Process for Accessing S2C2 Cryo-EM Resources

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 project evaluation outcomes, coordinate SLAC onboarding, invite microscope time requests, and confirm your scheduled microscope session(s) with the lead contact via email.
  • The S2C2 CryoEM Specialist supporting your microscope session is your scientific point of contact during steps 5-7 and will email the lead contact about 2 weeks before the microscope session to aid with logistics and answer any additional questions you may have.

​​1. Proposed Project Application, Submission, & Evaluation

Access to resources at S2C2 can be obtained by submitting a project application through the SLAC User Portal. All project participants, both new users and project collaborators, need to register on the SLAC User Portal before proceeding with a project application. Previous SLAC SSRL/LCLS Users should apply in the SLAC User portal under their previous username.

  • Cyclic Application Deadline

​Project applications are due the first day of each month. With few exceptions, applications will be reviewed within the same month and results communicated soon thereafter.

  • Application Materials

​Project application materials consist of a title and abstract, a project description covering aims & impact, feasibility & preliminary data, proposed experiments, goals & expectations, and project expertise & resources, supporting preliminary data figures, publication history, biosketch, biosafety information (further detailed biosafety information will be required for the microscope time request) & supporting documents, project personnel, 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 missions of the S2C2 are set forth here.

  • Evaluation Outcome 

​The outcome of your proposed project evaluation will be timely communicated to applicants by the S2C2 User Administrator and those awarded approval will be invited to request microscope time to be scheduled.

2. Institutional User Agreement

The Stanford SLAC Cryo-EM facility is located on the premises of a Department of Energy National Laboratory. The DOE requires that a stand-alone 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 the 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 your SLAC user onboarding. Onboarding involves requesting a SLAC ID number (prerequisite for other requirements), requesting SLAC Unix and Window 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 Request

Microscope Time Requests are submitted through the SLAC user portal after your proposed project is awarded cumulative microscope time. Sample details and deviations from the originally proposed project are to be included in the request. The details of the samples to be brought to SLAC must be provided in the microscope time request. This information is used to determine if biosafety requirements are satisfied. The S2C2 User Administrator will allocate time and schedule your microscope session after microscope time requests have been received and biosafety requirements satisfied. 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, scheduling requests, participating project personnel, and return shipping information. Further details may be found here.

5. Sample Shipment to & from SLAC

Sample(s) should be shipped overnight/express to SLAC Monday through Wednesday the week prior to the date of your assigned microscope session to ensure timely arrival before the weekend. Express packages are delivered to the SLAC Receiving Department at 10:00 am Monday - Friday (excluding holidays), and subsequently delivered to the cryoEM facility. Frozen samples left in transit over the weekend usually crystallize or thaw, rendering them completely unusable.

Complete the form linked here to generate the required shipping labels to & from SLAC. The dry cryogenic shipping dewar and sample boxes/buttons (and sample grids, if requested) will be sent back to the users one week after the microscope session. We can store frozen grids during the project period. The user is responsible for all shipping costs. See this shipping page for more details, including international shipments.

6. Microscope Session & Remote Access

Microscope sessions are coordinated with and supported by your Scientific Point of Contact (SPOC), i.e., the S2C2 cryoEM specialist supporting your microscope session. Typically, remote users are provided observational access over Zoom with their cryoEM specialist, who is operating and physically present at the microscope. A typical microscope session workflow can be found here.

Secured remote access to operate the cryo-electron microscopes is available for qualified users and can be provided based on their needs through the cryoEM specialist supporting the microscope session.

7. Data Access & Transfer

Experimental data will be made available to the user through SLAC's central data storage computer cluster. A SLAC Unix account is required to access the data (see quick links for users to request an account). Standard Unix tools like scp and rsync are available, as is Globus. Further details may be found here.

8. Data Storage & Preprocessing

SLAC will provide short-term storage, i.e., two months, on disk and long-term storage, i.e., two years, on magnetic tape. On-the-fly preprocessing, alignment, and CTF estimation to evaluate image quality is available via Slack Channel.