2018Sorzano_Swarm]]
| Quantifying the local resolution of cryo-EM density maps
+
| Consensus of several initial volumes by swarm optimization
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Pintilie_Probabilistic]]
+
| [[2019Zehni_Joint]]
| Probabilistic models and resolution
+
| Continuous angular refinement and reconstruction
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Sorzano_FourierProperties]]
+
| [[2019Zehni_Joint]]
| Statistical properties of resolution measures defined in Fourier space
+
| Continuous angular refinement and reconstruction
 
|-  
 
|-  
  
| Conference
+
 
| [[2018Avramov_DeepLearning]]
+
| Paper
| Deep learning classification of volumes into low, medium and high resolution
+
| [[2020Sharon_NonUniformKam]]
 +
| Reconstruction and angular distribution estimation without angular assignment (reference free)
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Carugo_BFactors]]
+
| [[2020Xie_Network]]
| How large can B-factors be in protein crystals
+
| Angular assignment considering a network of assignments
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Kim_FourierError]]
+
| [[2021Jimenez_DeepAlign]]
| Comparison between a gold standard and a reconstruction
+
| Angular alignment using deep learning
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Vilas_MonoRes]]
+
| [[2021Kojima_Preferred]]
| Local resolution by monogenic signals
+
| Identification of preferred orientations
 +
|-
 +
 
 +
| Conference
 +
| [[2021Nashed_CryoPoseNet]]
 +
| CryoPoseNet: Angular alignment with deep learning
 +
|-
 +
 
 +
| Conference
 +
| [[2021Zhong_CryoDRGN2]]
 +
| CryoDRGN2: Angular alignment with deep learning
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Yang_Multiscale]]
+
| [[2022Lu_SphericalEmbeddings]]
| Resolution from a multiscale spectral analysis
+
| Angular assignment through common lines and spherical embeddings
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2019Avramov_DeepLearning]]
+
| [[2022Wang_Thunder]]
| Deep learning classification of volumes into low, medium and high resolution
+
| Angular assignment implementation in GPU
 
|-  
 
|-  
  
 
|}
 
|}
  
=== Sharpening of high resolution information ===
+
=== 3D Reconstruction ===
 
{|
 
{|
+
 
 
| Paper
 
| Paper
| [[2003Rosenthal_DPR]]
+
| [[1972Gilbert_SIRT]]
| Contrast restoration and map sharpening
+
| Simultaneous Iterative Reconstruction Technique (SIRT)
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2008Fernandez_Bfactor]]
+
| [[1973Herman_ART]]
| Bfactor determination and restoration
+
| Algebraic Reconstruction Technique (ART)
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Fiddy_SaxtonAlgorithm]]
+
| [[1980Kam_SphericalHarmonics]]
| Phase retrieval or extension
+
| 3D Reconstruction using spherical harmonics
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2014Kishchenko_SphericalDeconvolution]]
+
| [[1984Andersen_SART]]
| Spherical deconvolution
+
| Simultaneous Algebraic Reconstruction Technique (SART)
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Spiegel_VISDEM]]
+
| [[1986Harauz_FBP]]
| Visualization improvement by the use of pseudoatomic profiles
+
| Exact filters for Filtered Back Projection
 +
|-
 +
 
 +
| Chapter
 +
| [[1992Radermacher_WBP]]
 +
| Exact filters for Weighted Back Projection
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Jonic_Pseudoatoms]]
+
| [[1997Zhu_RecCTF]]
| Approximation with pseudoatoms
+
| 3D Reconstruction (SIRT like) and simultaneous CTF correction
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Jonic_Denoising]]
+
| [[1998Boisset_Uneven]]
| Denoising and high-frequency boosting by pseudoatom approximation
+
| Artifacts in SIRT and WBP under uneven angular distributions
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Jakobi_LocScale]]
+
| [[1998Marabini_ART]]
| Sharpening based on an atomic model
+
| Algebraic Reconstruction Technique with blobs (Xmipp)
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2019Ramlaul_Filtering]]
+
| [[2001Sorzano_Uneven]]
| Local agreement filtering (denoising)
+
| Free parameter selection under uneven angular distributions
 
|-  
 
|-  
 
|}
 
 
=== CTF estimation and restoration ===
 
 
{|
 
  
 
| Paper
 
| Paper
| [[1982Schiske_Correction]]
+
| [[2005Sorzano_Parameters]]
| CTF correction for tilted objects
+
| Free parameter selection for optimizing multiple tasks
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1988Toyoshima_Model]]
+
| [[2008Sorzano_Constraints]]
| CTF estimation
+
| Mass, surface, positivity and symmetry constraints for real-space algorithms
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1995Frank_Wiener]]
+
| [[2009Bilbao_ParallelART]]
| CTF correction using Wiener filter
+
| Efficient parallelization of ART
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1996Skoglund_MaxEnt]]
+
| [[2011Li_GradientFlow]]
| CTF correction with Maximum Entropy
+
| Regularized 3D Reconstruction by Gradient Flow
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1996Zhou_Model]]
+
| [[2011Vonesch_Wavelets]]
| CTF model and user interface for manual fitting
+
| Fast wavelet-based 3D reconstruction
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1997Fernandez_AR]]
+
| [[2012Gopinath_ShapeRegularization]]
| PSD estimation using periodogram averaging and AR models
+
| Regularized 3D Reconstruction by Shape information
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1997Penczek_Wiener]]
+
| [[2012Kucukelbir_adaptiveBasis]]
| CTF correction using Wiener filter
+
| 3D reconstruction in an adaptive basis promoting sparsity
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1997Stark_Deconvolution]]
+
| [[2012Sindelar_NoiseReduction]]
| CTF correction using deconvolution
+
| Optimal noise reduction in 3D reconstructions
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1997Zhu_RecCTF]]
+
| [[2013Elmlund H_PRIME]]
| CTF correction and reconstruction
+
| PRIME: Probabilistic Initial 3D Model Generation for Single-Particle Cryo-Electron Microscopy
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2000DeRosier_EwaldCorrection]]
+
| [[2013Lyumkis_Optimod]]
| CTF correction considering the Ewald sphere
+
| Construction of initial volumes with Optimod
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2000Jensen_TiltedCorrection]]
+
| [[2013Wang FIRM]]
| CTF correction considering tilt in backprojection
+
| Fast 3D reconstruction in Fourier domain
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2001Saad_CTFEstimate]]
+
| [[2014Kunz_SART_OS]]
| CTF estimation
+
| Simultaneous ART with OS
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2003Huang_CTFEstimate]]
+
| [[2015Abrishami_Fourier]]
| CTF estimation
+
| 3D Reconstruction in Fourier space
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2003Mindell_CTFTILT]]
+
| [[2015Dvornek_SubspaceEM]]
| CTF estimation for tilted micrographs
+
| Fast Maximum a posteriori
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2003Sander_MSA]]
+
| [[2015Moriya_Bayesian]]
| CTF estimation through MSA classification of PSDs
+
| Bayesian approach to suppress limited angular artifacts
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2003Velazquez_ARMA]]
+
| [[2015Xu_GeometricFlow]]
| PSD and CTF estimation using ARMA models
+
| Multi-scale geometric flow
 
|-  
 
|-  
  
| Paper
+
| Arxiv
| [[2004Sorzano_IDR]]
+
| [[2016Ye_Cohomology]]
| CTF restoration and reconstruction with Iterative Data Refinement
+
| Cohomology properties of 3D reconstruction
 
|-  
 
|-  
  
| Conference
+
| Paper
| [[2004Wan_CTF]]
+
| [[2017Barnett_Marching]]
| Spatially variant CTF
+
| Initial volume through frequency marching
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2004Zubelli_Chahine]]
+
| [[2017Punjani_CryoSPARC]]
| CTF restoration and reconstruction with Chahine's multiplicative method
+
| CryoSPARC
 
|-  
 
|-  
  
| Conference
+
| Paper
| [[2005Dubowy_SpaceVariant]]
+
| [[2017Punjani_CryoSPARCTheory]]
| CTF correction when this is space variant
+
| Theory related to CryoSPARC
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2005Mallick_ACE]]
+
| [[2017Sorzano_SurveyIterative]]
| CTF estimation
+
| Survey of iterative reconstruction methods for EM
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2006Wolf_Ewald]]
+
| [[2018Bartesaghi_Refinement]]
| CTF correction considering Ewald sphere
+
| Refinement of CTF, frame weight and alignment for high resolution reconstruction
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007Jonic_EnhancedPSD]]
+
| [[2018Hu_ParticleFilter]]
| PSD enhancement for better identification of Thon rings; Vitreous ice diffracts in Thon rings
+
| A particle filter framework for 3D reconstruction
 
|-  
 
|-  
  
| Paper
+
| Conference
| [[2007Philippsen_Model]]
+
| [[2018Levin_Kam]]
| CTF Model for tilted specimens
+
| Ab initio reconstruction by autocorrelation analysis
 +
|-
 +
 
 +
| Conference
 +
| [[2018Michels_RBF]]
 +
| Ab-initio reconstruction with radial basis functions
 
|-  
 
|-  
 +
  
 
| Paper
 
| Paper
| [[2007Sorzano_CTF]]
+
| [[2018Reboul_Simple]]
| CTF estimation using enhanced PSDs
+
| Ab initio reconstruction with Simple
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2009Sorzano_Sensitivity]]
+
| [[2018Sorzano_Highres]]
| Error sensitivity of the CTF models, non-uniqueness of the CTF parameters
+
| New algorithm for 3D Reconstruction and alignment with emphasis on significance
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2010Jiang2010_CTFCorrection]]
+
| [[2018Sorzano_Swarm]]
| Amplitude correction method
+
| Consensus of several initial volumes by swarm optimization
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2010Kasantsev_CTFCorrection]]
+
| [[2018Zhu_Ewald]]
| Mathematical foundations of Kornberg and Jensen method
+
| 3D Reconstruction with Ewald sphere correction
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2010Leong_CTFCorrection]]
+
| [[2019Gomez_Initial]]
| Correction for spatially variant CTF
+
| Construction of initial models
 
|-  
 
|-  
  
| Paper
+
| Master
| [[2011Glaeser_Coma]]
+
| [[2019Havelkova_Regularization]]
| The effect of coma at high-resolution
+
| Regularization methods in 3D reconstruction
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2011Mariani_Tilted]]
+
| [[2019Wilkinson_Scales]]
| CTF simulation and correction of tilted specimens
+
| Combining data acquired at different scales
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2011Sindelar_Wiener]]
+
| [[2020Alazzawi_Auto]]
| CTF correction using a modified version of Wiener filter
+
| Automatic full processing of micrographs to yield a 3D reconstruction
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2011Voortman_Tilted]]
+
| [[2020Pan_TV]]
| CTF correction for tilted specimen
+
| 3D Reconstruction with total variation regularization
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2012Voortman_VaryingCTF]]
+
| [[2020Punjani_NonUniform]]
| Correcting a spatially varying CTF
+
| Non-uniform refinement
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Vargas_FastDef]]
+
| [[2020Ramlaul_Sidesplitter]]
| Fast defocus
+
| Local filtering along the reconstruction iterations
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Rohou_CTFFind4]]
+
| [[2020Xie_Automatic]]
| CTF Find 4
+
| Automatic 3D reconstruction from projections
 
|-  
 
|-  
  
| Paper
+
| Conference
| [[2015Sheth_CTFquality]]
+
| [[2020Venkatakrishnan_MBIR]]
| Visualization and quality assessment of CTF
+
| Model based image reconstruction
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Zhang_GCTF]]
+
| [[2020Zhou_AutomaticSelection]]
| gCTF
+
| Automatic selection of particles for 3D reconstruction
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Su_GoCTF]]
+
| [[2021Abrishami_Localized]]
| goCTF, CTF for tilted specimens
+
| Localized reconstruction in scipion expedites the analysis of symmetry mismatches in Cryo-EM data
 
|-  
 
|-  
 
|}
 
 
=== Segmentation ===
 
 
{|
 
  
 
| Paper
 
| Paper
| [[2006Baker_segmentation]]
+
| [[2021Gupta_CryoGAN]]
| Segmentation of molecular subunits
+
| 3D Reconstruction via Generative Adversarial Learning
 
|-  
 
|-  
  
| Conference
+
| Paper
| [[2017Nissenson_VolumeCut]]
+
| [[2021Luo_Opus]]
| Segmentation of an EM volume using an atomic model
+
| 3D Reconstruction with a sparse and smoothness constraint
 
|-  
 
|-  
 
|}
 
 
=== Fitting and docking ===
 
 
{|
 
  
 
| Paper
 
| Paper
| [[1999Volkmann_Fitting]]
+
| [[2021Kimanius_PriorKnowledge]]
| Fitting in real space
+
| Incorporation of prior knowledge during 3D reconstruction
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2001Baker_Review]]
+
| [[2021Sorzano_Uneven]]
| Review of protein structure prediction
+
| Algorithmic robustness to uneven angular distributions
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2001Jones_Review]]
+
| [[2022Havelkova_regularization]]
| Review of protein structure prediction
+
| Regularization of iterative reconstruction algorithms
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2003Kovacs_FRM3D]]
+
| [[2023Bendory_Autocorrelation]]
| Fast Rotational Alignment of two EM maps
+
| Initial volume through autocorrelation analysis with sparsity constraints
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2004Tama_NMA1]]
+
| [[2023Herreros_ZART]]
| Flexible fitting with Normal Modes (I)
+
| Correction of continuous heterogeneity during the 3D reconstruction
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2004Tama_NMA2]]
+
| [[2023Rangan_AbInitio]]
| Flexible fitting with Normal Modes (II)
+
| Robust ab initio reconstruction
 
|-  
 
|-  
  
| Paper
+
|}
| [[2005Velazquez_Superfamilies]]
 
| Recognition of the superfamily folding in medium-high resolution volumes
 
|-
 
  
| Paper
+
=== 3D Heterogeneity ===
| [[2007DeVries_Haddock]]
+
 
| Docking with Haddock 2.0
+
{|
|-
 
  
 
| Paper
 
| Paper
| [[2007Kleywegt_QualityControl]]
+
| [[2004White_Size]]
| Quality control and validation of fitting
+
| Heterogeneity classification of differently sized images
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2012Biswas_Secondary]]
+
| [[2006Penczek_Bootstrap]]
| Secondary structure determination in EM volumes
+
| 3D heterogeneity through bootstrap
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2012Velazquez_Constraints]]
+
| [[2007Leschziner_Review]]
| Multicomponent fitting by using constraints from other information sources
+
| Review of 3D heterogeneity handling algorithms
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Chapman MS_Atomicmodeling]]
+
| [[2007Scheres_ML3D]]
| Atomic modeling of cryo-electron microscopy reconstructions--joint refinement of model and imaging parameters
+
| Maximum Likelihood alignment and classification in 3D
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Esquivel_Modelling]]
+
| [[2008Herman_Graph]]
| Review on modelling (secondary structure, fitting, ...)
+
| Classification by graph partitioning
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Lopez_Imodfit]]
+
| [[2009Spahn_Bootstrap]]
| Fitting based on vibrational analysis
+
| 3D heterogeneity through bootstrap
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Nogales_3DEMLoupe]]
+
| [[2010Elmlund_AbInitio]]
| Normal Mode Analysis of reconstructed volumes
+
| Solving the initial volume problem with multiple conformations
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2014AlNasr_Secondary]]
+
| [[2010Shatsky_MultiVariate]]
| Identification of secondary structure elements in EM volumes
+
| Multivariate Statistical Analysis
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2014Politis_MassSpect]]
+
| [[2012Scheres_Bayesian]]
| Integration of mass spectroscopy information
+
| A Bayesian view on cryo-EM structure determination
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2014Rey_MassSpect]]
+
| [[2012Zheng_Covariance]]
| Integration of mass spectroscopy information
+
| Estimation of the volume covariance
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2014Villa_Review]]
+
| [[2013Wang_MLVariance]]
| Review of atomic fitting into EM volumes
+
| Maximum Likelihood estimate of the map variance
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Barad_EMRinger]]
+
| [[2013Lyumkis D_FREALIGN]]
| Validation of hybrid models
+
| Likelihood-based classification of cryo-EM images using FREALIGN.
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2015Bettadapura_PF2Fit]]
+
| [[2014Chen_Migration]]
| Fast rigid fitting of PDBs into EM maps
+
| Particle migration analysis in 3D classification
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Carrillo_CapsidMaps]]
+
| [[2014Dashti_Brownian]]
| Analysis of virus capsids using Google Maps
+
| Continuous heterogeneity through Brownian trajectories
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Hanson_Continuum]]
+
| [[2014Schwander_manifold]]
| Modelling assemblies with continuum mechanics
+
| Continuous heterogeneity through Manifold Analysis
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Lopez_Review]]
+
| [[2014Jin_NMA]]
| Review of structural modelling from EM data
+
| HEMNMA: Continuous heterogeneity through Normal Mode Analysis
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Schroeder_Hybrid]]
+
| [[2015Anden_Covariance]]
| Review on model building
+
| 3D Covariance matrix estimation for heterogeneity
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Tamo_Dynamics]]
+
| [[2015Bai_Focused]]
| Dynamics in integrative modeling
+
| Focused classification
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Sorzano_AtomsToVoxels]]
+
| [[2015Katsevich_Covariance]]
| Accurate conversion of an atomic model into a voxel density volume
+
| 3D Covariance matrix estimation for heterogeneity
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Joseph_Evolution]]
+
| [[2015Klaholz_MRA]]
| Evolutionary constraints for the fitting of atomic models into density maps
+
| Multivariate Statistical Analysis of Jackknife and Bootstrapping on random subsets
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Joseph_Refinement]]
+
| [[2015Liao_Covariance]]
| Refinement of atomic models in high-resolution EM reconstructions and using Flex-EM
+
| Estimation of the 3D covariance from 2D projections
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Segura_3Diana]]
+
| [[2015Tagare_Direct]]
| Validation of hybrid models
+
| Direct reconstruction of PCA components
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Singharoy_MDFF]]
+
| [[2016Gong_Mechanical]]
| Construction of hybrid models driven by EM density and molecular dynamics
+
| Mechanical model for macromolecules
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Wang_Rosetta]]
+
| [[2016Rawson_Movement]]
| Construction of hybrid models driven by EM density using Rosetta
+
| Movement and flexibility
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Chen_CoarseGraining]]
+
| [[2016Shan_Multibody]]
| Coarse graining of EM volumes
+
| Multibody refinement
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Joseph_Metrics]]
+
| [[2016Sorzano_StructMap]]
| Metrics analysis for the comparison of structures
+
| Sorting a discrete set of conformational states
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Hryc_WeightedAtoms]]
+
| [[2016Sorzano_Strain]]
| Construction of hybrid models by locally weighting the different atoms
+
| Calculate local stretches, strains and rotations from two conformational states
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Matsumoto_Distribution]]
+
| [[2017Punjani_CryoSPARC]]
| Estimating the distribution of conformations of atomic models
+
| CryoSPARC
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Michel_ContactPrediction]]
+
| [[2017Schillbach_Warpcraft]]
| Structure prediction by contact prediction
+
| Warpcraft: 3D Reconstruction in the presence of continuous heterogeneity
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Miyashita_EnsembleFitting]]
+
| [[2018Anden_Covariance]]
| Ensemble fitting using Molecular Dynamics
+
| Structural Variability from Noisy Tomographic Projections
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Turk_ModelBuilding]]
+
| [[2018Haselbach_FreeEnergy]]
| Tutorial on model building and protein visualization
+
| Analysis of the free energy landscape through PCA
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Wang_PartialCharges]]
+
| [[2018Nakane_MultiBody]]
| Appearance of partial charges in EM maps
+
| Structural Variability through multi-body refinement
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Wlodawer]]
+
| [[2019Serna_Review]]
| Comparison of X-ray and EM high resolution structures
+
| Review of classification tools
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Cassidy_review]]
+
| [[2018Solernou_FFEA]]
| Review of methods for hybrid modeling
+
| Fluctuating Finite Element Analysis, continuum approach to Molecular Dynamics
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Chen_SudeChains]]
+
| [[2019Sorzano_Review]]
| A comparison of side chains between X-ray and EM maps
+
| Review of continuous heterogeneity biophysics
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Kawabata_Pseudoatoms]]
+
| [[2019Zhang_Local]]
| Modelling the EM map with Gaussian pseudoatoms
+
| Local variability and covariance
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Kovacs_Medium]]
+
| [[2020Dashti_Landscape]]
| Modelling of medium resolution EM maps
+
| Retrieving functional pathways from single particle snapshots
 +
|-
 +
 
 +
| Conference
 +
| [[2020Gupta_MultiCryoGAN]]
 +
| Reconstruction of continuously heterogeneous structures with adversarial networks
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Neumann_validation]]
+
| [[2020Harastani_NMA]]
| Validation of fitting, resolution assessment and quality of fit
+
| HEMNMA in Scipion : Using HEMNMA for analyzing continuous heterogeneity with normal modes
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Terwilliger_map_to_model]]
+
| [[2020Maji_Propagation]]
| Phenix map_to_model, automatic modelling of EM volumes
+
| Propagation of conformational coordinates across angular space
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Wang_MD]]
+
| [[2020Moscovich_DiffusionMaps]]
| Constructing atomic models using molecular dynamics
+
| Heterogeneity analysis by diffusion maps and spectral volumes
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Xia_MVPENM]]
+
| [[2020Seitz_Polaris]]
| Multiscale Normal Mode Analysis
+
| Analysis of energy landscapes to find minimal action paths
 +
|-
 +
 
 +
| Conference
 +
| [[2020Zhong_CryoDRGN]]
 +
| CryoDRGN to analyze the continuous heterogeneity by CryoEM
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Yu_Atomic]]
+
| [[2020Verbeke_Separation]]
| Constructing atomic models using existing tools
+
| Heterogeneity analysis by comparing common lines
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2019Bonomi_Multiscale]]
+
| [[2021Chen_GM]]
| Bayesian multi-scale modelling
+
| Deep learning-based mixed-dimensional Gaussian mixture model for characterizing variability
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2019Zhang_CoarseGrained]]
+
| [[2021Giraldo_cryoBIFE]]
| Coarse-graining of EM maps
+
| A Bayesian approach to extracting free‑energy profiles
 
|-  
 
|-  
  
|}
+
| Conference
 +
| [[2021Hamitouche_NMADL]]
 +
| Continuous heterogeneity analysis through normal modes and deep learning
 +
|-
  
=== Books and reviews ===
+
| Paper
 +
| [[2021Herreros_Zernikes3D]]
 +
| Continuous heterogeneity analysis through Zernikes 3D
 +
|-
  
{|
+
| Paper
 +
| [[2021Kazemi_Enrich]]
 +
| ENRICH: A fast method to improve the quality of flexible macromolecular reconstructions
 +
|-
  
| Book
+
| Paper
| [[1980Herman_Tomography]]
+
| [[2021Matsumoto_DEFmap]]
| General book on tomography
+
| Prediction of RMSF of Molecular Dynamics from a CryoEM map using deep learning
 
|-  
 
|-  
  
| Book
+
| Chapter
| [[1988Kak_Tomography]]
+
| [[2021Nakasako_Landscape]]
| General book on tomography
+
| Estimation of free-energy landscape from images
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2000Tao_Review]]
+
| [[2021Punjani_3DVA]]
| Review of single particles
+
| 3D Variability analysis from images
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2000VanHeel_Review]]
+
| [[2021Sorzano_PCA]]
| Review of single particles
+
| PCA is limited to low-resolution
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2002Frank_Review]]
+
| [[2021Zhong_CryoDRGN]]
| Review of single particles
+
| CryoDRGN to analyze the continuous heterogeneity by CryoEM
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2002Schmid_Review]]
+
| [[2022Ecoffet_MorphOT]]
| Review of single particles
+
| More physically plausible morphing between two states
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2004Henderson_Review]]
+
| [[2022Gomez_Hierarchical]]
| Review of electron microscopy
+
| Hierarchical classification of particles
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2004Subramaniam_Review]]
+
| [[2022Hamitouche_DeepHEMNMA]]
| Review of single particles
+
| DeepHEMNMA: Continuous heterogeneity analysis through normal modes and deep learning
 +
|-
 +
 
 +
| Conference
 +
| [[2022Levy_CryoFire]]
 +
| CryoFire: heterogeneity and alignment through amortized inference
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2005Steven_Review]]
+
| [[2022Rabuck_Quant]]
| Review of electron microscopy
+
| Workflow for discrete heterogeneity analysis
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2006Fernandez_Review]]
+
| [[2022Skalidis_Endogenous]]
| Review of electron microscopy
+
| AI tools to recognize proteins in cellular fractions
 
|-  
 
|-  
  
| Book
+
| Paper
| [[2006Frank_book]]
+
| [[2022Wu_Manifold]]
| Book covering all aspects of electron microscopy of single particles
+
| Continuous heterogeneity through manifold learning
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2006Sorzano_Review]]
+
| [[2022Zhou_Data]]
| Review of optimization problems in electron microscopy
+
| Determination of the number of discrete 3D classes
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007Leschziner_Review]]
+
| [[2023Barchet_Focused]]
| Review of 3D heterogeneity handling algorithms
+
| Applications and strategies in focused classification and refinement
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007Sorzano_Review]]
+
| [[2023Chen_GMM]]
| Review of the image processing steps
+
| Continuous heterogeneity analysis with GMMs and neural networks
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2008Fanelli_ImageFormation]]
+
| [[2023Dsouza_benchmark]]
| Review on the image formation model from the electron waves and open inverse-problems in Electron Tomography
+
| Benchmark analysis of various continuous heterogeneity algorithms
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2008Fernandez_HPCReview]]
+
| [[2023Esteve_Spectral]]
| High performance computing in electron cryomicroscopy
+
| Continuous heterogeneity analysis through the spectral decomposition of the atomic structure
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2008Jonic_Review]]
+
| [[2023Fernandez_Subtraction]]
| Comparison between electron tomography and single particles
+
| Subtraction of unwanted signals to improve classification and alignment
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2008Mueller_Review]]
+
| [[2023Herreros_Hub]]
| Review of Electron microscopy
+
| Flexibility hub: an integrative platform for continuous heterogeneity
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2008Taylor_Review]]
+
| [[2023Luo_OpusDSD]]
| Review of Electron microscopy
+
| OPUS DSD: a neural network approach to continuous heterogeneity
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2010DeRosier_Review]]
+
| [[2023Kinman_Analysis]]
| Personal account of how 3DEM developed in the early days
+
| Analysis of the continuous heterogeneity results of CryoDrgn
 
|-  
 
|-  
  
| Chapter
+
| Paper
| [[2012Sorzano_Review]]
+
| [[2023Matsumoto_DEFmap]]
| Review of single particle analysis using Xmipp
+
| Quantitative analysis of the prediction of RMSF from a map using DefMap
 
|-  
 
|-  
  
| Chapter
+
| Paper
| [[2012Devaux_Protocol]]
+
| [[2023Punjani_3DFlex]]
| Protocols for performing single particle analysis
+
| Continuous heterogeneity through 3DFlex
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2014Bai_Review]]
+
| [[2023Seitz_Geometric]]
| Recent advances in cryo-EM
+
| Geometric relationships between manifold embeddings of a continuum of 3D molecular structures and their 2D projections
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Carazo_Review]]
+
| [[2023Seitz_ESPER]]
| Review of the reconstruction process
+
| Continuous heterogeneity through Embedded subspace partitioning and eigenfunction realignment
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Cheng_Review]]
+
| [[2023Tang_Reweighting]]
| A primer to Single Particle Cryo-EM
+
| Ensemble reweighting using Cryo-EM particles
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Cheng_Reviewb]]
+
| [[2023Vuillemot_MDSPACE]]
| Single Particle Cryo-EM at crystallographic resolution
+
| MDSPACE: Continuous heterogeneity analysis through normal modes and MD simulation
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Elmlund_Review]]
+
| [[2023Wang_Autoencoder]]
| Recent advances in cryo-EM
+
| Discrete heterogeneity based on autoencoders
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Henderson_Review]]
+
| [[2024Chen_Focused]]
| Recent advances in cryo-EM
+
| Focused reconstruction of heterogeneous macromolecules
 
|-  
 
|-  
 +
 +
|}
 +
 +
=== Validation ===
 +
 +
{|
  
 
| Paper
 
| Paper
| [[2015Nogales_Review]]
+
| [[2008Stagg_TestBed]]
| Recent advances in cryo-EM
+
| Effect of voltage, dosis, number of particles and Euler jumps on resolution
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Schroeder_Review]]
+
| [[2011Henderson]]
| Review of advances in the electron microscope
+
| Tilt Validation
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015VanDenBedem_Integrative]]
+
| [[2011Read]]
| Review of integrative structural biology
+
| Validation of PDBs
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Wu_Review]]
+
| [[2012Henderson]]
| Review of advances in cryo-EM
+
| EM Map Validation
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Carroni_CryoEM]]
+
| [[2013Cossio_Bayesian]]
| Review of advances in Cryo-EM
+
| EM Map Validation in a probabilistic setting
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Egelman_CryoEM]]
+
| [[2013Chen_NoiseSubstitution]]
| Review of advances in Cryo-EM
+
| Noise substitution at high resolution for measuring overfitting
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Eisenstein_CryoEM]]
+
| [[2013Ludtke_Validation]]
| News feature on the Method of the Year
+
| Structural validation, example of the Calcium release channel
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016FernandezLeiro_Review]]
+
| [[2013Murray_Validation]]
| Review of EM
+
| Validation of a 3DEM structure through a particular example
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Glaeser_HowGood]]
+
| [[2014Russo_StatisticalSignificance]]
| How good can cryo-EM become?
+
| EM Map Validation through the statistical significance of the tilt-pair angular assignment
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Jonic_PseudoAtoms]]
+
| [[2014Stagg_Reslog]]
| Review of the applications of the use of pseudoatoms in EM
+
| EM Map Validation through the resolution evolution with the number of particles
 
|-  
 
|-  
  
| Chapter
+
| Paper
| [[2016Mio_Review]]
+
| [[2014Wasilewski_Tilt]]
| Overview of the process to obtain EM reconstructions
+
| Web implementation of the tilt pair validation
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Jonic_Review]]
+
| [[2015Heymann_Alignability]]
| A review of computational ways to handle heterogeneity
+
| EM Map Validation through the resolution of reconstructions from particles and noise
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Nogales_Review]]
+
| [[2015Oliveira_FreqLimited]]
| Review of advances in cryo-EM
+
| Comparison of gold standard and frequency limited optimization
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Subramaniam_Review]]
+
| [[2015Rosenthal_Review]]
| Why cryo-EM is now suitable for crystallographic journals
+
| Review of validation methods
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Vinothkumar_Review]]
+
| [[2015Wriggers_Secondary]]
| Historical review and current limitations
+
| Validation by secondary structure
 
|-  
 
|-  
  
| Report
+
| Paper
| [[2017Brezinski_Nobel]]
+
| [[2016Degiacomi_IM]]
| Scientific background on the Nobel Prize in Chemistry 2017
+
| Comparison of Ion Mobility data and EM volumes
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Cheng_review]]
+
| [[2016Kim_SAXS]]
| Why CryoEM became so hot
+
| Comparison of SAXS data and EM projections
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Danev_Review]]
+
| [[2016Rosenthal_Review]]
| Review of the use of phase plates in EM
+
| Review of validation methods
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Elmlund_Review]]
+
| [[2016Vargas_Alignability]]
| Review of the main current difficulties of EM
+
| Validation by studying the tendency of an angular assignment to cluster in the projection space
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Frank_Review]]
+
| [[2017Monroe_PDBRefinement]]
| Historical review of EM
+
| Validation by comparison to a refined PDB
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Frank_TimeResolved]]
+
| [[2018Afonine_Phenix]]
| Review of time-resolved of EM
+
| Tools in Phenix for the validation of EM maps
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Jonic_Review]]
+
| [[2018Heymann_Bsoft]]
| Review of computational methods to analyze conformational variability
+
| Map validation using Bsoft
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Merino_DrugEM]]
+
| [[2018Heymann_Challenge]]
| Applications of EM for drug design
+
| A summary of the assessments of the 3D Map Challenge
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Rawson_Limitations]]
+
| [[2018Jonic_Gaussian]]
| Limitations of EM for drug design
+
| Assessment of sets of volumes by pseudoatomic structures
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Sorzano_FourierProperties]]
+
| [[2018Naydenova_AngularDistribution]]
| Review of statistical properties of resolution measures defined in Fourier space
+
| Evaluating the angular distribution of a 3D reconstruction
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Sorzano_SurveyIterative]]
+
| [[2018Pages_Symmetry]]
| Survey of iterative reconstruction methods for EM
+
| Looking for a symmetry axis in a PDB
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Bruggeman_Crowdsourcing]]
+
| [[2018Pintilie_SSE]]
| Exploring crowdsourcing for EM image processing
+
| Evaluating the quality of SSE and side chains
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Cheng_Review]]
+
| [[2019Herzik_Multimodel]]
| Review of EM and future ahead
+
| Local and global quality by multi-model fitting
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Cossio_ML]]
+
| [[2020Chen_Atomic]]
| Review of Maximum Likelihood methods
+
| Validation of the atomic models derived from CryoEM
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Grimes_Crystallography]]
+
| [[2020Cossio_CrossValidation]]
| Review of X-ray crystallography and its relationship to EM
+
| Need for cross validation
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Murata_Review]]
+
| [[2020Ortiz_CrossValidation]]
| Review of EM for structure dynamics
+
| Cross validation for SPA
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Quentin_Biomedical]]
+
| [[2020Sazzed_helices]]
| Review of EM as a tool for biomedical research
+
| Validation of helix quality
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Scapin_DrugDiscovery]]
+
| [[2020Stojkovic_PTM]]
| Review of EM as a tool for drug discovery
+
| Validation of post-translational modifications
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Vilas_ImageProcessing]]
+
| [[2020Tiwari_PixelSize]]
| Review of the recent developments in image processing for single particle analysis
+
| Fine determination of the pixel size
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018vonLoeffelholz_VPP]]
+
| [[2021Mendez_Graph]]
| Comparison of Volta Phase Plate reconstructions close to focus and with defocus
+
| Identification of incorrectly oriented particles
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Eisenstein_DrugDesigners]]
+
| [[2021Pintilie_Validation]]
| Drug designers embrace cryo-EM
+
| Review of map validation approaches
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2019Lyumkis_Review]]
+
| [[2021Olek_FDR]]
| Challenges and reviews
+
| Cryo-EM Map–Based Model Validation Using the False Discovery Rate Approach
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2019Sorzano_Review]]
+
| [[2022Garcia_DeepHand]]
| Review of cotinuous heterogeneity biophysics
+
| Checking the correct handedness with a neural network
 
|-  
 
|-  
  
|}
+
| Paper
 
+
| [[2022Sorzano_Bias]]
=== Software ===
+
| Bias, variance, gold-standard and overfitting in SPA
 
