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== Electron microscopy images ==
 
== Electron microscopy images ==
  
=== Online courses ===
+
=== Online courses and Learning material ===
  
[http://cryo-em-course.caltech.edu Caltech]
+
[http://cryo-em-course.caltech.edu Caltech] [https://www.coursera.org/learn/cryo-em (same course in Coursera)] [https://em-learning.com (latest version of the course in EM-learning)]
  
 
[ftp://ftp.mrc-lmb.cam.ac.uk/pub/scheres/EM-course MRC]
 
[ftp://ftp.mrc-lmb.cam.ac.uk/pub/scheres/EM-course MRC]
Line 83: Line 83:
 
[https://www.youtube.com/playlist?list=PL8_xPU5epJdfd5fM2CjQItR-iRlIEIJk8 Tutorial on how to prepare samples]
 
[https://www.youtube.com/playlist?list=PL8_xPU5epJdfd5fM2CjQItR-iRlIEIJk8 Tutorial on how to prepare samples]
  
[http://nramm.nysbc.org/2017-workshop-lectures NRAMM Workshop 2017]
+
[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://em-learning.com 70h of EM learning by Grant Jensen and Matthijn Vos]
+
[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]
 +
 
 +
[http://i2pc.es/coss/Docencia/ImageProcessing/imageProcessingInEM.pdf Madrid course on single particle analysis]
 +
 
 +
[https://www.youtube.com/watch?v=F1yXJaZ2H5o&list=PLFEB3YHuxu11I4Qgj6K5jmWcghsFnE09Q CCP-EM Spring symposium 2019]
 +
 
 +
[https://www.youtube.com/playlist?list=PLFEB3YHuxu11Jp_pOCIEtXxSqozFHve0O CCP-EM Spring symposium 2020]
 +
 
 +
[https://www.youtube.com/playlist?list=PLhiuGaXlZZel2mj6S4FPjWwsvj2LPqLYL NCCAT Single Particle short course 2020]
 +
 
 +
[https://www.cellstructureatlas.org Cell atlas book by Grant Jensen and Catherine Oikonomou]
 +
 
 +
[https://va.tech.purdue.edu/cryoVR/index.php Purdue CryoEM Virtual Reality Augmented Training]
 +
 
 +
[https://www.youtube.com/playlist?list=PLhiuGaXlZZek9D0SZk0OVtTeFVETa1sPG NCCAT Short course on Tomography]
 +
 
 +
[https://www.google.com/maps/d/u/0/viewer?mid=1eQ1r8BiDYfaK7D1S9EeFJEgkLggMyoaT&ll=-3.81666561775622e-14%2C-37.83892653579875&z=1 Map with CryoEM Facilities]
 +
 
 +
[https://www.youtube.com/playlist?list=PLhiuGaXlZZeliWnyp_wtRqPr_QkX00um7 NCCAT Single Particle Analysis short course]
  
 
=== Image formation ===
 
=== Image formation ===
Line 110: Line 130:
 
| CTF model
 
| CTF model
 
|-  
 
|-  
 +
 +
| Paper
 +
| [[1974Taylor_Diffraction]]
 +
| Electron diffraction of crystals
 +
|-
 +
  
 
| Paper
 
| Paper
Line 174: Line 200:
 
| [[2009Baxter_NoiseCharacterization]]
 
| [[2009Baxter_NoiseCharacterization]]
 
| Characterization of the different noise sources in cryo-EM  
 
| Characterization of the different noise sources in cryo-EM  
 +
|-
 +
 +
| Book
 +
| [[2009Rose_Optics]]
 +
| Geometrical Charged-Particle Optics
 
|-  
 
|-  
  
Line 329: Line 360:
 
| [[2017Mishyna_DNARadiation]]
 
| [[2017Mishyna_DNARadiation]]
 
| Review of radiation damage on DNA
 
| Review of radiation damage on DNA
 +
|-
 +
 +
| Paper
 +
| [[2018Anoshina_Simulation]]
 +
| Simulation of 2D and 3D EM images
 
|-  
 
|-  
  
Line 354: 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 381: Line 412:
 
|-  
 
|-  
  
|}
+
| Paper
 +
| [[2019Peet_EnergyDependence]]
 +
| Energy dependence of radiation damage
 +
|-
  
=== Collection geometry ===
+
| Paper
 
+
| [[2020Bromberg_Aberrations]]
{|
+
| 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
 
+
| [[2003Ludtke_FocusPairs]]
=== Sample preparation ===
+
| Focus pairs for single particles
 
+
|-
{|
 
  
 
| Paper
 
| Paper
| [[1982Dubochet_Sample]]
+
| [[2005Lanzavecchia_Conical]]
| Vitreous ice
+
| Conical tomography
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1986Lepault_Sample]]
+
| [[2005Zampighi_Conical]]
| Fast freezing
+
| Conical tomography
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1995Dubochet_Sample]]
+
| [[2006Leschziner_OT]]
| High-pressure freezing
+
| Orthogonal Tilt
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1995VanMarle_Sample]]
+
| [[2006Messaoudi_Multiple]]
| Sample damages in resin
+
| Multiple axis tomography
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1998Adrian_Sample]]
+
| [[2012Kudryashev_FocusPairs]]
| Cryo negative staining
+
| Focus pairs tomography
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2002DeCarlo_Damage]]
+
| [[2014Hovden_TiltFocus]]
| Radiation damage in cryonegative staining
+
| Combining tilt series with focus series
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2002Hsieh_Sample]]
+
| [[2015Sorzano_RandomConicalTilt]]
| Cryofixation
+
| General formulation of Random Conical Tilt
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2004AlAmoudi_Sample]]
+
| [[2017Hagen_DoseTomography]]
| CEMOVIS
+
| Dose optimization for subtomogram averaging
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2008Studer_Sample]]
+
| [[2017Tan_PreferredViews]]
| Review on high pressure freezing
+
| Solving preferred views problems through tilting
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2009Pierson_Sample]]
+
| [[2017Donati_Compressed]]
| Review on sample preparation for electron tomography
+
| Compressed sensing for STEM
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2010Zhang_NegativeStaining]]
+
| [[2018Oveisi_Stereo]]
| Negative staining for small protein imaging
+
| Stereo-vision with EM
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2012Zhang_PositiveStaining]]
+
| [[2018Cheng_BeamShift]]
| Positive staining
+
| Fast image acquisition through beam-shift
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2014Rames_NegativeStaining]]
+
| [[2019Wu_BeamShiftAndTilt]]
| Optimized negative staining
+
| Fast image acquisition through beam-shift and beam tilt control
 
|-  
 
|-  
 +
 +
|}
 +
 +
=== Sample preparation ===
 +
 +
{|
  
 
| Paper
 
| Paper
| [[2014Russo_GoldGrids]]
+
| [[1982Dubochet_Sample]]
| Gold grids for single particles
+
| 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
 +
| [[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
 
| Paper
| [[2018Dandey_Spotiton]]
+
| [[2017Earl_review]]
| Spotiton, a device for vitrification
+
| Review of sample preparation
 
|-
 
|-
  
 
| Paper
 
| Paper
| [[2018Gewering_Detergents]]
+
| [[2017Feng_SprayingPlunging]]
| Detergent background in negative stain
+
| Spraying plunging
 
|-
 
|-
  
 
| Paper
 
| Paper
| [[2018Li_CLEM]]
+
| [[2017He_FIB]]
| Correlated light and EM
+
| Cryo FIB lamella for TEM
 
|-
 
|-
  
 
| Paper
 
| Paper
| [[2018Noble_Reducing]]
+
| [[2017Peitsch_Sample]]
| Reducing particle adsorption
+
| iMEM: Isolation of Plasma Membrane for Cryoelectron Microscopy
 
|-
 
|-
  
 
| Paper
 
| Paper
| [[2018Rice_Ice]]
+
| [[2017Scapin_Storage]]
| Routine determination of ice thickness
+
| Cryo storage of samples
 
|-
 
|-
  
 
| Paper
 
| Paper
| [[2018Wei_Grids]]
+
| [[2017Schaffer_FocusedIonBeam]]
| "Self-wicking" nanowire grids
+
| Focused Ion Beam sample preparation for membrane proteins
 
|-
 
|-
  
|}
+
| Paper
 +
| [[2017Scherr_HydrogelNanomembranes]]
 +
| Sample preparation for membrane proteins
 +
|-
  
=== Automated data collection ===
+
| Paper
 +
| [[2018Anderson_CLEM]]
 +
| Correlated light and EM
 +
|-
  
{|
+
| Paper
 +
| [[2018Arnold_Review]]
 +
| Review on sample preparation with special emphasis on microfluidic approaches
 +
|-
  
 
| Paper
 
| Paper
| [[1992Dierksen_Automatic]]
+
| [[2018Ashtiani_femtolitre]]
| Automated data collection
+
| Delivery of femtolitre droplets using surface acoustic wave based atomisation for cryo-EM grid preparation
|-  
+
|-
  
 
| Paper
 
| Paper
| [[1992Koster_Automatic]]
+
| [[2018Dandey_Spotiton]]
| Automated data collection
+
| Spotiton, a device for vitrification
|-  
+
|-
  
 
| Paper
 
| Paper
| [[1996Fung_Automatic]]
+
| [[2018Gewering_Detergents]]
| Automated data collection for tomography
+
| Detergent background in negative stain
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2001Zhang_Automatic]]
+
| [[2018Li_CLEM]]
| Automated data collection: AutoEM
+
| Correlated light and EM
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2003Ziese_Automatic]]
+
| [[2018Noble_Reducing]]
| Automated autofocusing
+
| Reducing particle adsorption
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2004Potter_Automatic]]
+
| [[2018Palovcak_Graphene]]
| Automated sample loading
+
| Preparation of graphene-oxide cryo-EM grids
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2004Zheng_Automatic]]
+
| [[2018Rice_Ice]]
| Automated data collection
+
| Routine determination of ice thickness
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2005Lei_Automatic]]
+
| [[2018Schmidli_Miniaturized]]
| Automated data collection: AutoEM
+
| Protein isolation and sample preparation
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2005Suloway_Automatic]]
+
| [[2018Wei_Grids]]
| Automated data collection: Leginon
+
| "Self-wicking" nanowire grids
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2007Yoshioka_RCT]]
+
| [[2019DImprima_Denaturation]]
| Automated Random Conical Tilt
+
| Protein denaturation at the air-water interface and how to prevent it
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2011Korinek_TOM2]]
+
| [[2019Rubinstein_ultrasonic]]
| Automated acquisition with TOM2
+
| Ultrasonic specimen preparation device
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2015Li_UCSFImage]]
+
| [[2019Song_FalconIII]]
| Automated acquisition with UCSFImage
+
| Comparison of the modes of Falcon III
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2016Gil_Fuzzy]]
+
| [[2020Cianfrocco_Wrong]]
| Real time decisions during acquisition with neuro-fuzzy method
+
| What could go wrong?
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2016Liu_TiltControl]]
+
| [[2020Egelman_Ice]]
| Accurate control of the tilt angle for electron tomography
+
| Problems with the ice
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2016Vargas_FoilHole]]
+
| [[2020Fassler_Printing]]
| Determination of image quality at low magnification
+
| 3D printed cell culture grid holder
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2017Alewijnse_Best]]
+
| [[2020Klebl_Deposition]]
| Best practices for managing large CryoEM facilities
+
| Sample deposition onto CryoEM grids: sprays and jets
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2017Biyani_Focus]]
+
| [[2020Maeots_TimeResolved]]
| Automatic processing of micrographs
+
| Time resolved CryoEM by microfluidics
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2018Gomez_Facilities]]
+
| [[2020Tan_ThroughGrid]]
| Use of Scipion at facilities
+
| Through-grid wicking enables high-speed 1 cryoEM specimen preparation
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2018Sorzano_Gain]]
+
| [[2020Yoder_TimeResolved]]
| Estimation of the DDD camera gain or residual gain
+
| Time resolved CryoEM by light estimulation
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2019Thompson_Protocol]]
+
| [[2020Zachs_FIB]]
| Protocol for EM acquisition
+
| Automation for FIB milling
|-  
+
|-
  
|}
+
| Paper
 +
| [[2021Bieber_FIBET]]
 +
| Sample preparation for correlative FIB milling and CryoET
 +
|-
  
== Single particles ==
+
| Paper
 +
| [[2021Budell_TimeResolved]]
 +
| Time resolved CryoEM with Spotiton
 +
|-
  
=== Automatic particle picking ===
+
| Paper
 +
| [[2021Casasanta_Microchip]]
 +
| Microchip-based structure determination of low-molecular weight proteins using cryo-electron microscopy
 +
|-
  
{|
+
| Paper
 +
| [[2021Frechard_Preparation]]
 +
| Optimization of Sample Preparation
 +
|-
  
 
| Paper
 
| Paper
| [[1982VanHeel_Detection]]
+
| [[2021Engstrom_Nitrogen]]
| Detection of particles in micrographs
+
| Samples vitrified in boiling nitrogen
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2001Nicholson_Review]]
+
| [[2021Jagota_GoldNanoparticles]]
| Review on automatic particle picking
+
| Gold nanoparticles to assess flexibility
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2001Zhu_Filaments]]
+
| [[2021Jiang_MoAu]]
| Automatic identification of filaments in micrographs
+
| Holey Gold Films on Molybdenum Grids
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2004Sigworth_Detection]]
+
| [[2021Jonaid_Liquid]]
| Classical detection theory and the cryo-EM particle selection problem
+
| Liquid phase EM
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2004Volkmann_ParticlePicking]]
+
| [[2021Ki_Conformational]]
| An approach to automated particle picking from electron micrographs based on reduced representation templates
+
| Conformational Distribution of a Small Protein with Nanoparticle-Aided CryoEM
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2004Wong_ParticlePicking]]
+
| [[2021Li_detergents]]
| Model-based particle picking for cryo-electron microscopy
+
| The effect of detergents on preferential orientations
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2004Zhu_Review]]
+
| [[2021Voss_Melting]]
| Review on automatic particle picking
+
| Rapid melting and revitrification as an approach to microsecond time-resolved cryoEM
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2007Chen_Signature]]
+
| [[2021Zhang_Pegylation]]
| Automatic particle picking program: Signature
+
| Improving particle quality in cryo-EM by PEGylation
|-  
+
|-
 
 
  
 
| Paper
 
| Paper
| [[2007Woolford_SwarmPS]]
+
| [[2022Chen_Detergents]]
| Automatic particle picking with several criteria, implemented in EMAN Boxer
+
| Role of detergents in the air-water interface
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2009Sorzano_MachineLearning]]
+
| [[2022Levitz_Chameleon]]
| Automatic particle picking based on machine learning of rotational invariants
+
| Effects of dispense-to-plunge speed on particle concentration, complex formation, and final resolution
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2011Arbelaez_Comparison]]
+
| [[2022Naydenova_Grid]]
| Evaluation of the performance of software for automated particle-boxing
+
| Integrated wafer-scale manufacturing of electron cryomicroscopy specimen supports
 
|-
 
|-
  
 
| Paper
 
| Paper
| [[2013Abrishami_MachineLearning]]
+
| [[2022Scher_FIB]]
| A pattern matching approach to the automatic selection of particles from low-contrast electron micrographs
+
| Sample preparation for FIB-SEM and Correlative microscopy
 
|-
 
|-
  
| Paper
+
|}
| [[2013Hauer_2013]]
+
 
| Automatic tilt pair detection in Random Conical Tilt
+
=== Automated data collection ===
|-
+
 
