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I shall not copy-paste "Nature, Scientific Reports" on Saturdays<br>
I shall not copy-paste "Nature, Scientific Reports" on Saturdays<br>
I shall not copy-paste "Nature, Scientific Reports" on Saturdays<br>
I shall not copy-paste "Nature, Scientific Reports" on Saturdays<br>
<br>
Marin<br>
<br>
(and Ariel: "va te laver la bouche avec du savon")<br>
<br>
<br>
On 31/01/2016 16:56, Ariel Blocker wrote:<br>
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cite="mid:717E90EE-EACE-4E27-9547-CCA71BEBBB07@bristol.ac.uk"
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Sweet Sacha! And glad you did not write "Note to self: do not READ
to 3DEM emails on Sunday…”.
<div class=""> ;)</div>
<div class="">A.<br class="">
<div class="">
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class="">
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class="">
<div style="color: rgb(0, 0, 0);
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text-align: start; text-indent: 0px;
text-transform: none; white-space: normal;
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class="">
<div style="color: rgb(0, 0, 0);
letter-spacing: normal; orphans: auto;
text-align: start; text-indent: 0px;
text-transform: none; white-space:
normal; widows: auto; word-spacing: 0px;
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class="">
<div style="color: rgb(0, 0, 0);
letter-spacing: normal; orphans: auto;
text-align: start; text-indent: 0px;
text-transform: none; white-space:
normal; widows: auto; word-spacing:
0px; -webkit-text-stroke-width: 0px;
word-wrap: break-word;
-webkit-nbsp-mode: space;
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after-white-space;" class=""><span
style="font-size: 12px; orphans: 2;
widows: 2;" class="">Ariel J.
Blocker, PhD, FRSB</span><br
style="font-size: 12px; orphans: 2;
widows: 2;" class="">
<span style="font-size: 12px; orphans:
2; widows: 2;" class="">Reader in
Microbiology </span></div>
<div style="color: rgb(0, 0, 0);
letter-spacing: normal; orphans: auto;
text-align: start; text-indent: 0px;
text-transform: none; white-space:
normal; widows: auto; word-spacing:
0px; -webkit-text-stroke-width: 0px;
word-wrap: break-word;
-webkit-nbsp-mode: space;
-webkit-line-break:
after-white-space;" class=""><span
style="font-size: 12px; orphans: 2;
widows: 2;" class="">Wellcome Trust
Investigator</span><br
style="font-size: 12px; orphans: 2;
widows: 2;" class="">
<span style="font-size: 12px; orphans:
2; widows: 2;" class="">Schools of
Cellular & Molecular Medicine
and Biochemistry</span><br
style="font-size: 12px; orphans: 2;
widows: 2;" class="">
<span style="font-size: 12px; orphans:
2; widows: 2;" class="">Biomedical
Sciences Building</span><br
style="font-size: 12px; orphans: 2;
widows: 2;" class="">
<span style="font-size: 12px; orphans:
2; widows: 2;" class="">University
of Bristol</span><br
style="font-size: 12px; orphans: 2;
widows: 2;" class="">
<span style="font-size: 12px; orphans:
2; widows: 2;" class="">University
Walk</span><br style="font-size:
12px; orphans: 2; widows: 2;"
class="">
<span style="font-size: 12px; orphans:
2; widows: 2;" class="">Bristol BS8
1TD</span><br style="font-size:
12px; orphans: 2; widows: 2;"
class="">
<span style="font-size: 12px; orphans:
2; widows: 2;" class="">United
Kingdom</span><br style="font-size:
12px; orphans: 2; widows: 2;"
class="">
<br style="font-size: 12px; orphans:
2; widows: 2;" class="">
<span style="font-size: 12px; orphans:
2; widows: 2;" class="">Email: <a
moz-do-not-send="true"
href="mailto:ariel.blocker@bristol.ac.uk"
class=""><a class="moz-txt-link-abbreviated" href="mailto:ariel.blocker@bristol.ac.uk">ariel.blocker@bristol.ac.uk</a></a></span><br
style="font-size: 12px; orphans: 2;
widows: 2;" class="">
<span style="font-size: 12px; orphans:
2; widows: 2;" class="">Tel office
(D39a): +44 117 33 12063</span><br
style="font-size: 12px; orphans: 2;
widows: 2;" class="">
<span style="font-size: 12px; orphans:
2; widows: 2;" class="">Tel wetlab