+
|-
{|
 
  
 
| Paper
 
| Paper
| [[1996Frank_Spider]]
+
| [[2022Sorzano_Validation]]
| Spider
+
| Validation scheme and server for SPA
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1996VanHeel_Imagic]]
+
| [[2022Terashi_DAQ]]
| Imagic
+
| Validation of models fitted into CryoEM maps
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1999Lutdke_Eman]]
+
| [[2022Waarshamanage_EMDA]]
| Eman
+
| Validation of models fitted into CryoEM maps
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2004Sorzano_Xmipp]]
+
| [[2024Verbeke_SelfFSC]]
| Xmipp
+
| Self FSC: FSC with a single map
 
|-  
 
|-  
 +
 +
|}
 +
 +
=== Resolution ===
 +
 +
{|
  
 
| Paper
 
| Paper
| [[2007Baldwin_AngularTransformations]]
+
| [[1986Harauz_FBP]]
| The Transform Class in SPARX and EMAN2
+
| Fourier Shell Correlation
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007Heymann_Bsoft]]
+
| [[1987Unser_SSNR]]
| Bsoft
+
| 2D Spectral Signal to Noise Ratio
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007Grigorieff_Frealign]]
+
| [[2002Penczek_SSNR]]
| Frealign
+
| 3D Spectral Signal to Noise Ratio for Fourier based algorithms
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2008Scheres_XmippProtocols]]
+
| [[2003Rosenthal_DPR]]
| Xmipp Protocols
+
| Review of the FSC and establishment of a new threshold
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2008Shaikh_SpiderProtocols]]
+
| [[2005Unser_SSNR]]
| Spider Protocols
+
| 3D Spectral Signal to Noise Ratio for any kind of algorithms
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2012Wriggers_SitusConventions]]
+
| [[2005VanHeel_FSC]]
| Conventions and workflows in Situs
+
| Establishment of a new threshold for FSC
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013DeLaRosa_Xmipp30]]
+
| [[2007Sousa_AbInitio]]
| Xmipp 3.0
+
| Resolution measurement on neighbour Fourier voxels
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Cianfrocco_Cloud]]
+
| [[2014Kucukelbir_Local]]
| Software execution in the cloud
+
| Quantifying the local resolution of cryo-EM density maps
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Cheng_MRC2014]]
+
| [[2016Pintilie_Probabilistic]]
| Extensions to MRC file format
+
| Probabilistic models and resolution
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013DeLaRosa_Scipion]]
+
| [[2017Sorzano_FourierProperties]]
| Scipion
+
| Statistical properties of resolution measures defined in Fourier space
 
|-  
 
|-  
  
| Paper
+
| Conference
| [[2016Scheres_Relion]]
+
| [[2018Avramov_DeepLearning]]
| Tutorial on the use of Relion
+
| Deep learning classification of volumes into low, medium and high resolution
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Grigorieff_Frealign]]
+
| [[2018Carugo_BFactors]]
| Tutorial on the use of Frealign
+
| How large can B-factors be in protein crystals
 
|-  
 
|-  
  
| Paper
+
| Conference
| [[2017Moriya_Sphire]]
+
| [[2018Kim_FourierError]]
| Tutorial on the use of Sphire
+
| Comparison between a gold standard and a reconstruction
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Bell_EMAN2]]
+
| [[2018Rupp_Problems]]
| New tools in EMAN2
+
| Problems of resolution as a proxy number for map quality
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Cianfrocco_cloud]]
+
| [[2018Vilas_MonoRes]]
| CryoEM Cloud Tools
+
| Local resolution by monogenic signals
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Grant_cisTEM]]
+
| [[2018Yang_Multiscale]]
| cisTEM
+
| Resolution from a multiscale spectral analysis
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018McLeod_MRCZ]]
+
| [[2019Avramov_DeepLearning]]
| MRC Compression format
+
| Deep learning classification of volumes into low, medium and high resolution
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Zivanov_Relion3]]
+
| [[2019Heymann_Statistics]]
| Relion 3
+
| SNR, FSC, and related statistics
 
|-  
 
|-  
 
|}
 
 
== Electron tomography ==
 
 
=== Image preprocessing ===
 
 
{|
 
  
 
| Paper
 
| Paper
| [[2015Yan_thickness]]
+
| [[2019Ramirez_DeepRes]]
| Determination of thickness, tilt and electron mean free path
+
| Resolution determination by deep learning
 
|-  
 
|-  
 
|}
 
 
=== Image alignment ===
 
 
{|
 
  
 
| Paper
 
| Paper
| [[1982Guckenberger_commonOrigin]]
+
| [[2020Baldwin_Lyumkis_SCF]]
| Determination of a common origin in the micrographs of titl series in three-dimensional electron microscopy
+
| Resolution attenuation through non-uniform Fourier sampling
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1992Lawrence_leastSquares]]
+
| [[2020Beckers_Permutation]]
| Least squares solution of the alignment problem
+
| Permutation tests for the FSC
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1995Penczek_dual]]
+
| [[2020Penczek_mFSC]]
| Dual tilt alignment
+
| Modified FSC to avoid mask induced artifacts
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1996Owen_alignmentQuality]]
+
| [[2020Vilas_MonoDir]]
| Automatic alignment without fiducial markers and evaluation of alignment quality
+
| Local and directional resolution
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1998Grimm_normalization]]
+
| [[2023Dai_CryoRes]]
| Discussion of several gray level normalization methods for electron tomography
+
| Local resolution through deep learning
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2001Brandt_Automatic1]]
+
| [[2023Vilas_FSO]]
| Automatic alignment without fiducial markers
+
| Fourier Shell Occupancy to measure anisotropy
 
|-  
 
|-  
  
 +
|}
 +
 +
=== Sharpening of high resolution information ===
 +
{|
 +
 
| Paper
 
| Paper
| [[2001Brandt_Automatic2]]
+
| [[2003Rosenthal_DPR]]
| Automatic alignment with fiducial markers
+
| Contrast restoration and map sharpening
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2006Winkler_alignment]]
+
| [[2008Fernandez_Bfactor]]
| Marker-free alignment and refinement
+
| Bfactor determination and restoration
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2006Castano_alignment]]
+
| [[2013Fiddy_SaxtonAlgorithm]]
| Alignment with non-perpendicularity
+
| Phase retrieval or extension
|-
 
 
 
| Paper
 
| [[2007Castano_alignment]]
 
| Fiducial-less alignment of cryo-sections
 
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2009Sorzano_alignment]]
+
| [[2014Kishchenko_SphericalDeconvolution]]
| Marker-free alignment and refinement
+
| Spherical deconvolution
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2010Cantele_dualAlignment]]
+
| [[2015Spiegel_VISDEM]]
| Alignment of dual series
+
| Visualization improvement by the use of pseudoatomic profiles
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2014Tomonaga_Automatic]]
+
| [[2016Jonic_Pseudoatoms]]
| Automatic alignment of tilt series using the projection themselves
+
| Approximation with pseudoatoms
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2014Han_Automatic]]
+
| [[2016Jonic_Denoising]]
| Automatic alignment of tilt series using SIFT features
+
| Denoising and high-frequency boosting by pseudoatom approximation
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Han_Automatic]]
+
| [[2017Jakobi_LocScale]]
| Automatic alignment of tilt series using fiducials
+
| Sharpening based on an atomic model
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Mastronarde_Automatic]]
+
| [[2019Ramlaul_Filtering]]
| Automatic alignment and reconstruction of tilt series in IMOD
+
| Local agreement filtering (denoising)
 
|-  
 
|-  
  
| Paper
+
| Conference
| [[2018Fernadez_Beam]]
+
| [[2020Mullick_SuperResolution]]
| Image alignment considering beam induced motion
+
| Superresolution from a map
 
|-  
 
|-  
 +
  
 
| Paper
 
| Paper
| [[2018Han_Fast]]
+
| [[2020Ramirez_LocalDeblur]]
| Automatic alignment using fiducial markers
+
| Local deblur (local Wiener filter)
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2019Fernandez_residual]]
+
| [[2020Terwilliger_density]]
| Alignment of tilt series using residual interpolation
+
| Density modification of CryoEM maps
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2019Han_Dual]]
+
| [[2020Vilas_Bfactor]]
| Automatic alignment using fiducial markers in dual tilt series
+
| Global B-factor correction does not represent macromolecules
 
|-  
 
|-  
 
|}
 
 
=== CTF estimation and restoration ===
 
 
{|
 
  
 
| Paper
 
| Paper
| [[2003Winkler_CTF]]
+
| [[2021Beckers_Interpretation]]
| Focus gradient correction in electron tomography
+
| Improvements from the raw reconstruction to a structure to model
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2006Fernandez_CTF]]
+
| [[2021Kaur_LocSpiral]]
| CTF determination and correction in electron tomography
+
| LocSpiral, LocBsharpen, LocBfactor
 
|-  
 
|-  
 
  
 
| Paper
 
| Paper
| [[2009Zanetti_CTF]]
+
| [[2021Fernandez_Adjustment]]
| CTF determination and correction in electron tomography
+
| Map adjustment for subtraction, consensus and sharpening
 
|-  
 
|-  
 
  
 
| Paper
 
| Paper
| [[2009Xiong_CTF]]
+
| [[2021Sanchez_DeepEMhancer]]
| CTF determination and correction for low dose tomographic tilt series
+
| Deep learning algorithm for volume restoration
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2012Eibauer_CTF]]
+
| [[2022Gilles_Wilson]]
| CTF determination and correction
+
| A molecular prior distribution for Bayesian inference based on Wilson statistics
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Bharat_CTFCorrectedSubtomogramAveraging]]
+
| [[2022Vargas_tubular]]
| Subtomogram averaging with CTF correction using a Bayesian prior
+
| Map enhancement by multiscale tubular filter
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Turonova_3DCTF]]
+
| [[2023He_EMReady]]
| 3D CTF Correction
+
| Map enhancement with local and non-local deep learning (EMReady)
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Kunz_3DCTF]]
+
| [[2023Maddhuri_EMGan]]
| 3D CTF Correction
+
| Map enhancement with GANs (EMGan)
 
|-  
 
|-  
  
 
|}
 
|}
  
=== 3D reconstruction ===
+
=== CTF estimation and restoration ===
  
 
{|
 
{|
  
 
| Paper
 
| Paper
| [[1972Gilbert_SIRT]]
+
| [[1982Schiske_Correction]]
| Simultaneous Iterative Reconstruction Technique (SIRT)
+
| CTF correction for tilted objects
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1973Herman_ART]]
+
| [[1988Toyoshima_Model]]
| Algebraic Reconstruction Technique (ART)
+
| CTF estimation
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1984Andersen_SART]]
+
| [[1995Frank_Wiener]]
| Simultaneous Algebraic Reconstruction Technique (SART)
+
| CTF correction using Wiener filter
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1992Radermacher_WBP]]
+
| [[1996Skoglund_MaxEnt]]
| Weighted Backprojection in electron tomography
+
| CTF correction with Maximum Entropy
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1997Marabini_reconstruction]]
+
| [[1996Zhou_Model]]
| Iterative reconstruction in electron tomography
+
| CTF model and user interface for manual fitting
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2002Fernandez_reconstruction]]
+
| [[1997Fernandez_AR]]
| Iterative reconstruction in electron tomography
+
| PSD estimation using periodogram averaging and AR models
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007Radermacher_WBP]]
+
| [[1997Penczek_Wiener]]
| Weighted Backprojection in electron tomography
+
| CTF correction using Wiener filter
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2008Fernandez_CARP]]
+
| [[1997Stark_Deconvolution]]
| Component Averaged Row Projections (CARP)
+
| CTF correction using deconvolution
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2010Xu_Long]]
+
| [[1997Zhu_RecCTF]]
| Iterative reconstructions with long object correction and GPU implementation
+
| CTF correction and reconstruction
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2012Herman General Superiorization]]
+
| [[2000DeRosier_EwaldCorrection]]
| Superiorization: an optimization heuristic for medical physics
+
| CTF correction considering the Ewald sphere
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2012Zhang_IPET_FETR]]
+
| [[2000Jensen_TiltedCorrection]]
| IPET and FETR, a reconstruction algorithm for single molecule tomography
+
| CTF correction considering tilt in backprojection
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Goris_SIRT_TV_DART]]
+
| [[2001Saad_CTFEstimate]]
| Combination of SIRT, Total Variation and Discrete ART to reconstruct and segment at the same time
+
| CTF estimation
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Briegel A_Challenge]]
+
| [[2003Huang_CTFEstimate]]
| The challenge of determining handedness in electron tomography and the use of DNA origami gold nanoparticle helices as molecular standards
+
| CTF estimation
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Messaoudi_EnergyFiltered]]
+
| [[2003Mindell_CTFTILT]]
| 3D Reconstruction of Energy-Filtered TEM
+
| CTF estimation for tilted micrographs
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Venkatakrishnan_MBIR]]
+
| [[2003Sander_MSA]]
| 3D Reconstruction with priors
+
| CTF estimation through MSA classification of PSDs
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Deng_ICON]]
+
| [[2003Velazquez_ARMA]]
| 3D Reconstruction with missing information restoration
+
| PSD and CTF estimation using ARMA models
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Guay_Compressed]]
+
| [[2004Sorzano_IDR]]
| 3D Reconstruction using compressed sensing
+
| CTF restoration and reconstruction with Iterative Data Refinement
 
|-  
 
|-  
  
| Paper
+
| Conference
| [[2016Turonova_Artifacts]]
+
| [[2004Wan_CTF]]
| Artifacts observed during 3D reconstruction
+
| Spatially variant CTF
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2019Yan_MBIR]]
+
| [[2004Zubelli_Chahine]]
| 3D Reconstruction with priors and demonstration of its use in biological samples
+
| CTF restoration and reconstruction with Chahine's multiplicative method
 
|-  
 
|-  
  
|}
+
| Conference
 
+
| [[2005Dubowy_SpaceVariant]]
=== Noise reduction ===
+
| CTF correction when this is space variant
{|
+
|-
  
 
| Paper
 
| Paper
| [[2001Frangakis_NAD]]
+
| [[2005Mallick_ACE]]
| Noise reduction with Nonlinear Anisotropic Diffusion
+
| CTF estimation
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2003Fernandez_AND]]
+
| [[2006Wolf_Ewald]]
| Anisotropic nonlinear diffusion for electron tomography
+
| CTF correction considering Ewald sphere
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2003Jiang_Bilateral]]
+
| [[2007Jonic_EnhancedPSD]]
| Bilateral denoising filter in electron microscopy
+
| PSD enhancement for better identification of Thon rings; Vitreous ice diffracts in Thon rings
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2005Fernandez_AND]]
+
| [[2007Philippsen_Model]]
| Anisotropic nonlinear denoising in electron tomography
+
| CTF Model for tilted specimens
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007Heide_median]]
+
| [[2007Sorzano_CTF]]
| Iterative median filtering in electron tomography
+
| CTF estimation using enhanced PSDs
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2007Fernandez_autAND]]
+
| [[2009Sorzano_Sensitivity]]
| Anisotropic nonlinear diffusion with automated parameter tuning
+
| Error sensitivity of the CTF models, non-uniqueness of the CTF parameters
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2009Fernandez_Beltrami]]
+
| [[2010Jiang2010_CTFCorrection]]
| Nonlinear filtering based on Beltrami flow
+
| Amplitude correction method
 
|-  
 
|-  
+
 
 
| Paper
 
| Paper
| [[2010Bilbao_MeanShift]]
+
| [[2010Kasantsev_CTFCorrection]]
| Mean Shift Filtering
+
| Mathematical foundations of Kornberg and Jensen method
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2014Kovacik_wedgeArtefacts]]
+
| [[2010Leong_CTFCorrection]]
| Removal of wedge artefacts
+
| Correction for spatially variant CTF
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2014Maiorca_beadArtefacts]]
+
| [[2011Glaeser_Coma]]
| Removal of gold bead artefacts
+
| The effect of coma at high-resolution
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Trampert_Inpainting]]
+
| [[2011Mariani_Tilted]]
| Removal of the missing wedge by inpainting
+
| CTF simulation and correction of tilted specimens
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Moreno_TomoEED]]
+
| [[2011Sindelar_Wiener]]
| Fast Anisotropic Diffusion
+
| CTF correction using a modified version of Wiener filter
 
|-  
 
|-  
  
|}
+
| Paper
 
+
| [[2011Voortman_Tilted]]
=== Segmentation ===
+
| CTF correction for tilted specimen
 
+
|-
{|
 
  
 
| Paper
 
| Paper
| [[2002Frangakis_Eigenanalysis]]
+
| [[2012Voortman_VaryingCTF]]
| Segmentation using eigenvector analysis.
+
| Correcting a spatially varying CTF
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2002Volkmann_Watershed]]
+
| [[2013Vargas_FastDef]]
| Segmentation using watershed transform.
+
| Fast defocus
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2003Bajaj_BoundarySegmentation]]
+
| [[2014Penczek_CTER]]
| Segmentation based on fast marching.
+
| Estimation of the CTF errors
|-
 
 
 
| Paper
 
| [[2005Cyrklaff_Thresholding]]
 
| Segmentation using optimal thresholding.
 
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007Lebbink_TemplateMatching]]
+
| [[2015Rohou_CTFFind4]]
| Segmentation using template matching.
+
| CTF Find 4
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007Sandberg_OrientationFields]]
+
| [[2015Sheth_CTFquality]]
| Segmentation using orientation fields.
+
| Visualization and quality assessment of CTF
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007Sandberg_SegmentationReview]]
+
| [[2016Zhang_GCTF]]
| Review on segmentation in electron tomography.
+
| gCTF
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2008Garduno_FuzzySegmentation]]
+
| [[2018Su_GoCTF]]
| Segmentation using fuzzy set theory principles.
+
| goCTF, CTF for tilted specimens
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2009Lebbink_TemplateMatching2]]
+
| [[2020Heimowitz_Aspire]]
| Segmentation using template matching.
+
| CTF determination in Aspire
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2012RubbiyaAli_EdgeDetection]]
+
| [[2020Zivanov_HighOrder]]
| Parameter-Free Segmentation of Macromolecular Structures.
+
| Estimation of high order aberrations
 
|-  
 
|-  
  
| Conference
+
|}
| [[2015Xu_TemplateMatching]]
+
 
| Detection of macromolecular complexes with a reduced representation of the templates.
+
=== Segmentation ===
|-
+
 
 +
{|
  
 
| Paper
 
| Paper
| [[2017Ali_RAZA]]
+
| [[2006Baker_segmentation]]
| Automated segmentation of tomograms
+
| Segmentation of molecular subunits
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Chen_Annotation]]
+
| [[2010Pintilie_segger]]
| Automated annotation of tomograms
+
| Segmentation of molecular subunits
 
|-  
 
|-  
  
| Paper
+
| Conference
| [[2017Tasel_ActiveContours]]
+
| [[2017Nissenson_VolumeCut]]
| Segmentation with active contours
+
| Segmentation of an EM volume using an atomic model
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Xu_DeepLearning]]
+
| [[2019Beckers_FDR]]
| Finding proteins in tomograms using deep learning
+
| Segmentation of the protein using False Discovery Rate
 
|-  
 
|-  
 
  
 
| Paper
 
| Paper
| [[2018Zeng_DeepLearning]]
+
| [[2020Beckers_FDR]]
| Mining features in Electron Tomographt by deep learning
+
| Segmentation of the protein using False Discovery Rate (GUI)
 
|-  
 
|-  
 
|}
 
 
=== Resolution ===
 
{|
 
  
 
| Paper
 
| Paper
| [[2005Cardone_Resolution]]
+
| [[2020Farkas_MemBlob]]
| Resolution criterion for electron tomography
+
| Segmentation of membrane in membrane embedded proteins
 
|-  
 
|-  
  
| Chapter
+
| Paper
| [[2007Penczek_Resolution]]
+
| [[2020Terashi_MainMastSeg]]
| Review of resolution criteria for electron tomography
+
| Segmentation of proteins into domains
 
|-  
 
|-  
 
  
 
| Paper
 
| Paper
| [[2015Diebolder_ConicalFSC]]
+
| [[2021He_EMNUSS]]
| Conical Fourier Shell Correlation
+
| EMNUSS: Identification of secondary structure in CryoEM maps with deep learning
 
|-  
 
|-  
 
  
 
|}
 
|}
  
=== Subtomogram analysis ===
+
=== Fitting and docking ===
  
 
{|
 
{|
  
 
| Paper
 
| Paper
| [[2000Bohm_Template]]
+
| [[1999Volkmann_Fitting]]
| Macromolecule finding by template matching
+
| Fitting in real space
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2002Frangakis_Template]]
+
| [[2001Baker_Review]]
| Macromolecule finding by template matching
+
| Review of protein structure prediction
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2006Nickell_Review]]
+
| [[2001Jones_Review]]
| Review of macromolecule finding by template matching (Visual Proteomics)
+
| Review of protein structure prediction
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007Best_Review]]
+
| [[2003Kovacs_FRM3D]]
| Review of Localization of Protein Complexes by Pattern Recognition
+
| Fast Rotational Alignment of two EM maps
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007Forster_Review]]
+
| [[2004Tama_NMA1]]
| Review of structure determination by subtomogram averaging
+
| Flexible fitting with Normal Modes (I)
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2008Forster_Classification]]
+
| [[2004Tama_NMA2]]
| Classification of subtomograms using constrained correlation
+
| Flexible fitting with Normal Modes (II)
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2008Bartesaghi_Classification]]
+
| [[2005Velazquez_Superfamilies]]
| Classification and averaging of subtomograms
+
| Recognition of the superfamily folding in medium-high resolution volumes
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2008Schmid_Averaging]]
+
| [[2007DeVries_Haddock]]
| Alignment and averaging of subtomograms
+
| Docking with Haddock 2.0
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2010Amat_Averaging]]
+
| [[2007Kleywegt_QualityControl]]
| Alignment and averaging of subtomograms exploiting thresholding in Fourier space
+
| Quality control and validation of fitting
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2010Yu_PPCA]]
+
| [[2008Orzechowski_Flexible]]
| Probabilistic PCA for volume classification
+
| Flexible fitting with biased molecular dynamics
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2013Chen_Averaging]]
+
| [[2008Rusu_Interpolation]]
| Fast alignment of subtomograms using spherical harmonics
+
| Biomolecular pleiomorphism probed by spatial interpolation of coarse models
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2013Kuybeda_Averaging]]
+
| [[2012Biswas_Secondary]]
| Alignment and averaging of subtomograms using the nuclear norm of the cluster
+
| Secondary structure determination in EM volumes
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2013Shatsky_Averaging]]
+
| [[2012Velazquez_Constraints]]
| Alignment and averaging of subtomograms with constrained cross-correlation
+
| Multicomponent fitting by using constraints from other information sources
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2013Yu_Projection]]
+
| [[2013Chapman MS_Atomicmodeling]]
| Subtomogram averaging by aligning their projections
+
| Atomic modeling of cryo-electron microscopy reconstructions--joint refinement of model and imaging parameters
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2014Chen_Autofocus]]
+
| [[2013Esquivel_Modelling]]
| Subtomogram averaging and classification with special attention to differences
+
| Review on modelling (secondary structure, fitting, ...)
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2014Yu_ReferenceBias]]
+
| [[2013Lopez_Imodfit]]
| Scoring the reference bias
+
| Fitting based on vibrational analysis
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2014Voortman_LimitingFactors]]
+
| [[2013Nogales_3DEMLoupe]]
| Limiting factors of subtomogram averaging
+
| Normal Mode Analysis of reconstructed volumes
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2015Bharat_CTFCorrectedSubtomogramAveraging]]
+
| [[2014AlNasr_Secondary]]
| Subtomogram averaging with CTF correction using a Bayesian prior
+
| Identification of secondary structure elements in EM volumes
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Yu_ReferenceBias]]
+
| [[2014Politis_MassSpect]]
| Scoring the reference bias
+
| Integration of mass spectroscopy information
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2016Bharat_Relion]]
+
| [[2014Rey_MassSpect]]
| Subtomogram averaging with Relion
+
| Integration of mass spectroscopy information
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2016Song_MatrixNorm]]
+
| [[2014Villa_Review]]
| Matrix norm minimization for tomographic reconstruction and alignment
+
| Review of atomic fitting into EM volumes
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2017Castano_ParticlePicking]]
+
| [[2015Barad_EMRinger]]
| Particle picking in tomograms for subtomogram averaging
+
| Validation of hybrid models
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2017Frazier_Tomominer]]
+
| [[2015Bettadapura_PF2Fit]]
| TomoMiner a software platform for large-scale subtomogram analysis
+
| Fast rigid fitting of PDBs into EM maps
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2018Himes_emClarity]]
+
| [[2015Carrillo_CapsidMaps]]
| emClarity for subtomogram averaging
+
| Analysis of virus capsids using Google Maps
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2018Zhao_Fast]]
+
| [[2015Hanson_Continuum]]
| Fast alignment and maximum likelihod for subtomogram averaging
+
| Modelling assemblies with continuum mechanics
|-
+
|-  
  
|}
+
| Paper
 
+
| [[2015Lopez_Review]]
=== Single particle tomography ===
+
| Review of structural modelling from EM data
 
+
|-
{|
 
  
 
| Paper
 
| Paper
| [[2012Bartesaghi_Constrained]]
+
| [[2015Schroeder_Hybrid]]
| 3D reconstruction by imposing geometrical constraints
+
| Review on model building
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2015Galaz_SingleParticleTomography]]
+
| [[2015Tamo_Dynamics]]
| Set of tools for Single Particle Tomography in EMAN2
+
| Dynamics in integrative modeling
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Galaz_SingleParticleTomography]]
+
| [[2015Sorzano_AtomsToVoxels]]
| Alignment algorithms and CTF correction
+
| Accurate conversion of an atomic model into a voxel density volume
 
|-  
 
|-  
  
|}
+
| Paper
 +
| [[2016Joseph_Evolution]]
 +
| Evolutionary constraints for the fitting of atomic models into density maps
 +
|-
  