 +
{|
  
 
| Paper
 
| Paper
| [[2013Hoang_ParallelGPUPicking]]
+
| [[1992Dierksen_Automatic]]
| Parallel GPU-accelerated particle picking
+
| Automated data collection
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2013Shatsky_ParticlePicking]]
+
| [[1992Koster_Automatic]]
| Automated particle correspondence and accurate tilt-axis detection in tilted-image pairs
+
| Automated data collection
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2013Vargas_ParticleQuality]]
+
| [[1996Fung_Automatic]]
| Automatic determination of particle quality
+
| Automated data collection for tomography
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2014Langlois_ParticlePicking]]
+
| [[2001Zhang_Automatic]]
| Automatic particle picking
+
| Automated data collection: AutoEM
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Scheres_SemiAutoPicking]]
+
| [[2003Ziese_Automatic]]
| Semi-automated selection of cryo-EM particles
+
| Automated autofocusing
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Vilas_AutomaticTilt]]
+
| [[2004Potter_Automatic]]
| Automatic identification of image pairs in untilted-tilted micrograph pairs
+
| Automated sample loading
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Wang_DeepPicker]]
+
| [[2004Zheng_Automatic]]
| A deep learning approach for fully automated particle picking
+
| Automated data collection
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Zhu_DeepEM]]
+
| [[2005Lei_Automatic]]
| Deep learning approach to picking
+
| Automated data collection: AutoEM
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Huber_Helices]]
+
| [[2005Suloway_Automatic]]
| Automated tracing of helices
+
| Automated data collection: Leginon
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Heimowitz_ApplePicker]]
+
| [[2007Yoshioka_RCT]]
| Automated particle picking
+
| Automated Random Conical Tilt
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Sanchez_DeepConsensus]]
+
| [[2011Korinek_TOM2]]
| Deep learning consensus of multiple automatic pickers
+
| Automated acquisition with TOM2
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2019Zhang_Pixer]]
+
| [[2015Li_UCSFImage]]
| Deep learning for particle picking
+
| Automated acquisition with UCSFImage
 
|-  
 
|-  
 
|}
 
 
=== 2D Preprocessing ===
 
 
{|
 
  
 
| Paper
 
| Paper
| [[2003Rosenthal_DPR]]
+
| [[2016Gil_Fuzzy]]
| Contrast enhancement through DPR
+
| Real time decisions during acquisition with neuro-fuzzy method
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2004Sorzano_Normalization]]
+
| [[2016Liu_TiltControl]]
| Normalization procedures and their statistical properties.
+
| Accurate control of the tilt angle for electron tomography
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2006Sorzano_Denoising]]
+
| [[2016Vargas_FoilHole]]
| Strong denoising in wavelet space
+
| Determination of image quality at low magnification
 
|-  
 
|-  
  
| Conference
+
| Paper
| [[2009Sorzano_Downsampling]]
+
| [[2017Alewijnse_Best]]
| Differences between the different downsampling schemes
+
| Best practices for managing large CryoEM facilities
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2012Brilot_Movies]]
+
| [[2017Biyani_Focus]]
| Alignment of beam induced motion in direct detectors
+
| Automatic processing of micrographs
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2012Campbell_Movies]]
+
| [[2018Gomez_Facilities]]
| Alignment of beam induced motion in direct detectors
+
| Use of Scipion at facilities
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2012Zhao_Denoising]]
+
| [[2018Sorzano_Gain]]
| Denoising using an invariant Fourier-Bessel eigenspace
+
| Estimation of the DDD camera gain or residual gain
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Norousi_Screening]]
+
| [[2019Chreifi_TiltSeries]]
| Screening particles to identify outliers
+
| Rapid tilt-series acquisition for electron cryotomography
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Bai_ElectronCounting]]
+
| [[2019Eng_ImageCompression]]
| Electron counting and beam induced motion correction
+
| 3D Reconstruction from compressed images
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Li_ElectronCounting]]
+
| [[2019Eisenstein_FISE]]
| Electron counting and beam induced motion correction
+
| Improved applicability and robustness of fast cryo-electron tomography data acquisition
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Shigematsu_Movies]]
+
| [[2019Hamaguchi_CryoARM]]
| Drift correction for movies considering dark field
+
| CryoARM data acquisition
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Vargas_ParticleQuality]]
+
| [[2019Maluenda_Scipion]]
| Automatic determination of particle quality
+
| Automated workflow processing for facilities
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2014Scheres_Movies]]
+
| [[2019Schorb_ET]]
| Beam induced motion correction
+
| Automated acquisition in Electron Tomography
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Abrishami_Movies]]
+
| [[2019Tegunov_Warp]]
| Alignment of direct detection device micrographs
+
| Automatic micrograph processing with Warp
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Grant_Anisotropic]]
+
| [[2019Thompson_Protocol]]
| Automatic estimation and correction of anisotropic magnification
+
| Protocol for EM acquisition
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Grant_OptimalExposure]]
+
| [[2020Baxa_Facility]]
| Filter movies according to the radiation damage
+
| Operational workflow in a facility
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Rubinstein_Alignment]]
+
| [[2020Guo_EER]]
| Frame alignment at the level of particle
+
| Electron event representation for acquisition
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Spear_DoseCompensation]]
+
| [[2020Li_Workflow]]
| Effect of dose compensation on resolution
+
| Workflow for automatic reconstruction
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Zhao_AnisotropicMagnification]]
+
| [[2020Sader_Facility]]
| Correction of anisotropic magnification
+
| Microscope installation and operation in a facility
 
|-  
 
|-  
  
| Conference
+
| Paper
| [[2016Bajic_Denoising]]
+
| [[2020Schenk_CryoFlare]]
| Denoising and deconvolution of micrographs
+
| CryoFlare, automatic data acquisition
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Jensen_RemovalVesicles]]
+
| [[2020Stabrin_Transphire]]
| Removal of vesicles in membrane proteins
+
| TranSPHIRE: Automated and feedback-optimized on-the-fly processing for cryo-EM
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Bhamre_Denoising]]
+
| [[2020Yokoyama_Good]]
| Denoising by 2D covariance estimation
+
| Deep learning for determining good regions in a grid
 
|-  
 
|-  
 +
  
 
| Paper
 
| Paper
| [[2017Berndsen_EMPH]]
+
| [[2020Weis_Acquisition]]
| Automated hole masking algorithm
+
| Suggestions for high-quality and high-throughput acquisition
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017McLeod_Zorro]]
+
| [[2021Feathers_Superresolution]]
| Movie alignment by Zorro
+
| Effects of superresolution and magnification on final resolution
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Zheng_MotionCorr2]]
+
| [[2021Bouvette_Bisect]]
| Movie alignment by MotionCorr2
+
| Beam image-shift accelerated data acquisition for near-atomic resolution single-particle cryo-electron tomography
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Ouyang_Denoising]]
+
| [[2021Chreifi_FISE]]
| Denoising based on geodesic distance
+
| Rapid tilt-series method for cryo-electron tomography: Characterizing stage behavior during FISE acquisition
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Wu_ContrastEnhancement]]
+
| [[2021Efremov_ComaCorrected]]
| Contrast enhancement
+
| Coma-corrected rapid single-particle cryo-EM data collection on the CRYO ARM 300
 
|-  
 
|-  
  
|}
+
| Paper
 +
| [[2021Herzik_Setup]]
 +
| Setup for parallel illumination
 +
|-
  
=== 2D Alignment ===
+
| 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
 
| Paper
| [[1981Frank_Averaging]]
+
| [[2021Yang_CRIM]]
| 2D averaging and phase residual
+
| Computer readable image markers (CRIM) for correlative microscopy
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1982Saxton_Averaging]]
+
| [[2021Weis_Strategies]]
| 2D averaging using correlation
+
| Strategies for Optimization of Cryogenic Electron Tomography Data Acquisition
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1998Sigworth_ML2D]]
+
| [[2021Wypych_gP2S]]
| Maximum likelihood alignment in 2D
+
| LIMS of microscope sessions
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2003Cong_FRM2D]]
+
| [[2021Yang_CLEM]]
| Fast Rotational Matching in 2D
+
| Automated correlative microscopy
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2005Cong_FRM2D]]
+
| [[2021Yonekura_Hole]]
| Fast Rotational Matching in 2D introduced in a 3D Alignment algorithm
+
| Automated hole detection using YOLO
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2005Scheres_ML2D]]
+
| [[2022Peck_200]]
| Multireference alignment and classification in 2D
+
| High-speed high-resolution data collection on a 200 keV cryo-TEM
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2010Sorzano_CL2D]]
+
| [[2022Peck_Montage]]
| Multireference alignment and classification in 2D
+
| Montage electron tomography
 
|-  
 
|-  
  
| Conference
+
| Paper
| [[2017Anoshina_Correlation]]
+
| [[2022Zhu_ElectronCounting]]
| New correlation measure for aligning images
+
| New algorithm for electron counting at the microscope
 
|-  
 
|-  
  
 
|}
 
|}
  
=== 2D Classification and clustering ===
+
== Single particles ==
 +
 
 +
=== Automatic particle picking ===
  
 
{|
 
{|
  
 
| Paper
 
| Paper
| [[1981VanHeel_MSA]]
+
| [[1982VanHeel_Detection]]
| Multivariate Statistical Analysis
+
| Detection of particles in micrographs
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1984VanHeel_MSA]]
+
| [[2001Nicholson_Review]]
| Multivariate Statistical Analysis
+
| Review on automatic particle picking
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2005Scheres_ML2D]]
+
| [[2001Zhu_Filaments]]
| Multireference alignment and classification in 2D
+
| Automatic identification of filaments in micrographs
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2010Sorzano_CL2D]]
+
| [[2004Sigworth_Detection]]
| Multireference alignment and classification in 2D
+
| Classical detection theory and the cryo-EM particle selection problem
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2011Singer_DiffusionMaps]]
+
| [[2004Volkmann_ParticlePicking]]
| Classification in 2D based on graph analysis of the projections
+
| An approach to automated particle picking from electron micrographs based on reduced representation templates
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2012Yang_ISAC]]
+
| [[2004Wong_ParticlePicking]]
| Iterative Stable Alignment and clustering
+
| Model-based particle picking for cryo-electron microscopy
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2014Sorzano_Outlier]]
+
| [[2004Zhu_Review]]
| Outlier detection in 2D classifications.
+
| Review on automatic particle picking
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2014Zhao_Aspire]]
+
| [[2007Chen_Signature]]
| Fast classification based on rotational invariants and vector diffusion maps
+
| Automatic particle picking program: Signature
 
|-  
 
|-  
 +
  
 
| Paper
 
| Paper
| [[2015Huang_Robust]]
+
| [[2007Woolford_SwarmPS]]
| Robust w-estimators of 2D classes
+
| Automatic particle picking with several criteria, implemented in EMAN Boxer
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Kimanius_Accelerated]]
+
| [[2009Sorzano_MachineLearning]]
| GPU Accelerated image classification and high-resolution refinement
+
| Automatic particle picking based on machine learning of rotational invariants
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Reboul_Stochastic]]
+
| [[2011Arbelaez_Comparison]]
| Stochastic Hill Climbing for calculating 2D classes
+
| Evaluation of the performance of software for automated particle-boxing
|-  
+
|-
  
| Conference
+
| Paper
| [[2017Bhamre_Mahalanobis]]
+
| [[2013Abrishami_MachineLearning]]
| 2D classification using Mahalanobis distance
+
| A pattern matching approach to the automatic selection of particles from low-contrast electron micrographs
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2017Wu_GTM]]
+
| [[2013Hauer_2013]]
| 2D classification using Generative Topographic Mapping
+
| Automatic tilt pair detection in Random Conical Tilt
|-  
+
|-
|}
 
  
=== 3D Alignment ===
+
| Paper
 +
| [[2013Hoang_ParallelGPUPicking]]
 +
| Parallel GPU-accelerated particle picking
 +
|-
  
{|
+
| Paper
 +
| [[2013Shatsky_ParticlePicking]]
 +
| Automated particle correspondence and accurate tilt-axis detection in tilted-image pairs
 +
|- 
  
 
| Paper
 
| Paper
| [[1980Kam_AutoCorrelation]]
+
| [[2013Vargas_ParticleQuality]]
| Reconstruction without angular assignment from autocorrelation function (reference free)
+
| Automatic determination of particle quality
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1986Goncharov_CommonLines]]
+
| [[2014Langlois_ParticlePicking]]
| Angular assignment using common lines (reference free)
+
| Automatic particle picking
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1987VanHeel_CommonLines]]
+
| [[2015Scheres_SemiAutoPicking]]
| Angular assignment using common lines (reference free)
+
| Semi-automated selection of cryo-EM particles
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1988Provencher_Simultaneous]]
+
| [[2016Vilas_AutomaticTilt]]
| Simultaneaous alignment and reconstruction
+
| Automatic identification of image pairs in untilted-tilted micrograph pairs
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1988Radermacher_RCT]]
+
| [[2016Wang_DeepPicker]]
| Random Conical Tilt and Single axis tilt
+
| A deep learning approach for fully automated particle picking
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1988Vogel_Simultaneous]]
+
| [[2017Rickgauer_Detection]]
| Simultaneaous alignment and reconstruction
+
| Picking by correlation
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1990Gelfand_Moments]]
+
| [[2017Zhu_DeepEM]]
| Angular assignment using moments (reference free)
+
| Deep learning approach to picking
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1990Goncharov_Moments]]
+
| [[2018Huber_Helices]]
| Angular assignment using moments (reference free)
+
| Automated tracing of helices
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1990Harauz_Quaternions]]
+
| [[2018Heimowitz_ApplePicker]]
| Use of quaternions to represent rotations
+
| Automated particle picking
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1994Penczek_Real]]
+
| [[2018Sanchez_DeepConsensus]]
| Angular assignment using projection matching in real space
+
| Deep learning consensus of multiple automatic pickers
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1994Radermacher_Radon]]
+
| [[2019Alazzawi_Clustering]]
| Angular assignment in Radon space
+
| Use of clustering algorithms to find particles in micrographs
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1996Penczek_CommonLines]]
+
| [[2019Bepler_Topaz]]
| Angular assignment using common lines (reference free)
+
| Deep learning for particle picking
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2003Rosenthal_DPR]]
+
| [[2019Carrasco_IP]]
| Angular assignment using DPR
+
| Use of standard image processing for particle picking
 +
|-
 +
 
 +
| Conference
 +
| [[2019Li_Deep]]
 +
| Deep learning for particle picking without box size
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2004Sorzano_Wavelet]]
+
| [[2019Wagner_Cryolo]]
| Angular assignment in the wavelet space.
+
| Deep learning for particle picking
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2005Jonic_Splines]]
+
| [[2019Wang_Biobjective]]
| Angular assignment in Fourier space using spline interpolation.
+
| Biobjective function for robust signal detection
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2005Yang_Simultaneous]]
+
| [[2019Zhang_Pixer]]
| Simultaneaous alignment and reconstruction
+
| Deep learning for particle picking
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2006Ogura_SimulatedAnnealing]]
+
| [[2020Sanchez_Cleaner]]
| Angular asignment by simulated annealing
+
| Deep learning for removing particles from the carbon edges, aggregations, contaminations, ...
 
|-  
 
|-  
  
| Paper
+
| Conference
| [[2007Grigorieff_Continuous]]
+
| [[2021Li_PickerOptimizers]]
| Continuous angular assignment in Fourier space
+
| Removal of badly picked particles with Deep Learning
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2010Jaitly_Bayesian]]
+
| [[2021Ohashi_GRIPS]]
| Angular assignment by a Bayesian method and annealing
+
| Two-pass picking with GRIPS
|-
+
|-  
  
| Paper
+
| Conference
| [[2010Sanz_Random]]
+
| [[2022Huang_DenoisingAndPicking]]
| Random model method
+
| Simultaneous denoising and picking with deep learning
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2010Singer_Voting]]
+
| [[2022Olek_Icebreaker]]
| Detecting consistent common lines by voting (reference free)
+
| Ice thickness detection and its use for particle picking
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2011Singer_SDP]]
+
| [[2022Zhang_EPicker]]
| Angular assignment by semidefinite programming and eigenvectors (reference free)
+
| Particle picking based on continual learning
|-
+
|-  
 +
 
