Re: Memory allocation/speed of processing

Posted by lechristophe on Feb 19, 2015; 11:50am
URL: http://imagej.273.s1.nabble.com/Memory-allocation-speed-of-processing-tp5011680p5011683.html

Hi,

You can also check that the number of cores used by ImageJ (in the ImageJ
options) is optimal.

However, the speed of ThunderSTORM processing is likely due to the plugin
itself, i.e. the way it is coded, and the parameters you use for detection
and localization of blinking events. For example, the multiple-emitter
fitting option is extremely demanding and will slow processing considerably.

I suggest you compare with another STORM software (such as Octane,
QuickPALM in ImageJ, or rapidSTORM) to see if there is a big difference in
processing time with the same parameters (be careful it is sometimes
difficult to translate parameters from one soft to another).

In any case I suggest you ask more question on the ThunderSTORM google
group:
https://groups.google.com/forum/#!forum/thunderstorm-users


Christophe

--
Christophe Leterrier
Researcher
Axonal Domains Architecture Team
CRN2M CNRS UMR 7286
Aix Marseille University, France



On Thu, Feb 19, 2015 at 12:24 PM, Shannon, Michael <
[hidden email]> wrote:

> Hi there
>
> We use imageJ for certain image analysis techniques, in which each frame of
> a TIFF containing 30000 frames is processed.
>
> The specific plugin I am using is called 'ThunderSTORM'
>
> Our problem is that this takes an inordinate amount of time to do.
>
> We recently upgraded our computers, so now this one has 48 gb RAM, and its
> original intel xeon CPU (e5-1620 with 3.7GHz).
>
> I have upped the memory allocation in ImageJ - is there any other way to
> make this go faster?
>
> Thanks for any help anyone can offer,
>
> Mike?
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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