=== Books and reviews ===
+
| Paper
 
+
| [[2016Joseph_Refinement]]
{|
+
| Refinement of atomic models in high-resolution EM reconstructions using Flex-EM
 +
|-
  
 
| Paper
 
| Paper
| [[2000Baumeister_Review]]
+
| [[2016Murshudov_Refinement]]
| Review of electron tomography
+
| Refinement of atomic models in high-resolution EM reconstructions
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2003Koster_Review]]
+
| [[2016Segura_3Diana]]
| Review of electron tomography
+
| Validation of hybrid models
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2003Sali_Review]]
+
| [[2016Singharoy_MDFF]]
| Review of electron tomography
+
| Construction of hybrid models driven by EM density and molecular dynamics
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2004Henderson_Review]]
+
| [[2016Wang_Rosetta]]
| Review of electron microscopy
+
| Construction of hybrid models driven by EM density using Rosetta
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2005Lucic_Review]]
+
| [[2017Chen_CoarseGraining]]
| Review of electron tomography
+
| Coarse graining of EM volumes
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2006Fernandez_Review]]
+
| [[2017Joseph_Metrics]]
| Review of electron microscopy
+
| Metrics analysis for the comparison of structures
 
|-  
 
|-  
  
| Book
+
| Paper
| [[2006Frank_TomoBook]]
+
| [[2017Hryc_WeightedAtoms]]
| Electron Tomography
+
| Construction of hybrid models by locally weighting the different atoms
|-
 
 
 
| Book
 
| [[2007McIntosh_Book]]
 
| Cellular Electron Microscopy
 
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007Sorzano_Review]]
+
| [[2017Matsumoto_Distribution]]
| Review of the image processing steps
+
| Estimating the distribution of conformations of atomic models
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2008Fanelli_ImageFormation]]
+
| [[2017Michel_ContactPrediction]]
| Review on the image formation model from the electron waves and open inverse-problems
+
| Structure prediction by contact prediction
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2008Fernandez_HPCReview]]
+
| [[2017Miyashita_EnsembleFitting]]
| High performance computing in electron cryomicroscopy
+
| Ensemble fitting using Molecular Dynamics
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2008Jonic_Review]]
+
| [[2017Turk_ModelBuilding]]
| Comparison between electron tomography and single particles
+
| Tutorial on model building and protein visualization
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2012Kudryashev_Review]]
+
| [[2017Wang_PartialCharges]]
| Review of subtomogram averaging
+
| Appearance of partial charges in EM maps
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Briggs_Review]]
+
| [[2017Wlodawer]]
| Review of subtomogram averaging
+
| Comparison of X-ray and EM high resolution structures
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Beck_Review]]
+
| [[2018Cassidy_review]]
| Review of molecular sociology
+
| Review of methods for hybrid modeling
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Galaz_Review]]
+
| [[2018Chen_SudeChains]]
| Review of single particle tomography
+
| A comparison of side chains between X-ray and EM maps
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Plitzko_Review]]
+
| [[2018Kawabata_Pseudoatoms]]
| Review of electron tomography, FRET and FIB milling
+
| Modelling the EM map with Gaussian pseudoatoms
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2019Schur_Review]]
+
| [[2018Kovacs_Medium]]
| Review of electron tomography and subtomogram averaging
+
| Modelling of medium resolution EM maps
 
|-  
 
|-  
  
|}
+
| Paper
 
+
| [[2018Neumann_validation]]
=== Software ===
+
| Validation of fitting, resolution assessment and quality of fit
 
+
|-
{|
 
  
 
| Paper
 
| Paper
| [[1996Kremer_IMOD]]
+
| [[2018Terwilliger_map_to_model]]
| IMOD
+
| Phenix map_to_model, automatic modelling of EM volumes
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1996Chen_Priism/IVE]]
+
| [[2018Wang_MD]]
| Priism/IVE
+
| Constructing atomic models using molecular dynamics
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1996Frank_Spider]]
+
| [[2018Xia_MVPENM]]
| Spider
+
| Multiscale Normal Mode Analysis
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2004Sorzano_Xmipp]]
+
| [[2018Yu_Atomic]]
| Xmipp
+
| Constructing atomic models using existing tools
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2005Nickell_TOM]]
+
| [[2019Bonomi_Multiscale]]
| TOM Toolbox
+
| Bayesian multi-scale modelling
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007Messaoudi_TomoJ]]
+
| [[2019Kidmose_Namdinator]]
| TomoJ
+
| Namdinator: Flexible fitting with NAMD
 
|-  
 
|-  
 +
  
 
| Paper
 
| Paper
| [[2008Heymann_BsoftTomo]]
+
| [[2019Klaholz_Review]]
| Bsoft
+
| Review of Phenix tools to modelling
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Ding_CaltechTomography]]
+
| [[2019Subramaniya_DeepSSE]]
| Caltech tomography database
+
| Secondary structure prediction from maps using deep learning
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Noble_AppionProtomo]]
+
| [[2019Zhang_CoarseGrained]]
| Batch fiducial-less tilt-series alignment in Appion using Protomo
+
| Coarse-graining of EM maps
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015vanAarle_Astra]]
+
| [[2020Costa_MDeNM]]
| ASTRA Toolbox
+
| Flexible fitting with molecular dynamics and normal modes
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Han_AuTom]]
+
| [[2020Cragnolini_Tempy2]]
| Software platform for Electron Tomography
+
| TEMpy2 library for density-fitting and validation
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Wan_Simulator]]
+
| [[2020Dodd_ModelBuilding]]
| Electron Tomography Simulator
+
| Model building possibilities, with special emphasis on flexible fitting
 
|-  
 
|-  
  
|}
+
| Paper
 +
| [[2020Ho_CryoID]]
 +
| Identification of proteins in structural proteomics from cryoEM volumes
 +
|-
  
== 2D Crystals ==
+
| Paper
 +
| [[2020Hoh_Buccaneer]]
 +
| Structure modelling with Buccaneer
 +
|-
  
=== 2D Preprocessing ===
 
  
{|
+
| Paper
 +
| [[2020Joseph_comparison]]
 +
| Comparison of map and model, or two maps
 +
|-
  
 +
| Paper
 +
| [[2020Kim_Review]]
 +
| Review of the options for atomic modelling
 +
|-
  
 
| Paper
 
| Paper
| [[1986Henderson_Processing]]
+
| [[2020Leelananda_Constraints]]
| General 2D processing
+
| NMR Chemical Shifts and Cryo-EM Density Restraints in Iterative Rosetta-MD structure refinement
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2000He_PhaseAlignment]]
+
| [[2020Liebschner_Ceres]]
| Phase consistency and Alignment
+
| CERES: Web server of refined atomic maps of CryoEM deposited maps by Phenix
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2006Gil_Unbending]]
+
| [[2020Oroguchi]]
| Crystal unbending
+
| Assessment of Force Field Accuracy Using Cryogenic Electron Microscopy Data
 
|-  
 
|-  
 
|}
 
 
=== Classification ===
 
{|
 
  
 
| Paper
 
| Paper
| [[1988Frank_Classification]]
+
| [[2020Vant_Flexible]]
| MSA and classification in electron crystallography
+
| Flexible fitting with molecular dynamics and neural network potentials
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1996Fernandez_SOM]]
+
| [[2021Behkamal_Secondary]]
| Classification based on self organizing maps
+
| Secondary structure from medium resolution maps
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1998Sherman_MSA]]
+
| [[2021Chojnowski_quality]]
| Classification based on MSA
+
| Quality of models automatically fitted with ARP/wARP
 
|-  
 
|-  
 
|}
 
=== 3D Reconstruction ===
 
 
{|
 
  
 
| Paper
 
| Paper
| [[1985Wang_Solvent]]
+
| [[2021Han_Vesper]]
| Solvent flattening
+
| VESPER: global and local cryo-EM map alignment using local density vectors
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1990Henderson_Processing]]
+
| [[2021Lawson_Challenge]]
| General 3D processing
+
| Validation recommendations based on outcomes of the 2019 EMDataResource challenge
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2004Marabini_ART]]
+
| [[2021Mori_Flexible]]
| Algebraic Reconstruction Technique with blobs for crystals (Xmipp)
+
| Efficient Flexible Fitting Refinement with Automatic Error Fixing
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Biyani_Badlu]]
+
| [[2021Pfab_DeepTracer]]
| Image processing for badly ordered crystals
+
| DeepTracer for fast de novo cryo-EM protein structure modeling
 +
|-
 +
 
 +
| Paper
 +
| [[2021Saltzberg_IMP]]
 +
| Using the Integrative Modeling Platform to model a cryoEM map
 
|-  
 
|-  
  
|}
+
| Paper
 +
| [[2021Terwilliger_CryoID]]
 +
| Identification of sequence in a CryoEM map from a set of candidates
 +
|-
  
=== Books and reviews ===
+
| Paper
 +
| [[2021Titarenko_LocalCorr]]
 +
| Performance improvement of local correlation for docking
 +
|-
  
{|
+
| Conference
 +
| [[2021Vuillemot_NMA]]
 +
| Flexible fitting using a combined Bayesian and Normal Mode approach with Hamiltonian Monte Carlo sampling
 +
|-
  
 
| Paper
 
| Paper
| [[1998Walz_Review]]
+
| [[2022Antanasijevic_ab]]
| Review of 2D crystallography
+
| Sequence determination of antibodies bound to a map
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1999Glaeser_Review]]
+
| [[2022Behkamal_LPTD]]
| Review of 2D crystallography
+
| LPTD: Topology determination of CryoEM maps
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2001Ellis_Review]]
+
| [[2022Chojnowski_findMySeq]]
| Review of 2D crystallography
+
| Identify sequence in CryoEM map using Deep Learning
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2001Glaeser_Review]]
+
| [[2022Hryc_Pathwalking]]
| Review of 2D crystallography
+
| Atomic modelling with Pathwalking
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2004Henderson_Review]]
+
| [[2022He_EMBuild]]
| Review of electron microscopy
+
| Atomic modelling for complexes with EMbuild
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2006Fernandez_Review]]
+
| [[2022Krieger_Prody2]]
| Review of single particles, electron tomography and crystallography
+
| Protein dynamics developments for the large scale and cryoEM: case study of ProDy 2.0
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007Sorzano_Review]]
+
| [[2022Neijenhuis_Haddock]]
| Review of the image processing steps
+
| Protein-protein interface refinement in complex maps with Haddock2.4
 
|-  
 
|-  
  
|}
+
| Paper
 +
| [[2022Urzhumtsev_Direct]]
 +
| Calculation of the EM map from an atomic model
 +
|-
  
=== Software ===
+
| Paper
 
+
| [[2022Urzhumtsev_XrayEM]]
{|
+
| Effect of the local resolution on the atomic modeling
 +
|-
  
 
| Paper
 
| Paper
| [[1996Crowther_MRC]]
+
| [[2022Vuillemot_NMMD]]
| MRC
+
| NMMD: Flexible fitting with simultaneous Normal Mode and Molecular Dynamics displacements
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2004Sorzano_Xmipp]]
+
| [[2022Zhang_CRITASSER]]
| Xmipp
+
| Atomic models of assemble protein structures with deep learning
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007Gipson_2dx]]
+
| [[2023Blau_FittingML]]
| 2dx
+
| Maximum-likelihood fitting of atomic models in EM maps
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007Heymann_Bsoft]]
+
| [[2023Chang_CryoFold]]
| Bsoft
+
| Flexible fitting into cryo-EM maps with CryoFold (a MELD plugin)
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007Philippsen_IPLT]]
+
| [[2023Millan_LL]]
| IPLT
+
| Likelihood-based docking of models into cryo-EM maps
 
|-  
 
|-  
  
|}
+
| Paper
 +
| [[2023Park_CSA]]
 +
| Atomic model fitting using conformational space annealing
 +
|-
  
== 3D Crystals - MicroED ==
+
| Paper
 +
| [[2023Read_LL]]
 +
| Likelihood-based signal and noise analysis for docking of models into cryo-EM maps
 +
|-  
  
=== Sample Preparation ===
 
{|
 
 
| Paper
 
| Paper
| [[2016Shi_Preparation]]
+
| [[2023Reggiano_MEDIC]]
| Sample Preparation
+
| Evaluation of atomic models using MEDIC
|}
+
|-
=== Data Collection ===
+
 
{|
 
 
| Paper
 
| Paper
| [[2014Nannenga_CR]]  
+
| [[2023Terashi_DAQrefine]]
| Continuous rotation
+
| Atomic model refinement using AlphaFold2 and DAQ
 +
|-
  
|}
+
| Paper
=== Data Processing ===
+
| [[2023Terashi_DeepMainMast]]
{|
+
| DeepMainMast: de novo modelling of CryoEM maps
 +
|-
  
 
| Paper
 
| Paper
| [[2011Wisedchaisri_PhaseExtension]]
+
| [[2023Wang_CryoREAD]]
| Fragment-based phase extension
+
| CryoREAD: de novo modelling of nucleic acids
|-
+
|-  
  
| Paper
 
| [[2015Hattne_Processing]]
 
| Data Processing
 
|-
 
 
| Paper
 
| [[2016Hattne_Correction]]
 
| Image correction
 
 
|}
 
|}
  
=== Software ===
+
=== Books and reviews ===
 +
 
 
{|
 
{|
  
| Paper
+
| Book
| [[2014Iadanza_Processing]]
+
| [[1980Herman_Tomography]]
| Data Processing of still diffraction data
+
| General book on tomography
|}
+
|-
  
=== Books and Reviews ===
+
| Book
{|
+
| [[1988Kak_Tomography]]
| Paper
+
| General book on tomography
| [[2014Nannenga_Review ]]
+
|-  
| Review of MicroED
 
|-
 
  
 
| Paper
 
| Paper
| [[2016Liu_Review ]]
+
| [[2000Tao_Review]]
| Review of MicroED
+
| Review of single particles
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2016Rodriguez_Review ]]
+
| [[2000VanHeel_Review]]
| Review of MicroED
+
| Review of single particles
 
|-  
 
|-  
 
|}
 
 
== Helical particles ==
 
 
=== Filament corrections ===
 
 
{|
 
  
 
| Paper
 
| Paper
| [[1986Egelman_Curved]]
+
| [[2002Frank_Review]]
| Algorithm for correcting curved filaments
+
| Review of single particles
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1988Bluemke_Pitch]]
+
| [[2002Schmid_Review]]
| Algorithm for correcting filaments with different helical pitches
+
| Review of single particles
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2006Wang_Pitch]]
+
| [[2004Henderson_Review]]
| Algorithm for correcting filaments with different helical pitches
+
| Review of electron microscopy
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Yang_Flexible]]
+
| [[2004Subramaniam_Review]]
| Algorithm for correcting filaments with flexible subunits
+
| Review of single particles
 
|-  
 
|-  
  
|}
+
| Paper
 +
| [[2005Steven_Review]]
 +
| Review of electron microscopy
 +
|-
  
=== Reconstruction ===
+
| Paper
 +
| [[2006Fernandez_Review]]
 +
| Review of electron microscopy
 +
|-
  
{|
+
| Book
 +
| [[2006Frank_book]]
 +
| Book covering all aspects of electron microscopy of single particles
 +
|-
  
 
| Paper
 
| Paper
| [[1952Cochran_Fourier]]
+
| [[2006Sorzano_Review]]
| Fourier Bessel transform of filamentous structures
+
| Review of optimization problems in electron microscopy
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1958Klug_Fourier]]
+
| [[2007Leschziner_Review]]
| Fourier Bessel decomposition of the projection images
+
| Review of 3D heterogeneity handling algorithms
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1970DeRosier_Rec]]
+
| [[2007Sorzano_Review]]
| Image processing steps towards 3D reconstruction
+
| Review of the image processing steps
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1992Morgan_Rec]]
+
| [[2008Fanelli_ImageFormation]]
| Image processing steps towards 3D reconstruction
+
| Review on the image formation model from the electron waves and open inverse-problems in Electron Tomography
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2005Wang_Iterative]]
+
| [[2008Fernandez_HPCReview]]
| Iterative Fourier-Bessel algorithm
+
| High performance computing in electron cryomicroscopy
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007Egelman_Iterative]]
+
| [[2008Jonic_Review]]
| Iterative real-space algorithm
+
| Comparison between electron tomography and single particles
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Desfosses_Spring]]
+
| [[2008Mueller_Review]]
| Helical processing with Spring
+
| Review of Electron microscopy
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Zhang_seam]]
+
| [[2008Taylor_Review]]
| Workflow for the detection of the lattice seam
+
| Review of Electron microscopy
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Rohou_Frealix]]
+
| [[2010DeRosier_Review]]
| Helical processing with Frealix
+
| Personal account of how 3DEM developed in the early days
 +
|-
 +
 
 +
| Chapter
 +
| [[2012Sorzano_Review]]
 +
| Review of single particle analysis using Xmipp
 +
|-
 +
 
 +
| Chapter
 +
| [[2012Devaux_Protocol]]
 +
| Protocols for performing single particle analysis
 +
|-
 +
 
 +
| Paper
 +
| [[2014Bai_Review]]
 +
| Recent advances in cryo-EM
 +
|-
 +
 
 +
| Paper
 +
| [[2015Carazo_Review]]
 +
| Review of the reconstruction process
 +
|-
 +
 
 +
| Paper
 +
| [[2015Cheng_Review]]
 +
| A primer to Single Particle Cryo-EM
 +
|-
 +
 
 +
| Paper
 +
| [[2015Cheng_Reviewb]]
 +
| Single Particle Cryo-EM at crystallographic resolution
 +
|-
 +
 
 +
| Paper
 +
| [[2015Elmlund_Review]]
 +
| Recent advances in cryo-EM
 +
|-
 +
 
 +
| Paper
 +
| [[2015Henderson_Review]]
 +
| Recent advances in cryo-EM
 +
|-
 +
 
 +
| Paper
 +
| [[2015Nogales_Review]]
 +
| Recent advances in cryo-EM
 +
|-
 +
 
 +
| Paper
 +
| [[2015Schroeder_Review]]
 +
| Review of advances in the electron microscope
 +
|-
 +
 
 +
| Paper
 +
| [[2015VanDenBedem_Integrative]]
 +
| Review of integrative structural biology
 +
|-
 +
 
 +
| Paper
 +
| [[2015Wu_Review]]
 +
| Review of advances in cryo-EM
 +
|-
 +
 
 +
| Paper
 +
| [[2016Carroni_CryoEM]]
 +
| Review of advances in Cryo-EM
 +
|-
 +
 
 +
| Paper
 +
| [[2016Egelman_CryoEM]]
 +
| Review of advances in Cryo-EM
 +
|-
 +
 
 +
| Paper
 +
| [[2016Eisenstein_CryoEM]]
 +
| News feature on the Method of the Year
 +
|-
 +
 
 +
| Paper
 +
| [[2016FernandezLeiro_Review]]
 +
| Review of EM
 +
|-
 +
 
 +
| Paper
 +
| [[2016Glaeser_HowGood]]
 +
| How good can cryo-EM become?
 +
|-
 +
 
 +
| Paper
 +
| [[2016Jonic_PseudoAtoms]]
 +
| Review of the applications of the use of pseudoatoms in EM
 +
|-
 +
 
 +
| Chapter
 +
| [[2016Mio_Review]]
 +
| Overview of the process to obtain EM reconstructions
 +
|-
 +
 
 +
| Paper
 +
| [[2016Jonic_Review]]
 +
| A review of computational ways to handle heterogeneity
 +
|-
 +
 
 +
| Paper
 +
| [[2016Nogales_Review]]
 +
| Review of advances in cryo-EM
 +
|-
 +
 
 +
| Paper
 +
| [[2016Subramaniam_Review]]
 +
| Why cryo-EM is now suitable for crystallographic journals
 +
|-
 +
 
 +
| Paper
 +
| [[2016Vinothkumar_Review]]
 +
| Historical review and current limitations
 +
|-
 +
 
 +
| Report
 +
| [[2017Brezinski_Nobel]]
 +
| Scientific background on the Nobel Prize in Chemistry 2017
 +
|-
 +
 
 +
| Paper
 +
| [[2017Cheng_review]]
 +
| Why CryoEM became so hot
 +
|-
 +
 
 +
| Paper
 +
| [[2017Danev_Review]]
 +
| Review of the use of phase plates in EM
 +
|-
 +
 
 +
| Paper
 +
| [[2017Elmlund_Review]]
 +
| Review of the main current difficulties of EM
 +
|-
 +
 
 +
| Paper
 +
| [[2017Frank_Review]]
 +
| Historical review of EM
 +
|-
 +
 
 +
| Paper
 +
| [[2017Frank_TimeResolved]]
 +
| Review of time-resolved of EM
 +
|-
 +
 
 +
| Paper
 +
| [[2017Jonic_Review]]
 +
| Review of computational methods to analyze conformational variability
 +
|-
 +
 
 +
| Paper
 +
| [[2017Merino_DrugEM]]
 +
| Applications of EM for drug design
 +
|-
 +
 
 +
| Paper
 +
| [[2017Rawson_Limitations]]
 +
| Limitations of EM for drug design
 +
|-
 +
 
 +
| Paper
 +
| [[2017Sorzano_FourierProperties]]
 +
| Review of statistical properties of resolution measures defined in Fourier space
 +
|-
 +
 
 +
| Paper
 +
| [[2017Sorzano_SurveyIterative]]
 +
| Survey of iterative reconstruction methods for EM
 +
|-
 +
 
 +
| Paper
 +
| [[2018Bruggeman_Crowdsourcing]]
 +
| Exploring crowdsourcing for EM image processing
 +
|-
 +
 
 +
| Paper
 +
| [[2018Cheng_Review]]
 +
| Review of EM and future ahead
 +
|-
 +
 
 +
| Paper
 +
| [[2018Cossio_ML]]
 +
| Review of Maximum Likelihood methods
 +
|-
 +
 
 +
| Paper
 +
| [[2018Grimes_Crystallography]]
 +
| Review of X-ray crystallography and its relationship to EM
 +
|-
 +
 
 +
| Paper
 +
| [[2018Murata_Review]]
 +
| Review of EM for structure dynamics
 +
|-
 +
 
 +
| Paper
 +
| [[2018Quentin_Biomedical]]
 +
| Review of EM as a tool for biomedical research
 +
|-
 +
 
 +
| Paper
 +
| [[2018Scapin_DrugDiscovery]]
 +
| Review of EM as a tool for drug discovery
 +
|-
 +
 
 +
| Paper
 +
| [[2018Vilas_ImageProcessing]]
 +
| Review of the recent developments in image processing for single particle analysis
 +
|-
 +
 
 +
| Paper
 +
| [[2018vonLoeffelholz_VPP]]
 +
| Comparison of Volta Phase Plate reconstructions close to focus and with defocus
 +
|-
 +
 
 +
| Paper
 +
| [[2018Eisenstein_DrugDesigners]]
 +
| Drug designers embrace cryo-EM
 +
|-
 +
 
 +
| Paper
 +
| [[2019Benjin_Review]]
 +
| Review of SPA
 +
|-
 +
 
 +
| Paper
 +
| [[2019Danev_Review]]
 +
| Review of future directions
 +
|-
 +
 
 +
| Paper
 +
| [[2019Lyumkis_Review]]
 +
| Challenges and reviews
 +
|-
 +
 
 +
| Paper
 +
| [[2019Sorzano_Review]]
 +
| Review of continuous heterogeneity biophysics
 +
|-
 +
 
 +
| Paper
 +
| [[2020Abriata_Review]]
 +
| Considerations of structure prediction and CryoEM
 +
|-
 +
 
 +
| Paper
 +
| [[2020Akbar_Review]]
 +
| Review of membrane protein reconstructions
 +
|-
 +
 
 +
| Paper
 +
| [[2020Bendory_Review]]
 +
| Review of image processing problems
 +
|-
 +
 
 +
| Paper
 +
| [[2020Dubach_Review]]
 +
| Review of resolution in X-ray crystallography and CryoEM
 +
|-
 +
 
 +
| TechReport
 +
| [[2020Lai_Statistics]]
 +
| Review of statistical properties of image alignment
 +
|-
 +
 
 +
| Paper
 +
| [[2020Hu_Quaternions]]
 +
| Review of the use of quaternions to describe rotations
 +
|-
 +
 
 +
| Paper
 +
| [[2020McCafferty_Review]]
 +
| Review of SPA and Mass Spectroscopy
 +
|-
 +
 
 +
| Paper
 +
| [[2020Seffernick_Hybrid]]
 +
| Review of hybrid (computational and experimental) methods to get protein structure
 +
|-
 +
 
 +
| Paper
 +
| [[2020Nakane_Atomic]]
 +
| Single-particle cryo-EM at atomic resolution
 +
|-
 +
 
 +
| Paper
 +
| [[2020Vilas_Review]]
 +
| Review of local resolution
 +
|-
 +
 
 +
| Paper
 +
| [[2020Wu_Review]]
 +
| Review of current limitations, with special emphasis on protein size
 +
|-
 +
 
 +
| Paper
 +
| [[2020Singer_Sigworth_Review]]
 +
| Review of single particle analysis
 +
|-
 +
 
 +
| Paper
 +
| [[2021Bai_Review]]
 +
| Review of breakthroughs leading to atomic resolution
 +
|-
 +
 
 +
| Paper
 +
| [[2021DImprima_Review]]
 +
| Review of sample preparation for single particle analysis
 +
|-
 +
 
 +
| Paper
 +
| [[2021Lander_Review]]
 +
| Review of focused analysis in SPA
 +
|-
 +
 
 +
| Paper
 +
| [[2021Raimondi_Review]]
 +
| General review of SPA
 +
|-
 +
 
 +
| Paper
 +
| [[2022Beton_Fitting]]
 +
| Review of fitting in SPA
 +
|-
 +
 
 +
| Paper
 +
| [[2022Burley_PDB]]
 +
| Review of cryoEM derived structures at PDB
 +
|-
 +
 
 +
| Paper
 +
| [[2022Caldraft_Tilt]]
 +
| Review of applications of tilt pairs in SPA
 +
|-
 +
 
 +
| Paper
 +
| [[2022Donnat_GAN]]
 +
| Review of Generative modelling with neural networks
 +
|-
 +
 
 +
| Paper
 +
| [[2022Guaita_Review]]
 +
| Recent advances and current trends in cryo-electron microscopy
 +
|-
 +
 
 +
| Paper
 +
| [[2022Jones_Comment]]
 +
| Comment on the impact of AlphaFold and next challenges ahead
 +
|-
 +
 
 +
| Paper
 +
| [[2022Namba_Review]]
 +
| Review of the current state of SPA
 +
|-
 +
 
 +
| Paper
 +
| [[2022Ourmazd_Comment]]
 +
| Comment on the impact of AlphaFold and next challenges ahead
 +
|-
 +
 
 +
| Paper
 +
| [[2022Palmer_Local]]
 +
| Review of local methods in CryoEM
 +
|-
 +
 
 +
| Paper
 +
| [[2022Sorzano_1000]]
 +
| CryoEM is the field of 1000+ methods
 +
|-
 +
 
 +
| Paper
 +
| [[2022Subramaniam_Comment]]
 +
| Comment on the impact of AlphaFold and next challenges ahead
 +
|-
 +
 
 +
| Paper
 +
| [[2022Treder_DL]]
 +
| Review of Deep Learning applications in CryoEM
 +
|-
 +
 
 +
| Paper
 +
| [[2022Vant_MD]]
 +
| Review of Molecular Dynamics analysis of CryoEM maps
 +
|-
 +
 
 +
| Paper
 +
| [[2023Amann_TimeResolved]]
 +
| Review of time-resolved cryoEM
 +
|-
 +
 
 +
| Paper
 +
| [[2023Bai_Challenges]]
 +
| Challenges and opportunities in structure determination
 +
|-
 +
 
 +
| Paper
 +
| [[2023Liu_AWI]]
 +
| Review of the Air-Water Interface
 +
|-
 +
 
 +
| Paper
 +
| [[2023Lucas_Structureome]]
 +
| Review of the localization of proteins and complexes in their cellular context
 +
|-
 +
 
 +
| Paper
 +
| [[2023Miyashita_MD]]
 +
| Review of the use of molecular dynamics in atomic modelling
 +
|-
 +
 
 +
| Paper
 +
| [[2023Si_DeNovo]]
 +
| Review of the de-novo atomic modelling
 +
|-
 +
 
 +
| Paper
 +
| [[2023Tang_Conformational]]
 +
| Review of conformational heterogeneity and probability distributions
 +
|-
 +
 
 +
| Paper
 +
| [[2023Toader_Heterogeneity]]
 +
| Review of continuous heterogeneity
 +
|-
 +
 
 +
|}
 +
 
 +
=== Software ===
 +
 
 +
{|
 +
 
 +
| Paper
 +
| [[1996Frank_Spider]]
 +
| Spider
 +
|-
 +
 
 +
| Paper
 +
| [[1996VanHeel_Imagic]]
 +
| Imagic
 +
|-
 +
 
 +
| Paper
 +
| [[1999Lutdke_Eman]]
 +
| Eman
 +
|-
 +
 
 +
| Paper
 +
| [[2004Sorzano_Xmipp]]
 +
| Xmipp
 +
|-
 +
 
 +
| Paper
 +
| [[2007Baldwin_AngularTransformations]]
 +
| The Transform Class in SPARX and EMAN2
 +
|-
 +
 
 +
| Paper
 +
| [[2007Heymann_Bsoft]]
 +
| Bsoft
 +
|-
 +
 
 +
| Paper
 +
| [[2007Grigorieff_Frealign]]
 +
| Frealign
 +
|-
 +
 
 +
| Paper
 +
| [[2008Scheres_XmippProtocols]]
 +
| Xmipp Protocols
 +
|-
 +
 
 +
| Paper
 +
| [[2008Shaikh_SpiderProtocols]]
 +
| Spider Protocols
 +
|-
 +
 
 +
| Paper
 +
| [[2012Wriggers_SitusConventions]]
 +
| Conventions and workflows in Situs
 +
|-
 +
 
 +
| Paper
 +
| [[2013DeLaRosa_Xmipp30]]
 +
| Xmipp 3.0
 +
|-
 +
 
 +
| Paper
 +
| [[2015Cianfrocco_Cloud]]
 +
| Software execution in the cloud
 +
|-
 +
 
 +
| Paper
 +
| [[2015Cheng_MRC2014]]
 +
| Extensions to MRC file format
 +
|-
 +
 
 +
| Paper
 +
| [[2013DeLaRosa_Scipion]]
 +
| Scipion
 +
|-
 +
 
 +
| Paper
 +
| [[2016Scheres_Relion]]
 +
| Tutorial on the use of Relion
 +
|-
 +
 
 +
| Paper
 +
| [[2016Grigorieff_Frealign]]
 +
| Tutorial on the use of Frealign
 +
|-
 +
 
 +
| Paper
 +
| [[2017Moriya_Sphire]]
 +
| Tutorial on the use of Sphire
 +
|-
 +
 
 +
| Paper
 +
| [[2018Bell_EMAN2]]
 +
| New tools in EMAN2
 +
|-
 +
 
 +
| Paper
 +
| [[2018Cianfrocco_cloud]]
 +
| CryoEM Cloud Tools
 +
|-
 +
 
 +
| Paper
 +
| [[2018Grant_cisTEM]]
 +
| cisTEM
 +
|-
 +
 
 +
| Paper
 +
| [[2018McLeod_MRCZ]]
 +
| MRC Compression format
 +
|-
 +
 
 +
| Paper
 +
| [[2018Zivanov_Relion3]]
 +
| Relion 3
 +
|-
 +
 
 +
| Paper
 +
| [[2020Caesar_Simple3]]
 +
| Simple 3
 +
|-
 +
 
 +
| Paper
 +
| [[2021Baldwin_SCF]]
 +
| Visualizer of the Sampling Compensation Factor
 +
|-
 +
 
