SerialEM HowTo: Take Multiple Shots around A Hole Using Image Shift

Chen Xu

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SerialEM is a powerful program for EM data collection. Although it is maybe originally designed for tomography data collection, it is equally powerful and flexible for single particle EM tasks.

One of the scenarios in single particle low dose data collection is to take a few shots around a hole, rather than only take a single shot at that location. In this document, I would like to show how to do it using SerialEM's macro function.

You can also get pdf version of this document here.


Table of Contents
1 Task Description
2 The Macro

1 Task Description

After moving specimen to a location, for example, center of a hole on Quantifoil or C-flat grid, one might want to take more than one shot around the hole. Otherwise, the size of the detector like K2 camera can only capture small portion of the hole, it could wast quite some good area if only take a single shot.

There are two ways to take shots at different spots. One is to move stage and the other is to use Image Shift without moving stage. Moving stage and settling down cost more time. Therefore, using ImageShift seems to be an attractive option. However, we have to be aware of the two things in this setup.

  1. Image Shift means beam tilting above the specimen. This introduces image distortion. The large the Image Shift used, the more the distortion is. And it could also introduce extra coma of beam incident to specimen, even scope is well aligned.

  2. In order to take multiple shots around a single hole, we have to limit our beam size so it doesn't touch the adjacent area. If we don't have parallel beam, or if we cross beam too much to get small size, the convergent beam gives bad coma too. To avoid that, one of the good ways is to use very small C2 aperture.