The SerialEM Script Repository

Auto Acquire on Holey Carbon

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Name Auto Acquire on Holey Carbon
Category Single Particle
Language SerialEM Scripting
Description Automatic image acquisition in holes of a carbon film via the "acquire at points" function of SerialEM
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 434
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 script is intended to be run with "Acquire at points" function of the Navigator panel. Typically the user would define a grid of points (every hole of a Quantifoil or Cflat grid) and run this Macro to acquire an image at each point.

Buffer J should contain a View image of a centered hole (this image should be acquired using only the center of the field of view, adjust this in the Camera Properties). After moving to a new point/acquisition area, the stage position is aligned relative to this reference image. Defocus is changed by 0.01 micron after each image. This value should be adjusted depending on the starting defocus, the range to be covered and the number of of images acquired in each single run.


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