Re: [scipion-users] SCIPION dev - motion correction

[Jose M. de la R. T. <del...@gm...>]

Dear Dmitry,

Thanks for giving a try to Scipion devel. Nonetheless, I would suggest you
to use 'release-1.1' branch (recently branched out from devel) which is the
branch for the next stable release. This means that it will only contains
important bug-fixes and should be more stable than devel at this point.

Regarding your specific questions, in this new version we have separated
the protocols related to movie alignment. Before, they were added to the
same protocol...was does not follows the Scipion philosophy of modularity.
This change was also necessary for the streaming feature, that allows you
to launch several processing steps right after the first item of the set is
being produced and does not need to wait until all items are done. This
allows to overlap the acquisition time with the preprocessing time, that
save computing time and resources while giving you a quickly feedback on
the dataset.

Probably you are not seeing these new protocols because you still have an
old 'protocols.conf' file. Try to delete this file (at
$SCIPION/config/protocols.conf) and then generate it again with the
command: scipion config
After that you should have the complete list of movie alignment protocols
(see the attached screenshot) under the Movies section in the left panel of
the project GUI.

Hope this helps
Jose Miguel

[image: Inline image 1]

On Sat, Feb 11, 2017 at 8:26 PM, Dmitry Semchonok <sem...@gm...>
wrote:

> Dear colleagues,
>
> I tried SCIPION dev - wanted to experiment with GPU etc.
> And found some workflow differences.
>
>
> I used to do the motion correction with *xmipp3 movie alignment* based on
> motion core (cross-corr + optical correction using CPU)
>
>
> Now I can only see:
>
> *xmipp3 - optical alignment*; (this is probably local?)
> *grigoriefflab - unblur*
> *grigoriefflab - summovie*
>
>
> So, how do you do motion alignment (global and local) now after adding
> your movie to the project? Can I use GPU?
>
> And after how to sum the movies? (grigoriefflab - ?)
>
> Sincerely,
> Dmitry
>
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