Re: [scipion-users] java error opening the extraction particle file with built-in ImageJ

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

Thanks Dmitry for the feedback.
We might think about making these easier for the future, either to use
images in presentation/publication or to share with collaborators.

Best,
Jose Miguel



On Wed, May 6, 2020 at 9:59 AM Dmitry A. Semchonok <sem...@gm...>
wrote:

> Dear colleagues,
>
>
>
> Thank you all for your suggestions!
>
> My problem indeed was connected with the memory since the dataset was
> ~8000 particles.
>
>
>
> The solution was found.
>
> If you need to get an stk file out of your particles (the number doesn't
> matter much), you can use *relion-export particles* protocol in SCIPION.
>
> There you have several options. You can make 1 mrc stack file that Fiji
> (ImageJ) can easily read.
>
>
>
> I hope this helps.
>
>
>
> Sincerely,
>
> Dmitry
>
>
>
> Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for
> Windows 10
>
>
>
> *From: *Jose Miguel de la Rosa Trevin <del...@gm...>
> *Sent: *Tuesday, May 5, 2020 6:13 PM
> *To: *Mailing list for Scipion users <sci...@li...>
> *Subject: *Re: [scipion-users] java error opening the extraction particle
> file with built-in ImageJ
>
>
>
> Hi Dmitry,
>
>
>
> Depending on how many particles do you have and their dimensions, ImageJ
> can have some memory issues if the dataset is too big to be read into RAM
> memory.
>
>
>
> Hope this helps,
>
> Best,
>
> Jose Miguel
>
>
>
>
>
>
>
>
>
> On Tue, May 5, 2020 at 5:33 PM Dmitry A. Semchonok <sem...@gm...>
> wrote:
>
> Dear Grigory,
>
>
>
> Yes (please see the attachment), so
>
>
>
> Relion particles extraction protocol (analyze)à then see the particles
> gallery (open with imageJ) à then the program crashes with the java error.
>
>
>
>
>
> Thank you!
>
>
>
> Sincerely,
>
> Dmitry
>
>
>
> Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for
> Windows 10
>
>
>
> *From: *Grigory Sharov <sha...@gm...>
> *Sent: *Tuesday, May 5, 2020 1:41 PM
> *To: *Mailing list for Scipion users <sci...@li...>
> *Subject: *Re: [scipion-users] java error opening the extraction particle
> file with built-in ImageJ
>
>
>
> Hi,
>
>
>
> Could you be more specific? What is relion extraction file? Sqlite? Mrcs?
> Star ? What error?
>
>
>
>
>
>
>
> On Tue, May 5, 2020, 12:38 Dmitry A. Semchonok <sem...@gm...>
> wrote:
>
> Dear colleagues,
>
>
>
> While opening the relion-extraction file with ImageJ, I’m getting the java
> error.
>
> Are there any options to open this extracted particle file directly from
> the folder with ImageJ?
>
> I want to do stk from the extracted particles.
>
>
>
> Sincerely,
>
> Dmitry
>
>
>
>
>
> Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for
> Windows 10
>
>
>
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