 +
|}
  
| Paper
+
=== 2D Preprocessing ===
| [[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
 
| Paper
| [[2013Elmlund H_PRIME]]
+
| [[1978Carrascosa_matching]]
| PRIME: Probabilistic Initial 3D Model Generation for Single-Particle Cryo-Electron Microscopy
+
| Gray values matching by linear transformations
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Wang_LUD]]
+
| [[2003Rosenthal_DPR]]
| Angular assignment by least unsquared deviations (reference free)
+
| Contrast enhancement through DPR
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2014Vargas_RANSAC]]
+
| [[2004Sorzano_Normalization]]
| Initial model using RANSAC (reference free)
+
| Normalization procedures and their statistical properties.
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2015Joubert_Pseudoatoms]]
+
| [[2006Sorzano_Denoising]]
| Initial model based on pseudo-atoms
+
| Strong denoising in wavelet space
 
|-  
 
|-  
  
| Paper
+
| Conference
| [[2015Singer_Kam]]
+
| [[2009Sorzano_Downsampling]]
| Reconstruction without angular assignment from autocorrelation function (reference free)
+
| Differences between the different downsampling schemes
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Sorzano_Significant]]
+
| [[2012Brilot_Movies]]
| Statistical approach to the initial volume estimation (reconstruct significant)
+
| Alignment of beam induced motion in direct detectors
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Cossio_BayesianGPU]]
+
| [[2012Campbell_Movies]]
| GPU implementation of the Bayesian 3D reconstruction approach
+
| Alignment of beam induced motion in direct detectors
 
|-  
 
|-  
  
| Conference
+
| Paper
| [[2016Michels_Heterogeneous]]
+
| [[2012Zhao_Denoising]]
| Initial volume in the presence of heterogeneity
+
| Denoising using an invariant Fourier-Bessel eigenspace
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Pragier_Graph]]
+
| [[2013Norousi_Screening]]
| Graph partitioning approach to angular reconstitution
+
| Screening particles to identify outliers
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Greenberg_CommonLines]]
+
| [[2013Bai_ElectronCounting]]
| Common lines for reference free ab-initio reconstruction
+
| Electron counting and beam induced motion correction
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Sorzano_Highres]]
+
| [[2013Li_ElectronCounting]]
| New algorithm for 3D Reconstruction and alignment with emphasis on significance
+
| Electron counting and beam induced motion correction
 
|-  
 
|-  
 
|}
 
 
=== 3D Reconstruction ===
 
{|
 
  
 
| Paper
 
| Paper
| [[1972Gilbert_SIRT]]
+
| [[2013Shigematsu_Movies]]
| Simultaneous Iterative Reconstruction Technique (SIRT)
+
| Drift correction for movies considering dark field
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1973Herman_ART]]
+
| [[2013Vargas_ParticleQuality]]
| Algebraic Reconstruction Technique (ART)
+
| Automatic determination of particle quality
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1980Kam_SphericalHarmonics]]
+
| [[2014Scheres_Movies]]
| 3D Reconstruction using spherical harmonics
+
| Beam induced motion correction
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1984Andersen_SART]]
+
| [[2015Abrishami_Movies]]
| Simultaneous Algebraic Reconstruction Technique (SART)
+
| Alignment of direct detection device micrographs
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1986Harauz_FBP]]
+
| [[2015Grant_Anisotropic]]
| Exact filters for Filtered Back Projection
+
| Automatic estimation and correction of anisotropic magnification
 
|-  
 
|-  
  
| Chapter
+
| Paper
| [[1992Radermacher_WBP]]
+
| [[2015Grant_OptimalExposure]]
| Exact filters for Weighted Back Projection
+
| Filter movies according to the radiation damage
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1997Zhu_RecCTF]]
+
| [[2015Rubinstein_Alignment]]
| 3D Reconstruction (SIRT like) and simultaneous CTF correction
+
| Frame alignment at the level of particle
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1998Boisset_Uneven]]
+
| [[2015Spear_DoseCompensation]]
| Artifacts in SIRT and WBP under uneven angular distributions
+
| Effect of dose compensation on resolution
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1998Marabini_ART]]
+
| [[2015Zhao_AnisotropicMagnification]]
| Algebraic Reconstruction Technique with blobs (Xmipp)
+
| Correction of anisotropic magnification
 
|-  
 
|-  
  
| Paper
+
| Conference
| [[2001Sorzano_Uneven]]
+
| [[2016Bajic_Denoising]]
| Free parameter selection under uneven angular distributions
+
| Denoising and deconvolution of micrographs
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2005Sorzano_Parameters]]
+
| [[2016Jensen_RemovalVesicles]]
| Free parameter selection for optimizing multiple tasks
+
| Removal of vesicles in membrane proteins
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2008Sorzano_Constraints]]
+
| [[2016Bhamre_Denoising]]
| Mass, surface, positivity and symmetry constraints for real-space algorithms
+
| Denoising by 2D covariance estimation
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2009Bilbao_ParallelART]]
+
| [[2017Berndsen_EMPH]]
| Efficient parallelization of ART
+
| Automated hole masking algorithm
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2011Li_GradientFlow]]
+
| [[2017McLeod_Zorro]]
| Regularized 3D Reconstruction by Gradient Flow
+
| Movie alignment by Zorro
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2011Vonesch_Wavelets]]
+
| [[2017Zheng_MotionCorr2]]
| Fast wavelet-based 3D reconstruction
+
| Movie alignment by MotionCorr2
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2012Gopinath_ShapeRegularization]]
+
| [[2018Ouyang_Denoising]]
| Regularized 3D Reconstruction by Shape information
+
| Denoising based on geodesic distance
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2012Kucukelbir_adaptiveBasis]]
+
| [[2018Wu_ContrastEnhancement]]
| 3D reconstruction in an adaptive basis promoting sparsity
+
| Contrast enhancement
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2012Sindelar_NoiseReduction]]
+
| [[2019Zivanov_BayesianBIM]]
| Optimal noise reduction in 3D reconstructions
+
| Bayesian correction of beam induced movement
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Elmlund H_PRIME]]
+
| [[2020Bepler_TopazDenoise]]
| PRIME: Probabilistic Initial 3D Model Generation for Single-Particle Cryo-Electron Microscopy
+
| Preprocessing of micrographs for better picking
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Lyumkis_Optimod]]
+
| [[2020Chung_2SDR]]
| Construction of initial volumes with Optimod
+
| PCA to denoise particles
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Wang FIRM]]
+
| [[2020Chung_Prepro]]
| Fast 3D reconstruction in Fourier domain
+
| Preprocessing of particles for better alignment
 
|-  
 
|-  
  
| Paper
+
| Conference
| [[2014Kunz_SART_OS]]
+
| [[2020Huang_SuperResolution]]
| Simultaneous ART with OS
+
| Deep learning superresolution combination of frames
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Abrishami_Fourier]]
+
| [[2020Palovcak_noise2noise]]
| 3D Reconstruction in Fourier space
+
| Noise2noise denoising of micrographs
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Dvornek_SubspaceEM]]
+
| [[2020Strelak_FlexAlign]]
| Fast Maximum a posteriori
+
| Continuous deformation model for aligning movie frames
 
|-  
 
|-  
  
| Paper
+
| Conference
| [[2015Moriya_Bayesian]]
+
| [[2021Fan_Denoising]]
| Bayesian approach to suppress limited angular artifacts
+
| Particle denoising using vector diffusion maps
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Xu_GeometricFlow]]
+
| [[2022Heymann_ProgressiveSSNR]]
| Multi-scale geometric flow
+
| Progressive SSNR to assess quality and radiation damage
 
|-  
 
|-  
  
| Arxiv
+
|}
| [[2016Ye_Cohomology]]
+
 
| Cohomology properties of 3D reconstruction
+
=== 2D Alignment ===
|-
+
 
 +
{|
  
 
| Paper
 
| Paper
| [[2017Punjani_CryoSPARC]]
+
| [[1981Frank_Averaging]]
| CryoSPARC
+
| 2D averaging and phase residual
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Punjani_CryoSPARCTheory]]
+
| [[1982Saxton_Averaging]]
| Theory related to CryoSPARC
+
| 2D averaging using correlation
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Sorzano_SurveyIterative]]
+
| [[1998Sigworth_ML2D]]
| Survey of iterative reconstruction methods for EM
+
| Maximum likelihood alignment in 2D
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Reboul_Simple]]
+
| [[2003Cong_FRM2D]]
| Ab initio reconstruction with Simple
+
| Fast Rotational Matching in 2D
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Bartesaghi_Refinement]]
+
| [[2005Cong_FRM2D]]
| Refinement of CTF, frame weight and alignment for high resolution reconstruction
+
| Fast Rotational Matching in 2D introduced in a 3D Alignment algorithm
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Sorzano_Highres]]
+
| [[2005Scheres_ML2D]]
| New algorithm for 3D Reconstruction and alignment with emphasis on significance
+
| Multireference alignment and classification in 2D
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Zhu_Ewald]]
+
| [[2016Aguerrebere_Limits]]
| 3D Reconstruction with Ewald sphere correction
+
| Fundamental limits of 2D translational alignment
 
|-  
 
|-  
  
|}
+
| Paper
 +
| [[2010Sorzano_CL2D]]
 +
| Multireference alignment and classification in 2D
 +
|-
  
=== 3D Heterogeneity ===
+
| Conference
 
+
| [[2017Anoshina_Correlation]]
{|
+
| New correlation measure for aligning images
 +
|-
  
 
| Paper
 
| Paper
| [[2004White_Size]]
+
| [[2019Radermacher_Correlation]]
| Heterogeneity classification of differently sized images
+
| On the properties of cross correlation for the alignment of images
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2006Penczek_Bootstrap]]
+
| [[2020Lederman_representation]]
| 3D heterogeneity through bootstrap
+
| A representation theory perspective of alignment and classification
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007Leschziner_Review]]
+
| [[2020Marshall_Invariants]]
| Review of 3D heterogeneity handling algorithms
+
| Recovery of an image from its invariants
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007Scheres_ML3D]]
+
| [[2021Chen_Fast]]
| Maximum Likelihood alignment and classification in 3D
+
| Fast alignment through Power Spectrum
 
|-  
 
|-  
  
| Paper
+
| Conference
| [[2009Spahn_Bootstrap]]
+
| [[2021Chung_CryoRALIB]]
| 3D heterogeneity through bootstrap
+
| Image alignment acceleration
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2010Elmlund_AbInitio]]
+
| [[2021Heimowitz_Centering]]
| Solving the initial volume problem with multiple conformations
+
| Centering noisy images
 
|-  
 
|-  
 +
 +
|}
 +
 +
=== 2D Classification and clustering ===
 +
 +
{|
  
 
| Paper
 
| Paper
| [[2010Shatsky_MultiVariate]]
+
| [[1981VanHeel_MSA]]
 
| Multivariate Statistical Analysis
 
| Multivariate Statistical Analysis
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2012Scheres_Bayesian]]
+
| [[1984VanHeel_MSA]]
| A Bayesian view on cryo-EM structure determination
+
| Multivariate Statistical Analysis
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2012Zheng_Covariance]]
+
| [[2005Scheres_ML2D]]
| Estimation of the volume covariance
+
| Multireference alignment and classification in 2D
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Wang_MLVariance]]
+
| [[2010Sorzano_CL2D]]
| Maximum Likelihood estimate of the map variance
+
| Multireference alignment and classification in 2D
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Lyumkis D_FREALIGN]]
+
| [[2011Singer_DiffusionMaps]]
| Likelihood-based classification of cryo-EM images using FREALIGN.
+
| Classification in 2D based on graph analysis of the projections
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2014Jin_NMA]]
+
| [[2012Yang_ISAC]]
| Continuous heterogeneity through Normal Mode Analysis
+
| Iterative Stable Alignment and clustering
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2014Dashti_Brownian]]
+
| [[2014Sorzano_Outlier]]
| Continuous heterogeneity through Brownian trajectories
+
| Outlier detection in 2D classifications.
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2014Chen_Migration]]
+
| [[2014Zhao_Aspire]]
| Particle migration analysis in 3D classification
+
| Fast classification based on rotational invariants and vector diffusion maps
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Anden_Covariance]]
+
| [[2015Huang_Robust]]
| 3D Covariance matrix estimation for heterogeneity
+
| Robust w-estimators of 2D classes
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Bai_Focused]]
+
| [[2016Kimanius_Accelerated]]
| Focused classification  
+
| GPU Accelerated image classification and high-resolution refinement
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Katsevich_Covariance]]
+
| [[2016Reboul_Stochastic]]
| 3D Covariance matrix estimation for heterogeneity
+
| Stochastic Hill Climbing for calculating 2D classes
 
|-  
 
|-  
  
| Paper
+
| Conference
| [[2015Klaholz_MRA]]
+
| [[2017Bhamre_Mahalanobis]]
| Multivariate Statistical Analysis of Jackknife and Bootstrapping on random subsets
+
| 2D classification using Mahalanobis distance
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Liao_Covariance]]
+
| [[2017Wu_GTM]]
| Estimation of the 3D covariance from 2D projections
+
| 2D classification using Generative Topographic Mapping
 
|-  
 
|-  
  
| Paper
+
| Conference
| [[2015Tagare_Direct]]
+
| [[2018Boumal_SinglePass]]
| Direct reconstruction of PCA components
+
| Single pass classification
 
|-  
 
|-  
  
| Paper
+
| Conference
| [[2016Gong_Mechanical]]
+
| [[2018Shuo_Network]]
| Mechanical model for macromolecules
+
| 2D Clustering by network metrics
 
|-  
 
|-  
  
| Paper
+
| Conference
| [[2016Rawson_Movement]]
+
| [[2020Miolane_VAEGAN]]
| Movement and flexibility
+
| 2D Analysis by deep learning
 
|-  
 
|-  
  
| Paper
+
| Conference
| [[2016Shan_Multibody]]
+
| [[2021Rao_Wasserstein]]
| Multibody refinement
+
| Wasserstein K-Means for Clustering Tomographic Projections
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Sorzano_StructMap]]
+
| [[2022Wang_Spectral]]
| Sorting a discrete set of conformational states
+
| 2D classification with spectral clustering
 
|-  
 
|-  
  
| Paper
+
|}
| [[2016Sorzano_Strain]]
+
 
| Calculate local stretches, strains and rotations from two conformational states
+
=== 3D Alignment ===
|-
+
 
 +
{|
  
 
| Paper
 
| Paper
| [[2017Punjani_CryoSPARC]]
+
| [[1980Kam_AutoCorrelation]]
| CryoSPARC
+
| Reconstruction without angular assignment from autocorrelation function (reference free)
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Schillbach_Warpcraft]]
+
| [[1986Goncharov_CommonLines]]
| Warpcraft: 3D Reconstruction in the presence of continuous heterogeneity
+
| Angular assignment using common lines (reference free)
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Anden_Covariance]]
+
| [[1987VanHeel_CommonLines]]
| Structural Variability from Noisy Tomographic Projections
+
| Angular assignment using common lines (reference free)
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Haselbach_FreeEnergy]]
+
| [[1988Provencher_Simultaneous]]
| Analysis of the free energy landscape through PCA
+
| Simultaneaous alignment and reconstruction
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Nakane_MultiBody]]
+
| [[1988Radermacher_RCT]]
| Structural Variability through multi-body refinement
+
| Random Conical Tilt and Single axis tilt
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Solernou_FFEA]]
+
| [[1988Vogel_Simultaneous]]
| Fluctuating Finite Element Analysis, continuum approach to Molecular Dynamics
+
| Simultaneaous alignment and reconstruction
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2019Sorzano_Review]]
+
| [[1990Gelfand_Moments]]
| Review of cotinuous heterogeneity biophysics
+
| Angular assignment using moments (reference free)
 
|-  
 
|-  
 
|}
 
 
=== Validation ===
 
 
{|
 
  
 
| Paper
 
| Paper
| [[2008Stagg_TestBed]]
+
| [[1990Goncharov_Moments]]
| Effect of voltage, dosis, number of particles and Euler jumps on resolution
+
| Angular assignment using moments (reference free)
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2011Henderson]]
+
| [[1990Harauz_Quaternions]]
| Tilt Validation
+
| Use of quaternions to represent rotations
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2011Read]]
+
| [[1994Penczek_Real]]
| Validation of PDBs
+
| Angular assignment using projection matching in real space
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2012Henderson]]
+
| [[1994Radermacher_Radon]]
| EM Map Validation
+
| Angular assignment in Radon space
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Cossio_Bayesian]]
+
| [[1996Penczek_CommonLines]]
| EM Map Validation in a probabilistic setting
+
| Angular assignment using common lines (reference free)
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Chen_NoiseSubstitution]]
+
| [[2003Rosenthal_DPR]]
| Noise substitution at high resolution for measuring overfitting
+
| Angular assignment using DPR
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Ludtke_Validation]]
+
| [[2004Sorzano_Wavelet]]
| Structural validation, example of the Calcium release channel
+
| Angular assignment in the wavelet space.
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Murray_Validation]]
+
| [[2005Jonic_Splines]]
| Validation of a 3DEM structure through a particular example
+
| Angular assignment in Fourier space using spline interpolation.
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2014Russo_StatisticalSignificance]]
+
| [[2005Yang_Simultaneous]]
| EM Map Validation through the statistical significance of the tilt-pair angular assignment
+
| Simultaneaous alignment and reconstruction
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2014Stagg_Reslog]]
+
| [[2006Ogura_SimulatedAnnealing]]
| EM Map Validation through the resolution evolution with the number of particles
+
| Angular asignment by simulated annealing
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2014Wasilewski_Tilt]]
+
| [[2007Grigorieff_Continuous]]
| Web implementation of the tilt pair validation
+
| Continuous angular assignment in Fourier space
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Heymann_Alignability]]
+
| [[2010Jaitly_Bayesian]]
| EM Map Validation through the resolution of reconstructions from particles and noise
+
| Angular assignment by a Bayesian method and annealing
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2015Oliveira_FreqLimited]]
+
| [[2010Sanz_Random]]
| Comparison of gold standard and frequency limited optimization
+
| Random model method
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2015Wriggers_Secondary]]
+
| [[2010Singer_Voting]]
| Validation by secondary structure
+
| Detecting consistent common lines by voting (reference free)
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2016Degiacomi_IM]]
+
| [[2011Singer_SDP]]
| Comparison of Ion Mobility data and EM volumes
+
| Angular assignment by semidefinite programming and eigenvectors (reference free)
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2016Kim_SAXS]]
+
| [[2012Giannakis_Scattering]]
| Comparison of SAXS data and EM projections
+
| Construction of an initial volume, reference free, by graph analysis of the projections
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2016Rosenthal_Review]]
+
| [[2012Shkolnisky_Sync]]
| Review of validation methods
+
| Angular assignment by synchronization of rotations (reference free)
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2016Vargas_Alignability]]
+
| [[2013Elmlund H_PRIME]]
| Validation by studying the tendency of an angular assignment to cluster in the projection space
+
| PRIME: Probabilistic Initial 3D Model Generation for Single-Particle Cryo-Electron Microscopy
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Monroe_PDBRefinement]]
+
| [[2013Wang_LUD]]
| Validation by comparison to a refined PDB
+
| Angular assignment by least unsquared deviations (reference free)
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2018Heymann_Bsoft]]
+
| [[2014Vargas_RANSAC]]
| Map validation using Bsoft
+
| Initial model using RANSAC (reference free)
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2018Heymann_Challenge]]
+
| [[2015Joubert_Pseudoatoms]]
| A summary of the assessments of the 3D Map Challenge
+
| Initial model based on pseudo-atoms
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Jonic_Gaussian]]
+
| [[2015Singer_Kam]]
| Assessment of sets of volumes by pseudoatomic structures
+
| Reconstruction without angular assignment from autocorrelation function (reference free)
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Naydenova_AngularDistribution]]
+
| [[2015Sorzano_Significant]]
| Evaluating the angular distribution of a 3D reconstruction
+
| Statistical approach to the initial volume estimation (reconstruct significant)
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Pages_Symmetry]]
+
| [[2016Cossio_BayesianGPU]]
| Looking for a symmetry axis in a PDB
+
| GPU implementation of the Bayesian 3D reconstruction approach
 
