Leginon Data Collection

Category: Software
Sub-category: Data Collection

Use Leginon software to collect data from cryoEM grids for single particle analysis.


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 Data Collection (for review before demonstration)

Additional reference information:

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

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 thresholding to automate data collection. 
  • Appropriate targeting to maximize data collection efficiency.
  • Recognizing issues that require staff assistance.

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 before the demonstration.

Each center has additional specific Safety, Setup, and Shutdown procedures.  Below, you will find those protocols for each center.

  • PNCC Site Specific Procedures
  • NCCAT Site Specific Procedures
  • S2C2 Site Specific Procedures

Supervised Practice with Leginon

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.

Practical Test

Center staff will assist in arranging time for independence testing during your scheduled data collection session.

A data collection 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. Two staff must independently certify you have past the test before you can independently run your session.

Additional information:

Recertification period

  • Merit badges for independent Leginon data collection are valid for ~4 months.
  • Recertification (to maintain active status) requires you to demonstrate proper operation while a center staff member shadows you.

Furthering your knowledge

  • Other data collection software:
    • SerialEM
    • EPU