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[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]
Line 92: Line 92:
  
 
[https://www.youtube.com/watch?v=F1yXJaZ2H5o&list=PLFEB3YHuxu11I4Qgj6K5jmWcghsFnE09Q CCP-EM Spring symposium 2019]
 
[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.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]
  
 
=== Image formation ===
 
=== Image formation ===
Line 378: Line 390:
 
| [[2018Hettler_Charging]]
 
| [[2018Hettler_Charging]]
 
| Charging of carbon thin films
 
| Charging of carbon thin films
|-
 
 
| Paper
 
| [[2018Koeck_PhaseShift]]
 
| Design of a phase shift device
 
 
|-  
 
|-  
  
Line 410: Line 417:
 
|-  
 
|-  
  
|}
+
| Paper
 
+
| [[2020Bromberg_Aberrations]]
=== Collection geometry ===
+
| Estimation of strong high-order aberrations
 
 
{|
 
 
 
| Chapter
 
| [[1980Hoppe_Wedge]]
 
| Missing wedge
 
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1987Radermacher_RCT]]
+
| [[2020Gruza_Atomic]]
| Random Conical Tilt and Single axis tilt
+
| Detailed atomic models considering local charges and directional bonds
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1988Radermacher_RCT]]
+
| [[2020Naydenova_Buckling]]
| Random Conical Tilt and Single axis tilt
+
| Beam induced movement explained as ice buckling
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1995Penczek_Dual]]
+
| [[2020Zhang_LimitsSimulated]]
| Dual axis tomography
+
| Simulation of micrographs and 3D reconstruction for low weight proteins (14kDa)
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1997Mastronarde_Dual]]
+
| [[2020Tichelaar_Thick]]
| Dual axis tomography
+
| Effect of sample thickness on the CTF
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2003Ludtke_FocusPairs]]
+
| [[2020Yip_Atomic]]
| Focus pairs for single particles
+
| Atomic resolution by monochromator and a second-generation spherical aberration corrector
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2005Lanzavecchia_Conical]]
+
| [[2020Zhang_LimitsSimulated]]
| Conical tomography
+
| Simulation of micrographs and 3D reconstruction for low weight proteins (14kDa)
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2005Zampighi_Conical]]
+
| [[2021Egerton_Inelastic]]
| Conical tomography
+
| PSF of inelastic scattering
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2006Leschziner_OT]]
+
| [[2021Glaeser_Fading]]
| Orthogonal Tilt
+
| Defocus-dependent Thon-ring fading
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2006Messaoudi_Multiple]]
+
| [[2021Wieferig_Devitrification]]
| Multiple axis tomography
+
| Devitrification reduces beam-induced movement in cryo-EM
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2012Kudryashev_FocusPairs]]
+
| [[2022Dickerson_Inelastic]]
| Focus pairs tomography
+
| The role of inelastic scattering in thick specimens
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2014Hovden_TiltFocus]]
+
| [[2022Ravikumar_SideChains]]
| Combining tilt series with focus series
+
| Comparison of side-chain dispersion in protein structures determined by cryo-EM and X-ray crystallography
 
|-  
 
|-  
  
| Paper
+
|}
| [[2015Sorzano_RandomConicalTilt]]
+
 
| General formulation of Random Conical Tilt
+
=== Collection geometry ===
 +
 
 +
{|
 +
 
 +
| Chapter
 +
| [[1980Hoppe_Wedge]]
 +
| Missing wedge
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Hagen_DoseTomography]]
+
| [[1987Radermacher_RCT]]
| Dose optimization for subtomogram averaging
+
| Random Conical Tilt and Single axis tilt
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Tan_PreferredViews]]
+
| [[1988Radermacher_RCT]]
| Solving preferred views problems through tilting
+
| Random Conical Tilt and Single axis tilt
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Donati_Compressed]]
+
| [[1995Penczek_Dual]]
| Compressed sensing for STEM
+
| Dual axis tomography
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Oveisi_Stereo]]
+
| [[1997Mastronarde_Dual]]
| Stereo-vision with EM
+
| Dual axis tomography
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Cheng_BeamShift]]
+
| [[2003Ludtke_FocusPairs]]
| Fast image acquisition through beam-shift
+
| Focus pairs for single particles
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2019Wu_BeamShiftAndTilt]]
+
| [[2005Lanzavecchia_Conical]]
| Fast image acquisition through beam-shift and beam tilt control
+
| Conical tomography
 
|-  
 
|-  
 
|}
 
 
=== Sample preparation ===
 
 
{|
 
  
 
| Paper
 
| Paper
| [[1982Dubochet_Sample]]
+
| [[2005Zampighi_Conical]]
| Vitreous ice
+
| Conical tomography
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1986Lepault_Sample]]
+
| [[2006Leschziner_OT]]
| Fast freezing
+
| Orthogonal Tilt
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1995Dubochet_Sample]]
+
| [[2006Messaoudi_Multiple]]
| High-pressure freezing
+
| Multiple axis tomography
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1995VanMarle_Sample]]
+
| [[2012Kudryashev_FocusPairs]]
| Sample damages in resin
+
| Focus pairs tomography
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1998Adrian_Sample]]
+
| [[2014Hovden_TiltFocus]]
| Cryo negative staining
+
| Combining tilt series with focus series
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2002DeCarlo_Damage]]
+
| [[2015Sorzano_RandomConicalTilt]]
| Radiation damage in cryonegative staining
+
| General formulation of Random Conical Tilt
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2002Hsieh_Sample]]
+
| [[2017Hagen_DoseTomography]]
| Cryofixation
+
| Dose optimization for subtomogram averaging
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2004AlAmoudi_Sample]]
+
| [[2017Tan_PreferredViews]]
| CEMOVIS
+
| Solving preferred views problems through tilting
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2008Studer_Sample]]
+
| [[2017Donati_Compressed]]
| Review on high pressure freezing
+
| Compressed sensing for STEM
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2009Pierson_Sample]]
+
| [[2018Oveisi_Stereo]]
| Review on sample preparation for electron tomography
+
| Stereo-vision with EM
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2010Zhang_NegativeStaining]]
+
| [[2018Cheng_BeamShift]]
| Negative staining for small protein imaging
+
| Fast image acquisition through beam-shift
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2012Zhang_PositiveStaining]]
+
| [[2019Wu_BeamShiftAndTilt]]
| Positive staining
+
| Fast image acquisition through beam-shift and beam tilt control
 
|-  
 
|-  
  
| Paper
+
|}
| [[2014Rames_NegativeStaining]]
+
 
| Optimized negative staining
+
=== Sample preparation ===
|-
 
  
| Paper
+
{|
| [[2014Russo_GoldGrids]]
+
 
| Gold grids for single particles
+
| Paper
 +
| [[1982Dubochet_Sample]]
 +
| Vitreous ice
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Cabra_Sample]]
+
| [[1986Lepault_Sample]]
| Review on sample preparation for single particles with videos
+
| Fast freezing
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Chari_ProteoPlex]]
+
| [[1995Dubochet_Sample]]
| Fast evaluation of the structural stability
+
| High-pressure freezing
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Passmore_Review]]
+
| [[1995VanMarle_Sample]]
| Tutorial chapter on sample preparation
+
| Sample damages in resin
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Razinkov_Vitrification]]
+
| [[1998Adrian_Sample]]
| New vitrification method
+
| Cryo negative staining
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Takizawa_Sample]]
+
| [[2002DeCarlo_Damage]]
| Review on sample preparation for EM
+
| Radiation damage in cryonegative staining
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Thompson_Sample]]
+
| [[2002Hsieh_Sample]]
| Review on sample preparation for EM
+
| Cryofixation
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Arnold_BlottingFree]]
+
| [[2004AlAmoudi_Sample]]
| Blotting-free preparation
+
| CEMOVIS
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2017Earl_review]]
+
| [[2008Studer_Sample]]
| Review of sample preparation
+
| Review on high pressure freezing
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2017Feng_SprayingPlunging]]
+
| [[2009Pierson_Sample]]
| Spraying plunging
+
| Review on sample preparation for electron tomography
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2017He_FIB]]
+
| [[2010Zhang_OpNS]]
| Cryo FIB lamella for TEM
+
| Optimized negative staining (OpNS) for small protein and lipoprotein imaging
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2017Peitsch_Sample]]
+
| [[2012Zhang_Cryo-PS]]
| iMEM: Isolation of Plasma Membrane for Cryoelectron Microscopy
+
| Cryo-positive staining (Cryo-PS)
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2017Scapin_Storage]]
+
| [[2014Russo_GoldGrids]]
| Cryo storage of samples
+
| Gold grids for single particles
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2017Schaffer_FocusedIonBeam]]
+
| [[2015Cabra_Sample]]
| Focused Ion Beam sample preparation for membrane proteins
+
| Review on sample preparation for single particles with videos
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2017Scherr_HydrogelNanomembranes]]
+
| [[2015Chari_ProteoPlex]]
| Sample preparation for membrane proteins
+
| Fast evaluation of the structural stability
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2018Anderson_CLEM]]
+
| [[2016Passmore_Review]]
| Correlated light and EM
+
| Tutorial chapter on sample preparation
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2018Arnold_Review]]
+
| [[2016Razinkov_Vitrification]]
| Review on sample preparation with special emphasis on microfluidic approaches
+
| New vitrification method
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2018Dandey_Spotiton]]
+
| [[2016Takizawa_Sample]]
| Spotiton, a device for vitrification
+
| Review on sample preparation for EM
|-
+
|-
 +
 
 +
| Paper
 +
| [[2016Thompson_Sample]]
 +
| Review on sample preparation for EM
 +
|-  
  
 
| Paper
 
| Paper
| [[2018Gewering_Detergents]]
+
| [[2017Arnold_BlottingFree]]
| Detergent background in negative stain
+
| Blotting-free preparation
 
|-
 
|-
  
 
| Paper
 
| Paper
| [[2018Li_CLEM]]
+
| [[2017Earl_review]]
| Correlated light and EM
+
| Review of sample preparation
 
|-
 
|-
  
 
| Paper
 
| Paper
| [[2018Noble_Reducing]]
+
| [[2017Feng_SprayingPlunging]]
| Reducing particle adsorption
+
| Spraying plunging
 
|-
 
|-
  
 
| Paper
 
| Paper
| [[2018Rice_Ice]]
+
| [[2017He_FIB]]
| Routine determination of ice thickness
+
| Cryo FIB lamella for TEM
 
|-
 
|-
  
 
| Paper
 
| Paper
| [[2018Schmidli_Miniaturized]]
+
| [[2017Peitsch_Sample]]
| Protein isolation and sample preparation
+
| iMEM: Isolation of Plasma Membrane for Cryoelectron Microscopy
 
|-
 
|-
  
 
| Paper
 
| Paper
| [[2018Wei_Grids]]
+
| [[2017Scapin_Storage]]
| "Self-wicking" nanowire grids
+
| Cryo storage of samples
 
|-
 
|-
  
 
| Paper
 
| Paper
| [[2019DImprima_Denaturation]]
+
| [[2017Schaffer_FocusedIonBeam]]
| Protein denaturation at the air-water interface and how to prevent it
+
| Focused Ion Beam sample preparation for membrane proteins
 
|-
 
|-
  
 
| Paper
 
| Paper
| [[2019Song_FalconIII]]
+
| [[2017Scherr_HydrogelNanomembranes]]
| Comparison of the modes of Falcon III
+
| Sample preparation for membrane proteins
 
|-
 
|-
  
 
| Paper
 
| Paper
| [[2020Cianfrocco_Wrong]]
+
| [[2018Anderson_CLEM]]
| What could go wrong?
+
| Correlated light and EM
 
|-
 
|-
  
|}
+
| Paper
 +
| [[2018Arnold_Review]]
 +
| Review on sample preparation with special emphasis on microfluidic approaches
 +
|-
  
=== Automated data collection ===
+
| Paper
 
+
| [[2018Ashtiani_femtolitre]]
{|
+
| Delivery of femtolitre droplets using surface acoustic wave based atomisation for cryo-EM grid preparation
 +
|-
  
 
| Paper
 
| Paper
| [[1992Dierksen_Automatic]]
+
| [[2018Dandey_Spotiton]]
| Automated data collection
+
| Spotiton, a device for vitrification
|-  
+
|-
  
 
| Paper
 
| Paper
| [[1992Koster_Automatic]]
+
| [[2018Gewering_Detergents]]
| Automated data collection
+
| Detergent background in negative stain
|-  
+
|-
  
 
| Paper
 
| Paper
| [[1996Fung_Automatic]]
+
| [[2018Li_CLEM]]
| Automated data collection for tomography
+
| Correlated light and EM
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2001Zhang_Automatic]]
+
| [[2018Noble_Reducing]]
| Automated data collection: AutoEM
+
| Reducing particle adsorption
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2003Ziese_Automatic]]
+
| [[2018Palovcak_Graphene]]
| Automated autofocusing
+
| Preparation of graphene-oxide cryo-EM grids
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2004Potter_Automatic]]
+
| [[2018Rice_Ice]]
| Automated sample loading
+
| Routine determination of ice thickness
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2004Zheng_Automatic]]
+
| [[2018Schmidli_Miniaturized]]
| Automated data collection
+
| Protein isolation and sample preparation
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2005Lei_Automatic]]
+
| [[2018Wei_Grids]]
| Automated data collection: AutoEM
+
| "Self-wicking" nanowire grids
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2005Suloway_Automatic]]
+
| [[2019DImprima_Denaturation]]
| Automated data collection: Leginon
+
| Protein denaturation at the air-water interface and how to prevent it
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2007Yoshioka_RCT]]
+
| [[2019Rubinstein_ultrasonic]]
| Automated Random Conical Tilt
+
| Ultrasonic specimen preparation device
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2011Korinek_TOM2]]
+
| [[2019Song_FalconIII]]
| Automated acquisition with TOM2
+
| Comparison of the modes of Falcon III
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2015Li_UCSFImage]]
+
| [[2020Cianfrocco_Wrong]]
| Automated acquisition with UCSFImage
+
| What could go wrong?
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2016Gil_Fuzzy]]
+
| [[2020Egelman_Ice]]
| Real time decisions during acquisition with neuro-fuzzy method
+
| Problems with the ice
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2016Liu_TiltControl]]
+
| [[2020Fassler_Printing]]
| Accurate control of the tilt angle for electron tomography
+
| 3D printed cell culture grid holder
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2016Vargas_FoilHole]]
+
| [[2020Klebl_Deposition]]
| Determination of image quality at low magnification
+
| Sample deposition onto CryoEM grids: sprays and jets
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2017Alewijnse_Best]]
+
| [[2020Maeots_TimeResolved]]
| Best practices for managing large CryoEM facilities
+
| Time resolved CryoEM by microfluidics
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2017Biyani_Focus]]
+
| [[2020Tan_ThroughGrid]]
| Automatic processing of micrographs
+
| Through-grid wicking enables high-speed 1 cryoEM specimen preparation
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2018Gomez_Facilities]]
+
| [[2020Yoder_TimeResolved]]
| Use of Scipion at facilities
+
| Time resolved CryoEM by light estimulation
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2018Sorzano_Gain]]
+
| [[2020Zachs_FIB]]
| Estimation of the DDD camera gain or residual gain
+
| Automation for FIB milling
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2019Chreifi_TiltSeries]]
+
| [[2021Bieber_FIBET]]
| Rapid tilt-series acquisition for electron cryotomography
+
| Sample preparation for correlative FIB milling and CryoET
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2019Eng_ImageCompression]]
+
| [[2021Budell_TimeResolved]]
| 3D Reconstruction from compressed images
+
| Time resolved CryoEM with Spotiton
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2019Hamaguchi_CryoARM]]
+
| [[2021Casasanta_Microchip]]
| CryoARM data acquisition
+
| Microchip-based structure determination of low-molecular weight proteins using cryo-electron microscopy
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2019Maluenda_Scipion]]
+
| [[2021Frechard_Preparation]]
| Automated workflow processing for facilities
+
| Optimization of Sample Preparation
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2019Tegunov_Warp]]
+
| [[2021Engstrom_Nitrogen]]
| Automatic micrograph processing with Warp
+
| Samples vitrified in boiling nitrogen
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2019Thompson_Protocol]]
+
| [[2021Jagota_GoldNanoparticles]]
| Protocol for EM acquisition
+
| Gold nanoparticles to assess flexibility
|-  
+
|-
  
|}
+
| Paper
 +
| [[2021Jiang_MoAu]]
 +
| Holey Gold Films on Molybdenum Grids
 +
|-
  
== Single particles ==
+
| Paper
 +
| [[2021Jonaid_Liquid]]
 +
| Liquid phase EM
 +
|-
  
=== Automatic particle picking ===
+
| Paper
 +
| [[2021Ki_Conformational]]
 +
| Conformational Distribution of a Small Protein with Nanoparticle-Aided CryoEM
 +
|-
  
{|
+
| Paper
 +
| [[2021Li_detergents]]
 +
| The effect of detergents on preferential orientations
 +
|-
  
 
| Paper
 
| Paper
| [[1982VanHeel_Detection]]
+
| [[2021Voss_Melting]]
| Detection of particles in micrographs
+
| Rapid melting and revitrification as an approach to microsecond time-resolved cryoEM
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2001Nicholson_Review]]
+
| [[2021Zhang_Pegylation]]
| Review on automatic particle picking
+
| Improving particle quality in cryo-EM by PEGylation
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2001Zhu_Filaments]]
+
| [[2022Chen_Detergents]]
| Automatic identification of filaments in micrographs
+
| Role of detergents in the air-water interface
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2004Sigworth_Detection]]
+
| [[2022Levitz_Chameleon]]
| Classical detection theory and the cryo-EM particle selection problem
+
| Effects of dispense-to-plunge speed on particle concentration, complex formation, and final resolution
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2004Volkmann_ParticlePicking]]
+
| [[2022Naydenova_Grid]]
| An approach to automated particle picking from electron micrographs based on reduced representation templates
+
| Integrated wafer-scale manufacturing of electron cryomicroscopy specimen supports
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2004Wong_ParticlePicking]]
+
| [[2022Scher_FIB]]
| Model-based particle picking for cryo-electron microscopy
+
| Sample preparation for FIB-SEM and Correlative microscopy
|-  
+
|-
 +
 