(D57/D59): +44 117 33 12404</span><br
style="font-size: 12px; orphans: 2;
widows: 2;" class="">
<span style="font-size: 12px; orphans:
2; widows: 2;" class="">Tel wetlab
office (D53): +44 117 33 12059</span><br
style="font-size: 12px; orphans: 2;
widows: 2;" class="">
<span style="font-size: 12px; orphans:
2; widows: 2;" class="">Tel drylab
(D51): +44 117 33 12097</span><br
style="font-size: 12px; orphans: 2;
widows: 2;" class="">
<span style="font-size: 12px; orphans:
2; widows: 2;" class="">Tel
Tecnai20: +44 117 33 12357</span><br
style="font-size: 12px; orphans: 2;
widows: 2;" class="">
<span style="font-size: 12px; orphans:
2; widows: 2;" class="">Dept. fax:
+44 117 3312091</span><br
style="font-size: 12px; orphans: 2;
widows: 2;" class="">
<span style="font-size: 12px; orphans:
2; widows: 2;" class="">Room: D39a</span><br
style="font-size: 12px; orphans: 2;
widows: 2;" class="">
<span style="font-size: 12px; orphans:
2; widows: 2;" class="">Personal
webpage: </span><a
moz-do-not-send="true"
href="http://www.bristol.ac.uk/cellmolmed/research/infect-immune/blocker.html"
class=""><a class="moz-txt-link-freetext" href="http://www.bristol.ac.uk/cellmolmed/research/infect-immune/blocker.html">http://www.bristol.ac.uk/cellmolmed/research/infect-immune/blocker.html</a></a><br
style="font-size: 12px; orphans: 2;
widows: 2;" class="">
<span style="font-size: 12px; orphans:
2; widows: 2;" class="">Group page: </span><a
moz-do-not-send="true"
href="http://www.bristol.ac.uk/cellmolmed/research/infect-immune/blocker/"
class=""><a class="moz-txt-link-freetext" href="http://www.bristol.ac.uk/cellmolmed/research/infect-immune/blocker/">http://www.bristol.ac.uk/cellmolmed/research/infect-immune/blocker/</a></a><br
style="font-size: 12px; orphans: 2;
widows: 2;" class="">
<span style="font-size: 12px; orphans:
2; widows: 2;" class="">Postgraduate
students searching for a PhD please
look here:</span><br
style="font-size: 12px; orphans: 2;
widows: 2;" class="">
<a moz-do-not-send="true"
href="http://www.bris.ac.uk/fmvs/gradschool/"
class="">http://www.bris.ac.uk/fmvs/gradschool/</a></div>
<div style="color: rgb(0, 0, 0);
letter-spacing: normal; orphans: auto;
text-align: start; text-indent: 0px;
text-transform: none; white-space:
normal; widows: auto; word-spacing:
0px; -webkit-text-stroke-width: 0px;
word-wrap: break-word;
-webkit-nbsp-mode: space;
-webkit-line-break:
after-white-space;" class=""><span
style="font-size: 12px; orphans: 2;
widows: 2;" class="">Twitter:
@T3Secreton</span></div>
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<br class="">
<div>
<blockquote type="cite" class="">
<div class="">On 31 Jan 2016, at 16:53, De Carlo, Sacha <<a
moz-do-not-send="true"
href="mailto:Sacha.DeCarlo@fei.com" class=""><a class="moz-txt-link-abbreviated" href="mailto:Sacha.DeCarlo@fei.com">Sacha.DeCarlo@fei.com</a></a>>
wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div class="">Note to self: do not reply to 3DEM emails on
Sunday...<br class="">
<br class="">
Sacha De Carlo, Ph.D.<br class="">
EMEAI SSD LS Apps Manager<br class="">
-sent from my mobile<br class="">
<a moz-do-not-send="true" href="http://fei.com" class="">FEI.com</a><<a
moz-do-not-send="true" href="http://fei.com" class=""><a class="moz-txt-link-freetext" href="http://fei.com">http://fei.com</a></a>><br
class="">
<br class="">
On 31 Jan 2016, at 16:51, Ariel Blocker <<a
moz-do-not-send="true"
href="mailto:Ariel.Blocker@bristol.ac.uk" class=""><a class="moz-txt-link-abbreviated" href="mailto:Ariel.Blocker@bristol.ac.uk">Ariel.Blocker@bristol.ac.uk</a></a><<a
moz-do-not-send="true"
href="mailto:Ariel.Blocker@bristol.ac.uk" class=""><a class="moz-txt-link-freetext" href="mailto:Ariel.Blocker@bristol.ac.uk">mailto:Ariel.Blocker@bristol.ac.uk</a></a>>>
wrote:<br class="">
<br class="">
As associate editor of Scientific Reports, I, for once,
entirely agree with you, Ed! ;)<br class="">
Indeed, in French we have a rather dirty saying:
“Faudrait voir à ne pas péter plus haut que son cul!”<br
class="">
