Screening with Leginon

Category: Microscope operations
Sub-category: Screening and software

Use Leginon software to screen cryoEM grids for assessing quality.


You must complete all required safety training at the center you are visiting before hands on training. Coordinate this with the user office or training coordinator.


Relevant Training Modules (to review until you can pass the knowledge test):

SOP for Leginon grid screening (for review before demonstration)

Additional reference information:

  • A full Leginon manual (with more detail than is necessary for this badge) can be found at:

The pass/fail knowledge assessment will test your understanding of the following concepts:

  • The Leginon interface and “node-ledge”: what nodes to use to perform different tasks).
  • Principles of multi-scale imaging.
  • Recognizing issues that require staff assistance.
  • Recognizing “good” screening images.

Here is the current quiz:

A workflow demonstration should be scheduled with center staff. The demonstration will cover all points of the SOP. You must have passed the knowledge quiz and reviewed the SOP and tutorial videos before the demonstration.

The Screening with Leginon badge is specific for use at NCCAT, so there is no added site specific SOP.

Schedule your supervised practice with the user office or appointed user coordinator. This can be scheduled for the same session as the demonstration. During supervised practice, center staff will be present for the full duration of the session to provide feedback and answer questions with the goal that you can pass the practical test for independence with no assistance. The number of supervised practice sessions will be tailored to the user, and if necessary, more than one session can be scheduled before taking the practical test.

Center staff will assist in arranging time for access to the necessary equipment and testing for independence. The practical test can not be scheduled during the same session as supervised practice.

A screening with Leginon checklist will be used by the certifying staff to test for proper use of the instrument with a pass/fail outcome. All steps on the checklist must be performed to pass. You may use any instructions normally posted as a guide during the session.

Additional information:

Recertification period

  • Microscope operation merit badges are valid for 9 months.
  • Recertification (to maintain active status) requires demonstrating proper use and care in front of a center staff member.