May 2023 CryoEM Image Processing Workshop

Workshop & Lecture Archive

2019 Archive
2020 Archive
2021 Archive
2022 Archive
2023 Archive

S²C² CryoEM Image Processing Workshop: SCIPION
In-Person/Zoom \| November 18-20, 2019
Speaker	Institution	Talk Title/Slide Deck	Recording(s)
Monday, November 18, 2019
David DeRosier	Brandeis University	General Principles of cryoEM 3D reconstructions	Video 1/Video 2/Video 3
Jose Maria Carazo	CNB-CSIC	Basic image processing for EM Part 1, Part 2	Video 1/Video 2/Video 3
Carlos Sanchez- Sorzano	CNB-CSIC	Image processing principles	Video 1/Video 2/Video 3/ Video 4/Video 5
Tuesday, November 19, 2019
Yiorgio Skiniotis	Stanford	Dealing with heterogeneity in single-particle data/examples	Not Available
Wednesday, November 20, 2019
Greg Pintilie	Stanford	Model building and map validation	Not Available

S²C² CryoEM Training for Beginners Workshop
In-Person Workshop \| September 11 - 13, 2019
Speaker	Institution	Talk Title/Slide Deck	Recording
Wednesday, September 11, 2019
Juegen Plitzko	Max Planck Insitute	EM Basics	Not Available
Yiorgio Skiniotis	Stanford	Freezing Basics	Not Available
Thursday, September 12, 2019
Christopher Booth	Gatan	Camera	Not Available
Yee Ting Li	SLAC	eLogbook and data transfer	Not Available
Robert Glaeser	LBNL	Radiation damage	Not Available
Friday, September 13, 2019
Zoltan Metlagel	FEI	EPU and phase plate	Not Available
Corey Hecksel	SLAC	Data collection (Serial EM)	Not Available

S²C² CryoEM Modeling Workshop: ChimeraX & Phenix
In-Person Workshop \| July 10-12, 2019 Materials: properly weighted map t20s \| model validation tutorial \| model optimization tutorial
Speaker	Institution	Talk Title/Slide Deck	Recording
Wednesday, July 10, 2019
Tom Goddard Elaine Meng Eric Pettersen	UCSF UCSF UCSF	ChimeraX - visualization of cryoEM Maps and Models	Not Available
Greg Pintilie	Stanford	Rigid body and flexible fitting	Not Available
Thursday, July 11, 2019
Paul Adams	LBNL	Phenix introduction	Not Available
Paul Adams	LBNL	Automated model docking and building	Not Available
Pavel Afonine	LBNL	Phenix tools for cryoEM: refinement and validation	Not Available
Paul Adams	LBNL	Model validation for cryo-EM	Not Available
Nigel Moriarty	LBNL	Restraints in Phenix	Not Available
Friday, July 12, 2019
Corey Hyrc	Baylor College of Medicine	Accurate representation of cryoEM Structures	Not Available
Greg Pintilie	Stanford	Assessment of high resolution of cryoEM Features	Not Available
Michael Roberston	Stanford	CryoEM structure and ligand modeling	Not available
Cathy Lawson	Rutgers	CryoEM archives, challenges and validation	Not Available

S²C² CryoEM Image Processing Workshop: SCIPION
In-Person Workshop \| November 18-20, 2019
Speaker	Institution	Talk Title/Slide Deck	Recording
Monday, November 18-20, 2019
David DeRosier	Brandeis University	General principles of CryoEM image reconstruction	Not Available
Yee Ting Li	SLAC	Data Acquisition and pre-processing software logging on and computers basics	Not Available
Cornelius Gati	SLAC	Image Processing with Relion - Introduction	Not Available
Tuesday, November 19, 2019
Cornelius Gati	SLAC	Practical 2 & 3	Not Available
Wednesday, November 20, 2019
Greg Pintilie Wah Chiu	Stanford Stanford/SLAC	Map visualization and validation	Not Available
Cathy Lawson	Rutgers University	Cryo-EM map challenge, map deposition and archiving	Not Available
Yiorgio Skiniotis	Stanford	Dealing with heterogeneity in single-particle cryoEM data	Not Available
Cornelius Gati	SLAC	Different image processing software packages	Not Available

