3 Determine Eucentric Focus and Set to it

The key is to determine what the value of Standard Focus at Eucentric Focus is for a magnification and how to use this value to set the objective lens from anywhere to the Eucentric Focus when needed. And this needs to be done at any one of the multiple magnifications.

SerialEM provides two commands for this. They are ReportFocus and SetStandardFocus #. Lets take a look how to use them.

If we first make sure the specimen is at eucentricity and we precisely focus the image, we can then get the Standard Focus value for Eucentric Focus by running a SerialEM macro command ReportFocus.

Example 1. ReportFocus


MacroName ReportFocus
# find the standard value at the current objective condition.

ReportFocus

The above macro command outputs a value like -0.000038. This value defines the objective strength specifically. In this case, it is linked with Eucentric Focus. With this value, we can set the objective lens to a Eucentric Focus by running another SerialEM macro command called SetStandardFocus, at any time.

Example 2. SetStandardFocus


MacroName SetStandardFocus
# set objective to a specific level

Std_Focus = -0.000038
SetStandardFocus $Std_Focus

As you have probably realized, these two commands can be used to determine and later reset to an (any) objective lens condition. Eucentric Focus is just one special case.

Since Feb 7, 2013, SerialEM beta version has provided a calibration Standard Focus to allow one record Standard Focus values for Eucentric Focus at all magnifications and save them as part of calibration. This Standard Focus calibration menu replaces the old Standard LM Focus which only allows for LM mag range. There is also a new macro command SetEucentricFocus to retrieve a value for current magnification and set objective lens to. These two new features make our task more conveniently.