 +
| Paper
 +
| [[2021Jimenez_Scipion]]
 +
| Scipion workflow example for image processing
 +
|-
 +
 
 +
| Paper
 +
| [[2021Kimanius_Relion4]]
 +
| Changes in Relion 4.0
 +
|-
 +
 
 +
| Paper
 +
| [[2021Maji_BlackBox]]
 +
| Exploration of image processing concepts
 +
|-
 +
 
 +
| Paper
 +
| [[2021Sharov_Relion]]
 +
| Use of Relion within Scipion
 +
|-
 +
 
 +
| Paper
 +
| [[2021Sorzano_Scipion]]
 +
| Use of Scipion as a way to compare the results of multiple methods
 +
|-
 +
 
 +
| Paper
 +
| [[2021Strelak_Xmipp]]
 +
| Advances in Xmipp
 +
|-
 +
 
 +
| Paper
 +
| [[2022DiIorio_Multiple]]
 +
| A Robust Single-Particle Cryo-Electron Microscopy (cryo-EM) Processing Workflow with cryoSPARC, RELION, and Scipion.
 +
|-
 +
 
 +
| Paper
 +
| [[2022Fluty_Precision]]
 +
| Precision requirements and data compression
 +
|-
 +
 
 +
| Paper
 +
| [[2022Harastani_ContinuousFlex]]
 +
| ContinuousFlex: Software for continuous heterogeneity analysis in cryo-EM and cryo-ET
 +
|-
 +
 
 +
| Paper
 +
| [[2023Cheng_AutoEMage]]
 +
| AutoEMage: a system for processing in streaming (SPA)
 +
|-
 +
 
 +
| Paper
 +
| [[2023Conesa_Scipion3]]
 +
| Scipion3: A workflow engine for cryoEM
 +
|-
 +
 
 +
| Paper
 +
| [[2023Krieger_ScipionPrody]]
 +
| Scipion-EM-Prody: Interface between Scipion and Prody (Structural Analysis)
 +
|-
 +
 
 +
| Paper
 +
| [[2023Short_MRC2020]]
 +
| MRC2020: improvements to Ximdisp and the MRC image-processing programs
 +
|-
 +
 
 +
| Paper
 +
| [[2024Vuillemot_MDSPACE]]
 +
| MDSpace and MDTomo to analyze continuous heterogeneity
 +
|-
 +
 
 +
|}
 +
 
 +
== Electron tomography ==
 +
 
 +
=== Image preprocessing ===
 +
 
 +
{|
 +
 
 +
| Paper
 +
| [[2015Yan_thickness]]
 +
| Determination of thickness, tilt and electron mean free path
 +
|-
 +
 
 +
| Paper
 +
| [[2018Wu_contrast]]
 +
| Contrast enhancement to improve alignability
 +
|-
 +
 
 +
|}
 +
 
 +
=== Image alignment ===
 +
 
 +
{|
 +
 
 +
| Paper
 +
| [[1982Guckenberger_commonOrigin]]
 +
| Determination of a common origin in the micrographs of titl series in three-dimensional electron microscopy
 +
|-
 +
 
 +
| Paper
 +
| [[1992Lawrence_leastSquares]]
 +
| Least squares solution of the alignment problem
 +
|-
 +
 
 +
| Paper
 +
| [[1995Penczek_dual]]
 +
| Dual tilt alignment
 +
|-
 +
 
 +
| Paper
 +
| [[1996Owen_alignmentQuality]]
 +
| Automatic alignment without fiducial markers and evaluation of alignment quality
 +
|-
 +
 
 +
| Paper
 +
| [[1998Grimm_normalization]]
 +
| Discussion of several gray level normalization methods for electron tomography
 +
|-
 +
 
 +
| Paper
 +
| [[2001Brandt_Automatic1]]
 +
| Automatic alignment without fiducial markers
 +
|-
 +
 
 +
| Paper
 +
| [[2001Brandt_Automatic2]]
 +
| Automatic alignment with fiducial markers
 +
|-
 +
 
 +
| Paper
 +
| [[2006Winkler_alignment]]
 +
| Marker-free alignment and refinement
 +
|-
 +
 
 +
| Paper
 +
| [[2006Castano_alignment]]
 +
| Alignment with non-perpendicularity
 +
|-
 +
 
 +
| Paper
 +
| [[2007Castano_alignment]]
 +
| Fiducial-less alignment of cryo-sections
 +
|-
 +
 
 +
| Paper
 +
| [[2009Sorzano_alignment]]
 +
| Marker-free alignment and refinement
 +
|-
 +
 
 +
| Paper
 +
| [[2010Cantele_dualAlignment]]
 +
| Alignment of dual series
 +
|-
 +
 
 +
| Paper
 +
| [[2014Tomonaga_Automatic]]
 +
| Automatic alignment of tilt series using the projection themselves
 +
|-
 +
 
 +
| Paper
 +
| [[2014Han_Automatic]]
 +
| Automatic alignment of tilt series using SIFT features
 +
|-
 +
 
 +
| Paper
 +
| [[2015Han_Automatic]]
 +
| Automatic alignment of tilt series using fiducials
 +
|-
 +
 
 +
| Paper
 +
| [[2017Mastronarde_Automatic]]
 +
| Automatic alignment and reconstruction of tilt series in IMOD
 +
|-
 +
 
 +
| Paper
 +
| [[2018Fernadez_Beam]]
 +
| Image alignment considering beam induced motion
 +
|-
 +
 
 +
| Paper
 +
| [[2018Han_Fast]]
 +
| Automatic alignment using fiducial markers
 +
|-
 +
 
 +
| Paper
 +
| [[2019Fernandez_residual]]
 +
| Alignment of tilt series using residual interpolation
 +
|-
 +
 
 +
| Paper
 +
| [[2019Han_Dual]]
 +
| Automatic alignment using fiducial markers in dual tilt series
 +
|-
 +
 
 +
| Paper
 +
| [[2020Sorzano_automatic]]
 +
| Automatic alignment considering several geometrical distortions
 +
|-
 +
 
 +
| Paper
 +
| [[2021Han_LocalConstraints]]
 +
| Automatic alignment considering local constraints
 +
|-
 +
 
 +
| Paper
 +
| [[2022Zheng_Aretomo]]
 +
| Automatic alignment based on projection matching
 +
|-
 +
 
 +
|}
 +
 
 +
=== CTF estimation and restoration ===
 +
 
 +
{|
 +
 
 +
| Paper
 +
| [[2003Winkler_CTF]]
 +
| Focus gradient correction in electron tomography
 +
|-
 +
 
 +
| Paper
 +
| [[2006Fernandez_CTF]]
 +
| CTF determination and correction in electron tomography
 +
|-
 +
 
 +
 
 +
| Paper
 +
| [[2009Zanetti_CTF]]
 +
| CTF determination and correction in electron tomography
 +
|-
 +
 
 +
 
 +
| Paper
 +
| [[2009Xiong_CTF]]
 +
| CTF determination and correction for low dose tomographic tilt series
 +
|-
 +
 
 +
| Paper
 +
| [[2012Eibauer_CTF]]
 +
| CTF determination and correction
 +
|-
 +
 
 +
| Paper
 +
| [[2015Bharat_CTFCorrectedSubtomogramAveraging]]
 +
| Subtomogram averaging with CTF correction using a Bayesian prior
 +
|-
 +
 
 +
| Paper
 +
| [[2017Turonova_3DCTF]]
 +
| 3D CTF Correction
 +
|-
 +
 
 +
| Paper
 +
| [[2017Kunz_3DCTF]]
 +
| 3D CTF Correction
 +
|-
 +
 
 +
|}
 +
 
 +
=== 3D reconstruction ===
 +
 
 +
{|
 +
 
 +
| Paper
 +
| [[1972Gilbert_SIRT]]
 +
| Simultaneous Iterative Reconstruction Technique (SIRT)
 +
|-
 +
 
 +
| Paper
 +
| [[1973Herman_ART]]
 +
| Algebraic Reconstruction Technique (ART)
 +
|-
 +
 
 +
| Paper
 +
| [[1984Andersen_SART]]
 +
| Simultaneous Algebraic Reconstruction Technique (SART)
 +
|-
 +
 
 +
| Paper
 +
| [[1992Radermacher_WBP]]
 +
| Weighted Backprojection in electron tomography
 +
|-
 +
 
 +
| Paper
 +
| [[1997Marabini_reconstruction]]
 +
| Iterative reconstruction in electron tomography
 +
|-
 +
 
 +
| Paper
 +
| [[2002Fernandez_reconstruction]]
 +
| Iterative reconstruction in electron tomography
 +
|-
 +
 
 +
| Paper
 +
| [[2007Radermacher_WBP]]
 +
| Weighted Backprojection in electron tomography
 +
|-
 +
 
 +
| Paper
 +
| [[2008Fernandez_CARP]]
 +
| Component Averaged Row Projections (CARP)
 +
|-
 +
 
 +
| Paper
 +
| [[2010Xu_Long]]
 +
| Iterative reconstructions with long object correction and GPU implementation
 +
|-
 +
 
 +
| Paper
 +
| [[2012Herman General Superiorization]]
 +
| Superiorization: an optimization heuristic for medical physics
 +
|-
 +
 
 +
| Paper
 +
| [[2012Zhang_IPET_FETR]]
 +
| IPET and FETR, a reconstruction algorithm for a single particle structure determination without any averaging
 +
|-
 +
 
 +
| Paper
 +
| [[2013Goris_SIRT_TV_DART]]
 +
| Combination of SIRT, Total Variation and Discrete ART to reconstruct and segment at the same time
 +
|-
 +
 
 +
| Paper
 +
| [[2013Briegel A_Challenge]]
 +
| The challenge of determining handedness in electron tomography and the use of DNA origami gold nanoparticle helices as molecular standards
 +
|-
 +
 
 +
| Paper
 +
| [[2013Messaoudi_EnergyFiltered]]
 +
| 3D Reconstruction of Energy-Filtered TEM
 +
|-
 +
 
 +
| Paper
 +
| [[2014Paavolainen_Missing]]
 +
| Compensation of the missing wedge
 +
|-
 +
 
 +
| Paper
 +
| [[2015Venkatakrishnan_MBIR]]
 +
| 3D Reconstruction with priors
 +
|-
 +
 
 +
| Paper
 +
| [[2016Deng_ICON]]
 +
| 3D Reconstruction with missing information restoration
 +
|-
 +
 
 +
| Paper
 +
| [[2016Guay_Compressed]]
 +
| 3D Reconstruction using compressed sensing
 +
|-
 +
 
 +
| Paper
 +
| [[2016Turonova_Artifacts]]
 +
| Artifacts observed during 3D reconstruction
 +
|-
 +
 
 +
| Paper
 +
| [[2019Yan_MBIR]]
 +
| 3D Reconstruction with priors and demonstration of its use in biological samples
 +
|-
 +
 
 +
| Paper
 +
| [[2020Sanchez_Hybrid]]
 +
| 3D reconstruction with a special acquisition and alignment scheme
 +
|-
 +
 
 +
| Paper
 +
| [[2020Song_Tygress]]
 +
| 3D reconstruction with a special acquisition and alignment scheme
 +
|-
 +
 
 +
| Paper
 +
| [[2021Fernandez_TomoAlign]]
 +
| 3D reconstruction with sample motion and CTF correction
 +
|-
 +
 
 +
| Paper
 +
| [[2021Geng_Nudim]]
 +
| Non-uniform FFT reconstruction and total variation to fill the missing wedge
 +
|-
 +
 
 +
|}
 +
 
 +
=== Noise reduction ===
 +
{|
 +
 
 +
| Paper
 +
| [[2001Frangakis_NAD]]
 +
| Noise reduction with Nonlinear Anisotropic Diffusion
 +
|-
 +
 
 +
| Paper
 +
| [[2003Fernandez_AND]]
 +
| Anisotropic nonlinear diffusion for electron tomography
 +
|-
 +
 
 +
| Paper
 +
| [[2003Jiang_Bilateral]]
 +
| Bilateral denoising filter in electron microscopy
 +
|-
 +
 
 +
| Paper
 +
| [[2005Fernandez_AND]]
 +
| Anisotropic nonlinear denoising in electron tomography
 +
|-
 +
 
 +
| Paper
 +
| [[2007Heide_median]]
 +
| Iterative median filtering in electron tomography
 +
|-
 +
 
 +
| Paper
 +
| [[2007Fernandez_autAND]]
 +
| Anisotropic nonlinear diffusion with automated parameter tuning
 +
|-
 +
 
 +
| Paper
 +
| [[2009Fernandez_Beltrami]]
 +
| Nonlinear filtering based on Beltrami flow
 +
|-
 +
 +
| Paper
 +
| [[2010Bilbao_MeanShift]]
 +
| Mean Shift Filtering
 +
|-
 +
 
 +
| Paper
 +
| [[2014Kovacik_wedgeArtefacts]]
 +
| Removal of wedge artefacts
 +
|-
 +
 
 +
| Paper
 +
| [[2014Maiorca_beadArtefacts]]
 +
| Removal of gold bead artefacts
 +
|-
 +
 
 +
| Paper
 +
| [[2018Trampert_Inpainting]]
 +
| Removal of the missing wedge by inpainting
 +
|-
 +
 
 +
| Paper
 +
| [[2018Moreno_TomoEED]]
 +
| Fast Anisotropic Diffusion
 +
|-
 +
 
 +
| Paper
 +
| [[2018Wu_Enhancement]]
 +
| Enhancing the image contrast of electron tomography
 +
|-
 +
 
 +
| Paper
 +
| [[2022Liu_Isonet]]
 +
| Isotropic reconstructions using deep learning
 +
|-
 +
 
 +
|}
 +
 
 +
=== Segmentation ===
 +
 
 +
{|
 +
 
 +
| Paper
 +
| [[2002Frangakis_Eigenanalysis]]
 +
| Segmentation using eigenvector analysis.
 +
|-
 +
 
 +
| Paper
 +
| [[2002Volkmann_Watershed]]
 +
| Segmentation using watershed transform.
 +
|-
 +
 
 +
| Paper
 +
| [[2003Bajaj_BoundarySegmentation]]
 +
| Segmentation based on fast marching.
 +
|-
 +
 
 +
| Paper
 +
| [[2005Cyrklaff_Thresholding]]
 +
| Segmentation using optimal thresholding.
 +
|-
 +
 
 +
| Paper
 +
| [[2007Lebbink_TemplateMatching]]
 +
| Segmentation using template matching.
 +
|-
 +
 
 +
| Paper
 +
| [[2007Sandberg_OrientationFields]]
 +
| Segmentation using orientation fields.
 +
|-
 +
 
 +
| Paper
 +
| [[2007Sandberg_SegmentationReview]]
 +
| Review on segmentation in electron tomography.
 +
|-
 +
 
 +
| Paper
 +
| [[2008Garduno_FuzzySegmentation]]
 +
| Segmentation using fuzzy set theory principles.
 +
|-
 +
 
 +
| Paper
 +
| [[2009Lebbink_TemplateMatching2]]
 +
| Segmentation using template matching.
 +
|-
 +
 
 +
| Paper
 +
| [[2012RubbiyaAli_EdgeDetection]]
 +
| Parameter-Free Segmentation of Macromolecular Structures.
 +
|-
 +
 
 +
| Conference
 +
| [[2015Xu_TemplateMatching]]
 +
| Detection of macromolecular complexes with a reduced representation of the templates.
 +
|-
 +
 
 +
| Paper
 +
| [[2017Ali_RAZA]]
 +
| Automated segmentation of tomograms
 +
|-
 +
 
 +
| Paper
 +
| [[2017Chen_Annotation]]
 +
| Automated annotation of tomograms
 +
|-
 +
 
 +
| Paper
 +
| [[2017Tasel_ActiveContours]]
 +
| Segmentation with active contours
 +
|-
 +
 
 +
| Paper
 +
| [[2017Xu_DeepLearning]]
 +
| Finding proteins in tomograms using deep learning
 +
|-
 +
 
 +
| Paper
 +
| [[2018Zeng_DeepLearning]]
 +
| Mining features in Electron Tomography by deep learning
 +
|-
 +
 
 +
| Paper
 +
| [[2020Salfer_PyCurv]]
 +
| Curvature analysis of segmented tomograms
 +
|-
 +
 
 +
| Paper
 +
| [[2021Dimchev_filaments]]
 +
| Segmentation of filaments in tomograms
 +
|-
 +
 
 +
| Paper
 +
| [[2022Frangakis_Curvature]]
 +
| Use of mean curvature for segmentation and visualization of tomograms
 +
|-
 +
 
 +
| Paper
 +
| [[2022Lamm_MemBrain]]
 +
| Membrane segmentation using deep learning
 +
|-
 +
 
 +
| Paper
 +
| [[2023Zeng_AITOM]]
 +
| Structural pattern mining by unsupervised deep iterative subtomogram clustering
 +
|-
 +
 
 +
|}
 +
 
 +
=== Resolution ===
 +
{|
 +
 
 +
| Paper
 +
| [[2005Cardone_Resolution]]
 +
| Resolution criterion for electron tomography
 +
|-
 +
 
 +
| Chapter
 +
| [[2007Penczek_Resolution]]
 +
| Review of resolution criteria for electron tomography
 +
|-
 +
 
 +
| Paper
 +
| [[2015Diebolder_ConicalFSC]]
 +
| Conical Fourier Shell Correlation
 +
|-
 +
 
 +
| Paper
 +
| [[2020Vilas_Monotomo]]
 +
| Resolution determination in tomograms
 +
|-
 +
 
 +
|}
 +
 
 +
=== Subtomogram analysis ===
 +
 
 +
{|
 +
 
 +
| Paper
 +
| [[2000Bohm_Template]]
 +
| Macromolecule finding by template matching
 +
|-
 +
 
 +
| Paper
 +
| [[2002Frangakis_Template]]
 +
| Macromolecule finding by template matching
 +
|-
 +
 
 +
| Paper
 +
| [[2006Nickell_Review]]
 +
| Review of macromolecule finding by template matching (Visual Proteomics)
 +
|-
 +
 
 +
| Paper
 +
| [[2007Best_Review]]
 +
| Review of Localization of Protein Complexes by Pattern Recognition
 +
|-
 +
 
 +
| Paper
 +
| [[2007Forster_Review]]
 +
| Review of structure determination by subtomogram averaging
 +
|-
 +
 
 +
| Paper
 +
| [[2008Forster_Classification]]
 +
| Classification of subtomograms using constrained correlation
 +
|-
 +
 
 +
| Paper
 +
| [[2008Bartesaghi_Classification]]
 +
| Classification and averaging of subtomograms
 +
|-
 +
 
 +
| Paper
 +
| [[2008Schmid_Averaging]]
 +
| Alignment and averaging of subtomograms
 +
|-
 +
 
 +
| Paper
 +
| [[2010Amat_Averaging]]
 +
| Alignment and averaging of subtomograms exploiting thresholding in Fourier space
 +
|-
 +
 
 +
| Paper
 +
| [[2010Yu_PPCA]]
 +
| Probabilistic PCA for volume classification
 +
|-
 +
 
 +
| Paper
 +
| [[2013Chen_Averaging]]
 +
| Fast alignment of subtomograms using spherical harmonics
 +
|-
 +
 
 +
| Paper
 +
| [[2013Kuybeda_Averaging]]
 +
| Alignment and averaging of subtomograms using the nuclear norm of the cluster
 +
|-
 +
 
 +
| Paper
 +
| [[2013Shatsky_Averaging]]
 +
| Alignment and averaging of subtomograms with constrained cross-correlation
 +
|-
 +
 
 +
| Paper
 +
| [[2013Yu_Projection]]
 +
| Subtomogram averaging by aligning their projections
 +
|-
 +
 
 +
| Paper
 +
| [[2014Chen_Autofocus]]
 +
| Subtomogram averaging and classification with special attention to differences
 +
|-
 +
 
 +
| Paper
 +
| [[2014Yu_ReferenceBias]]
 +
| Scoring the reference bias
 +
|-
 +
 
 +
| Paper
 +
| [[2014Voortman_LimitingFactors]]
 +
| Limiting factors of subtomogram averaging
 +
|-
 +
 
 +
| Paper
 +
| [[2015Bharat_CTFCorrectedSubtomogramAveraging]]
 +
| Subtomogram averaging with CTF correction using a Bayesian prior
 +
|-
 +
 
 +
| Paper
 +
| [[2015Yu_ReferenceBias]]
 +
| Scoring the reference bias
 +
|-
 +
 
 +
| Paper
 +
| [[2016Bharat_Relion]]
 +
| Subtomogram averaging with Relion
 +
|-
 +
 
 +
| Paper
 +
| [[2016Song_MatrixNorm]]
 +
| Matrix norm minimization for tomographic reconstruction and alignment
 +
|-
 +
 
 +
| Paper
 +
| [[2017Castano_ParticlePicking]]
 +
| Particle picking in tomograms for subtomogram averaging
 +
|-
 +
 
 +
| Paper
 +
| [[2017Frazier_Tomominer]]
 +
| TomoMiner a software platform for large-scale subtomogram analysis
 +
|-
 +
 
 +
| Paper
 +
| [[2018Himes_emClarity]]
 +
| emClarity for subtomogram averaging
 +
|-
 +
 
 +
| Paper
 +
| [[2018Zhao_Fast]]
 +
| Fast alignment and maximum likelihod for subtomogram averaging
 +
|-
 +
 
 +
| Paper
 +
| [[2019Fokine_Enhancement]]
 +
| Subtomogram enhancement through the locked self-rotation
 +
|-
 +
 
 +
| Paper
 +
| [[2019Han_Constrained]]
 +
| Constrained reconstruction to enhance resolution
 +
|-
 +
 
 +
| Paper
 +
| [[2020Basanta_workflow]]
 +
| Workflow for subtomogram averaging
 +
|-
 +
 
 +
| Paper
 +
| [[2021Cheng_Native]]
 +
| 3D reconstruction only with 0-tilt images
 +
|-
 +
 
 +
| Paper
 +
| [[2021Du_Active]]
 +
| Active learning to reduce the need of annotated samples
 +
|-
 +
 
 +
| Paper
 +
| [[2021Harastani_HEMNMA3D]]
 +
| HEMNMA-3D: Continuous flexibility analysis of subtomograms using normal modes
 +
|-
 +
 
 +
| Paper
 +
| [[2021Lucas_Cistem]]
 +
| Identification of particles in tomograms using Cistem
 +
|-
 +
 
 +
| Paper
 +
| [[2021Scaramuzza_Dynamo]]
 +
| Subtomogram averaging workflow using Dynamo
 +
|-
 +
 
 +
| Paper
 +
| [[2021Singla_Measures]]
 +
| Analysis of different measures to analyze subtomogram clusters
 +
|-
 +
 
 +
| Paper
 +
| [[2021Tegunov_M]]
 +
| Image processing workflow for tilt-series (introduction of M)
 +
|-
 +
 
 +
| Conference
 +
| [[2021Zeng_OpenSet]]
 +
| Unsupervised open set classification using deep learning
 +
|-
 +
 
 +
| Paper
 +
| [[2022Boehning_CompressedSensing]]
 +
| Compressed sensing for subtomogram averaging
 +
|-
 +
 
 +
| Paper
 +
| [[2022Hao_Picking]]
 +
| Detection of molecules in tomograms
 +
|-
 +
 
 +
| Paper
 +
| [[2022Harastani_TomoFlow]]
 +
| TomoFlow: Continuous flexibility analysis of subtomograms using 3D dense optical flow
 +
|-
 +
 
 +
| Paper
 +
| [[2022Metskas_STA]]
 +
| Tricks for a better Subtomogram Averaging
 +
|-
 +
 
 +
| Paper
 +
| [[2022Moebel_unsupervised]]
 +
| Unsupervised classification of subtomograms using neural networks
 +
|-
 +
 
 +
| Paper
 +
| [[2022Peters_Feature]]
 +
| Feature guided, focused 3D signal permutation for STA
 +
|-
 +
 
 +
| Paper
 +
| [[2023Balyschew_TomoBEAR]]
 +
| TomoBEAR: tilt series alignment, reconstruction and subtomogram averaging
 +
|-
 +
 
 +
| Paper
 +
| [[2023Chaillet_Extensive]]
 +
| Extensive angular sampling for picking in tomograms
 +
|-
 +
 
 +
| Paper
 +
| [[2023Cheng_GisSPA]]
 +
| Detection of protein targets in 0-tilt images
 +
|-
 +
 
 +
| Paper
 +
| [[2023Genthe_PickYolo]]
 +
| Subtomogram picking in tomograms
 +
|-
 +
 
 +
|}
 +
 
 +
=== Single particle tomography ===
 +
 
 +
{|
 +
 
 +
| Paper
 +
| [[2012Bartesaghi_Constrained]]
 +
| 3D reconstruction by imposing geometrical constraints
 +
|-
 +
 
 +
| Paper
 +
| [[2012Zhang_IPET_FETR]]
 +
| FETR: a focused reconstruction algorithm for a single molecule 3D structure determination without any averaging
 +
|-
 +
 
 +
| Paper
 +
| [[2015Galaz_SingleParticleTomography]]
 +
| Set of tools for Single Particle Tomography in EMAN2
 +
|-
 +
 
 +
| Paper
 +
| [[2016Galaz_SingleParticleTomography]]
 +
| Alignment algorithms and CTF correction
 +
|-
 +
 
 +
|}
 +
 
 +
=== Missing-wedge correction ===
 +
 
 +
{|
 +
 
 +
| Paper
 +
| [[2020Kovacs_Filaments]]
 +
| Removal of missing wedge artifacts in filamentous tomograms
 +
|-
 +
 
 +
| Paper
 +
| [[2020Moebel_MCMC]]
 +
| Missing wedge correction with Monte Carlo Markov Chains
 +
|-
 +
 
 +
| Paper
 +
| [[2020Zhai_LoTTor]]
 +
| Missing-wedge correction by LoTTor ('''Lo'''w-'''T'''ilt '''T'''omographic 3D '''R'''econstruction for a single molecule structure)
 +
|-
 +
 
 +
| Paper
 +
| [[2023Zhang_REST]]
 +
| Missing-wedge correction with neural networks
 +
|-
 +
 
 +
|}
 +
 
 +
=== Molecular 3D dynamics  ===
 +
 
 +
{|
 +
 
 +
| Paper
 +
| [[2015Zhang_IPET]]
 +
| 3D Structural Dynamics of Macromolecules by individual-particle structures without averaging
 +
|-
 +
 
 +
| Paper
 +
| [[2023Vuillemot_MDTOMO]]
 +
| 3D Structural Dynamics of using molecular dynamics and normal modes
 +
|-
 +
 
 +
|}
 +
 
 +
=== Books and reviews ===
 +
 
 +
{|
 +
 
 +
| Paper
 +
| [[2000Baumeister_Review]]
 +
| Review of electron tomography
 +
|-
 +
 
 +
| Paper
 +
| [[2003Koster_Review]]
 +
| Review of electron tomography
 +
|-
 +
 
 +
| Paper
 +
| [[2003Sali_Review]]
 +
| Review of electron tomography
 +
|-
 +
 
 +
| Paper
 +
| [[2004Henderson_Review]]
 +
| Review of electron microscopy
 +
|-
 +
 
 +
| Paper
 +
| [[2005Lucic_Review]]
 +
| Review of electron tomography
 +
|-
 +
 
 +
| Paper
 +
| [[2006Fernandez_Review]]
 +
| Review of electron microscopy
 +
|-
 +
 
 +
| Book
 +
| [[2006Frank_TomoBook]]
 +
| Electron Tomography
 +
|-
 +
 
 +
| Book
 +
| [[2007McIntosh_Book]]
 +
| Cellular Electron Microscopy
 +
|-
 +
 
 +
| Paper
 +
| [[2007Sorzano_Review]]
 +
| Review of the image processing steps
 +
|-
 +
 
 +
| Paper
 +
| [[2008Fanelli_ImageFormation]]
 +
| Review on the image formation model from the electron waves and open inverse-problems
 +
|-
 +
 
 +
| Paper
 +
| [[2008Fernandez_HPCReview]]
 +
| High performance computing in electron cryomicroscopy
 +
|-
 +
 
 +
| Paper
 +
| [[2008Jonic_Review]]
 +
| Comparison between electron tomography and single particles
 +
|-
 +
 
 +
| Paper
 +
| [[2012Kudryashev_Review]]
 +
| Review of subtomogram averaging
 +
|-
 +
 
 +
| Paper
 +
| [[2013Briggs_Review]]
 +
| Review of subtomogram averaging
 +
|-
 +
 
 +
| Paper
 +
| [[2016Beck_Review]]
 +
| Review of molecular sociology
 +
|-
 +
 
 +
| Paper
 +
| [[2016Ercius_Review]]
 +
| Electron tomography for hard and soft materials research
 +
|-
 +
 
 +
| Paper
 +
| [[2017Galaz_Review]]
 +
| Review of single particle tomography
 +
|-
 +
 
 +
| Paper
 +
| [[2017Plitzko_Review]]
 +
| Review of electron tomography, FRET and FIB milling
 +
|-
 +
 
 +
| Paper
 +
| [[2019Schur_Review]]
 +
| Review of electron tomography and subtomogram averaging
 +
|-
 +
 
 +
| Paper
 +
| [[2021Frangakis_Review]]
 +
| Review of tomogram denoising in electron tomography
 +
|-
 +
 
 +
| Paper
 +
| [[2022Forster_Review]]
 +
| Review of subtomogram averaging
 +
|-
 +
 
 +
| Paper
 +
| [[2022Liedtke_Review]]
 +
| Review of electron tomography in bacterial cell biology
 +
|-
 +
 
 +
| Paper
 +
| [[2022Liu_Review]]
 +
| Review of beam image shift and subtomogram averaging
 +
|-
 +
 
 +
| Paper
 +
| [[2023Kim_Review]]
 +
| Review of particle picking and volume segmentation
 +
|-
 +
 
 +
| Paper
 +
| [[2023Ochner_Review]]
 +
| Review of electron tomography as a way to visualize macromolecules in their native environment
 +
|-
 +
 
 +
| Paper
 +
| [[2023Zhao_Review]]
 +
| Review of computational methods for electron tomography
 +
|-
 +
 
