SerialEM Screening

Category: Software
Sub-category: Screening

SerialEM is a program that can acquire a variety of data from electron microscopes: tilt series for electron tomography, large image areas for 3-D reconstruction from serial sections, and images for reconstruction of macromolecules by single-particle methods.


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 SerialEM Screening (for review before demonstration)

Additional Information

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

  • The SerialEM User Interface
  • The Standard Operating Procedure
  • Troubleshooting
  • Screening Image Assessment

Here is the current quiz version:

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.

The video below is an introduction to the SerialEM screening workflow.

Supervised Practice with SerialEM

PNCC hosts semi-monthly online workshops on sample screening with SerialEM

For more information on workshops & training at PNCC: 

In addition to workshops, PNCC offers shadowing sessions for approved proposals

Practical Test

SerialEM mastery requires a significant time investment.  After you have attended a workshop and completed your follow-up training, staff will shadow you as you screen your own samples.  We will access your understanding of the software and workflow by following an evaluator checklist.

Staff may determine that you need additional shadowing sessions before granting you the SerialEM Screening Merit Badge.

Additional information:

Recertification period

  • Merit badges for independent SerialEM screening are valid for ~1yr.
  • Recertification (to maintain active status) requires you to demonstrate proper operation while a center staff member shadows you, either in-person or remotely.

Furthering your knowledge

  • Other data collection software:
    • Leginon
    • EPU