serialEM Macros

serialEM Macros and Scripts

We have collected several very simple serialEM macros (aka scripts) here as examples of sequences of events that serialEM can be programmed to do automatically.

Sweep Through Magnifications and Measure Defocus

A perfectly parfocal lens or set of lenses stays in focus when the magnification and/or focal length is changed. Most electron microscopes are relatively parfocal, but few (likely none) are perfectly parfocal. The important thing to keep in mind is that defocus differences as the magnification is changed are quite reproducible and involve a consistent offset when the mag is changed. For example, if the defocus is X at 200kx, the defocus at (say) 50kx will be X + offset. The following serialEM script determines these offsets by determining the defocus at each magnification over a range.

View data collected from the Electron Microscopy Center (EMC) using this script

Move Stage, Wait and Record Image(s)

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Move Stage, Allow Drift to Settle and Record Image(s)

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