 +
|}
 +
 
 +
=== Software ===
 +
 
 +
{|
 +
 
 +
| Paper
 +
| [[1996Kremer_IMOD]]
 +
| IMOD
 +
|-
 +
 
 +
| Paper
 +
| [[1996Chen_Priism/IVE]]
 +
| Priism/IVE
 +
|-
 +
 
 +
| Paper
 +
| [[1996Frank_Spider]]
 +
| Spider
 +
|-
 +
 
 +
| Paper
 +
| [[2004Sorzano_Xmipp]]
 +
| Xmipp
 +
|-
 +
 
 +
| Paper
 +
| [[2005Nickell_TOM]]
 +
| TOM Toolbox
 +
|-
 +
 
 +
| Paper
 +
| [[2007Messaoudi_TomoJ]]
 +
| TomoJ
 +
|-
 +
 
 +
| Paper
 +
| [[2008Heymann_BsoftTomo]]
 +
| Bsoft
 +
|-
 +
 
 +
| Paper
 +
| [[2012Zhang IPET FETR]]
 +
| IPET
 +
|-
 +
 
 +
| Paper
 +
| [[2015Ding_CaltechTomography]]
 +
| Caltech tomography database
 +
|-
 +
 
 +
| Paper
 +
| [[2015Noble_AppionProtomo]]
 +
| Batch fiducial-less tilt-series alignment in Appion using Protomo
 +
|-
 +
 
 +
| Paper
 +
| [[2015vanAarle_Astra]]
 +
| ASTRA Toolbox
 +
|-
 +
 
 +
| Paper
 +
| [[2016Liu_FullMechTomo]]
 +
| Fully mechanically controlled automated electron microscopic tomography
 +
|-
 +
 
 +
| Paper
 +
| [[2017Han_AuTom]]
 +
| Software platform for Electron Tomography
 +
|-
 +
 
 +
| Paper
 +
| [[2017Wan_Simulator]]
 +
| Electron Tomography Simulator
 +
|-
 +
 
 +
| Paper
 +
| [[2021Burt_RWD]]
 +
| Interoperability between Relion, Warp M, and Dynamo
 +
|-
 +
 
 +
| Paper
 +
| [[2022Jimenez_ScipionTomo]]
 +
| Electron tomography within Scipion
 +
|-
 +
 
 +
 
 +
| Paper
 +
| [[2022Martinez_PyOrg]]
 +
| Point pattern analysis for coordinates in tomograms
 +
|-
 +
 
 +
| Paper
 +
| [[2022Ni_EmClarity]]
 +
| Processing protocols with EmClarity
 +
|-
 +
 
 +
| Paper
 +
| [[2023Liu_NextPYP]]
 +
| NextPYP: a software platform for cryoET
 +
|-
 +
 
 +
|}
 +
 
 +
== 2D Crystals ==
 +
 
 +
=== 2D Preprocessing ===
 +
 
 +
{|
 +
 
 +
| Paper
 +
| [[1982Saxton_Averaging]]
 +
| Radial Correlation Function
 +
|-
 +
 
 +
| Paper
 +
| [[1984Saxton_Distortions]]
 +
| 3D Reconstruction of distorted crystals
 +
|-
 +
 
 +
| Paper
 +
| [[1986Henderson_Processing]]
 +
| General 2D processing
 +
|-
 +
 
 +
| Paper
 +
| [[2000He_PhaseAlignment]]
 +
| Phase consistency and Alignment
 +
|-
 +
 
 +
| Paper
 +
| [[2006Gil_Unbending]]
 +
| Crystal unbending
 +
|-
 +
 
 +
|}
 +
 
 +
=== Classification ===
 +
{|
 +
 
 +
| Paper
 +
| [[1988Frank_Classification]]
 +
| MSA and classification in electron crystallography
 +
|-
 +
 
 +
| Paper
 +
| [[1996Fernandez_SOM]]
 +
| Classification based on self organizing maps
 +
|-
 +
 
 +
| Paper
 +
| [[1998Sherman_MSA]]
 +
| Classification based on MSA
 +
|-
 +
 
 +
|}
 +
=== 3D Reconstruction ===
 +
 
 +
{|
 +
 
 +
| Paper
 +
| [[1985Wang_Solvent]]
 +
| Solvent flattening
 +
|-
 +
 
 +
| Paper
 +
| [[1990Henderson_Processing]]
 +
| General 3D processing
 +
|-
 +
 
 +
| Paper
 +
| [[2004Marabini_ART]]
 +
| Algebraic Reconstruction Technique with blobs for crystals (Xmipp)
 +
|-
 +
 
 +
| Paper
 +
| [[2018Biyani_Badlu]]
 +
| Image processing for badly ordered crystals
 +
|-
 +
 
 +
|}
 +
 
 +
=== Books and reviews ===
 +
 
 +
{|
 +
 
 +
| Paper
 +
| [[1998Walz_Review]]
 +
| Review of 2D crystallography
 +
|-
 +
 
 +
| Paper
 +
| [[1999Glaeser_Review]]
 +
| Review of 2D crystallography
 +
|-
 +
 
 +
| Paper
 +
| [[2001Ellis_Review]]
 +
| Review of 2D crystallography
 +
|-
 +
 
 +
| Paper
 +
| [[2001Glaeser_Review]]
 +
| Review of 2D crystallography
 +
|-
 +
 
 +
| Paper
 +
| [[2004Henderson_Review]]
 +
| Review of electron microscopy
 +
|-
 +
 
 +
| Paper
 +
| [[2006Fernandez_Review]]
 +
| Review of single particles, electron tomography and crystallography
 +
|-
 +
 
 +
| Paper
 +
| [[2007Sorzano_Review]]
 +
| Review of the image processing steps
 +
|-
 +
 
 +
|}
 +
 
 +
=== Software ===
 +
 
 +
{|
 +
 
 +
| Paper
 +
| [[1996Crowther_MRC]]
 +
| MRC
 +
|-
 +
 
 +
| Paper
 +
| [[2004Sorzano_Xmipp]]
 +
| Xmipp
 +
|-
 +
 
 +
| Paper
 +
| [[2007Gipson_2dx]]
 +
| 2dx
 +
|-
 +
 
 +
| Paper
 +
| [[2007Heymann_Bsoft]]
 +
| Bsoft
 +
|-
 +
 
 +
| Paper
 +
| [[2007Philippsen_IPLT]]
 +
| IPLT
 +
|-
 +
 
 +
|}
 +
 
 +
== 3D Crystals - MicroED ==
 +
 
 +
=== Sample Preparation ===
 +
{|
 +
| Paper
 +
| [[2016Shi_Preparation]]
 +
| Sample Preparation
 +
|}
 +
=== Data Collection ===
 +
{|
 +
| Paper
 +
| [[2014Nannenga_CR]]
 +
| Continuous rotation
 +
 
 +
|}
 +
=== Data Processing ===
 +
{|
 +
 
 +
| Paper
 +
| [[2011Wisedchaisri_PhaseExtension]]
 +
| Fragment-based phase extension
 +
|-
 +
 
 +
| Paper
 +
| [[2015Hattne_Processing]]
 +
| Data Processing
 +
|-
 +
 +
| Paper
 +
| [[2016Hattne_Correction]]
 +
| Image correction
 +
|}
 +
 
 +
=== Software ===
 +
{|
 +
 
 +
| Paper
 +
| [[2014Iadanza_Processing]]
 +
| Data Processing of still diffraction data
 +
|}
 +
 
 +
=== Books and Reviews ===
 +
{|
 +
|  Paper
 +
| [[2014Nannenga_Review ]]
 +
| Review of MicroED
 +
|-
 +
 
 +
| Paper
 +
| [[2016Liu_Review ]]
 +
| Review of MicroED
 +
|-
 +
 
 +
| Paper
 +
| [[2016Rodriguez_Review ]]
 +
| Review of MicroED
 +
|-
 +
 
 +
|}
 +
 
 +
== Helical particles ==
 +
 
 +
=== Filament picking ===
 +
 
 +
{|
 +
 
 +
| Paper
 +
| [[2021Thurber_Automated]]
 +
| Automated picking of filaments
 +
|-
 +
 
 +
|}
 +
 
 +
=== Filament corrections ===
 +
 
 +
{|
 +
 
 +
| Paper
 +
| [[1986Egelman_Curved]]
 +
| Algorithm for correcting curved filaments
 +
|-
 +
 
 +
| Paper
 +
| [[1988Bluemke_Pitch]]
 +
| Algorithm for correcting filaments with different helical pitches
 +
|-
 +
 
 +
| Paper
 +
| [[2006Wang_Pitch]]
 +
| Algorithm for correcting filaments with different helical pitches
 +
|-
 +
 
 +
| Paper
 +
| [[2016Yang_Flexible]]
 +
| Algorithm for correcting filaments with flexible subunits
 +
|-
 +
 
 +
| Paper
 +
| [[2019Ohashi_SoftBody]]
 +
| Algorithm for correcting filaments with flexible helices
 +
|-
 +
 
 +
|}
 +
 
 +
=== Reconstruction ===
 +
 
 +
{|
 +
 
 +
| Paper
 +
| [[1952Cochran_Fourier]]
 +
| Fourier Bessel transform of filamentous structures
 +
|-
 +
 
 +
| Paper
 +
| [[1958Klug_Fourier]]
 +
| Fourier Bessel decomposition of the projection images
 +
|-
 +
 
 +
| Paper
 +
| [[1970DeRosier_Rec]]
 +
| Image processing steps towards 3D reconstruction
 +
|-
 +
 
 +
| Paper
 +
| [[1988Stewart_Rec]]
 +
| Image processing steps towards 3D reconstruction
 +
|-
 +
 
 +
| Paper
 +
| [[1992Morgan_Rec]]
 +
| Image processing steps towards 3D reconstruction
 +
|-
 +
 
 +
| Paper
 +
| [[2005Wang_Iterative]]
 +
| Iterative Fourier-Bessel algorithm
 +
|-
 +
 
 +
| Paper
 +
| [[2007Egelman_Iterative]]
 +
| Iterative real-space algorithm
 +
|-
 +
 
 +
| Paper
 +
| [[2010Egelman_Pitfalls]]
 +
| Pitfalls in helical reconstruction
 +
|-
 +
 
 +
| Paper
 +
| [[2013Desfosses_Spring]]
 +
| Helical processing with Spring
 +
|-
 +
 
 +
| Paper
 +
| [[2015Zhang_seam]]
 +
| Workflow for the detection of the lattice seam
 +
|-
 +
 
 +
| Paper
 +
| [[2016Rohou_Frealix]]
 +
| Helical processing with Frealix
 +
|-
 +
 
 +
| Paper
 +
| [[2017_He]]
 +
| Helical processing with Relion
 +
|-
 +
 
 +
| Paper
 +
| [[2019_Pothula]]
 +
| 3D Classification through 2D analysis
 +
|-
 +
 
 +
|}
 +
 
 +
=== Validation ===
 +
 
 +
{|
 +
 
 +
| Paper
 +
| [[2014Egelman_ambiguity]]
 +
| How to detect incorrect models
 +
|-
 +
 
 +
|}
 +
 
 +
=== Books and reviews ===
 +
 
 +
{|
 +
 
 +
| Paper
 +
| [[1970DeRosier_Rec]]
 +
| Image processing steps towards 3D reconstruction
 +
|-
 +
 
 +
| Paper
 +
| [[1992Morgan_Rec]]
 +
| Image processing steps towards 3D reconstruction
 +
|-
 +
 
 +
| Paper
 +
| [[2004Henderson_Review]]
 +
| Review of electron microscopy
 +
|-
 +
 
 +
| Paper
 +
| [[2015Sachse_Review]]
 +
| Review of the image processing steps in helical particles
 +
|-
 +
 
 +
| Paper
 +
| [[2021Egelman_Review]]
 +
| Review of reconstruction problems in helical structures
 +
|-
 +
 
 +
| Paper
 +
| [[2022Wang_Review]]
 +
| Review of reconstruction problems in helical structures
 +
|-
 +
 
 +
|}
 +
 
 +
=== Software ===
 +
 
 +
{|
 +
 
 +
| Paper
 +
| [[1996Carragher_Phoelix]]
 +
| Phoelix
 +
|-
 +
 
 +
| Paper
 +
| [[1996Crowther_MRC]]
 +
| MRC
 +
|-
 +
 
 +
| Paper
 +
| [[1996Owen_Brandeis]]
 +
| Brandeis
 +
|-
 +
 
 +
|}
 +
 
 +
== Icosahedral particles ==
 +
 
 +
=== Reconstruction ===
 +
 
 +
{|
 +
 
 +
| Paper
 +
| [[1970Crowther_Rec]]
 +
| Reconstruction of icosahedral viruses in Fourier space
 +
|-
 +
 
 +
| Paper
 +
| [[1971Crowther_Rec]]
 +
| Reconstruction of icosahedral viruses in Fourier space
 +
|-
 +
 
 +
| Paper
 +
| [[1996Fuller_Rec]]
 +
| Reconstruction of icosahedral viruses in Fourier space
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017_He]]
+
| [[1997Thuman_Rec]]
| Helical processing with Relion
+
| Reconstruction of icosahedral viruses in Fourier space
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2019_Pothula]]
+
| [[2019Goetschius_Asymmetric]]
| 3D Classification through 2D analysis
+
| Approaches to reconstruct asymmetric features in viruses
 
|-  
 
|-  
  
 
|}
 
|}
  
=== Validation ===
+
=== Classification ===
  
 
{|
 
{|
  
 
| Paper
 
| Paper
| [[2014Egelman_ambiguity]]
+
| [[2005Scheres_Virus]]
| How to detect incorrect models
+
| Classification of virus capsids in real space
 
|-  
 
|-  
  
Line 4,088: Line 6,291:
  
 
| Paper
 
| Paper
| [[1970DeRosier_Rec]]
+
| [[1999Baker_Review]]
| Image processing steps towards 3D reconstruction
+
| Review of reconstruction of icosahedral viruses
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1992Morgan_Rec]]
+
| [[1999Conway_Review]]
| Image processing steps towards 3D reconstruction
+
| Review of reconstruction of icosahedral viruses
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2004Henderson_Review]]
+
| [[2000Thuman_Review]]
| Review of electron microscopy
+
| Review of reconstruction of icosahedral viruses
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Sachse_Review]]
+
| [[2003Lee_Review]]
| Review of the image processing steps in helical particles
+
| Review of reconstruction of icosahedral viruses
 
|-  
 
|-  
  
|}
+
| Paper
 +
| [[2003Navaza_Review]]
 +
| Review of reconstruction of icosahedral viruses
 +
|-
 +
 
 +
| Paper
 +
| [[2006Grunewald_Review]]
 +
| Review of reconstruction of icosahedral viruses
 +
|-
 +
 
 +
|}
  
 
=== Software ===
 
=== Software ===
Line 4,114: Line 6,327:
  
 
| Paper
 
| Paper
| [[1996Carragher_Phoelix]]
+
| [[1996Baker_EMPFT]]
| Phoelix
+
| EMPFT
 
|-  
 
|-  
  
Line 4,124: Line 6,337:
  
 
| Paper
 
| Paper
| [[1996Owen_Brandeis]]
+
| [[1996Frank_Spider]]
| Brandeis
+
| Spider
 
|-  
 
|-  
 
|}
 
 
== Icosahedral particles ==
 
 
=== Reconstruction ===
 
 
{|
 
  
 
| Paper
 
| Paper
| [[1970Crowther_Rec]]
+
| [[1996VanHeel_Imagic]]
| Reconstruction of icosahedral viruses in Fourier space
+
| Imagic
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1971Crowther_Rec]]
+
| [[2004Sorzano_Xmipp]]
| Reconstruction of icosahedral viruses in Fourier space
+
| Xmipp
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1996Fuller_Rec]]
+
| [[2013DeLaRosa_Xmipp30]]
| Reconstruction of icosahedral viruses in Fourier space
+
| Xmipp 3.0
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1997Thuman_Rec]]
+
| [[2013Morin_Sliz SBGrid]]
| Reconstruction of icosahedral viruses in Fourier space
+
| SBGrid presentation for eLife
 
|-  
 
|-  
  
 
|}
 
|}
  
=== Classification ===
+
== Liquid-cell TEM / in-situ TEM ==
 +
 
  
 
{|
 
{|
  
 
| Paper
 
| Paper
| [[2005Scheres_Virus]]
+
| [[2020Ren_LTEM]]
| Classification of virus capsids in real space
+
| Real-time dynamic imaging of sample in liquid phase
 
|-  
 
|-  
  
 
|}
 
|}
  
=== Books and reviews ===
+
== Databases ==
  
 
{|
 
{|
  
 
| Paper
 
| Paper
| [[1999Baker_Review]]
+
| [[2003Boutselakis_EMSD]]
| Review of reconstruction of icosahedral viruses
+
| EMSD database
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1999Conway_Review]]
+
| [[2005Heymann_Conventions]]
| Review of reconstruction of icosahedral viruses
+
| Conventions for software interoperability
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2000Thuman_Review]]
+
| [[2005Heymann_Conventions]]
| Review of reconstruction of icosahedral viruses
+
| Conventions for software interoperability
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2003Lee_Review]]
+
| [[2011Kim_CDDB]]
| Review of reconstruction of icosahedral viruses
+
| Conformational Dynamics Data Bank
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2003Navaza_Review]]
+
| [[2011Lawson_EMDB]]
| Review of reconstruction of icosahedral viruses
+
| Electron Microscopy Data Bank
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2006Grunewald_Review]]
+
| [[2013Ison_EDAM]]
| Review of reconstruction of icosahedral viruses
+
| EDAM, an ontology of bioinformatics operations
 
|-  
 
|-  
  
|}
+
| Paper
 
+
| [[2016Iudin_EMPIAR]]
=== Software ===
+
| EMPIAR raw data database
 
+
|-
{|
 
  
 
| Paper
 
| Paper
| [[1996Baker_EMPFT]]
+
| [[2016Patwhardan_EMDB]]
| EMPFT
+
| EMDB, PDB, ...
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1996Crowther_MRC]]
+
| [[2017Gore_Validation]]
| MRC
+
| Validations of PDB submissions
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1996Frank_Spider]]
+
| [[2017Patwhardan_Trends]]
| Spider
+
| Trends at EMDB
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1996VanHeel_Imagic]]
+
| [[2017Shao_PDBQuality]]
| Imagic
+
| Quality metrics in PDB
 +
|-
 +
 
 +
| Paper
 +
| [[2018Tawari_search]]
 +
| Search of 3D structures in a database using 2D experimental images
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2004Sorzano_Xmipp]]
+
| [[2018wwwPDB_PDB]]
| Xmipp
+
| Review of PDB advances
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013DeLaRosa_Xmipp30]]
+
| [[2022Wang_EMDB]]
| Xmipp 3.0
+
| Validation analysis of EMDB entries
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Morin_Sliz SBGrid]]
+
| [[2022Westbrook_mmCIF]]
| SBGrid presentation for eLife
+
| PDBx/mmCIF ecosystem
 +
|-
 +
 
 +
| Blog
 +
| http://www.mybiosoftware.com
 +
| Huge list of bioinformatics programs (many of them structural bioinformatics)
 
|-  
 
|-  
  
 
|}
 
|}
  
== Databases ==
+
== Relationship to other structural information sources ==
  
 
{|
 
{|
  
 
| Paper
 
| Paper
| [[2003Boutselakis_EMSD]]
+
| [[2000Engel_AFM]]
| EMSD database
+
| Review of Atomic Force Microscopy
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2005Heymann_Conventions]]
+
| [[2001Dimmeler_AFM]]
| Conventions for software interoperability
+
| Constraints from Atomic Force Microscopy
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2005Heymann_Conventions]]
+
| [[2003Mobus_EnergyLoss]]
| Conventions for software interoperability
+
| Chemical mapping by energy loss electron tomography
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2011Kim_CDDB]]
+
| [[2004Leapman_EnergyLoss]]
| Conformational Dynamics Data Bank
+
| Chemical mapping by energy loss electron tomography
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2011Lawson_EMDB]]
+
| [[2004Leapman_Review]]
| Electron Microscopy Data Bank
+
| Review on correlative microscopy
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Ison_EDAM]]
+
| [[2005Boudier_EFTETJ]]
| EDAM, an ontology of bioinformatics operations
+
| Software for Chemical mapping by energy loss electron tomography
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Iudin_EMPIAR]]
+
| [[2005Vestergaard_SAXS]]
| EMPIAR raw data database
+
| Example of comparison of 3DEM and Small-angle X-ray scattering
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Patwhardan_EMDB]]
+
| [[2007Hamada_SAXS]]
| EMDB, PDB, ...
+
| Constraints from Small-angle X-ray scattering
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Gore_Validation]]
+
| [[2013Xu_FRET]]
| Validations of PDB submissions
+
| EM+FRET
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Patwhardan_Trends]]
+
| [[2017Kim_SAXS]]
| Trends at EMDB
+
| Compatibility of EM experimental images and SAXS curves
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Shao_PDBQuality]]
+
| [[2018Ando_Correlative]]
| Quality metrics in PDB
+
| Review of correlative microscopy techniques
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Tawari_search]]
+
| [[2018Sieben_Multicolor]]
| Search of 3D structures in a database using 2D experimental images
+
| Correlative microscopy with superresolution optical images
|-
 
 
 
| Paper
 
| [[2018wwwPDB_PDB]]
 
| Review of PDB advances
 
|-
 
 
 
| Blog
 
| http://www.mybiosoftware.com
 
| Huge list of bioinformatics programs (many of them structural bioinformatics)
 
|-
 
 
 
|}
 
 
 
== Relationship to other structural information sources ==
 
 
 
{|
 
 
 
| Paper
 
| [[2000Engel_AFM]]
 
| Review of Atomic Force Microscopy
 
|-
 
 
 
| Paper
 
| [[2001Dimmeler_AFM]]
 
| Constraints from Atomic Force Microscopy
 
|-
 
 
 
| Paper
 
| [[2003Mobus_EnergyLoss]]
 
| Chemical mapping by energy loss electron tomography
 
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2004Leapman_EnergyLoss]]
+
| [[2019Huber_EDXS_HAADF]]
| Chemical mapping by energy loss electron tomography
+
| Combined reconstruction using EDXS and HAADF data
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2004Leapman_Review]]
+
| [[2019Jimenez_SAXS]]
| Review on correlative microscopy
+
| Selection of EM initial volumes by SAXS curves
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2005Boudier_EFTETJ]]
+
| [[2022Graziadei_CrossLinking]]
| Software for Chemical mapping by energy loss electron tomography
+
| Review on the use of crosslinking mass spectrometry in CryoEM
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2005Vestergaard_SAXS]]
+
| [[2022Klumpe_FIB]]
| Example of comparison of 3DEM and Small-angle X-ray scattering
+
| A modular platform for automated cryo-FIB workflows
|-
 
 
 
| Paper
 
| [[2007Hamada_SAXS]]
 
| Constraints from Small-angle X-ray scattering
 
|-
 
 
 
| Paper
 
| [[2013Xu_FRET]]
 
| EM+FRET
 
|-
 
 
 
| Paper
 
| [[2018Ando_Correlative]]
 
| Review of correlative microscopy techniques
 
|-
 
 
 
| Paper
 
| [[2018Sieben_Multicolor]]
 
| Correlative microscopy with superresolution optical images
 
 
|-  
 
|-  
  
Line 4,391: Line 6,555:
 
| Image formation model in X-ray cell microscopy
 
| Image formation model in X-ray cell microscopy
 
|-  
 
|-  
 
 
  
 
|}
 
|}
Line 4,418: Line 6,580:
  
 
[Vahid Abrishami]: CSIC, Madrid, Spain <br>
 
[Vahid Abrishami]: CSIC, Madrid, Spain <br>
 +
 +
[https://rengroup.lbl.gov/ Gang (Gary) Ren]: The Molecular Foundry, LBNL, USA<br>
  
 
== 3DEM sites ==
 
== 3DEM sites ==

Latest revision as of 07:43, 19 January 2024

Contents

Presentation

This web page is intended to be an extensive repository of three-dimensional electron microscopy (3DEM) methods. The advantages of having such a repository are

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Please:

  • Add your articles at the right place (you can add a single article in several topics if it is relevant to all of them). The easiest way to add an article is by editing the corresponding topic in the main page, adding your entry, then save the main page. Click on the red link that appears on your new entry, copy and paste the Wiki following code, add the information of your article
== Citation ==

== Abstract ==

== Keywords ==

== Links ==

== Related software ==

== Related methods ==

== Comments ==
  • Maintain the information of each article as complete as possible.
  • Sort articles by years and authors.
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Electron microscopy images

Online courses and Learning material

Caltech (same course in Coursera) (latest version of the course in EM-learning)

MRC

MRC training channel

CNB-CSIC

Workshop on Computational methods for CryoEM

Workshop on Management of large CryoEM facilities

Icknield Course on Model Building and Refinement for High Resolution EM Maps

Tutorial on how to prepare negative staining samples

Tutorial on how to prepare samples

Do's and don'ts on sample preparation

NRAMM Workshop 2017 (course slides)

SBGrid videos about the programs they offer

Madrid course on single particle analysis

CCP-EM Spring symposium 2019

CCP-EM Spring symposium 2020

NCCAT Single Particle short course 2020

Cell atlas book by Grant Jensen and Catherine Oikonomou

Purdue CryoEM Virtual Reality Augmented Training

NCCAT Short course on Tomography

Map with CryoEM Facilities

NCCAT Single Particle Analysis short course

Algorithms for Structural Bioinformatics, AlgoSB2023, Cargese

One world CryoEM technical talks

Image formation

Paper 1971Erickson_CTF CTF model
Paper 1971Glaeser_Damage Radiation damage
Chapter 1971Hanszen_CTF Image formation model
Paper 1971Thon_Model CTF model
Paper 1974Taylor_Diffraction Electron diffraction of crystals
Paper 1975Unwin_Imaging Radiation dose
Paper 1977Wade_Model CTF model
Paper 1978Wade_Model CTF model
Paper 1979Hayward_Radiation Radiation damage
Paper 1984Cohen_Validity Validity of the CTF model at high frequencies
Paper 1988Toyoshima_Model Amplitud constrast
Paper 1992Wade_Model CTF model
Paper 1993Toyoshima_Model Amplitud constrast
Paper 2002DeCarlo_Damage Radiation damage in cryonegative staining
Paper 2004Egerton_Damage Radiation damage
Paper 2004Sorzano_Normalization Background noise is Gaussian
Paper 2008Fanelli_ImageFormation Review on the image formation model from the electron waves and open inverse-problems
Paper 2009Baxter_NoiseCharacterization Characterization of the different noise sources in cryo-EM
Book 2009Rose_Optics Geometrical Charged-Particle Optics
Paper 2010Baker_Damage Radiation damage dependence on resolution
Paper 2010Bammes_Damage Radiation damage dependence on temperature
Paper 2010Gomez_Multislice Simulation of the multi slice model
Paper 2010Zewail_FourDimensional Review on the use of ultrafast EM
Paper 2011Bammes_CCD Performance of CCD cameras
Paper 2011Glaeser_Coma Image formation model including coma
Paper 2011Milazzo_DirectDetectors Evaluation of Direct Detectors
Paper 2011Rullgard_ImageSimulation Accurate simulation of EM images
Paper 2011Zhang LimitingFactors Limiting factor for atomic resolution in EM
Paper 2012Bammes_DirectDetection Performance of Direct detectors
Paper 2012Campbell_MotionCorrection Beam induced motion correction and direct detectors
Paper 2012Shang_HydrationLayer Simulation of PDB volumes explicitly considering the hydration layer
Paper 2013Egerton_RadiationDamage Review of TEM radiation damage and experimental ways of reducing it
Paper 2013Bai_ElectronCounting Electron counting and beam induced motion correction
Paper 2013Li_ElectronCounting Electron counting and beam induced motion correction
Paper 2013Shigematsu H_Noisemodels Noise models and cryo-EM drift correction with a direct-electron camera
Paper 2013Li X K2 noisemodels Influence of electron dose rate on electron counting images recorded with the K2 camera
Paper 2013Vulovic_CTFApproximations When to use the different approximations performed so that a projection with linear CTF is valid
Thesis 2013Vulovic_ImageFormation Ph.D. Thesis on the image formation in cryo-EM
Paper 2014Danev_PhasePlate Volta potential phase plate
Paper 2015Chiu_K2 Characterization of K2
Paper 2015Hawkes_AberrationCorrection Historical account of the development of lens corrections
Paper 2015Koeck_Quadratic Limitations of the linear approximation and use of the quadratic terms
Paper 2015Kuijper_FEI Description of the FEI Falcons
Paper 2015Lobato_MULTEM Simulation of multislice diffraction
Paper 2015McMullan_AmorphousIce Beam induced movement is caused by Brownian motion
Paper 2016Glaeser_Behaviour Behaviour of the specimen under the electron beam
Paper 2016Koeck_ADF Simulations of Annular Dark Field TEM
Paper 2017Fan_VPP 3D Reconstruction with under-focus and over-focus Volta Phase Plate micrographs
Paper 2017Koeck_ApertureDesign Aperture design for singe side band imaging
Paper 2017Mishyna_DNARadiation Review of radiation damage on DNA
Paper 2018Anoshina_Simulation Simulation of 2D and 3D EM images
Paper 2018Downing_DepthOfField Effects of the Depth of Field
Paper 2018DeJonge_SpatialResolution Theory of spatial resolution in liquid water or ice layers
Paper 2018Faruqi_DED Review of Direct Detectors
Paper 2018Hattne_RadiationDamage Analysis of radiation damage in EM
Paper 2018Hettler_Charging Charging of carbon thin films
Paper 2018Koeck_PhaseShift Design of a phase shift device
Paper 2018Noble_ParticleDistribution Particle distribution and ice thickness for Single Particles
Paper 2018Russo_ChargeAccumulation Charge accumulation in electron cryomicroscopy
Paper 2018Russo_SingleBandEM Ewald sphere correcion using single-side band image processing
Paper 2019Peet_EnergyDependence Energy dependence of radiation damage
Paper 2020Bromberg_Aberrations Estimation of strong high-order aberrations
Paper 2020Gruza_Atomic Detailed atomic models considering local charges and directional bonds
Paper 2020Naydenova_Buckling Beam induced movement explained as ice buckling
Paper 2020Zhang_LimitsSimulated Simulation of micrographs and 3D reconstruction for low weight proteins (14kDa)
Paper 2020Tichelaar_Thick Effect of sample thickness on the CTF
Paper 2020Yip_Atomic Atomic resolution by monochromator and a second-generation spherical aberration corrector
Paper 2020Zhang_LimitsSimulated Simulation of micrographs and 3D reconstruction for low weight proteins (14kDa)
Paper 2021Egerton_Inelastic PSF of inelastic scattering
Paper 2021Glaeser_Fading Defocus-dependent Thon-ring fading
Paper 2021Wieferig_Devitrification Devitrification reduces beam-induced movement in cryo-EM
Paper 2022Heymann_PSSNR Progressive Spectral Signal-to-Noise Ratio to assess quality and radiation damage
Paper 2022Dickerson_Inelastic The role of inelastic scattering in thick specimens
Paper 2022Kulik_TAAM Theoretical 3D electron diffraction electrostatic potential maps of proteins
Paper 2022Ravikumar_SideChains Comparison of side-chain dispersion in protein structures determined by cryo-EM and X-ray crystallography
Paper 2023Bromberg_Complex CTF and Ewald sphere correction using complex-valued images
Paper 2023Heymann_Ewald The Ewald sphere/focus gradient does not limit the resolution of cryoEM reconstructions
Paper 2023Schreiber_charge Time dynamics of charge buildup

