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<p>Hi Philip,</p>
<p>
<blockquote type="cite"><span lang="EN-US">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.</span></blockquote>
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.<br>
</p>
<p>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.<br>
</p>
<p>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. <a class="moz-txt-link-freetext" href="https://doi.org/10.1016/j.jsb.2009.02.012">https://doi.org/10.1016/j.jsb.2009.02.012</a></p>
<p>Cheers,<br>
Alexis<br>
</p>
<br>
<div class="moz-cite-prefix">On 06/07/2017 01:22 AM, Philip Koeck
wrote:<br>
</div>
<blockquote type="cite"
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<p class="MsoNormal">Hi.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span lang="EN-US">I’ve recently
encountered a bit of a conundrum:<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">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.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">The CTF describes the
contrast transfer for both signal and noise in the same way.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">So, what is the point of
changing the CTF by defocusing and/or using a phase plate.<br>
The SNR should be unchanged.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">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<br>
resolution bands where the difference is big.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Else: Is there some
other factor that affects visibility of the molecule than
SNR?<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">All the best,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Philip<o:p></o:p></span></p>
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