Posted by
Guy Cox-2 on
URL: http://confocal-microscopy-list.275.s1.nabble.com/GPU-based-deconvolution-tp7582498p7582505.html
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Look, this is normal for 'academic' or research programs. Many years ago I worked on (and published) a 1D (z) deconvolution scheme for confocal images. It worked, and gave great results - but it you tried it on too large a dataset it overwrote important memory areas and crashed the computer! Obviously I wasn't going to distribute it to anyone but it gave the research results I needed. (And some very pretty 3D reconstructions).
Guy
Guy Cox, Honorary Associate Professor
School of Medical Sciences
Australian Centre for Microscopy and Microanalysis,
Madsen, F09, University of Sydney, NSW 2006
-----Original Message-----
From: Confocal Microscopy List [mailto:
[hidden email]] On Behalf Of George McNamara
Sent: Thursday, 14 August 2014 10:35 AM
To:
[hidden email]
Subject: Re: GPU-based deconvolution
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Hi Sergey,
Manish's "academic" program has a nasty bug for production size
(2048x2048x32 planes) - illustrated in large results file, downloadable here
http://works.bepress.com/gmcnamara/56/that he has not replied to me about this problem. I encountered it on my NVidia TITAN card with 6 Gb ram, which ought to handle this size data (the 'academic' ImageJ plugin does not give any out of memory or any other warning or error messages). also, the software runs through an ImageJ dialog that does not remember X or Y pixel size -- tese need to be typed in every time it is run.
As for someone sending it to you, I believe the material transfer agreement forbid re-distribution.
Manish Butte's web site now states:
http://tcell.stanford.edu/software.htmlBruce MA, Butte MJ. Real-time GPU-based 3D Deconvolution. Optics Express, Vol. 21, Issue 4, pp. 4766-4773 (2013).
http://dx.doi.org/10.1364/OE.21.004766.
(c) 2013 The Board of Trustees of the Leland Stanford Junior University
After one year of freely distributing the executable version of this software, Stanford is licensing the software to Microvolution, Inc.
<
http://www.microvolution.com/>. Because of the burden of maintaining the software in my lab, we will no longer be distributing the executable. Please contact Microvolution <
http://www.microvolution.com/#contact> for information about the availability of the software.
http://www.microvolution.com/#contactMicrovolution's goal is to enable manufacturers of microscopy devices to offer almost instantaneous deconvolution to their customers by incorporating our software into their instrumentation. We also seek to work with users of multiple microscopy platforms in order to enable faster deconvolution and discovery. We are committed to delivering a quality product that generates a competitive advantage.
Cassandra Boyer, MT (ASCP)
CEO & Co-Founder
Cassandra has a 20-year track record as a proven commercial leader at GEHC and Beckman Coulter in the cellular analysis markets. She is also a board certified Medical Technologist by the American Society of Clinical Pathology (Clinical Laboratory Scientist) and has laboratory experience in clinical hematology. Her experience working with scientists using high content analysis microscopy systems enables her to have a keen understanding of our customers' goals and objectives. She drives our team to deliver quality products while ensuring excellence in customer satisfaction.
Marc Bruce, PhD
CTO & Co-Founder
Invented the software technology to solve problems in analyzing microscopy problems in immunology and cell biology research. He has extensive experience in software development in C++, Java, CUDA, and other programming languages. During his PhD studies at Stanford University, he has gained unique insight into bridging advanced wet lab techniques with computation.
Manish Butte, MD, PhD
Advisor & Co-Founder
Supervised and assists in software development. Dr. Butte is an Assistant Professor in the Department of Pediatrics at Stanford University. His research lab at Stanford conducting basic research in Immunology, Biophysics, and Materials Science. He has 30+ years of software experience including work as a software engineer for Microsoft and Apple, Inc.
//
For open source deconvolution code, you can try UNC's Clarity deconvolution library
http://cismm.cs.unc.edu/resources/software-manuals/clarity-deconvolution-library/ER-Decon / IVE / Priism might have source code and might work with GPU(s)
http://msg.ucsf.edu/IVE/Download/... I'm still waiting for our internal paperwork to clear the material transfer agreement before I can get ER-Decon and send it to our UNIX Administrator to run it on a local Linux cluster.
I do not believe COSMOS uses GPU(s), you can get it from
http://cirl.memphis.edu/cosmos.phpHoppe 2008's 3DFSR is 61 lines of Matlab code, which you could "tweak"
to use the MatLab parallel (GPU) toolbox,
http://www.ncbi.nlm.nih.gov/pubmed/18339754source code is available at
http://sitemaker.umich.edu/4dimagingcenter/3dfsr<
http://sitemaker.umich.edu/4dimagingcenter/3dfsr>
3DFSR was slow in 2008, but does 'joint' spatial deconvolution and spectral unmixing, for 10x improvement in signal to noise ratio. PC's are a bit faster now. My colleagues and I recently submitted a proposal to Intel to fund parallelizing it for Xeon CPUs, Xeon Phi cards (maybe the ~7000 in TACC Stampede,
https://www.tacc.utexas.edu/stampede/ - as part of UT, we have free access), and next year's Knights Landing CPU(s)
- and our's will be fully open source AND functional program(s) for Windows and hopefully Linux ... I am especially psyched about the latter, since will have 72 cores, 16 Gb 'on package' very fast RAM (that is in with the CPU), fast interconnects to other components in its node:
local RAM (ex. 384 Gb per CPU), Intel's new P3700 data center SSDs (2 Tb), 40 Gbit Ethernet. We should herr back from Intel in the next three months, and if funded may be able to get out a Matlab program (using runtime library like CellProfiler) and a way to have the Matlab -> C-compiler to use Intel MKL calls to send instructions and data to Xeon CPUs and Phi card(s) - and hopefully TACC Stampede. Then move forward with porting it to Python or similar language/libraries (or maybe Intel C and MKL) and get it to work with ImageJ2 (especially headless).
Sincerely,
George
On 8/13/2014 4:33 PM, Sergey Tauger wrote:
> *****
> To join, leave or search the confocal microscopy listserv, go to:
>
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy> Post images on
http://www.imgur.com and include the link in your posting.
> *****
>
> Dear colleagues,
>
> Could you please share a open source software for PSF generation
> and/or deconvolution that runs on GPU? If somebody has a copy of the
> one described in "Real-time GPU-based 3D Deconvolution" (Bruce&Brutte,
> 2013) it will be brilliant.
>
> Looking forward for reply,
> Sergey Tauger
> Dept. of Biology, MSU
>
>
--
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