S²C² CryoEM Training for Begineers Workshop
In-Person Workshop \| September 11-13, 2019
Speaker	Institution	Talk Title/Slide Deck	Recording
Wednesday, September 11, 2019
Juergen Plitzko	Max Planck Institute	EM Basics	Not Available
Yiorgo Skiniotis	Stanford	Freezing Basics	Not Available
Thursday, September 12, 2019
Chris Booth	Gatan	Camera	Not Available
Yee-Ting Li	SLAC	eLogbook and data transfer	Not Available
Robert Glaeser	LBNL	Radiation Damage	Not Available
Friday, September 13, 2019
Zoltan Metlagel	Thermofisher	EPU and Phase Plate	Not Available
Corey Hecksel	SLAC	Data Collection (Serial EM)	Not Available

S²C² Modeling Workshop: ChimeraX & Phenix
In-Person Workshop \| July 10-12, 2019
Speaker	Institution	Talk Title/Slide Deck	Recording
Wednesday, July 10, 2019
Tom Ferrin Tom Goddard	UCSF	ChimeraX - Visualization of CryoEM maps & models	Not Available
Greg Pintilie	Stanford	Rigid Body and Flexible Fitting	Not Available
Michael Schmid	SLAC	Hands on VR to Visualize CryoEM Structures	Not Available
Thursday, July 11, 2019
Paul Adams	LBNL	Phenix Intro/Automated Model Docking & Building	Not Available
Pavel Afonine	LBNL	Structure Refinement	Not Available
Dorothee Liebschner	LBNL	Validation and Refinement	Not Available
Paul Adams	LBNL	Intro to Phenix Cryo-EM Tools Practical/Automated Model Building	Not Available
Pavel Afonine	LBNL	Structure Refinement Practical	Not Available
Dorothee Liebschner	LBNL	Validation and Refinement Practical	Not Available
Friday, July 12, 2019
Corey Hyrc	Baylor College of Medicine	Accurate Representation of CryoEM Structures	Not Available
Greg Pintilie	Stanford	Assessment of High Resolution CryoEM Features	Not Available
Mike Robertson	Stanford	CryoEM Structure Ligand Modeling	Not Available
Cathy Lawson	Rutgers	CryoEM Structural Validation	Not Available

S²C² Cryo-EM Image Processing Workshop
In-Person Workshop \| March 11-13, 2019
Speaker	Institution	Talk Title/Slide Deck	Recording
Monday, March 11, 2019
David DeRosier	Brandeis University	General Principles of CryoEM Image Reconstruction	Not Available
Yee-Ting Li	SLAC	Data Acquistion and pre-processing software, logging on and computer basics	Not Available
Cornelius Gati	SLAC	Image Processing with Relion Intro/Practical 1: Images, MotionCor, CTF	Not Available
Tuesday, March 12, 2019
Cornelius Gati	SLAC	Practical 2: 2D/3D Classification/Practical 3: 3D Refinement & Map Improvement	Not Available
Wednesday, March 13, 2019
Greg Pintilie Wah Chiu	SLAC	Map Visualization and Validation	Not Available
Cathy Lawson	Rutgers	Map Challenge and Map Deposition and Archival	Not Available
Yiorgio Skiniotis	Stanford	Dealing with Heterogeneity in single-particle cryoEM data	Not Available
Kaiming Zhang	Stanford	Image Processing of Heterogeneous Particle Images	Not Available
Bart Buijsse	Thermofisher	Update on Volta Phase Plate	Not Available

2019 Workshop/Lectures
S²C²Cryo-EM Training for Beginners Workshop In-Person Workshop \| January 22-25, 2019
Speaker	Institution	Talk Title/Slide Deck	Recording(s)
Tuesday, January 22, 2019
Yiorgo Skiniotis	Stanford	Cryo-Specimen Preparation	Not Available
Wah Chiu	Stanford/SLAC	Radiation Damage in cryoEM	Not Available
Christopher Booth	Gatan	Detection technologies for cryo-electron microscopy	Not Available
Wednesday, January 23, 2019
Juergen Plitzko	Max Planck Institute	TEM Basics and column alignment	Not Available
David Bushnell	Stanford/SLAC	Low dose imaging via serial EM and EPU	Not Available
Wah Chiu	Stanford/SLAC	Image contrast theory in CryoEM	Not Available
Thursday, January 24, 2019
John Spear	Thermofisher	Krios and Talos alignment	Not Available
Yee Ting Li	SLAC	eLogbook, data collection monitoring & pre-processing	Not Available

