Posted by
George McNamara on
URL: http://confocal-microscopy-list.275.s1.nabble.com/GPU-based-deconvolution-tp7582498p7582510.html
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Hi Sergey,
One great point Manish emphasized to me is that anytime we are using
FFT's, to give the FFT routines data with power of two dimensions. So,
instead of 256*256*40, you would be better off with 256*256*32, and
might be better off with 256*256*64.
If COSMOS is no longer being developed by Prof. Preza, all the more
reason for you to adopt it! It is using a GNU General Public License,
http://cirl.memphis.edu/cosmos_faqs.phpLikewise the Clarity deconvolution library at UNC is no longer being
developed, consider taking over that.
Adam Hoppe told me several months ago that he is continuing to work on
3DFSR, so consider contacting him at
http://www.sdstate.edu/chem/faculty/adam-hoppe/I forgot to mention in yesterday's email the BoaDeconvolution -- already
Parallel Deconvolution -- at
http://pawliczek.net.pl/deconvolution/http://onlinelibrary.wiley.com/doi/10.1002/jemt.20773/abstractI've previously posted to the listserv more on GPU (and Xeon, Xeon Phi,
Knights Landing proposal).
best wishes,
George
On 8/14/2014 4:14 AM, Sergey Tauger wrote:
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>
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>
> George,
>
> Thank you for useful links. I'm going to write my own deconvolution software or
> contribute to existing. At the moment I use DeconvolutionLab and COSMOS for
> PSF generation. To my regret, COSMOS is a legacy software, but the only that
> supports PSF generation according to Haeberle and Török models. I'd like to
> speedup PSF generation, 1hr for 256*256*40 is too much.
>
> I do not overestimate my programming skills, so I'd better use a existing GPU-
> based PSF generation software as a "best practice" guide than writing my own
> implementation from scratch. If I succeed in speeding up PSF generation, I'll post
> a link to github in this thread.
>
> Best,
> Sergey
>
>
--
George McNamara, Ph.D.
Single Cells Analyst
L.J.N. Cooper Lab
University of Texas M.D. Anderson Cancer Center
Houston, TX 77054
Tattletales
http://works.bepress.com/gmcnamara/42