Re: [scipion-users] Problems with my software

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

Dear Robin, all.

We are close to release tomography plugins... actually, they are 
silently released (intentionally) to test the release process and for us 
to get used to release our code.

So, anyone willing to test tomography plugins, feel free to use them 
(kind of in BETA/production state) and report any issue. Grigory 
suggestion should also work.


As for the streaming tab in import tilt series.... it has been removed. 
If you want to do streaming processing of tilt series you should follow 
the more tested path:


Import movies (as if they where SPA)

Motion correct them (as if they were SPA)

Compose tilt series (THis one is new in tomo and is feed with 
"micrographs" and "mdoc path"). This one composes the tilt series on the 
fly stacking the images.

Aretomo is on its way to be streamified, and more to come.

NovaCTF and cryoCARE, might need some time to verify its status. You can 
always use Grigory's link to have them in devel mode.

On 12/5/23 10:48, Grigory Sharov wrote:
> Dear Robin,
>
> all tomography plugins are not listed in the Plugin manager because 
> they are still in beta testing. You can install them in development 
> mode from github (see here 
> <https://docs.google.com/document/d/119yxa9Wz4hksjIrAb26YA8rFJPzx-Rq0oy8VNQvp3kE/edit?usp=sharing>). 
>
>
> As for streaming, import tomo protocols do not have this tab. Instead 
> you should do the streaming via SPA (import and motion correction) and 
> then use the "tilt series composer" protocol.
>
> Best regards,
> Grigory
>
> --------------------------------------------------------------------------------
> Grigory Sharov, Ph.D.
>
> MRC Laboratory of Molecular Biology,
> Francis Crick Avenue,
> Cambridge Biomedical Campus,
> Cambridge CB2 0QH, UK.
> tel. +44 (0) 1223 267228 <tel:+44%201223%20267228>
> e-mail: gs...@mr...
>
>
> On Fri, May 12, 2023 at 9:22 AM robin <rob...@u-...> wrote:
>
>     Hello,
>
>     I am contacting you because I have some problems with my Scipion
>     software (v3.0.12 and Eugenius v3.0.31).
>
>     The first one is that I don't have the complete list of plugins in
>     the plugin manager, for example I'm missing novaCTF or cryoCARE.
>
>     The second one is that I don't have the streaming tab in the job
>     tomo-import tilt series movies or tomo-import tilt series.
>
>     My Scipion software is installed on a Linux workstation (no
>     cluster). Are these problems due to an installation problem?
>
>     Best regards,
>
>     Robin ANGER
>
>     Robin ANGER, PhD
>     Ingénieur de Recherche
>     Institut Européen de Chimie et de Biologie
>     2 rue Robert Escarpit
>     33607 Pessac, France
>
>
>
>
>
>
>
>
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-- 
Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*