[3dem] Magnification anisotropy at low mag settings on Titan Krios

Marin van Heel marin.vanheel at googlemail.com
Mon May 19 05:53:45 PDT 2014

Dear All,

I have spoken to Max Haider about the issue and he told me there is a 
straight-forward reason for this magnification behavior with the Cs 
corrector.  The combination of a quadrupole lens at the beginning of the 
corrector and another one at the end of the corrector can jointly cause 
this effect.  On our NeCEN Cs corrected instrument, we measured up to 7% 
magnification difference in two orthogonal directions in the first data 
sets we collected with a new Falcon-2 camera on our Cs-corrected 
instrument. This large difference in magnification has since been 
corrected by re-adjusting the corrector but this issue remains a concern 
for high resolution work. In particular, Rishi and Sacha found that the 
fine tuning of the Cs Corrector is only effective/stable after the high 
tension has been on and constant for some 10-12 hours.



On 04/04/2014 08:10, Marin van Heel wrote:
> Dear All,
> This could also be due to astigmatism in the illumination system. Such 
> astigmatism would mean that the illumination is not parallel to the 
> optical axis in (at least) one direction leading to anisotropic 
> magnification effects as per our paper:
> G. van Duinen,  M. van Heel, and A. Patwardhan,* Magnification 
> variations due to illumination curvature and object defocus in 
> transmission electron microscopy, */Opt. Express /*13 *(2005) 
> 9085-9093*. *
> Hope this helps,
> Marin
> =======================================================
> On 04/04/2014 02:17, Nikolaus Grigorieff wrote:
>> Dear Colleagues,
>> We have recently noticed a problem with anisotropic magnification on one
>> of our Titan Krios microscopes. When recording data at a nominal
>> magnification of 29,000x, there seems to be an image distortion that
>> produces variable magnification in different directions of the image.
>> These variations were estimated using diffraction from gold particles to
>> be about 2%, a significant amount especially when working on large
>> assemblies such as viruses. The distortions can be approximately
>> corrected using image interpolation but this is not desirable, of
>> course. In one case, the resolution of a 700 Angstrom virus
>> reconstruction with data collected on a Gatan K2 direct electron
>> detector improved from 7 to 4 Angstrom after correcting for the distortions.
>> The severity of the distortion depends on the magnification setting. At
>> 37000x magnification the magnification anisotropy is about 1% and
>> 59,000x it appears to be undetectable. Since most Krios microscopes are
>> only calibrated for magnifications of 59,000x and higher, it is possible
>> that the problem we have observed also occurs on other instruments. This
>> will be particularly relevant for instruments that operate with the K2
>> detector mentioned above. The pixel size of this detector (5 microns)
>> usually demands magnifications settings of 29,000x and lower where the
>> distortions are significant. Users of detectors with a larger pixel size
>> (e.g. the Falcon direct electron detector) are less likely to experience
>> the distortions since they will typically use magnifications of 59,000x
>> and higher.
>> FEI have acknowledged the problem but at this point the cause is not
>> clear. We hope that the distortions can be corrected with a simple
>> recalibration of the projector lenses. We would be grateful if other
>> Titan Krios users could share their experience and possibly check if
>> distortions are detectable at lower magnification settings.
>>       Thanks,
>>            Niko.
>> _______________________________________________
>> 3dem mailing list
>> 3dem at ncmir.ucsd.edu
>> https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem


     Prof Dr Ir Marin van Heel

     Professor of Cryo-EM Data Processing

     Leiden University
     NeCEN Building Room 05.27
     Einsteinweg 55
     2333 CC Leiden
     The Netherlands
     Tel. NL: +31(0)715271424 // Mobile NL: +31(0)652736618
     Skype:    Marin.van.Heel
     email:  marin.vanheel(A_T)gmail.com
     and:    mvh.office(A_T)gmail.com


     Emeritus Professor of Structural Biology

     Imperial College London
     Faculty of Natural Sciences
     Biochemistry Building (Room 512)
     South Kensington Campus
     London SW7 2AZ,  UK
     email:  m.vanheel(A_T)ic.ac.uk

     Tel. UK:   +44(0)2075945316 //Mobile: +44(0)7941540625

     Visiting Professor at:

     Laboratório Nacional de Nanotecnologia - LNNano
     CNPEM/ABTLuS, Campinas, Brazil
     Brazilian mobile phone  +55-19-99369051


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