Project Application

Steps to Access Cryo-EM


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 preliminary cryo-EM results (images or maps), the cryo-EM research experience of the investigators, and the status of access to cryo-EM elsewhere.

Who can apply for training?

Trainees can be established investigators, staff, postdocs or students.

What is the cost of usage and training?


User Obligations

Users must acknowledge the NIH grant (U24GM129564) and the Stanford-SLAC cryo-EM Center staff in publications.

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 1-year period. As we await delivery of our new cryo-EM instruments specifically for this new Center (expected in the fall of 2019), we shall be providing limited access to our existing cryo-EM resources. Once your proposal has been approved, you may submit Microscope Time Requests to schedule time on the microscopes.

  • Application Deadline: November 1 is the next user access application deadline for this year. Proposals can be submitted at any time, and will be reviewed within a month of the application deadline.

  • 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 expect the earliest time to be scheduled for a microscope usage is two months after the project and biosafety approval 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 possible.  

  • 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 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.

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 a part of the 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 (3 months) storage on disk and long term (3 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 cover experiments at the SSRL and the 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.