Posted by
vbindokas on
Feb 19, 2015; 1:24pm
URL: http://imagej.273.s1.nabble.com/Memory-allocation-speed-of-processing-tp5011680p5011687.html
Hi Mike,
What do you consider "inordinate" times?
We run ThunderSTORM on far lesser machines with very good
performance [12GB RAM, 8 threads, 2.8GHz x3460] on 100k frames of 3-D
data. The plugin does slow appreciably if there are very dense SMLs to
be fit per frame and/or you are asking for multiple peak testing/fitting
as Christophe mentioned in his reply. You might want to compare results
with the multi-emitter feature turned off, with it set to 2, to 3, etc.
Just because it can fit 5 peaks, doesn't mean you should start with
that, for example.
Fitting data in RAM is a bit faster than from virtual stack, but
virtual mode seems just fine and allows other operations to be run
during the wait time.
regards,
Vytas
On 2/19/2015 5:24 AM, Shannon, Michael 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?
>
>
> --
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__
Vytas Bindokas, Ph.D.
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Director, BSD Light Microscopy Core Facility
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