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Hi Philip,<br>
<br>
Admittedly, the wave-particle duality of nature is a confusing
matter! All wave functions and (complex) transmission functions
in the object plane and in diffraction plane (back-focal plane of
the lens) are only probability functions. They only become real
entities when they are measured in the image plane (the waves
squared, are actually measured). It is there where we introduce
the counting of the arriving electrons (particles), a counting
which is subject to Poisson statistics. Thus Poisson statistics
is NOT subject to the CTF. (See Alexis' post below)<br>
<br>
Cheers<br>
<br>
Marin<br>
<br>
================================================<br>
<br>
<br>
On 09/06/2017 10:32, Philip Koeck wrote:<br>
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<p class="MsoNormal"><span style="color:#1F497D">Hi again.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D" lang="EN-US">Several
people have pointed out that shot-noise is the main noise
contribution and that it isn’t modulated by the CTF.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D" lang="EN-US">I’m
having a hard time understanding why it wouldn’t be
modulated by the CTF.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D" lang="EN-US">All
shot noise that occurs before the imaging by the objective
lens should somehow affect the exit wave, shouldn’t it?<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D" lang="EN-US">(I
know I’m switching from a particle to a wave description
here.)<br>
Since the whole exit wave (signal and noise contributions)
is multiplied by the same phase factor containing the<br>
lens aberration function, the noise in it should be affected
by the CTF just as much as the signal.<br>
Now I’m thinking about shot noise produced mainly during
elastic scattering in the specimen.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D" lang="EN-US">I’m
trying not to think of inelastic scattering to keep things
simpler.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D" lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D" lang="EN-US">All
the best,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D" lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D" lang="EN-US">Philip<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D" lang="EN-US"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span
style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext;mso-fareast-language:SV">Från:</span></b><span
style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext;mso-fareast-language:SV">
3dem [<a class="moz-txt-link-freetext" href="mailto:3dem-bounces@ncmir.ucsd.edu">mailto:3dem-bounces@ncmir.ucsd.edu</a>] <b>För </b>Alexis
Rohou<br>
<b>Skickat:</b> den 7 juni 2017 15:25<br>
<b>Till:</b> <a class="moz-txt-link-abbreviated" href="mailto:3dem@ncmir.ucsd.edu">3dem@ncmir.ucsd.edu</a><br>
<b>Ämne:</b> Re: [3dem] [TEM] CTF and SNR<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p>Hi Philip,<o:p></o:p></p>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<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.</span><o:p></o:p></p>
</blockquote>
<p class="MsoNormal">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.<o:p></o:p></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.<o:p></o:p></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 href="https://doi.org/10.1016/j.jsb.2009.02.012"
moz-do-not-send="true">https://doi.org/10.1016/j.jsb.2009.02.012</a><o:p></o:p></p>
<p>Cheers,<br>
Alexis<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On 06/07/2017 01:22 AM, Philip Koeck
wrote:<o:p></o:p></p>
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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:</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US"> </span><o:p></o:p></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.</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US">The CTF describes the
contrast transfer for both signal and noise in the same
way.</span><o:p></o:p></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.</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US"> </span><o:p></o:p></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.</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US">Else: Is there some
other factor that affects visibility of the molecule than
SNR?</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US">All the best,</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US">Philip</span><o:p></o:p></p>
<p class="MsoNormal"><span
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<br>
<br>
<o:p></o:p></span></p>
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<pre class="moz-signature" cols="72">--
==============================================================
Prof Dr Ir Marin van Heel
Research Professor at:
Laboratório Nacional de Nanotecnologia - LNNano
CNPEM/ABTLuS, Campinas, Brazil
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