 +
|}
 +
 
 +
=== Automated data collection ===
 +
 
 +
{|
  
 
| Paper
 
| Paper
| [[2004Zhu_Review]]
+
| [[1992Dierksen_Automatic]]
| Review on automatic particle picking
+
| Automated data collection
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007Chen_Signature]]
+
| [[1992Koster_Automatic]]
| Automatic particle picking program: Signature
+
| Automated data collection
 
|-  
 
|-  
 
  
 
| Paper
 
| Paper
| [[2007Woolford_SwarmPS]]
+
| [[1996Fung_Automatic]]
| Automatic particle picking with several criteria, implemented in EMAN Boxer
+
| Automated data collection for tomography
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2009Sorzano_MachineLearning]]
+
| [[2001Zhang_Automatic]]
| Automatic particle picking based on machine learning of rotational invariants
+
| Automated data collection: AutoEM
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2011Arbelaez_Comparison]]
+
| [[2003Ziese_Automatic]]
| Evaluation of the performance of software for automated particle-boxing
+
| Automated autofocusing
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2013Abrishami_MachineLearning]]
+
| [[2004Potter_Automatic]]
| A pattern matching approach to the automatic selection of particles from low-contrast electron micrographs
+
| Automated sample loading
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2013Hauer_2013]]
+
| [[2004Zheng_Automatic]]
| Automatic tilt pair detection in Random Conical Tilt
+
| Automated data collection
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2013Hoang_ParallelGPUPicking]]
+
| [[2005Lei_Automatic]]
| Parallel GPU-accelerated particle picking
+
| Automated data collection: AutoEM
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2013Shatsky_ParticlePicking]]
+
| [[2005Suloway_Automatic]]
| Automated particle correspondence and accurate tilt-axis detection in tilted-image pairs
+
| Automated data collection: Leginon
|- 
 
 
 
| Paper
 
| [[2013Vargas_ParticleQuality]]
 
| Automatic determination of particle quality
 
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2014Langlois_ParticlePicking]]
+
| [[2007Yoshioka_RCT]]
| Automatic particle picking
+
| Automated Random Conical Tilt
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Scheres_SemiAutoPicking]]
+
| [[2011Korinek_TOM2]]
| Semi-automated selection of cryo-EM particles
+
| Automated acquisition with TOM2
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Vilas_AutomaticTilt]]
+
| [[2015Li_UCSFImage]]
| Automatic identification of image pairs in untilted-tilted micrograph pairs
+
| Automated acquisition with UCSFImage
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Wang_DeepPicker]]
+
| [[2016Gil_Fuzzy]]
| A deep learning approach for fully automated particle picking
+
| Real time decisions during acquisition with neuro-fuzzy method
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Zhu_DeepEM]]
+
| [[2016Liu_TiltControl]]
| Deep learning approach to picking
+
| Accurate control of the tilt angle for electron tomography
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Huber_Helices]]
+
| [[2016Vargas_FoilHole]]
| Automated tracing of helices
+
| Determination of image quality at low magnification
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Heimowitz_ApplePicker]]
+
| [[2017Alewijnse_Best]]
| Automated particle picking
+
| Best practices for managing large CryoEM facilities
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Sanchez_DeepConsensus]]
+
| [[2017Biyani_Focus]]
| Deep learning consensus of multiple automatic pickers
+
| Automatic processing of micrographs
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2019Alazzawi_Clustering]]
+
| [[2018Gomez_Facilities]]
| Use of clustering algorithms to find particles in micrographs
+
| Use of Scipion at facilities
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2019Bepler_Topaz]]
+
| [[2018Sorzano_Gain]]
| Deep learning for particle picking
+
| Estimation of the DDD camera gain or residual gain
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2019Carrasco_IP]]
+
| [[2019Chreifi_TiltSeries]]
| Use of standard image processing for particle picking
+
| Rapid tilt-series acquisition for electron cryotomography
|-  
 
 
 
| Conference
 
| [[2019Li_Deep]]
 
| Deep learning for particle picking without box size
 
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2019Wagner_Cryolo]]
+
| [[2019Eng_ImageCompression]]
| Deep learning for particle picking
+
| 3D Reconstruction from compressed images
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2019Wang_Biobjective]]
+
| [[2019Eisenstein_FISE]]
| Biobjective function for robust signal detection
+
| Improved applicability and robustness of fast cryo-electron tomography data acquisition
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2019Zhang_Pixer]]
+
| [[2019Hamaguchi_CryoARM]]
| Deep learning for particle picking
+
| CryoARM data acquisition
 
|-  
 
|-  
 
|}
 
 
=== 2D Preprocessing ===
 
 
{|
 
  
 
| Paper
 
| Paper
| [[1978Carrascosa_matching]]
+
| [[2019Maluenda_Scipion]]
| Gray values matching by linear transformations
+
| Automated workflow processing for facilities
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2003Rosenthal_DPR]]
+
| [[2019Schorb_ET]]
| Contrast enhancement through DPR
+
| Automated acquisition in Electron Tomography
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2004Sorzano_Normalization]]
+
| [[2019Tegunov_Warp]]
| Normalization procedures and their statistical properties.
+
| Automatic micrograph processing with Warp
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2006Sorzano_Denoising]]
+
| [[2019Thompson_Protocol]]
| Strong denoising in wavelet space
+
| Protocol for EM acquisition
 
|-  
 
|-  
  
| Conference
+
| Paper
| [[2009Sorzano_Downsampling]]
+
| [[2020Baxa_Facility]]
| Differences between the different downsampling schemes
+
| Operational workflow in a facility
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2012Brilot_Movies]]
+
| [[2020Guo_EER]]
| Alignment of beam induced motion in direct detectors
+
| Electron event representation for acquisition
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2012Campbell_Movies]]
+
| [[2020Li_Workflow]]
| Alignment of beam induced motion in direct detectors
+
| Workflow for automatic reconstruction
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2012Zhao_Denoising]]
+
| [[2020Sader_Facility]]
| Denoising using an invariant Fourier-Bessel eigenspace
+
| Microscope installation and operation in a facility
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Norousi_Screening]]
+
| [[2020Schenk_CryoFlare]]
| Screening particles to identify outliers
+
| CryoFlare, automatic data acquisition
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Bai_ElectronCounting]]
+
| [[2020Stabrin_Transphire]]
| Electron counting and beam induced motion correction
+
| TranSPHIRE: Automated and feedback-optimized on-the-fly processing for cryo-EM
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Li_ElectronCounting]]
+
| [[2020Yokoyama_Good]]
| Electron counting and beam induced motion correction
+
| Deep learning for determining good regions in a grid
|-  
+
|-  
 +
 
  
 
| Paper
 
| Paper
| [[2013Shigematsu_Movies]]
+
| [[2020Weis_Acquisition]]
| Drift correction for movies considering dark field
+
| Suggestions for high-quality and high-throughput acquisition
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Vargas_ParticleQuality]]
+
| [[2021Feathers_Superresolution]]
| Automatic determination of particle quality
+
| Effects of superresolution and magnification on final resolution
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2014Scheres_Movies]]
+
| [[2021Bouvette_Bisect]]
| Beam induced motion correction
+
| Beam image-shift accelerated data acquisition for near-atomic resolution single-particle cryo-electron tomography
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Abrishami_Movies]]
+
| [[2021Chreifi_FISE]]
| Alignment of direct detection device micrographs
+
| Rapid tilt-series method for cryo-electron tomography: Characterizing stage behavior during FISE acquisition
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Grant_Anisotropic]]
+
| [[2021Efremov_ComaCorrected]]
| Automatic estimation and correction of anisotropic magnification
+
| Coma-corrected rapid single-particle cryo-EM data collection on the CRYO ARM 300
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Grant_OptimalExposure]]
+
| [[2021Herzik_Setup]]
| Filter movies according to the radiation damage
+
| Setup for parallel illumination
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Rubinstein_Alignment]]
+
| [[2021Kayama_Multipurpose]]
| Frame alignment at the level of particle
+
| Below 3 Å structure of apoferritin using a multipurpose TEM with a side entry cryoholder
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Spear_DoseCompensation]]
+
| [[2021Lane_NegativeBias]]
| Effect of dose compensation on resolution
+
| Negative potential bias for faster imaging
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Zhao_AnisotropicMagnification]]
+
| [[2021Rheinberger_IceThickness]]
| Correction of anisotropic magnification
+
| Scripts to measure ice thickness
|-
 
 
 
| Conference
 
| [[2016Bajic_Denoising]]
 
| Denoising and deconvolution of micrographs
 
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Jensen_RemovalVesicles]]
+
| [[2021Yang_CRIM]]
| Removal of vesicles in membrane proteins
+
| Computer readable image markers (CRIM) for correlative microscopy
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Bhamre_Denoising]]
+
| [[2021Weis_Strategies]]
| Denoising by 2D covariance estimation
+
| Strategies for Optimization of Cryogenic Electron Tomography Data Acquisition
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Berndsen_EMPH]]
+
| [[2021Wypych_gP2S]]
| Automated hole masking algorithm
+
| LIMS of microscope sessions
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017McLeod_Zorro]]
+
| [[2021Yang_CLEM]]
| Movie alignment by Zorro
+
| Automated correlative microscopy
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Zheng_MotionCorr2]]
+
| [[2021Yonekura_Hole]]
| Movie alignment by MotionCorr2
+
| Automated hole detection using YOLO
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Ouyang_Denoising]]
+
| [[2022Peck_200]]
| Denoising based on geodesic distance
+
| High-speed high-resolution data collection on a 200 keV cryo-TEM
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Wu_ContrastEnhancement]]
+
| [[2022Peck_Montage]]
| Contrast enhancement
+
| Montage electron tomography
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2019Zivanov_BayesianBIM]]
+
| [[2022Zhu_ElectronCounting]]
| Bayesian correction of beam induced movement
+
| New algorithm for electron counting at the microscope
 
|-  
 
|-  
  
 
|}
 
|}
  
=== 2D Alignment ===
+
== Single particles ==
 +
 
 +
=== Automatic particle picking ===
  
 
{|
 
{|
  
 
| Paper
 
| Paper
| [[1981Frank_Averaging]]
+
| [[1982VanHeel_Detection]]
| 2D averaging and phase residual
+
| Detection of particles in micrographs
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1982Saxton_Averaging]]
+
| [[2001Nicholson_Review]]
| 2D averaging using correlation
+
| Review on automatic particle picking
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1998Sigworth_ML2D]]
+
| [[2001Zhu_Filaments]]
| Maximum likelihood alignment in 2D
+
| Automatic identification of filaments in micrographs
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2003Cong_FRM2D]]
+
| [[2004Sigworth_Detection]]
| Fast Rotational Matching in 2D
+
| Classical detection theory and the cryo-EM particle selection problem
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2005Cong_FRM2D]]
+
| [[2004Volkmann_ParticlePicking]]
| Fast Rotational Matching in 2D introduced in a 3D Alignment algorithm
+
| An approach to automated particle picking from electron micrographs based on reduced representation templates
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2005Scheres_ML2D]]
+
| [[2004Wong_ParticlePicking]]
| Multireference alignment and classification in 2D
+
| Model-based particle picking for cryo-electron microscopy
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Aguerrebere_Limits]]
+
| [[2004Zhu_Review]]
| Fundamental limits of 2D translational alignment
+
| Review on automatic particle picking
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2010Sorzano_CL2D]]
+
| [[2007Chen_Signature]]
| Multireference alignment and classification in 2D
+
| Automatic particle picking program: Signature
 
|-  
 
|-  
  
| Conference
+
 
| [[2017Anoshina_Correlation]]
+
| Paper
| New correlation measure for aligning images
+
| [[2007Woolford_SwarmPS]]
 +
| Automatic particle picking with several criteria, implemented in EMAN Boxer
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2019Radermacher_Correlation]]
+
| [[2009Sorzano_MachineLearning]]
| On the properties of cross correlation for the alignment of images
+
| Automatic particle picking based on machine learning of rotational invariants
 
|-  
 
|-  
  
|}
+
| Paper
 +
| [[2011Arbelaez_Comparison]]
 +
| Evaluation of the performance of software for automated particle-boxing
 +
|-
  
=== 2D Classification and clustering ===
+
| 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
 
| Paper
| [[1981VanHeel_MSA]]
+
| [[2013Hoang_ParallelGPUPicking]]
| Multivariate Statistical Analysis
+
| Parallel GPU-accelerated particle picking
|-  
+
|-
  
 
| Paper
 
| Paper
| [[1984VanHeel_MSA]]
+
| [[2013Shatsky_ParticlePicking]]
| Multivariate Statistical Analysis
+
| Automated particle correspondence and accurate tilt-axis detection in tilted-image pairs
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2005Scheres_ML2D]]
+
| [[2013Vargas_ParticleQuality]]
| Multireference alignment and classification in 2D
+
| Automatic determination of particle quality
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2010Sorzano_CL2D]]
+
| [[2014Langlois_ParticlePicking]]
| Multireference alignment and classification in 2D
+
| Automatic particle picking
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2011Singer_DiffusionMaps]]
+
| [[2015Scheres_SemiAutoPicking]]
| Classification in 2D based on graph analysis of the projections
+
| Semi-automated selection of cryo-EM particles
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2012Yang_ISAC]]
+
| [[2016Vilas_AutomaticTilt]]
| Iterative Stable Alignment and clustering
+
| Automatic identification of image pairs in untilted-tilted micrograph pairs
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2014Sorzano_Outlier]]
+
| [[2016Wang_DeepPicker]]
| Outlier detection in 2D classifications.
+
| A deep learning approach for fully automated particle picking
 +
|-
 +
 
 +
| Paper
 +
| [[2017Rickgauer_Detection]]
 +
| Picking by correlation
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2014Zhao_Aspire]]
+
| [[2017Zhu_DeepEM]]
| Fast classification based on rotational invariants and vector diffusion maps
+
| Deep learning approach to picking
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Huang_Robust]]
+
| [[2018Huber_Helices]]
| Robust w-estimators of 2D classes
+
| Automated tracing of helices
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Kimanius_Accelerated]]
+
| [[2018Heimowitz_ApplePicker]]
| GPU Accelerated image classification and high-resolution refinement
+
| Automated particle picking
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Reboul_Stochastic]]
+
| [[2018Sanchez_DeepConsensus]]
| Stochastic Hill Climbing for calculating 2D classes
+
| Deep learning consensus of multiple automatic pickers
 
|-  
 
|-  
  
| Conference
+
| Paper
| [[2017Bhamre_Mahalanobis]]
+
| [[2019Alazzawi_Clustering]]
| 2D classification using Mahalanobis distance
+
| Use of clustering algorithms to find particles in micrographs
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Wu_GTM]]
+
| [[2019Bepler_Topaz]]
| 2D classification using Generative Topographic Mapping
+
| Deep learning for particle picking
 
|-  
 
|-  
  
| Conference
+
| Paper
| [[2018Boumal_SinglePass]]
+
| [[2019Carrasco_IP]]
| Single pass classification
+
| Use of standard image processing for particle picking
 
|-  
 
|-  
  
 
| Conference
 
| Conference
| [[2018Shuo_Network]]
+
| [[2019Li_Deep]]
| 2D Clustering by network metrics
+
| Deep learning for particle picking without box size
 
|-  
 
|-  
  
|}
+
| Paper
 
+
| [[2019Wagner_Cryolo]]
=== 3D Alignment ===
+
| Deep learning for particle picking
 
+
|-
{|
 
  
 
| Paper
 
| Paper
| [[1980Kam_AutoCorrelation]]
+
| [[2019Wang_Biobjective]]
| Reconstruction without angular assignment from autocorrelation function (reference free)
+
| Biobjective function for robust signal detection
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1986Goncharov_CommonLines]]
+
| [[2019Zhang_Pixer]]
| Angular assignment using common lines (reference free)
+
| Deep learning for particle picking
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1987VanHeel_CommonLines]]
+
| [[2020Sanchez_Cleaner]]
| Angular assignment using common lines (reference free)
+
| Deep learning for removing particles from the carbon edges, aggregations, contaminations, ...
 
|-  
 
|-  
  
| Paper
+
| Conference
| [[1988Provencher_Simultaneous]]
+
| [[2021Li_PickerOptimizers]]
| Simultaneaous alignment and reconstruction
+
| Removal of badly picked particles with Deep Learning
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1988Radermacher_RCT]]
+
| [[2021Ohashi_GRIPS]]
| Random Conical Tilt and Single axis tilt
+
| Two-pass picking with GRIPS
 
|-  
 
|-  
  
| Paper
+
| Conference
| [[1988Vogel_Simultaneous]]
+
| [[2022Huang_DenoisingAndPicking]]
| Simultaneaous alignment and reconstruction
+
| Simultaneous denoising and picking with deep learning
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1990Gelfand_Moments]]
+
| [[2022Olek_Icebreaker]]
| Angular assignment using moments (reference free)
+
| Ice thickness detection and its use for particle picking
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1990Goncharov_Moments]]
+
| [[2022Zhang_EPicker]]
| Angular assignment using moments (reference free)
+
| Particle picking based on continual learning
 
|-  
 
|-  
 +
 +
|}
 +
 +
=== 2D Preprocessing ===
 +
 +
{|
  
 
| Paper
 
| Paper
| [[1990Harauz_Quaternions]]
+
| [[1978Carrascosa_matching]]
| Use of quaternions to represent rotations
+
| Gray values matching by linear transformations
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1994Penczek_Real]]
+
| [[2003Rosenthal_DPR]]
| Angular assignment using projection matching in real space
+
| Contrast enhancement through DPR
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1994Radermacher_Radon]]
+
| [[2004Sorzano_Normalization]]
| Angular assignment in Radon space
+
| Normalization procedures and their statistical properties.
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1996Penczek_CommonLines]]
+
| [[2006Sorzano_Denoising]]
| Angular assignment using common lines (reference free)
+
| Strong denoising in wavelet space
 
