[3dem] [TEM] amplitude contrast

Tue Aug 15 05:47:46 PDT 2017

On Aug 15, 2017, at 7:22 AM, Philip Koeck <Philip.Koeck at ki.se<mailto:Philip.Koeck at ki.se>> wrote:
I see many open questions:
If it’s due to scattering outside the aperture, shouldn’t it depend strongly on the aperture size?
The objective aperture basically positioned so it is in Fourier space (for eleastically scattered electrons). That is, the aperture is the equivalent of a low-pass filter at the resolution corresponding to its radius. The typical aperture is at high enough resolution that this doesn't normally impinge on the resolutions studied in CryoEM. Physically it is removing some electrons which might otherwise contribute to background noise.

Once an electron has scattered inelastically (by more than a very small amount), it can no longer contribute coherently to the image, but its absence can (amplitude contrast and beam attenuation). Thus we'd like to get rid of it physically so it doesn't contribute instead to background noise, hence we have objective apertures and energy filters.

If it’s due to multiple scattering, it must depend strongly on specimen thickness.
If it’s due to inelastic scattering, why is it so weak (about 10%)? Inelastic scattering has a larger cross section than elastic, I believe.

Clearly the attenuation of the beam is impacted strongly by specimen thickness. However, the effect you are referring to as amplitude contrast is due to the difference in scattering in one part of the specimen vs another. That is, uniform solvent added above or below the feature producing contrast simply attenuates the beam uniformly, and doesn't produce "contrast".

The way we handle it in the weak phase approximation, as a cos() term is an approximation, as you could argue that it should be treated as an exponential decay with thickness as it is in optics. However, since we're talking about contrast bewteen different scatterers in the X-Y plane rather than total attenuation by the specimen, for single particle work, it's a good approximation.  For tomography of thick specimens, however, we should probably be thinking about the issue a bit deeper.

All the best,

Philip

Från: Sacha De Carlo [mailto:sacha.decarlo at dectris.com]
Skickat: den 15 augusti 2017 13:11
Till: Philip Koeck
Kopia: 3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu>
Ämne: Re: [3dem] [TEM] amplitude contrast

A good reference which may provide you with an answer... I am sure many other people will provide more recent studies...

Enjoy !

Best,
Sacha

On Tue, Aug 15, 2017 at 12:55 PM, Philip Koeck <Philip.Koeck at ki.se<mailto:Philip.Koeck at ki.se>> wrote:
Dear all.

Is there any agreement on the cause of amplitude contrast when imaging proteins in cryo-TEM?

Is it the second order term in the expansion of a weak phase object or is it due to inelastic scattering or the aperture or something else?

Al the best.

Philip

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