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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">
<meta content="text/html; charset=UTF-8" http-equiv="Content-Type">
<div class="moz-cite-prefix"><br>
<meta http-equiv="Content-Type" content="text/html;
charset=UTF-8">
<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">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 class="moz-txt-link-abbreviated" href="mailto:michael@imagescience.de">michael@imagescience.de</a></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 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">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)gmail.com
and: mvh.office(A_T)gmail.com
</pre>
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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""><br>
<o:p></o:p></span></p>
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