Posted by
George McNamara on
URL: http://confocal-microscopy-list.275.s1.nabble.com/GPU-based-deconvolution-tp7582498p7582502.html
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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.
© 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