SerialEM Note: More on MMM Centering

Author:

Chen Xu

Contact:

<chen.xu@umassmed.edu>

Date_Created:

March 2, 2026

Last_Updated:

March 2, 2026

Abstract

Now Realign in LM range works better due to two recent improvements is SerialEM. 1) The property “RealignItemMaxLMField” is taken care of automatically for LM range, and 2) The aperture sizes for both condenser and objective lenses are now properties for the Map item in navigator. Thus, realign routine becomes a more convenient way for positioning a mesh accurately.

However, there is another source of MMM’s off-centered problem I did not realize much before - the lateral shift! If your mesh Z height changed a lot from initial Z of LMM map, your MMM will be off centered due to this lateral shift. If the Z change is 100 micron or more, the lateral shift becomes fairly noticeable. This needs to be taken care of for accurate centering for MMM mapping. It is not uncommon for meshes to have quite different Z heights acrossing a grid.

This issue can be simply addressed by another round of Realign.

The Script to Run after Z change

One can use Realign or just use stage shift only to move to a mesh initially. Before acquiring the MMM map, the Z height must be properly adjusted. We normally use “Eucentricity by Focus” to correct the Z height for the selected mesh.

After that, Realign can be run again to fine-tune the XY position of the mesh, correcting the XY offset caused by the Z-height adjustment before starting MMM montaging. The key point is to skip any Z adjustment during this second realignment so that the stage does not revert to the original Z height of the LMM grid map.

ScriptName MMM_Centering

ReportStageXYZ
Z0 = $repVal3

RealignToNavItem 0
Eucentricity -1

ReportStageXYZ
Z1 = $repVal3

If ABS ( $Z1 - $Z0 ) >= 70
   SkipZMoveNextNavRealign
   RealignToNavItem 0
Endif