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I would not have corrected you, just Marin!<br>
Regards,<br>
Ed<br>
<br>
<div class="moz-cite-prefix">On 1/31/16 4:18 PM, Nancy Meyer wrote:<br>
</div>
<blockquote cite="mid:79621E8C-B53E-4C7E-9B05-D56E82284E5A@ohsu.edu"
type="cite">
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
<div>Well, since *I'm* the guilty "people" (and apparently have
company), I thought I should say that it was a casual error and
that I'd no reason to think Schors wouldn't know exactly what I
meant. Apologies for my unfamiliarity mostly to Scientific
Reports. Glad we're keeping pretentiousness in check. And that
ya'll are having this debate on Sunday. ;-) But thanks in all
sincerity for the dialogue - I stand corrected!</div>
<div><br>
</div>
<div>Very best,</div>
<div>Nancy<br>
<br>
Sent from my iPhone</div>
<div><br>
On Jan 31, 2016, at 8:35 AM, Edward Egelman <<a
moz-do-not-send="true" href="mailto:egelman@virginia.edu"><a class="moz-txt-link-abbreviated" href="mailto:egelman@virginia.edu">egelman@virginia.edu</a></a>>
wrote:<br>
<br>
</div>
<blockquote type="cite">
<div> Why are people using "Nature, Scientific Reports"? The
journal's name is Scientific Reports, and Nature is the
publisher. By this logic I could say that I was the
Editor-in-Chief of Cell, Biophysical Journal, since Cell is
the publisher of BJ. Not to rain on Marin's parade, but If one
looks at Peer Review Policy for Nature publications, it
states:<br>
"The policy outlined on this page applies to Nature journals
(those with the word "Nature" in their title). NPG publishes
many other journals, each of which has separate publication
policies described on its website."<br>
The policy for Nature journals goes on to explain the need for
novelty, significance and likely impact. In stark contrast,
this is what they say about Scientific Reports:<br>
"To be considered for publication in Scientific Reports, a
paper must be technically sound original research, without any
requirement for impact or a conceptual advance."<br>
Just my two cents (which are worth less and less).<br>
Ed<br>
<br>
<div class="moz-cite-prefix">On 1/30/16 8:07 AM, Marin van
Heel wrote:<br>
</div>
<blockquote cite="mid:56ACB5AE.5010807@googlemail.com"
type="cite">
<div class="moz-cite-prefix"><br>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt
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595.4pt 641.2pt 687.0pt 732.8pt">
<span style="font-size:10.0pt;font-family:"Courier
New";mso-fareast-font-family:"Times New
Roman"; mso-fareast-language:EN-GB">Dear Nancy,<o:p></o:p></span></p>
<span style="font-size:10.0pt;font-family:"Courier
New";mso-fareast-font-family:"Times New
Roman"; mso-fareast-language:EN-GB"><o:p></o:p></span>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt
274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt
595.4pt 641.2pt 687.0pt 732.8pt">
<span style="font-size:10.0pt;font-family:"Courier
New";mso-fareast-font-family:"Times New
Roman"; mso-fareast-language:EN-GB">What Sjors is
suggesting is a simplified version of what we
suggested in:<o:p></o:p></span></p>
<span style="font-size:10.0pt;font-family:"Courier
New";mso-fareast-font-family:"Times New
Roman"; mso-fareast-language:EN-GB"><o:p></o:p></span>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt
274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt
595.4pt 641.2pt 687.0pt 732.8pt">
<span style="font-size:10.0pt;font-family:"Courier
New";mso-fareast-font-family:"Times New
Roman"; mso-fareast-language:EN-GB">"A posteriori
correction of camera characteristics from large image
data sets", P. Afanasyev et al, Nature, Scientific
Reports.<o:p></o:p></span><span
style="font-size:10.0pt;font-family:"Courier
New";mso-fareast-font-family:"Times New
Roman"; mso-fareast-language:EN-GB"><o:p> </o:p></span>
</p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt
274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt
595.4pt 641.2pt 687.0pt 732.8pt">
<span style="font-size:10.0pt;font-family:"Courier
