[3dem] [ccpem] Adequate particle normalization prior to 2D classification?

[Ariel Blocker]

 All that now being said, I do think SREP is a good, and rapidly improving journal. See for instance a recent paper by Steve Matthews' lab on curli I had the honour to edit (hope it's out already!) So, watch this IF space!
Best,
Ariel.

Sent from my iPad

> On 31 Jan 2016, at 19:30, Marin van Heel <marin.vanheel at googlemail.com> wrote:
> 
> 
> I shall not copy-paste "Nature, Scientific Reports" on Saturdays
> I shall not copy-paste "Nature, Scientific Reports" on Saturdays
> I shall not copy-paste "Nature, Scientific Reports" on Saturdays
> I shall not copy-paste "Nature, Scientific Reports" on Saturdays
> 
> Marin
> 
> (and Ariel: "va te laver la bouche avec du savon")
>  
> 
>> On 31/01/2016 16:56, Ariel Blocker wrote:
>> Sweet Sacha! And glad you did not write "Note to self: do not READ to 3DEM emails on Sunday…”.
>>  ;)
>> A.
>> Ariel J. Blocker, PhD, FRSB
>> Reader in Microbiology 
>> Wellcome Trust Investigator
>> Schools of Cellular & Molecular Medicine and Biochemistry
>> Biomedical Sciences Building
>> University of Bristol
>> University Walk
>> Bristol  BS8 1TD
>> United Kingdom
>> 
>> Email: ariel.blocker at bristol.ac.uk
>> Tel office (D39a): +44 117 33 12063
>> Tel wetlab (D57/D59): +44 117 33 12404
>> Tel wetlab office (D53): +44 117 33 12059
>> Tel drylab (D51): +44 117 33 12097
>> Tel Tecnai20: +44 117 33 12357
>> Dept. fax: +44 117 3312091
>> Room: D39a
>> Personal webpage: http://www.bristol.ac.uk/cellmolmed/research/infect-immune/blocker.html
>> Group page: http://www.bristol.ac.uk/cellmolmed/research/infect-immune/blocker/
>> Postgraduate students searching for a PhD please look here:
>> http://www.bris.ac.uk/fmvs/gradschool/
>> Twitter: @T3Secreton
>> 
>>> On 31 Jan 2016, at 16:53, De Carlo, Sacha <Sacha.DeCarlo at fei.com> wrote:
>>> 
>>> Note to self: do not reply to 3DEM emails on Sunday...
>>> 
>>> Sacha De Carlo, Ph.D.
>>> EMEAI SSD LS Apps Manager
>>> -sent from my mobile
>>> FEI.com<http://fei.com>
>>> 
>>> On 31 Jan 2016, at 16:51, Ariel Blocker <Ariel.Blocker at bristol.ac.uk<mailto:Ariel.Blocker at bristol.ac.uk>> wrote:
>>> 
>>> As associate editor of Scientific Reports, I, for once, entirely agree with you, Ed! ;)
>>> Indeed, in French we have a rather dirty saying: “Faudrait voir à ne pas péter plus haut que son cul!”
>>> 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!)
>>> Bonne fin de Dimanche!
>>> Best,
>>> Ariel.
>>> Ariel J. Blocker, PhD, FRSB
>>> Reader in Microbiology
>>> Wellcome Trust Investigator
>>> Schools of Cellular & Molecular Medicine and Biochemistry
>>> Biomedical Sciences Building
>>> University of Bristol
>>> University Walk
>>> Bristol  BS8 1TD
>>> United Kingdom
>>> 
>>> Email: ariel.blocker at bristol.ac.uk<mailto:ariel.blocker at bristol.ac.uk>
>>> Tel office (D39a): +44 117 33 12063
>>> Tel wetlab (D57/D59): +44 117 33 12404
>>> Tel wetlab office (D53): +44 117 33 12059
>>> Tel drylab (D51): +44 117 33 12097
>>> Tel Tecnai20: +44 117 33 12357
>>> Dept. fax: +44 117 3312091
>>> Room: D39a
>>> Personal webpage: http://www.bristol.ac.uk/cellmolmed/research/infect-immune/blocker.html
>>> Group page: http://www.bristol.ac.uk/cellmolmed/research/infect-immune/blocker/
>>> Postgraduate students searching for a PhD please look here:
>>> http://www.bris.ac.uk/fmvs/gradschool/
>>> Twitter: @T3Secreton
>>> 
>>> On 31 Jan 2016, at 16:34, Edward Egelman <egelman at virginia.edu<mailto:egelman at virginia.edu>> wrote:
>>> 
>>>    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:
>>> "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."
>>> 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:
>>> "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."
>>>  Just my two cents (which are worth less and less).
>>> Ed
>>> 
>>> On 1/30/16 8:07 AM, Marin van Heel wrote:
>>> 
>>> Dear Nancy,
>>> What Sjors is suggesting is a simplified version of what we suggested in:
>>> "A posteriori correction of camera characteristics from large image data sets", P. Afanasyev et al, Nature, Scientific Reports.
>>> 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.
>>> If you want to test the a posteriori camera correction programs, contact <mailto:michael at imagescience.de> michael at imagescience.de<mailto:michael at imagescience.de>!
>>> Hope this helps!
>>> Marin
>>> 
>>> =====================================
>>> 
>>> On 28/01/2016 00:48, Nancy Meyer wrote:
>>> 
>>> 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
> 
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