|-  
 
|-  
  
| Paper
+
| Conference
| [[2003Rosenthal_DPR]]
+
| [[2009Sorzano_Downsampling]]
| Angular assignment using DPR
+
| Differences between the different downsampling schemes
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2004Sorzano_Wavelet]]
+
| [[2012Brilot_Movies]]
| Angular assignment in the wavelet space.
+
| Alignment of beam induced motion in direct detectors
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2005Jonic_Splines]]
+
| [[2012Campbell_Movies]]
| Angular assignment in Fourier space using spline interpolation.
+
| Alignment of beam induced motion in direct detectors
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2005Yang_Simultaneous]]
+
| [[2012Zhao_Denoising]]
| Simultaneaous alignment and reconstruction
+
| Denoising using an invariant Fourier-Bessel eigenspace
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2006Ogura_SimulatedAnnealing]]
+
| [[2013Norousi_Screening]]
| Angular asignment by simulated annealing
+
| Screening particles to identify outliers
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007Grigorieff_Continuous]]
+
| [[2013Bai_ElectronCounting]]
| Continuous angular assignment in Fourier space
+
| Electron counting and beam induced motion correction
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2010Jaitly_Bayesian]]
+
| [[2013Li_ElectronCounting]]
| Angular assignment by a Bayesian method and annealing
+
| Electron counting and beam induced motion correction
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2010Sanz_Random]]
+
| [[2013Shigematsu_Movies]]
| Random model method
+
| Drift correction for movies considering dark field
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2010Singer_Voting]]
+
| [[2013Vargas_ParticleQuality]]
| Detecting consistent common lines by voting (reference free)
+
| Automatic determination of particle quality
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2011Singer_SDP]]
+
| [[2014Scheres_Movies]]
| Angular assignment by semidefinite programming and eigenvectors (reference free)
+
| Beam induced motion correction
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2012Giannakis_Scattering]]
+
| [[2015Abrishami_Movies]]
| Construction of an initial volume, reference free, by graph analysis of the projections
+
| Alignment of direct detection device micrographs
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2012Shkolnisky_Sync]]
+
| [[2015Grant_Anisotropic]]
| Angular assignment by synchronization of rotations (reference free)
+
| Automatic estimation and correction of anisotropic magnification
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2013Elmlund H_PRIME]]
+
| [[2015Grant_OptimalExposure]]
| PRIME: Probabilistic Initial 3D Model Generation for Single-Particle Cryo-Electron Microscopy
+
| Filter movies according to the radiation damage
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Wang_LUD]]
+
| [[2015Rubinstein_Alignment]]
| Angular assignment by least unsquared deviations (reference free)
+
| Frame alignment at the level of particle
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2014Vargas_RANSAC]]
+
| [[2015Spear_DoseCompensation]]
| Initial model using RANSAC (reference free)
+
| Effect of dose compensation on resolution
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2015Joubert_Pseudoatoms]]
+
| [[2015Zhao_AnisotropicMagnification]]
| Initial model based on pseudo-atoms
+
| Correction of anisotropic magnification
 
|-  
 
|-  
  
| Paper
+
| Conference
| [[2015Singer_Kam]]
+
| [[2016Bajic_Denoising]]
| Reconstruction without angular assignment from autocorrelation function (reference free)
+
| Denoising and deconvolution of micrographs
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Sorzano_Significant]]
+
| [[2016Jensen_RemovalVesicles]]
| Statistical approach to the initial volume estimation (reconstruct significant)
+
| Removal of vesicles in membrane proteins
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Cossio_BayesianGPU]]
+
| [[2016Bhamre_Denoising]]
| GPU implementation of the Bayesian 3D reconstruction approach
+
| Denoising by 2D covariance estimation
 
|-  
 
|-  
  
| Conference
+
| Paper
| [[2016Michels_Heterogeneous]]
+
| [[2017Berndsen_EMPH]]
| Initial volume in the presence of heterogeneity
+
| Automated hole masking algorithm
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Pragier_Graph]]
+
| [[2017McLeod_Zorro]]
| Graph partitioning approach to angular reconstitution
+
| Movie alignment by Zorro
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Greenberg_CommonLines]]
+
| [[2017Zheng_MotionCorr2]]
| Common lines for reference free ab-initio reconstruction
+
| Movie alignment by MotionCorr2
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Sorzano_Highres]]
+
| [[2018Ouyang_Denoising]]
| New algorithm for 3D Reconstruction and alignment with emphasis on significance
+
| Denoising based on geodesic distance
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Sorzano_Swarm]]
+
| [[2018Wu_ContrastEnhancement]]
| Consensus of several initial volumes by swarm optimization
+
| Contrast enhancement
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2019Zehni_Joint]]
+
| [[2019Zivanov_BayesianBIM]]
| Continuous angular refinement and reconstruction
+
| Bayesian correction of beam induced movement
 
|-  
 
|-  
 
|}
 
 
=== 3D Reconstruction ===
 
{|
 
  
 
| Paper
 
| Paper
| [[1972Gilbert_SIRT]]
+
| [[2020Bepler_TopazDenoise]]
| Simultaneous Iterative Reconstruction Technique (SIRT)
+
| Preprocessing of micrographs for better picking
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1973Herman_ART]]
+
| [[2020Chung_2SDR]]
| Algebraic Reconstruction Technique (ART)
+
| PCA to denoise particles
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1980Kam_SphericalHarmonics]]
+
| [[2020Chung_Prepro]]
| 3D Reconstruction using spherical harmonics
+
| Preprocessing of particles for better alignment
 +
|-
 +
 
 +
| Conference
 +
| [[2020Huang_SuperResolution]]
 +
| Deep learning superresolution combination of frames
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1984Andersen_SART]]
+
| [[2020Palovcak_noise2noise]]
| Simultaneous Algebraic Reconstruction Technique (SART)
+
| Noise2noise denoising of micrographs
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1986Harauz_FBP]]
+
| [[2020Strelak_FlexAlign]]
| Exact filters for Filtered Back Projection
+
| Continuous deformation model for aligning movie frames
 
|-  
 
|-  
  
| Chapter
+
| Conference
| [[1992Radermacher_WBP]]
+
| [[2021Fan_Denoising]]
| Exact filters for Weighted Back Projection
+
| Particle denoising using vector diffusion maps
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1997Zhu_RecCTF]]
+
| [[2022Heymann_ProgressiveSSNR]]
| 3D Reconstruction (SIRT like) and simultaneous CTF correction
+
| Progressive SSNR to assess quality and radiation damage
 
|-  
 
|-  
 +
 +
|}
 +
 +
=== 2D Alignment ===
 +
 +
{|
  
 
| Paper
 
| Paper
| [[1998Boisset_Uneven]]
+
| [[1981Frank_Averaging]]
| Artifacts in SIRT and WBP under uneven angular distributions
+
| 2D averaging and phase residual
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1998Marabini_ART]]
+
| [[1982Saxton_Averaging]]
| Algebraic Reconstruction Technique with blobs (Xmipp)
+
| 2D averaging using correlation
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2001Sorzano_Uneven]]
+
| [[1998Sigworth_ML2D]]
| Free parameter selection under uneven angular distributions
+
| Maximum likelihood alignment in 2D
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2005Sorzano_Parameters]]
+
| [[2003Cong_FRM2D]]
| Free parameter selection for optimizing multiple tasks
+
| Fast Rotational Matching in 2D
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2008Sorzano_Constraints]]
+
| [[2005Cong_FRM2D]]
| Mass, surface, positivity and symmetry constraints for real-space algorithms
+
| Fast Rotational Matching in 2D introduced in a 3D Alignment algorithm
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2009Bilbao_ParallelART]]
+
| [[2005Scheres_ML2D]]
| Efficient parallelization of ART
+
| Multireference alignment and classification in 2D
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2011Li_GradientFlow]]
+
| [[2016Aguerrebere_Limits]]
| Regularized 3D Reconstruction by Gradient Flow
+
| Fundamental limits of 2D translational alignment
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2011Vonesch_Wavelets]]
+
| [[2010Sorzano_CL2D]]
| Fast wavelet-based 3D reconstruction
+
| Multireference alignment and classification in 2D
 +
|-  
 +
 
 +
| Conference
 +
| [[2017Anoshina_Correlation]]
 +
| New correlation measure for aligning images
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2012Gopinath_ShapeRegularization]]
+
| [[2019Radermacher_Correlation]]
| Regularized 3D Reconstruction by Shape information
+
| On the properties of cross correlation for the alignment of images
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2012Kucukelbir_adaptiveBasis]]
+
| [[2020Lederman_representation]]
| 3D reconstruction in an adaptive basis promoting sparsity
+
| A representation theory perspective of alignment and classification
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2012Sindelar_NoiseReduction]]
+
| [[2020Marshall_Invariants]]
| Optimal noise reduction in 3D reconstructions
+
| Recovery of an image from its invariants
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Elmlund H_PRIME]]
+
| [[2021Chen_Fast]]
| PRIME: Probabilistic Initial 3D Model Generation for Single-Particle Cryo-Electron Microscopy
+
| Fast alignment through Power Spectrum
 
|-  
 
|-  
  
| Paper
+
| Conference
| [[2013Lyumkis_Optimod]]
+
| [[2021Chung_CryoRALIB]]
| Construction of initial volumes with Optimod
+
| Image alignment acceleration
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Wang FIRM]]
+
| [[2021Heimowitz_Centering]]
| Fast 3D reconstruction in Fourier domain
+
| Centering noisy images
 
|-  
 
|-  
 +
 +
|}
 +
 +
=== 2D Classification and clustering ===
 +
 +
{|
  
 
| Paper
 
| Paper
| [[2014Kunz_SART_OS]]
+
| [[1981VanHeel_MSA]]
| Simultaneous ART with OS
+
| Multivariate Statistical Analysis
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Abrishami_Fourier]]
+
| [[1984VanHeel_MSA]]
| 3D Reconstruction in Fourier space
+
| Multivariate Statistical Analysis
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Dvornek_SubspaceEM]]
+
| [[2005Scheres_ML2D]]
| Fast Maximum a posteriori
+
| Multireference alignment and classification in 2D
 
|-  
 
|-  
  
| Conference
+
| Paper
| [[2018Michels_RBF]]
+
| [[2010Sorzano_CL2D]]
| Ab-initio reconstruction with radial basis functions
+
| Multireference alignment and classification in 2D
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Moriya_Bayesian]]
+
| [[2011Singer_DiffusionMaps]]
| Bayesian approach to suppress limited angular artifacts
+
| Classification in 2D based on graph analysis of the projections
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Xu_GeometricFlow]]
+
| [[2012Yang_ISAC]]
| Multi-scale geometric flow
+
| Iterative Stable Alignment and clustering
|-
 
 
 
| Arxiv
 
| [[2016Ye_Cohomology]]
 
| Cohomology properties of 3D reconstruction
 
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Punjani_CryoSPARC]]
+
| [[2014Sorzano_Outlier]]
| CryoSPARC
+
| Outlier detection in 2D classifications.
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Punjani_CryoSPARCTheory]]
+
| [[2014Zhao_Aspire]]
| Theory related to CryoSPARC
+
| Fast classification based on rotational invariants and vector diffusion maps
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Sorzano_SurveyIterative]]
+
| [[2015Huang_Robust]]
| Survey of iterative reconstruction methods for EM
+
| Robust w-estimators of 2D classes
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Bartesaghi_Refinement]]
+
| [[2016Kimanius_Accelerated]]
| Refinement of CTF, frame weight and alignment for high resolution reconstruction
+
| GPU Accelerated image classification and high-resolution refinement
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Hu_ParticleFilter]]
+
| [[2016Reboul_Stochastic]]
| A particle filter framework for 3D reconstruction
+
| Stochastic Hill Climbing for calculating 2D classes
 
|-  
 
|-  
  
 
| Conference
 
| Conference
| [[2018Levin_Kam]]
+
| [[2017Bhamre_Mahalanobis]]
| Ab initio reconstruction by autocorrelation analysis
+
| 2D classification using Mahalanobis distance
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Reboul_Simple]]
+
| [[2017Wu_GTM]]
| Ab initio reconstruction with Simple
+
| 2D classification using Generative Topographic Mapping
 
|-  
 
|-  
  
| Paper
+
| Conference
| [[2018Sorzano_Highres]]
+
| [[2018Boumal_SinglePass]]
| New algorithm for 3D Reconstruction and alignment with emphasis on significance
+
| Single pass classification
 
|-  
 
|-  
  
| Paper
+
| Conference
| [[2018Sorzano_Swarm]]
+
| [[2018Shuo_Network]]
| Consensus of several initial volumes by swarm optimization
+
| 2D Clustering by network metrics
 
|-  
 
|-  
  
| Paper
+
| Conference
| [[2018Zhu_Ewald]]
+
| [[2020Miolane_VAEGAN]]
| 3D Reconstruction with Ewald sphere correction
+
| 2D Analysis by deep learning
 
|-  
 
|-  
  
| Paper
+
| Conference
| [[2019Gomez_Initial]]
+
| [[2021Rao_Wasserstein]]
| Construction of initial models
+
| Wasserstein K-Means for Clustering Tomographic Projections
|-  
 
 
 
| Master
 
| [[2019Havelkova_Regularization]]
 
| Regularization methods in 3D reconstruction
 
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2019Wilkinson_Scales]]
+
| [[2022Wang_Spectral]]
| Combining data acquired at different scales
+
| 2D classification with spectral clustering
 
|-  
 
|-  
  
 
|}
 
|}
  
=== 3D Heterogeneity ===
+
=== 3D Alignment ===
  
 
{|
 
{|
  
 
| Paper
 
| Paper
| [[2004White_Size]]
+
| [[1980Kam_AutoCorrelation]]
| Heterogeneity classification of differently sized images
+
| Reconstruction without angular assignment from autocorrelation function (reference free)
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2006Penczek_Bootstrap]]
+
| [[1986Goncharov_CommonLines]]
| 3D heterogeneity through bootstrap
+
| Angular assignment using common lines (reference free)
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007Leschziner_Review]]
+
| [[1987VanHeel_CommonLines]]
| Review of 3D heterogeneity handling algorithms
+
| Angular assignment using common lines (reference free)
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007Scheres_ML3D]]
+
| [[1988Provencher_Simultaneous]]
| Maximum Likelihood alignment and classification in 3D
+
| Simultaneaous alignment and reconstruction
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2008Herman_Graph]]
+
| [[1988Radermacher_RCT]]
| Classification by graph partitioning
+
| Random Conical Tilt and Single axis tilt
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2009Spahn_Bootstrap]]
+
| [[1988Vogel_Simultaneous]]
| 3D heterogeneity through bootstrap
+
| Simultaneaous alignment and reconstruction
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2010Elmlund_AbInitio]]
+
| [[1990Gelfand_Moments]]
| Solving the initial volume problem with multiple conformations
+
| Angular assignment using moments (reference free)
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2010Shatsky_MultiVariate]]
+
| [[1990Goncharov_Moments]]
| Multivariate Statistical Analysis
+
| Angular assignment using moments (reference free)
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2012Scheres_Bayesian]]
+
| [[1990Harauz_Quaternions]]
| A Bayesian view on cryo-EM structure determination
+
| Use of quaternions to represent rotations
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2012Zheng_Covariance]]
+
| [[1994Penczek_Real]]
| Estimation of the volume covariance
+
| Angular assignment using projection matching in real space
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Wang_MLVariance]]
+
| [[1994Radermacher_Radon]]
| Maximum Likelihood estimate of the map variance
+
| Angular assignment in Radon space
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Lyumkis D_FREALIGN]]
+
| [[1996Penczek_CommonLines]]
| Likelihood-based classification of cryo-EM images using FREALIGN.
+
| Angular assignment using common lines (reference free)
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2014Jin_NMA]]
+
| [[2003Rosenthal_DPR]]
| Continuous heterogeneity through Normal Mode Analysis
+
| Angular assignment using DPR
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2014Dashti_Brownian]]
+
| [[2004Sorzano_Wavelet]]
| Continuous heterogeneity through Brownian trajectories
+
| Angular assignment in the wavelet space.
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2014Chen_Migration]]
+
| [[2005Jonic_Splines]]
| Particle migration analysis in 3D classification
+
| Angular assignment in Fourier space using spline interpolation.
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Anden_Covariance]]
+
| [[2005Yang_Simultaneous]]
| 3D Covariance matrix estimation for heterogeneity
+
| Simultaneaous alignment and reconstruction
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Bai_Focused]]
+
| [[2006Ogura_SimulatedAnnealing]]
| Focused classification
+
| Angular asignment by simulated annealing
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Katsevich_Covariance]]
+
| [[2007Grigorieff_Continuous]]
| 3D Covariance matrix estimation for heterogeneity
+
| Continuous angular assignment in Fourier space
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Klaholz_MRA]]
+
| [[2010Jaitly_Bayesian]]
| Multivariate Statistical Analysis of Jackknife and Bootstrapping on random subsets
+
| Angular assignment by a Bayesian method and annealing
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2015Liao_Covariance]]
+
| [[2010Sanz_Random]]
| Estimation of the 3D covariance from 2D projections
+
| Random model method
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2015Tagare_Direct]]
+
| [[2010Singer_Voting]]
| Direct reconstruction of PCA components
+
| Detecting consistent common lines by voting (reference free)
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2016Gong_Mechanical]]
+
| [[2011Singer_SDP]]
| Mechanical model for macromolecules
+
| Angular assignment by semidefinite programming and eigenvectors (reference free)
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2016Rawson_Movement]]
+
| [[2012Giannakis_Scattering]]
| Movement and flexibility
+
| Construction of an initial volume, reference free, by graph analysis of the projections
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2016Shan_Multibody]]
+
| [[2012Shkolnisky_Sync]]
| Multibody refinement
+
| Angular assignment by synchronization of rotations (reference free)
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2016Sorzano_StructMap]]
+
| [[2013Elmlund H_PRIME]]
| Sorting a discrete set of conformational states
+
| PRIME: Probabilistic Initial 3D Model Generation for Single-Particle Cryo-Electron Microscopy
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Sorzano_Strain]]
+
| [[2013Wang_LUD]]
| Calculate local stretches, strains and rotations from two conformational states
+
| Angular assignment by least unsquared deviations (reference free)
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2017Punjani_CryoSPARC]]
+
| [[2014Vargas_RANSAC]]
| CryoSPARC
+
| Initial model using RANSAC (reference free)
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2017Schillbach_Warpcraft]]
+
| [[2015Joubert_Pseudoatoms]]
| Warpcraft: 3D Reconstruction in the presence of continuous heterogeneity
+
| Initial model based on pseudo-atoms
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Anden_Covariance]]
+
| [[2015Singer_Kam]]
| Structural Variability from Noisy Tomographic Projections
+
| Reconstruction without angular assignment from autocorrelation function (reference free)
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Haselbach_FreeEnergy]]
+
| [[2015Sorzano_Significant]]
| Analysis of the free energy landscape through PCA
+
| Statistical approach to the initial volume estimation (reconstruct significant)
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Nakane_MultiBody]]
+
| [[2016Cossio_BayesianGPU]]
| Structural Variability through multi-body refinement
+
| GPU implementation of the Bayesian 3D reconstruction approach
 