CryoEM In-Residence Training and Public Lecture: Tomgraphy and Volta Phase Plate
Virtual Workshop Only \| December 10-11, 2020 Provided Agenda

S²C² CryoEM CCP-EM Modeling Workshop
Virtual Workshop Only \| November 10-13, 2020 Workshop Materials: computing instructions
Speaker	Institution	Talk Title/Slide Deck	Recording(s)
Tuesday, November 10, 2020
Colin Palmer	CCP-EM	Lecture: Intro to workshop and CCP-EM	Video 1
Kevin Cowtan	University of York	Lecture: Automated model building with Buccaneer & Nautilus Tutorial: Buccaneer	Video 1 Video 1/Video 2/Video3
Paul Emsley	MRC, LMB	Lecture: Cryo-EM model building with modern COOT Tutorial: COOT (Part 1)	Video 1 Video 1
Wednesday, November 11, 2020
Paul Emsley	MRC, LMB	Tutorial: COOT (Part 2)	Video 1/Video 2
Maya Topf	ISMB, Birkbeck	Lecture: Flexible fitting of Atomic Models	Video 1
Tristan Cragnolini	ISMB, Birkbeck	Tutorial: Flex-EM (Part 1)	Video 1
Aaron Sweeney	University College of London	Tutorial: Flex-EM (Part 2)	Video 1
Andrea Thorn	University of Wurzburg	Lecture: Finding secondary structure in cryo-EM maps: HARUSPEX	Video 1
Thursday, November 12, 2020
Rob Nicholls	MRC, LMB	Lecture: Refinement against cryo-EM Maps Tutorial: Refmac (Part 1) Tutorial: Refmac (Part 2)	Video 1 Video 2 Video 3
Ardan Patwardhan	EMBL-EBI	Lecture: PDB, EMDB, & Empiar: Public archiving of cryoEM data	Video 1
Arjen Jakobi	TU Delft	Lecture: Map sharpening tools for cryo-EM density maps Tutorial: LocScale	Video 1 Video 2
Friday, November 13, 2020
Agnel Joseph	CCP-EM	Lecture: Validation of cryo-EM maps and Models Lecture: Model Validation Tutorial: Model Validation	Video 1 Video 2 Video 3
All Speakers		General Q&A Session

SSRL/LCLS Users' Meeting: Cryo-EM of COVID-related Macromolecules
Virtual Workshop Only \| September 28, 2020
Speaker	Institution	Talk Title/Slide Deck	Recording(s)
David Veesler	University of Washington	Structural Studies of the SARS-CoV Spike Glycoprotein	Video 1/Video 2
David Stuart	Oxford University/ Diamond Light Source	The use of cryoEM structural information to advance SARS2-CoV-2 biology and therapy	Video 1/Video 2
Goran Kokic	Max Planck Institute	Structure of replicating SARS-COV-2 polymerase	Video 1
Erica O. Saphire Adrian Enriquez	La Jolla Institute	Antibodies against emerging viral disease	Video 1/Q&A
Rhiju Das Ivan Zheludev	Stanford	CryoEM of previously unsolvable RNA structures including coronavirus genome elements	Video 1/Q&A
Stephan Wilkens	SUNY Upsate Medical University	Targeting Vacuolar H+-ATPase for Antivral Therapy	Video 1/Video 2/Video3

Fundamentals of Single Particle CryoEM Workshop
Virtual Workshop Only \| August 11 - 12, 2020
Speaker	Institution	Talk Title/Slide Deck	Recording(s)
Tuesday, August 11, 2020
Mark Herzik	UC San Diego	Sample preparation for cryo-EM	Video 1/Video 2
David DeRosier	Brandeis University	Image contrast theory and reconstruction	Video 1/Video 2
Alexis Rohou	Genentech	Principles of image processing	Video 1/Video 2
Andres Leschziner	UC San Diego	Determining structures of challenging samples Part 1/Part 2/Part 3	Video 1/Video 2
Wednesday, August 12, 2020
Dmity Lyumkis	Salk Institute	Dealing with resolution anisotropy and considerations for high resolution structure determination	Video 1/Video 2/Video 3
Wah Chiu	Stanford/SLAC	Atomic modeling and the importance of validation	Video 1/Video 2
Ali Punjani	Structural Biotechnology	CryoSPARC demonstration/tutorial (see below June workshop for slides)	Video 1/Video 2/Video 3/ Video 4

