Re: [scipion-users] Export particles from cryosparc

[Grigory S. <sha...@gm...>]

Hi,

I don't use cryosparc.

You need to rename mrc to mrcs. MRC format was never designed for stacks,
mrc is only for a single 2D image or a 3D volume. 2D stacks should be mrcs
(as in relion & eman2).

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 <+44%201223%20267228>
e-mail: gs...@mr...


On Tue, May 18, 2021 at 8:53 AM Dmitry Semchonok <Sem...@gm...>
wrote:

> Dear Grigory,
>
>
>
> The files are in mrc format.
>
>
>
> Please, let me try to explain more plan:
>
>  I have a project in cryosparc. There I have cryosparc selected 2D
> classes. I want to export the particles of those classes into SCIPION.
>
>  So I I pressed Export (fig 1) and the program(cryosparc) created the
> folder with mrc  + other files (fig 2;3). I looked into J48 and found many
> *.mrc files of the particles. But it is not 1 mrc = 1 particle. It seems to
> be a mrc stuck - so I have several files inside 1 *.mrc  (fig 4) (you can
> also notice that they all have different sizes)
>
>  So I need to export them somehow in SCIPION
>
>  For that, I used the SCIPION export - images protocol where for the files
> to add I put *.mrc. But the protocol seems to be added only 1 mrc as 1
> picture and instead of having 46392 particles I have ~600 particles.
>
>  (Also the geometry seems not preserved).
>
>
>
> So my question how to export the particles from cryosparc into SCIPION
> correctly?
>
>
>
>  Thank you!
>
>
>
>  https://disk.yandex.com/d/Fv3Q1lpwEzSisg
>
>  Sincerely,
>
> Dmitry
>
>
>
> On 17. May 2021, at 18:12, Grigory Sharov <sha...@gm...>
> wrote:
>
> Hi Dmitry,
>
> mrc stacks should have "mrcs" extension. Is this the problem you are
> getting?
>
> 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 <+44%201223%20267228>
> e-mail: gs...@mr...
>
>
> On Mon, May 17, 2021 at 4:49 PM Dmitry Semchonok <Sem...@gm...>
> wrote:
>
>> Dear colleagues,
>>
>>  I would like to export the particles from cryosparc to SCIPION.
>>
>>  How to do that?
>>
>>
>>
>>
>> What I tried:
>>
>>
>> 1.     In cryosparc I pressed Export – to export the particles I am
>> interested in.
>>
>> 2.     In the folder Export – I found many mrc stacks with particles in
>> each.
>>
>> 3.     I tried to export them to SCIPION using Export particles but
>> instead of reading each stack and combine them in the 1 dataset I received
>> 1 particle / per each mrc stack.
>>
>>
>> Any ideas?
>>
>>
>> Thank you
>>
>>  Sincerely,
>>
>> Dmitry
>>
>> _______________________________________________
>> scipion-users mailing list
>> sci...@li...
>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>
>
>