|-  
 
|-  
  
| Paper
+
| Conference
| [[2019Serna_Review]]
+
| [[2016Michels_Heterogeneous]]
| Review of classification tools
+
| Initial volume in the presence of heterogeneity
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Solernou_FFEA]]
+
| [[2016Pragier_Graph]]
| Fluctuating Finite Element Analysis, continuum approach to Molecular Dynamics
+
| Graph partitioning approach to angular reconstitution
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2019Sorzano_Review]]
+
| [[2017Greenberg_CommonLines]]
| Review of continuous heterogeneity biophysics
+
| Common lines for reference free ab-initio reconstruction
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2019Zhang_Local]]
+
| [[2018Sorzano_Highres]]
| Local variability and covariance
+
| New algorithm for 3D Reconstruction and alignment with emphasis on significance
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2020Harastani_NMA]]
+
| [[2018Sorzano_Swarm]]
| Using Scipion for analyzing local heterogeneity with normal modes
+
| Consensus of several initial volumes by swarm optimization
 
|-  
 
|-  
 
|}
 
 
=== Validation ===
 
 
{|
 
  
 
| Paper
 
| Paper
| [[2008Stagg_TestBed]]
+
| [[2019Zehni_Joint]]
| Effect of voltage, dosis, number of particles and Euler jumps on resolution
+
| Continuous angular refinement and reconstruction
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2011Henderson]]
+
| [[2019Zehni_Joint]]
| Tilt Validation
+
| Continuous angular refinement and reconstruction
 
|-  
 
|-  
  
| Paper
 
| [[2011Read]]
 
| Validation of PDBs
 
|-
 
  
 
| Paper
 
| Paper
| [[2012Henderson]]
+
| [[2020Sharon_NonUniformKam]]
| EM Map Validation
+
| Reconstruction and angular distribution estimation without angular assignment (reference free)
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Cossio_Bayesian]]
+
| [[2020Xie_Network]]
| EM Map Validation in a probabilistic setting
+
| Angular assignment considering a network of assignments
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Chen_NoiseSubstitution]]
+
| [[2021Jimenez_DeepAlign]]
| Noise substitution at high resolution for measuring overfitting
+
| Angular alignment using deep learning
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Ludtke_Validation]]
+
| [[2021Kojima_Preferred]]
| Structural validation, example of the Calcium release channel
+
| Identification of preferred orientations
 
|-  
 
|-  
  
| Paper
+
| Conference
| [[2013Murray_Validation]]
+
| [[2021Nashed_CryoPoseNet]]
| Validation of a 3DEM structure through a particular example
+
| CryoPoseNet: Angular alignment with deep learning
 
|-  
 
|-  
  
| Paper
+
| Conference
| [[2014Russo_StatisticalSignificance]]
+
| [[2021Zhong_CryoDRGN2]]
| EM Map Validation through the statistical significance of the tilt-pair angular assignment
+
| CryoDRGN2: Angular alignment with deep learning
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2014Stagg_Reslog]]
+
| [[2022Lu_SphericalEmbeddings]]
| EM Map Validation through the resolution evolution with the number of particles
+
| Angular assignment through common lines and spherical embeddings
 
|-  
 
|-  
 +
 +
|}
 +
 +
=== 3D Reconstruction ===
 +
{|
  
 
| Paper
 
| Paper
| [[2014Wasilewski_Tilt]]
+
| [[1972Gilbert_SIRT]]
| Web implementation of the tilt pair validation
+
| Simultaneous Iterative Reconstruction Technique (SIRT)
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Heymann_Alignability]]
+
| [[1973Herman_ART]]
| EM Map Validation through the resolution of reconstructions from particles and noise
+
| Algebraic Reconstruction Technique (ART)
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Oliveira_FreqLimited]]
+
| [[1980Kam_SphericalHarmonics]]
| Comparison of gold standard and frequency limited optimization
+
| 3D Reconstruction using spherical harmonics
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Rosenthal_Review]]
+
| [[1984Andersen_SART]]
| Review of validation methods
+
| Simultaneous Algebraic Reconstruction Technique (SART)
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Wriggers_Secondary]]
+
| [[1986Harauz_FBP]]
| Validation by secondary structure
+
| Exact filters for Filtered Back Projection
 
|-  
 
|-  
  
| Paper
+
| Chapter
| [[2016Degiacomi_IM]]
+
| [[1992Radermacher_WBP]]
| Comparison of Ion Mobility data and EM volumes
+
| Exact filters for Weighted Back Projection
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Kim_SAXS]]
+
| [[1997Zhu_RecCTF]]
| Comparison of SAXS data and EM projections
+
| 3D Reconstruction (SIRT like) and simultaneous CTF correction
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Rosenthal_Review]]
+
| [[1998Boisset_Uneven]]
| Review of validation methods
+
| Artifacts in SIRT and WBP under uneven angular distributions
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Vargas_Alignability]]
+
| [[1998Marabini_ART]]
| Validation by studying the tendency of an angular assignment to cluster in the projection space
+
| Algebraic Reconstruction Technique with blobs (Xmipp)
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Monroe_PDBRefinement]]
+
| [[2001Sorzano_Uneven]]
| Validation by comparison to a refined PDB
+
| Free parameter selection under uneven angular distributions
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Afonine_Phenix]]
+
| [[2005Sorzano_Parameters]]
| Tools in Phenix for the validation of EM maps
+
| Free parameter selection for optimizing multiple tasks
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Heymann_Bsoft]]
+
| [[2008Sorzano_Constraints]]
| Map validation using Bsoft
+
| Mass, surface, positivity and symmetry constraints for real-space algorithms
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Heymann_Challenge]]
+
| [[2009Bilbao_ParallelART]]
| A summary of the assessments of the 3D Map Challenge
+
| Efficient parallelization of ART
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Jonic_Gaussian]]
+
| [[2011Li_GradientFlow]]
| Assessment of sets of volumes by pseudoatomic structures
+
| Regularized 3D Reconstruction by Gradient Flow
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Naydenova_AngularDistribution]]
+
| [[2011Vonesch_Wavelets]]
| Evaluating the angular distribution of a 3D reconstruction
+
| Fast wavelet-based 3D reconstruction  
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Pages_Symmetry]]
+
| [[2012Gopinath_ShapeRegularization]]
| Looking for a symmetry axis in a PDB
+
| Regularized 3D Reconstruction by Shape information
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Pintilie_SSE]]
+
| [[2012Kucukelbir_adaptiveBasis]]
| Evaluating the quality of SSE and side chains
+
| 3D reconstruction in an adaptive basis promoting sparsity
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2019Herzik_Multimodel]]
+
| [[2012Sindelar_NoiseReduction]]
| Local and global quality by multi-model fitting
+
| Optimal noise reduction in 3D reconstructions
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2020Stojkovic_PTM]]
+
| [[2013Elmlund H_PRIME]]
| Validation of post-translational modifications
+
| PRIME: Probabilistic Initial 3D Model Generation for Single-Particle Cryo-Electron Microscopy
 
|-  
 
|-  
 
|}
 
 
=== Resolution ===
 
 
{|
 
  
 
| Paper
 
| Paper
| [[1986Harauz_FBP]]
+
| [[2013Lyumkis_Optimod]]
| Fourier Shell Correlation
+
| Construction of initial volumes with Optimod
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1987Unser_SSNR]]
+
| [[2013Wang FIRM]]
| 2D Spectral Signal to Noise Ratio
+
| Fast 3D reconstruction in Fourier domain
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2002Penczek_SSNR]]
+
| [[2014Kunz_SART_OS]]
| 3D Spectral Signal to Noise Ratio for Fourier based algorithms
+
| Simultaneous ART with OS
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2003Rosenthal_DPR]]
+
| [[2015Abrishami_Fourier]]
| Review of the FSC and establishment of a new threshold
+
| 3D Reconstruction in Fourier space
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2005Unser_SSNR]]
+
| [[2015Dvornek_SubspaceEM]]
| 3D Spectral Signal to Noise Ratio for any kind of algorithms
+
| Fast Maximum a posteriori
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2005VanHeel_FSC]]
+
| [[2015Moriya_Bayesian]]
| Establishment of a new threshold for FSC
+
| Bayesian approach to suppress limited angular artifacts
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007Sousa_AbInitio]]
+
| [[2015Xu_GeometricFlow]]
| Resolution measurement on neighbour Fourier voxels
+
| Multi-scale geometric flow
 
|-  
 
|-  
  
| Paper
+
| Arxiv
| [[2014Kucukelbir_Local]]
+
| [[2016Ye_Cohomology]]
| Quantifying the local resolution of cryo-EM density maps
+
| Cohomology properties of 3D reconstruction
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Pintilie_Probabilistic]]
+
| [[2017Punjani_CryoSPARC]]
| Probabilistic models and resolution
+
| CryoSPARC
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Sorzano_FourierProperties]]
+
| [[2017Punjani_CryoSPARCTheory]]
| Statistical properties of resolution measures defined in Fourier space
+
| Theory related to CryoSPARC
 
|-  
 
|-  
  
| Conference
+
| Paper
| [[2018Avramov_DeepLearning]]
+
| [[2017Sorzano_SurveyIterative]]
| Deep learning classification of volumes into low, medium and high resolution
+
| Survey of iterative reconstruction methods for EM
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Carugo_BFactors]]
+
| [[2018Bartesaghi_Refinement]]
| How large can B-factors be in protein crystals
+
| Refinement of CTF, frame weight and alignment for high resolution reconstruction
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Kim_FourierError]]
+
| [[2018Hu_ParticleFilter]]
| Comparison between a gold standard and a reconstruction
+
| A particle filter framework for 3D reconstruction
 
|-  
 
|-  
  
| Paper
+
| Conference
| [[2018Rupp_Problems]]
+
| [[2018Levin_Kam]]
| Problems of resolution as a proxy number for map quality
+
| Ab initio reconstruction by autocorrelation analysis
 
|-  
 
|-  
  
| Paper
+
| Conference
| [[2018Vilas_MonoRes]]
+
| [[2018Michels_RBF]]
| Local resolution by monogenic signals
+
| Ab-initio reconstruction with radial basis functions
 
|-  
 
|-  
 +
  
 
| Paper
 
| Paper
| [[2018Yang_Multiscale]]
+
| [[2018Reboul_Simple]]
| Resolution from a multiscale spectral analysis
+
| Ab initio reconstruction with Simple
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2019Avramov_DeepLearning]]
+
| [[2018Sorzano_Highres]]
| Deep learning classification of volumes into low, medium and high resolution
+
| New algorithm for 3D Reconstruction and alignment with emphasis on significance
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2019Ramirez_DeepRes]]
+
| [[2018Sorzano_Swarm]]
| Resolution determination by deep learning
+
| Consensus of several initial volumes by swarm optimization
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2020Baldwin_Lyumkis_SCF]]
+
| [[2018Zhu_Ewald]]
| Resolution attenuation through non-uniform Fourier sampling
+
| 3D Reconstruction with Ewald sphere correction
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2020Vilas_MonoDir]]
+
| [[2019Gomez_Initial]]
| Local and directional resolution
+
| Construction of initial models
 
|-  
 
|-  
  
|}
+
| Master
 +
| [[2019Havelkova_Regularization]]
 +
| Regularization methods in 3D reconstruction
 +
|-
  
=== Sharpening of high resolution information ===
 
{|
 
 
 
| Paper
 
| Paper
| [[2003Rosenthal_DPR]]
+
| [[2019Wilkinson_Scales]]
| Contrast restoration and map sharpening
+
| Combining data acquired at different scales
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2008Fernandez_Bfactor]]
+
| [[2020Alazzawi_Auto]]
| Bfactor determination and restoration
+
| Automatic full processing of micrographs to yield a 3D reconstruction
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Fiddy_SaxtonAlgorithm]]
+
| [[2020Pan_TV]]
| Phase retrieval or extension
+
| 3D Reconstruction with total variation regularization
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2014Kishchenko_SphericalDeconvolution]]
+
| [[2020Punjani_NonUniform]]
| Spherical deconvolution
+
| Non-uniform refinement
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Spiegel_VISDEM]]
+
| [[2020Ramlaul_Sidesplitter]]
| Visualization improvement by the use of pseudoatomic profiles
+
| Local filtering along the reconstruction iterations
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Jonic_Pseudoatoms]]
+
| [[2020Xie_Automatic]]
| Approximation with pseudoatoms
+
| Automatic 3D reconstruction from projections
 +
|-
 +
 
 +
| Conference
 +
| [[2020Venkatakrishnan_MBIR]]
 +
| Model based image reconstruction
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Jonic_Denoising]]
+
| [[2020Zhou_AutomaticSelection]]
| Denoising and high-frequency boosting by pseudoatom approximation
+
| Automatic selection of particles for 3D reconstruction
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Jakobi_LocScale]]
+
| [[2021Abrishami_Localized]]
| Sharpening based on an atomic model
+
| Localized reconstruction in scipion expedites the analysis of symmetry mismatches in Cryo-EM data
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2019Ramlaul_Filtering]]
+
| [[2021Gupta_CryoGAN]]
| Local agreement filtering (denoising)
+
| 3D Reconstruction via Generative Adversarial Learning
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2020Vilas_Bfactor]]
+
| [[2021Luo_Opus]]
| Global B-factor correction does not represent macromolecules
+
| 3D Reconstruction with a sparse and smoothness constraint
 
|-  
 
|-  
  
|}
+
| Paper
 +
| [[2021Kimanius_PriorKnowledge]]
 +
| Incorporation of prior knowledge during 3D reconstruction
 +
|-
  
=== CTF estimation and restoration ===
+
| Paper
 +
| [[2021Sorzano_Uneven]]
 +
| Algorithmic robustness to uneven angular distributions
 +
|-
 +
 
 +
|}
 +
 
 +
=== 3D Heterogeneity ===
  
 
{|
 
{|
  
 
| Paper
 
| Paper
| [[1982Schiske_Correction]]
+
| [[2004White_Size]]
| CTF correction for tilted objects
+
| Heterogeneity classification of differently sized images
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1988Toyoshima_Model]]
+
| [[2006Penczek_Bootstrap]]
| CTF estimation
+
| 3D heterogeneity through bootstrap
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1995Frank_Wiener]]
+
| [[2007Leschziner_Review]]
| CTF correction using Wiener filter
+
| Review of 3D heterogeneity handling algorithms
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1996Skoglund_MaxEnt]]
+
| [[2007Scheres_ML3D]]
| CTF correction with Maximum Entropy
+
| Maximum Likelihood alignment and classification in 3D
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1996Zhou_Model]]
+
| [[2008Herman_Graph]]
| CTF model and user interface for manual fitting
+
| Classification by graph partitioning
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1997Fernandez_AR]]
+
| [[2009Spahn_Bootstrap]]
| PSD estimation using periodogram averaging and AR models
+
| 3D heterogeneity through bootstrap
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1997Penczek_Wiener]]
+
| [[2010Elmlund_AbInitio]]
| CTF correction using Wiener filter
+
| Solving the initial volume problem with multiple conformations
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1997Stark_Deconvolution]]
+
| [[2010Shatsky_MultiVariate]]
| CTF correction using deconvolution
+
| Multivariate Statistical Analysis
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1997Zhu_RecCTF]]
+
| [[2012Scheres_Bayesian]]
| CTF correction and reconstruction
+
| A Bayesian view on cryo-EM structure determination
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2000DeRosier_EwaldCorrection]]
+
| [[2012Zheng_Covariance]]
| CTF correction considering the Ewald sphere
+
| Estimation of the volume covariance
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2000Jensen_TiltedCorrection]]
+
| [[2013Wang_MLVariance]]
| CTF correction considering tilt in backprojection
+
| Maximum Likelihood estimate of the map variance
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2001Saad_CTFEstimate]]
+
| [[2013Lyumkis D_FREALIGN]]
| CTF estimation
+
| Likelihood-based classification of cryo-EM images using FREALIGN.
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2003Huang_CTFEstimate]]
+
| [[2014Chen_Migration]]
| CTF estimation
+
| Particle migration analysis in 3D classification
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2003Mindell_CTFTILT]]
+
| [[2014Dashti_Brownian]]
| CTF estimation for tilted micrographs
+
| Continuous heterogeneity through Brownian trajectories
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2003Sander_MSA]]
+
| [[2014Schwander_manifold]]
| CTF estimation through MSA classification of PSDs
+
| Continuous heterogeneity through Manifold Analysis
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2003Velazquez_ARMA]]
+
| [[2014Jin_NMA]]
| PSD and CTF estimation using ARMA models
+
| Continuous heterogeneity through Normal Mode Analysis
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2004Sorzano_IDR]]
+
| [[2015Anden_Covariance]]
| CTF restoration and reconstruction with Iterative Data Refinement
+
| 3D Covariance matrix estimation for heterogeneity
 
|-  
 
|-  
  
| Conference
+
| Paper
| [[2004Wan_CTF]]
+
| [[2015Bai_Focused]]
| Spatially variant CTF
+
| Focused classification
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2004Zubelli_Chahine]]
+
| [[2015Katsevich_Covariance]]
| CTF restoration and reconstruction with Chahine's multiplicative method
+
| 3D Covariance matrix estimation for heterogeneity
 
|-  
 
|-  
  
| Conference
+
| Paper
| [[2005Dubowy_SpaceVariant]]
+
| [[2015Klaholz_MRA]]
| CTF correction when this is space variant
+
| Multivariate Statistical Analysis of Jackknife and Bootstrapping on random subsets
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2005Mallick_ACE]]
+
| [[2015Liao_Covariance]]
| CTF estimation
+
| Estimation of the 3D covariance from 2D projections
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2006Wolf_Ewald]]
+
| [[2015Tagare_Direct]]
| CTF correction considering Ewald sphere
+
| Direct reconstruction of PCA components
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007Jonic_EnhancedPSD]]
+
| [[2016Gong_Mechanical]]
| PSD enhancement for better identification of Thon rings; Vitreous ice diffracts in Thon rings
+
| Mechanical model for macromolecules
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007Philippsen_Model]]
+
| [[2016Rawson_Movement]]
| CTF Model for tilted specimens
+
| Movement and flexibility
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007Sorzano_CTF]]
+
| [[2016Shan_Multibody]]
| CTF estimation using enhanced PSDs
+
| Multibody refinement
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2009Sorzano_Sensitivity]]
+
| [[2016Sorzano_StructMap]]
| Error sensitivity of the CTF models, non-uniqueness of the CTF parameters
+
| Sorting a discrete set of conformational states
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2010Jiang2010_CTFCorrection]]
+
| [[2016Sorzano_Strain]]
| Amplitude correction method
+
| Calculate local stretches, strains and rotations from two conformational states
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2010Kasantsev_CTFCorrection]]
+
| [[2017Punjani_CryoSPARC]]
| Mathematical foundations of Kornberg and Jensen method
+
| CryoSPARC
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2010Leong_CTFCorrection]]
+
| [[2017Schillbach_Warpcraft]]
| Correction for spatially variant CTF
+
| Warpcraft: 3D Reconstruction in the presence of continuous heterogeneity
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2011Glaeser_Coma]]
+
| [[2018Anden_Covariance]]
| The effect of coma at high-resolution
+
| Structural Variability from Noisy Tomographic Projections
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2011Mariani_Tilted]]
+
| [[2018Haselbach_FreeEnergy]]
| CTF simulation and correction of tilted specimens
+
| Analysis of the free energy landscape through PCA
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2011Sindelar_Wiener]]
+
| [[2018Nakane_MultiBody]]
| CTF correction using a modified version of Wiener filter
+
| Structural Variability through multi-body refinement
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2011Voortman_Tilted]]
+
| [[2019Serna_Review]]
| CTF correction for tilted specimen
+
| Review of classification tools
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2012Voortman_VaryingCTF]]
+
| [[2018Solernou_FFEA]]
| Correcting a spatially varying CTF
+
| Fluctuating Finite Element Analysis, continuum approach to Molecular Dynamics
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Vargas_FastDef]]
+
| [[2019Sorzano_Review]]
| Fast defocus
+
| Review of continuous heterogeneity biophysics
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Rohou_CTFFind4]]
+
| [[2019Zhang_Local]]
| CTF Find 4
+
| Local variability and covariance
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Sheth_CTFquality]]
+
| [[2020Dashti_Landscape]]
| Visualization and quality assessment of CTF
+
| Retrieving functional pathways from single particle snapshots
 +
|-
 +
 
