3 Using SerialEM's built-in function "Realign"

As you can see, the macro ZeroIS can only work for a single position, as you have to manually "drag" to that position first. And you might have the question in your mind already: "why not use the SerialEM built-in function realign?". Indeed, as an very important part of navigator, realign can get to the position of a point item nicely if the point item is inside a valid map. And this realign function can even be used repeatedly for multiple point items by Navigator → Acquire at Points → Realign to item.

However, due to mechanical inaccuracy of stage movement, in order to get the point precisely, realign procedure always leaves a small amount of IS value in the end. If we want 0 IS for imaging condition of microscope state, we can simply call the macro ZeroIS afterwards.

Here is an example of using macro command for realign function together with ZeroIS.

Example 2. Realign.txt


MacroName Realign
# a macro to realign to a nav item and then clear
# out any ImageShift afterwards.

RealignToNavItem 0
Call ZeroIS

Lets look at this macro. As usual, all the macro commands in the macro get executed line by line when we run this macro. Here, the line


RealignToNavItem 0

is a macro command. It has an argument, 0. It brings an navigator item to the center of CCD view by combining Image Shift and Stage Shift. This involves taking some images at the same magnification as map was created. The argument 0 here means that after the procedure the scope will NOT resume to the original state right before the procedure. The line after it


Call ZeroIS

calls another macro. As we see from the previous example, macro ZeroIS will clear out any IS left and still make the target spot centered. It uses V shots in this case.

The macro will work nicely, but the scope will be left at the mag of that of the map, even it starts from a different mag. It doesn't sound anything problematic. However, in the case of Low-Dose mode, the argument 0 will result in leaving Low-Dose mode and not coming back in. That might not be what we wanted.