[3dem] Newbie question - Defocus mistmatch

rg2502 at columbia.edu rg2502 at columbia.edu
Sun Oct 26 07:34:24 PDT 2008

I assume that you are using the low dose program on your tecnai when  
you say that you use the series option.  One cause of the defocus  
mismatch is that you are using a different magnification to focus than  
the one you are using to take the exposure.  The large descrepancy in  
resulting defocus is likely related to the fact that you do not have a  
parfocal lens series.  A way to check this is to go to the  
magnification that you use to focus and check what the objective lens  
current readout is.  Now change the magnification to what you are  
using for exposure and check what the value is there.  My guess is  
that they differ by the amount that you observe.  There is a step in  
the alignment procedure where you can correct for this (right now I  
can not recall exactly where, but you should be able to find it out  
from FEI).  The second reason that defocus settings can go astray  
,assuming the grid is flat and you are consistently at the eucentric  
plane, is the calibration of the difference in lens value as compared  
to what defocus it gives you.  This value is set in the registry and  
generally is only set by the service engineer with help from the  
factory.  I hope that helps.  These are the main reasons for these  
inconsistencies that are related to the software.  Shixin's  
suggestions are related to the electron optics.  Good luck.

Quoting shixinwang at micron.com:

> 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.
> Shixin
> ________________________________
> 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
> micrograph.
> 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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