 +
| Conference
 +
| [[2020Gupta_MultiCryoGAN]]
 +
| Reconstruction of continuously heterogeneous structures with adversarial networks
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Zhang_GCTF]]
+
| [[2020Harastani_NMA]]
| gCTF
+
| Using Scipion for analyzing local heterogeneity with normal modes
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Su_GoCTF]]
+
| [[2020Maji_Propagation]]
| goCTF, CTF for tilted specimens
+
| Propagation of conformational coordinates across angular space
 
|-  
 
|-  
 
|}
 
 
=== Segmentation ===
 
 
{|
 
  
 
| Paper
 
| Paper
| [[2006Baker_segmentation]]
+
| [[2020Moscovich_DiffusionMaps]]
| Segmentation of molecular subunits
+
| Heterogeneity analysis by diffusion maps and spectral volumes
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2010Pintilie_segger]]
+
| [[2020Seitz_Polaris]]
| Segmentation of molecular subunits
+
| Analysis of energy landscapes to find minimal action paths
 
|-  
 
|-  
  
 
| Conference
 
| Conference
| [[2017Nissenson_VolumeCut]]
+
| [[2020Zhong_CryoDRGN]]
| Segmentation of an EM volume using an atomic model
+
| CryoDRGN to analyze the continuous heterogeneity by CryoEM
 
|-  
 
|-  
  
|}
+
| Paper
 
+
| [[2020Verbeke_Separation]]
=== Fitting and docking ===
+
| Heterogeneity analysis by comparing common lines
 
+
|-
{|
 
  
 
| Paper
 
| Paper
| [[1999Volkmann_Fitting]]
+
| [[2021Chen_GM]]
| Fitting in real space
+
| Deep learning-based mixed-dimensional Gaussian mixture model for characterizing variability
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2001Baker_Review]]
+
| [[2021Giraldo_cryoBIFE]]
| Review of protein structure prediction
+
| A Bayesian approach to extracting free‑energy profiles
 
|-  
 
|-  
  
| Paper
+
| Conference
| [[2001Jones_Review]]
+
| [[2021Hamitouche_NMADL]]
| Review of protein structure prediction
+
| Continuous heterogeneity analysis through normal modes and deep learning
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2003Kovacs_FRM3D]]
+
| [[2021Herreros_Zernikes3D]]
| Fast Rotational Alignment of two EM maps
+
| Continuous heterogeneity analysis through Zernikes 3D
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2004Tama_NMA1]]
+
| [[2021Kazemi_Enrich]]
| Flexible fitting with Normal Modes (I)
+
| ENRICH: A fast method to improve the quality of flexible macromolecular reconstructions
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2004Tama_NMA2]]
+
| [[2021Matsumoto_DEFmap]]
| Flexible fitting with Normal Modes (II)
+
| Prediction of RMSF of Molecular Dynamics from a CryoEM map using deep learning
 
|-  
 
|-  
  
| Paper
+
| Chapter
| [[2005Velazquez_Superfamilies]]
+
| [[2021Nakasako_Landscape]]
| Recognition of the superfamily folding in medium-high resolution volumes
+
| Estimation of free-energy landscape from images
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007DeVries_Haddock]]
+
| [[2021Punjani_3DVA]]
| Docking with Haddock 2.0
+
| 3D Variability analysis from images
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007Kleywegt_QualityControl]]
+
| [[2021Sorzano_PCA]]
| Quality control and validation of fitting
+
| PCA is limited to low-resolution
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2012Biswas_Secondary]]
+
| [[2021Zhong_CryoDRGN]]
| Secondary structure determination in EM volumes
+
| CryoDRGN to analyze the continuous heterogeneity by CryoEM
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2012Velazquez_Constraints]]
+
| [[2022Ecoffet_MorphOT]]
| Multicomponent fitting by using constraints from other information sources
+
| More physically plausible morphing between two states
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Chapman MS_Atomicmodeling]]
+
| [[2022Gomez_Hierarchical]]
| Atomic modeling of cryo-electron microscopy reconstructions--joint refinement of model and imaging parameters
+
| Hierarchical classification of particles
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Esquivel_Modelling]]
+
| [[2022Rabuck_Quant]]
| Review on modelling (secondary structure, fitting, ...)
+
| Workflow for discrete heterogeneity analysis
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Lopez_Imodfit]]
+
| [[2022Skalidis_Endogenous]]
| Fitting based on vibrational analysis
+
| AI tools to recognize proteins in cellular fractions
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Nogales_3DEMLoupe]]
+
| [[2022Zhou_Data]]
| Normal Mode Analysis of reconstructed volumes
+
| Determination of the number of discrete 3D classes
 
|-  
 
|-  
  
| Paper
+
|}
| [[2014AlNasr_Secondary]]
+
 
| Identification of secondary structure elements in EM volumes
+
=== Validation ===
|-
 
  
| Paper
+
{|
| [[2014Politis_MassSpect]]
 
| Integration of mass spectroscopy information
 
|-
 
  
 
| Paper
 
| Paper
| [[2014Rey_MassSpect]]
+
| [[2008Stagg_TestBed]]
| Integration of mass spectroscopy information
+
| Effect of voltage, dosis, number of particles and Euler jumps on resolution
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2014Villa_Review]]
+
| [[2011Henderson]]
| Review of atomic fitting into EM volumes
+
| Tilt Validation
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Barad_EMRinger]]
+
| [[2011Read]]
| Validation of hybrid models
+
| Validation of PDBs
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Bettadapura_PF2Fit]]
+
| [[2012Henderson]]
| Fast rigid fitting of PDBs into EM maps
+
| EM Map Validation
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Carrillo_CapsidMaps]]
+
| [[2013Cossio_Bayesian]]
| Analysis of virus capsids using Google Maps
+
| EM Map Validation in a probabilistic setting
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Hanson_Continuum]]
+
| [[2013Chen_NoiseSubstitution]]
| Modelling assemblies with continuum mechanics
+
| Noise substitution at high resolution for measuring overfitting
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Lopez_Review]]
+
| [[2013Ludtke_Validation]]
| Review of structural modelling from EM data
+
| Structural validation, example of the Calcium release channel
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Schroeder_Hybrid]]
+
| [[2013Murray_Validation]]
| Review on model building
+
| Validation of a 3DEM structure through a particular example
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Tamo_Dynamics]]
+
| [[2014Russo_StatisticalSignificance]]
| Dynamics in integrative modeling
+
| EM Map Validation through the statistical significance of the tilt-pair angular assignment
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Sorzano_AtomsToVoxels]]
+
| [[2014Stagg_Reslog]]
| Accurate conversion of an atomic model into a voxel density volume
+
| EM Map Validation through the resolution evolution with the number of particles
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Joseph_Evolution]]
+
| [[2014Wasilewski_Tilt]]
| Evolutionary constraints for the fitting of atomic models into density maps
+
| Web implementation of the tilt pair validation
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Joseph_Refinement]]
+
| [[2015Heymann_Alignability]]
| Refinement of atomic models in high-resolution EM reconstructions using Flex-EM
+
| EM Map Validation through the resolution of reconstructions from particles and noise
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Murshudov_Refinement]]
+
| [[2015Oliveira_FreqLimited]]
| Refinement of atomic models in high-resolution EM reconstructions
+
| Comparison of gold standard and frequency limited optimization
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Segura_3Diana]]
+
| [[2015Rosenthal_Review]]
| Validation of hybrid models
+
| Review of validation methods
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Singharoy_MDFF]]
+
| [[2015Wriggers_Secondary]]
| Construction of hybrid models driven by EM density and molecular dynamics
+
| Validation by secondary structure
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Wang_Rosetta]]
+
| [[2016Degiacomi_IM]]
| Construction of hybrid models driven by EM density using Rosetta
+
| Comparison of Ion Mobility data and EM volumes
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Chen_CoarseGraining]]
+
| [[2016Kim_SAXS]]
| Coarse graining of EM volumes
+
| Comparison of SAXS data and EM projections
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Joseph_Metrics]]
+
| [[2016Rosenthal_Review]]
| Metrics analysis for the comparison of structures
+
| Review of validation methods
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Hryc_WeightedAtoms]]
+
| [[2016Vargas_Alignability]]
| Construction of hybrid models by locally weighting the different atoms
+
| Validation by studying the tendency of an angular assignment to cluster in the projection space
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Matsumoto_Distribution]]
+
| [[2017Monroe_PDBRefinement]]
| Estimating the distribution of conformations of atomic models
+
| Validation by comparison to a refined PDB
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Michel_ContactPrediction]]
+
| [[2018Afonine_Phenix]]
| Structure prediction by contact prediction
+
| Tools in Phenix for the validation of EM maps
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Miyashita_EnsembleFitting]]
+
| [[2018Heymann_Bsoft]]
| Ensemble fitting using Molecular Dynamics
+
| Map validation using Bsoft
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Turk_ModelBuilding]]
+
| [[2018Heymann_Challenge]]
| Tutorial on model building and protein visualization
+
| A summary of the assessments of the 3D Map Challenge
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Wang_PartialCharges]]
+
| [[2018Jonic_Gaussian]]
| Appearance of partial charges in EM maps
+
| Assessment of sets of volumes by pseudoatomic structures
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Wlodawer]]
+
| [[2018Naydenova_AngularDistribution]]
| Comparison of X-ray and EM high resolution structures
+
| Evaluating the angular distribution of a 3D reconstruction
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Cassidy_review]]
+
| [[2018Pages_Symmetry]]
| Review of methods for hybrid modeling
+
| Looking for a symmetry axis in a PDB
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Chen_SudeChains]]
+
| [[2018Pintilie_SSE]]
| A comparison of side chains between X-ray and EM maps
+
| Evaluating the quality of SSE and side chains
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Kawabata_Pseudoatoms]]
+
| [[2019Herzik_Multimodel]]
| Modelling the EM map with Gaussian pseudoatoms
+
| Local and global quality by multi-model fitting
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Kovacs_Medium]]
+
| [[2020Chen_Atomic]]
| Modelling of medium resolution EM maps
+
| Validation of the atomic models derived from CryoEM
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Neumann_validation]]
+
| [[2020Cossio_CrossValidation]]
| Validation of fitting, resolution assessment and quality of fit
+
| Need for cross validation
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Terwilliger_map_to_model]]
+
| [[2020Ortiz_CrossValidation]]
| Phenix map_to_model, automatic modelling of EM volumes
+
| Cross validation for SPA
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Wang_MD]]
+
| [[2020Sazzed_helices]]
| Constructing atomic models using molecular dynamics
+
| Validation of helix quality
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Xia_MVPENM]]
+
| [[2020Stojkovic_PTM]]
| Multiscale Normal Mode Analysis
+
| Validation of post-translational modifications
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Yu_Atomic]]
+
| [[2020Tiwari_PixelSize]]
| Constructing atomic models using existing tools
+
| Fine determination of the pixel size
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2019Bonomi_Multiscale]]
+
| [[2021Mendez_Graph]]
| Bayesian multi-scale modelling
+
| Identification of incorrectly oriented particles
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2019Klaholz_Review]]
+
| [[2021Pintilie_Validation]]
| Review of Phenix tools to modelling
+
| Review of map validation approaches
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2019Zhang_CoarseGrained]]
+
| [[2021Olek_FDR]]
| Coarse-graining of EM maps
+
| Cryo-EM Map–Based Model Validation Using the False Discovery Rate Approach
 +
|-
 +
 
 +
| Paper
 +
| [[2022Sorzano_Bias]]
 +
| Bias, variance, gold-standard and overfitting in SPA
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2020Joseph_comparison]]
+
| [[2022Waarshamanage_EMDA]]
| Comparison of map and model, or two maps
+
| Validation of models fitted into CryoEM maps
 
|-  
 
|-  
  
 
|}
 
|}
  
=== Books and reviews ===
+
=== Resolution ===
  
 
{|
 
{|
  
| Book
+
| Paper
| [[1980Herman_Tomography]]
+
| [[1986Harauz_FBP]]
| General book on tomography
+
| Fourier Shell Correlation
 
|-  
 
|-  
  
| Book
+
| Paper
| [[1988Kak_Tomography]]
+
| [[1987Unser_SSNR]]
| General book on tomography
+
| 2D Spectral Signal to Noise Ratio
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2000Tao_Review]]
+
| [[2002Penczek_SSNR]]
| Review of single particles
+
| 3D Spectral Signal to Noise Ratio for Fourier based algorithms
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2000VanHeel_Review]]
+
| [[2003Rosenthal_DPR]]
| Review of single particles
+
| Review of the FSC and establishment of a new threshold
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2002Frank_Review]]
+
| [[2005Unser_SSNR]]
| Review of single particles
+
| 3D Spectral Signal to Noise Ratio for any kind of algorithms
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2002Schmid_Review]]
+
| [[2005VanHeel_FSC]]
| Review of single particles
+
| Establishment of a new threshold for FSC
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2004Henderson_Review]]
+
| [[2007Sousa_AbInitio]]
| Review of electron microscopy
+
| Resolution measurement on neighbour Fourier voxels
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2004Subramaniam_Review]]
+
| [[2014Kucukelbir_Local]]
| Review of single particles
+
| Quantifying the local resolution of cryo-EM density maps
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2005Steven_Review]]
+
| [[2016Pintilie_Probabilistic]]
| Review of electron microscopy
+
| Probabilistic models and resolution
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2006Fernandez_Review]]
+
| [[2017Sorzano_FourierProperties]]
| Review of electron microscopy
+
| Statistical properties of resolution measures defined in Fourier space
 
|-  
 
|-  
  
| Book
+
| Conference
| [[2006Frank_book]]
+
| [[2018Avramov_DeepLearning]]
| Book covering all aspects of electron microscopy of single particles
+
| Deep learning classification of volumes into low, medium and high resolution
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2006Sorzano_Review]]
+
| [[2018Carugo_BFactors]]
| Review of optimization problems in electron microscopy
+
| How large can B-factors be in protein crystals
 +
|-
 +
 
 +
| Conference
 +
| [[2018Kim_FourierError]]
 +
| Comparison between a gold standard and a reconstruction
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007Leschziner_Review]]
+
| [[2018Rupp_Problems]]
| Review of 3D heterogeneity handling algorithms
+
| Problems of resolution as a proxy number for map quality
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007Sorzano_Review]]
+
| [[2018Vilas_MonoRes]]
| Review of the image processing steps
+
| Local resolution by monogenic signals
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2008Fanelli_ImageFormation]]
+
| [[2018Yang_Multiscale]]
| Review on the image formation model from the electron waves and open inverse-problems in Electron Tomography
+
| Resolution from a multiscale spectral analysis
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2008Fernandez_HPCReview]]
+
| [[2019Avramov_DeepLearning]]
| High performance computing in electron cryomicroscopy
+
| Deep learning classification of volumes into low, medium and high resolution
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2008Jonic_Review]]
+
| [[2019Heymann_Statistics]]
| Comparison between electron tomography and single particles
+
| SNR, FSC, and related statistics
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2008Mueller_Review]]
+
| [[2019Ramirez_DeepRes]]
| Review of Electron microscopy
+
| Resolution determination by deep learning
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2008Taylor_Review]]
+
| [[2020Baldwin_Lyumkis_SCF]]
| Review of Electron microscopy
+
| Resolution attenuation through non-uniform Fourier sampling
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2010DeRosier_Review]]
+
| [[2020Beckers_Permutation]]
| Personal account of how 3DEM developed in the early days
+
| Permutation tests for the FSC
 
|-  
 
|-  
  
| Chapter
+
| Paper
| [[2012Sorzano_Review]]
+
| [[2020Penczek_mFSC]]
| Review of single particle analysis using Xmipp
+
| Modified FSC to avoid mask induced artifacts
 
|-  
 
|-  
  
| Chapter
+
| Paper
| [[2012Devaux_Protocol]]
+
| [[2020Vilas_MonoDir]]
| Protocols for performing single particle analysis
+
| Local and directional resolution
 
|-  
 
|-  
  
 +
|}
 +
 +
=== Sharpening of high resolution information ===
 +
{|
 +
 
| Paper
 
| Paper
| [[2014Bai_Review]]
+
| [[2003Rosenthal_DPR]]
| Recent advances in cryo-EM
+
| Contrast restoration and map sharpening
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Carazo_Review]]
+
| [[2008Fernandez_Bfactor]]
| Review of the reconstruction process
+
| Bfactor determination and restoration
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Cheng_Review]]
+
| [[2013Fiddy_SaxtonAlgorithm]]
| A primer to Single Particle Cryo-EM
+
| Phase retrieval or extension
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Cheng_Reviewb]]
+
| [[2014Kishchenko_SphericalDeconvolution]]
| Single Particle Cryo-EM at crystallographic resolution
+
| Spherical deconvolution
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Elmlund_Review]]
+
| [[2015Spiegel_VISDEM]]
| Recent advances in cryo-EM
+
| Visualization improvement by the use of pseudoatomic profiles
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Henderson_Review]]
+
| [[2016Jonic_Pseudoatoms]]
| Recent advances in cryo-EM
+
| Approximation with pseudoatoms
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Nogales_Review]]
+
| [[2016Jonic_Denoising]]
| Recent advances in cryo-EM
+
| Denoising and high-frequency boosting by pseudoatom approximation
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Schroeder_Review]]
+
| [[2017Jakobi_LocScale]]
| Review of advances in the electron microscope
+
| Sharpening based on an atomic model
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015VanDenBedem_Integrative]]
+
| [[2019Ramlaul_Filtering]]
| Review of integrative structural biology
+
| Local agreement filtering (denoising)
 
|-  
 
|-  
  
| Paper
+
| Conference
| [[2015Wu_Review]]
+
| [[2020Mullick_SuperResolution]]
| Review of advances in cryo-EM
+
| Superresolution from a map
 
|-  
 
|-  
  
| Paper
 
| [[2016Carroni_CryoEM]]
 
| Review of advances in Cryo-EM
 
|-
 
  
 
| Paper
 
| Paper
| [[2016Egelman_CryoEM]]
+
| [[2020Ramirez_LocalDeblur]]
| Review of advances in Cryo-EM
+
| Local deblur (local Wiener filter)
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Eisenstein_CryoEM]]
+
| [[2020Terwilliger_density]]
| News feature on the Method of the Year
+
| Density modification of CryoEM maps
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016FernandezLeiro_Review]]
+
| [[2020Vilas_Bfactor]]
| Review of EM
+
| Global B-factor correction does not represent macromolecules
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Glaeser_HowGood]]
+
| [[2021Beckers_Interpretation]]
| How good can cryo-EM become?
+
| Improvements from the raw reconstruction to a structure to model
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Jonic_PseudoAtoms]]
+
| [[2021Kaur_LocSpiral]]
| Review of the applications of the use of pseudoatoms in EM
+
| LocSpiral, LocBsharpen, LocBfactor
|-
 
