User Access

Types of Project Proposals (i.e. Applications to use S2C2 cryoEM Facilities):

Service Project: This data collection service project is carried out by S2C2 staff, or by qualified facility users. Preliminary cryoEM data (images, 2D class averages, and/or 3D maps at lower resolution) are a prerequisite for a favorable application review. The duration of approved projects is valid for a period of two years with an option of renewal. Select 'Service Project' when submitting your application via the SLAC User Portal.

 

Exploratory Freezing & Screening Project: This cryo-specimen preparation project is provided to users whose projects do not yet qualify as a Service Project due to a lack of compelling preliminary cryoEM results. Project scenarios include: i) completely independent users who can perform freezing and TEM grid screening using S2C2 instrumentation (after being certified by S2C2 staff), ii) facility users who require S2C2 staff support for freezing and/or screening, or iii) a purely service-oriented engagement of S2C2 staff without the experimental involvement of the users. Exploratory freezing & screening project applications need to provide evidence of the readiness of the biological samples for freezing to receive a favorable review. The duration of approved projects is valid for a period of one year with a possible extension depending on project progress and resource availability. Select 'Exploratory Freezing & Screening Project' when submitting an application in the SLAC User Portal.

 

Training Project: This training service project is offered to individuals who would like to become familiar with the entire workflow of cryoEM single particle analysis (cryoEM SPA). This includes cryo-specimen preparation and screening, data collection and processing, and structure reconstruction, modeling, and validation. Trainees from different experience levels and professional backgrounds, such as primary investigators, faculty, staff, postdocs or graduate and undergraduate students, are eligible to apply. Typically, the training will take one-plus months to complete with additional guidance provided by S2C2 staff for an extended period up to one year. Trainees are embedded in the S2C2 for a period of one month to a year with non-contiguous training sessions over a period of time. Remote training is available for cryo-specimen screening, data collection and processing, and structure reconstruction, modeling, and validation; although in-person training is preferred for sample preparation. Priority is given to trainees who will share the expertise they gain at the S2C2 with their home institution. Select "Training Project" when submitting an application in the SLAC User Portal. Indicate your choice of i) Project-Tailored Training or ii) Comprehensive Training in the project description.

  1. Project-Tailored Training: This training program is offered to individuals who have a specific biological research project intended for cryoEM SPA. It covers any or all aspects of cryoEM SPA as needed for the trainee's particular project.
  2. Comprehensive Training: This training program is offered to individuals who would like to become familiar with all aspects of cryoEM SPA not directed toward any specific project. Typically, a standard biological sample is used for comprehensive training, such as apoferritin.

 

Who can apply to us S2Ccryo-EM Facilities?

S2C2 resources are open to the global scientific community, however, priority is given to NIH-funded projects, then nonprofit projects, followed by proprietary for-profit projects.

What are the project application review criteria?

All project applications are reviewed and approved by an external project evaluation committee. Review criteria are based on the mission of the S2C2 set forth here. Briefly, access to this resource is based on the feasibility and scientific merit of the project proposed, project readiness, the cryoEM research experience of the investigators, geographic diversity, and the status of the applicants' access to SPA-capable cryo-EM facilities at either their home institution or elsewhere.

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

How is microscope time allocated?

Microscope time for each approved project will be allocated cumulatively from a few days to weeks divided into multiple, continuous 24-hour allotments as appropriate for the project (e.g., 1, 2, or 3 consecutive days) and resource availability permits. All microscope sessions start or end at 9:00 am pacific time and are scheduled on a first requested first served basis.

User 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 acknowledgment wording, grant number, and co-authorship policy can be found here. Please inform us of your published results by emailing S2C2@slac.stanford.edu.

What is the cost of usage and training?

None, for academic & nonprofit users. The expenses associated with running and maintaining the facility and staff compensation are borne by S2C2 federal funding from NIH; however, expenses for biological sample procurement or production, user transportation, local room and board for users, and shipping of samples (and dewar return shipping) will be borne by the project applicants. For proprietary for-profit research, industry users will be charged a fee for microscope time and staff support.

Process for accessing S2CcryoEM resources

Communication with the S2C2 Operations Team

  • The S2C2 User Administrator is your administrative point of contact during steps 1 - 3 listed below and will timely share project evaluation outcomes, 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 4 - 6 listed below and will email the lead contact about two weeks before the microscope session to aid with logistics and answer any additional questions you may have.

1. Proposed Project Application, Submission, & Evaluation

Experimental 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.

  • Cyclic Application Deadline

    Project applications are due on 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 & supporting documents, project personnel, and funding sources. Further details may be found here.

  • Project Evaluation

    Proposed projects are sent to an external project evaluation committee and review criteria based on the mission 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 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, supporting preliminary data, 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