[3dem] [TEM] CTF and SNR

[Slavica Jonic]

Dear John,

We showed in 2007 that pure water ice produces Thon rings and that their 
visibility depends on ice thickness (Fig. 7 in 
http://www.sciencedirect.com/science/article/pii/S104784770600236X). The 
visibility of rings can be improved using the method proposed in that 
paper.

Best regards,

Slavica


Le 07/06/2017 à 15:43, John Rubinstein a écrit :
> Hi Steve,
>
> As Greg McMullan and Richard Henderson showed recently, amorphous ice 
> does give Thon rings. However, ice also exhibits a beam induced 
> ‘Brownian’-like movement so that the power spectrum from the average 
> of DDD frames does not often show Thon rings.
> https://www.ncbi.nlm.nih.gov/pubmed/26103047
> Alexis Rohou modified CTF find in order to allow use of this signal in 
> CTF estimation.
>
> Best regards,
> John
>
>
>
> -- 
> John Rubinstein
> Molecular Medicine Program
> The Hospital for Sick Children Research Institute
> 686 Bay Street, Rm. 20-9705
> Toronto, ON
> Canada
> M5G 0A4
> Tel: (+001) 416-813-7255
> Fax: (+001) 416-813-5022
> www.sickkids.ca/research/rubinstein 
> <http://www.sickkids.ca/research/rubinstein>
>
>> On Jun 7, 2017, at 9:33 AM, Ludtke, Steven J <sludtke at bcm.edu 
>> <mailto:sludtke at bcm.edu>> wrote:
>>
>> Hi Philip,
>> pure water ice, alas, does not exhibit Thon rings (at least not 
>> significantly). Other buffer constituents may. This makes modeling 
>> noise a bit tricky.
>>
>> Many of the methods in the field start with the assumption that the 
>> image consists of a true projection of a macromolecule, convolved 
>> with the CTF with added uncorrelated Gaussian noise. That is, noise 
>> with a flat power spectrum and no correlation among nearby pixels. 
>> Prior to direct detectors and counting, the background noise power 
>> spectrum in typical cryoEM images had an exponential decay, and could 
>> with a little processing be "flattened" to produce something more or 
>> less like uncorrelated Gaussian noise.  The problem with this 
>> assumption, even then, is that CryoEM images actually contain a lot 
>> of other stuff, and from the perspective of single particle 
>> reconstruction, noise isn't just the scattering off the solvent, it's 
>> anything present in the image which is not a perfect projection of 
>> the particle.
>>
>> This is what led to EMAN2's approach of computing the power spectrum 
>> of masked out particles, and masked out regions outside particles to 
>> compute an accurate estimate of the SNR of the particles within the 
>> images. Whether having this really produces better reconstructions is 
>> a separate question, but making this estimate DOES tell you quite a 
>> lot about particle data quality and whether you should expect to be 
>> able to achieve high resolution from your data.
>>
>> I'm attaching some slides from about 10 years ago showing how SSNR 
>> estimates assuming a pretty flat background can give completely 
>> inaccurate estimates of the actual SSNR of the images. Hope they are 
>> reasonably self-explanatory. This compares the approach of 
>> considering noise to be anything in the power spectrum without Thon 
>> rings to be noise, with the approach of computing the noise from 
>> regions of the image not containing particles.
>>
>> https://drive.google.com/file/d/0BxreryX3Fp-ZUVJtTFlYX0lmbzg/view?usp=sharing
>>
>> ----------------------------------------------------------------------------
>> Steven Ludtke, Ph.D.
>> Professor, Dept of Biochemistry and Mol. Biol.     
>>   (www.bcm.edu/biochem <http://www.bcm.edu/biochem>)
>> Co-Director National Center For Macromolecular Imaging (ncmi.bcm.edu 
>> <http://ncmi.bcm.edu/>)
>> Co-Director CIBR Center (www.bcm.edu/research/cibr 
>> <http://www.bcm.edu/research/cibr>)
>> Baylor College of Medicine
>> sludtke at bcm.edu <mailto:sludtke at bcm.edu>
>>
>>
>>
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-- 
Dr Slavica JONIC
CNRS Associate Scientist

IMPMC, Sorbonne Universités
CNRS UMR 7590, UPMC Univ Paris 6, MNHN, IRD UMR 206

Université Pierre et Marie Curie
Case courrier 115
4 Place Jussieu
75005 Paris, France

Tel: +33 1 44 27 72 05
Fax: +33 1 44 27 37 85

E-mail: Slavica.Jonic at impmc.upmc.fr
URL: http://www.impmc.upmc.fr/~jonic

Frontiers Research Topic:
http://frontiersin.org/Biophysics/researchtopics/Hybrid_Biomolecular_Modeling/4799


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