Re: [scipion-users] About particle picking with Xmipp and EMAN2 through Scipion

[Pablo C. <pc...@cn...>]

Dear Luigi, please follow this thread. Jose Miguel, I already replied to 
Luigi, and asked for the same thing. Let's keep this thread since 
situation is better explained.

Cheers, Pablo

Scipion Team

On 03/02/17 11:32, Jose Miguel de la Rosa Trevin wrote:
>
> Dear Luigi,
>
> Thanks for providing feedback to us. Regarding your specific issues 
> with picking, what do you mean by "after providing the references" in 
> Xmipp and Eman pickers? To the best of my knowledge, both programs 
> generate the references on-the-fly, after the selection of some 
> particles manually. So, there is not need to provide pre-computed 
> references such as 2D class averages.
>
> In the case of EMAN2-Box, both the manual/supervised steps are 
> interwinned in a very interactive way. On the other hand, in Xmipp3 
> picker, those steps are separated in two phases. You first need to 
> picking manually some micrographs entirely (or a well-defined box in 
> one micrograph is its contains many particles)...and then switch to 
> "Supervised" mode, where the algorithm will propose you some particle 
> candidates and you can correct it (either removing bad proposed 
> particles or adding missing one). The algorithm will "learn" from that 
> and then in another protocol you can launch the automatic picking 
> based on that training.
>
> Anyway, if you provide a few micrographs we could try to help about 
> the parameters selection.
>
> Hope this helps,
>
> Jose Miguel
>
> Scipion Team
>
>
> -----------------------------------------
>
> My name is Luigi De Colibus and I’m Post Doc at the Division of 
> Structural Biology of Oxford University.
> I’m writing you because I’m trying to run automated particle picking 
> programs on my micrographs trough SCIPION.
> Surprisingly, despite the fact my virus particle is very big and 
> evident on the micrographs, neither Xmipp particle picking program nor 
> Boxer in EMAN2 is able to pick correctly the particles after providing 
> the reference.
> I guess my settings could be wrong and trying different values has not 
> helped so far.
>
> It would be great if you could point me in the right direction.
> I can send you one of my micrographs if you need to do a test run.
>
> Thanks a lot in advance for your help!
>
> Best Regards
>
> Reply to: luigi at strubi.ox.ac.uk <http://strubi.ox.ac.uk>
>
>
>
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