[OpenSPIM] Deconvolution on cluster

[Pavel Tomancak]

Dear Graham,

Are you using GPU acceleration? Is there any error message? How big is the image you are trying to deconvolve?

It may be advisable to use blocks instead of the deconvolving the entire image at once, but at this point its just a hunch.

I am cc'ing Stephan Preibisch who should be able to help, but we need more information.

All the best

PAvel

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Pavel Tomancak, Ph.D.

Group Leader
Max Planck Institute of Molecular Cell Biology and Genetics
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email: tomancak at mpi-cbg.de
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twitter: @PavelTomancak
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On Oct 21, 2014, at 8:32 PM, "Marquart, Gregory (NIH/NICHD) [F]" <gregory.marquart at nih.gov> wrote:

> We have been trying to run deconvolution on a cluster at the NIH without much luck.  Although we have run the process on a 256GB node and Fiji says the deconvolution should only take ~80GB, Fiji still crashes.  How accurate are these memory estimates?  Is it possible that we are still running out of memory?  Or is it more likely that our settings just aren't right?  Any help or suggestions would be much appreciated.
> 
> Cheers,
> Graham
> 
> Gregory (Graham) Marquart
> Unit on Behavioral Neurogenetics, NICHD
> Building 6B, 3B-308
> 6 Center Drive, Bethesda, MD 20892
> 
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