3 Rough positioning, but faster

SerialEM's realign routine works well, very robust. It leaves certain amount of Image Shift in the end, for accuracy purpose. As I mentioned before, for high resolution images, we better off get rid of the Image Shift. We can do this using a macro as following:

Example 2. ZeroIS.txt


MacroName ZeroIS
# 
# Align one more round and get rid of IS 
# using the last image as ref

Copy A P
ResetImageShift
Loop 2
V
AlignTo P
ResetImageShift
EndLoop

This macro basically uses stage shift to compensate the image shift value. Due to inaccuracy of stage movement, we usually need to iterate. In this case, we loop twice. However, this involves taking single shots twice, which consumes some time too.

In the case which we don't need to be on target exactly, we can replace this macro with a quick version.

Example 3. ZeroIS-quick.txt


MacroName ZeroIS-quick
# position off limit in micron
limit = 0.3

ReportImageShift
X = $reportedValue1
Y = $reportedValue2
IS = sqrt $X * $X + $Y * $Y

Loop 1
If $IS <= $limit
   ClearAlignment
Else 
   ResetImageShift
Endif
EndLoop

This macro doesn't take any shot. Instead, it either clears the alignment and image shift or just compensates the image shift using stage shift for once, based on the Image Shift limit you set.