The SerialEM Script Repository

Manual Acquisition

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Name Manual Acquisition
Category Single Particle
Language SerialEM Scripting
Description Manual data collection on a user centered area
Author Juha Huiskonen
Website link

Version History

Version 1.0


This script requires additional scripts to be run – please refer to the Required Scripts section below.

Upload date March 01, 2018
Download count 410
SerialEM version ≥ (untested)


Required Scripts

The following scripts are required to run this script, either because the are called directly or they provide functions:

Related Scripts

The following scripts provide a similar or related functionality, but are not required to run this script:


This macro is intended for manual data collection, where the user centers the acquisition area manually in View mode. This centering may involve a large image shift, which is first minimized by moving the stage. Then the same steps as in fully automated mode are run (beam centering, drift settling, focus pair acquisition).

Effectively, the user only has to center a feature of interest, run the macro and repeat. This is beneficial if the sample is not fully covering the grid, is present only in some holes etc.

Defocus is changed by 0.02 micron after each image. Typically we start collecting at -2.5 micron defocus and collect data gardually closer and closer to focus, finishing around -1.5 micron defocus.


This code can be shared and adapted under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) License (