|-  
 
|-  
  
| Paper
+
| Conference
| [[2018Pintilie_SSE]]
+
| [[2016Michels_Heterogeneous]]
| Evaluating the quality of SSE and side chains
+
| Initial volume in the presence of heterogeneity
 
|-  
 
|-  
 
|}
 
 
=== Resolution ===
 
 
{|
 
  
 
| Paper
 
| Paper
| [[1986Harauz_FBP]]
+
| [[2016Pragier_Graph]]
| Fourier Shell Correlation
+
| Graph partitioning approach to angular reconstitution
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1987Unser_SSNR]]
+
| [[2017Greenberg_CommonLines]]
| 2D Spectral Signal to Noise Ratio
+
| Common lines for reference free ab-initio reconstruction
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2002Penczek_SSNR]]
+
| [[2018Sorzano_Highres]]
| 3D Spectral Signal to Noise Ratio for Fourier based algorithms
+
| New algorithm for 3D Reconstruction and alignment with emphasis on significance
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2003Rosenthal_DPR]]
+
| [[2018Sorzano_Swarm]]
| Review of the FSC and establishment of a new threshold
+
| Consensus of several initial volumes by swarm optimization
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2005Unser_SSNR]]
+
| [[2019Zehni_Joint]]
| 3D Spectral Signal to Noise Ratio for any kind of algorithms
+
| Continuous angular refinement and reconstruction
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2005VanHeel_FSC]]
+
| [[2019Zehni_Joint]]
| Establishment of a new threshold for FSC
+
| Continuous angular refinement and reconstruction
 
|-  
 
|-  
 +
  
 
| Paper
 
| Paper
| [[2007Sousa_AbInitio]]
+
| [[2020Sharon_NonUniformKam]]
| Resolution measurement on neighbour Fourier voxels
+
| Reconstruction and angular distribution estimation without angular assignment (reference free)
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2014Kucukelbir_Local]]
+
| [[2020Xie_Network]]
| Quantifying the local resolution of cryo-EM density maps
+
| Angular assignment considering a network of assignments
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Pintilie_Probabilistic]]
+
| [[2021Jimenez_DeepAlign]]
| Probabilistic models and resolution
+
| Angular alignment using deep learning
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Sorzano_FourierProperties]]
+
| [[2021Kojima_Preferred]]
| Statistical properties of resolution measures defined in Fourier space
+
| Identification of preferred orientations
 
|-  
 
|-  
  
 
| Conference
 
| Conference
| [[2018Avramov_DeepLearning]]
+
| [[2021Nashed_CryoPoseNet]]
| Deep learning classification of volumes into low, medium and high resolution
+
| CryoPoseNet: Angular alignment with deep learning
 
|-  
 
|-  
  
| Paper
+
| Conference
| [[2018Kim_FourierError]]
+
| [[2021Zhong_CryoDRGN2]]
| Comparison between a gold standard and a reconstruction
+
| CryoDRGN2: Angular alignment with deep learning
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Yang_Multiscale]]
+
| [[2022Lu_SphericalEmbeddings]]
| Resolution from a multiscale spectral analysis
+
| Angular assignment through common lines and spherical embeddings
 
|-  
 
|-  
  
 
|}
 
|}
  
=== Sharpening of high resolution information ===
+
=== 3D Reconstruction ===
 
{|
 
{|
 
| Paper
 
| [[2003Rosenthal_DPR]]
 
| Contrast restoration and map sharpening
 
|-
 
  
 
| Paper
 
| Paper
| [[2008Fernandez_Bfactor]]
+
| [[1972Gilbert_SIRT]]
| Bfactor determination and restoration
+
| Simultaneous Iterative Reconstruction Technique (SIRT)
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Fiddy_SaxtonAlgorithm]]
+
| [[1973Herman_ART]]
| Phase retrieval or extension
+
| Algebraic Reconstruction Technique (ART)
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2014Kishchenko_SphericalDeconvolution]]
+
| [[1980Kam_SphericalHarmonics]]
| Spherical deconvolution
+
| 3D Reconstruction using spherical harmonics
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Spiegel_VISDEM]]
+
| [[1984Andersen_SART]]
| Visualization improvement by the use of pseudoatomic profiles
+
| Simultaneous Algebraic Reconstruction Technique (SART)
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Jonic_Pseudoatoms]]
+
| [[1986Harauz_FBP]]
| Approximation with pseudoatoms
+
| Exact filters for Filtered Back Projection
 
|-  
 
|-  
  
| Paper
+
| Chapter
| [[2016Jonic_Denoising]]
+
| [[1992Radermacher_WBP]]
| Denoising and high-frequency boosting by pseudoatom approximation
+
| Exact filters for Weighted Back Projection
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Jakobi_LocScale]]
+
| [[1997Zhu_RecCTF]]
| Sharpening based on an atomic model
+
| 3D Reconstruction (SIRT like) and simultaneous CTF correction
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2019Ramlaul_Filtering]]
+
| [[1998Boisset_Uneven]]
| Local agreement filtering (denoising)
+
| Artifacts in SIRT and WBP under uneven angular distributions
 
|-  
 
|-  
 
|}
 
 
=== CTF estimation and restoration ===
 
 
{|
 
  
 
| Paper
 
| Paper
| [[1982Schiske_Correction]]
+
| [[1998Marabini_ART]]
| CTF correction for tilted objects
+
| Algebraic Reconstruction Technique with blobs (Xmipp)
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1988Toyoshima_Model]]
+
| [[2001Sorzano_Uneven]]
| CTF estimation
+
| Free parameter selection under uneven angular distributions
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1995Frank_Wiener]]
+
| [[2005Sorzano_Parameters]]
| CTF correction using Wiener filter
+
| Free parameter selection for optimizing multiple tasks
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1996Skoglund_MaxEnt]]
+
| [[2008Sorzano_Constraints]]
| CTF correction with Maximum Entropy
+
| Mass, surface, positivity and symmetry constraints for real-space algorithms
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1996Zhou_Model]]
+
| [[2009Bilbao_ParallelART]]
| CTF model and user interface for manual fitting
+
| Efficient parallelization of ART
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1997Fernandez_AR]]
+
| [[2011Li_GradientFlow]]
| PSD estimation using periodogram averaging and AR models
+
| Regularized 3D Reconstruction by Gradient Flow
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1997Penczek_Wiener]]
+
| [[2011Vonesch_Wavelets]]
| CTF correction using Wiener filter
+
| Fast wavelet-based 3D reconstruction
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1997Stark_Deconvolution]]
+
| [[2012Gopinath_ShapeRegularization]]
| CTF correction using deconvolution
+
| Regularized 3D Reconstruction by Shape information
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1997Zhu_RecCTF]]
+
| [[2012Kucukelbir_adaptiveBasis]]
| CTF correction and reconstruction
+
| 3D reconstruction in an adaptive basis promoting sparsity
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2000DeRosier_EwaldCorrection]]
+
| [[2012Sindelar_NoiseReduction]]
| CTF correction considering the Ewald sphere
+
| Optimal noise reduction in 3D reconstructions
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2000Jensen_TiltedCorrection]]
+
| [[2013Elmlund H_PRIME]]
| CTF correction considering tilt in backprojection
+
| PRIME: Probabilistic Initial 3D Model Generation for Single-Particle Cryo-Electron Microscopy
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2001Saad_CTFEstimate]]
+
| [[2013Lyumkis_Optimod]]
| CTF estimation
+
| Construction of initial volumes with Optimod
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2003Huang_CTFEstimate]]
+
| [[2013Wang FIRM]]
| CTF estimation
+
| Fast 3D reconstruction in Fourier domain
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2003Mindell_CTFTILT]]
+
| [[2014Kunz_SART_OS]]
| CTF estimation for tilted micrographs
+
| Simultaneous ART with OS
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2003Sander_MSA]]
+
| [[2015Abrishami_Fourier]]
| CTF estimation through MSA classification of PSDs
+
| 3D Reconstruction in Fourier space
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2003Velazquez_ARMA]]
+
| [[2015Dvornek_SubspaceEM]]
| PSD and CTF estimation using ARMA models
+
| Fast Maximum a posteriori
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2004Sorzano_IDR]]
+
| [[2015Moriya_Bayesian]]
| CTF restoration and reconstruction with Iterative Data Refinement
+
| Bayesian approach to suppress limited angular artifacts
|-
 
 
 
| Conference
 
| [[2004Wan_CTF]]
 
| Spatially variant CTF
 
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2004Zubelli_Chahine]]
+
| [[2015Xu_GeometricFlow]]
| CTF restoration and reconstruction with Chahine's multiplicative method
+
| Multi-scale geometric flow
 
|-  
 
|-  
  
| Conference
+
| Arxiv
| [[2005Dubowy_SpaceVariant]]
+
| [[2016Ye_Cohomology]]
| CTF correction when this is space variant
+
| Cohomology properties of 3D reconstruction
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2005Mallick_ACE]]
+
| [[2017Punjani_CryoSPARC]]
| CTF estimation
+
| CryoSPARC
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2006Wolf_Ewald]]
+
| [[2017Punjani_CryoSPARCTheory]]
| CTF correction considering Ewald sphere
+
| Theory related to CryoSPARC
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007Jonic_EnhancedPSD]]
+
| [[2017Sorzano_SurveyIterative]]
| PSD enhancement for better identification of Thon rings; Vitreous ice diffracts in Thon rings
+
| Survey of iterative reconstruction methods for EM
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007Philippsen_Model]]
+
| [[2018Bartesaghi_Refinement]]
| CTF Model for tilted specimens
+
| Refinement of CTF, frame weight and alignment for high resolution reconstruction
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007Sorzano_CTF]]
+
| [[2018Hu_ParticleFilter]]
| CTF estimation using enhanced PSDs
+
| A particle filter framework for 3D reconstruction
 
|-  
 
|-  
  
| Paper
+
| Conference
| [[2009Sorzano_Sensitivity]]
+
| [[2018Levin_Kam]]
| Error sensitivity of the CTF models, non-uniqueness of the CTF parameters
+
| Ab initio reconstruction by autocorrelation analysis
 +
|-
 +
 
 +
| Conference
 +
| [[2018Michels_RBF]]
 +
| Ab-initio reconstruction with radial basis functions
 
|-  
 
|-  
  
| Paper
 
| [[2010Jiang2010_CTFCorrection]]
 
| Amplitude correction method
 
|-
 
  
 
| Paper
 
| Paper
| [[2010Kasantsev_CTFCorrection]]
+
| [[2018Reboul_Simple]]
| Mathematical foundations of Kornberg and Jensen method
+
| Ab initio reconstruction with Simple
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2010Leong_CTFCorrection]]
+
| [[2018Sorzano_Highres]]
| Correction for spatially variant CTF
+
| New algorithm for 3D Reconstruction and alignment with emphasis on significance
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2011Glaeser_Coma]]
+
| [[2018Sorzano_Swarm]]
| The effect of coma at high-resolution
+
| Consensus of several initial volumes by swarm optimization
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2011Mariani_Tilted]]
+
| [[2018Zhu_Ewald]]
| CTF simulation and correction of tilted specimens
+
| 3D Reconstruction with Ewald sphere correction
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2011Sindelar_Wiener]]
+
| [[2019Gomez_Initial]]
| CTF correction using a modified version of Wiener filter
+
| Construction of initial models
 
|-  
 
|-  
  
| Paper
+
| Master
| [[2011Voortman_Tilted]]
+
| [[2019Havelkova_Regularization]]
| CTF correction for tilted specimen
+
| Regularization methods in 3D reconstruction
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2012Voortman_VaryingCTF]]
+
| [[2019Wilkinson_Scales]]
| Correcting a spatially varying CTF
+
| Combining data acquired at different scales
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Vargas_FastDef]]
+
| [[2020Alazzawi_Auto]]
| Fast defocus
+
| Automatic full processing of micrographs to yield a 3D reconstruction
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Rohou_CTFFind4]]
+
| [[2020Pan_TV]]
| CTF Find 4
+
| 3D Reconstruction with total variation regularization
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Sheth_CTFquality]]
+
| [[2020Punjani_NonUniform]]
| Visualization and quality assessment of CTF
+
| Non-uniform refinement
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Zhang_GCTF]]
+
| [[2020Ramlaul_Sidesplitter]]
| gCTF
+
| Local filtering along the reconstruction iterations
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Su_GoCTF]]
+
| [[2020Xie_Automatic]]
| goCTF, CTF for tilted specimens
+
| Automatic 3D reconstruction from projections
 
|-  
 
|-  
  
|}
+
| Conference
 +
| [[2020Venkatakrishnan_MBIR]]
 +
| Model based image reconstruction
 +
|-
  
=== Segmentation ===
+
| 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
 
| Paper
| [[2006Baker_segmentation]]
+
| [[2021Gupta_CryoGAN]]
| Segmentation of molecular subunits
+
| 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
 
|-  
 
|-  
  
| Conference
+
| Paper
| [[2017Nissenson_VolumeCut]]
+
| [[2021Sorzano_Uneven]]
| Segmentation of an EM volume using an atomic model
+
| Algorithmic robustness to uneven angular distributions
 
|-  
 
|-  
  
 
|}
 
|}
  
=== Fitting and docking ===
+
=== 3D Heterogeneity ===
  
 
{|
 
{|
  
 
| Paper
 
| Paper
| [[1999Volkmann_Fitting]]
+
| [[2004White_Size]]
| Fitting in real space
+
| Heterogeneity classification of differently sized images
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2001Baker_Review]]
+
| [[2006Penczek_Bootstrap]]
| Review of protein structure prediction
+
| 3D heterogeneity through bootstrap
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2001Jones_Review]]
+
| [[2007Leschziner_Review]]
| Review of protein structure prediction
+
| Review of 3D heterogeneity handling algorithms
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2003Kovacs_FRM3D]]
+
| [[2007Scheres_ML3D]]
| Fast Rotational Alignment of two EM maps
+
| Maximum Likelihood alignment and classification in 3D
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2004Tama_NMA1]]
+
| [[2008Herman_Graph]]
| Flexible fitting with Normal Modes (I)
+
| Classification by graph partitioning
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2004Tama_NMA2]]
+
| [[2009Spahn_Bootstrap]]
| Flexible fitting with Normal Modes (II)
+
| 3D heterogeneity through bootstrap
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2005Velazquez_Superfamilies]]
+
| [[2010Elmlund_AbInitio]]
| Recognition of the superfamily folding in medium-high resolution volumes
+
| Solving the initial volume problem with multiple conformations
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007DeVries_Haddock]]
+
| [[2010Shatsky_MultiVariate]]
| Docking with Haddock 2.0
+
| Multivariate Statistical Analysis
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007Kleywegt_QualityControl]]
+
| [[2012Scheres_Bayesian]]
| Quality control and validation of fitting
+
| A Bayesian view on cryo-EM structure determination
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2012Biswas_Secondary]]
+
| [[2012Zheng_Covariance]]
| Secondary structure determination in EM volumes
+
| Estimation of the volume covariance
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2012Velazquez_Constraints]]
+
| [[2013Wang_MLVariance]]
| Multicomponent fitting by using constraints from other information sources
+
| Maximum Likelihood estimate of the map variance
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Chapman MS_Atomicmodeling]]
+
| [[2013Lyumkis D_FREALIGN]]
| Atomic modeling of cryo-electron microscopy reconstructions--joint refinement of model and imaging parameters
+
| Likelihood-based classification of cryo-EM images using FREALIGN.
|-  
+
|-
  