 
 
| Chapter
 
| [[2016Mio_Review]]
 
| Overview of the process to obtain EM reconstructions
 
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Jonic_Review]]
+
| [[2021Fernandez_Adjustment]]
| A review of computational ways to handle heterogeneity
+
| Map adjustment for subtraction, consensus and sharpening
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Nogales_Review]]
+
| [[2021Sanchez_DeepEMhancer]]
| Review of advances in cryo-EM
+
| Deep learning algorithm for volume restoration
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Subramaniam_Review]]
+
| [[2022Vargas_tubular]]
| Why cryo-EM is now suitable for crystallographic journals
+
| Map enhancement by multiscale tubular filter
 
|-  
 
|-  
  
| Paper
+
|}
| [[2016Vinothkumar_Review]]
+
 
| Historical review and current limitations
+
=== CTF estimation and restoration ===
|-
+
 
 +
{|
  
| Report
+
| Paper
| [[2017Brezinski_Nobel]]
+
| [[1982Schiske_Correction]]
| Scientific background on the Nobel Prize in Chemistry 2017
+
| CTF correction for tilted objects
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Cheng_review]]
+
| [[1988Toyoshima_Model]]
| Why CryoEM became so hot
+
| CTF estimation
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Danev_Review]]
+
| [[1995Frank_Wiener]]
| Review of the use of phase plates in EM
+
| CTF correction using Wiener filter
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Elmlund_Review]]
+
| [[1996Skoglund_MaxEnt]]
| Review of the main current difficulties of EM
+
| CTF correction with Maximum Entropy
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Frank_Review]]
+
| [[1996Zhou_Model]]
| Historical review of EM
+
| CTF model and user interface for manual fitting
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Frank_TimeResolved]]
+
| [[1997Fernandez_AR]]
| Review of time-resolved of EM
+
| PSD estimation using periodogram averaging and AR models
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Jonic_Review]]
+
| [[1997Penczek_Wiener]]
| Review of computational methods to analyze conformational variability
+
| CTF correction using Wiener filter
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Merino_DrugEM]]
+
| [[1997Stark_Deconvolution]]
| Applications of EM for drug design
+
| CTF correction using deconvolution
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Rawson_Limitations]]
+
| [[1997Zhu_RecCTF]]
| Limitations of EM for drug design
+
| CTF correction and reconstruction
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Sorzano_FourierProperties]]
+
| [[2000DeRosier_EwaldCorrection]]
| Review of statistical properties of resolution measures defined in Fourier space
+
| CTF correction considering the Ewald sphere
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Sorzano_SurveyIterative]]
+
| [[2000Jensen_TiltedCorrection]]
| Survey of iterative reconstruction methods for EM
+
| CTF correction considering tilt in backprojection
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Bruggeman_Crowdsourcing]]
+
| [[2001Saad_CTFEstimate]]
| Exploring crowdsourcing for EM image processing
+
| CTF estimation
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Cheng_Review]]
+
| [[2003Huang_CTFEstimate]]
| Review of EM and future ahead
+
| CTF estimation
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Cossio_ML]]
+
| [[2003Mindell_CTFTILT]]
| Review of Maximum Likelihood methods
+
| CTF estimation for tilted micrographs
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Grimes_Crystallography]]
+
| [[2003Sander_MSA]]
| Review of X-ray crystallography and its relationship to EM
+
| CTF estimation through MSA classification of PSDs
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Murata_Review]]
+
| [[2003Velazquez_ARMA]]
| Review of EM for structure dynamics
+
| PSD and CTF estimation using ARMA models
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Quentin_Biomedical]]
+
| [[2004Sorzano_IDR]]
| Review of EM as a tool for biomedical research
+
| CTF restoration and reconstruction with Iterative Data Refinement
 
|-  
 
|-  
  
| Paper
+
| Conference
| [[2018Scapin_DrugDiscovery]]
+
| [[2004Wan_CTF]]
| Review of EM as a tool for drug discovery
+
| Spatially variant CTF
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Vilas_ImageProcessing]]
+
| [[2004Zubelli_Chahine]]
| Review of the recent developments in image processing for single particle analysis
+
| CTF restoration and reconstruction with Chahine's multiplicative method
 
|-  
 
|-  
  
| Paper
+
| Conference
| [[2018vonLoeffelholz_VPP]]
+
| [[2005Dubowy_SpaceVariant]]
| Comparison of Volta Phase Plate reconstructions close to focus and with defocus
+
| CTF correction when this is space variant
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Eisenstein_DrugDesigners]]
+
| [[2005Mallick_ACE]]
| Drug designers embrace cryo-EM
+
| CTF estimation
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2019Benjin_Review]]
+
| [[2006Wolf_Ewald]]
| Review of SPA
+
| CTF correction considering Ewald sphere
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2019Danev_Review]]
+
| [[2007Jonic_EnhancedPSD]]
| Review of future directions
+
| PSD enhancement for better identification of Thon rings; Vitreous ice diffracts in Thon rings
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2019Lyumkis_Review]]
+
| [[2007Philippsen_Model]]
| Challenges and reviews
+
| CTF Model for tilted specimens
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2019Sorzano_Review]]
+
| [[2007Sorzano_CTF]]
| Review of continuous heterogeneity biophysics
+
| CTF estimation using enhanced PSDs
 
|-  
 
|-  
 
|}
 
 
=== Software ===
 
 
{|
 
  
 
| Paper
 
| Paper
| [[1996Frank_Spider]]
+
| [[2009Sorzano_Sensitivity]]
| Spider
+
| Error sensitivity of the CTF models, non-uniqueness of the CTF parameters
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1996VanHeel_Imagic]]
+
| [[2010Jiang2010_CTFCorrection]]
| Imagic
+
| Amplitude correction method
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1999Lutdke_Eman]]
+
| [[2010Kasantsev_CTFCorrection]]
| Eman
+
| Mathematical foundations of Kornberg and Jensen method
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2004Sorzano_Xmipp]]
+
| [[2010Leong_CTFCorrection]]
| Xmipp
+
| Correction for spatially variant CTF
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007Baldwin_AngularTransformations]]
+
| [[2011Glaeser_Coma]]
| The Transform Class in SPARX and EMAN2
+
| The effect of coma at high-resolution
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007Heymann_Bsoft]]
+
| [[2011Mariani_Tilted]]
| Bsoft
+
| CTF simulation and correction of tilted specimens
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007Grigorieff_Frealign]]
+
| [[2011Sindelar_Wiener]]
| Frealign
+
| CTF correction using a modified version of Wiener filter
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2008Scheres_XmippProtocols]]
+
| [[2011Voortman_Tilted]]
| Xmipp Protocols
+
| CTF correction for tilted specimen
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2008Shaikh_SpiderProtocols]]
+
| [[2012Voortman_VaryingCTF]]
| Spider Protocols
+
| Correcting a spatially varying CTF
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2012Wriggers_SitusConventions]]
+
| [[2013Vargas_FastDef]]
| Conventions and workflows in Situs
+
| Fast defocus
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013DeLaRosa_Xmipp30]]
+
| [[2014Penczek_CTER]]
| Xmipp 3.0
+
| Estimation of the CTF errors
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Cianfrocco_Cloud]]
+
| [[2015Rohou_CTFFind4]]
| Software execution in the cloud
+
| CTF Find 4
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Cheng_MRC2014]]
+
| [[2015Sheth_CTFquality]]
| Extensions to MRC file format
+
| Visualization and quality assessment of CTF
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013DeLaRosa_Scipion]]
+
| [[2016Zhang_GCTF]]
| Scipion
+
| gCTF
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Scheres_Relion]]
+
| [[2018Su_GoCTF]]
| Tutorial on the use of Relion
+
| goCTF, CTF for tilted specimens
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Grigorieff_Frealign]]
+
| [[2020Heimowitz_Aspire]]
| Tutorial on the use of Frealign
+
| CTF determination in Aspire
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Moriya_Sphire]]
+
| [[2020Zivanov_HighOrder]]
| Tutorial on the use of Sphire
+
| Estimation of high order aberrations
 +
|-
 +
 
 +
|}
 +
 
 +
=== Segmentation ===
 +
 
 +
{|
 +
 
 +
| Paper
 +
| [[2006Baker_segmentation]]
 +
| Segmentation of molecular subunits
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Bell_EMAN2]]
+
| [[2010Pintilie_segger]]
| New tools in EMAN2
+
| Segmentation of molecular subunits
 +
|-
 +
 
 +
| Conference
 +
| [[2017Nissenson_VolumeCut]]
 +
| Segmentation of an EM volume using an atomic model
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Cianfrocco_cloud]]
+
| [[2019Beckers_FDR]]
| CryoEM Cloud Tools
+
| Segmentation of the protein using False Discovery Rate
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Grant_cisTEM]]
+
| [[2020Beckers_FDR]]
| cisTEM
+
| Segmentation of the protein using False Discovery Rate (GUI)
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018McLeod_MRCZ]]
+
| [[2020Farkas_MemBlob]]
| MRC Compression format
+
| Segmentation of membrane in membrane embedded proteins
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Zivanov_Relion3]]
+
| [[2020Terashi_MainMastSeg]]
| Relion 3
+
| Segmentation of proteins into domains
 
|-  
 
|-  
 
|}
 
 
== Electron tomography ==
 
 
=== Image preprocessing ===
 
 
{|
 
  
 
| Paper
 
| Paper
| [[2015Yan_thickness]]
+
| [[2021He_EMNUSS]]
| Determination of thickness, tilt and electron mean free path
+
| EMNUSS: Identification of secondary structure in CryoEM maps with deep learning
 
|-  
 
|-  
  
 
|}
 
|}
  
=== Image alignment ===
+
=== Fitting and docking ===
  
 
{|
 
{|
  
 
| Paper
 
| Paper
| [[1982Guckenberger_commonOrigin]]
+
| [[1999Volkmann_Fitting]]
| Determination of a common origin in the micrographs of titl series in three-dimensional electron microscopy
+
| Fitting in real space
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1992Lawrence_leastSquares]]
+
| [[2001Baker_Review]]
| Least squares solution of the alignment problem
+
| Review of protein structure prediction
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1995Penczek_dual]]
+
| [[2001Jones_Review]]
| Dual tilt alignment
+
| Review of protein structure prediction
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1996Owen_alignmentQuality]]
+
| [[2003Kovacs_FRM3D]]
| Automatic alignment without fiducial markers and evaluation of alignment quality
+
| Fast Rotational Alignment of two EM maps
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1998Grimm_normalization]]
+
| [[2004Tama_NMA1]]
| Discussion of several gray level normalization methods for electron tomography
+
| Flexible fitting with Normal Modes (I)
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2001Brandt_Automatic1]]
+
| [[2004Tama_NMA2]]
| Automatic alignment without fiducial markers
+
| Flexible fitting with Normal Modes (II)
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2001Brandt_Automatic2]]
+
| [[2005Velazquez_Superfamilies]]
| Automatic alignment with fiducial markers
+
| Recognition of the superfamily folding in medium-high resolution volumes
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2006Winkler_alignment]]
+
| [[2007DeVries_Haddock]]
| Marker-free alignment and refinement
+
| Docking with Haddock 2.0
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2006Castano_alignment]]
+
| [[2007Kleywegt_QualityControl]]
| Alignment with non-perpendicularity
+
| Quality control and validation of fitting
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2007Castano_alignment]]
+
| [[2008Rusu_Interpolation]]
| Fiducial-less alignment of cryo-sections
+
| Biomolecular pleiomorphism probed by spatial interpolation of coarse models
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2009Sorzano_alignment]]
+
| [[2012Biswas_Secondary]]
| Marker-free alignment and refinement
+
| Secondary structure determination in EM volumes
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2010Cantele_dualAlignment]]
+
| [[2012Velazquez_Constraints]]
| Alignment of dual series
+
| Multicomponent fitting by using constraints from other information sources
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2014Tomonaga_Automatic]]
+
| [[2013Chapman MS_Atomicmodeling]]
| Automatic alignment of tilt series using the projection themselves
+
| Atomic modeling of cryo-electron microscopy reconstructions--joint refinement of model and imaging parameters
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2014Han_Automatic]]
+
| [[2013Esquivel_Modelling]]
| Automatic alignment of tilt series using SIFT features
+
| Review on modelling (secondary structure, fitting, ...)
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Han_Automatic]]
+
| [[2013Lopez_Imodfit]]
| Automatic alignment of tilt series using fiducials
+
| Fitting based on vibrational analysis
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Mastronarde_Automatic]]
+
| [[2013Nogales_3DEMLoupe]]
| Automatic alignment and reconstruction of tilt series in IMOD
+
| Normal Mode Analysis of reconstructed volumes
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Fernadez_Beam]]
+
| [[2014AlNasr_Secondary]]
| Image alignment considering beam induced motion
+
| Identification of secondary structure elements in EM volumes
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Han_Fast]]
+
| [[2014Politis_MassSpect]]
| Automatic alignment using fiducial markers
+
| Integration of mass spectroscopy information
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2019Fernandez_residual]]
+
| [[2014Rey_MassSpect]]
| Alignment of tilt series using residual interpolation
+
| Integration of mass spectroscopy information
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2019Han_Dual]]
+
| [[2014Villa_Review]]
| Automatic alignment using fiducial markers in dual tilt series
+
| Review of atomic fitting into EM volumes
 
|-  
 
|-  
 
|}
 
 
=== CTF estimation and restoration ===
 
 
{|
 
  
 
| Paper
 
| Paper
| [[2003Winkler_CTF]]
+
| [[2015Barad_EMRinger]]
| Focus gradient correction in electron tomography
+
| Validation of hybrid models
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2006Fernandez_CTF]]
+
| [[2015Bettadapura_PF2Fit]]
| CTF determination and correction in electron tomography
+
| Fast rigid fitting of PDBs into EM maps
 
|-  
 
|-  
 
  
 
| Paper
 
| Paper
| [[2009Zanetti_CTF]]
+
| [[2015Carrillo_CapsidMaps]]
| CTF determination and correction in electron tomography
+
| Analysis of virus capsids using Google Maps
 
|-  
 
|-  
 
  
 
| Paper
 
| Paper
| [[2009Xiong_CTF]]
+
| [[2015Hanson_Continuum]]
| CTF determination and correction for low dose tomographic tilt series
+
| Modelling assemblies with continuum mechanics
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2012Eibauer_CTF]]
+
| [[2015Lopez_Review]]
| CTF determination and correction
+
| Review of structural modelling from EM data
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Bharat_CTFCorrectedSubtomogramAveraging]]
+
| [[2015Schroeder_Hybrid]]
| Subtomogram averaging with CTF correction using a Bayesian prior
+
| Review on model building
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Turonova_3DCTF]]
+
| [[2015Tamo_Dynamics]]
| 3D CTF Correction
+
| Dynamics in integrative modeling
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Kunz_3DCTF]]
+
| [[2015Sorzano_AtomsToVoxels]]
| 3D CTF Correction
+
| Accurate conversion of an atomic model into a voxel density volume
 
|-  
 
|-  
 
|}
 
 
=== 3D reconstruction ===
 
 
{|
 
  
 
