US CryoEM Center Merit Badges

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

What are cryoEM merit badges?

Receipt of a merit badge qualifies a user for independent use of specified instrumentation and is cross-honored at all of the US cryoEM service centers. These proficiency badges are awarded in three main skill areas:

  • sample preparation
  • microscope operations
  • data processing

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

All users with training proposals at a national cryoEM center can earn merit badges as part of their training. Users should coordinate with the User Office at the respective center before a training visit to plan what badges will be earned. Completion of the merit badge requires passing a knowledge quiz and a practical independence test. Review of the SOP and 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 user/training coordinator during your time at the center. 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.

  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 available checklist)

Obtaining a merit badge certifies that you are independent on a particular instrument or skill area to operational staff. Also, merit badges will be cross-honored at other 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.

What merit badges are available?

Available merit badges reflect current instrumentation and best practices. Each badge has associated background reference material, a full 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. Currently available badges have colored buttons below that link to the individual badge 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 you don’t see here, send us a message!

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,


In development, coming soon:

  • Working with cryogens
  • Autoloaders (nanocab handling & care; sample loading/recovery)

In development, planning stages:

  • Negative staining
  • Support films
  • Chameleon
  • Vitrojet

Microscope Operations

Microscope use and data collection

In development, coming soon:

  • SerialEM for remote screening

In development, planning stages:

  • SerialEM for screening
  • Leginon for screening
  • EPU for screening
  • SerialEM for data collection, levels I & II
  • Leginon for screening, levels I & II
  • PU for screening, 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



Data management and basic linux command line.




Use of center specific on-the-fly packages.


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