Collection geometry

Chapter 1980Hoppe_Wedge Missing wedge
Paper 1987Radermacher_RCT Random Conical Tilt and Single axis tilt
Paper 1988Radermacher_RCT Random Conical Tilt and Single axis tilt
Paper 1995Penczek_Dual Dual axis tomography
Paper 1997Mastronarde_Dual Dual axis tomography
Paper 2003Ludtke_FocusPairs Focus pairs for single particles
Paper 2005Lanzavecchia_Conical Conical tomography
Paper 2005Zampighi_Conical Conical tomography
Paper 2006Leschziner_OT Orthogonal Tilt
Paper 2006Messaoudi_Multiple Multiple axis tomography
Paper 2012Kudryashev_FocusPairs Focus pairs tomography
Paper 2014Hovden_TiltFocus Combining tilt series with focus series
Paper 2015Sorzano_RandomConicalTilt General formulation of Random Conical Tilt
Paper 2017Hagen_DoseTomography Dose optimization for subtomogram averaging
Paper 2017Tan_PreferredViews Solving preferred views problems through tilting
Paper 2017Donati_Compressed Compressed sensing for STEM
Paper 2018Oveisi_Stereo Stereo-vision with EM
Paper 2018Cheng_BeamShift Fast image acquisition through beam-shift
Paper 2019Wu_BeamShiftAndTilt Fast image acquisition through beam-shift and beam tilt control
Paper 2023Seifer_RevisedSaxton Revised Saxton geometry for tilt series acquisition

Sample preparation

Paper 1982Dubochet_Sample Vitreous ice
Paper 1986Lepault_Sample Fast freezing
Paper 1995Dubochet_Sample High-pressure freezing
Paper 1995VanMarle_Sample Sample damages in resin
Paper 1998Adrian_Sample Cryo negative staining
Paper 2002DeCarlo_Damage Radiation damage in cryonegative staining
Paper 2002Hsieh_Sample Cryofixation
Paper 2004AlAmoudi_Sample CEMOVIS
Paper 2008Studer_Sample Review on high pressure freezing
Paper 2009Pierson_Sample Review on sample preparation for electron tomography
Paper 2010Zhang_OpNS Optimized negative staining (OpNS) for small protein and lipoprotein imaging
Paper 2012Zhang_Cryo-PS Cryo-positive staining (Cryo-PS)
Paper 2014Russo_GoldGrids Gold grids for single particles
Paper 2015Cabra_Sample Review on sample preparation for single particles with videos
Paper 2015Chari_ProteoPlex Fast evaluation of the structural stability
Paper 2016Passmore_Review Tutorial chapter on sample preparation
Paper 2016Razinkov_Vitrification New vitrification method
Paper 2016Takizawa_Sample Review on sample preparation for EM
Paper 2016Thompson_Sample Review on sample preparation for EM
Paper 2017Arnold_BlottingFree Blotting-free preparation
Paper 2017Earl_review Review of sample preparation
Paper 2017Feng_SprayingPlunging Spraying plunging
Paper 2017He_FIB Cryo FIB lamella for TEM
Paper 2017Peitsch_Sample iMEM: Isolation of Plasma Membrane for Cryoelectron Microscopy
Paper 2017Scapin_Storage Cryo storage of samples
Paper 2017Schaffer_FocusedIonBeam Focused Ion Beam sample preparation for membrane proteins
Paper 2017Scherr_HydrogelNanomembranes Sample preparation for membrane proteins
Paper 2018Anderson_CLEM Correlated light and EM
Paper 2018Arnold_Review Review on sample preparation with special emphasis on microfluidic approaches
Paper 2018Ashtiani_femtolitre Delivery of femtolitre droplets using surface acoustic wave based atomisation for cryo-EM grid preparation
Paper 2018Dandey_Spotiton Spotiton, a device for vitrification
Paper 2018Gewering_Detergents Detergent background in negative stain
Paper 2018Li_CLEM Correlated light and EM
Paper 2018Noble_Reducing Reducing particle adsorption
Paper 2018Palovcak_Graphene Preparation of graphene-oxide cryo-EM grids
Paper 2018Rice_Ice Routine determination of ice thickness
Paper 2018Schmidli_Miniaturized Protein isolation and sample preparation
Paper 2018Wei_Grids "Self-wicking" nanowire grids
Paper 2019DImprima_Denaturation Protein denaturation at the air-water interface and how to prevent it
Paper 2019Rubinstein_ultrasonic Ultrasonic specimen preparation device
Paper 2019Song_FalconIII Comparison of the modes of Falcon III
Paper 2020Cianfrocco_Wrong What could go wrong?
Paper 2020Egelman_Ice Problems with the ice
Paper 2020Fassler_Printing 3D printed cell culture grid holder
Paper 2020Klebl_Deposition Sample deposition onto CryoEM grids: sprays and jets
Paper 2020Maeots_TimeResolved Time resolved CryoEM by microfluidics
Paper 2020Tan_ThroughGrid Through-grid wicking enables high-speed 1 cryoEM specimen preparation
Paper 2020Yoder_TimeResolved Time resolved CryoEM by light estimulation
Paper 2020Zachs_FIB Automation for FIB milling
Paper 2021Bieber_FIBET Sample preparation for correlative FIB milling and CryoET
Paper 2021Budell_TimeResolved Time resolved CryoEM with Spotiton
Paper 2021Casasanta_Microchip Microchip-based structure determination of low-molecular weight proteins using cryo-electron microscopy
Paper 2021Frechard_Preparation Optimization of Sample Preparation
Paper 2021Engstrom_Nitrogen Samples vitrified in boiling nitrogen
Paper 2021Jagota_GoldNanoparticles Gold nanoparticles to assess flexibility
Paper 2021Jiang_MoAu Holey Gold Films on Molybdenum Grids
Paper 2021Jonaid_Liquid Liquid phase EM
Paper 2021Ki_Conformational Conformational Distribution of a Small Protein with Nanoparticle-Aided CryoEM
Paper 2021Li_detergents The effect of detergents on preferential orientations
Paper 2021Voss_Melting Rapid melting and revitrification as an approach to microsecond time-resolved cryoEM
Paper 2021Zhang_Pegylation Improving particle quality in cryo-EM by PEGylation
Paper 2022Chen_Detergents Role of detergents in the air-water interface
Paper 2022Levitz_Chameleon Effects of dispense-to-plunge speed on particle concentration, complex formation, and final resolution
Paper 2022Naydenova_Grid Integrated wafer-scale manufacturing of electron cryomicroscopy specimen supports
Paper 2022Russo_Review Review of sample preparation issues
Paper 2022Scher_FIB Sample preparation for FIB-SEM and Correlative microscopy
Paper 2023Basanta_Graphene Fabrication of Monolayer Graphene-Coated Grids
Paper 2023Han_Sample Challenges in making ideal cryo-EM samples
Paper 2023Liu_AirWater Review on sample preparation techniques to deal with the air-water interface
Paper 2023Neselu_IceThickness Effect of ice thickness on resolution
Paper 2023Torino_TimeResolved Device for the preparation of time-resolved CryoEM experiments
Paper 2023Venien_Membrane Review on the preparation of membrane proteins
Paper 2023Zheng_Ultraflat Uniform thin ice on ultraflat graphene grids

Automated data collection

Paper 1992Dierksen_Automatic Automated data collection
Paper 1992Koster_Automatic Automated data collection
Paper 1996Fung_Automatic Automated data collection for tomography
Paper 2001Zhang_Automatic Automated data collection: AutoEM
Paper 2003Ziese_Automatic Automated autofocusing
Paper 2004Potter_Automatic Automated sample loading
Paper 2004Zheng_Automatic Automated data collection
Paper 2005Lei_Automatic Automated data collection: AutoEM
Paper 2005Suloway_Automatic Automated data collection: Leginon
Paper 2007Yoshioka_RCT Automated Random Conical Tilt
Paper 2011Korinek_TOM2 Automated acquisition with TOM2
Paper 2015Li_UCSFImage Automated acquisition with UCSFImage
Paper 2016Gil_Fuzzy Real time decisions during acquisition with neuro-fuzzy method
Paper 2016Liu_TiltControl Accurate control of the tilt angle for electron tomography
Paper 2016Vargas_FoilHole Determination of image quality at low magnification
Paper 2017Alewijnse_Best Best practices for managing large CryoEM facilities
Paper 2017Biyani_Focus Automatic processing of micrographs
Paper 2018Gomez_Facilities Use of Scipion at facilities
Paper 2018Sorzano_Gain Estimation of the DDD camera gain or residual gain
Paper 2019Chreifi_TiltSeries Rapid tilt-series acquisition for electron cryotomography
Paper 2019Eng_ImageCompression 3D Reconstruction from compressed images
Paper 2019Eisenstein_FISE Improved applicability and robustness of fast cryo-electron tomography data acquisition
Paper 2019Hamaguchi_CryoARM CryoARM data acquisition
Paper 2019Maluenda_Scipion Automated workflow processing for facilities
Paper 2019Schorb_ET Automated acquisition in Electron Tomography
Paper 2019Tegunov_Warp Automatic micrograph processing with Warp
Paper 2019Thompson_Protocol Protocol for EM acquisition
Paper 2020Baxa_Facility Operational workflow in a facility
Paper 2020Guo_EER Electron event representation for acquisition
Paper 2020Li_Workflow Workflow for automatic reconstruction
Paper 2020Sader_Facility Microscope installation and operation in a facility
Paper 2020Schenk_CryoFlare CryoFlare, automatic data acquisition
Paper 2020Stabrin_Transphire TranSPHIRE: Automated and feedback-optimized on-the-fly processing for cryo-EM
Paper 2020Yokoyama_Good Deep learning for determining good regions in a grid
Paper 2020Weis_Acquisition Suggestions for high-quality and high-throughput acquisition
Paper 2021Feathers_Superresolution Effects of superresolution and magnification on final resolution
Paper 2021Bouvette_Bisect Beam image-shift accelerated data acquisition for near-atomic resolution single-particle cryo-electron tomography
Paper 2021Chreifi_FISE Rapid tilt-series method for cryo-electron tomography: Characterizing stage behavior during FISE acquisition
Paper 2021Efremov_ComaCorrected Coma-corrected rapid single-particle cryo-EM data collection on the CRYO ARM 300
Paper 2021Herzik_Setup Setup for parallel illumination
Paper 2021Kayama_Multipurpose Below 3 Å structure of apoferritin using a multipurpose TEM with a side entry cryoholder
Paper 2021Lane_NegativeBias Negative potential bias for faster imaging
Paper 2021Rheinberger_IceThickness Scripts to measure ice thickness
Paper 2021Yang_CRIM Computer readable image markers (CRIM) for correlative microscopy
Paper 2021Weis_Strategies Strategies for Optimization of Cryogenic Electron Tomography Data Acquisition
Paper 2021Wypych_gP2S LIMS of microscope sessions
Paper 2021Yang_CLEM Automated correlative microscopy
Paper 2021Yonekura_Hole Automated hole detection using YOLO
Paper 2022Bepler_Smart Smart data collection
Paper 2022Bouvette_SmartScope SmartScope
Paper 2022Flutty_bits Bit-precision for SPA and ET
Paper 2022Hagen_Screening Screening of ice thickness using energy filter-based plasmon imaging
Paper 2022Hohle_Ice Screening of ice thickness using interferometry
Paper 2022Peck_200 High-speed high-resolution data collection on a 200 keV cryo-TEM
Paper 2022Peck_Montage Montage electron tomography
Paper 2022Zhu_ElectronCounting New algorithm for electron counting at the microscope
Paper 2023Cheng_Leginon Smart data collection with Leginon
Paper 2023Kim_Ptolemy Smart data collection with Ptolemy
Paper 2023Last_Ice Measuring the ice thickness with an optical device and a neural network

Single particles

Automatic particle picking

Paper 1982VanHeel_Detection Detection of particles in micrographs
Paper 2001Nicholson_Review Review on automatic particle picking
Paper 2001Zhu_Filaments Automatic identification of filaments in micrographs
Paper 2004Sigworth_Detection Classical detection theory and the cryo-EM particle selection problem
Paper 2004Volkmann_ParticlePicking An approach to automated particle picking from electron micrographs based on reduced representation templates
Paper 2004Wong_ParticlePicking Model-based particle picking for cryo-electron microscopy
Paper 2004Zhu_Review Review on automatic particle picking
Paper 2007Chen_Signature Automatic particle picking program: Signature
Paper 2007Woolford_SwarmPS Automatic particle picking with several criteria, implemented in EMAN Boxer
Paper 2009Sorzano_MachineLearning Automatic particle picking based on machine learning of rotational invariants
Paper 2011Arbelaez_Comparison Evaluation of the performance of software for automated particle-boxing
Paper 2013Abrishami_MachineLearning A pattern matching approach to the automatic selection of particles from low-contrast electron micrographs
Paper 2013Hauer_2013 Automatic tilt pair detection in Random Conical Tilt
Paper 2013Hoang_ParallelGPUPicking Parallel GPU-accelerated particle picking
Paper 2013Shatsky_ParticlePicking Automated particle correspondence and accurate tilt-axis detection in tilted-image pairs
Paper 2013Vargas_ParticleQuality Automatic determination of particle quality
Paper 2014Langlois_ParticlePicking Automatic particle picking
Paper 2015Scheres_SemiAutoPicking Semi-automated selection of cryo-EM particles
Paper 2016Vilas_AutomaticTilt Automatic identification of image pairs in untilted-tilted micrograph pairs
Paper 2016Wang_DeepPicker A deep learning approach for fully automated particle picking
Paper 2017Rickgauer_Detection Picking by correlation
Paper 2017Zhu_DeepEM Deep learning approach to picking
Paper 2018Huber_Helices Automated tracing of helices
Paper 2018Heimowitz_ApplePicker Automated particle picking
Paper 2018Sanchez_DeepConsensus Deep learning consensus of multiple automatic pickers
Paper 2019Alazzawi_Clustering Use of clustering algorithms to find particles in micrographs
Paper 2019Bepler_Topaz Deep learning for particle picking
Paper 2019Carrasco_IP Use of standard image processing for particle picking
Conference 2019Li_Deep Deep learning for particle picking without box size
Paper 2019Wagner_Cryolo Deep learning for particle picking
Paper 2019Wang_Biobjective Biobjective function for robust signal detection
Paper 2019Zhang_Pixer Deep learning for particle picking
Paper 2020Sanchez_Cleaner Deep learning for removing particles from the carbon edges, aggregations, contaminations, ...
Conference 2021Li_PickerOptimizers Removal of badly picked particles with Deep Learning
Paper 2021Ohashi_GRIPS Two-pass picking with GRIPS
Paper 2022Eldar_ASOCEM Automatic segmentation of contaminations
Conference 2022Huang_DenoisingAndPicking Simultaneous denoising and picking with deep learning
Paper 2022Olek_Icebreaker Ice thickness detection and its use for particle picking
Paper 2022Zhang_EPicker Particle picking based on continual learning
Paper 2023Dhakal_CryoPPP A public database for particle picking

2D Preprocessing

Paper 1978Carrascosa_matching Gray values matching by linear transformations
Paper 2003Rosenthal_DPR Contrast enhancement through DPR
Paper 2004Sorzano_Normalization Normalization procedures and their statistical properties.
Paper 2006Sorzano_Denoising Strong denoising in wavelet space
Conference 2009Sorzano_Downsampling Differences between the different downsampling schemes
Paper 2012Brilot_Movies Alignment of beam induced motion in direct detectors
Paper 2012Campbell_Movies Alignment of beam induced motion in direct detectors
Paper 2012Zhao_Denoising Denoising using an invariant Fourier-Bessel eigenspace
Paper 2013Norousi_Screening Screening particles to identify outliers
Paper 2013Bai_ElectronCounting Electron counting and beam induced motion correction
Paper 2013Li_ElectronCounting Electron counting and beam induced motion correction
Paper 2013Shigematsu_Movies Drift correction for movies considering dark field
Paper 2013Vargas_ParticleQuality Automatic determination of particle quality
Paper 2014Scheres_Movies Beam induced motion correction
Paper 2015Abrishami_Movies Alignment of direct detection device micrographs
Paper 2015Grant_Anisotropic Automatic estimation and correction of anisotropic magnification
Paper 2015Grant_OptimalExposure Filter movies according to the radiation damage
Paper 2015Rubinstein_Alignment Frame alignment at the level of particle
Paper 2015Spear_DoseCompensation Effect of dose compensation on resolution
Paper 2015Zhao_AnisotropicMagnification Correction of anisotropic magnification
Conference 2016Bajic_Denoising Denoising and deconvolution of micrographs
Paper 2016Jensen_RemovalVesicles Removal of vesicles in membrane proteins
Paper 2016Bhamre_Denoising Denoising by 2D covariance estimation
Paper 2017Berndsen_EMPH Automated hole masking algorithm
Paper 2017McLeod_Zorro Movie alignment by Zorro
Paper 2017Zheng_MotionCorr2 Movie alignment by MotionCorr2
Paper 2018Ouyang_Denoising Denoising based on geodesic distance
Paper 2018Wu_ContrastEnhancement Contrast enhancement
Paper 2019Zivanov_BayesianBIM Bayesian correction of beam induced movement
Paper 2020Bepler_TopazDenoise Preprocessing of micrographs for better picking
Paper 2020Chung_2SDR PCA to denoise particles
Paper 2020Chung_Prepro Preprocessing of particles for better alignment
Conference 2020Huang_SuperResolution Deep learning superresolution combination of frames
Paper 2020Palovcak_noise2noise Noise2noise denoising of micrographs
Paper 2020Strelak_FlexAlign Continuous deformation model for aligning movie frames
Conference 2021Fan_Denoising Particle denoising using vector diffusion maps
Paper 2022Heymann_ProgressiveSSNR Progressive SSNR to assess quality and radiation damage
Paper 2022Shi_Denoising Contrast estimation and denoising in SPA
Paper 2023Huang_ZSSR Multiple image super-resolution, upsampling with deep learning
Paper 2023Marshall_PCA Fast PCA on single particle images
Paper 2023Sharon_Enhancement Signal enhancement of SPA particles
Paper 2023Strelak_MovieAlignment Comparison of movie alignment programs

2D Alignment

Paper 1981Frank_Averaging 2D averaging and phase residual
Paper 1982Saxton_Averaging 2D averaging using correlation
Paper 1998Sigworth_ML2D Maximum likelihood alignment in 2D
Paper 2003Cong_FRM2D Fast Rotational Matching in 2D
Paper 2005Cong_FRM2D Fast Rotational Matching in 2D introduced in a 3D Alignment algorithm
Paper 2005Scheres_ML2D Multireference alignment and classification in 2D
Paper 2016Aguerrebere_Limits Fundamental limits of 2D translational alignment
Paper 2010Sorzano_CL2D Multireference alignment and classification in 2D
Conference 2017Anoshina_Correlation New correlation measure for aligning images
Paper 2019Radermacher_Correlation On the properties of cross correlation for the alignment of images
Paper 2020Lederman_representation A representation theory perspective of alignment and classification
Paper 2020Marshall_Invariants Recovery of an image from its invariants
Paper 2021Chen_Fast Fast alignment through Power Spectrum
Conference 2021Chung_CryoRALIB Image alignment acceleration
Paper 2021Heimowitz_Centering Centering noisy images

2D Classification and clustering

Paper 1981VanHeel_MSA Multivariate Statistical Analysis
Paper 1984VanHeel_MSA Multivariate Statistical Analysis
Paper 2005Scheres_ML2D Multireference alignment and classification in 2D
Paper 2010Sorzano_CL2D Multireference alignment and classification in 2D
Paper 2011Singer_DiffusionMaps Classification in 2D based on graph analysis of the projections
Paper 2012Yang_ISAC Iterative Stable Alignment and clustering
Paper 2014Sorzano_Outlier Outlier detection in 2D classifications.
Paper 2014Zhao_Aspire Fast classification based on rotational invariants and vector diffusion maps
Paper 2015Huang_Robust Robust w-estimators of 2D classes
Paper 2016Kimanius_Accelerated GPU Accelerated image classification and high-resolution refinement
Paper 2016Reboul_Stochastic Stochastic Hill Climbing for calculating 2D classes
Conference 2017Bhamre_Mahalanobis 2D classification using Mahalanobis distance
Paper 2017Wu_GTM 2D classification using Generative Topographic Mapping
Conference 2018Boumal_SinglePass Single pass classification
Conference 2018Shuo_Network 2D Clustering by network metrics
Conference 2020Miolane_VAEGAN 2D Analysis by deep learning
Conference 2021Rao_Wasserstein Wasserstein K-Means for Clustering Tomographic Projections
Paper 2022Wang_Spectral 2D classification with spectral clustering
Paper 2022Zhang_DRVAE 2D classification with deep learning and K-means++
Paper 2023Chen_Joint 2D classification with deep learning and joint unsupervised difference learning

3D Alignment

Paper 1980Kam_AutoCorrelation Reconstruction without angular assignment from autocorrelation function (reference free)
Paper 1986Goncharov_CommonLines Angular assignment using common lines (reference free)
Paper 1987VanHeel_CommonLines Angular assignment using common lines (reference free)
Paper 1988Provencher_Simultaneous Simultaneaous alignment and reconstruction
Paper 1988Radermacher_RCT Random Conical Tilt and Single axis tilt
Paper 1988Vogel_Simultaneous Simultaneaous alignment and reconstruction
Paper 1990Gelfand_Moments Angular assignment using moments (reference free)
Paper 1990Goncharov_Moments Angular assignment using moments (reference free)
Paper 1990Harauz_Quaternions Use of quaternions to represent rotations
Paper 1994Penczek_Real Angular assignment using projection matching in real space
Paper 1994Radermacher_Radon Angular assignment in Radon space
Paper 1996Penczek_CommonLines Angular assignment using common lines (reference free)
Paper 2003Rosenthal_DPR Angular assignment using DPR
Paper 2004Sorzano_Wavelet Angular assignment in the wavelet space.
Paper 2005Jonic_Splines Angular assignment in Fourier space using spline interpolation.
Paper 2005Yang_Simultaneous Simultaneaous alignment and reconstruction
Paper 2006Ogura_SimulatedAnnealing Angular asignment by simulated annealing
Paper 2007Grigorieff_Continuous Continuous angular assignment in Fourier space
Paper 2010Jaitly_Bayesian Angular assignment by a Bayesian method and annealing
Paper 2010Sanz_Random Random model method
Paper 2010Singer_Voting Detecting consistent common lines by voting (reference free)
Paper 2011Singer_SDP Angular assignment by semidefinite programming and eigenvectors (reference free)
Paper 2012Giannakis_Scattering Construction of an initial volume, reference free, by graph analysis of the projections
Paper 2012Shkolnisky_Sync Angular assignment by synchronization of rotations (reference free)
Paper 2013Elmlund H_PRIME PRIME: Probabilistic Initial 3D Model Generation for Single-Particle Cryo-Electron Microscopy
Paper 2013Wang_LUD Angular assignment by least unsquared deviations (reference free)
Paper 2014Vargas_RANSAC Initial model using RANSAC (reference free)
Paper 2015Joubert_Pseudoatoms Initial model based on pseudo-atoms
Paper 2015Singer_Kam Reconstruction without angular assignment from autocorrelation function (reference free)
Paper 2015Sorzano_Significant Statistical approach to the initial volume estimation (reconstruct significant)
Paper 2016Cossio_BayesianGPU GPU implementation of the Bayesian 3D reconstruction approach
Conference 2016Michels_Heterogeneous Initial volume in the presence of heterogeneity
Paper 2016Pragier_Graph Graph partitioning approach to angular reconstitution
Paper 2017Greenberg_CommonLines Common lines for reference free ab-initio reconstruction
Paper 2018Sorzano_Highres New algorithm for 3D Reconstruction and alignment with emphasis on significance
Paper 2018Sorzano_Swarm Consensus of several initial volumes by swarm optimization
Paper 2019Zehni_Joint Continuous angular refinement and reconstruction
Paper 2019Zehni_Joint Continuous angular refinement and reconstruction
Paper 2020Sharon_NonUniformKam Reconstruction and angular distribution estimation without angular assignment (reference free)
Paper 2020Xie_Network Angular assignment considering a network of assignments
Paper 2021Jimenez_DeepAlign Angular alignment using deep learning
Paper 2021Kojima_Preferred Identification of preferred orientations
Conference 2021Nashed_CryoPoseNet CryoPoseNet: Angular alignment with deep learning
Conference 2021Zhong_CryoDRGN2 CryoDRGN2: Angular alignment with deep learning
Paper 2022Lu_SphericalEmbeddings Angular assignment through common lines and spherical embeddings
Paper 2022Wang_Thunder Angular assignment implementation in GPU

3D Reconstruction

Paper 1972Gilbert_SIRT Simultaneous Iterative Reconstruction Technique (SIRT)
Paper 1973Herman_ART Algebraic Reconstruction Technique (ART)
Paper 1980Kam_SphericalHarmonics 3D Reconstruction using spherical harmonics
Paper 1984Andersen_SART Simultaneous Algebraic Reconstruction Technique (SART)
Paper 1986Harauz_FBP Exact filters for Filtered Back Projection
Chapter 1992Radermacher_WBP Exact filters for Weighted Back Projection
Paper 1997Zhu_RecCTF 3D Reconstruction (SIRT like) and simultaneous CTF correction
Paper 1998Boisset_Uneven Artifacts in SIRT and WBP under uneven angular distributions
Paper 1998Marabini_ART Algebraic Reconstruction Technique with blobs (Xmipp)
Paper 2001Sorzano_Uneven Free parameter selection under uneven angular distributions
Paper 2005Sorzano_Parameters Free parameter selection for optimizing multiple tasks
Paper 2008Sorzano_Constraints Mass, surface, positivity and symmetry constraints for real-space algorithms
Paper 2009Bilbao_ParallelART Efficient parallelization of ART
Paper 2011Li_GradientFlow Regularized 3D Reconstruction by Gradient Flow
Paper 2011Vonesch_Wavelets Fast wavelet-based 3D reconstruction
Paper 2012Gopinath_ShapeRegularization Regularized 3D Reconstruction by Shape information
Paper 2012Kucukelbir_adaptiveBasis 3D reconstruction in an adaptive basis promoting sparsity
Paper 2012Sindelar_NoiseReduction Optimal noise reduction in 3D reconstructions
Paper 2013Elmlund H_PRIME PRIME: Probabilistic Initial 3D Model Generation for Single-Particle Cryo-Electron Microscopy
Paper 2013Lyumkis_Optimod Construction of initial volumes with Optimod
Paper 2013Wang FIRM Fast 3D reconstruction in Fourier domain
Paper 2014Kunz_SART_OS Simultaneous ART with OS
Paper 2015Abrishami_Fourier 3D Reconstruction in Fourier space
Paper 2015Dvornek_SubspaceEM Fast Maximum a posteriori
Paper 2015Moriya_Bayesian Bayesian approach to suppress limited angular artifacts
Paper 2015Xu_GeometricFlow Multi-scale geometric flow
Arxiv 2016Ye_Cohomology Cohomology properties of 3D reconstruction
Paper 2017Barnett_Marching Initial volume through frequency marching
Paper 2017Punjani_CryoSPARC CryoSPARC
Paper 2017Punjani_CryoSPARCTheory Theory related to CryoSPARC
Paper 2017Sorzano_SurveyIterative Survey of iterative reconstruction methods for EM
Paper 2018Bartesaghi_Refinement Refinement of CTF, frame weight and alignment for high resolution reconstruction
Paper 2018Hu_ParticleFilter A particle filter framework for 3D reconstruction
Conference 2018Levin_Kam Ab initio reconstruction by autocorrelation analysis
Conference 2018Michels_RBF Ab-initio reconstruction with radial basis functions
Paper 2018Reboul_Simple Ab initio reconstruction with Simple
Paper 2018Sorzano_Highres New algorithm for 3D Reconstruction and alignment with emphasis on significance
Paper 2018Sorzano_Swarm Consensus of several initial volumes by swarm optimization
Paper 2018Zhu_Ewald 3D Reconstruction with Ewald sphere correction
Paper 2019Gomez_Initial Construction of initial models
Master 2019Havelkova_Regularization Regularization methods in 3D reconstruction
Paper 2019Wilkinson_Scales Combining data acquired at different scales
Paper 2020Alazzawi_Auto Automatic full processing of micrographs to yield a 3D reconstruction
Paper 2020Pan_TV 3D Reconstruction with total variation regularization
Paper 2020Punjani_NonUniform Non-uniform refinement
Paper 2020Ramlaul_Sidesplitter Local filtering along the reconstruction iterations
Paper 2020Xie_Automatic Automatic 3D reconstruction from projections
Conference 2020Venkatakrishnan_MBIR Model based image reconstruction
Paper 2020Zhou_AutomaticSelection Automatic selection of particles for 3D reconstruction
Paper 2021Abrishami_Localized Localized reconstruction in scipion expedites the analysis of symmetry mismatches in Cryo-EM data
Paper 2021Gupta_CryoGAN 3D Reconstruction via Generative Adversarial Learning
Paper 2021Luo_Opus 3D Reconstruction with a sparse and smoothness constraint
Paper 2021Kimanius_PriorKnowledge Incorporation of prior knowledge during 3D reconstruction
Paper 2021Sorzano_Uneven Algorithmic robustness to uneven angular distributions
Paper 2022Havelkova_regularization Regularization of iterative reconstruction algorithms
Paper 2023Bendory_Autocorrelation Initial volume through autocorrelation analysis with sparsity constraints
Paper 2023Herreros_ZART Correction of continuous heterogeneity during the 3D reconstruction
Paper 2023Rangan_AbInitio Robust ab initio reconstruction

