Project Application

New project applications are due the first day of each month.  With few exceptions applications will be reviewed within the same month.  COVID-19 related proposals will have no deadline and will be reviewed expeditiously.


Types of application to use our cryo-EM facilities:

Large scale data collection: This is for projects which have preliminary cryoEM results (images, 2D class averages and/or 3D maps at lower resolution). The approved projects will be allocated cumulatively from a few days to weeks of data collection in different allotments depending on the availability of the instruments. The data collection will be performed by the users and/or the Center staff.


Exploratory data collection: This is for projects which may not have compelling cryoEM results but have sufficient biochemical data to suggest that preliminary data can be obtained to support subsequent application for large scale data collection. The allocations of instrument times will be determined by the progress of the projects and the availability of the resources. The data collection will be performed by the users and/or the Center staff.


Project-tailored training program: We offer training to individuals who have specific biological projects intended for cryoEM structure determination. This a-la-carte style of training can cover any or all aspects of cryo-specimen preparation and screening and data collection for their particular project, using our facility. Generally, the training will take 2+months to complete and additional guidance by our staff will be provided for an extended period of 2-3 months. Trainees can be established investigators, staff, postdocs or students. 


Comprehensive cryoEM training: This program is designed to train individuals who would like to become familiar with all aspects of cryoEM from cryo-specimen preparation, data collection and processing, modeling and structure validation, not directed toward a specific project. Generally, the trainee can be embedded in our Center for a period of 1 month to a year. It is also possible for the trainee to divide their training into multiple shorter intervals to learn different steps in the entire workflow of cryoEM structure determination. The curriculum of training is tailored to the individuals needs and backgrounds. Trainees can be established investigators, staff, postdocs or students. Priority will be given to underserved geographical regions, and the likelihood that the trainees will carry back and share the expertise they gained with their home institution. 

Who can apply for cryo-EM usage?

S2C2 resources are open to the global scientific community but priority is given to NIH-funded projects. Access to this resource is based on the merit of the proposal, the cryo-EM research experience of the investigators, geographic diversity, and the status of access to cryo-EM elsewhere.

What are the project review criteria?

Review criteria are based on the missions of S2C2.

What is the cost of usage and training?

None. Expenses for transportation, local lodging, and shipping of samples will be borne by the participants.

User Obligations

S2C2 provides technical tools for world-leading science at no charge with the understanding that significant results are to be publicly disseminated. Users must acknowledge the NIH grant (U24GM129564) and the Stanford-SLAC Cryo-EM Center staff in publications.  Please inform us of your published results by sending a message to

Instructions for requesting S2C2 cryo-EM resources

1. Proposal Submission

Experimental access to resources at the Stanford-SLAC Cryo-EM Center (S2C2) can be obtained by submitting a project proposal through the User Portal (see example of proposal form). Both new users and team members need to register before proceeding with a project proposal. Presently, each approved Proposal permits the use of our cryo-EM facilities over a 2-year period.  Once your proposal has been approved, you will be invited to submit Microscope Time Requests to schedule time on the microscopes.

  • Application Deadline: Proposals can be submitted at any time, and will be reviewed monthly.

  • Project Merit Evaluation: Project proposals are sent to an external panel to review the feasibility and scientific merit of the proposed research and the readiness of the project. Safety and hazardous material concerns will be reviewed by SLAC/Stanford staff. The outcome of these reviews will be communicated to the users and a call sent out to invite users to request microscope time.

2. Microscope Time Request

Request for on-site or remote time to collect images from your samples must be submitted through a Microscope Time Request (available through the user portal after your project proposal is accepted). Sample details and variations from the original project Proposal are to be included in the Microscope Time Request. The management team will make allocation determinations after Microscope Time Requests have been submitted. The details of the samples to be brought to SLAC must be provided at this point. This information will be combined with that from the Proposal to determine if biosafety concerns are satisfied. Depending on the load on our instruments, we will schedule a microscope slot as soon as possible after the project and biosafety approvals are made.

  • Frequency of Usage: Each recurring time allocation request will be made by the Center staff on the basis of the availability of the instrument, the progress of the previous data sets and the review ranking of the proposal. Remote data collection is routine.

  • Communication prior to Data Collection: A conference call will be scheduled with our Center Staff two weeks prior to the scheduled microscope time to aid with logistics and any questions you may have.

3. Sample Shipment to and from SLAC: Users will ship the frozen grid to SLAC Bldg. 57 one week prior to the date of data collection. The sample and the dry shipper will be sent back to the users after one week of the data collection - please ensure a pre-paid return label is included with your shipment. We can archive the frozen grid during the period of the project. If the user desires to have the sample and its Dewar back, the user is responsible for all shipping costs.  See shipping page for more details.

4. Remote Access: Secured remote access to operate the cryo-electron microscopes is available. Users who wish to make use of this must apply for a SLAC unix account and indicate remote data collection as part of the Microscope Time Request. Further details here.

5. Data Transfer: As soon as your experiment has started, your experimental data will be made available on our central data storage. A SLAC unix account is required to access the data. Standard unix tools like scp and rsync are available, as is Globus. Further details here.

6. Data Storage and Analysis: SLAC will provide a short term (2 months) storage on disk and long term (2 years) on magnetic tape. On-the-fly data analysis to evaluate image quality is available. The more extensive computing resources required for 3-D reconstruction are available through a competitive application process.

7. User Agreement: The Stanford SLAC Cryo-EM Center is located on the premises of a Department of Energy laboratory site. As such a Cryo-EM 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 cryo-EM experiments for any group from that institution. The list of institutions that have User Agreements with SLAC can be found here.

Are you still interested? Here is how to access Cryo-EM.


Coming to SLAC for Cryo-EM

 Information for Visitor/User/Employee