SerialEM Data Collection

Category: Software
Sub-category: Data Collection

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

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

Helpful videos referenced in the SOP:

The SerialEM data collection workflow

Gatan GIF Tuning & K3 DED Gain Collection

Record-View Offset Adjustment

Supervised Practice with SerialEM

PNCC hosts semi-annual on-site workshops on data collection 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 a evaluation checklist.

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

Additional information:

Recertification period

  • Merit badges for independent SerialEM data collection 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