 
| Paper
 
| Paper
| [[2013Esquivel_Modelling]]
+
| [[2014Chen_Migration]]
| Review on modelling (secondary structure, fitting, ...)
+
| Particle migration analysis in 3D classification
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Lopez_Imodfit]]
+
| [[2014Dashti_Brownian]]
| Fitting based on vibrational analysis
+
| Continuous heterogeneity through Brownian trajectories
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Nogales_3DEMLoupe]]
+
| [[2014Schwander_manifold]]
| Normal Mode Analysis of reconstructed volumes
+
| Continuous heterogeneity through Manifold Analysis  
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2014AlNasr_Secondary]]
+
| [[2014Jin_NMA]]
| Identification of secondary structure elements in EM volumes
+
| Continuous heterogeneity through Normal Mode Analysis
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2014Politis_MassSpect]]
+
| [[2015Anden_Covariance]]
| Integration of mass spectroscopy information
+
| 3D Covariance matrix estimation for heterogeneity
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2014Rey_MassSpect]]
+
| [[2015Bai_Focused]]
| Integration of mass spectroscopy information
+
| Focused classification
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2014Villa_Review]]
+
| [[2015Katsevich_Covariance]]
| Review of atomic fitting into EM volumes
+
| 3D Covariance matrix estimation for heterogeneity
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Barad_EMRinger]]
+
| [[2015Klaholz_MRA]]
| Validation of hybrid models
+
| Multivariate Statistical Analysis of Jackknife and Bootstrapping on random subsets
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Bettadapura_PF2Fit]]
+
| [[2015Liao_Covariance]]
| Fast rigid fitting of PDBs into EM maps
+
| Estimation of the 3D covariance from 2D projections
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Carrillo_CapsidMaps]]
+
| [[2015Tagare_Direct]]
| Analysis of virus capsids using Google Maps
+
| Direct reconstruction of PCA components
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Hanson_Continuum]]
+
| [[2016Gong_Mechanical]]
| Modelling assemblies with continuum mechanics
+
| Mechanical model for macromolecules
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Lopez_Review]]
+
| [[2016Rawson_Movement]]
| Review of structural modelling from EM data
+
| Movement and flexibility
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Schroeder_Hybrid]]
+
| [[2016Shan_Multibody]]
| Review on model building
+
| Multibody refinement
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Tamo_Dynamics]]
+
| [[2016Sorzano_StructMap]]
| Dynamics in integrative modeling
+
| Sorting a discrete set of conformational states
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Sorzano_AtomsToVoxels]]
+
| [[2016Sorzano_Strain]]
| Accurate conversion of an atomic model into a voxel density volume
+
| Calculate local stretches, strains and rotations from two conformational states
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Joseph_Evolution]]
+
| [[2017Punjani_CryoSPARC]]
| Evolutionary constraints for the fitting of atomic models into density maps
+
| CryoSPARC
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Joseph_Refinement]]
+
| [[2017Schillbach_Warpcraft]]
| Refinement of atomic models in high-resolution EM reconstructions and using Flex-EM
+
| Warpcraft: 3D Reconstruction in the presence of continuous heterogeneity
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Segura_3Diana]]
+
| [[2018Anden_Covariance]]
| Validation of hybrid models
+
| Structural Variability from Noisy Tomographic Projections
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Singharoy_MDFF]]
+
| [[2018Haselbach_FreeEnergy]]
| Construction of hybrid models driven by EM density and molecular dynamics
+
| Analysis of the free energy landscape through PCA
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Wang_Rosetta]]
+
| [[2018Nakane_MultiBody]]
| Construction of hybrid models driven by EM density using Rosetta
+
| Structural Variability through multi-body refinement
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Chen_CoarseGraining]]
+
| [[2019Serna_Review]]
| Coarse graining of EM volumes
+
| Review of classification tools
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Joseph_Metrics]]
+
| [[2018Solernou_FFEA]]
| Metrics analysis for the comparison of structures
+
| Fluctuating Finite Element Analysis, continuum approach to Molecular Dynamics
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Hryc_WeightedAtoms]]
+
| [[2019Sorzano_Review]]
| Construction of hybrid models by locally weighting the different atoms
+
| Review of continuous heterogeneity biophysics
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Matsumoto_Distribution]]
+
| [[2019Zhang_Local]]
| Estimating the distribution of conformations of atomic models
+
| Local variability and covariance
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Michel_ContactPrediction]]
+
| [[2020Dashti_Landscape]]
| Structure prediction by contact prediction
+
| Retrieving functional pathways from single particle snapshots
 
|-  
 
|-  
  
| Paper
+
| Conference
| [[2017Miyashita_EnsembleFitting]]
+
| [[2020Gupta_MultiCryoGAN]]
| Ensemble fitting using Molecular Dynamics
+
| Reconstruction of continuously heterogeneous structures with adversarial networks
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Turk_ModelBuilding]]
+
| [[2020Harastani_NMA]]
| Tutorial on model building and protein visualization
+
| Using Scipion for analyzing local heterogeneity with normal modes
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Wang_PartialCharges]]
+
| [[2020Maji_Propagation]]
| Appearance of partial charges in EM maps
+
| Propagation of conformational coordinates across angular space
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Wlodawer]]
+
| [[2020Moscovich_DiffusionMaps]]
| Comparison of X-ray and EM high resolution structures
+
| Heterogeneity analysis by diffusion maps and spectral volumes
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Cassidy_review]]
+
| [[2020Seitz_Polaris]]
| Review of methods for hybrid modeling
+
| Analysis of energy landscapes to find minimal action paths
 
|-  
 
|-  
  
| Paper
+
| Conference
| [[2018Chen_SudeChains]]
+
| [[2020Zhong_CryoDRGN]]
| A comparison of side chains between X-ray and EM maps
+
| CryoDRGN to analyze the continuous heterogeneity by CryoEM
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Kawabata_Pseudoatoms]]
+
| [[2020Verbeke_Separation]]
| Modelling the EM map with Gaussian pseudoatoms
+
| Heterogeneity analysis by comparing common lines
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Kovacs_Medium]]
+
| [[2021Chen_GM]]
| Modelling of medium resolution EM maps
+
| Deep learning-based mixed-dimensional Gaussian mixture model for characterizing variability
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Neumann_validation]]
+
| [[2021Giraldo_cryoBIFE]]
| Validation of fitting, resolution assessment and quality of fit
+
| A Bayesian approach to extracting free‑energy profiles
 
|-  
 
|-  
  
| Paper
+
| Conference
| [[2018Terwilliger_map_to_model]]
+
| [[2021Hamitouche_NMADL]]
| Phenix map_to_model, automatic modelling of EM volumes
+
| Continuous heterogeneity analysis through normal modes and deep learning
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Wang_MD]]
+
| [[2021Herreros_Zernikes3D]]
| Constructing atomic models using molecular dynamics
+
| Continuous heterogeneity analysis through Zernikes 3D
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Xia_MVPENM]]
+
| [[2021Kazemi_Enrich]]
| Multiscale Normal Mode Analysis
+
| ENRICH: A fast method to improve the quality of flexible macromolecular reconstructions
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Yu_Atomic]]
+
| [[2021Matsumoto_DEFmap]]
| Constructing atomic models using existing tools
+
| Prediction of RMSF of Molecular Dynamics from a CryoEM map using deep learning
 
|-  
 
|-  
  
|}
+
| Chapter
 
+
| [[2021Nakasako_Landscape]]
=== Books and reviews ===
+
| Estimation of free-energy landscape from images
 
 
{|
 
 
 
| Book
 
| [[1980Herman_Tomography]]
 
| General book on tomography
 
|-  
 
 
 
| Book
 
| [[1988Kak_Tomography]]
 
| General book on tomography
 
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2000Tao_Review]]
+
| [[2021Punjani_3DVA]]
| Review of single particles
+
| 3D Variability analysis from images
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2000VanHeel_Review]]
+
| [[2021Sorzano_PCA]]
| Review of single particles
+
| PCA is limited to low-resolution
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2002Frank_Review]]
+
| [[2021Zhong_CryoDRGN]]
| Review of single particles
+
| CryoDRGN to analyze the continuous heterogeneity by CryoEM
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2002Schmid_Review]]
+
| [[2022Ecoffet_MorphOT]]
| Review of single particles
+
| More physically plausible morphing between two states
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2004Henderson_Review]]
+
| [[2022Gomez_Hierarchical]]
| Review of electron microscopy
+
| Hierarchical classification of particles
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2004Subramaniam_Review]]
+
| [[2022Rabuck_Quant]]
| Review of single particles
+
| Workflow for discrete heterogeneity analysis
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2005Steven_Review]]
+
| [[2022Skalidis_Endogenous]]
| Review of electron microscopy
+
| AI tools to recognize proteins in cellular fractions
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2006Fernandez_Review]]
+
| [[2022Zhou_Data]]
| Review of electron microscopy
+
| Determination of the number of discrete 3D classes
 
|-  
 
|-  
  
| Book
+
|}
| [[2006Frank_book]]
+
 
| Book covering all aspects of electron microscopy of single particles
+
=== Validation ===
|-
+
 
 +
{|
  
 
| Paper
 
| Paper
| [[2006Sorzano_Review]]
+
| [[2008Stagg_TestBed]]
| Review of optimization problems in electron microscopy
+
| Effect of voltage, dosis, number of particles and Euler jumps on resolution
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007Leschziner_Review]]
+
| [[2011Henderson]]
| Review of 3D heterogeneity handling algorithms
+
| Tilt Validation
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007Sorzano_Review]]
+
| [[2011Read]]
| Review of the image processing steps
+
| Validation of PDBs
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2008Fanelli_ImageFormation]]
+
| [[2012Henderson]]
| Review on the image formation model from the electron waves and open inverse-problems in Electron Tomography
+
| EM Map Validation
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2008Fernandez_HPCReview]]
+
| [[2013Cossio_Bayesian]]
| High performance computing in electron cryomicroscopy
+
| EM Map Validation in a probabilistic setting
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2008Jonic_Review]]
+
| [[2013Chen_NoiseSubstitution]]
| Comparison between electron tomography and single particles
+
| Noise substitution at high resolution for measuring overfitting
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2008Mueller_Review]]
+
| [[2013Ludtke_Validation]]
| Review of Electron microscopy
+
| Structural validation, example of the Calcium release channel
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2008Taylor_Review]]
+
| [[2013Murray_Validation]]
| Review of Electron microscopy
+
| Validation of a 3DEM structure through a particular example
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2010DeRosier_Review]]
+
| [[2014Russo_StatisticalSignificance]]
| Personal account of how 3DEM developed in the early days
+
| EM Map Validation through the statistical significance of the tilt-pair angular assignment
 
|-  
 
|-  
  
| Chapter
+
| Paper
| [[2012Sorzano_Review]]
+
| [[2014Stagg_Reslog]]
| Review of single particle analysis using Xmipp
+
| EM Map Validation through the resolution evolution with the number of particles
 
|-  
 
|-  
  
| Chapter
+
| Paper
| [[2012Devaux_Protocol]]
+
| [[2014Wasilewski_Tilt]]
| Protocols for performing single particle analysis
+
| Web implementation of the tilt pair validation
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2014Bai_Review]]
+
| [[2015Heymann_Alignability]]
| Recent advances in cryo-EM
+
| EM Map Validation through the resolution of reconstructions from particles and noise
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Carazo_Review]]
+
| [[2015Oliveira_FreqLimited]]
| Review of the reconstruction process
+
| Comparison of gold standard and frequency limited optimization
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Cheng_Review]]
+
| [[2015Rosenthal_Review]]
| A primer to Single Particle Cryo-EM
+
| Review of validation methods
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Cheng_Reviewb]]
+
| [[2015Wriggers_Secondary]]
| Single Particle Cryo-EM at crystallographic resolution
+
| Validation by secondary structure
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Elmlund_Review]]
+
| [[2016Degiacomi_IM]]
| Recent advances in cryo-EM
+
| Comparison of Ion Mobility data and EM volumes
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Henderson_Review]]
+
| [[2016Kim_SAXS]]
| Recent advances in cryo-EM
+
| Comparison of SAXS data and EM projections
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Nogales_Review]]
+
| [[2016Rosenthal_Review]]
| Recent advances in cryo-EM
+
| Review of validation methods
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Schroeder_Review]]
+
| [[2016Vargas_Alignability]]
| Review of advances in the electron microscope
+
| Validation by studying the tendency of an angular assignment to cluster in the projection space
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015VanDenBedem_Integrative]]
+
| [[2017Monroe_PDBRefinement]]
| Review of integrative structural biology
+
| Validation by comparison to a refined PDB
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Wu_Review]]
+
| [[2018Afonine_Phenix]]
| Review of advances in cryo-EM
+
| Tools in Phenix for the validation of EM maps
 +
|-  
 +
 
 +
| Paper
 +
| [[2018Heymann_Bsoft]]
 +
| Map validation using Bsoft
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Carroni_CryoEM]]
+
| [[2018Heymann_Challenge]]
| Review of advances in Cryo-EM
+
| A summary of the assessments of the 3D Map Challenge
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Egelman_CryoEM]]
+
| [[2018Jonic_Gaussian]]
| Review of advances in Cryo-EM
+
| Assessment of sets of volumes by pseudoatomic structures
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Eisenstein_CryoEM]]
+
| [[2018Naydenova_AngularDistribution]]
| News feature on the Method of the Year
+
| Evaluating the angular distribution of a 3D reconstruction
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016FernandezLeiro_Review]]
+
| [[2018Pages_Symmetry]]
| Review of EM
+
| Looking for a symmetry axis in a PDB
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Glaeser_HowGood]]
+
| [[2018Pintilie_SSE]]
| How good can cryo-EM become?
+
| Evaluating the quality of SSE and side chains
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Jonic_PseudoAtoms]]
+
| [[2019Herzik_Multimodel]]
| Review of the applications of the use of pseudoatoms in EM
+
| Local and global quality by multi-model fitting
 
|-  
 
|-  
  
| Chapter
+
| Paper
| [[2016Mio_Review]]
+
| [[2020Chen_Atomic]]
| Overview of the process to obtain EM reconstructions
+
| Validation of the atomic models derived from CryoEM
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Jonic_Review]]
+
| [[2020Cossio_CrossValidation]]
| A review of computational ways to handle heterogeneity
+
| Need for cross validation
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Nogales_Review]]
+
| [[2020Ortiz_CrossValidation]]
| Review of advances in cryo-EM
+
| Cross validation for SPA
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Subramaniam_Review]]
+
| [[2020Sazzed_helices]]
| Why cryo-EM is now suitable for crystallographic journals
+
| Validation of helix quality
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Vinothkumar_Review]]
+
| [[2020Stojkovic_PTM]]
| Historical review and current limitations
+
| Validation of post-translational modifications
 
|-  
 
|-  
  
| Report
+
| Paper
| [[2017Brezinski_Nobel]]
+
| [[2020Tiwari_PixelSize]]
| Scientific background on the Nobel Prize in Chemistry 2017
+
| Fine determination of the pixel size
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Cheng_review]]
+
| [[2021Mendez_Graph]]
| Why CryoEM became so hot
+
| Identification of incorrectly oriented particles
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Danev_Review]]
+
| [[2021Pintilie_Validation]]
| Review of the use of phase plates in EM
+
| Review of map validation approaches
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Elmlund_Review]]
+
| [[2021Olek_FDR]]
| Review of the main current difficulties of EM
+
| Cryo-EM Map–Based Model Validation Using the False Discovery Rate Approach
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Frank_Review]]
+
| [[2022Sorzano_Bias]]
| Historical review of EM
+
| Bias, variance, gold-standard and overfitting in SPA
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Frank_TimeResolved]]
+
| [[2022Waarshamanage_EMDA]]
| Review of time-resolved of EM
+
| Validation of models fitted into CryoEM maps
 
|-  
 
|-  
 +
 +
|}
 +
 +
=== Resolution ===
 +
 +
{|
  
 
| Paper
 
| Paper
| [[2017Jonic_Review]]
+
| [[1986Harauz_FBP]]
| Review of computational methods to analyze conformational variability
+
| Fourier Shell Correlation
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Merino_DrugEM]]
+
| [[1987Unser_SSNR]]
| Applications of EM for drug design
+
| 2D Spectral Signal to Noise Ratio
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Rawson_Limitations]]
+
| [[2002Penczek_SSNR]]
| Limitations of EM for drug design
+
| 3D Spectral Signal to Noise Ratio for Fourier based algorithms
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Sorzano_FourierProperties]]
+
| [[2003Rosenthal_DPR]]
| Review of statistical properties of resolution measures defined in Fourier space
+
| Review of the FSC and establishment of a new threshold
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Sorzano_SurveyIterative]]
+
| [[2005Unser_SSNR]]
| Survey of iterative reconstruction methods for EM
+
| 3D Spectral Signal to Noise Ratio for any kind of algorithms
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Bruggeman_Crowdsourcing]]
+
| [[2005VanHeel_FSC]]
| Exploring crowdsourcing for EM image processing
+
| Establishment of a new threshold for FSC
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Cheng_Review]]
+
| [[2007Sousa_AbInitio]]
| Review of EM and future ahead
+
| Resolution measurement on neighbour Fourier voxels
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Cossio_ML]]
+
| [[2014Kucukelbir_Local]]
| Review of Maximum Likelihood methods
+
| Quantifying the local resolution of cryo-EM density maps
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Grimes_Crystallography]]
+
| [[2016Pintilie_Probabilistic]]
| Review of X-ray crystallography and its relationship to EM
+
| Probabilistic models and resolution
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Murata_Review]]
+
| [[2017Sorzano_FourierProperties]]
| Review of EM for structure dynamics
+
| Statistical properties of resolution measures defined in Fourier space
 
