SerialEM Training - Basic, Tomography, Single Particle, Advanced¶
(Each session is set 2 - 2.5 hours)
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)¶
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)
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.
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 …
SerialEM - Tomography (5 sessions)¶
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.)
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
demo and explain dual axis tomography data collection
demo how to rotate grid 90 degree and find the same location (registration transformation)
Low dose mode setup for Cryo Tomography applications
refresh cryo sample and holder handeling
LMM, MMM in low dose mode
bi-directional tilting series collection
batch mode for cryo data collection.
SerialEM - Single Particle (5 sessions)¶
positioning X,Y, Image Shift and Stage Shift, backlash
dragging to a new position, with Script/Macro
positioning for preselected multiple location using
positioning Z, using stage and using tilted beam image pair
demo and explain scripts
demo center beam using keyboard and script
demo simple script
LD, and explain actions
refine hole centering using template
draw grid point - manual picking and using hole finder
LD-groupand explain the ideas
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
go through whole single particle procedure
LMM, LD setup, MMM with “Z_byV2”, draw grid point, prepare hole template
supervising user practise session to go through all the steps
explain script command to limit defocus changing range
SerialEM - Advanced Topics (3 sessions)¶
SerialEM installation and Calibration
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
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