S²C² CryoEM Image Processing Workshop: cryoSPARC
Virtual Workshop Only \| June 10 - 12, 2020 Workshop Materials: user interface overview; cryoSPARC Instructions Day 1/Day 2/ Q& A Day 1, Day 2, Day 3
Speaker	Institution	Talk Title/Slide Deck	Recording(s)
Wednesday, June 10, 2020
David DeRosier	Brandeis University	If only...	Video 1/Video 2/Video 3/
Ali Punjabi	Structural Biotechnology	CryoSPARC (AM) User Interface overview/ Day 1 CryoSPARC Instructions	Video 1/Video 2/Video 3/ Video 4/Video 5/Video 6
Ali Punjabi	Structural Biotechnology	CryoSPARC (PM)	Video 7/Video 8/Video 9/ Video 10/Video 11/Video 12
Thursday, June 11, 2020
Ali Punjabi	Structural Biotechnology	CryoSPARC (AM)	Video 1/Video 2/Video 3/ Video 4/Video 5/Video 6/ Video 7/Video 8
Ali Punjabi	Structural Biotechnology	CryoSPARC (PM)	Video 9/Video 10/Video 11/ Video 12
Stephan Arulthasan	Structural Biotechnology	CryoSPARC architecture & managment	Video 1
Ali Punjabi	Structural Biotechnology	CryoSPARC (PM)	Video 13/Video 14/Video 15/ Video 16
Friday, June 12, 2020
Greg Pintilie	Stanford University	CryoEM map resolution assessment, validation, visualization, and segmentation	Video 1/Video 2/Video 3
Cathy Lawson	Rutgers	EMDataResource: structure data archiving, validation challenges	Video 1/Video 2

Basics of Sample Preparations & Detection Technologies for Cryo-Electron Microscopy
Virtual Lecture Only \| May 29, 2020
Speaker	Institution	Talk Title/Slide Deck	Recording(s)
Yifan Cheng	HHMI UC San Francisco	Basics of sample preparation	Not Available
Christopher Booth	Amtek	Detection technologies for cryo-electron microscopy	Video 1/Video 2/ Video 3/Video 4/ Video 5/ Video 6

General Principles of Phase Contract and Phase Plates & Single-Particle Grid Preparation
Virtual Lecture Only \| April 20, 2020
Speaker	Institution	Talk Title/Slide Deck	Recording(s)
Robert Glaeser	LBNL	General Principles of phase contrast and phase plates Single-particle grid preparation	Video 1 Video 2

Specimen Prep and Data Collection Workshop

In-Person Workshop | March 2020 (CANCELLED DUE TO COVID)

S²C² CryoEM Modeling Workshop: ChimeraX & Phenix
In-Person Workshop \| January 15-17, 2020
Speaker	Institution	Talk Title/Slide Deck	Recording
Wednesday, January 15, 2020
Tom Goddard Elaine Meng Eric Pettersen	UCSF UCSF UCSF	ChimeraX-Visualization of cryoEM maps and models	Not Available
Greg Pintilie	Stanford	Segmentation, rigid body and flexible fitting	Not Available
Tom Goddard Elaine Meng Eric Pettersen	UCSF UCSF UCSF	Refinement of cryoEM maps with Isolde	Not Available
Tom Goddard	UCSF	Publication-quality images and movies	Not Available
Thursday, January 16, 2020
Paul Adams	LBNL	Phenix Introduction (The entire day is include in one video) Atomic models from cryo-EM data	Video 1
Pavel Afonine	LBNL	Structure Refinement	see above
Paul Adams	LBNL	Model validation for cryo-EM	see above
Pavel Afonine	LBNL	Structure refinement and validation practical	see above
Nigel Moriarty	LBNL	Ligands	see above
Friday, January 17, 2020
Greg Pintilie	Stanford	Assessment of high resolution cryoEM features	Video 1
Helen Berman	Rutgers	Validation of biological sctructures	Not available
Cathy Lawson	Rutgers	EM structure archives, validation and challenges	see above

