S2C2 CryoEM Image Processing Workshop Agenda - June 10-12, 2020 (Zoom only Participation)

Contacts

General Questions:

s2c2@slac.stanford.edu

Contacts for Cryo-EM Services

 

CONTACTS

General Questions: S2C2@slac.stanford.edu Web Contacts for Cryo-EM Services
 

Stanford-SLAC Cryo-EM Center (S2C2) will offer a zoom training workshop from June 10 to 12, 2020. This workshop will include all steps of image reconstruction and the practical use of software for single particle image reconstruction available using CryoSPARC. This workshop will consist of three days of lectures and hands-on training sessions led by Dr. David DeRosier, Ali Punjani, Saara Virani, Suhail Dawood, Stephan Arulthasan, Dr. Greg Pintilie and Dr. Cathy Lawson.  Zoom teleconferencing will be available for the lectures, demonstration of the practical material and the practical participation.
 

We can accept 60 participants for the training portion of the workshop, which works through the reconstruction pipeline with an image training set, while there is no enrollment limit for the lectures given in the mornings of the workshop days. However, all Zoom participants must pre-register. The deadline is May 24, 2020 for practical applications and June 1, 2020 for lecture only applicants.
 

 All applicants must submit required documents by 5:00 PM (PDT) on June 1, 2020.

Please note:  Due to the shelter-in-place mandate, attendance to be conducted via Zoom webinar only at this June workshop lecture and practical.

Agenda

Wednesday, June 10, 2020

Time

Title

Speaker

Workshop Reference Materials

8:30 AM

Fundamental principles in 3D reconstruction in electron microscopy (Attendance by All)

  • David DeRosier

David's Presentation

CryoSPARC Presentation Part 1

CryoSPARC Presentation Part 2

Day cryoSparc 1 Instructions

User Interface Overview

Videorecording

Audio Transcript AM Session

 

10:30 AM

cryoSPARC tutorial (Attendance by All)

  • Basic techniques for the standard processing pipeline, working with T20S proteasome data to reach ~2.8 Å reconstruction tutorial
  • Explanation and theory information about motion correction algorithms, CTF estimation
  • CryoSPARC UI details, parameter choices, project and instance management
  • Ali Punjani
  • Saara Virani
  • Suhail Dawood
  • Stephan Arulthasan

CryoSPARC Presentation Part 1

CryoSPARC Presentation Part 2

Day cryoSparc 1 Instructions

User Interface Overview

Videorecording

12:00 PM

Lunch break (if needed computing issues)

 

1:00 PM

cryoSPARC tutorial (cont'd)(Attendance by All)

 

 

  • Ali Punjani
  • Saara Virani
  • Suhail Dawood
  • Stephan Arulthasan

Q&A Day 1

Audio Transcript PM Session

3:30 PM Break  
3:50 PM Interactiive time (Practical attendees only)  


Thursday, June 11, 2020 (CryoSPARC tutorial runs ~all day)

Time

Title

Speaker

Workshop Reference Materials

8:30 AM

Q&A Session (continued) (Attendance by All)

 

9:00 AM

Processing using shared tutorial data (movies)(Attendance by All)

  • Motion correction & CTF estimation interpretation
  • Raw data curation
  • Particle picking methods
  •  Ali Punjani

Day 2 cryoSPARC Instructions

cryoSPARC Presentation Part 1

cryoSPARC Presentation Part 2

Stephan's Presentation

Videorecording

Videorecording

10:30 AM

Break

 

10:45 AM

  • Custom/Advanced 2D classification for curating particles
  • Discrete heterogeneity using multi-class ab initio reconstruction and heterogeneous refinement    (Attendance by All)
  •  Ali Punjani
Audio Transcript AM Session

12:00 PM

Lunch Break

 
1:00PM

Processing using shared tutorial data (particle stacks) (Attendance by All)

  • Homogeneous refinement to high resolution
  • Diagnosing orientation distributions
  • CTF refinement and aberration correction
  • Ali Punjani
2:30 PM

Break

 
2:45 PM

Advanced Topics (Attendance by All)

  • Masking and local refinement
  • Non-uniform refinement
  • Local resolution estimation and filtering
  • Advanced heterogeneity classification strategies
  • Flexible and continuous heterogeneity using 3D variability analysis
  • Ali Punjani
  • Stephan Arulthasan

Q&A Day 2

Audio Transcript PM Session

 

4:00 PM Interactive Time (Practical Attendees only)  
 


Friday, June 12, 2020

Time

Title

Speaker

Workshop Reference Materials

9:00 AM

CryoEM map resolution assessment, validation, visualization and segmentation (Attendance by All)

  •  Greg Pintilie

Greg's Presentation

Videorecording

Audio Transcript Pintilie Session

10:30 AM

CryoEM map deposition, validation report and retrieval (Attendance by All)

  •  Cathy Lawson

Cathy's Presentation

Videorecording

Audio Transcript Lawson Session

11:45 AM Lunch break  
12:45 PM General Discussion with Q&A (Attendance by All)  

Videorecording

Q&A Day 3

Audio Transcript Q&A

2:15 PM General Audience Webinar Closes (Practical attendees move to Zoom meeting conference site - sent to you earlier this week)  
2:30 PM Practical Participants presentations of materials (Practical attendees only) Zoom Meeting forum

Beginning Feb. 1, 2019, the Department of Energy (DOE) requires that all foreign nationals (non-U.S. citizens) looking to conduct work on-site at SLAC must provide their curriculum vitae (CV).  Please go to following link for more details on other information on visiting SLAC:  https://vue.slac.stanford.edu/foreign-nationals

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