|-  
 
|-  
  
| Paper
+
| Conference
| [[2018Quentin_Biomedical]]
+
| [[2018Avramov_DeepLearning]]
| Review of EM as a tool for biomedical research
+
| Deep learning classification of volumes into low, medium and high resolution
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Scapin_DrugDiscovery]]
+
| [[2018Carugo_BFactors]]
| Review of EM as a tool for drug discovery
+
| How large can B-factors be in protein crystals
 
|-  
 
|-  
  
| Paper
+
| Conference
| [[2018Vilas_ImageProcessing]]
+
| [[2018Kim_FourierError]]
| Review of the recent developments in image processing for single particle analysis
+
| Comparison between a gold standard and a reconstruction
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018vonLoeffelholz_VPP]]
+
| [[2018Rupp_Problems]]
| Comparison of Volta Phase Plate reconstructions close to focus and with defocus
+
| Problems of resolution as a proxy number for map quality
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Eisenstein_DrugDesigners]]
+
| [[2018Vilas_MonoRes]]
| Drug designers embrace cryo-EM
+
| Local resolution by monogenic signals
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2019Sorzano_Review]]
+
| [[2018Yang_Multiscale]]
| Review of cotinuous heterogeneity biophysics
+
| Resolution from a multiscale spectral analysis
 
|-  
 
|-  
 
|}
 
 
=== Software ===
 
 
{|
 
  
 
| Paper
 
| Paper
| [[1996Frank_Spider]]
+
| [[2019Avramov_DeepLearning]]
| Spider
+
| Deep learning classification of volumes into low, medium and high resolution
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1996VanHeel_Imagic]]
+
| [[2019Heymann_Statistics]]
| Imagic
+
| SNR, FSC, and related statistics
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1999Lutdke_Eman]]
+
| [[2019Ramirez_DeepRes]]
| Eman
+
| Resolution determination by deep learning
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2004Sorzano_Xmipp]]
+
| [[2020Baldwin_Lyumkis_SCF]]
| Xmipp
+
| Resolution attenuation through non-uniform Fourier sampling
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007Baldwin_AngularTransformations]]
+
| [[2020Beckers_Permutation]]
| The Transform Class in SPARX and EMAN2
+
| Permutation tests for the FSC
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007Heymann_Bsoft]]
+
| [[2020Penczek_mFSC]]
| Bsoft
+
| Modified FSC to avoid mask induced artifacts
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007Grigorieff_Frealign]]
+
| [[2020Vilas_MonoDir]]
| Frealign
+
| Local and directional resolution
 
|-  
 
|-  
  
 +
|}
 +
 +
=== Sharpening of high resolution information ===
 +
{|
 +
 
| Paper
 
| Paper
| [[2008Scheres_XmippProtocols]]
+
| [[2003Rosenthal_DPR]]
| Xmipp Protocols
+
| Contrast restoration and map sharpening
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2008Shaikh_SpiderProtocols]]
+
| [[2008Fernandez_Bfactor]]
| Spider Protocols
+
| Bfactor determination and restoration
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2012Wriggers_SitusConventions]]
+
| [[2013Fiddy_SaxtonAlgorithm]]
| Conventions and workflows in Situs
+
| Phase retrieval or extension
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013DeLaRosa_Xmipp30]]
+
| [[2014Kishchenko_SphericalDeconvolution]]
| Xmipp 3.0
+
| Spherical deconvolution
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Cianfrocco_Cloud]]
+
| [[2015Spiegel_VISDEM]]
| Software execution in the cloud
+
| Visualization improvement by the use of pseudoatomic profiles
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Cheng_MRC2014]]
+
| [[2016Jonic_Pseudoatoms]]
| Extensions to MRC file format
+
| Approximation with pseudoatoms
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013DeLaRosa_Scipion]]
+
| [[2016Jonic_Denoising]]
| Scipion
+
| Denoising and high-frequency boosting by pseudoatom approximation
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Scheres_Relion]]
+
| [[2017Jakobi_LocScale]]
| Tutorial on the use of Relion
+
| Sharpening based on an atomic model
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Grigorieff_Frealign]]
+
| [[2019Ramlaul_Filtering]]
| Tutorial on the use of Frealign
+
| Local agreement filtering (denoising)
 +
|-
 +
 
 +
| Conference
 +
| [[2020Mullick_SuperResolution]]
 +
| Superresolution from a map
 
|-  
 
|-  
 +
  
 
| Paper
 
| Paper
| [[2017Moriya_Sphire]]
+
| [[2020Ramirez_LocalDeblur]]
| Tutorial on the use of Sphire
+
| Local deblur (local Wiener filter)
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Cianfrocco_cloud]]
+
| [[2020Terwilliger_density]]
| CryoEM Cloud Tools
+
| Density modification of CryoEM maps
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Grant_cisTEM]]
+
| [[2020Vilas_Bfactor]]
| cisTEM
+
| Global B-factor correction does not represent macromolecules
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018McLeod_MRCZ]]
+
| [[2021Beckers_Interpretation]]
| MRC Compression format
+
| Improvements from the raw reconstruction to a structure to model
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Zivanov_Relion3]]
+
| [[2021Kaur_LocSpiral]]
| Relion 3
+
| LocSpiral, LocBsharpen, LocBfactor
 
|-  
 
|-  
  
|}
+
| Paper
 +
| [[2021Fernandez_Adjustment]]
 +
| Map adjustment for subtraction, consensus and sharpening
 +
|-
  
== Electron tomography ==
+
| Paper
 
+
| [[2021Sanchez_DeepEMhancer]]
=== Image preprocessing ===
+
| Deep learning algorithm for volume restoration
 
+
|-
{|
 
  
 
| Paper
 
| Paper
| [[2015Yan_thickness]]
+
| [[2022Vargas_tubular]]
| Determination of thickness, tilt and electron mean free path
+
| Map enhancement by multiscale tubular filter
 
|-  
 
|-  
  
 
|}
 
|}
  
=== Image alignment ===
+
=== CTF estimation and restoration ===
  
 
{|
 
{|
  
 
| Paper
 
| Paper
| [[1982Guckenberger_commonOrigin]]
+
| [[1982Schiske_Correction]]
| Determination of a common origin in the micrographs of titl series in three-dimensional electron microscopy
+
| CTF correction for tilted objects
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1992Lawrence_leastSquares]]
+
| [[1988Toyoshima_Model]]
| Least squares solution of the alignment problem
+
| CTF estimation
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1995Penczek_dual]]
+
| [[1995Frank_Wiener]]
| Dual tilt alignment
+
| CTF correction using Wiener filter
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1996Owen_alignmentQuality]]
+
| [[1996Skoglund_MaxEnt]]
| Automatic alignment without fiducial markers and evaluation of alignment quality
+
| CTF correction with Maximum Entropy
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1998Grimm_normalization]]
+
| [[1996Zhou_Model]]
| Discussion of several gray level normalization methods for electron tomography
+
| CTF model and user interface for manual fitting
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2001Brandt_Automatic1]]
+
| [[1997Fernandez_AR]]
| Automatic alignment without fiducial markers
+
| PSD estimation using periodogram averaging and AR models
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2001Brandt_Automatic2]]
+
| [[1997Penczek_Wiener]]
| Automatic alignment with fiducial markers
+
| CTF correction using Wiener filter
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2006Winkler_alignment]]
+
| [[1997Stark_Deconvolution]]
| Marker-free alignment and refinement
+
| CTF correction using deconvolution
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2006Castano_alignment]]
+
| [[1997Zhu_RecCTF]]
| Alignment with non-perpendicularity
+
| CTF correction and reconstruction
|-
 
 
 
| Paper
 
| [[2007Castano_alignment]]
 
| Fiducial-less alignment of cryo-sections
 
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2009Sorzano_alignment]]
+
| [[2000DeRosier_EwaldCorrection]]
| Marker-free alignment and refinement
+
| CTF correction considering the Ewald sphere
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2010Cantele_dualAlignment]]
+
| [[2000Jensen_TiltedCorrection]]
| Alignment of dual series
+
| CTF correction considering tilt in backprojection
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2014Tomonaga_Automatic]]
+
| [[2001Saad_CTFEstimate]]
| Automatic alignment of tilt series using the projection themselves
+
| CTF estimation
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2014Han_Automatic]]
+
| [[2003Huang_CTFEstimate]]
| Automatic alignment of tilt series using SIFT features
+
| CTF estimation
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Han_Automatic]]
+
| [[2003Mindell_CTFTILT]]
| Automatic alignment of tilt series using fiducials
+
| CTF estimation for tilted micrographs
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Mastronarde_Automatic]]
+
| [[2003Sander_MSA]]
| Automatic alignment and reconstruction of tilt series in IMOD
+
| CTF estimation through MSA classification of PSDs
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Fernadez_Beam]]
+
| [[2003Velazquez_ARMA]]
| Image alignment considering beam induced motion
+
| PSD and CTF estimation using ARMA models
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Han_Fast]]
+
| [[2004Sorzano_IDR]]
| Automatic alignment using fiducial markers
+
| CTF restoration and reconstruction with Iterative Data Refinement
 +
|-
 +
 
 +
| Conference
 +
| [[2004Wan_CTF]]
 +
| Spatially variant CTF
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2019Han_Dual]]
+
| [[2004Zubelli_Chahine]]
| Automatic alignment using fiducial markers in dual tilt series
+
| CTF restoration and reconstruction with Chahine's multiplicative method
 
|-  
 
|-  
  
|}
+
| Conference
 
+
| [[2005Dubowy_SpaceVariant]]
=== CTF estimation and restoration ===
+
| CTF correction when this is space variant
 
+
|-
{|
 
  
 
| Paper
 
| Paper
| [[2003Winkler_CTF]]
+
| [[2005Mallick_ACE]]
| Focus gradient correction in electron tomography
+
| CTF estimation
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2006Fernandez_CTF]]
+
| [[2006Wolf_Ewald]]
| CTF determination and correction in electron tomography
+
| CTF correction considering Ewald sphere
 
|-  
 
|-  
 
  
 
| Paper
 
| Paper
| [[2009Zanetti_CTF]]
+
| [[2007Jonic_EnhancedPSD]]
| CTF determination and correction in electron tomography
+
| PSD enhancement for better identification of Thon rings; Vitreous ice diffracts in Thon rings
 
|-  
 
|-  
 
  
 
| Paper
 
| Paper
| [[2009Xiong_CTF]]
+
| [[2007Philippsen_Model]]
| CTF determination and correction for low dose tomographic tilt series
+
| CTF Model for tilted specimens
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2012Eibauer_CTF]]
+
| [[2007Sorzano_CTF]]
| CTF determination and correction
+
| CTF estimation using enhanced PSDs
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Bharat_CTFCorrectedSubtomogramAveraging]]
+
| [[2009Sorzano_Sensitivity]]
| Subtomogram averaging with CTF correction using a Bayesian prior
+
| Error sensitivity of the CTF models, non-uniqueness of the CTF parameters
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Turonova_3DCTF]]
+
| [[2010Jiang2010_CTFCorrection]]
| 3D CTF Correction
+
| Amplitude correction method
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Kunz_3DCTF]]
+
| [[2010Kasantsev_CTFCorrection]]
| 3D CTF Correction
+
| Mathematical foundations of Kornberg and Jensen method
 
|-  
 
|-  
 
|}
 
 
=== 3D reconstruction ===
 
 
{|
 
  
 
| Paper
 
| Paper
| [[1972Gilbert_SIRT]]
+
| [[2010Leong_CTFCorrection]]
| Simultaneous Iterative Reconstruction Technique (SIRT)
+
| Correction for spatially variant CTF
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1973Herman_ART]]
+
| [[2011Glaeser_Coma]]
| Algebraic Reconstruction Technique (ART)
+
| The effect of coma at high-resolution
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1984Andersen_SART]]
+
| [[2011Mariani_Tilted]]
| Simultaneous Algebraic Reconstruction Technique (SART)
+
| CTF simulation and correction of tilted specimens
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1992Radermacher_WBP]]
+
| [[2011Sindelar_Wiener]]
| Weighted Backprojection in electron tomography
+
| CTF correction using a modified version of Wiener filter
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1997Marabini_reconstruction]]
+
| [[2011Voortman_Tilted]]
| Iterative reconstruction in electron tomography
+
| CTF correction for tilted specimen
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2002Fernandez_reconstruction]]
+
| [[2012Voortman_VaryingCTF]]
| Iterative reconstruction in electron tomography
+
| Correcting a spatially varying CTF
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007Radermacher_WBP]]
+
| [[2013Vargas_FastDef]]
| Weighted Backprojection in electron tomography
+
| Fast defocus
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2008Fernandez_CARP]]
+
| [[2014Penczek_CTER]]
| Component Averaged Row Projections (CARP)
+
| Estimation of the CTF errors
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2012Herman General Superiorization]]
+
| [[2015Rohou_CTFFind4]]
| Superiorization: an optimization heuristic for medical physics
+
| CTF Find 4
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2012Zhang_IPET_FETR]]
+
| [[2015Sheth_CTFquality]]
| IPET and FETR, a reconstruction algorithm for single molecule tomography
+
| Visualization and quality assessment of CTF
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Goris_SIRT_TV_DART]]
+
| [[2016Zhang_GCTF]]
| Combination of SIRT, Total Variation and Discrete ART to reconstruct and segment at the same time
+
| gCTF
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Briegel A_Challenge]]
+
| [[2018Su_GoCTF]]
| The challenge of determining handedness in electron tomography and the use of DNA origami gold nanoparticle helices as molecular standards
+
| goCTF, CTF for tilted specimens
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Messaoudi_EnergyFiltered]]
+
| [[2020Heimowitz_Aspire]]
| 3D Reconstruction of Energy-Filtered TEM
+
| CTF determination in Aspire
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Deng_ICON]]
+
| [[2020Zivanov_HighOrder]]
| 3D Reconstruction with missing information restoration
+
| Estimation of high order aberrations
 
|-  
 
|-  
  
| Paper
+
|}
| [[2016Guay_Compressed]]
+
 
| 3D Reconstruction using compressed sensing
+
=== Segmentation ===
|-
 
 
 
|}
 
  
=== Noise reduction ===
 
 
{|
 
{|
  
 
| Paper
 
| Paper
| [[2001Frangakis_NAD]]
+
| [[2006Baker_segmentation]]
| Noise reduction with Nonlinear Anisotropic Diffusion
+
| Segmentation of molecular subunits
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2003Fernandez_AND]]
+
| [[2010Pintilie_segger]]
| Anisotropic nonlinear diffusion for electron tomography
+
| Segmentation of molecular subunits
 
|-  
 
|-  
  
| Paper
+
| Conference
| [[2003Jiang_Bilateral]]
+
| [[2017Nissenson_VolumeCut]]
| Bilateral denoising filter in electron microscopy
+
| Segmentation of an EM volume using an atomic model
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2005Fernandez_AND]]
+
| [[2019Beckers_FDR]]
| Anisotropic nonlinear denoising in electron tomography
+
| Segmentation of the protein using False Discovery Rate
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007Heide_median]]
+
| [[2020Beckers_FDR]]
| Iterative median filtering in electron tomography
+
| Segmentation of the protein using False Discovery Rate (GUI)
|-
 
 
 
| 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
 
| Paper
| [[2014Kovacik_wedgeArtefacts]]
+
| [[2020Farkas_MemBlob]]
| Removal of wedge artefacts
+
| Segmentation of membrane in membrane embedded proteins
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2014Maiorca_beadArtefacts]]
+
| [[2020Terashi_MainMastSeg]]
| Removal of gold bead artefacts
+
| Segmentation of proteins into domains
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Trampert_Inpainting]]
+
| [[2021He_EMNUSS]]
| Removal of the missing wedge by inpainting
+
| EMNUSS: Identification of secondary structure in CryoEM maps with deep learning
|-
 
 
 
| Paper
 
| [[2018Moreno_TomoEED]]
 
| Fast Anisotropic Diffusion
 
 
|-  
 
|-  
  
 
|}
 
|}
  
=== Segmentation ===
+
=== Fitting and docking ===
  
 
{|
 
{|
  
 
| Paper
 
| Paper
| [[2002Frangakis_Eigenanalysis]]
+
| [[1999Volkmann_Fitting]]
| Segmentation using eigenvector analysis.
+
| Fitting in real space
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2002Volkmann_Watershed]]
+
| [[2001Baker_Review]]
| Segmentation using watershed transform.
+
| Review of protein structure prediction
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2003Bajaj_BoundarySegmentation]]
+
| [[2001Jones_Review]]
| Segmentation based on fast marching.
+
| Review of protein structure prediction
|-
 
 
 
| Paper
 
| [[2005Cyrklaff_Thresholding]]
 
| Segmentation using optimal thresholding.
 