SSRL/LCLS Users' Meeting: CryoEM of Macromolecules and Cells Workshop
Virtual Workshop Only \| September 21, 2021
Speaker	Institution	Talk Title/Slide Deck	Recording(s)
Alfonso Mondragon	Northwestern University	Structural Studies of a Type III-A CRISPR effector compleex	Not Available
Seyed Torabi	Yale University	Integration of biochemical and structural data to investigate stabilizing triplex-forming elements in RNA	Video 1
Kalli Kappel	MIT Broad Institute	Accelerating RNA structure determination with cryo-EM and DRRAFTER computational modeling	Video 1
Zhaoming Su	Schuan University	Cryo-EM reveals multiple states in splicing reaction of Tetrahymena intron	Video 1
Kaiming Zhang	University of S&T of China	Determination of small RNA-only 3D structures by Cryo-EM	Video 1

S²C² CryoEM Map Modeling and Validation Workshop
Virtual Workshop Only \| September 8-10, 2021 Workshop Material: Computer Setup & Instructions Q&A Day 1, Day 2, Day 3
Speaker	Institution	Talk Title/Slide Deck	Recording(s)
Wednesday, September 8, 2021
Christopher Schlicksup	LBNL	Phenix tools for improving maps, and building, refining, and validating models	Video 1
Tom Goddard	UCSF	Using AlphaFold predicted structures in ChimeraX for cryoEM modeling	Video 1
Greg Pintilie	Stanford	Model fitting and assessment in CryoEM maps with Segger, Segfit, and Q-scores	Video 1
Jasmine Young Justin Flatt	Rutgers Rutgers	Deposition, Validation, and Biocuration at the wwPDB	Video 1
Thursday, September 9, 2021
Paul Emsley	MRC Laboratory of Molecular Biology	Coot Tools for Cryo-EM Model-building, Refinement, Validation, and Analysis	Video 1
Tristan Croll	Cambridge	Interactive physics-based model building with ISOLDE	Video 1
Maximilian Edich Jola Mirecka	Universitat Hamburg STFC UKRI	Secondary	Video 1
Grzegorz Chojnowski	EMBL, Hamburg	Macromolecular models automatically built into cryo- EM maps and how to use them	Video 1
Jane Richardson	Duke University	CryoEM model validation, to avoid or correct errors at various resolutions	Video 1
Friday, September 10, 2021
Tristan Cragnolini	Birbeck College	Improving and validating map/model fits with TEMPy	Video 1
Brinda Vallat	Rutgers	Virtual Torsion Plots to Validate Coarse RNA Conformation	Video 1
Andriy Kryshtafovych	UC Davis	Model comparisons	Video 1
Ardan Patwardhan	EMBL-EBI	Cryo-EM validation from the perspective of the EMDB and EMPIAR archives	Video 1
Abhishek Singharoy	Arizona State University	Molecular dynamics flexible fitting extended: structures, ensembles and free energy of proteins and small molecules Part 1, Part 2	Video 1

S²C² CryoEM Specimen Preparation and Data Collection Workshop
Virtual Workshop Only \| March 3-4, 2021 Workshop Materials: Understanding the invisible hands of sample preparation, Unanswered Q&A from Prof. Peter's Lecture
Speaker	Institution	Talk Title/Slide Deck	Recording(s)
Wednesday, March 3, 2021
Peter J. Peters	(M4i) Maastricht University	Understanding the invisible hands of sample preparation for cryo-EM	Video 1/Video 2/Video 3/ Video 4
Benjamin Bammes	Direct Electron, LP	Optimizing Direct Detector Design for a Range of Cryo-EM Techniques	Video 1/Video 2/Video 3/ Video 4
Jeffrey Lengyel	Thermofisher	The latest generation technology for CryoEM allowing for unparalleled scientific breakthroughs	Video 1/Video 2/Video 3/ Video 4
Thursday, March 4, 2021
Christopher Russo	LMB, MRC	Principles of information loss in cryoEM and how eliminating specimen movement can improve cryomicrographs	Video 1/Video 2/Video3
Sahil Gulati	Ametek	Advances in direct electron detection: getting the most out of your microscope	Video 1/Video 2/Video 3/ Video 4/Video 5
Yee Ting Li	SLAC	Data Management at S²C²	Video 1/Video 2
Patrick Mitchell	SLAC	S²C² data collection	Video 1
		Final Q&A	Video 1, Video 2, Video3