New";mso-fareast-font-family:"Times New
Roman"; mso-fareast-language:EN-GB">The camera
correction should preferably include the subtraction
of the average background and the normalization of the
standard deviations of the pixel vectors, especially
if you are operating your DE camera in integrating
mode. The movie alignments can improve significantly
after the a posteriori camera correction.<span
style="mso-spacerun:yes">
</span>The other aspect is the FRC validation of the
camera correction. The FRC is then not used as a ‘gold
standard’ 2D resolution criterion but rather as an
indicator of the independence of different images
collected with the same sensor. The FRC should not
cross the 3-sigma threshold indicating the expected
random noise fluctuations around FRC=0. For details
see the paper.<o:p></o:p></span></p>
<span style="font-size:10.0pt;font-family:"Courier
New";mso-fareast-font-family:"Times New
Roman"; mso-fareast-language:EN-GB"><o:p></o:p></span>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt
274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt
595.4pt 641.2pt 687.0pt 732.8pt">
<span style="font-size:10.0pt;font-family:"Courier
New";mso-fareast-font-family:"Times New
Roman"; mso-fareast-language:EN-GB">If you want
to test the a posteriori camera correction programs,
contact
<a moz-do-not-send="true"
class="moz-txt-link-abbreviated"
href="mailto:michael@imagescience.de">
</a><a moz-do-not-send="true"
class="moz-txt-link-abbreviated"
href="mailto:michael@imagescience.de">michael@imagescience.de</a>!<o:p></o:p></span></p>
<span style="font-size:10.0pt;font-family:"Courier
New";mso-fareast-font-family:"Times New
Roman"; mso-fareast-language:EN-GB"><o:p></o:p></span>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt
274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt
595.4pt 641.2pt 687.0pt 732.8pt">
<span style="font-size:10.0pt;font-family:"Courier
New";mso-fareast-font-family:"Times New
Roman"; mso-fareast-language:EN-GB">Hope this
helps!<o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt
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595.4pt 641.2pt 687.0pt 732.8pt">
<span style="font-size:10.0pt;font-family:"Courier
New";mso-fareast-font-family:"Times New
Roman"; mso-fareast-language:EN-GB">Marin<o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt
274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt
595.4pt 641.2pt 687.0pt 732.8pt">
<span style="font-size:10.0pt;font-family:"Courier
New";mso-fareast-font-family:"Times New
Roman"; mso-fareast-language:EN-GB"><o:p> </o:p></span></p>
=====================================<br>
<br>
On 28/01/2016 00:48, Nancy Meyer wrote:<br>
</div>
<blockquote
cite="mid:7B6DD4F49731AB4691DC21234C3BAE985641108A@EXMB06.ohsu.edu"
type="cite">
<pre wrap="">Again, thank you for the reassuring response! Maybe I've lucked out with similar image intensities in previous datasets - I should probably look at a few min/max, mean, and stdev values to convince myself.
I was pretty careful to remove particles on that horiz artefact and if restoring their inclusion is the biggest gain from redoing gain correction, I can maybe let that slide for now. I did just see "A posteriori correction of camera
characteristics from large image data sets", P. Afanasyev et al, Nature, Scientific Reports, after looking up your recommendation - looks like they've implemented it in Imagic - wonder if you could do the same correction in just ImageJ...
Thank you for taking the time to look at the images... slowly getting the hang of Relion, but the input is so invaluable!
Best,
Nancy
______________________________________
From: Sjors Scheres [<a moz-do-not-send="true" class="moz-txt-link-abbreviated" href="mailto:scheres@mrc-lmb.cam.ac.uk">scheres@mrc-lmb.cam.ac.uk</a>]
Sent: Wednesday, January 27, 2016 1:10 PM
To: Nancy Meyer
Cc: <a moz-do-not-send="true" class="moz-txt-link-abbreviated" href="mailto:ccpem@jiscmail.ac.uk">ccpem@jiscmail.ac.uk</a>
Subject: Re: [ccpem] Adequate particle normalization prior to 2D classification?
