SerialEM Note: Take Images At Two Different Mags For A Grid
- Author:
Chen Xu
- Contact:
- Date_Created:
March 14, 2026
- Last_Updated:
March 15, 2026
- Abstract
There is a need to collect images at two different magnifications for some of the LNP samples. For example, we like to take 20 items at 130kX, and then 50 items at 49kX. This is not hard to do it manually, but how to do this automatically without human intervention? With multigrid, we want to do this for each grid selected, also automatically. This can be very nice for screening purpose too.
In this note, I share what I figured out for this.
Prepare Imaging State
If our Low Dose areas are setup for LD_R at 130kX, and LD_V at 2000x, we need another set of imaging states for 49kX. Say we have prepared image state for LD_R at 49kX, and its related LD_V at 2000X, with state names as “49k” and “V-for-49k”, respectively. It not only takes care of mag, but also exposure time and dose etc too. So we are ready to go.
The reason for another state at LD_V is that R and V need to be lined up. If only switch LD_R, the new R and old V might not line up.
Three Places to Make This Happen
This is Acquire dialog windows of Multigrid operation.
The first 20 items with current LD setup can be defined in General Option - [v] Do subset. This part is straightforward.
Now after 20 items are done, we need to switch to new image state and continue Acquire. This can be done from General Option - [v] Run Script at end. And you define a script like this:
ScriptName SwitchTo_49kX
# script to load new image states and continue acquiring
GoToImagingState 49k
GotoImagingState V-for-49k
StartNavAcquireAtEnd
This is a little funny. At the “end”, we use a command to continue. So collection is going on.
The another ending number needs to be controlled. There are maybe many items with A flag, but we only collect 50 items at the new mag. So total items to collect in total at both magnifications are 70.
We can run another script as “[v] Run Script after Action”. The script can be something like below:
ScriptName EndAcquire
# Report how many A has been acquired.
ReportNavItem
if $navAcqIndex == 70
EndAcquireAtItems
Endif
This script is run at every item, the variable $navAcqIndex gives number of how many A items has been acquired. When the number is reached, we end the acquire completely using command “EndAcquireAtItems”.