SSRL/LCLS Users' Meeting - CryoEM Workshop
Virtual Workshop Only \| September 26, 2022 Workshop Presentations (not including River Xiao) (no PDFs of talks)
Speaker	Institution	Talk Title/Slide Deck	Recording(s)
Monday, September 26, 2022
Peter Peters	Maastricht University	Sample preparation for Single Particle Analysis and cryo-EM tomography	See above
Chu-Young Kim	Yale University	Detection and repair of noncovalent DNA modifications	See above
Chencheng Fan	University of Michigan	Neutralizing monoclonal antibodies elicted by mosaic RBD nanoparticles bind conserved sarbecovirus epitope	See above
River Xiao	University of Texas	Structural studies of giant icosahedral eukaryotic dsDNA viruses	Not Aavailable
David Chmielewski	Stanford	Chikungunya virus assembly and budding visualized in situ using cryoET	See above

S²C² High Resolution CryoET Image Processing Virtual Workshop
Virtual Workshop Only \| March 1-3, 2022 Workshop Materials: DeRosier's Fourier Transform Treastise Booklet; Goddard's Materials Zip folder; Ludtke's Tutorial Zip Folder
Speaker	Institution	Talk Title/Slide Deck	Recording(s)
Tuesday, March 1, 2022
David DeRosier	Brandeis University	EM Images: what you want vs what you get and why	Video 1
Frederick Sigworth	Yale University	Basics of Image Processing: from the data you have to the structures you'd like	Video 1
Thomas Goddard	UCSF	Visualizing proteasomes in tomograms with ChimeraX	Video 1
Wednesday, March 2, 2022
Steven Ludtke	Baylor College of Medicine	CryoET processing toward atomic resolution (EMAN2) Part 1, Part 2	Video 1/Video 2/Video 3
Thursday, March 3, 2022
Dimitry Tegunov	Genentech	Using the WARP-RELION-M pipeline to obtain high- resolution structures from tilt series	Video 1/Video 2/Video 3

2023 Image Processing Workshop
In-Person/Virtual Workshop \| May 17-19, 2023 Materials: Scipion Agenda; Scipion Slide Decks: Course Motivation; Validation Server; Marcos Gragera
Speaker	Institution	Talk Title/Slide Deck (see above links)	Recording(s)
Wednesday, May 17, 2023
Carlos Sorzano Marcos Cabezudo	CSIC CSIC	Theory and Practices: Understanding the effects of the low SNR on the cryoEM images and the ways to reduce bias. Introduction to the different softwares to be used in these sections, namely: SCIPION, Xmipp, Relion, CryoSPARC, Cryolo, GCTF, CTFFind4, GAutomatch, and Topaz	Video 1/Video 2/Video 3
		Practical Exercise: Image processing, particle identification, intial map, angular refinement	Video 1/Video 2/Video3/ Video 4
Thursday, May 18, 2023
Carlos Sorzano Marcos Cabezudo	CSIC CSIC	Theory and Practices: Discrete classification, polishing, map validation	Video 1/Video 2
		Theory and Practices: Off the beaten path - Beyond discrete classification: Continuous flexibility analysis (Zernikes, CryoDrgn, Normal Modes, and GMM+AI)	Video 1/Video 2
Friday, May 19, 2023
Carlos Sorzano Marcos Cabezudo	CSIC CSIC	Theory and Practices: Variability characterization	Video 1
Muyuan Chen	SLAC	Gaussian mixture models for single particle refinement and heterogeneity analysis (EMANs)	Video 1
Greg Pinitilie	Stanford	CryoEM map and model assessment	Video 1/Video 2
Tom Goddard	UCSF	ChimeraX cryoEM Visualization Hands-on Tutorial looking at Bacterial ATP Synthase	Video 1

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