Comprehensive CryoEM Training Program

Program Objective

This training program is offered to individuals who would like to become familiar with all aspects of cryoEM methods, but not necessarily directed toward any specific project.  This program is best suited for scientists early on in their own research and training, where biospecimens of interest have yet to be procured, but the scientist is ready for in-person hands-on learning of cryoEM workflows.  A standard biological sample is used for comprehensive training, such as apoferritin. We invite researchers of all electron microscopy skill levels to apply for our comprehensive cryoEM training program, which is offered by a team of cryoEM experts.  Residency may vary in length and different aspects of cryoEM workflows can be emphasized, as requested by the trainee.

What aspects of cryoEM are covered?

As this training program is comprehensive, we cover all aspects of cryoEM workflows using a standard biological sample (e.g., apoferritn).  This includes cryo-specimen preparation and screening, data collection and processing, and image reconstruction, modeling, and structure validation.

Who can apply for comprehensive training?

Trainees from different experience levels and professional backgrounds, such as principal investigators, faculty, staff, postdocs, or graduate and undergraduate students, are eligible to apply.

What are the training application review criteria?

All project applications are reviewed and approved by an external project review committee.  Review criteria are based on the mission of the S2C2 set forth here.  Briefly, access to this resource is based on the cryoEM research experience of the investigators, geographic diversity, and the status of the applicants' access to cryoEM facilities at either their home institution or elsewhere.

Safety and biohazardous material concerns will be reviewed by the Stanford health and Safety Department's Biosafety & Biosecurity Group and the SLAC Environment, Safety, and Health Division's Biological Safety Program.

What length of residency can be requested?

  • ​Any suitable period from one week to one year.
  • The period of residency will be determined by the applicant's need and available space at S2C2.

​Trainee Obligations?

All users must be registered in the SLAC User Portal and meet all SLAC/DOE access requirements to use the cryoEM facility which includes safety training, an institutional user agreement, and additional documents to be uploaded.

S2C2 provides technical tools and staff support for world-leading science at no charge with the understanding that significant results are to be publicly disseminated.  Users must therefore acknowledge in publications the NIH grant that supports facility operations, the supporting S2C2 CryoEM Specialist, and the specific microscope(s) used.  Acknowledging the supporting S2C2 CryoEM Specialist is especially appreciated.  Expected acknowledgement wording, grant number, and co-authorship policy can be found here.  Please inform us of your published results by emails S2C2@slac.stanford.edu.

What is the cost of training?

None, for academic & non-profit trainees.  No fees will be charged for in-residence training, microscope time, or study materials.  The expenses associated with running and maintaining the facility and staff compensation are borne by S2C2 federal funding from NIH; however, expenses for trainee transportation and local room and board will be borne by the trainee and their home institution.  

Will any reading material be provided?

Successful training applicants will receive online reading material, including video clips and PDF copies of material, as needed.

Process for Accessing the Comprehensive Training Program

Communication with the S2C2 Operations Team

  • The S2C2 User Administrator is your administrative point of contact during steps 1-4 listed below and will timely share evaluation outcomes, coordinate SLAC user onboarding, invite microscope time requests, and confirm your scheduled microscope session(s) with the trainee via email.
  • the S2C2 CryoEM Specialist running the comprehensive training program is your scientific point of contact during steps 6-7 and will email the trainee about 2 weeks before your residency to aid with logistics and answer any additional questions you may have.

1. Comprehensive Training Program Application, Submission, & Evaluation

Participation in the comprehensive SPA training program at S2C2 can be obtained by submitting a comprehensive training project application through the SLAC User Portal.  All project participants, both new trainees and principal investigators, need to register on the SLAC User Portal before proceeding with a comprehensive training project application.

Cyclic Application Deadline: Comprehensive training project applications are due the first day of each month.  With few exceptions, applications will be reviewed within the same month and results communicated by the following deadline.

Application Materials: Comprehensive training project application materials consist of a title and abstract, a proposed length of training residency, a training and experience document covering goals & motivation, current research, institutional impact, cryogenic electron microscopy experience, other electron microscopy experience, and operational experience, and support documents consisting of a trainee biosketch or curriculum vitae and a PI biosketch or curriculum vitae (optional), project personnel details, and funding sources.  Further details may be found here.

Project Evaluation: Proposed projects are sent to an external project review committee and review criteria based on the mission of the S2C2 are set forth here.

Evalution Outcome: The outcome of your comprehensive training project evaluation will be timely communicated to applicants by the S2C2 User Administrator and those awarded approval will be invited to request microscope time and proceed with onboarding.

2. Institutional User Agreement

The Stanford-SLAC Cryo-EM Center is located on the premises of a Department of Energy national Laboratory.  The DOE requires that a CryoEM User Agreement, or addendum to an existing DOE User Agreement that covers experiments at SSRL and LCLS, must be executed before the beginning of any experiment.  Once executed, the agreement will cover cryoEM experiments for any group from that institution.  The list of institutions that have existing User Agreements with SLAC can be found here with instructions on obtaining institutional user agreements if your institution doesn't yet have an existing agreement on file.

3. SLAC User Onboarding

The S2C2 User Administrator will coordinate the trainee's SLAC user onboarding.  Onboarding involves requesting a SLAC ID number (prerequisite for other requirements), requesting SLAC Unix and Windows accounts, and taking an initial online safety and security training.  A user security/safety badge is obtained after completing the in-person safety orientation once you are onsite.

4. Microscope Time Requests

Microscope Time Requests are submitted through the SLAC user portal after your comprehensive training project is awarded cumulative microscope time.  Sample details of the specific biological standards employed in comprehensive training are to be included in the request.  The S2C2 user Administrator will allocate time and schedule your microscope session after microscope time requests have been received.  All microscope sessions start or end at 9:00 am pacific time and are scheduled on a first requested first scheduled basis.

Time Request Materials: Time request materials consist of project information, instrument information, sample information, supporting preliminary data, scheduling requests, and participating project personnel.  Further details may be found here.

5. Lodging and Traveling to SLAC

Rooms are reserved for users of our CryoEM Facility at the Stanford Guest House situated at SLAC.  You will be asked to provide information about the dates of your scheduled session and your assigned proposal/project number.  SLAC's Visitor, User, and Employee (VUE) Center has an Accommodations page with alternative lodging options.  For assistance in arranging transportation to SLAC and local accommodations, trainees should contact our administrative associate, as needed.

6. Comprehensive Training - Residency Schedule

The daily agenda/schedule for your residency is coordinated with your Scientific Point of Contact (SPOC), i.e., the S2C2 cryoEM specialist providing your comprehensive training.  Your SPOC will provide reading materials and training in cryo-specimen preparation and screening, data collection and processing, and image reconstruction, modeling, and structure validation, and will reserve the appropriate equipment, as needed.

7. Post Residency Support

After your training residency concludes, our cryoEM specialists will continue providing remote support via emails and Zoom, as needed, for up to one year post residency.