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007Lebbink_TemplateMatching]]
+
| [[2003Kovacs_FRM3D]]
| Segmentation using template matching.
+
| Fast Rotational Alignment of two EM maps
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007Sandberg_OrientationFields]]
+
| [[2004Tama_NMA1]]
| Segmentation using orientation fields.
+
| Flexible fitting with Normal Modes (I)
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007Sandberg_SegmentationReview]]
+
| [[2004Tama_NMA2]]
| Review on segmentation in electron tomography.
+
| Flexible fitting with Normal Modes (II)
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2008Garduno_FuzzySegmentation]]
+
| [[2005Velazquez_Superfamilies]]
| Segmentation using fuzzy set theory principles.
+
| Recognition of the superfamily folding in medium-high resolution volumes
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2009Lebbink_TemplateMatching2]]
+
| [[2007DeVries_Haddock]]
| Segmentation using template matching.
+
| Docking with Haddock 2.0
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2012RubbiyaAli_EdgeDetection]]
+
| [[2007Kleywegt_QualityControl]]
| Parameter-Free Segmentation of Macromolecular Structures.
+
| Quality control and validation of fitting
 
|-  
 
|-  
  
| Conference
+
| Paper
| [[2015Xu_TemplateMatching]]
+
| [[2008Rusu_Interpolation]]
| Detection of macromolecular complexes with a reduced representation of the templates.
+
| Biomolecular pleiomorphism probed by spatial interpolation of coarse models
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Ali_RAZA]]
+
| [[2012Biswas_Secondary]]
| Automated segmentation of tomograms
+
| Secondary structure determination in EM volumes
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Chen_Annotation]]
+
| [[2012Velazquez_Constraints]]
| Automated annotation of tomograms
+
| Multicomponent fitting by using constraints from other information sources
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Tasel_ActiveContours]]
+
| [[2013Chapman MS_Atomicmodeling]]
| Segmentation with active contours
+
| Atomic modeling of cryo-electron microscopy reconstructions--joint refinement of model and imaging parameters
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Xu_DeepLearning]]
+
| [[2013Esquivel_Modelling]]
| Finding proteins in tomograms using deep learning
+
| Review on modelling (secondary structure, fitting, ...)
 
|-  
 
|-  
 
  
 
| Paper
 
| Paper
| [[2018Zeng_DeepLearning]]
+
| [[2013Lopez_Imodfit]]
| Mining features in Electron Tomographt by deep learning
+
| Fitting based on vibrational analysis
 
|-  
 
|-  
 
|}
 
 
=== Resolution ===
 
{|
 
  
 
| Paper
 
| Paper
| [[2005Cardone_Resolution]]
+
| [[2013Nogales_3DEMLoupe]]
| Resolution criterion for electron tomography
+
| Normal Mode Analysis of reconstructed volumes
 
|-  
 
|-  
  
| Chapter
+
| Paper
| [[2007Penczek_Resolution]]
+
| [[2014AlNasr_Secondary]]
| Review of resolution criteria for electron tomography
+
| Identification of secondary structure elements in EM volumes
 
|-  
 
|-  
 
  
 
| Paper
 
| Paper
| [[2015Diebolder_ConicalFSC]]
+
| [[2014Politis_MassSpect]]
| Conical Fourier Shell Correlation
+
| Integration of mass spectroscopy information
 
|-  
 
|-  
  
 +
| Paper
 +
| [[2014Rey_MassSpect]]
 +
| Integration of mass spectroscopy information
 +
|-
  
|}
+
| Paper
 +
| [[2014Villa_Review]]
 +
| Review of atomic fitting into EM volumes
 +
|-
  
=== Subtomogram analysis ===
+
| Paper
 
+
| [[2015Barad_EMRinger]]
{|
+
| Validation of hybrid models
 +
|-
  
 
| Paper
 
| Paper
| [[2000Bohm_Template]]
+
| [[2015Bettadapura_PF2Fit]]
| Macromolecule finding by template matching
+
| Fast rigid fitting of PDBs into EM maps
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2002Frangakis_Template]]
+
| [[2015Carrillo_CapsidMaps]]
| Macromolecule finding by template matching
+
| Analysis of virus capsids using Google Maps
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2006Nickell_Review]]
+
| [[2015Hanson_Continuum]]
| Review of macromolecule finding by template matching (Visual Proteomics)
+
| Modelling assemblies with continuum mechanics
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007Best_Review]]
+
| [[2015Lopez_Review]]
| Review of Localization of Protein Complexes by Pattern Recognition
+
| Review of structural modelling from EM data
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007Forster_Review]]
+
| [[2015Schroeder_Hybrid]]
| Review of structure determination by subtomogram averaging
+
| Review on model building
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2008Forster_Classification]]
+
| [[2015Tamo_Dynamics]]
| Classification of subtomograms using constrained correlation
+
| Dynamics in integrative modeling
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2008Bartesaghi_Classification]]
+
| [[2015Sorzano_AtomsToVoxels]]
| Classification and averaging of subtomograms
+
| Accurate conversion of an atomic model into a voxel density volume
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2008Schmid_Averaging]]
+
| [[2016Joseph_Evolution]]
| Alignment and averaging of subtomograms
+
| Evolutionary constraints for the fitting of atomic models into density maps
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2010Amat_Averaging]]
+
| [[2016Joseph_Refinement]]
| Alignment and averaging of subtomograms exploiting thresholding in Fourier space
+
| Refinement of atomic models in high-resolution EM reconstructions using Flex-EM
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2013Chen_Averaging]]
+
| [[2016Murshudov_Refinement]]
| Fast alignment of subtomograms using spherical harmonics
+
| Refinement of atomic models in high-resolution EM reconstructions
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2013Kuybeda_Averaging]]
+
| [[2016Segura_3Diana]]
| Alignment and averaging of subtomograms using the nuclear norm of the cluster
+
| Validation of hybrid models
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2013Shatsky_Averaging]]
+
| [[2016Singharoy_MDFF]]
| Alignment and averaging of subtomograms with constrained cross-correlation
+
| Construction of hybrid models driven by EM density and molecular dynamics
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2014Chen_Autofocus]]
+
| [[2016Wang_Rosetta]]
| Subtomogram averaging and classification with special attention to differences
+
| Construction of hybrid models driven by EM density using Rosetta
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2014Yu_ReferenceBias]]
+
| [[2017Chen_CoarseGraining]]
| Scoring the reference bias
+
| Coarse graining of EM volumes
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2014Voortman_LimitingFactors]]
+
| [[2017Joseph_Metrics]]
| Limiting factors of subtomogram averaging
+
| Metrics analysis for the comparison of structures
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2015Bharat_CTFCorrectedSubtomogramAveraging]]
+
| [[2017Hryc_WeightedAtoms]]
| Subtomogram averaging with CTF correction using a Bayesian prior
+
| Construction of hybrid models by locally weighting the different atoms
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Yu_ReferenceBias]]
+
| [[2017Matsumoto_Distribution]]
| Scoring the reference bias
+
| Estimating the distribution of conformations of atomic models
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2016Bharat_Relion]]
+
| [[2017Michel_ContactPrediction]]
| Subtomogram averaging with Relion
+
| Structure prediction by contact prediction
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2016Song_MatrixNorm]]
+
| [[2017Miyashita_EnsembleFitting]]
| Matrix norm minimization for tomographic reconstruction and alignment
+
| Ensemble fitting using Molecular Dynamics
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2017Castano_ParticlePicking]]
+
| [[2017Turk_ModelBuilding]]
| Particle picking in tomograms for subtomogram averaging
+
| Tutorial on model building and protein visualization
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2017Frazier_Tomominer]]
+
| [[2017Wang_PartialCharges]]
| TomoMiner a software platform for large-scale subtomogram analysis
+
| Appearance of partial charges in EM maps
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2018Himes_emClarity]]
+
| [[2017Wlodawer]]
| emClarity for subtomogram averaging
+
| Comparison of X-ray and EM high resolution structures
|-
+
|-  
  
|}
+
| Paper
 
+
| [[2018Cassidy_review]]
=== Single particle tomography ===
+
| Review of methods for hybrid modeling
 
+
|-
{|
 
  
 
| Paper
 
| Paper
| [[2012Bartesaghi_Constrained]]
+
| [[2018Chen_SudeChains]]
| 3D reconstruction by imposing geometrical constraints
+
| A comparison of side chains between X-ray and EM maps
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2015Galaz_SingleParticleTomography]]
+
| [[2018Kawabata_Pseudoatoms]]
| Set of tools for Single Particle Tomography in EMAN2
+
| Modelling the EM map with Gaussian pseudoatoms
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Galaz_SingleParticleTomography]]
+
| [[2018Kovacs_Medium]]
| Alignment algorithms and CTF correction
+
| Modelling of medium resolution EM maps
 
|-  
 
|-  
 
|}
 
 
=== Books and reviews ===
 
 
{|
 
  
 
| Paper
 
| Paper
| [[2000Baumeister_Review]]
+
| [[2018Neumann_validation]]
| Review of electron tomography
+
| Validation of fitting, resolution assessment and quality of fit
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2003Koster_Review]]
+
| [[2018Terwilliger_map_to_model]]
| Review of electron tomography
+
| Phenix map_to_model, automatic modelling of EM volumes
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2003Sali_Review]]
+
| [[2018Wang_MD]]
| Review of electron tomography
+
| Constructing atomic models using molecular dynamics
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2004Henderson_Review]]
+
| [[2018Xia_MVPENM]]
| Review of electron microscopy
+
| Multiscale Normal Mode Analysis
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2005Lucic_Review]]
+
| [[2018Yu_Atomic]]
| Review of electron tomography
+
| Constructing atomic models using existing tools
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2006Fernandez_Review]]
+
| [[2019Bonomi_Multiscale]]
| Review of electron microscopy
+
| Bayesian multi-scale modelling
 
|-  
 
|-  
  
| Book
+
| Paper
| [[2006Frank_TomoBook]]
+
| [[2019Kidmose_Namdinator]]
| Electron Tomography
+
| Namdinator: Flexible fitting with NAMD
 
|-  
 
|-  
  
| Book
+
 
| [[2007McIntosh_Book]]
+
| Paper
| Cellular Electron Microscopy
+
| [[2019Klaholz_Review]]
 +
| Review of Phenix tools to modelling
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007Sorzano_Review]]
+
| [[2019Subramaniya_DeepSSE]]
| Review of the image processing steps
+
| Secondary structure prediction from maps using deep learning
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2008Fanelli_ImageFormation]]
+
| [[2019Zhang_CoarseGrained]]
| Review on the image formation model from the electron waves and open inverse-problems
+
| Coarse-graining of EM maps
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2008Fernandez_HPCReview]]
+
| [[2020Costa_MDeNM]]
| High performance computing in electron cryomicroscopy
+
| Flexible fitting with molecular dynamics and normal modes
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2008Jonic_Review]]
+
| [[2020Cragnolini_Tempy2]]
| Comparison between electron tomography and single particles
+
| TEMpy2 library for density-fitting and validation
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2012Kudryashev_Review]]
+
| [[2020Dodd_ModelBuilding]]
| Review of subtomogram averaging
+
| Model building possibilities, with special emphasis on flexible fitting
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Briggs_Review]]
+
| [[2020Ho_CryoID]]
| Review of subtomogram averaging
+
| Identification of proteins in structural proteomics from cryoEM volumes
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Beck_Review]]
+
| [[2020Hoh_Buccaneer]]
| Review of molecular sociology
+
| Structure modelling with Buccaneer
 
|-  
 
|-  
 +
  
 
| Paper
 
| Paper
| [[2017Galaz_Review]]
+
| [[2020Joseph_comparison]]
| Review of single particle tomography
+
| Comparison of map and model, or two maps
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Plitzko_Review]]
+
| [[2020Kim_Review]]
| Review of electron tomography, FRET and FIB milling
+
| Review of the options for atomic modelling
 
|-  
 
|-  
  
|}
+
| Paper
 
+
| [[2020Leelananda_Constraints]]
=== Software ===
+
| NMR Chemical Shifts and Cryo-EM Density Restraints in Iterative Rosetta-MD structure refinement
 
+
|-
{|
 
  
 
| Paper
 
| Paper
| [[1996Kremer_IMOD]]
+
| [[2020Liebschner_Ceres]]
| IMOD
+
| CERES: Web server of refined atomic maps of CryoEM deposited maps by Phenix
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1996Chen_Priism/IVE]]
+
| [[2020Oroguchi]]
| Priism/IVE
+
| Assessment of Force Field Accuracy Using Cryogenic Electron Microscopy Data
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1996Frank_Spider]]
+
| [[2020Vant_Flexible]]
| Spider
+
| Flexible fitting with molecular dynamics and neural network potentials
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2004Sorzano_Xmipp]]
+
| [[2021Behkamal_Secondary]]
| Xmipp
+
| Secondary structure from medium resolution maps
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2005Nickell_TOM]]
+
| [[2021Chojnowski_quality]]
| TOM Toolbox
+
| Quality of models automatically fitted with ARP/wARP
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007Messaoudi_TomoJ]]
+
| [[2021Han_Vesper]]
| TomoJ
+
| VESPER: global and local cryo-EM map alignment using local density vectors
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2008Heymann_BsoftTomo]]
+
| [[2021Lawson_Challenge]]
| Bsoft
+
| Validation recommendations based on outcomes of the 2019 EMDataResource challenge
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Ding_CaltechTomography]]
+
| [[2021Mori_Flexible]]
| Caltech tomography database
+
| Efficient Flexible Fitting Refinement with Automatic Error Fixing
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Noble_AppionProtomo]]
+
| [[2021Pfab_DeepTracer]]
| Batch fiducial-less tilt-series alignment in Appion using Protomo
+
| DeepTracer for fast de novo cryo-EM protein structure modeling
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015vanAarle_Astra]]
+
| [[2021Saltzberg_IMP]]
| ASTRA Toolbox
+
| Using the Integrative Modeling Platform to model a cryoEM map
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Han_AuTom]]
+
| [[2021Terwilliger_CryoID]]
| Software platform for Electron Tomography
+
| Identification of sequence in a CryoEM map from a set of candidates
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Wan_Simulator]]
+
| [[2021Titarenko_LocalCorr]]
| Electron Tomography Simulator
+
| Performance improvement of local correlation for docking
 
|-  
 
|-  
  
|}
+
| Conference
 +
| [[2021Vuillemot_NMA]]
 +
| Flexible fitting using Normal Modes
 +
|-
  
== 2D Crystals ==
+
| Paper
 +
| [[2022Antanasijevic_ab]]
 +
| Sequence determination of antibodies bound to a map
 +
|-
  
=== 2D Preprocessing ===
+
| Paper
 
+
| [[2022Behkamal_LPTD]]
{|
+
| LPTD: Topology determination of CryoEM maps
 +
|-
  
  
 
| Paper
 
| Paper
| [[1986Henderson_Processing]]
+
| [[2022Chojnowski_findMySeq]]
| General 2D processing
+
| Identify sequence in CryoEM map using Deep Learning
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2000He_PhaseAlignment]]
+
| [[2022Krieger_Prody2]]
| Phase consistency and Alignment
+
| Protein dynamics developments for the large scale and cryoEM: case study of ProDy 2.0
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2006Gil_Unbending]]
+
| [[2022Neijenhuis_Haddock]]
| Crystal unbending
+
| Protein-protein interface refinement in complex maps with Haddock2.4
|-  
 
 
 
|}
 
 
 
=== Classification ===
 
{|
 
 
 
| Paper
 
| [[1988Frank_Classification]]
 
| MSA and classification in electron crystallography
 
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1996Fernandez_SOM]]
+
| [[2022Vuillemot_NMMD]]
| Classification based on self organizing maps
+
| Flexible fitting with simultaneous Normal Mode and Molecular Dynamics displacements
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1998Sherman_MSA]]
+
| [[2022Zhang_CRITASSER]]
| Classification based on MSA
+
| Atomic models of assemble protein structures with deep learning
 
|-  
 
|-  
  
 
|}
 
|}
=== 3D Reconstruction ===
+
 
 +
=== Books and reviews ===
  
 
{|
 
{|
  
| Paper
+
| Book
| [[1985Wang_Solvent]]
+
| [[1980Herman_Tomography]]
| Solvent flattening
+
| General book on tomography
 +
|-
 +
 
