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
  • Low-level troubleshooting
  • What good screening images are

Here is the current quiz:


Example Questions:

  1. SerialEM Crashed, why are all images the same magnification?
    1. Low Dose Mode needs to be enabled in order to tie the optics settings and camera settings together into imaging states
  2. You just loaded a grid and took a search image, why is it all black?
    1. Column Valves, Thick Grid, Low Dose Mode is off
  3. You have extra time and want to collect a bunch of MMMs, why should you not do this?
    1. View contributes a minor about of dose per Å^2 and should be avoided until data collection
  4. I can’t access the microscope pC, can I still continue?
    1. Yes only need it for changing the C2 aperture
  5. Why do we leave the 150um C2 aperture in during screening?
    1. Simplify things so only need to use serialEM interface. Don’t need a parallel beam for screening
  6. Does serialEM automatically save the screening images you acquire?
    1. No, you need to manually save screening images
  7. How do you switch grids?
    1. SerialEM UI: One-line Scripts -> Load Cartridge #
    2. TEM UI: Autoloader OCX -> click slot, click load
  8. How do you make a stage movement?
    1. Shift + Right-Click drag
    2. Left-click place marker, “Go To Marker” in Navigator window
  9. What does right click drag do?
    1. Image shift until IS limit, then will stage shift
  10. What does shift + left-click do?
    1. Measuring Tool
  11. What can you learn from View images?
    1. Local ice conditions of your holes
    2. sometimes particle density
  12. Do I need to take record images? Why not just skip those?
    1. You sometimes cannot see crystalline ice until taking a record image and checking the FFT
  13. From this FFT, does this look like a good image?
    1. Show crystalline fft image
  14. Hexagonal Ice vs Cubic Ice
    1. could be various images but could also just group it all as crystalline ice
  15. Identify the vitreous ice ring
    1. probably should not use since you need a nicely aligned image
  16. What routine corrects Z-Height?
    1. Eucentric-Rough
    2. Eucentric-Fine (don’t need to use)
  17. What defocus target should I use for screening
    1. >-3 – could be a range.  Could also leave out

SerialEM Demonstration

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