SerialEM HowTo: Positioning X, Y

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 most frequently needed tasks is to go to an area on an EM grid. For example, after you take an image shot, you want to move to a new location with interested feature in the image view. Or you might want to go to a new location that is far a way from current location, say, another end of the mesh or a position in a different mesh. Usually, the way we do this is to drive stage trackball or joystick on the right pad while watching the moving on large screen, on an analog TV camera or on a CCD camera running in continuous mode. It can get job done this way. However, there are a few drawbacks including time and dose consuming. Apparently, as you can see, it is impossible to perform efficient, automatic data collection in this manual fashion.

Due to the mechanical inaccuracy of the stage movement, going to a target position accurately is perhaps the most challenging job in SerialEM and any other computer control program.

In this document, I want to show you some tips with SerialEM how to go to an area accurately enough, and conveniently.

You can also get pdf version of this document here.


Table of Contents
1 The Task
2 Using Macro, for a single point
3 Using SerialEM's built-in function "Realign"
4 In Low-Dose Mode

1 The Task

If there is one or more feature spots in a CCD image view, we want to move specimen stage to each spot accurately.

With SerialEM, one can accomplish this task manually by going through the following steps.

  1. Drag the image by holding down the right mouse and move the image until the interested spot is at the center of the CCD area.

  2. Click on ResetImageShift button in Image Alignment & Focus control panel.

  3. Take a shot, View in this example.

  4. Repeat last three steps until the spot is centered.

This is already better than manually driving the stage continuously. It is more convenient and saves dose for the specimen. However, the above procedure is still not ideal for advanced control such as automation. It has too many steps that require human interaction, let alone there are more than one spot we want to move to. Therefore, we need to make it even easier, if possible.