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

[Marin van Heel]

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 <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 16:53, De Carlo, Sacha <Sacha.DeCarlo at fei.com 
>> <mailto: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><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><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><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
>>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ncmir.ucsd.edu/pipermail/3dem/attachments/20160131/2cb7661e/attachment-0001.html>