Re: Lightsheet imaging analysis Workstation Specs

Posted by Niyanta Kumar on
URL: http://confocal-microscopy-list.275.s1.nabble.com/Lightsheet-imaging-analysis-Workstation-Specs-tp7590391p7590402.html

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Thanks Gary, Pavak, Vincent, and Francesco! I'm fairly new to the field so this is great. I was wondering if you'll could comment on your experience and related recommended PC specs needed when using Imaris or Arivis Vision 4D software in particular for lightsheet data analysis? I think Imaris only uses a single GPU. My typical data set is ~ 0.5 to 1 TB - labeled, cleared tumors/organs. A lot of the processing will involve fusion and analysis will be segmentation based. We are finalizing the purchase of a lightsheet instrument for inhouse use and currently generating data through a CRO (LifeCanvas) but will need to analyze data in house. I'm not working in a core setting in terms of throughput and my analysis station will handle a couple of data sets of the size mentioned over a month at a time. I think to your point I want to find a sweet spot between something to start with and what we can upgrade to over time if/as our needs increase. Any recommendations on monitors? I was thinking of a dual Lenovo Think Vision P32u-10. Does a full LED array help or is edge lit fine?

Best,
Niyanta

Niyanta Kumar, Ph.D.
Senior Scientist - Pharmacokinetics and ADME
Merck Research Laboratories, WP75B-2215
770 Sumneytown Pike, West Point, PA 19486
Phone: [phone]

-----Original Message-----
From: Confocal Microscopy List <[hidden email]> On Behalf Of Francesco Pasqualini
Sent: Wednesday, January 15, 2020 10:22 AM
To: [hidden email]
Subject: Re: Lightsheet imaging analysis Workstation Specs

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Pavak, Vincent Gary, et al - thanks for the clarification. Best, Francesco


On Wed, Jan 15, 2020 at 4:13 PM PAVAK SHAH <[hidden email]> wrote:

> *****
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> *****
>
> Hi Francesco,
>
> I should clarify that it depends a lot on the software pipeline being used.
> The ones I am most familiar with for diSPIM data (MIPAV, Shroff lab
> software, and Stephan Preibisch's Multiview Reconstruction) don't
> inherently support parallel processing of a single dataset on multiple
> GPU's but multiple instances can be run separately on different
> datasets (or different segments of the same dataset). I have not kept
> up as closely with what folks use for fusing data from Z1, openSPIM,
> MuVi SPIM, or bespoke multiview systems.
>
> With enough memory, multiple fusions can also be performed on the same
> GPU, albeit with sub-linear gains in performance. In the case of MVR,
> my understanding is that GPU support may have become deprecated (at
> least I haven't succeeded in running the CUDA libraries it depends on
> in several
> years) and most users run it on CPU clusters now. I've been meaning to
> take a stab at recompiling the CUDA libraries to see if they'll run as
> is on 10.1, but haven't found the time to do so.
>
> Best,
> Pavak
>
> On Wed, Jan 15, 2020, 12:33 AM Francesco Pasqualini <
> [hidden email]> 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.
> > *****
> >
> > Hi Pavak et al,
> > This is very interesting and helpful.
> >
> > Do I understand you correctly that multiple GPU won't help with
> > multiview deconvolution?
> >
> > If there is a reference for deconvolution performances as a function
> > of various hardware options can anyone point it out?
> >
> > Thanks
> > Francesco
> >
> >
> >
> > On Wed, Jan 15, 2020, 12:57 AM PAVAK SHAH <[hidden email]> 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.
> > > *****
> > >
> > > Hi Niyanta,
> > >
> > > What lightsheet instrument and what is the size of your typical
> dataset?
> > Is
> > > your processing pipeline primarily for segmentation or multiview
> > > deconvolution? This will dictate, to a large extent, the kind of
> > > memory
> > and
> > > CPU you need.
> > >
> > > An RTX 2080ti or Titan RTX will be competitively performant but
> > > much cheaper than a Quadro card, which offers no benefits for an
> > > image
> > analysis
> > > workflow unless you're running virtual machines. If your workflow
> > > is primarily single view deconvolution, multiple GPUs can also be
> > > a huge
> > boon
> > > in terms of processing throughput, especially if individual
> > > volumes can
> > fit
> > > in 11 GB of VRAM since you can fill a large workstation to
> > > bursting
> with
> > > 2080ti's for the price of 1 Quadro card. Even 2x Titan RTX can be
> > > had
> for
> > > less than the price of 1x Quadro 6000.
> > >
> > > Depending on the specific piece of software, many will not scale
> > > efficiently to >16 cores and a faster clocked CPU with fewer cores
> > > may
> be
> > > advantageous. If you can benchmark it on a high core count system,
> > > that should show whether your pipelines are able to keep that many
> > > cores fed before running into algorithmic, disk access or memory
> > > throughput bottlenecks.
> > >
> > > Best,
> > > Pavak
> > >
> > > On Tue, Jan 14, 2020, 1:27 PM Niyanta Kumar <
> > > [hidden email]> 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.
> > > > *****
> > > >
> > > > Hi all,
> > > > I plan to get a workstation that can handle confocal and
> > > > lightsheet
> > data
> > > > analysis using Imaris and/or Arivis. Lightsheet data clearly has
> > > > the
> > > higher
> > > > bar/needs in terms of specs. Below are the specs I am considering.
> Can
> > > you
> > > > please let me know if you have any recommendations?
> > > >
> > > > Lenovo Think Station P920
> > > > 3.7 GHz CPUs (Intel) 48 cores
> > > > Graphics: NVIDIA Quadro RTX 6000 or 8000
> > > > 4 X 3 TB of local SSD (multiple drives - one for the OS, one for
> > writing,
> > > > one for reading)
> > > > RAM: 500 GB
> > > > Monitor: dual 1920 x 1200
> > > > 300 TB NAS via 10 GB ethernet – file sharing
> > > > Mouse: 3 button wheel
> > > >
> > > > Monitor: thinking of a dual Lenovo Think Vision P32u-10 but it
> doesn’t
> > > > have a full array LED. Any suggestions? I hear the curved
> > > > monitors
> can
> > > > cause issues with display when sharing screens over Webex etc.
> > > > Thanks,
> > > > Niyanta
> > > >
> > >
> >
>

--
Francesco S. Pasqualini
Visiting Professor University of Pavia
Associate Harvard University

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