Hi Nancy,
The particles look perfectly fine to me. The overall differences in
greyscale you see is because each of the particles is scaled from white to
black with their own min and max values, which are susceptible to
outliers. The mean will probably be perfectly fine. You can get rid of
this with removing white and black dust, but it will not be necessary to
do so.
The classes also look quite OK. Just select all the nice ones and proceed
with another 2D classification or go into 3D already. Some details are
already coming up, so the 3D structure will look nice.
The micrographs show a sign of a bad gain correction. If you have many of
them (> several hundreds) you could correct the gain a-posteriori by
calculating the average of all micrographs and then divide each micrograph
by that average. This should get rid of the horizontal artefact (as long
as it is present in all micrographs). That may save some particles that
lie on that line.
HTH,
Sjors
</pre>
<br>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
================================================================
Prof Dr Ir Marin van Heel
Professor of Cryo-EM Data Processing
Leiden University
NeCEN Building Room 05.27
Einsteinweg 55
2333 CC Leiden
The Netherlands
Tel. NL: +31(0)715271424 // Mobile NL: +31(0)652736618
Skype: Marin.van.Heel
email: marin.vanheel(A_T)<a moz-do-not-send="true" href="http://gmail.com">gmail.com</a>
and: mvh.office(A_T)<a moz-do-not-send="true" href="http://gmail.com">gmail.com</a>
</pre>
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</pre>
</blockquote>
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<p class="MsoNormal">Edward H. Egelman, Ph.D.<u5:p></u5:p></p>
<p class="MsoNormal">Harrison Distinguished Professor<u5:p></u5:p></p>
<p class="MsoNormal">Dept. of Biochemistry and Molecular
Genetics<u5:p></u5:p></p>
<p class="MsoNormal">University of Virginia<u5:p></u5:p><o:p></o:p></p>
<p class="MsoNormal"><u5:p> </u5:p></p>
<p class="MsoNormal">President<u5:p></u5:p></p>
<p class="MsoNormal">Biophysical Society<u5:p></u5:p><o:p></o:p></p>
<p class="MsoNormal"><u5:p> </u5:p></p>
<p class="MsoNormal"><span class="GramE">phone</span>:
434-924-8210<u5:p></u5:p></p>
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434-924-5069<u5:p></u5:p></p>
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<div><span>_______________________________________________</span><br>
<span>3dem mailing list</span><br>
<span><a moz-do-not-send="true"
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<span><a moz-do-not-send="true"
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<p class="MsoNormal">Edward H. Egelman, Ph.D.<u5:p></u5:p></p>
<p class="MsoNormal">Harrison Distinguished Professor<u5:p></u5:p></p>
<p class="MsoNormal">Dept. of Biochemistry and Molecular
Genetics<u5:p></u5:p></p>
<p class="MsoNormal">University of Virginia<u5:p></u5:p><o:p></o:p></p>
<p class="MsoNormal"><u5:p> </u5:p></p>
<p class="MsoNormal">President<u5:p></u5:p></p>
<p class="MsoNormal">Biophysical Society<u5:p></u5:p><o:p></o:p></p>
<p class="MsoNormal"><u5:p> </u5:p></p>
<p class="MsoNormal"><span class="GramE">phone</span>:
434-924-8210<u5:p></u5:p></p>
<p class="MsoNormal"><span class="GramE">fax</span>:
434-924-5069<u5:p></u5:p></p>
<p class="MsoNormal"><a class="moz-txt-link-abbreviated" href="mailto:egelman@virginia.edu">egelman@virginia.edu</a><u5:p></u5:p></p>
<p class="MsoNormal"><a
href="http://www.people.virginia.edu/%7Eehe2n"><a class="moz-txt-link-freetext" href="http://www.people.virginia.edu/~ehe2n">http://www.people.virginia.edu/~ehe2n</a></a></p>
<u5:p></u5:p>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:Times;mso-fareast-font-family:
"Times New
Roman";mso-bidi-font-family:"Times New
Roman""><img id="_x0000_i1025"
src="cid:part15.01060900.09020308@virginia.edu"
alt="icture" border="0" width="373" height="102"><o:p></o:p></span></p>
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