Just my own two cents (which are indeed worth less &
less and may well be worth nothing more from me at all,
after you all have read this!)<br class="">
Bonne fin de Dimanche!<br class="">
Best,<br class="">
Ariel.<br class="">
Ariel J. Blocker, PhD, FRSB<br class="">
Reader in Microbiology<br class="">
Wellcome Trust Investigator<br class="">
Schools of Cellular & Molecular Medicine and
Biochemistry<br class="">
Biomedical Sciences Building<br class="">
University of Bristol<br class="">
University Walk<br class="">
Bristol BS8 1TD<br class="">
United Kingdom<br class="">
<br class="">
Email: <a moz-do-not-send="true"
href="mailto:ariel.blocker@bristol.ac.uk" class="">ariel.blocker@bristol.ac.uk</a><<a
moz-do-not-send="true"
href="mailto:ariel.blocker@bristol.ac.uk" class=""><a class="moz-txt-link-freetext" href="mailto:ariel.blocker@bristol.ac.uk">mailto:ariel.blocker@bristol.ac.uk</a></a>><br
class="">
Tel office (D39a): +44 117 33 12063<br class="">
Tel wetlab (D57/D59): +44 117 33 12404<br class="">
Tel wetlab office (D53): +44 117 33 12059<br class="">
Tel drylab (D51): +44 117 33 12097<br class="">
Tel Tecnai20: +44 117 33 12357<br class="">
Dept. fax: +44 117 3312091<br class="">
Room: D39a<br class="">
Personal webpage: <a moz-do-not-send="true"
href="http://www.bristol.ac.uk/cellmolmed/research/infect-immune/blocker.html"
class="">http://www.bristol.ac.uk/cellmolmed/research/infect-immune/blocker.html</a><br
class="">
Group page: <a moz-do-not-send="true"
href="http://www.bristol.ac.uk/cellmolmed/research/infect-immune/blocker/"
class="">http://www.bristol.ac.uk/cellmolmed/research/infect-immune/blocker/</a><br
class="">
Postgraduate students searching for a PhD please look
here:<br class="">
<a moz-do-not-send="true"
href="http://www.bris.ac.uk/fmvs/gradschool/" class="">http://www.bris.ac.uk/fmvs/gradschool/</a><br
class="">
Twitter: @T3Secreton<br class="">
<br class="">
On 31 Jan 2016, at 16:34, Edward Egelman
<<a class="moz-txt-link-abbreviated" href="mailto:egelman@virginia.edu">egelman@virginia.edu</a><a class="moz-txt-link-rfc2396E" href="mailto:egelman@virginia.edu"><mailto:egelman@virginia.edu></a>>
wrote:<br class="">
<br class="">
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 class="">
"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
class="">
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 class="">
"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 class="">
Just my two cents (which are worth less and less).<br
class="">
Ed<br class="">
<br class="">
On 1/30/16 8:07 AM, Marin van Heel wrote:<br class="">
<br class="">
Dear Nancy,<br class="">
What Sjors is suggesting is a simplified version of what
we suggested in:<br class="">
"A posteriori correction of camera characteristics from
large image data sets", P. Afanasyev et al, Nature,
Scientific Reports.<br class="">
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.
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.<br class="">
If you want to test the a posteriori camera correction
programs, contact <a class="moz-txt-link-rfc2396E" href="mailto:michael@imagescience.de"><mailto:michael@imagescience.de></a>
<a class="moz-txt-link-abbreviated" href="mailto:michael@imagescience.de">michael@imagescience.de</a><a class="moz-txt-link-rfc2396E" href="mailto:michael@imagescience.de"><mailto:michael@imagescience.de></a>!<br
class="">
Hope this helps!<br class="">
Marin<br class="">
<br class="">
=====================================<br class="">
<br class="">
On 28/01/2016 00:48, Nancy Meyer wrote:<br class="">
<br class="">
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.<br class="">
<br class="">
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<br class="">
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...<br class="">
<br class="">
Thank you for taking the time to look at the images...
slowly getting the hang of Relion, but the input is so
invaluable!<br class="">
<br class="">
Best,<br class="">
Nancy<br class="">
<br>
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