US CryoEM Center Merit Badges

          Broadening access to high-resolution cryoEM for biomedical researchers and cultivating a skilled workforce.

What are cryoEM merit badges?

A merit badge is a proficiency qualification that allows for independent use of specified instrumentation and is cross-honored at the three US cryoEM service centers. Badges are awarded in three main skill areas:

  • sample preparation
  • microscope operations
  • data processing

If you are not a user of the national cryoEM centers, we hope the merit badge framework may still be useful by organizing cryoEM training materials into practical units relevant for specific steps of a cryoEM workflow.

How can I earn a merit badge?

Earning a merit badge requires successful completion of 5 steps:

  1. Review theoretical background information and SOP (independent study)
  2. Take the knowledge quiz (a pass/fail test)
  3. Have a practical demonstration (in-person training with center staff)
  4. Hands on Practice (supervised instrument use until you are ready for the independence test)
  5. Take the Practical test (2 separate staff at separate times evaluate using a standard checklist)

Obtaining a merit badge certifies to our operational staff that you are independent on a particular instrument or skill area. Merit badges are cross-honored at any national service centers after completing an orientation program and verifying proficiency (a trust-but-verify agreement). A researcher may need to obtain several merit badges to have sufficient skills to conduct a cryoEM research project but not all merit badges are needed to be an effective cryoEM practitioner. Work with your training coordinator to decide what badges are helpful for your training.

All users with active proposals at a national cryoEM center can earn merit badges as part of cross-training. Users should coordinate with the User Office at the respective center before a visit to plan what badges will be earned. Completion of the merit badge requires passing a knowledge quiz and a practical independence test. The background knowledge quiz can be completed at any time (including before on-site arrival). Demonstration, supervised practice, and independence tests should be scheduled with the user office or appointed training coordinator during your training visit. After successful completion of the merit badge knowledge quiz and independence test, the user has earned a merit badge – a designation shared between the centers.

Available Merit Badges?

Available merit badges reflect current instrumentation and best practices at the US national cryoEM centers. Each badge has associated background reference material, a standard SOP agreed upon by the three national centers, a knowledge quiz to test familiarity with essential theoretical background and the SOP, and an independence test checklist to guide practical training and supervised practice. They are in constant revision and construction and may evolve over time (versions are dated to keep track). Currently available badges are below with links to their individual pages. Badges still under construction will become available as they are completed. If you have particular requests for badges you would like to see expedited or that you don’t see here, let us know!

Sample Preparation

The start of a cryoEM project

TFS Vitrobot

Plunge freezing and instrument certification for Vitrobot Mark IV


Leica EM GP

Plunge freezing and instrument certification for Leica EM GP or GP2


Grid Clipping

Grid Clipping Certification



Cassette Loading and Autoloader Docking Certification


Coming soon:

  • Chameleon
  • Vitrojet

In the planning stage:

  • Working with cryogens
  • Negative staining
  • Support films

Microscope Operations

Microscope use and data collection

SerialEM Screening


Software Operation and Grid Assessment Certification for SerialEM


Leginon Screening


Software Operation and Grid Assessment Certification for Leginon


EPU Screening


Software Operation and Grid Assessment Certification for EPU


SerialEM Data Collection


Data Collection Certification for SerialEM


Coming soon:

  • Leginon for screening
  • EPU for screening

In the planning stage:

  • SerialEM for data collection, levels I & II
  • Leginon for data collection, levels I & II
  • EPU for data collection, levels I & II
  • Autoloader systems (inventory, TUI, etc.)
  • Gatan direct electron devices (Use of the Gatan K3 summit or K3 detector and DM)
  • TFS direct electron devices (Use of the Falcon3 or Falcon4 detector and TIA)

Data Pre-Processing

Feedback during data collection

In the planning stage:

  • General pre-processing (Data management, using the linux command line, useful software)
  • On-the-fly pre-processing (Getting feedback during your data collection)

How long is merit badge certification valid for?

Each merit badge has an expiration date to ensure a high level of proficiency is maintained. There is no one-time interval that fits each category. After a merit badge’s certification period elapses center staff will verify proficiency to renew the certification.


Sample preparation:

  • Room temperature work: ~1 year
  • Cryogenic work: ~6 months

Microscope operations:

  • General: ~3 months
  • Direct detectors: ~6 months
  • Side entry systems: ~3 months
  • Autoloader systems: ~1 year
  • Data collection programs: ~1 year


  • General ~1 year