| Paper
 
| Paper
| [[1972Gilbert_SIRT]]
+
| [[2016Joseph_Evolution]]
| Simultaneous Iterative Reconstruction Technique (SIRT)
+
| Evolutionary constraints for the fitting of atomic models into density maps
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1973Herman_ART]]
+
| [[2016Joseph_Refinement]]
| Algebraic Reconstruction Technique (ART)
+
| Refinement of atomic models in high-resolution EM reconstructions using Flex-EM
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1984Andersen_SART]]
+
| [[2016Murshudov_Refinement]]
| Simultaneous Algebraic Reconstruction Technique (SART)
+
| Refinement of atomic models in high-resolution EM reconstructions
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1992Radermacher_WBP]]
+
| [[2016Segura_3Diana]]
| Weighted Backprojection in electron tomography
+
| Validation of hybrid models
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1997Marabini_reconstruction]]
+
| [[2016Singharoy_MDFF]]
| Iterative reconstruction in electron tomography
+
| Construction of hybrid models driven by EM density and molecular dynamics
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2002Fernandez_reconstruction]]
+
| [[2016Wang_Rosetta]]
| Iterative reconstruction in electron tomography
+
| Construction of hybrid models driven by EM density using Rosetta
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007Radermacher_WBP]]
+
| [[2017Chen_CoarseGraining]]
| Weighted Backprojection in electron tomography
+
| Coarse graining of EM volumes
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2008Fernandez_CARP]]
+
| [[2017Joseph_Metrics]]
| Component Averaged Row Projections (CARP)
+
| Metrics analysis for the comparison of structures
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2010Xu_Long]]
+
| [[2017Hryc_WeightedAtoms]]
| Iterative reconstructions with long object correction and GPU implementation
+
| Construction of hybrid models by locally weighting the different atoms
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2012Herman General Superiorization]]
+
| [[2017Matsumoto_Distribution]]
| Superiorization: an optimization heuristic for medical physics
+
| Estimating the distribution of conformations of atomic models
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2012Zhang_IPET_FETR]]
+
| [[2017Michel_ContactPrediction]]
| IPET and FETR, a reconstruction algorithm for single molecule tomography
+
| Structure prediction by contact prediction
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Goris_SIRT_TV_DART]]
+
| [[2017Miyashita_EnsembleFitting]]
| Combination of SIRT, Total Variation and Discrete ART to reconstruct and segment at the same time
+
| Ensemble fitting using Molecular Dynamics
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Briegel A_Challenge]]
+
| [[2017Turk_ModelBuilding]]
| The challenge of determining handedness in electron tomography and the use of DNA origami gold nanoparticle helices as molecular standards
+
| Tutorial on model building and protein visualization
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Messaoudi_EnergyFiltered]]
+
| [[2017Wang_PartialCharges]]
| 3D Reconstruction of Energy-Filtered TEM
+
| Appearance of partial charges in EM maps
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Venkatakrishnan_MBIR]]
+
| [[2017Wlodawer]]
| 3D Reconstruction with priors
+
| Comparison of X-ray and EM high resolution structures
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Deng_ICON]]
+
| [[2018Cassidy_review]]
| 3D Reconstruction with missing information restoration
+
| Review of methods for hybrid modeling
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Guay_Compressed]]
+
| [[2018Chen_SudeChains]]
| 3D Reconstruction using compressed sensing
+
| A comparison of side chains between X-ray and EM maps
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Turonova_Artifacts]]
+
| [[2018Kawabata_Pseudoatoms]]
| Artifacts observed during 3D reconstruction
+
| Modelling the EM map with Gaussian pseudoatoms
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2019Yan_MBIR]]
+
| [[2018Kovacs_Medium]]
| 3D Reconstruction with priors and demonstration of its use in biological samples
+
| Modelling of medium resolution EM maps
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2020Song_Tygress]]
+
| [[2018Neumann_validation]]
| 3D reconstruction with a special acquisition and alignment scheme
+
| Validation of fitting, resolution assessment and quality of fit
 
|-  
 
|-  
 
|}
 
 
=== Noise reduction ===
 
{|
 
  
 
| Paper
 
| Paper
| [[2001Frangakis_NAD]]
+
| [[2018Terwilliger_map_to_model]]
| Noise reduction with Nonlinear Anisotropic Diffusion
+
| Phenix map_to_model, automatic modelling of EM volumes
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2003Fernandez_AND]]
+
| [[2018Wang_MD]]
| Anisotropic nonlinear diffusion for electron tomography
+
| Constructing atomic models using molecular dynamics
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2003Jiang_Bilateral]]
+
| [[2018Xia_MVPENM]]
| Bilateral denoising filter in electron microscopy
+
| Multiscale Normal Mode Analysis
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2005Fernandez_AND]]
+
| [[2018Yu_Atomic]]
| Anisotropic nonlinear denoising in electron tomography
+
| Constructing atomic models using existing tools
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007Heide_median]]
+
| [[2019Bonomi_Multiscale]]
| Iterative median filtering in electron tomography
+
| Bayesian multi-scale modelling
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2007Fernandez_autAND]]
+
| [[2019Kidmose_Namdinator]]
| Anisotropic nonlinear diffusion with automated parameter tuning
+
| Namdinator: Flexible fitting with NAMD
|-
+
|-  
 +
 
  
 
| Paper
 
| Paper
| [[2009Fernandez_Beltrami]]
+
| [[2019Klaholz_Review]]
| Nonlinear filtering based on Beltrami flow
+
| Review of Phenix tools to modelling
 
|-  
 
|-  
+
 
 
| Paper
 
| Paper
| [[2010Bilbao_MeanShift]]
+
| [[2019Subramaniya_DeepSSE]]
| Mean Shift Filtering
+
| Secondary structure prediction from maps using deep learning
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2014Kovacik_wedgeArtefacts]]
+
| [[2019Zhang_CoarseGrained]]
| Removal of wedge artefacts
+
| Coarse-graining of EM maps
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2014Maiorca_beadArtefacts]]
+
| [[2020Costa_MDeNM]]
| Removal of gold bead artefacts
+
| Flexible fitting with molecular dynamics and normal modes
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Trampert_Inpainting]]
+
| [[2020Cragnolini_Tempy2]]
| Removal of the missing wedge by inpainting
+
| TEMpy2 library for density-fitting and validation
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Moreno_TomoEED]]
+
| [[2020Dodd_ModelBuilding]]
| Fast Anisotropic Diffusion
+
| Model building possibilities, with special emphasis on flexible fitting
 
|-  
 
|-  
  
|}
+
| Paper
 +
| [[2020Ho_CryoID]]
 +
| Identification of proteins in structural proteomics from cryoEM volumes
 +
|-
  
=== Segmentation ===
+
| Paper
 +
| [[2020Hoh_Buccaneer]]
 +
| Structure modelling with Buccaneer
 +
|-
  
{|
 
  
 
| Paper
 
| Paper
| [[2002Frangakis_Eigenanalysis]]
+
| [[2020Joseph_comparison]]
| Segmentation using eigenvector analysis.
+
| Comparison of map and model, or two maps
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2002Volkmann_Watershed]]
+
| [[2020Kim_Review]]
| Segmentation using watershed transform.
+
| Review of the options for atomic modelling
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2003Bajaj_BoundarySegmentation]]
+
| [[2020Leelananda_Constraints]]
| Segmentation based on fast marching.
+
| NMR Chemical Shifts and Cryo-EM Density Restraints in Iterative Rosetta-MD structure refinement
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2005Cyrklaff_Thresholding]]
+
| [[2020Liebschner_Ceres]]
| Segmentation using optimal thresholding.
+
| CERES: Web server of refined atomic maps of CryoEM deposited maps by Phenix
|-  
+
|-  
  
 
| Paper
 
| Paper
| [[2007Lebbink_TemplateMatching]]
+
| [[2020Oroguchi]]
| Segmentation using template matching.
+
| Assessment of Force Field Accuracy Using Cryogenic Electron Microscopy Data
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007Sandberg_OrientationFields]]
+
| [[2020Vant_Flexible]]
| Segmentation using orientation fields.
+
| Flexible fitting with molecular dynamics and neural network potentials
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007Sandberg_SegmentationReview]]
+
| [[2021Behkamal_Secondary]]
| Review on segmentation in electron tomography.
+
| Secondary structure from medium resolution maps
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2008Garduno_FuzzySegmentation]]
+
| [[2021Chojnowski_quality]]
| Segmentation using fuzzy set theory principles.
+
| Quality of models automatically fitted with ARP/wARP
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2009Lebbink_TemplateMatching2]]
+
| [[2021Han_Vesper]]
| Segmentation using template matching.
+
| VESPER: global and local cryo-EM map alignment using local density vectors
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2012RubbiyaAli_EdgeDetection]]
+
| [[2021Lawson_Challenge]]
| Parameter-Free Segmentation of Macromolecular Structures.
+
| Validation recommendations based on outcomes of the 2019 EMDataResource challenge
 
|-  
 
|-  
  
| Conference
+
| Paper
| [[2015Xu_TemplateMatching]]
+
| [[2021Mori_Flexible]]
| Detection of macromolecular complexes with a reduced representation of the templates.
+
| Efficient Flexible Fitting Refinement with Automatic Error Fixing
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Ali_RAZA]]
+
| [[2021Pfab_DeepTracer]]
| Automated segmentation of tomograms
+
| DeepTracer for fast de novo cryo-EM protein structure modeling
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Chen_Annotation]]
+
| [[2021Saltzberg_IMP]]
| Automated annotation of tomograms
+
| Using the Integrative Modeling Platform to model a cryoEM map
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Tasel_ActiveContours]]
+
| [[2021Terwilliger_CryoID]]
| Segmentation with active contours
+
| Identification of sequence in a CryoEM map from a set of candidates
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Xu_DeepLearning]]
+
| [[2021Titarenko_LocalCorr]]
| Finding proteins in tomograms using deep learning
+
| Performance improvement of local correlation for docking
 
|-  
 
|-  
  
 +
| Conference
 +
| [[2021Vuillemot_NMA]]
 +
| Flexible fitting using Normal Modes
 +
|-
  
 
| Paper
 
| Paper
| [[2018Zeng_DeepLearning]]
+
| [[2022Antanasijevic_ab]]
| Mining features in Electron Tomographt by deep learning
+
| Sequence determination of antibodies bound to a map
 
|-  
 
|-  
  
|}
+
| Paper
 +
| [[2022Behkamal_LPTD]]
 +
| LPTD: Topology determination of CryoEM maps
 +
|-
  
=== Resolution ===
 
{|
 
  
 
| Paper
 
| Paper
| [[2005Cardone_Resolution]]
+
| [[2022Chojnowski_findMySeq]]
| Resolution criterion for electron tomography
+
| Identify sequence in CryoEM map using Deep Learning
 
|-  
 
|-  
  
| Chapter
+
| Paper
| [[2007Penczek_Resolution]]
+
| [[2022Krieger_Prody2]]
| Review of resolution criteria for electron tomography
+
| 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
 
| Paper
| [[2015Diebolder_ConicalFSC]]
+
| [[2022Vuillemot_NMMD]]
| Conical Fourier Shell Correlation
+
| Flexible fitting with simultaneous Normal Mode and Molecular Dynamics displacements
 
|-  
 
|-  
  
 +
| Paper
 +
| [[2022Zhang_CRITASSER]]
 +
| Atomic models of assemble protein structures with deep learning
 +
|-
  
 
|}
 
|}
  
=== Subtomogram analysis ===
+
=== Books and reviews ===
  
 
{|
 
{|
  
| Paper
+
| Book
| [[2000Bohm_Template]]
+
| [[1980Herman_Tomography]]
| Macromolecule finding by template matching
+
| General book on tomography
 +
|-
 +
 
 +
| Book
 +
| [[1988Kak_Tomography]]
 +
| General book on tomography
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2002Frangakis_Template]]
+
| [[2000Tao_Review]]
| Macromolecule finding by template matching
+
| Review of single particles
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2006Nickell_Review]]
+
| [[2000VanHeel_Review]]
| Review of macromolecule finding by template matching (Visual Proteomics)
+
| Review of single particles
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007Best_Review]]
+
| [[2002Frank_Review]]
| Review of Localization of Protein Complexes by Pattern Recognition
+
| Review of single particles
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007Forster_Review]]
+
| [[2002Schmid_Review]]
| Review of structure determination by subtomogram averaging
+
| Review of single particles
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2008Forster_Classification]]
+
| [[2004Henderson_Review]]
| Classification of subtomograms using constrained correlation
+
| Review of electron microscopy
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2008Bartesaghi_Classification]]
+
| [[2004Subramaniam_Review]]
| Classification and averaging of subtomograms
+
| Review of single particles
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2008Schmid_Averaging]]
+
| [[2005Steven_Review]]
| Alignment and averaging of subtomograms
+
| Review of electron microscopy
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2010Amat_Averaging]]
+
| [[2006Fernandez_Review]]
| Alignment and averaging of subtomograms exploiting thresholding in Fourier space
+
| Review of electron microscopy
|-
+
|-  
  
| Paper
+
| Book
| [[2010Yu_PPCA]]
+
| [[2006Frank_book]]
| Probabilistic PCA for volume classification
+
| Book covering all aspects of electron microscopy of single particles
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2013Chen_Averaging]]
+
| [[2006Sorzano_Review]]
| Fast alignment of subtomograms using spherical harmonics
+
| Review of optimization problems in electron microscopy
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2013Kuybeda_Averaging]]
+
| [[2007Leschziner_Review]]
| Alignment and averaging of subtomograms using the nuclear norm of the cluster
+
| Review of 3D heterogeneity handling algorithms
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2013Shatsky_Averaging]]
+
| [[2007Sorzano_Review]]
| Alignment and averaging of subtomograms with constrained cross-correlation
+
| Review of the image processing steps
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2013Yu_Projection]]
+
| [[2008Fanelli_ImageFormation]]
| Subtomogram averaging by aligning their projections
+
| Review on the image formation model from the electron waves and open inverse-problems in Electron Tomography
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2014Chen_Autofocus]]
+
| [[2008Fernandez_HPCReview]]
| Subtomogram averaging and classification with special attention to differences
+
| High performance computing in electron cryomicroscopy
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2014Yu_ReferenceBias]]
+
| [[2008Jonic_Review]]
| Scoring the reference bias
+
| Comparison between electron tomography and single particles
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2014Voortman_LimitingFactors]]
+
| [[2008Mueller_Review]]
| Limiting factors of subtomogram averaging
+
| Review of Electron microscopy
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2015Bharat_CTFCorrectedSubtomogramAveraging]]
+
| [[2008Taylor_Review]]
| Subtomogram averaging with CTF correction using a Bayesian prior
+
| Review of Electron microscopy
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Yu_ReferenceBias]]
+
| [[2010DeRosier_Review]]
| Scoring the reference bias
+
| 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
 
| Paper
| [[2016Bharat_Relion]]
+
| [[2014Bai_Review]]
| Subtomogram averaging with Relion
+
| Recent advances in cryo-EM
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2016Song_MatrixNorm]]
+
| [[2015Carazo_Review]]
| Matrix norm minimization for tomographic reconstruction and alignment
+
| Review of the reconstruction process
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2017Castano_ParticlePicking]]
+
| [[2015Cheng_Review]]
| Particle picking in tomograms for subtomogram averaging
+
| A primer to Single Particle Cryo-EM
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2017Frazier_Tomominer]]
+
| [[2015Cheng_Reviewb]]
| TomoMiner a software platform for large-scale subtomogram analysis
+
| Single Particle Cryo-EM at crystallographic resolution
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2018Himes_emClarity]]
+
| [[2015Elmlund_Review]]
| emClarity for subtomogram averaging
+
| Recent advances in cryo-EM
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2018Zhao_Fast]]
+
| [[2015Henderson_Review]]
| Fast alignment and maximum likelihod for subtomogram averaging
+
| Recent advances in cryo-EM
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2019Fokine_Enhancement]]
+
| [[2015Nogales_Review]]
| Subtomogram enhancement through the locked self-rotation
+
| Recent advances in cryo-EM
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2019Han_Constrained]]
+
| [[2015Schroeder_Review]]
| Constrained reconstruction to enhance resolution
+
| Review of advances in the electron microscope
|-
+
|-  
  
|}
+
| Paper
 
+
| [[2015VanDenBedem_Integrative]]
=== Single particle tomography ===
+
| Review of integrative structural biology
 
+
|-
{|
 
  
 
| Paper
 
| Paper
| [[2012Bartesaghi_Constrained]]
+
| [[2015Wu_Review]]
| 3D reconstruction by imposing geometrical constraints
+
| Review of advances in cryo-EM
|-
 
 
 
| Paper
 
| [[2015Galaz_SingleParticleTomography]]
 
| Set of tools for Single Particle Tomography in EMAN2
 
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Galaz_SingleParticleTomography]]
+
| [[2016Carroni_CryoEM]]
| Alignment algorithms and CTF correction
+
| Review of advances in Cryo-EM
 
|-  
 
|-  
 
|}
 
 
=== Books and reviews ===
 
 
{|
 
  
 
| Paper
 
| Paper
| [[2000Baumeister_Review]]
+
| [[2016Egelman_CryoEM]]
| Review of electron tomography
+
| Review of advances in Cryo-EM
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2003Koster_Review]]
+
| [[2016Eisenstein_CryoEM]]
| Review of electron tomography
+
| News feature on the Method of the Year
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2003Sali_Review]]
+
| [[2016FernandezLeiro_Review]]
| Review of electron tomography
+
| Review of EM
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2004Henderson_Review]]
+
| [[2016Glaeser_HowGood]]
| Review of electron microscopy
+
| How good can cryo-EM become?
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2005Lucic_Review]]
+
| [[2016Jonic_PseudoAtoms]]
| Review of electron tomography
+
| Review of the applications of the use of pseudoatoms in EM
 +
|-
 +
 
 +
| Chapter
 +
| [[2016Mio_Review]]
 +
| Overview of the process to obtain EM reconstructions
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2006Fernandez_Review]]
+
| [[2016Jonic_Review]]
| Review of electron microscopy
+
| A review of computational ways to handle heterogeneity
 
|-  
 
|-  
  
| Book
+
| Paper
| [[2006Frank_TomoBook]]
+
| [[2016Nogales_Review]]
| Electron Tomography
+
| Review of advances in cryo-EM
 
|-  
 
|-  
  
| Book
+
| Paper
| [[2007McIntosh_Book]]
+
| [[2016Subramaniam_Review]]
| Cellular Electron Microscopy
+
| Why cryo-EM is now suitable for crystallographic journals
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007Sorzano_Review]]
+
| [[2016Vinothkumar_Review]]
| Review of the image processing steps
+
| Historical review and current limitations
 
|-  
 
|-  
  
| Paper
+
| Report
| [[2008Fanelli_ImageFormation]]
+
| [[2017Brezinski_Nobel]]
| Review on the image formation model from the electron waves and open inverse-problems
+
| Scientific background on the Nobel Prize in Chemistry 2017
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2008Fernandez_HPCReview]]
+
| [[2017Cheng_review]]
| High performance computing in electron cryomicroscopy
+
| Why CryoEM became so hot
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2008Jonic_Review]]
+
| [[2017Danev_Review]]
| Comparison between electron tomography and single particles
+
| Review of the use of phase plates in EM
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2012Kudryashev_Review]]
+
| [[2017Elmlund_Review]]
| Review of subtomogram averaging
+
| Review of the main current difficulties of EM
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Briggs_Review]]
+
| [[2017Frank_Review]]
| Review of subtomogram averaging
+
| Historical review of EM
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Beck_Review]]
+
| [[2017Frank_TimeResolved]]
| Review of molecular sociology
+
| Review of time-resolved of EM
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Galaz_Review]]
+
| [[2017Jonic_Review]]
| Review of single particle tomography
+
| Review of computational methods to analyze conformational variability
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Plitzko_Review]]
+
| [[2017Merino_DrugEM]]
| Review of electron tomography, FRET and FIB milling
+
| Applications of EM for drug design
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2019Schur_Review]]
+
| [[2017Rawson_Limitations]]
| Review of electron tomography and subtomogram averaging
+
| Limitations of EM for drug design
 
|-  
 
|-  
  
|}
+
| Paper
 
+
| [[2017Sorzano_FourierProperties]]
=== Software ===
+
| Review of statistical properties of resolution measures defined in Fourier space
 
