March 11-13, 2019

S2C2 Workshop – Cryo-EM Imaging Process workshop March 11-13, 2019 (Registration Closed)


The Stanford-SLAC cryoEM Center (S2C2 - is sponsoring a single particle cryoEM image processing workshop at SLAC National Accelerator Laboratory (Menlo Park, CA), from March 11 to March 13 2019. The first part of the course will cover theoretical aspects of image processing (Electron scattering, Fourier transform, CTF, etc.), held by our invited speaker David DeRosier (Brandeis University). This will be followed by a hands-on workshop on Relion 3, held by Cornelius Gati (SLAC/Stanford University), covering all aspects from raw images, motion correction, CTF estimation, classification to final reconstructions. The third day of the course will cover Map validation and modeling (Greg Pintilie and Wah Chiu Stanford/SLAC), Map deposition and archival (Cathy Lawson, Rutgers University) and further talks by advanced users (Georgios Skiniotis and Kaiming Zhang, Stanford University) with useful tips for how to tackle your image processing problems. The course is aimed at beginners in single particle cryoEM image analysis and will be going through a relion tutorial, while participants are encouraged to prepare questions regarding their own datasets (time permitted). Attendance in person is preferable, although a Zoom link for remote participants will be provided as well. Applicants will be selected based on a short description of their scientific background and motivation letter. The course will be free of charge, while accommodation will have be covered by the participants

Please note new Location:  Redwood Room, Bldg. 048

Lecture Agenda

Day 1: Mar. 11, 2019

Time Title Speaker
8:30 AM -10:45 AM   General principles of cryoEM image reconstruction (PDF) David DeRosier             
11:00 AM -12:00 PM  Data acquistion and pre-processing software, logging on and computer basics (PDF) Yee Ting Li
12:00 PM - 1:00 PM  Lunch  
1:00 PM - 2:00 PM  Image processing with relion - Introduction Cornelius Gati
3:00 PM - 5:00 PM 

Practical: 1 - Images, MotionCor, CTF

Cornelius Gati

Day 2: Mar. 12, 2019

Time Title Speaker
8:30 AM - 12:00 PM

Practical 2:  2D Classification, 3D Classification                                 

Cornelius Gati             
12:00 PM - 1:00 PM Lunch  
1:00 PM - 5:00 PM Practical 3:  3D Refinement and map improvement Cornelius Gati

Day 3: Mar. 13, 2019

Time Title Speaker
8:30 AM -10:30 AM

Map visualization and validation   (PDF)                                          

Greg Pintilie/Wah Chu 
11:00 AM - 11:45 AM Map challenge and map deposition and archival (PDF) Cathy Lawson
11:45 AM - 1:00 PM Lunch provided for Practical attendees only: Sponsored by ThermoFisher  
1:00 PM - 1:45 PM

Dealing with heterogeneity in single-particle cryoEM data (PDF)

Georgios Skiniotis
1:45 PM - 2:30 PM Image processing of heterogeneous particle images (not available for public viewing) Kaiming Zhang
2:30 PM - 3:10 PM Update on Volta Phase Plate (not available for public viewing) Bart Buijsse
3:10 PM - 4:10 PM Different image processing software packages Cornelius Gati

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