3D Heterogeneity

Paper 2004White_Size Heterogeneity classification of differently sized images
Paper 2006Penczek_Bootstrap 3D heterogeneity through bootstrap
Paper 2007Leschziner_Review Review of 3D heterogeneity handling algorithms
Paper 2007Scheres_ML3D Maximum Likelihood alignment and classification in 3D
Paper 2008Herman_Graph Classification by graph partitioning
Paper 2009Spahn_Bootstrap 3D heterogeneity through bootstrap
Paper 2010Elmlund_AbInitio Solving the initial volume problem with multiple conformations
Paper 2010Shatsky_MultiVariate Multivariate Statistical Analysis
Paper 2012Scheres_Bayesian A Bayesian view on cryo-EM structure determination
Paper 2012Zheng_Covariance Estimation of the volume covariance
Paper 2013Wang_MLVariance Maximum Likelihood estimate of the map variance
Paper 2013Lyumkis D_FREALIGN Likelihood-based classification of cryo-EM images using FREALIGN.
Paper 2014Chen_Migration Particle migration analysis in 3D classification
Paper 2014Dashti_Brownian Continuous heterogeneity through Brownian trajectories
Paper 2014Schwander_manifold Continuous heterogeneity through Manifold Analysis
Paper 2014Jin_NMA HEMNMA: Continuous heterogeneity through Normal Mode Analysis
Paper 2015Anden_Covariance 3D Covariance matrix estimation for heterogeneity
Paper 2015Bai_Focused Focused classification
Paper 2015Katsevich_Covariance 3D Covariance matrix estimation for heterogeneity
Paper 2015Klaholz_MRA Multivariate Statistical Analysis of Jackknife and Bootstrapping on random subsets
Paper 2015Liao_Covariance Estimation of the 3D covariance from 2D projections
Paper 2015Tagare_Direct Direct reconstruction of PCA components
Paper 2016Gong_Mechanical Mechanical model for macromolecules
Paper 2016Rawson_Movement Movement and flexibility
Paper 2016Shan_Multibody Multibody refinement
Paper 2016Sorzano_StructMap Sorting a discrete set of conformational states
Paper 2016Sorzano_Strain Calculate local stretches, strains and rotations from two conformational states
Paper 2017Punjani_CryoSPARC CryoSPARC
Paper 2017Schillbach_Warpcraft Warpcraft: 3D Reconstruction in the presence of continuous heterogeneity
Paper 2018Anden_Covariance Structural Variability from Noisy Tomographic Projections
Paper 2018Haselbach_FreeEnergy Analysis of the free energy landscape through PCA
Paper 2018Nakane_MultiBody Structural Variability through multi-body refinement
Paper 2019Serna_Review Review of classification tools
Paper 2018Solernou_FFEA Fluctuating Finite Element Analysis, continuum approach to Molecular Dynamics
Paper 2019Sorzano_Review Review of continuous heterogeneity biophysics
Paper 2019Zhang_Local Local variability and covariance
Paper 2020Dashti_Landscape Retrieving functional pathways from single particle snapshots
Conference 2020Gupta_MultiCryoGAN Reconstruction of continuously heterogeneous structures with adversarial networks
Paper 2020Harastani_NMA HEMNMA in Scipion : Using HEMNMA for analyzing continuous heterogeneity with normal modes
Paper 2020Maji_Propagation Propagation of conformational coordinates across angular space
Paper 2020Moscovich_DiffusionMaps Heterogeneity analysis by diffusion maps and spectral volumes
Paper 2020Seitz_Polaris Analysis of energy landscapes to find minimal action paths
Conference 2020Zhong_CryoDRGN CryoDRGN to analyze the continuous heterogeneity by CryoEM
Paper 2020Verbeke_Separation Heterogeneity analysis by comparing common lines
Paper 2021Chen_GM Deep learning-based mixed-dimensional Gaussian mixture model for characterizing variability
Paper 2021Giraldo_cryoBIFE A Bayesian approach to extracting free‑energy profiles
Conference 2021Hamitouche_NMADL Continuous heterogeneity analysis through normal modes and deep learning
Paper 2021Herreros_Zernikes3D Continuous heterogeneity analysis through Zernikes 3D
Paper 2021Kazemi_Enrich ENRICH: A fast method to improve the quality of flexible macromolecular reconstructions
Paper 2021Matsumoto_DEFmap Prediction of RMSF of Molecular Dynamics from a CryoEM map using deep learning
Chapter 2021Nakasako_Landscape Estimation of free-energy landscape from images
Paper 2021Punjani_3DVA 3D Variability analysis from images
Paper 2021Sorzano_PCA PCA is limited to low-resolution
Paper 2021Zhong_CryoDRGN CryoDRGN to analyze the continuous heterogeneity by CryoEM
Paper 2022Ecoffet_MorphOT More physically plausible morphing between two states
Paper 2022Gomez_Hierarchical Hierarchical classification of particles
Paper 2022Hamitouche_DeepHEMNMA DeepHEMNMA: Continuous heterogeneity analysis through normal modes and deep learning
Conference 2022Levy_CryoFire CryoFire: heterogeneity and alignment through amortized inference
Paper 2022Rabuck_Quant Workflow for discrete heterogeneity analysis
Paper 2022Skalidis_Endogenous AI tools to recognize proteins in cellular fractions
Paper 2022Wu_Manifold Continuous heterogeneity through manifold learning
Paper 2022Zhou_Data Determination of the number of discrete 3D classes
Paper 2023Barchet_Focused Applications and strategies in focused classification and refinement
Paper 2023Chen_GMM Continuous heterogeneity analysis with GMMs and neural networks
Paper 2023Dsouza_benchmark Benchmark analysis of various continuous heterogeneity algorithms
Paper 2023Esteve_Spectral Continuous heterogeneity analysis through the spectral decomposition of the atomic structure
Paper 2023Fernandez_Subtraction Subtraction of unwanted signals to improve classification and alignment
Paper 2023Herreros_Hub Flexibility hub: an integrative platform for continuous heterogeneity
Paper 2023Luo_OpusDSD OPUS DSD: a neural network approach to continuous heterogeneity
Paper 2023Kinman_Analysis Analysis of the continuous heterogeneity results of CryoDrgn
Paper 2023Matsumoto_DEFmap Quantitative analysis of the prediction of RMSF from a map using DefMap
Paper 2023Punjani_3DFlex Continuous heterogeneity through 3DFlex
Paper 2023Seitz_Geometric Geometric relationships between manifold embeddings of a continuum of 3D molecular structures and their 2D projections
Paper 2023Seitz_ESPER Continuous heterogeneity through Embedded subspace partitioning and eigenfunction realignment
Paper 2023Tang_Reweighting Ensemble reweighting using Cryo-EM particles
Paper 2023Vuillemot_MDSPACE MDSPACE: Continuous heterogeneity analysis through normal modes and MD simulation
Paper 2023Wang_Autoencoder Discrete heterogeneity based on autoencoders
Paper 2024Chen_Focused Focused reconstruction of heterogeneous macromolecules

Validation

Paper 2008Stagg_TestBed Effect of voltage, dosis, number of particles and Euler jumps on resolution
Paper 2011Henderson Tilt Validation
Paper 2011Read Validation of PDBs
Paper 2012Henderson EM Map Validation
Paper 2013Cossio_Bayesian EM Map Validation in a probabilistic setting
Paper 2013Chen_NoiseSubstitution Noise substitution at high resolution for measuring overfitting
Paper 2013Ludtke_Validation Structural validation, example of the Calcium release channel
Paper 2013Murray_Validation Validation of a 3DEM structure through a particular example
Paper 2014Russo_StatisticalSignificance EM Map Validation through the statistical significance of the tilt-pair angular assignment
Paper 2014Stagg_Reslog EM Map Validation through the resolution evolution with the number of particles
Paper 2014Wasilewski_Tilt Web implementation of the tilt pair validation
Paper 2015Heymann_Alignability EM Map Validation through the resolution of reconstructions from particles and noise
Paper 2015Oliveira_FreqLimited Comparison of gold standard and frequency limited optimization
Paper 2015Rosenthal_Review Review of validation methods
Paper 2015Wriggers_Secondary Validation by secondary structure
Paper 2016Degiacomi_IM Comparison of Ion Mobility data and EM volumes
Paper 2016Kim_SAXS Comparison of SAXS data and EM projections
Paper 2016Rosenthal_Review Review of validation methods
Paper 2016Vargas_Alignability Validation by studying the tendency of an angular assignment to cluster in the projection space
Paper 2017Monroe_PDBRefinement Validation by comparison to a refined PDB
Paper 2018Afonine_Phenix Tools in Phenix for the validation of EM maps
Paper 2018Heymann_Bsoft Map validation using Bsoft
Paper 2018Heymann_Challenge A summary of the assessments of the 3D Map Challenge
Paper 2018Jonic_Gaussian Assessment of sets of volumes by pseudoatomic structures
Paper 2018Naydenova_AngularDistribution Evaluating the angular distribution of a 3D reconstruction
Paper 2018Pages_Symmetry Looking for a symmetry axis in a PDB
Paper 2018Pintilie_SSE Evaluating the quality of SSE and side chains
Paper 2019Herzik_Multimodel Local and global quality by multi-model fitting
Paper 2020Chen_Atomic Validation of the atomic models derived from CryoEM
Paper 2020Cossio_CrossValidation Need for cross validation
Paper 2020Ortiz_CrossValidation Cross validation for SPA
Paper 2020Sazzed_helices Validation of helix quality
Paper 2020Stojkovic_PTM Validation of post-translational modifications
Paper 2020Tiwari_PixelSize Fine determination of the pixel size
Paper 2021Mendez_Graph Identification of incorrectly oriented particles
Paper 2021Pintilie_Validation Review of map validation approaches
Paper 2021Olek_FDR Cryo-EM Map–Based Model Validation Using the False Discovery Rate Approach
Paper 2022Garcia_DeepHand Checking the correct handedness with a neural network
Paper 2022Sorzano_Bias Bias, variance, gold-standard and overfitting in SPA
Paper 2022Sorzano_Validation Validation scheme and server for SPA
Paper 2022Terashi_DAQ Validation of models fitted into CryoEM maps
Paper 2022Waarshamanage_EMDA Validation of models fitted into CryoEM maps
Paper 2024Verbeke_SelfFSC Self FSC: FSC with a single map

Resolution

Paper 1986Harauz_FBP Fourier Shell Correlation
Paper 1987Unser_SSNR 2D Spectral Signal to Noise Ratio
Paper 2002Penczek_SSNR 3D Spectral Signal to Noise Ratio for Fourier based algorithms
Paper 2003Rosenthal_DPR Review of the FSC and establishment of a new threshold
Paper 2005Unser_SSNR 3D Spectral Signal to Noise Ratio for any kind of algorithms
Paper 2005VanHeel_FSC Establishment of a new threshold for FSC
Paper 2007Sousa_AbInitio Resolution measurement on neighbour Fourier voxels
Paper 2014Kucukelbir_Local Quantifying the local resolution of cryo-EM density maps
Paper 2016Pintilie_Probabilistic Probabilistic models and resolution
Paper 2017Sorzano_FourierProperties Statistical properties of resolution measures defined in Fourier space
Conference 2018Avramov_DeepLearning Deep learning classification of volumes into low, medium and high resolution
Paper 2018Carugo_BFactors How large can B-factors be in protein crystals
Conference 2018Kim_FourierError Comparison between a gold standard and a reconstruction
Paper 2018Rupp_Problems Problems of resolution as a proxy number for map quality
Paper 2018Vilas_MonoRes Local resolution by monogenic signals
Paper 2018Yang_Multiscale Resolution from a multiscale spectral analysis
Paper 2019Avramov_DeepLearning Deep learning classification of volumes into low, medium and high resolution
Paper 2019Heymann_Statistics SNR, FSC, and related statistics
Paper 2019Ramirez_DeepRes Resolution determination by deep learning
Paper 2020Baldwin_Lyumkis_SCF Resolution attenuation through non-uniform Fourier sampling
Paper 2020Beckers_Permutation Permutation tests for the FSC
Paper 2020Penczek_mFSC Modified FSC to avoid mask induced artifacts
Paper 2020Vilas_MonoDir Local and directional resolution
Paper 2023Dai_CryoRes Local resolution through deep learning
Paper 2023Vilas_FSO Fourier Shell Occupancy to measure anisotropy

Sharpening of high resolution information

Paper 2003Rosenthal_DPR Contrast restoration and map sharpening
Paper 2008Fernandez_Bfactor Bfactor determination and restoration
Paper 2013Fiddy_SaxtonAlgorithm Phase retrieval or extension
Paper 2014Kishchenko_SphericalDeconvolution Spherical deconvolution
Paper 2015Spiegel_VISDEM Visualization improvement by the use of pseudoatomic profiles
Paper 2016Jonic_Pseudoatoms Approximation with pseudoatoms
Paper 2016Jonic_Denoising Denoising and high-frequency boosting by pseudoatom approximation
Paper 2017Jakobi_LocScale Sharpening based on an atomic model
Paper 2019Ramlaul_Filtering Local agreement filtering (denoising)
Conference 2020Mullick_SuperResolution Superresolution from a map
Paper 2020Ramirez_LocalDeblur Local deblur (local Wiener filter)
Paper 2020Terwilliger_density Density modification of CryoEM maps
Paper 2020Vilas_Bfactor Global B-factor correction does not represent macromolecules
Paper 2021Beckers_Interpretation Improvements from the raw reconstruction to a structure to model
Paper 2021Kaur_LocSpiral LocSpiral, LocBsharpen, LocBfactor
Paper 2021Fernandez_Adjustment Map adjustment for subtraction, consensus and sharpening
Paper 2021Sanchez_DeepEMhancer Deep learning algorithm for volume restoration
Paper 2022Gilles_Wilson A molecular prior distribution for Bayesian inference based on Wilson statistics
Paper 2022Vargas_tubular Map enhancement by multiscale tubular filter
Paper 2023He_EMReady Map enhancement with local and non-local deep learning (EMReady)
Paper 2023Maddhuri_EMGan Map enhancement with GANs (EMGan)

CTF estimation and restoration

Paper 1982Schiske_Correction CTF correction for tilted objects
Paper 1988Toyoshima_Model CTF estimation
Paper 1995Frank_Wiener CTF correction using Wiener filter
Paper 1996Skoglund_MaxEnt CTF correction with Maximum Entropy
Paper 1996Zhou_Model CTF model and user interface for manual fitting
Paper 1997Fernandez_AR PSD estimation using periodogram averaging and AR models
Paper 1997Penczek_Wiener CTF correction using Wiener filter
Paper 1997Stark_Deconvolution CTF correction using deconvolution
Paper 1997Zhu_RecCTF CTF correction and reconstruction
Paper 2000DeRosier_EwaldCorrection CTF correction considering the Ewald sphere
Paper 2000Jensen_TiltedCorrection CTF correction considering tilt in backprojection
Paper 2001Saad_CTFEstimate CTF estimation
Paper 2003Huang_CTFEstimate CTF estimation
Paper 2003Mindell_CTFTILT CTF estimation for tilted micrographs
Paper 2003Sander_MSA CTF estimation through MSA classification of PSDs
Paper 2003Velazquez_ARMA PSD and CTF estimation using ARMA models
Paper 2004Sorzano_IDR CTF restoration and reconstruction with Iterative Data Refinement
Conference 2004Wan_CTF Spatially variant CTF
Paper 2004Zubelli_Chahine CTF restoration and reconstruction with Chahine's multiplicative method
Conference 2005Dubowy_SpaceVariant CTF correction when this is space variant
Paper 2005Mallick_ACE CTF estimation
Paper 2006Wolf_Ewald CTF correction considering Ewald sphere
Paper 2007Jonic_EnhancedPSD PSD enhancement for better identification of Thon rings; Vitreous ice diffracts in Thon rings
Paper 2007Philippsen_Model CTF Model for tilted specimens
Paper 2007Sorzano_CTF CTF estimation using enhanced PSDs
Paper 2009Sorzano_Sensitivity Error sensitivity of the CTF models, non-uniqueness of the CTF parameters
Paper 2010Jiang2010_CTFCorrection Amplitude correction method
Paper 2010Kasantsev_CTFCorrection Mathematical foundations of Kornberg and Jensen method
Paper 2010Leong_CTFCorrection Correction for spatially variant CTF
Paper 2011Glaeser_Coma The effect of coma at high-resolution
Paper 2011Mariani_Tilted CTF simulation and correction of tilted specimens
Paper 2011Sindelar_Wiener CTF correction using a modified version of Wiener filter
Paper 2011Voortman_Tilted CTF correction for tilted specimen
Paper 2012Voortman_VaryingCTF Correcting a spatially varying CTF
Paper 2013Vargas_FastDef Fast defocus
Paper 2014Penczek_CTER Estimation of the CTF errors
Paper 2015Rohou_CTFFind4 CTF Find 4
Paper 2015Sheth_CTFquality Visualization and quality assessment of CTF
Paper 2016Zhang_GCTF gCTF
Paper 2018Su_GoCTF goCTF, CTF for tilted specimens
Paper 2020Heimowitz_Aspire CTF determination in Aspire
Paper 2020Zivanov_HighOrder Estimation of high order aberrations

Segmentation

Paper 2006Baker_segmentation Segmentation of molecular subunits
Paper 2010Pintilie_segger Segmentation of molecular subunits
Conference 2017Nissenson_VolumeCut Segmentation of an EM volume using an atomic model
Paper 2019Beckers_FDR Segmentation of the protein using False Discovery Rate
Paper 2020Beckers_FDR Segmentation of the protein using False Discovery Rate (GUI)
Paper 2020Farkas_MemBlob Segmentation of membrane in membrane embedded proteins
Paper 2020Terashi_MainMastSeg Segmentation of proteins into domains
Paper 2021He_EMNUSS EMNUSS: Identification of secondary structure in CryoEM maps with deep learning

Fitting and docking

Paper 1999Volkmann_Fitting Fitting in real space
Paper 2001Baker_Review Review of protein structure prediction
Paper 2001Jones_Review Review of protein structure prediction
Paper 2003Kovacs_FRM3D Fast Rotational Alignment of two EM maps
Paper 2004Tama_NMA1 Flexible fitting with Normal Modes (I)
Paper 2004Tama_NMA2 Flexible fitting with Normal Modes (II)
Paper 2005Velazquez_Superfamilies Recognition of the superfamily folding in medium-high resolution volumes
Paper 2007DeVries_Haddock Docking with Haddock 2.0
Paper 2007Kleywegt_QualityControl Quality control and validation of fitting
Paper 2008Orzechowski_Flexible Flexible fitting with biased molecular dynamics
Paper 2008Rusu_Interpolation Biomolecular pleiomorphism probed by spatial interpolation of coarse models
Paper 2012Biswas_Secondary Secondary structure determination in EM volumes
Paper 2012Velazquez_Constraints Multicomponent fitting by using constraints from other information sources
Paper 2013Chapman MS_Atomicmodeling Atomic modeling of cryo-electron microscopy reconstructions--joint refinement of model and imaging parameters
Paper 2013Esquivel_Modelling Review on modelling (secondary structure, fitting, ...)
Paper 2013Lopez_Imodfit Fitting based on vibrational analysis
Paper 2013Nogales_3DEMLoupe Normal Mode Analysis of reconstructed volumes
Paper 2014AlNasr_Secondary Identification of secondary structure elements in EM volumes
Paper 2014Politis_MassSpect Integration of mass spectroscopy information
Paper 2014Rey_MassSpect Integration of mass spectroscopy information
Paper 2014Villa_Review Review of atomic fitting into EM volumes
Paper 2015Barad_EMRinger Validation of hybrid models
Paper 2015Bettadapura_PF2Fit Fast rigid fitting of PDBs into EM maps
Paper 2015Carrillo_CapsidMaps Analysis of virus capsids using Google Maps
Paper 2015Hanson_Continuum Modelling assemblies with continuum mechanics
Paper 2015Lopez_Review Review of structural modelling from EM data
Paper 2015Schroeder_Hybrid Review on model building
Paper 2015Tamo_Dynamics Dynamics in integrative modeling
Paper 2015Sorzano_AtomsToVoxels Accurate conversion of an atomic model into a voxel density volume
Paper 2016Joseph_Evolution Evolutionary constraints for the fitting of atomic models into density maps
Paper 2016Joseph_Refinement Refinement of atomic models in high-resolution EM reconstructions using Flex-EM
Paper 2016Murshudov_Refinement Refinement of atomic models in high-resolution EM reconstructions
Paper 2016Segura_3Diana Validation of hybrid models
Paper 2016Singharoy_MDFF Construction of hybrid models driven by EM density and molecular dynamics
Paper 2016Wang_Rosetta Construction of hybrid models driven by EM density using Rosetta
Paper 2017Chen_CoarseGraining Coarse graining of EM volumes
Paper 2017Joseph_Metrics Metrics analysis for the comparison of structures
Paper 2017Hryc_WeightedAtoms Construction of hybrid models by locally weighting the different atoms
Paper 2017Matsumoto_Distribution Estimating the distribution of conformations of atomic models
Paper 2017Michel_ContactPrediction Structure prediction by contact prediction
Paper 2017Miyashita_EnsembleFitting Ensemble fitting using Molecular Dynamics
Paper 2017Turk_ModelBuilding Tutorial on model building and protein visualization
Paper 2017Wang_PartialCharges Appearance of partial charges in EM maps
Paper 2017Wlodawer Comparison of X-ray and EM high resolution structures
Paper 2018Cassidy_review Review of methods for hybrid modeling
Paper 2018Chen_SudeChains A comparison of side chains between X-ray and EM maps
Paper 2018Kawabata_Pseudoatoms Modelling the EM map with Gaussian pseudoatoms
Paper 2018Kovacs_Medium Modelling of medium resolution EM maps
Paper 2018Neumann_validation Validation of fitting, resolution assessment and quality of fit
Paper 2018Terwilliger_map_to_model Phenix map_to_model, automatic modelling of EM volumes
Paper 2018Wang_MD Constructing atomic models using molecular dynamics
Paper 2018Xia_MVPENM Multiscale Normal Mode Analysis
Paper 2018Yu_Atomic Constructing atomic models using existing tools
Paper 2019Bonomi_Multiscale Bayesian multi-scale modelling
Paper 2019Kidmose_Namdinator Namdinator: Flexible fitting with NAMD
Paper 2019Klaholz_Review Review of Phenix tools to modelling
Paper 2019Subramaniya_DeepSSE Secondary structure prediction from maps using deep learning
Paper 2019Zhang_CoarseGrained Coarse-graining of EM maps
Paper 2020Costa_MDeNM Flexible fitting with molecular dynamics and normal modes
Paper 2020Cragnolini_Tempy2 TEMpy2 library for density-fitting and validation
Paper 2020Dodd_ModelBuilding Model building possibilities, with special emphasis on flexible fitting
Paper 2020Ho_CryoID Identification of proteins in structural proteomics from cryoEM volumes
Paper 2020Hoh_Buccaneer Structure modelling with Buccaneer
Paper 2020Joseph_comparison Comparison of map and model, or two maps
Paper 2020Kim_Review Review of the options for atomic modelling
Paper 2020Leelananda_Constraints NMR Chemical Shifts and Cryo-EM Density Restraints in Iterative Rosetta-MD structure refinement
Paper 2020Liebschner_Ceres CERES: Web server of refined atomic maps of CryoEM deposited maps by Phenix
Paper 2020Oroguchi Assessment of Force Field Accuracy Using Cryogenic Electron Microscopy Data
Paper 2020Vant_Flexible Flexible fitting with molecular dynamics and neural network potentials
Paper 2021Behkamal_Secondary Secondary structure from medium resolution maps
Paper 2021Chojnowski_quality Quality of models automatically fitted with ARP/wARP
Paper 2021Han_Vesper VESPER: global and local cryo-EM map alignment using local density vectors
Paper 2021Lawson_Challenge Validation recommendations based on outcomes of the 2019 EMDataResource challenge
Paper 2021Mori_Flexible Efficient Flexible Fitting Refinement with Automatic Error Fixing
Paper 2021Pfab_DeepTracer DeepTracer for fast de novo cryo-EM protein structure modeling
Paper 2021Saltzberg_IMP Using the Integrative Modeling Platform to model a cryoEM map
Paper 2021Terwilliger_CryoID Identification of sequence in a CryoEM map from a set of candidates
Paper 2021Titarenko_LocalCorr Performance improvement of local correlation for docking
Conference 2021Vuillemot_NMA Flexible fitting using a combined Bayesian and Normal Mode approach with Hamiltonian Monte Carlo sampling
Paper 2022Antanasijevic_ab Sequence determination of antibodies bound to a map
Paper 2022Behkamal_LPTD LPTD: Topology determination of CryoEM maps
Paper 2022Chojnowski_findMySeq Identify sequence in CryoEM map using Deep Learning
Paper 2022Hryc_Pathwalking Atomic modelling with Pathwalking
Paper 2022He_EMBuild Atomic modelling for complexes with EMbuild
Paper 2022Krieger_Prody2 Protein dynamics developments for the large scale and cryoEM: case study of ProDy 2.0
Paper 2022Neijenhuis_Haddock Protein-protein interface refinement in complex maps with Haddock2.4
Paper 2022Urzhumtsev_Direct Calculation of the EM map from an atomic model
Paper 2022Urzhumtsev_XrayEM Effect of the local resolution on the atomic modeling
Paper 2022Vuillemot_NMMD NMMD: Flexible fitting with simultaneous Normal Mode and Molecular Dynamics displacements
Paper 2022Zhang_CRITASSER Atomic models of assemble protein structures with deep learning
Paper 2023Blau_FittingML Maximum-likelihood fitting of atomic models in EM maps
Paper 2023Chang_CryoFold Flexible fitting into cryo-EM maps with CryoFold (a MELD plugin)
Paper 2023Millan_LL Likelihood-based docking of models into cryo-EM maps
Paper 2023Park_CSA Atomic model fitting using conformational space annealing
Paper 2023Read_LL Likelihood-based signal and noise analysis for docking of models into cryo-EM maps
Paper 2023Reggiano_MEDIC Evaluation of atomic models using MEDIC
Paper 2023Terashi_DAQrefine Atomic model refinement using AlphaFold2 and DAQ
Paper 2023Terashi_DeepMainMast DeepMainMast: de novo modelling of CryoEM maps
Paper 2023Wang_CryoREAD CryoREAD: de novo modelling of nucleic acids

Books and reviews

Book 1980Herman_Tomography General book on tomography
Book 1988Kak_Tomography General book on tomography
Paper 2000Tao_Review Review of single particles
Paper 2000VanHeel_Review Review of single particles
Paper 2002Frank_Review Review of single particles
Paper 2002Schmid_Review Review of single particles
Paper 2004Henderson_Review Review of electron microscopy
Paper 2004Subramaniam_Review Review of single particles
Paper 2005Steven_Review Review of electron microscopy
Paper 2006Fernandez_Review Review of electron microscopy
Book 2006Frank_book Book covering all aspects of electron microscopy of single particles
Paper 2006Sorzano_Review Review of optimization problems in electron microscopy
Paper 2007Leschziner_Review Review of 3D heterogeneity handling algorithms
Paper 2007Sorzano_Review Review of the image processing steps
Paper 2008Fanelli_ImageFormation Review on the image formation model from the electron waves and open inverse-problems in Electron Tomography
Paper 2008Fernandez_HPCReview High performance computing in electron cryomicroscopy
Paper 2008Jonic_Review Comparison between electron tomography and single particles
Paper 2008Mueller_Review Review of Electron microscopy
Paper 2008Taylor_Review Review of Electron microscopy
Paper 2010DeRosier_Review Personal account of how 3DEM developed in the early days
Chapter 2012Sorzano_Review Review of single particle analysis using Xmipp
Chapter 2012Devaux_Protocol Protocols for performing single particle analysis
Paper 2014Bai_Review Recent advances in cryo-EM
Paper 2015Carazo_Review Review of the reconstruction process
Paper 2015Cheng_Review A primer to Single Particle Cryo-EM
Paper 2015Cheng_Reviewb Single Particle Cryo-EM at crystallographic resolution
Paper 2015Elmlund_Review Recent advances in cryo-EM
Paper 2015Henderson_Review Recent advances in cryo-EM
Paper 2015Nogales_Review Recent advances in cryo-EM
Paper 2015Schroeder_Review Review of advances in the electron microscope
Paper 2015VanDenBedem_Integrative Review of integrative structural biology
Paper 2015Wu_Review Review of advances in cryo-EM
Paper 2016Carroni_CryoEM Review of advances in Cryo-EM
Paper 2016Egelman_CryoEM Review of advances in Cryo-EM
Paper 2016Eisenstein_CryoEM News feature on the Method of the Year
Paper 2016FernandezLeiro_Review Review of EM
Paper 2016Glaeser_HowGood How good can cryo-EM become?
Paper 2016Jonic_PseudoAtoms Review of the applications of the use of pseudoatoms in EM
Chapter 2016Mio_Review Overview of the process to obtain EM reconstructions
Paper 2016Jonic_Review A review of computational ways to handle heterogeneity
Paper 2016Nogales_Review Review of advances in cryo-EM
Paper 2016Subramaniam_Review Why cryo-EM is now suitable for crystallographic journals
Paper 2016Vinothkumar_Review Historical review and current limitations
Report 2017Brezinski_Nobel Scientific background on the Nobel Prize in Chemistry 2017
Paper 2017Cheng_review Why CryoEM became so hot
Paper 2017Danev_Review Review of the use of phase plates in EM
Paper 2017Elmlund_Review Review of the main current difficulties of EM
Paper 2017Frank_Review Historical review of EM
Paper 2017Frank_TimeResolved Review of time-resolved of EM
Paper 2017Jonic_Review Review of computational methods to analyze conformational variability
Paper 2017Merino_DrugEM Applications of EM for drug design
Paper 2017Rawson_Limitations Limitations of EM for drug design
Paper 2017Sorzano_FourierProperties Review of statistical properties of resolution measures defined in Fourier space
Paper 2017Sorzano_SurveyIterative Survey of iterative reconstruction methods for EM
Paper 2018Bruggeman_Crowdsourcing Exploring crowdsourcing for EM image processing
Paper 2018Cheng_Review Review of EM and future ahead
Paper 2018Cossio_ML Review of Maximum Likelihood methods
Paper 2018Grimes_Crystallography Review of X-ray crystallography and its relationship to EM
Paper 2018Murata_Review Review of EM for structure dynamics
Paper 2018Quentin_Biomedical Review of EM as a tool for biomedical research
Paper 2018Scapin_DrugDiscovery Review of EM as a tool for drug discovery
Paper 2018Vilas_ImageProcessing Review of the recent developments in image processing for single particle analysis
Paper 2018vonLoeffelholz_VPP Comparison of Volta Phase Plate reconstructions close to focus and with defocus
Paper 2018Eisenstein_DrugDesigners Drug designers embrace cryo-EM
Paper 2019Benjin_Review Review of SPA
Paper 2019Danev_Review Review of future directions
Paper 2019Lyumkis_Review Challenges and reviews
Paper 2019Sorzano_Review Review of continuous heterogeneity biophysics
Paper 2020Abriata_Review Considerations of structure prediction and CryoEM
Paper 2020Akbar_Review Review of membrane protein reconstructions
Paper 2020Bendory_Review Review of image processing problems
Paper 2020Dubach_Review Review of resolution in X-ray crystallography and CryoEM
TechReport 2020Lai_Statistics Review of statistical properties of image alignment
Paper 2020Hu_Quaternions Review of the use of quaternions to describe rotations
Paper 2020McCafferty_Review Review of SPA and Mass Spectroscopy
Paper 2020Seffernick_Hybrid Review of hybrid (computational and experimental) methods to get protein structure
Paper 2020Nakane_Atomic Single-particle cryo-EM at atomic resolution
Paper 2020Vilas_Review Review of local resolution
Paper 2020Wu_Review Review of current limitations, with special emphasis on protein size
Paper 2020Singer_Sigworth_Review Review of single particle analysis
Paper 2021Bai_Review Review of breakthroughs leading to atomic resolution
Paper 2021DImprima_Review Review of sample preparation for single particle analysis
Paper 2021Lander_Review Review of focused analysis in SPA
Paper 2021Raimondi_Review General review of SPA
Paper 2022Beton_Fitting Review of fitting in SPA
Paper 2022Burley_PDB Review of cryoEM derived structures at PDB
Paper 2022Caldraft_Tilt Review of applications of tilt pairs in SPA
Paper 2022Donnat_GAN Review of Generative modelling with neural networks
Paper 2022Guaita_Review Recent advances and current trends in cryo-electron microscopy
Paper 2022Jones_Comment Comment on the impact of AlphaFold and next challenges ahead
Paper 2022Namba_Review Review of the current state of SPA
Paper 2022Ourmazd_Comment Comment on the impact of AlphaFold and next challenges ahead
Paper 2022Palmer_Local Review of local methods in CryoEM
Paper 2022Sorzano_1000 CryoEM is the field of 1000+ methods
Paper 2022Subramaniam_Comment Comment on the impact of AlphaFold and next challenges ahead
Paper 2022Treder_DL Review of Deep Learning applications in CryoEM
Paper 2022Vant_MD Review of Molecular Dynamics analysis of CryoEM maps
Paper 2023Amann_TimeResolved Review of time-resolved cryoEM
Paper 2023Bai_Challenges Challenges and opportunities in structure determination
Paper 2023Liu_AWI Review of the Air-Water Interface
Paper 2023Lucas_Structureome Review of the localization of proteins and complexes in their cellular context
Paper 2023Miyashita_MD Review of the use of molecular dynamics in atomic modelling
Paper 2023Si_DeNovo Review of the de-novo atomic modelling
Paper 2023Tang_Conformational Review of conformational heterogeneity and probability distributions
Paper 2023Toader_Heterogeneity Review of continuous heterogeneity