+
|-
{|
 
  
 
| Paper
 
| Paper
| [[1996Kremer_IMOD]]
+
| [[2017Sorzano_SurveyIterative]]
| IMOD
+
| Survey of iterative reconstruction methods for EM
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1996Chen_Priism/IVE]]
+
| [[2018Bruggeman_Crowdsourcing]]
| Priism/IVE
+
| Exploring crowdsourcing for EM image processing
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1996Frank_Spider]]
+
| [[2018Cheng_Review]]
| Spider
+
| Review of EM and future ahead
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2004Sorzano_Xmipp]]
+
| [[2018Cossio_ML]]
| Xmipp
+
| Review of Maximum Likelihood methods
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2005Nickell_TOM]]
+
| [[2018Grimes_Crystallography]]
| TOM Toolbox
+
| Review of X-ray crystallography and its relationship to EM
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007Messaoudi_TomoJ]]
+
| [[2018Murata_Review]]
| TomoJ
+
| Review of EM for structure dynamics
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2008Heymann_BsoftTomo]]
+
| [[2018Quentin_Biomedical]]
| Bsoft
+
| Review of EM as a tool for biomedical research
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Ding_CaltechTomography]]
+
| [[2018Scapin_DrugDiscovery]]
| Caltech tomography database
+
| Review of EM as a tool for drug discovery
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Noble_AppionProtomo]]
+
| [[2018Vilas_ImageProcessing]]
| Batch fiducial-less tilt-series alignment in Appion using Protomo
+
| Review of the recent developments in image processing for single particle analysis
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015vanAarle_Astra]]
+
| [[2018vonLoeffelholz_VPP]]
| ASTRA Toolbox
+
| Comparison of Volta Phase Plate reconstructions close to focus and with defocus
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Han_AuTom]]
+
| [[2018Eisenstein_DrugDesigners]]
| Software platform for Electron Tomography
+
| Drug designers embrace cryo-EM
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Wan_Simulator]]
+
| [[2019Benjin_Review]]
| Electron Tomography Simulator
+
| Review of SPA
 
|-  
 
|-  
 
|}
 
 
== 2D Crystals ==
 
 
=== 2D Preprocessing ===
 
 
{|
 
  
 
| Paper
 
| Paper
| [[1982Saxton_Averaging]]
+
| [[2019Danev_Review]]
| Radial Correlation Function
+
| Review of future directions
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1984Saxton_Distortions]]
+
| [[2019Lyumkis_Review]]
| 3D Reconstruction of distorted crystals
+
| Challenges and reviews
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1986Henderson_Processing]]
+
| [[2019Sorzano_Review]]
| General 2D processing  
+
| 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
 +
| [[2022Caldraft_Tilt]]
 +
| Review of applications of tilt pairs in SPA
 +
|-
 +
 
 +
| 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
 +
|-
 +
 
 +
|}
 +
 
 +
=== 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.
 +
|-
 +
 
 +
|}
 +
 
 +
== 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
 +
|-
 +
 
 +
|}
 +
 
 +
=== 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 single molecule tomography
 +
|-
 +
 
 +
| 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
 +
|-
 +
 
 +
|}
 +
 
 +
=== 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
 +
|-
 +
 
 +
|}
 +
 
 +
=== 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
 +
| [[2021Du_Active]]
 +
| Active learning to reduce the need of annotated samples
 +
|-
 +
 
 +
| Paper
 +
| [[2021Harastani_NMA]]
 +
| 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
 +
| [[2022Harastani_TomoFlow]]
 +
| Continuous flexibility analysis of subtomograms using 3D dense optical flow
 +
|-
 +
 
 +
| Paper
 +
| [[2022Peters_Feature]]
 +
| Feature guided, focused 3D signal permutation for STA
 +
|-
 +
 
 +
|}
 +
 
 +
=== 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
 +
|-
 +
 
 +
| 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)
 +
|-
 +
 
 +
|}
 +
 
 +
=== Molecular 3D dynamics  ===
 +
 
 +
{|
 +
 
 +
| Paper
 +
| [[2015Zhang_IPET]]
 +
| 3D structural fluctuation of macromoles)
 +
|-
 +
 
 +
|}
 +
 
 +
=== 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
 +
|-
 +
 
 +
|}
 +
 
 +
=== 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
 +
| [[2022Ni_EmClarity]]
 +
| Processing protocols with EmClarity
 +
|-
 +
 
 +
|}
 +
 
 +
== 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
 
| Paper
| [[2000He_PhaseAlignment]]
+
| [[2001Glaeser_Review]]
| Phase consistency and Alignment
+
| Review of 2D crystallography
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2006Gil_Unbending]]
+
| [[2004Henderson_Review]]
| Crystal unbending
+
| Review of electron microscopy
 
|-  
 
|-  
 
|}
 
 
=== Classification ===
 
{|
 
  
 
| Paper
 
| Paper
| [[1988Frank_Classification]]
+
| [[2006Fernandez_Review]]
| MSA and classification in electron crystallography
+
| Review of single particles, electron tomography and crystallography
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1996Fernandez_SOM]]
+
| [[2007Sorzano_Review]]
| Classification based on self organizing maps
+
| Review of the image processing steps
 
|-  
 
|-  
  
| Paper
+
|}
| [[1998Sherman_MSA]]
 
| Classification based on MSA
 
|-
 
  
|}
+
=== Software ===
=== 3D Reconstruction ===
 
  
 
{|
 
{|
  
 
| Paper
 
| Paper
| [[1985Wang_Solvent]]
+
| [[1996Crowther_MRC]]
| Solvent flattening
+
| MRC
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1990Henderson_Processing]]
+
| [[2004Sorzano_Xmipp]]
| General 3D processing
+
| Xmipp
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2004Marabini_ART]]
+
| [[2007Gipson_2dx]]
| Algebraic Reconstruction Technique with blobs for crystals (Xmipp)
+
| 2dx
 +
|-
 +
 
 +
| Paper
 +
| [[2007Heymann_Bsoft]]
 +
| Bsoft
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Biyani_Badlu]]
+
| [[2007Philippsen_IPLT]]
| Image processing for badly ordered crystals
+
| IPLT
 
|-  
 
|-  
  
 
|}
 
|}
  
=== Books and reviews ===
+
== 3D Crystals - MicroED ==
  
 +
=== Sample Preparation ===
 
{|
 
{|
 
 
| Paper
 
| Paper
| [[1998Walz_Review]]
+
| [[2016Shi_Preparation]]
| Review of 2D crystallography
+
| Sample Preparation
|-
+
|}
 
+
=== Data Collection ===
 +
{|
 
| Paper
 
| Paper
| [[1999Glaeser_Review]]
+
| [[2014Nannenga_CR]]  
| Review of 2D crystallography
+
| Continuous rotation
|-
 
  
| Paper
+
|}
| [[2001Ellis_Review]]
+
=== Data Processing ===
| Review of 2D crystallography
+
{|
|-
 
  
 
| Paper
 
| Paper
| [[2001Glaeser_Review]]
+
| [[2011Wisedchaisri_PhaseExtension]]
| Review of 2D crystallography
+
| Fragment-based phase extension
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2004Henderson_Review]]
+
| [[2015Hattne_Processing]]
| Review of electron microscopy
+
| 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
 
| Paper
| [[2006Fernandez_Review]]
+
| [[2016Liu_Review ]]
| Review of single particles, electron tomography and crystallography
+
| Review of MicroED
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2007Sorzano_Review]]
+
| [[2016Rodriguez_Review ]]
| Review of the image processing steps
+
| Review of MicroED
 
|-  
 
|-  
  
 
|}
 
|}
  
=== Software ===
+
== Helical particles ==
 +
 
 +
=== Filament picking ===
  
 
{|
 
{|
  
 
| Paper
 
| Paper
| [[1996Crowther_MRC]]
+
| [[2021Thurber_Automated]]
| MRC
+
| Automated picking of filaments
 
|-  
 
|-  
  
| Paper
+
|}
| [[2004Sorzano_Xmipp]]
+
 
| Xmipp
+
=== Filament corrections ===
|-
+
 
 +
{|
  
 
| Paper
 
| Paper
| [[2007Gipson_2dx]]
+
| [[1986Egelman_Curved]]
| 2dx
+
| Algorithm for correcting curved filaments
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007Heymann_Bsoft]]
+
| [[1988Bluemke_Pitch]]
| Bsoft
+
| Algorithm for correcting filaments with different helical pitches
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007Philippsen_IPLT]]
+
| [[2006Wang_Pitch]]
| IPLT
+
| Algorithm for correcting filaments with different helical pitches
 
|-  
 
|-  
  
|}
+
| Paper
 +
| [[2016Yang_Flexible]]
 +
| Algorithm for correcting filaments with flexible subunits
 +
|-
  
== 3D Crystals - MicroED ==
+
| Paper
 +
| [[2019Ohashi_SoftBody]]
 +
| Algorithm for correcting filaments with flexible helices
 +
|-  
  
=== Sample Preparation ===
 
{|
 
| Paper
 
| [[2016Shi_Preparation]]
 
| Sample Preparation
 
 
|}
 
|}
=== Data Collection ===
 
{|
 
| Paper
 
| [[2014Nannenga_CR]]
 
| Continuous rotation
 
  
|}
+
=== Reconstruction ===
=== Data Processing ===
+
 
 
{|
 
{|
  
 
| Paper
 
| Paper
| [[2011Wisedchaisri_PhaseExtension]]
+
| [[1952Cochran_Fourier]]
| Fragment-based phase extension
+
| Fourier Bessel transform of filamentous structures
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2015Hattne_Processing]]  
+
| [[1958Klug_Fourier]]
| Data Processing
+
| Fourier Bessel decomposition of the projection images
|-
+
|-  
+
 
 
| Paper
 
| Paper
| [[2016Hattne_Correction]]
+
| [[1970DeRosier_Rec]]
| Image correction
+
| Image processing steps towards 3D reconstruction
|}
+
|-
  
=== Software ===
+
| Paper
{|
+
| [[1988Stewart_Rec]]
 +
| Image processing steps towards 3D reconstruction
 +
|-
  
 
| Paper
 
| Paper
| [[2014Iadanza_Processing]]
+
| [[1992Morgan_Rec]]
| Data Processing of still diffraction data
+
| Image processing steps towards 3D reconstruction
|}
+
|-
  
=== Books and Reviews ===
+
| Paper
{|
+
| [[2005Wang_Iterative]]
| Paper
+
| Iterative Fourier-Bessel algorithm
| [[2014Nannenga_Review ]]
+
|-  
| Review of MicroED
 
|-
 
  
 
| Paper
 
| Paper
| [[2016Liu_Review ]]
+
| [[2007Egelman_Iterative]]
| Review of MicroED
+
| Iterative real-space algorithm
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2016Rodriguez_Review ]]
+
| [[2010Egelman_Pitfalls]]
| Review of MicroED
+
| Pitfalls in helical reconstruction
 
|-  
 
|-  
 
|}
 
 
== Helical particles ==
 
 
=== Filament corrections ===
 
 
{|
 
  
 
| Paper
 
| Paper
| [[1986Egelman_Curved]]
+
| [[2013Desfosses_Spring]]
| Algorithm for correcting curved filaments
+
| Helical processing with Spring
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1988Bluemke_Pitch]]
+
| [[2015Zhang_seam]]
| Algorithm for correcting filaments with different helical pitches
+
| Workflow for the detection of the lattice seam
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2006Wang_Pitch]]
+
| [[2016Rohou_Frealix]]
| Algorithm for correcting filaments with different helical pitches
+
| Helical processing with Frealix
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Yang_Flexible]]
+
| [[2017_He]]
| Algorithm for correcting filaments with flexible subunits
+
| Helical processing with Relion
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2019Ohashi_SoftBody]]
+
| [[2019_Pothula]]
| Algorithm for correcting filaments with flexible helices
+
| 3D Classification through 2D analysis
 
|-  
 
|-  
  
 
|}
 
|}
  
=== Reconstruction ===
+
=== Validation ===
  
 
{|
 
{|
  
 
| Paper
 
| Paper
| [[1952Cochran_Fourier]]
+
| [[2014Egelman_ambiguity]]
| Fourier Bessel transform of filamentous structures
+
| How to detect incorrect models
 
|-  
 
|-  
  
| Paper
+
|}
| [[1958Klug_Fourier]]
+
 
| Fourier Bessel decomposition of the projection images
+
=== Books and reviews ===
|-
+
 
 +
{|
  
 
| Paper
 
| Paper
Line 4,200: Line 5,591:
  
 
| Paper
 
| Paper
| [[1988Stewart_Rec]]
+
| [[1992Morgan_Rec]]
 
| Image processing steps towards 3D reconstruction
 
| Image processing steps towards 3D reconstruction
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1992Morgan_Rec]]
+
| [[2004Henderson_Review]]
| Image processing steps towards 3D reconstruction
+
| Review of electron microscopy
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2005Wang_Iterative]]
+
| [[2015Sachse_Review]]
| Iterative Fourier-Bessel algorithm
+
| Review of the image processing steps in helical particles
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007Egelman_Iterative]]
+
| [[2021Egelman_Review]]
| Iterative real-space algorithm
+
| Review of reconstruction problems in helical structures
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2010Egelman_Pitfalls]]
+
| [[2022Wang_Review]]
| Pitfalls in helical reconstruction
+
| Review of reconstruction problems in helical structures
 
|-  
 
|-  
  
| Paper
+
|}
| [[2013Desfosses_Spring]]
+
 
| Helical processing with Spring
+
=== Software ===
|-
 
  
| Paper
+
{|
| [[2015Zhang_seam]]
 
| Workflow for the detection of the lattice seam
 
|-
 
  
 
| Paper
 
| Paper
| [[2016Rohou_Frealix]]
+
| [[1996Carragher_Phoelix]]
| Helical processing with Frealix
+
| Phoelix
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017_He]]
+
| [[1996Crowther_MRC]]
| Helical processing with Relion
+
| MRC
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2019_Pothula]]
+
| [[1996Owen_Brandeis]]
| 3D Classification through 2D analysis
+
| Brandeis
 
|-  
 
|-  
  
 
|}
 
|}
  
=== Validation ===
+
== Icosahedral particles ==
 +
 
 +
=== Reconstruction ===
  
 
{|
 
{|
  
 
| Paper
 
| Paper
| [[2014Egelman_ambiguity]]
+
| [[1970Crowther_Rec]]
| How to detect incorrect models
+
| Reconstruction of icosahedral viruses in Fourier space
 
|-  
 
|-  
  
|}
+
| Paper
 
 
=== 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
 
|-
 
 
 
|}
 
 
 
=== 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]]
 
| [[1971Crowther_Rec]]
 
| Reconstruction of icosahedral viruses in Fourier space
 
| Reconstruction of icosahedral viruses in Fourier space
Line 4,426: Line 5,755:
 
| [[2013Morin_Sliz SBGrid]]
 
| [[2013Morin_Sliz SBGrid]]
 
| SBGrid presentation for eLife  
 
| SBGrid presentation for eLife  
 +
|-
 +
 +
|}
 +
 +
== Liquid-cell TEM / in-situ TEM ==
 +
 +
 +
{|
 +
 +
| Paper
 +
| [[2020Ren_LTEM]]
 +
| Real-time dynamic imaging of sample in liquid phase
 
|-  
 
|-  
  
Line 4,497: Line 5,838:
 
| [[2018wwwPDB_PDB]]
 
| [[2018wwwPDB_PDB]]
 
| Review of PDB advances
 
| Review of PDB advances
 +
|-
 +
 +
| Paper
 +
| [[2022Wang_EMDB]]
 +
| Validation analysis of EMDB entries
 
|-  
 
|-  
  
Line 4,578: Line 5,924:
 
| [[2019Jimenez_SAXS]]
 
| [[2019Jimenez_SAXS]]
 
| Selection of EM initial volumes by SAXS curves
 
| 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
 
|-  
 
|-  
  
Line 4,590: Line 5,946:
 
| Image formation model in X-ray cell microscopy
 
| Image formation model in X-ray cell microscopy
 
|-  
 
|-  
 
 
  
 
|}
 
|}
Line 4,617: Line 5,971:
  
 
[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 ==

Revision as of 14:53, 9 June 2022

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

  • You know which are the relevant articles in a particular topic, therefore, paper introductions, reviews, etc. are easier to write and you make sure you will cite all the related articles.
  • You will be sure that your paper has more chances of being cited.
  • You can add whatever information you find relevant to your method, external links, links to other papers, etc.
  • You can link your method to a web page providing the corresponding software, so you know people can use your algorithms.
  • You can use the Wiki search capabilities to locate relevant articles even if they are not at the topic you are looking at.
  • As a community we will "reconstruct" our history.
  • You can select the "watch" option above to receive notifications in case of further changes in the Main Page.

Developing image processing methods for 3DEM is not "well-paid" in terms of citations and impact factor. However, it is crucial for the advance of the field. Gathering methodological papers in a portal will help to increase the recognition of the field.

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.
  • Be respectful to other people's work.

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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

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 2022Dickerson_Inelastic The role of inelastic scattering in thick specimens
Paper 2022Ravikumar_SideChains Comparison of side-chain dispersion in protein structures determined by cryo-EM and X-ray crystallography

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

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 2022Scher_FIB Sample preparation for FIB-SEM and Correlative microscopy

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 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

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
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

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

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

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

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 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

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 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 Using Scipion for analyzing local 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 2022Rabuck_Quant Workflow for discrete heterogeneity analysis
Paper 2022Skalidis_Endogenous AI tools to recognize proteins in cellular fractions
Paper 2022Zhou_Data Determination of the number of discrete 3D classes

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 2022Sorzano_Bias Bias, variance, gold-standard and overfitting in SPA
Paper 2022Waarshamanage_EMDA Validation of models fitted into CryoEM maps

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

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 2022Vargas_tubular Map enhancement by multiscale tubular filter

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 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 Normal Modes
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 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 2022Vuillemot_NMMD Flexible fitting with simultaneous Normal Mode and Molecular Dynamics displacements
Paper 2022Zhang_CRITASSER Atomic models of assemble protein structures with deep learning

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 2022Caldraft_Tilt Review of applications of tilt pairs in SPA
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

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.

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

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 single molecule tomography
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

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

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 2021Du_Active Active learning to reduce the need of annotated samples
Paper 2021Harastani_NMA 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 2022Harastani_TomoFlow Continuous flexibility analysis of subtomograms using 3D dense optical flow
Paper 2022Peters_Feature Feature guided, focused 3D signal permutation for STA

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
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)

Molecular 3D dynamics

Paper 2015Zhang_IPET 3D structural fluctuation of macromoles)

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

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 2022Ni_EmClarity Processing protocols with EmClarity

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
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