SerialEM HowTo: Drift Control

Chen Xu

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For advanced operation, especially in single particle application, drift control is a must have. There are obvious reasons for this. After stage moved, it needs some time to settle down. Without drift control, the image taken could be completely useless and a waste of time. Visually watching it might work in manual mode, but users can be subjective about what is slow and fast. Quantitative measurement is needed.

In this document, I try to show you how to do drift control before each and every final shot using macros of SerialEM. It demonstrates how powerful and flexible the macro can provide.

You can also get pdf version of this document here.

Table of Contents
1 The Task Description
2 Macro Drift
3 Integrate macro Drift into main macro

1 The Task Description

What we want to do is that after getting to each location and after Autofocus is done we measure the drifting rate. This can be done by cross-correlating two images by some time apart.

If the drifting rate is high, wait certain mount of time and measure it again. If the drifting rate reaches below the set threshold, then jump out of the drifting macro and execute the following line in the main macro which usually is taking a shot. If the drifting rate is still above the threshold after certain numbers of measurements, then skip to the end of main macro, which is to end at this location.