Re: [scipion-users] 1. binning; 2. cryoSPARC

[Carlos O. S. <co...@cn...>]

Dear Dmitry,


On 07/02/2017 11:40, Dmitry Semchonok wrote:
> Dear colleagues,
>
> could you please explain me the strategy of binning usage?
>
> Apart of the fact that binning speeds up the processing. I would like 
> to use the binning to see my particles better (some of my data is very 
> close to focus)
Binning, or better downsampling (the difference is in the filter used 
before the decimation of the signal) is not only used for speeding up 
the processes, but also to remove high frequency noise, and smoothing 
the objective function of many algorithms. Actually, binning is not the 
best option as it has negative effects in many subsequent steps (see 
http://biocomp.cnb.csic.es/~coss/Articulos/Sorzano2009d.pdf)
>
> In the SCIPION tutorial - Mix-and-Match Tutorial 
> <https://github.com/biocompwebs/scipion/wiki/tutorials/scipion_tutorial_betagal.pdf> 
> on the page 12 stands the *Preprocess particles protocol *that sugests 
> to do binning before CTF estimation.
>
> My questions are:
>
> 1. When do you do unbinning of the dataset?
The set is never unbinned, you can extract particles again at the 
original size and reuse the part of the processing that you did with the 
downsampled particles.
>
> 2. Do you also need to estimate the CTF for the unbinned dataset?
No. Actually, the best way is to estimate the CTF on the original 
micrographs and use the same CTF for all particles (regardless their 
downsampling). Scipion knows the sampling rate of the particles and the 
sampling rate at which the CTF was estimated and acts accordingly.
>
> 3. How / when do you do the binning if you work with movies (stucks) - 
> after the motion correction?
>
Again, better do the movie alignment before extracting at a downsampled 
size.
>
>
>
> Another issue:
>
> there is a new soft calling cryoSPARC
>
> see the link about cryoSPARC 
> <http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.4169.html?WT.feed_name=subjects_systems-biology>
>
>
> Do you have plans to incorporate it in the SCIPION?
>
>
We have contacted the authors of cryoSparc and we will see how far we 
can go from both sides.

Kind regards, Carlos Oscar
> Sincerely,
> Dmitry
>
>
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Carlos Oscar Sánchez Sorzano                  e-mail:   co...@cn...
Biocomputing unit                             http://biocomp.cnb.csic.es
National Center of Biotechnology (CSIC)
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Campus Universidad Autónoma (Cantoblanco)     Tlf: 34-91-585 4510
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