[3dem] amplitude contrast valuesHi,

[Marin van Heel]

Dear David

The amplitude and phase information are two independent properties of 
the sample which are transferred through a linear optical system by the 
Amplitude Transfer Function (ATF) and the Phase Contrast Transfer 
Function (PhCTF), respectively. That is standard Fourier Optics. Merging 
of the amplitude and phase information transfer into a single hybrid 
contrast transfer function necessarily implies assuming a 
proportionality between the phase and amplitude information of the 
sample over all spatial frequencies. Assuming such a proportionality is 
certainly incorrect in general and the experimental evidence supporting 
such assumptions fail to convince me, even in the cases where one is 
only looking at low-resolution negative-stain images. The practical 
solution is simple: ignore the fiddle-factor "Q" altogether by setting 
it to zero and first take out all irrelevant and disturbing 
low-resolution amplitudes by high-pass filtering the images prior to the 
CTF determination. Reference: M. van Heel: On the imaging of relatively 
strong objects in partially coherent illumination in optics and electron 
optics, Optik 47 (1978) 389-408) and paper in preparation.

Hope this helps

Marin

On 21/07/2014 14:02, David Gene Morgan wrote:
> Hi,
>
>     I'm trying to do some automated defocus determination (initially 
> trying Niko's ctffind3 program) and would like some input on 
> appropriate amplitude contrast values for various types of samples.  I 
> know that ice embedded images usually are said to have an amplitude 
> contrast of 0.07 to 0.1.  I also know that with protein/nucleic acid 
> complexes in ice, amplitude contrast may need to be set a bit higher 
> (say to as much as 0.15 for some data I worked on awhile ago).
>
>     But I don't have any sort of feeling for appropriate values of 
> amp;itude contrast for different sorts of negative stains (either cryo 
> negative stain or standard negative stain).  It should be "high," but 
> I don't know how high might be appropriate.
>
>     If anyone has either some practical or theoretical insight into 
> this, I'd appreciate some suggestions.  Also, does anyone know about 
> an appropriate amplitude contrast for a standard Au/Pd waffle grid?
>
>     Thanks in advance for all your help.
>


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================================================================

     Prof Dr Ir Marin van Heel

     Professor of Cryo-EM Data Processing

     Leiden University
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