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<p>Dear John,<br>
</p>
<p>We showed in 2007 that pure water ice produces Thon rings and
that their visibility depends on ice thickness (Fig. 7 in <a
class="moz-txt-link-freetext"
href="http://www.sciencedirect.com/science/article/pii/S104784770600236X">http://www.sciencedirect.com/science/article/pii/S104784770600236X</a>).
The visibility of rings can be improved using the method proposed
in that paper.
</p>
<p>Best regards,</p>
<p>Slavica</p>
<br>
<div class="moz-cite-prefix">Le 07/06/2017 à 15:43, John Rubinstein
a écrit :<br>
</div>
<blockquote
cite="mid:DD10FFF9-B62B-4345-B479-E6F3CD06F15A@utoronto.ca"
type="cite">
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Hi Steve,
<div class=""><br class="">
</div>
<div class="">As Greg McMullan and Richard Henderson showed
recently, amorphous ice does give Thon rings. However, ice also
exhibits a beam induced ‘Brownian’-like movement so that the
power spectrum from the average of DDD frames does not often
show Thon rings.</div>
<div class=""><a moz-do-not-send="true"
href="https://www.ncbi.nlm.nih.gov/pubmed/26103047" class="">https://www.ncbi.nlm.nih.gov/pubmed/26103047</a></div>
<div class="">Alexis Rohou modified CTF find in order to allow use
of this signal in CTF estimation.</div>
<div class=""><br class="">
</div>
<div class="">Best regards,</div>
<div class="">John</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
<div class="">
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<div class="">
<div class="">-- </div>
<div class="">John Rubinstein</div>
<div class="">Molecular Medicine Program</div>
<div class="">The Hospital for Sick Children Research
Institute</div>
<div class="">686 Bay Street, Rm. 20-9705</div>
<div class="">Toronto, ON</div>
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<div class="">Fax: (+001) 416-813-5022</div>
<div class=""><a moz-do-not-send="true"
href="http://www.sickkids.ca/research/rubinstein"
class="">www.sickkids.ca/research/rubinstein</a></div>
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<br class="">
<div>
<blockquote type="cite" class="">
<div class="">On Jun 7, 2017, at 9:33 AM, Ludtke, Steven J
<<a moz-do-not-send="true"
href="mailto:sludtke@bcm.edu" class="">sludtke@bcm.edu</a>>
wrote:</div>
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charset=windows-1252" class="">
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Hi Philip,
<div class="">pure water ice, alas, does not exhibit
Thon rings (at least not significantly). Other buffer
constituents may. This makes modeling noise a bit
tricky. </div>
<div class=""><br class="">
</div>
<div class="">Many of the methods in the field start
with the assumption that the image consists of a true
projection of a macromolecule, convolved with the CTF
with added uncorrelated Gaussian noise. That is, noise
with a flat power spectrum and no correlation among
nearby pixels. Prior to direct detectors and counting,
the background noise power spectrum in typical cryoEM
images had an exponential decay, and could with a
little processing be "flattened" to produce something
more or less like uncorrelated Gaussian noise. The
problem with this assumption, even then, is that
CryoEM images actually contain a lot of other stuff,
and from the perspective of single particle
reconstruction, noise isn't just the scattering off
the solvent, it's anything present in the image which
is not a perfect projection of the particle. </div>
<div class=""><br class="">
</div>
<div class="">This is what led to EMAN2's approach of
computing the power spectrum of masked out particles,
and masked out regions outside particles to compute an
accurate estimate of the SNR of the particles within
the images. Whether having this really produces better
reconstructions is a separate question, but making
this estimate DOES tell you quite a lot about particle
data quality and whether you should expect to be able
to achieve high resolution from your data.</div>
<div class=""><br class="">
</div>
<div class="">I'm attaching some slides from about 10
years ago showing how SSNR estimates assuming a pretty
flat background can give completely inaccurate
estimates of the actual SSNR of the images. Hope they
are reasonably self-explanatory. This compares the
approach of considering noise to be anything in the
power spectrum without Thon rings to be noise, with
the approach of computing the noise from regions of
the image not containing particles.</div>
<div class=""><br class="">
</div>
<div class=""><a moz-do-not-send="true"
href="https://drive.google.com/file/d/0BxreryX3Fp-ZUVJtTFlYX0lmbzg/view?usp=sharing"
class="">https://drive.google.com/file/d/0BxreryX3Fp-ZUVJtTFlYX0lmbzg/view?usp=sharing</a></div>
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Steven Ludtke, Ph.D.</div>
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" class="">
Professor, Dept of
Biochemistry and Mol. Biol.
(<a
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href="http://www.bcm.edu/biochem"
class="">www.bcm.edu/biochem</a>)</div>
<div style="margin: 0px;
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" class="">
Co-Director National Center
For Macromolecular Imaging
<span
class="Apple-converted-space"> </span>(<a
moz-do-not-send="true"
href="http://ncmi.bcm.edu/"
class="">ncmi.bcm.edu</a>)</div>
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Co-Director CIBR Center
<span
class="Apple-converted-space"> </span>(<a
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href="http://www.bcm.edu/research/cibr"
class="">www.bcm.edu/research/cibr</a>)</div>
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Baylor College of Medicine<span
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class="">sludtke@bcm.edu</a></div>
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<pre class="moz-signature" cols="72">--
Dr Slavica JONIC
CNRS Associate Scientist
IMPMC, Sorbonne Universités
CNRS UMR 7590, UPMC Univ Paris 6, MNHN, IRD UMR 206
Université Pierre et Marie Curie
Case courrier 115
4 Place Jussieu
75005 Paris, France
Tel: +33 1 44 27 72 05
Fax: +33 1 44 27 37 85
E-mail: <a class="moz-txt-link-abbreviated" href="mailto:Slavica.Jonic@impmc.upmc.fr">Slavica.Jonic@impmc.upmc.fr</a>
URL: <a class="moz-txt-link-freetext" href="http://www.impmc.upmc.fr/~jonic">http://www.impmc.upmc.fr/~jonic</a>
Frontiers Research Topic:
<a class="moz-txt-link-freetext" href="http://frontiersin.org/Biophysics/researchtopics/Hybrid_Biomolecular_Modeling/4799">http://frontiersin.org/Biophysics/researchtopics/Hybrid_Biomolecular_Modeling/4799</a>
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