http://confocal-microscopy-list.275.s1.nabble.com/Lightsheet-imaging-analysis-Workstation-Specs-tp7590391p7590399.html
with Huygens allows using multiple GPU cards simultaneously. There is even
deconvolution of light sheet data, and CPU and GPU use. You can join via our
Op wo 15 jan. 2020 11:13 schreef Gary Laevsky <
> *****
> 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,
>
> We've been through three iterations of this.
>
> What we have found critical is to try and determine what software you are
> going to be using for analysis.
>
> Some are all CPU intensive.
> Some are GPU intensive.
> Some will use multiple GPU's
> Some will not use multiple GPU's, so we had to get one beasty GPU (RTX 8000
> 48Gb).
>
> And of course HD and RAM are important.
>
> And as state, read/write is a rate limiter on transfer. SSD good. We have
> 10 Gb fiber cards, but never get that speed ...
>
> I now have three different light-sheet analysis PC's, depending on the size
> of the dataset and software.
>
> On Wed, Jan 15, 2020 at 3:32 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
> > > >
> > >
> >
>
>
> --
> Best,
>
> Gary Laevsky, Ph.D.
> Director, Confocal Imaging Facility
> Nikon Center of Excellence
> Co-Founder, North Atlantic Microscopy Society (NAMS)
>
https://namsmicroscopy.com/> Dept. of Molecular Biology
> Washington Rd.
> Princeton University
> Princeton, New Jersey, 08544-1014
> (O) 609 258 5432
> (C) 508 507 1310
>
> North Atlantic Microscopy Society Spring Meeting at UPENN, April 23, 2020.
>