[3dem] Newbie question - Defocus mistmatch

shixinwang at micron.com shixinwang at micron.com
Sat Oct 25 13:56:44 PDT 2008

The defocus value reading from the scope is normally not the real
distance along the optical axis. It is proportional to the Z value, but
the ratio is normally not 1. 
You may run a test to roughly calibrate the defocus value against the
sample height Z (by moving sample up and down). Or you can use a tilted
flat sample: focus it a one location, move to another location (with
known distance from the first location), set the focus again. The real
height change is to be calculated from tilt angle and the distance
moved. This will give you the ratio to calibrate the focus value. 
Is the power spectrum a good way to calculate defocus value? I am not
sure about this. Theoretically, it should work for a thin amorphous
sample, to a certain defocus range. In your case, are you trying to use
it to measure the sample thickness? It won't work. Because it ignores
the thickness of the sample (correct me if I am wrong on this). The
defocus reading from the scope won't work either, because your sample
cannot be that thick. 


From: 3dem-bounces at ncmir.ucsd.edu [mailto:3dem-bounces at ncmir.ucsd.edu]
On Behalf Of Eduardo Sanz Garcia
Sent: Friday, October 24, 2008 6:17 PM
To: 3dem at ucsd.edu
Subject: [3dem] Newbie question - Defocus mistmatch

Dear 3DEM users,

Has anyone observe a mismatch between the defocus values reported by the
electron microscope software and the real defocus values computed from
the powerspectrum?

Example of a pair of micrographs:

First micrograph (this one is the reference):

*	Reported defocus value by the microscope: -2 microns 
*	Defocus value computed from the powerspectrum: -2.2 microns 

I use the "series" option to change the defocus and take the other

Second micrograph:

*	Reported defocus value by the microscope: -4 microns
*	Defocus value computed from the powerspectrum: -2.6 microns
(here is the problem, it should be closer to -4 microns). 

We use a Tecnai F30.
Is this a problem of  hysteresis?
Thank you very much.

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