 +
| Book
 +
| [[1988Kak_Tomography]]
 +
| General book on tomography
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1990Henderson_Processing]]
+
| [[2000Tao_Review]]
| General 3D processing
+
| Review of single particles
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2004Marabini_ART]]
+
| [[2000VanHeel_Review]]
| Algebraic Reconstruction Technique with blobs for crystals (Xmipp)
+
| Review of single particles
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Biyani_Badlu]]
+
| [[2002Frank_Review]]
| Image processing for badly ordered crystals
+
| Review of single particles
 
|-  
 
|-  
  
|}
+
| Paper
 +
| [[2002Schmid_Review]]
 +
| Review of single particles
 +
|-
  
=== Books and reviews ===
+
| Paper
 
+
| [[2004Henderson_Review]]
{|
+
| Review of electron microscopy
 +
|-
  
 
| Paper
 
| Paper
| [[1998Walz_Review]]
+
| [[2004Subramaniam_Review]]
| Review of 2D crystallography
+
| Review of single particles
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1999Glaeser_Review]]
+
| [[2005Steven_Review]]
| Review of 2D crystallography
+
| Review of electron microscopy
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2001Ellis_Review]]
+
| [[2006Fernandez_Review]]
| Review of 2D crystallography
+
| Review of electron microscopy
 
|-  
 
|-  
  
| Paper
+
| Book
| [[2001Glaeser_Review]]
+
| [[2006Frank_book]]
| Review of 2D crystallography
+
| Book covering all aspects of electron microscopy of single particles
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2004Henderson_Review]]
+
| [[2006Sorzano_Review]]
| Review of electron microscopy
+
| Review of optimization problems in electron microscopy
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2006Fernandez_Review]]
+
| [[2007Leschziner_Review]]
| Review of single particles, electron tomography and crystallography
+
| Review of 3D heterogeneity handling algorithms
 
|-  
 
|-  
  
Line 3,660: Line 3,732:
 
|-  
 
|-  
  
|}
+
| Paper
 
+
| [[2008Fanelli_ImageFormation]]
=== Software ===
+
| Review on the image formation model from the electron waves and open inverse-problems in Electron Tomography
 
+
|-
{|
 
  
 
| Paper
 
| Paper
| [[1996Crowther_MRC]]
+
| [[2008Fernandez_HPCReview]]
| MRC
+
| High performance computing in electron cryomicroscopy
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2004Sorzano_Xmipp]]
+
| [[2008Jonic_Review]]
| Xmipp
+
| Comparison between electron tomography and single particles
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007Gipson_2dx]]
+
| [[2008Mueller_Review]]
| 2dx
+
| Review of Electron microscopy
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007Heymann_Bsoft]]
+
| [[2008Taylor_Review]]
| Bsoft
+
| Review of Electron microscopy
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007Philippsen_IPLT]]
+
| [[2010DeRosier_Review]]
| IPLT
+
| Personal account of how 3DEM developed in the early days
 
|-  
 
|-  
  
|}
+
| Chapter
 +
| [[2012Sorzano_Review]]
 +
| Review of single particle analysis using Xmipp
 +
|-
  
== 3D Crystals - MicroED ==
+
| Chapter
 +
| [[2012Devaux_Protocol]]
 +
| Protocols for performing single particle analysis
 +
|-  
  
=== Sample Preparation ===
 
{|
 
 
| Paper
 
| Paper
| [[2016Shi_Preparation]]
+
| [[2014Bai_Review]]
| Sample Preparation
+
| Recent advances in cryo-EM
|}
+
|-
=== Data Collection ===
+
 
{|
 
 
| Paper
 
| Paper
| [[2014Nannenga_CR]]  
+
| [[2015Carazo_Review]]
| Continuous rotation
+
| Review of the reconstruction process
 +
|-
  
|}
+
| Paper
=== Data Processing ===
+
| [[2015Cheng_Review]]
{|
+
| A primer to Single Particle Cryo-EM
 +
|-
  
 
| Paper
 
| Paper
| [[2011Wisedchaisri_PhaseExtension]]
+
| [[2015Cheng_Reviewb]]
| Fragment-based phase extension
+
| Single Particle Cryo-EM at crystallographic resolution
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2015Hattne_Processing]]  
+
| [[2015Elmlund_Review]]
| Data Processing
+
| Recent advances in cryo-EM
|-
+
|-  
+
 
 
| Paper
 
| Paper
| [[2016Hattne_Correction]]
+
| [[2015Henderson_Review]]
| Image correction
+
| Recent advances in cryo-EM
|}
+
|-
  
=== Software ===
+
| Paper
{|
+
| [[2015Nogales_Review]]
 +
| Recent advances in cryo-EM
 +
|-
  
 
| Paper
 
| Paper
| [[2014Iadanza_Processing]]
+
| [[2015Schroeder_Review]]
| Data Processing of still diffraction data
+
| Review of advances in the electron microscope
|}
+
|-
  
=== Books and Reviews ===
+
| Paper
{|
+
| [[2015VanDenBedem_Integrative]]
| Paper
+
| Review of integrative structural biology
| [[2014Nannenga_Review ]]
+
|-  
| Review of MicroED
 
|-
 
  
 
| Paper
 
| Paper
| [[2016Liu_Review ]]
+
| [[2015Wu_Review]]
| Review of MicroED
+
| Review of advances in cryo-EM
|-
+
|-  
  
 
| Paper
 
| Paper
| [[2016Rodriguez_Review ]]
+
| [[2016Carroni_CryoEM]]
| Review of MicroED
+
| Review of advances in Cryo-EM
 
|-  
 
|-  
 
|}
 
 
== Helical particles ==
 
 
=== Filament corrections ===
 
 
{|
 
  
 
| Paper
 
| Paper
| [[1986Egelman_Curved]]
+
| [[2016Egelman_CryoEM]]
| Algorithm for correcting curved filaments
+
| Review of advances in Cryo-EM
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1988Bluemke_Pitch]]
+
| [[2016Eisenstein_CryoEM]]
| Algorithm for correcting filaments with different helical pitches
+
| News feature on the Method of the Year
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2006Wang_Pitch]]
+
| [[2016FernandezLeiro_Review]]
| Algorithm for correcting filaments with different helical pitches
+
| Review of EM
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Yang_Flexible]]
+
| [[2016Glaeser_HowGood]]
| Algorithm for correcting filaments with flexible subunits
+
| How good can cryo-EM become?
 
|-  
 
|-  
  
|}
+
| Paper
 +
| [[2016Jonic_PseudoAtoms]]
 +
| Review of the applications of the use of pseudoatoms in EM
 +
|-
  
=== Reconstruction ===
+
| Chapter
 
+
| [[2016Mio_Review]]
{|
+
| Overview of the process to obtain EM reconstructions
 +
|-
  
 
| Paper
 
| Paper
| [[1952Cochran_Fourier]]
+
| [[2016Jonic_Review]]
| Fourier Bessel transform of filamentous structures
+
| A review of computational ways to handle heterogeneity
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1958Klug_Fourier]]
+
| [[2016Nogales_Review]]
| Fourier Bessel decomposition of the projection images
+
| Review of advances in cryo-EM
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1970DeRosier_Rec]]
+
| [[2016Subramaniam_Review]]
| Image processing steps towards 3D reconstruction
+
| Why cryo-EM is now suitable for crystallographic journals
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1992Morgan_Rec]]
+
| [[2016Vinothkumar_Review]]
| Image processing steps towards 3D reconstruction
+
| Historical review and current limitations
 
|-  
 
|-  
  
| Paper
+
| Report
| [[2005Wang_Iterative]]
+
| [[2017Brezinski_Nobel]]
| Iterative Fourier-Bessel algorithm
+
| Scientific background on the Nobel Prize in Chemistry 2017
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2007Egelman_Iterative]]
+
| [[2017Cheng_review]]
| Iterative real-space algorithm
+
| Why CryoEM became so hot
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Desfosses_Spring]]
+
| [[2017Danev_Review]]
| Helical processing with Spring
+
| Review of the use of phase plates in EM
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Zhang_seam]]
+
| [[2017Elmlund_Review]]
| Workflow for the detection of the lattice seam
+
| 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 ('''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
 +
| [[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
 
| Paper
| [[2016Rohou_Frealix]]
+
| [[1996Fuller_Rec]]
| Helical processing with Frealix
+
| Reconstruction of icosahedral viruses in Fourier space
 +
|-
 +
 
 +
| Paper
 +
| [[1997Thuman_Rec]]
 +
| Reconstruction of icosahedral viruses in Fourier space
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017_He]]
+
| [[2019Goetschius_Asymmetric]]
| Helical processing with Relion
+
| Approaches to reconstruct asymmetric features in viruses
 
|-  
 
|-  
  
 
|}
 
|}
  
=== Validation ===
+
=== Classification ===
  
 
{|
 
{|
  
 
| Paper
 
| Paper
| [[2014Egelman_ambiguity]]
+
| [[2005Scheres_Virus]]
| How to detect incorrect models
+
| Classification of virus capsids in real space
 
|-  
 
|-  
  
Line 3,853: Line 5,687:
  
 
| Paper
 
| Paper
| [[1970DeRosier_Rec]]
+
| [[1999Baker_Review]]
| Image processing steps towards 3D reconstruction
+
| Review of reconstruction of icosahedral viruses
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1992Morgan_Rec]]
+
| [[1999Conway_Review]]
| Image processing steps towards 3D reconstruction
+
| Review of reconstruction of icosahedral viruses
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2004Henderson_Review]]
+
| [[2000Thuman_Review]]
| Review of electron microscopy
+
| Review of reconstruction of icosahedral viruses
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2015Sachse_Review]]
+
| [[2003Lee_Review]]
| Review of the image processing steps in helical particles
+
| Review of reconstruction of icosahedral viruses
 +
|-
 +
 
 +
| Paper
 +
| [[2003Navaza_Review]]
 +
| Review of reconstruction of icosahedral viruses
 +
|-
 +
 
 +
| Paper
 +
| [[2006Grunewald_Review]]
 +
| Review of reconstruction of icosahedral viruses
 
|-  
 
|-  
  
Line 3,879: Line 5,723:
  
 
| Paper
 
| Paper
| [[1996Carragher_Phoelix]]
+
| [[1996Baker_EMPFT]]
| Phoelix
+
| EMPFT
 
|-  
 
|-  
  
Line 3,889: Line 5,733:
  
 
| Paper
 
| Paper
| [[1996Owen_Brandeis]]
+
| [[1996Frank_Spider]]
| Brandeis
+
| Spider
 
|-  
 
|-  
 
|}
 
 
== Icosahedral particles ==
 
 
=== Reconstruction ===
 
 
{|
 
  
 
| Paper
 
| Paper
| [[1970Crowther_Rec]]
+
| [[1996VanHeel_Imagic]]
| Reconstruction of icosahedral viruses in Fourier space
+
| Imagic
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1971Crowther_Rec]]
+
| [[2004Sorzano_Xmipp]]
| Reconstruction of icosahedral viruses in Fourier space
+
| Xmipp
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1996Fuller_Rec]]
+
| [[2013DeLaRosa_Xmipp30]]
| Reconstruction of icosahedral viruses in Fourier space
+
| Xmipp 3.0
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1997Thuman_Rec]]
+
| [[2013Morin_Sliz SBGrid]]
| Reconstruction of icosahedral viruses in Fourier space
+
| SBGrid presentation for eLife
 
|-  
 
|-  
  
 
|}
 
|}
  
=== Classification ===
+
== Liquid-cell TEM / in-situ TEM ==
 +
 
  
 
{|
 
{|
  
 
| Paper
 
| Paper
| [[2005Scheres_Virus]]
+
| [[2020Ren_LTEM]]
| Classification of virus capsids in real space
+
| Real-time dynamic imaging of sample in liquid phase
 
|-  
 
|-  
  
 
|}
 
|}
  
=== Books and reviews ===
+
== Databases ==
  
 
{|
 
{|
  
 
| Paper
 
| Paper
| [[1999Baker_Review]]
+
| [[2003Boutselakis_EMSD]]
| Review of reconstruction of icosahedral viruses
+
| EMSD database
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1999Conway_Review]]
+
| [[2005Heymann_Conventions]]
| Review of reconstruction of icosahedral viruses
+
| Conventions for software interoperability
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2000Thuman_Review]]
+
| [[2005Heymann_Conventions]]
| Review of reconstruction of icosahedral viruses
+
| Conventions for software interoperability
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2003Lee_Review]]
+
| [[2011Kim_CDDB]]
| Review of reconstruction of icosahedral viruses
+
| Conformational Dynamics Data Bank
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2003Navaza_Review]]
+
| [[2011Lawson_EMDB]]
| Review of reconstruction of icosahedral viruses
+
| Electron Microscopy Data Bank
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2006Grunewald_Review]]
+
| [[2013Ison_EDAM]]
| Review of reconstruction of icosahedral viruses
+
| EDAM, an ontology of bioinformatics operations
 
|-  
 
|-  
 
|}
 
 
=== Software ===
 
 
{|
 
  
 
| Paper
 
| Paper
| [[1996Baker_EMPFT]]
+
| [[2016Iudin_EMPIAR]]
| EMPFT
+
| EMPIAR raw data database
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1996Crowther_MRC]]
+
| [[2016Patwhardan_EMDB]]
| MRC
+
| EMDB, PDB, ...
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1996Frank_Spider]]
+
| [[2017Gore_Validation]]
| Spider
+
| Validations of PDB submissions
 +
|-
 +
 
 +
| Paper
 +
| [[2017Patwhardan_Trends]]
 +
| Trends at EMDB
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[1996VanHeel_Imagic]]
+
| [[2017Shao_PDBQuality]]
| Imagic
+
| Quality metrics in PDB
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2004Sorzano_Xmipp]]
+
| [[2018Tawari_search]]
| Xmipp
+
| Search of 3D structures in a database using 2D experimental images
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013DeLaRosa_Xmipp30]]
+
| [[2018wwwPDB_PDB]]
| Xmipp 3.0
+
| Review of PDB advances
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Morin_Sliz SBGrid]]
+
| [[2022Wang_EMDB]]
| SBGrid presentation for eLife
+
| Validation analysis of EMDB entries
 +
|-
 +
 
 +
| Blog
 +
| http://www.mybiosoftware.com
 +
| Huge list of bioinformatics programs (many of them structural bioinformatics)
 
|-  
 
|-  
  
 
|}
 
|}
  
== Databases ==
+
== Relationship to other structural information sources ==
  
 
{|
 
{|
  
 
| Paper
 
| Paper
| [[2003Boutselakis_EMSD]]
+
| [[2000Engel_AFM]]
| EMSD database
+
| Review of Atomic Force Microscopy
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2005Heymann_Conventions]]
+
| [[2001Dimmeler_AFM]]
| Conventions for software interoperability
+
| Constraints from Atomic Force Microscopy
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2005Heymann_Conventions]]
+
| [[2003Mobus_EnergyLoss]]
| Conventions for software interoperability
+
| Chemical mapping by energy loss electron tomography
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2011Kim_CDDB]]
+
| [[2004Leapman_EnergyLoss]]
| Conformational Dynamics Data Bank
+
| Chemical mapping by energy loss electron tomography
 +
|-
 +
 
 +
| Paper
 +
| [[2004Leapman_Review]]
 +
| Review on correlative microscopy
 +
|-
 +
 
 +
| Paper
 +
| [[2005Boudier_EFTETJ]]
 +
| Software for Chemical mapping by energy loss electron tomography
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2011Lawson_EMDB]]
+
| [[2005Vestergaard_SAXS]]
| Electron Microscopy Data Bank
+
| Example of comparison of 3DEM and Small-angle X-ray scattering
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2013Ison_EDAM]]
+
| [[2007Hamada_SAXS]]
| EDAM, an ontology of bioinformatics operations
+
| Constraints from Small-angle X-ray scattering
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Iudin_EMPIAR]]
+
| [[2013Xu_FRET]]
| EMPIAR raw data database
+
| EM+FRET
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2016Patwhardan_EMDB]]
+
| [[2017Kim_SAXS]]
| EMDB, PDB, ...
+
| Compatibility of EM experimental images and SAXS curves
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Gore_Validation]]
+
| [[2018Ando_Correlative]]
| Validations of PDB submissions
+
| Review of correlative microscopy techniques
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Patwhardan_Trends]]
+
| [[2018Sieben_Multicolor]]
| Trends at EMDB
+
| Correlative microscopy with superresolution optical images
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2017Shao_PDBQuality]]
+
| [[2019Huber_EDXS_HAADF]]
| Quality metrics in PDB
+
| Combined reconstruction using EDXS and HAADF data
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018Tawari_search]]
+
| [[2019Jimenez_SAXS]]
| Search of 3D structures in a database using 2D experimental images
+
| Selection of EM initial volumes by SAXS curves
 
|-  
 
|-  
  
 
| Paper
 
| Paper
| [[2018wwwPDB_PDB]]
+
| [[2022Graziadei_CrossLinking]]
| Review of PDB advances
+
| Review on the use of crosslinking mass spectrometry in CryoEM
 
|-  
 
|-  
  
| Blog
+
| Paper
| http://www.mybiosoftware.com
+
| [[2022Klumpe_FIB]]
| Huge list of bioinformatics programs (many of them structural bioinformatics)
+
| A modular platform for automated cryo-FIB workflows
|-
 
 
 
|}
 
 
 
== 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
 
| [[2018Ando_Correlative]]
 
| Review of correlative microscopy techniques
 
|-
 
 
 
| Paper
 
| [[2018Sieben_Multicolor]]
 
| Correlative microscopy with superresolution optical images
 
 
|-  
 
|-  
  
Line 4,156: Line 5,946:
 
| Image formation model in X-ray cell microscopy
 
| Image formation model in X-ray cell microscopy
 
|-  
 
|-  
 
 
  
 
|}
 
|}
Line 4,183: 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

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== Citation ==

== Abstract ==

== Keywords ==

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== Related software ==

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== Comments ==
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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