Project Application

Steps to Access Cryo-EM

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Instructions for requesting National Center for Macromolecular Imaging Center resources:

1. Proposal Submission

Investigators who are interested in establishing a collaboration to use cryo-EM for their structure determination can submit a project application form through the User Portal.  We will assess the appropriateness of the proposed project as either a driving biomedical project or a user project. A driving biomedical project will involve significant effort of our staff in planning, engaging and conducting the research while a user project will utilize our established protocol to perform the research. Both new users and team members need to register before proceeding with a project proposal. Project proposals may be submitted at any time and will usually be reviewed within a month of application.

In addition to being reviewed for scientific merit the proposed research will also be reviewed for safety and hazardous material concerns. The outcome of these reviews will be communicated to users with an invitation to request microscope time.

Questions regarding proposal submittal can be directed to the Cryo-EM User Office.

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.  The user is responsible for all shipping costs - for non-hazardous shipments please ensure a prepaid return label is included with your shipment to SLAC.  We can archive the frozen grid during the period of the project.  Shipping instructions

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 NCMI cryo-EM facilities are 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 covering 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.