SerialEM Training - Basic, Tomography, Single Particle, Advanced

(Each session is set 2 - 2.5 hours)


Chen Xu






This is to provide hands-on training on SerialEM. I will teach basic functions of the program. And I will teach how to use the powerful program for electron tomography data collection, and for single particle application as well.


You are required to have basic knowledge for TEM operation, preferred for Tecnai/Titan/Talos system. You should be able to operate scope independently to get a properly foused image. You are not required, however, to have pre-knowledge of SerialEM itself.

This document lists the training contents that are covered in the four catagories - basics, tomography, single particle and advanced topic.


If you have any thought and suggetion to improvement the training, I love to hear them.

SerialEM - Basics (3 sessions)

Session 1

  • Introduction to SerialEM, launch and exit the program. Explain system files and user setting file.

  • Explain how SerialEM controls microscope and camera, and its relationship with microscope and camera control software interfaces.

  • Explain SerialEM interface and layout - control panels and menus

  • Camera setup, how to acquire an image from SerialEM interface

  • Demo basic function such as Eucentricity (and shift beam to tilting axis)

Session 2

  • Refresh Tune-scope procedure

  • Prepare gain reference file in SerialEM

  • Explain image buffers and how to save buffer image into file, explain MRC stack and modes

  • Image Shift and Stage Shift

  • Eucentricity, Autofocus and montaging

  • Explain pixelsize and dose/dose rate.

Session 3

  • Introduce Navigator - navigater items: map, point and polygon

  • Demo full grid montage, Medium Map Montage (Using Image Shift and Stage Shift)

  • Realign To Nav Item, demo and explain

  • demo acquire map or image at multiple points …

  • introduce script/macro

SerialEM - Tomography (5 sessions)

Session 1

  • demo and explain how to collect a tilting series

  • explain cooking resin specimen, defocus and other parameters (mag, binning etc.)

  • explain proper sample preparation for platic sections (thickness, gold beads etc.)

Session 2

  • Supervise user to acquire MMM maps and collect a tilting series, answer questions and comment on the condition used.

  • Setup montage tilting series

  • Setup batch mode for multiple locations

Session 3

  • demo and explain dual axis tomography data collection

  • demo how to rotate grid 90 degree and find the same location (registration transformation)

Session 4

  • Low dose mode setup for Cryo Tomography applications

  • refresh cryo sample and holder handeling

Session 5

  • LMM, MMM in low dose mode

  • bi-directional tilting series collection

  • batch mode for cryo data collection.

SerialEM - Single Particle (5 sessions)

Session 1

  • positioning X,Y, Image Shift and Stage Shift, backlash

  • dragging to a new position, with Script/Macro

  • positioning for preselected multiple location using RealignToItem and ZeroIS.

  • positioning Z, using stage and using tilted beam image pair

  • demo and explain scripts Z_byG and Z_byV

  • demo center beam using keyboard and script

Session 2

  • demo simple script LD, and explain actions

  • refine hole centering using template

  • draw grid point - manual picking and using hole finder

  • introduce script LD-group and explain the ideas

Session 3

  • K2/3 specific - image format(MRC, TIFF), Compression, 4-bit special for Super-res frames

  • Asynchronize mode for K2/3 imaging, separate gain reference from raw image frame stack

  • Consideration for dose - total dose, dose per frame, frame time

  • In-fly frame aligning option

Session 4

  • go through whole single particle procedure

  • LMM, LD setup, MMM with “Z_byV2”, draw grid point, prepare hole template

  • run LD-group

Session 5

  • supervising user practise session to go through all the steps

  • answer question

  • explain script command to limit defocus changing range

SerialEM - Advanced Topics (3 sessions)

Session 1

  • SerialEM installation and Calibration

Session 2

  • Setup multiple accounts

  • Setup multiple system files

  • Setup executables for production and tests

  • Setup Dummy instance to pick target holes while main instance is busy collecting

Session 3

  • Explain SerialEM scripting interface and major functions

  • Explain example script to control LN2refilling and obtain K2/3 hardware dark background

  • Setup email alert system

  • in-fly aligning frames using standalone GPU server computer