<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
<meta name="Generator" content="Microsoft Word 14 (filtered medium)">
<style><!--
/* Font Definitions */
@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:Tahoma;
panose-1:2 11 6 4 3 5 4 4 2 4;}
@font-face
{font-family:Consolas;
panose-1:2 11 6 9 2 2 4 3 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
margin-bottom:.0001pt;
font-size:11.0pt;
font-family:"Calibri","sans-serif";
color:black;
mso-fareast-language:EN-US;}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
p
{mso-style-priority:99;
mso-margin-top-alt:auto;
margin-right:0cm;
mso-margin-bottom-alt:auto;
margin-left:0cm;
font-size:11.0pt;
font-family:"Calibri","sans-serif";
color:black;
mso-fareast-language:EN-US;}
pre
{mso-style-priority:99;
mso-style-link:"HTML - förformaterad Char";
margin:0cm;
margin-bottom:.0001pt;
font-size:10.0pt;
font-family:"Courier New";
color:black;
mso-fareast-language:SV;}
p.MsoAcetate, li.MsoAcetate, div.MsoAcetate
{mso-style-priority:99;
mso-style-link:"Ballongtext Char";
margin:0cm;
margin-bottom:.0001pt;
font-size:8.0pt;
font-family:"Tahoma","sans-serif";
color:black;
mso-fareast-language:EN-US;}
span.HTML-frformateradChar
{mso-style-name:"HTML - förformaterad Char";
mso-style-priority:99;
mso-style-link:"HTML - förformaterad";
font-family:Consolas;
color:black;
mso-fareast-language:EN-US;}
span.E-postmall20
{mso-style-type:personal;
font-family:"Calibri","sans-serif";
color:windowtext;}
span.E-postmall21
{mso-style-type:personal;
font-family:"Calibri","sans-serif";
color:#1F497D;}
span.E-postmall22
{mso-style-type:personal-reply;
font-family:"Calibri","sans-serif";
color:#1F497D;}
span.BallongtextChar
{mso-style-name:"Ballongtext Char";
mso-style-priority:99;
mso-style-link:Ballongtext;
font-family:"Tahoma","sans-serif";
color:black;
mso-fareast-language:EN-US;}
.MsoChpDefault
{mso-style-type:export-only;
font-size:10.0pt;}
@page WordSection1
{size:612.0pt 792.0pt;
margin:70.85pt 70.85pt 70.85pt 70.85pt;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
</head>
<body bgcolor="white" lang="SV" link="blue" vlink="purple">
<div class="WordSection1">
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D">I see. I was trying to think of scattering as a process involving particles.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D">Thanks,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D">Philip<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D"><o:p> </o:p></span></p>
<div>
<div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm">
<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"> Marin
van Heel [mailto:marin.vanheel@googlemail.com] <br>
<b>Skickat:</b> den 9 juni 2017 11:57<br>
<b>Till:</b> Philip Koeck; 3dem@ncmir.ucsd.edu<br>
<b>Kopia:</b> CCPEM@JISCMAIL.AC.UK<br>
<b>Ämne:</b> Re: [3dem] [TEM] CTF and SNR<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<p class="MsoNormal"><br>
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:<o:p></o:p></p>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<p class="MsoNormal"><span style="color:#1F497D">Hi again.</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D">Several people have pointed out that shot-noise is the main noise contribution and that it isn’t modulated by the CTF.</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D">I’m having a hard time understanding why it wouldn’t be modulated by the CTF.</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D">All shot noise that occurs before the imaging by the objective lens should somehow affect the exit wave, shouldn’t it?</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D">(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.</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D">I’m trying not to think of inelastic scattering to keep things simpler.</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D">All the best,</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D">Philip</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D"> </span><o:p></o:p></p>
<div>
<div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm">
<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 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 href="mailto:3dem@ncmir.ucsd.edu">3dem@ncmir.ucsd.edu</a><br>
<b>Ämne:</b> Re: [3dem] [TEM] CTF and SNR</span><o:p></o:p></p>
</div>
</div>
<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">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>
<div>
<p class="MsoNormal">On 06/07/2017 01:22 AM, Philip Koeck wrote:<o:p></o:p></p>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<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 style="font-size:12.0pt"><br>
<br>
<br>
<br>
</span><o:p></o:p></p>
<pre>_______________________________________________<o:p></o:p></pre>
<pre>3dem mailing list<o:p></o:p></pre>
<pre><a href="mailto:3dem@ncmir.ucsd.edu">3dem@ncmir.ucsd.edu</a><o:p></o:p></pre>
<pre><a href="https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem">https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem</a><o:p></o:p></pre>
</blockquote>
<p class="MsoNormal"><span style="font-size:12.0pt"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif";mso-fareast-language:SV"><br>
<br>
<br>
<o:p></o:p></span></p>
<pre>_______________________________________________<o:p></o:p></pre>
<pre>3dem mailing list<o:p></o:p></pre>
<pre><a href="mailto:3dem@ncmir.ucsd.edu">3dem@ncmir.ucsd.edu</a><o:p></o:p></pre>
<pre><a href="https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem">https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem</a><o:p></o:p></pre>
</blockquote>
<p><o:p> </o:p></p>
<pre>-- <o:p></o:p></pre>
<pre>==============================================================<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre> Prof Dr Ir Marin van Heel<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre> Research Professor at:<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre> Laboratório Nacional de Nanotecnologia - LNNano<o:p></o:p></pre>
<pre> CNPEM/ABTLuS, Campinas, Brazil<o:p></o:p></pre>
<pre> <o:p></o:p></pre>
</div>
</body>
</html>