[3dem] [TEM] CTF and SNR

[Alexis Rohou]

Hi Philip,

> I’ll assume most of the noise in an image of an ice-embedded
> bio-molecule is due to variations in the ice, so called structural noise.
This is not a safe assumption. In fact most of the noise is shot noise,
which is Poisson distributed (so, Gaussian for our total exposures), and
not modulated by the CTF. Hence the CTF does modulate the SSNR.

A few years ago, Joachim Frank and colleagues attempted a quantification
of this and other sources of noise. You may find this a good read. They
come up with a shot noise SNR of ~ 0.1, and a combined shot+structural
noise SNR of ~1, if I read them correctly.

Baxter, W. T., Grassucci, R. A., Gao, H., & Frank, J. (2009).
Determination of signal-to-noise ratios and spectral SNRs in cryo-EM
low-dose imaging of molecules. Journal of Structural Biology, 166(2),
126–32. https://doi.org/10.1016/j.jsb.2009.02.012

Cheers,
Alexis


On 06/07/2017 01:22 AM, Philip Koeck wrote:
>
> Hi.
>
>  
>
> I’ve recently encountered a bit of a conundrum:
>
>  
>
> I’ll assume most of the noise in an image of an ice-embedded
> bio-molecule is due to variations in the ice, so called structural noise.
>
> The CTF describes the contrast transfer for both signal and noise in
> the same way.
>
> So, what is the point of changing the CTF by defocusing and/or using a
> phase plate.
> The SNR should be unchanged.
>
>  
>
> I can think of one explanation: If the signal spectrum is very
> different from the noise spectrum one could chose a CTF that enhances the
> resolution bands where the difference is big.
>
>  
>
> Else: Is there some other factor that affects visibility of the
> molecule than SNR?
>
>  
>
> All the best,
>
>  
>
> Philip
>
>
>
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