Software

Paper 1996Frank_Spider Spider
Paper 1996VanHeel_Imagic Imagic
Paper 1999Lutdke_Eman Eman
Paper 2004Sorzano_Xmipp Xmipp
Paper 2007Baldwin_AngularTransformations The Transform Class in SPARX and EMAN2
Paper 2007Heymann_Bsoft Bsoft
Paper 2007Grigorieff_Frealign Frealign
Paper 2008Scheres_XmippProtocols Xmipp Protocols
Paper 2008Shaikh_SpiderProtocols Spider Protocols
Paper 2012Wriggers_SitusConventions Conventions and workflows in Situs
Paper 2013DeLaRosa_Xmipp30 Xmipp 3.0
Paper 2015Cianfrocco_Cloud Software execution in the cloud
Paper 2015Cheng_MRC2014 Extensions to MRC file format
Paper 2013DeLaRosa_Scipion Scipion
Paper 2016Scheres_Relion Tutorial on the use of Relion
Paper 2016Grigorieff_Frealign Tutorial on the use of Frealign
Paper 2017Moriya_Sphire Tutorial on the use of Sphire
Paper 2018Bell_EMAN2 New tools in EMAN2
Paper 2018Cianfrocco_cloud CryoEM Cloud Tools
Paper 2018Grant_cisTEM cisTEM
Paper 2018McLeod_MRCZ MRC Compression format
Paper 2018Zivanov_Relion3 Relion 3
Paper 2020Caesar_Simple3 Simple 3
Paper 2021Baldwin_SCF Visualizer of the Sampling Compensation Factor
Paper 2021Jimenez_Scipion Scipion workflow example for image processing
Paper 2021Kimanius_Relion4 Changes in Relion 4.0
Paper 2021Maji_BlackBox Exploration of image processing concepts
Paper 2021Sharov_Relion Use of Relion within Scipion
Paper 2021Sorzano_Scipion Use of Scipion as a way to compare the results of multiple methods
Paper 2021Strelak_Xmipp Advances in Xmipp
Paper 2022DiIorio_Multiple A Robust Single-Particle Cryo-Electron Microscopy (cryo-EM) Processing Workflow with cryoSPARC, RELION, and Scipion.
Paper 2022Fluty_Precision Precision requirements and data compression
Paper 2022Harastani_ContinuousFlex ContinuousFlex: Software for continuous heterogeneity analysis in cryo-EM and cryo-ET
Paper 2023Cheng_AutoEMage AutoEMage: a system for processing in streaming (SPA)
Paper 2023Conesa_Scipion3 Scipion3: A workflow engine for cryoEM
Paper 2023Krieger_ScipionPrody Scipion-EM-Prody: Interface between Scipion and Prody (Structural Analysis)
Paper 2023Short_MRC2020 MRC2020: improvements to Ximdisp and the MRC image-processing programs
Paper 2024Vuillemot_MDSPACE MDSpace and MDTomo to analyze continuous heterogeneity

Electron tomography

Image preprocessing

Paper 2015Yan_thickness Determination of thickness, tilt and electron mean free path
Paper 2018Wu_contrast Contrast enhancement to improve alignability

Image alignment

Paper 1982Guckenberger_commonOrigin Determination of a common origin in the micrographs of titl series in three-dimensional electron microscopy
Paper 1992Lawrence_leastSquares Least squares solution of the alignment problem
Paper 1995Penczek_dual Dual tilt alignment
Paper 1996Owen_alignmentQuality Automatic alignment without fiducial markers and evaluation of alignment quality
Paper 1998Grimm_normalization Discussion of several gray level normalization methods for electron tomography
Paper 2001Brandt_Automatic1 Automatic alignment without fiducial markers
Paper 2001Brandt_Automatic2 Automatic alignment with fiducial markers
Paper 2006Winkler_alignment Marker-free alignment and refinement
Paper 2006Castano_alignment Alignment with non-perpendicularity
Paper 2007Castano_alignment Fiducial-less alignment of cryo-sections
Paper 2009Sorzano_alignment Marker-free alignment and refinement
Paper 2010Cantele_dualAlignment Alignment of dual series
Paper 2014Tomonaga_Automatic Automatic alignment of tilt series using the projection themselves
Paper 2014Han_Automatic Automatic alignment of tilt series using SIFT features
Paper 2015Han_Automatic Automatic alignment of tilt series using fiducials
Paper 2017Mastronarde_Automatic Automatic alignment and reconstruction of tilt series in IMOD
Paper 2018Fernadez_Beam Image alignment considering beam induced motion
Paper 2018Han_Fast Automatic alignment using fiducial markers
Paper 2019Fernandez_residual Alignment of tilt series using residual interpolation
Paper 2019Han_Dual Automatic alignment using fiducial markers in dual tilt series
Paper 2020Sorzano_automatic Automatic alignment considering several geometrical distortions
Paper 2021Han_LocalConstraints Automatic alignment considering local constraints
Paper 2022Zheng_Aretomo Automatic alignment based on projection matching

CTF estimation and restoration

Paper 2003Winkler_CTF Focus gradient correction in electron tomography
Paper 2006Fernandez_CTF CTF determination and correction in electron tomography
Paper 2009Zanetti_CTF CTF determination and correction in electron tomography
Paper 2009Xiong_CTF CTF determination and correction for low dose tomographic tilt series
Paper 2012Eibauer_CTF CTF determination and correction
Paper 2015Bharat_CTFCorrectedSubtomogramAveraging Subtomogram averaging with CTF correction using a Bayesian prior
Paper 2017Turonova_3DCTF 3D CTF Correction
Paper 2017Kunz_3DCTF 3D CTF Correction

3D reconstruction

Paper 1972Gilbert_SIRT Simultaneous Iterative Reconstruction Technique (SIRT)
Paper 1973Herman_ART Algebraic Reconstruction Technique (ART)
Paper 1984Andersen_SART Simultaneous Algebraic Reconstruction Technique (SART)
Paper 1992Radermacher_WBP Weighted Backprojection in electron tomography
Paper 1997Marabini_reconstruction Iterative reconstruction in electron tomography
Paper 2002Fernandez_reconstruction Iterative reconstruction in electron tomography
Paper 2007Radermacher_WBP Weighted Backprojection in electron tomography
Paper 2008Fernandez_CARP Component Averaged Row Projections (CARP)
Paper 2010Xu_Long Iterative reconstructions with long object correction and GPU implementation
Paper 2012Herman General Superiorization Superiorization: an optimization heuristic for medical physics
Paper 2012Zhang_IPET_FETR IPET and FETR, a reconstruction algorithm for a single particle structure determination without any averaging
Paper 2013Goris_SIRT_TV_DART Combination of SIRT, Total Variation and Discrete ART to reconstruct and segment at the same time
Paper 2013Briegel A_Challenge The challenge of determining handedness in electron tomography and the use of DNA origami gold nanoparticle helices as molecular standards
Paper 2013Messaoudi_EnergyFiltered 3D Reconstruction of Energy-Filtered TEM
Paper 2014Paavolainen_Missing Compensation of the missing wedge
Paper 2015Venkatakrishnan_MBIR 3D Reconstruction with priors
Paper 2016Deng_ICON 3D Reconstruction with missing information restoration
Paper 2016Guay_Compressed 3D Reconstruction using compressed sensing
Paper 2016Turonova_Artifacts Artifacts observed during 3D reconstruction
Paper 2019Yan_MBIR 3D Reconstruction with priors and demonstration of its use in biological samples
Paper 2020Sanchez_Hybrid 3D reconstruction with a special acquisition and alignment scheme
Paper 2020Song_Tygress 3D reconstruction with a special acquisition and alignment scheme
Paper 2021Fernandez_TomoAlign 3D reconstruction with sample motion and CTF correction
Paper 2021Geng_Nudim Non-uniform FFT reconstruction and total variation to fill the missing wedge

Noise reduction

Paper 2001Frangakis_NAD Noise reduction with Nonlinear Anisotropic Diffusion
Paper 2003Fernandez_AND Anisotropic nonlinear diffusion for electron tomography
Paper 2003Jiang_Bilateral Bilateral denoising filter in electron microscopy
Paper 2005Fernandez_AND Anisotropic nonlinear denoising in electron tomography
Paper 2007Heide_median Iterative median filtering in electron tomography
Paper 2007Fernandez_autAND Anisotropic nonlinear diffusion with automated parameter tuning
Paper 2009Fernandez_Beltrami Nonlinear filtering based on Beltrami flow
Paper 2010Bilbao_MeanShift Mean Shift Filtering
Paper 2014Kovacik_wedgeArtefacts Removal of wedge artefacts
Paper 2014Maiorca_beadArtefacts Removal of gold bead artefacts
Paper 2018Trampert_Inpainting Removal of the missing wedge by inpainting
Paper 2018Moreno_TomoEED Fast Anisotropic Diffusion
Paper 2018Wu_Enhancement Enhancing the image contrast of electron tomography
Paper 2022Liu_Isonet Isotropic reconstructions using deep learning

Segmentation

Paper 2002Frangakis_Eigenanalysis Segmentation using eigenvector analysis.
Paper 2002Volkmann_Watershed Segmentation using watershed transform.
Paper 2003Bajaj_BoundarySegmentation Segmentation based on fast marching.
Paper 2005Cyrklaff_Thresholding Segmentation using optimal thresholding.
Paper 2007Lebbink_TemplateMatching Segmentation using template matching.
Paper 2007Sandberg_OrientationFields Segmentation using orientation fields.
Paper 2007Sandberg_SegmentationReview Review on segmentation in electron tomography.
Paper 2008Garduno_FuzzySegmentation Segmentation using fuzzy set theory principles.
Paper 2009Lebbink_TemplateMatching2 Segmentation using template matching.
Paper 2012RubbiyaAli_EdgeDetection Parameter-Free Segmentation of Macromolecular Structures.
Conference 2015Xu_TemplateMatching Detection of macromolecular complexes with a reduced representation of the templates.
Paper 2017Ali_RAZA Automated segmentation of tomograms
Paper 2017Chen_Annotation Automated annotation of tomograms
Paper 2017Tasel_ActiveContours Segmentation with active contours
Paper 2017Xu_DeepLearning Finding proteins in tomograms using deep learning
Paper 2018Zeng_DeepLearning Mining features in Electron Tomography by deep learning
Paper 2020Salfer_PyCurv Curvature analysis of segmented tomograms
Paper 2021Dimchev_filaments Segmentation of filaments in tomograms
Paper 2022Frangakis_Curvature Use of mean curvature for segmentation and visualization of tomograms
Paper 2022Lamm_MemBrain Membrane segmentation using deep learning
Paper 2023Zeng_AITOM Structural pattern mining by unsupervised deep iterative subtomogram clustering

Resolution

Paper 2005Cardone_Resolution Resolution criterion for electron tomography
Chapter 2007Penczek_Resolution Review of resolution criteria for electron tomography
Paper 2015Diebolder_ConicalFSC Conical Fourier Shell Correlation
Paper 2020Vilas_Monotomo Resolution determination in tomograms

Subtomogram analysis

Paper 2000Bohm_Template Macromolecule finding by template matching
Paper 2002Frangakis_Template Macromolecule finding by template matching
Paper 2006Nickell_Review Review of macromolecule finding by template matching (Visual Proteomics)
Paper 2007Best_Review Review of Localization of Protein Complexes by Pattern Recognition
Paper 2007Forster_Review Review of structure determination by subtomogram averaging
Paper 2008Forster_Classification Classification of subtomograms using constrained correlation
Paper 2008Bartesaghi_Classification Classification and averaging of subtomograms
Paper 2008Schmid_Averaging Alignment and averaging of subtomograms
Paper 2010Amat_Averaging Alignment and averaging of subtomograms exploiting thresholding in Fourier space
Paper 2010Yu_PPCA Probabilistic PCA for volume classification
Paper 2013Chen_Averaging Fast alignment of subtomograms using spherical harmonics
Paper 2013Kuybeda_Averaging Alignment and averaging of subtomograms using the nuclear norm of the cluster
Paper 2013Shatsky_Averaging Alignment and averaging of subtomograms with constrained cross-correlation
Paper 2013Yu_Projection Subtomogram averaging by aligning their projections
Paper 2014Chen_Autofocus Subtomogram averaging and classification with special attention to differences
Paper 2014Yu_ReferenceBias Scoring the reference bias
Paper 2014Voortman_LimitingFactors Limiting factors of subtomogram averaging
Paper 2015Bharat_CTFCorrectedSubtomogramAveraging Subtomogram averaging with CTF correction using a Bayesian prior
Paper 2015Yu_ReferenceBias Scoring the reference bias
Paper 2016Bharat_Relion Subtomogram averaging with Relion
Paper 2016Song_MatrixNorm Matrix norm minimization for tomographic reconstruction and alignment
Paper 2017Castano_ParticlePicking Particle picking in tomograms for subtomogram averaging
Paper 2017Frazier_Tomominer TomoMiner a software platform for large-scale subtomogram analysis
Paper 2018Himes_emClarity emClarity for subtomogram averaging
Paper 2018Zhao_Fast Fast alignment and maximum likelihod for subtomogram averaging
Paper 2019Fokine_Enhancement Subtomogram enhancement through the locked self-rotation
Paper 2019Han_Constrained Constrained reconstruction to enhance resolution
Paper 2020Basanta_workflow Workflow for subtomogram averaging
Paper 2021Cheng_Native 3D reconstruction only with 0-tilt images
Paper 2021Du_Active Active learning to reduce the need of annotated samples
Paper 2021Harastani_HEMNMA3D HEMNMA-3D: Continuous flexibility analysis of subtomograms using normal modes
Paper 2021Lucas_Cistem Identification of particles in tomograms using Cistem
Paper 2021Scaramuzza_Dynamo Subtomogram averaging workflow using Dynamo
Paper 2021Singla_Measures Analysis of different measures to analyze subtomogram clusters
Paper 2021Tegunov_M Image processing workflow for tilt-series (introduction of M)
Conference 2021Zeng_OpenSet Unsupervised open set classification using deep learning
Paper 2022Boehning_CompressedSensing Compressed sensing for subtomogram averaging
Paper 2022Hao_Picking Detection of molecules in tomograms
Paper 2022Harastani_TomoFlow TomoFlow: Continuous flexibility analysis of subtomograms using 3D dense optical flow
Paper 2022Metskas_STA Tricks for a better Subtomogram Averaging
Paper 2022Moebel_unsupervised Unsupervised classification of subtomograms using neural networks
Paper 2022Peters_Feature Feature guided, focused 3D signal permutation for STA
Paper 2023Balyschew_TomoBEAR TomoBEAR: tilt series alignment, reconstruction and subtomogram averaging
Paper 2023Chaillet_Extensive Extensive angular sampling for picking in tomograms
Paper 2023Cheng_GisSPA Detection of protein targets in 0-tilt images
Paper 2023Genthe_PickYolo Subtomogram picking in tomograms

Single particle tomography

Paper 2012Bartesaghi_Constrained 3D reconstruction by imposing geometrical constraints
Paper 2012Zhang_IPET_FETR FETR: a focused reconstruction algorithm for a single molecule 3D structure determination without any averaging
Paper 2015Galaz_SingleParticleTomography Set of tools for Single Particle Tomography in EMAN2
Paper 2016Galaz_SingleParticleTomography Alignment algorithms and CTF correction

Missing-wedge correction

Paper 2020Kovacs_Filaments Removal of missing wedge artifacts in filamentous tomograms
Paper 2020Moebel_MCMC Missing wedge correction with Monte Carlo Markov Chains
Paper 2020Zhai_LoTTor Missing-wedge correction by LoTTor (Low-Tilt Tomographic 3D Reconstruction for a single molecule structure)
Paper 2023Zhang_REST Missing-wedge correction with neural networks

Molecular 3D dynamics

Paper 2015Zhang_IPET 3D Structural Dynamics of Macromolecules by individual-particle structures without averaging
Paper 2023Vuillemot_MDTOMO 3D Structural Dynamics of using molecular dynamics and normal modes

Books and reviews

Paper 2000Baumeister_Review Review of electron tomography
Paper 2003Koster_Review Review of electron tomography
Paper 2003Sali_Review Review of electron tomography
Paper 2004Henderson_Review Review of electron microscopy
Paper 2005Lucic_Review Review of electron tomography
Paper 2006Fernandez_Review Review of electron microscopy
Book 2006Frank_TomoBook Electron Tomography
Book 2007McIntosh_Book Cellular Electron Microscopy
Paper 2007Sorzano_Review Review of the image processing steps
Paper 2008Fanelli_ImageFormation Review on the image formation model from the electron waves and open inverse-problems
Paper 2008Fernandez_HPCReview High performance computing in electron cryomicroscopy
Paper 2008Jonic_Review Comparison between electron tomography and single particles
Paper 2012Kudryashev_Review Review of subtomogram averaging
Paper 2013Briggs_Review Review of subtomogram averaging
Paper 2016Beck_Review Review of molecular sociology
Paper 2016Ercius_Review Electron tomography for hard and soft materials research
Paper 2017Galaz_Review Review of single particle tomography
Paper 2017Plitzko_Review Review of electron tomography, FRET and FIB milling
Paper 2019Schur_Review Review of electron tomography and subtomogram averaging
Paper 2021Frangakis_Review Review of tomogram denoising in electron tomography
Paper 2022Forster_Review Review of subtomogram averaging
Paper 2022Liedtke_Review Review of electron tomography in bacterial cell biology
Paper 2022Liu_Review Review of beam image shift and subtomogram averaging
Paper 2023Kim_Review Review of particle picking and volume segmentation
Paper 2023Ochner_Review Review of electron tomography as a way to visualize macromolecules in their native environment
Paper 2023Zhao_Review Review of computational methods for electron tomography

Software

Paper 1996Kremer_IMOD IMOD
Paper 1996Chen_Priism/IVE Priism/IVE
Paper 1996Frank_Spider Spider
Paper 2004Sorzano_Xmipp Xmipp
Paper 2005Nickell_TOM TOM Toolbox
Paper 2007Messaoudi_TomoJ TomoJ
Paper 2008Heymann_BsoftTomo Bsoft
Paper 2012Zhang IPET FETR IPET
Paper 2015Ding_CaltechTomography Caltech tomography database
Paper 2015Noble_AppionProtomo Batch fiducial-less tilt-series alignment in Appion using Protomo
Paper 2015vanAarle_Astra ASTRA Toolbox
Paper 2016Liu_FullMechTomo Fully mechanically controlled automated electron microscopic tomography
Paper 2017Han_AuTom Software platform for Electron Tomography
Paper 2017Wan_Simulator Electron Tomography Simulator
Paper 2021Burt_RWD Interoperability between Relion, Warp M, and Dynamo
Paper 2022Jimenez_ScipionTomo Electron tomography within Scipion
Paper 2022Martinez_PyOrg Point pattern analysis for coordinates in tomograms
Paper 2022Ni_EmClarity Processing protocols with EmClarity
Paper 2023Liu_NextPYP NextPYP: a software platform for cryoET

2D Crystals

2D Preprocessing

Paper 1982Saxton_Averaging Radial Correlation Function
Paper 1984Saxton_Distortions 3D Reconstruction of distorted crystals
Paper 1986Henderson_Processing General 2D processing
Paper 2000He_PhaseAlignment Phase consistency and Alignment
Paper 2006Gil_Unbending Crystal unbending

Classification

Paper 1988Frank_Classification MSA and classification in electron crystallography
Paper 1996Fernandez_SOM Classification based on self organizing maps
Paper 1998Sherman_MSA Classification based on MSA

3D Reconstruction

Paper 1985Wang_Solvent Solvent flattening
Paper 1990Henderson_Processing General 3D processing
Paper 2004Marabini_ART Algebraic Reconstruction Technique with blobs for crystals (Xmipp)
Paper 2018Biyani_Badlu Image processing for badly ordered crystals

Books and reviews

Paper 1998Walz_Review Review of 2D crystallography
Paper 1999Glaeser_Review Review of 2D crystallography
Paper 2001Ellis_Review Review of 2D crystallography
Paper 2001Glaeser_Review Review of 2D crystallography
Paper 2004Henderson_Review Review of electron microscopy
Paper 2006Fernandez_Review Review of single particles, electron tomography and crystallography
Paper 2007Sorzano_Review Review of the image processing steps

Software

Paper 1996Crowther_MRC MRC
Paper 2004Sorzano_Xmipp Xmipp
Paper 2007Gipson_2dx 2dx
Paper 2007Heymann_Bsoft Bsoft
Paper 2007Philippsen_IPLT IPLT

3D Crystals - MicroED

Sample Preparation

Paper 2016Shi_Preparation Sample Preparation

Data Collection

Paper 2014Nannenga_CR Continuous rotation

Data Processing

Paper 2011Wisedchaisri_PhaseExtension Fragment-based phase extension
Paper 2015Hattne_Processing Data Processing
Paper 2016Hattne_Correction Image correction

Software

Paper 2014Iadanza_Processing Data Processing of still diffraction data

Books and Reviews

Paper 2014Nannenga_Review Review of MicroED
Paper 2016Liu_Review Review of MicroED
Paper 2016Rodriguez_Review Review of MicroED

Helical particles

Filament picking

Paper 2021Thurber_Automated Automated picking of filaments

Filament corrections

Paper 1986Egelman_Curved Algorithm for correcting curved filaments
Paper 1988Bluemke_Pitch Algorithm for correcting filaments with different helical pitches
Paper 2006Wang_Pitch Algorithm for correcting filaments with different helical pitches
Paper 2016Yang_Flexible Algorithm for correcting filaments with flexible subunits
Paper 2019Ohashi_SoftBody Algorithm for correcting filaments with flexible helices

Reconstruction

Paper 1952Cochran_Fourier Fourier Bessel transform of filamentous structures
Paper 1958Klug_Fourier Fourier Bessel decomposition of the projection images
Paper 1970DeRosier_Rec Image processing steps towards 3D reconstruction
Paper 1988Stewart_Rec Image processing steps towards 3D reconstruction
Paper 1992Morgan_Rec Image processing steps towards 3D reconstruction
Paper 2005Wang_Iterative Iterative Fourier-Bessel algorithm
Paper 2007Egelman_Iterative Iterative real-space algorithm
Paper 2010Egelman_Pitfalls Pitfalls in helical reconstruction
Paper 2013Desfosses_Spring Helical processing with Spring
Paper 2015Zhang_seam Workflow for the detection of the lattice seam
Paper 2016Rohou_Frealix Helical processing with Frealix
Paper 2017_He Helical processing with Relion
Paper 2019_Pothula 3D Classification through 2D analysis

Validation

Paper 2014Egelman_ambiguity How to detect incorrect models

Books and reviews

Paper 1970DeRosier_Rec Image processing steps towards 3D reconstruction
Paper 1992Morgan_Rec Image processing steps towards 3D reconstruction
Paper 2004Henderson_Review Review of electron microscopy
Paper 2015Sachse_Review Review of the image processing steps in helical particles
Paper 2021Egelman_Review Review of reconstruction problems in helical structures
Paper 2022Wang_Review Review of reconstruction problems in helical structures

Software

Paper 1996Carragher_Phoelix Phoelix
Paper 1996Crowther_MRC MRC
Paper 1996Owen_Brandeis Brandeis

Icosahedral particles

Reconstruction

Paper 1970Crowther_Rec Reconstruction of icosahedral viruses in Fourier space
Paper 1971Crowther_Rec Reconstruction of icosahedral viruses in Fourier space
Paper 1996Fuller_Rec Reconstruction of icosahedral viruses in Fourier space
Paper 1997Thuman_Rec Reconstruction of icosahedral viruses in Fourier space
Paper 2019Goetschius_Asymmetric Approaches to reconstruct asymmetric features in viruses

Classification

Paper 2005Scheres_Virus Classification of virus capsids in real space

Books and reviews

Paper 1999Baker_Review Review of reconstruction of icosahedral viruses
Paper 1999Conway_Review Review of reconstruction of icosahedral viruses
Paper 2000Thuman_Review Review of reconstruction of icosahedral viruses
Paper 2003Lee_Review Review of reconstruction of icosahedral viruses
Paper 2003Navaza_Review Review of reconstruction of icosahedral viruses
Paper 2006Grunewald_Review Review of reconstruction of icosahedral viruses

Software

Paper 1996Baker_EMPFT EMPFT
Paper 1996Crowther_MRC MRC
Paper 1996Frank_Spider Spider
Paper 1996VanHeel_Imagic Imagic
Paper 2004Sorzano_Xmipp Xmipp
Paper 2013DeLaRosa_Xmipp30 Xmipp 3.0
Paper 2013Morin_Sliz SBGrid SBGrid presentation for eLife

Liquid-cell TEM / in-situ TEM

Paper 2020Ren_LTEM Real-time dynamic imaging of sample in liquid phase

Databases

Paper 2003Boutselakis_EMSD EMSD database
Paper 2005Heymann_Conventions Conventions for software interoperability
Paper 2005Heymann_Conventions Conventions for software interoperability
Paper 2011Kim_CDDB Conformational Dynamics Data Bank
Paper 2011Lawson_EMDB Electron Microscopy Data Bank
Paper 2013Ison_EDAM EDAM, an ontology of bioinformatics operations
Paper 2016Iudin_EMPIAR EMPIAR raw data database
Paper 2016Patwhardan_EMDB EMDB, PDB, ...
Paper 2017Gore_Validation Validations of PDB submissions
Paper 2017Patwhardan_Trends Trends at EMDB
Paper 2017Shao_PDBQuality Quality metrics in PDB
Paper 2018Tawari_search Search of 3D structures in a database using 2D experimental images
Paper 2018wwwPDB_PDB Review of PDB advances
Paper 2022Wang_EMDB Validation analysis of EMDB entries
Paper 2022Westbrook_mmCIF PDBx/mmCIF ecosystem
Blog http://www.mybiosoftware.com Huge list of bioinformatics programs (many of them structural bioinformatics)

Relationship to other structural information sources

Paper 2000Engel_AFM Review of Atomic Force Microscopy
Paper 2001Dimmeler_AFM Constraints from Atomic Force Microscopy
Paper 2003Mobus_EnergyLoss Chemical mapping by energy loss electron tomography
Paper 2004Leapman_EnergyLoss Chemical mapping by energy loss electron tomography
Paper 2004Leapman_Review Review on correlative microscopy
Paper 2005Boudier_EFTETJ Software for Chemical mapping by energy loss electron tomography
Paper 2005Vestergaard_SAXS Example of comparison of 3DEM and Small-angle X-ray scattering
Paper 2007Hamada_SAXS Constraints from Small-angle X-ray scattering
Paper 2013Xu_FRET EM+FRET
Paper 2017Kim_SAXS Compatibility of EM experimental images and SAXS curves
Paper 2018Ando_Correlative Review of correlative microscopy techniques
Paper 2018Sieben_Multicolor Correlative microscopy with superresolution optical images
Paper 2019Huber_EDXS_HAADF Combined reconstruction using EDXS and HAADF data
Paper 2019Jimenez_SAXS Selection of EM initial volumes by SAXS curves
Paper 2022Graziadei_CrossLinking Review on the use of crosslinking mass spectrometry in CryoEM
Paper 2022Klumpe_FIB A modular platform for automated cryo-FIB workflows

X-ray tomography

Paper 2012Oton_ImageFormation Image formation model in X-ray cell microscopy

Mathematical tools necessary

People developing methods

Please, add yourself to this list (due to privacy reasons, please, do not add anyone else to the list without his/her explicit consent). Sort by first name alphabetical order.

Carlos Oscar S. Sorzano: CSIC, Madrid, Spain

Cédric Messaoudi: Institute Curie, Paris, France

Javier Vargas:: CSIC, Madrid, Spain

Joaquín Otón: CSIC, Madrid, Spain

[José Román Bilbao-Castro]: UAL, Almería, Spain; CSIC, Madrid, Spain

[José Miguel de la Rosa Trevín]: Biocomputing Unit CNB-CSIC, Madrid, Spain

Tamir Gonen: Howard Hughes Medical Institute, Ashburn, VA, USA

Tomas Majtner: Biocomputing Unit CNB-CSIC, Madrid, Spain

[Vahid Abrishami]: CSIC, Madrid, Spain

Gang (Gary) Ren: The Molecular Foundry, LBNL, USA

3DEM sites

Editing useful links