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As Oliver says, an SSD can help speed things along. You can get PCI-e
cards which are SSD's rather than relying on the SATA bus for data
transfer. They can be quite speedy depending on what you are doing:
http://www.ocztechnology.com/products/solid_state_drives/pci-e_solid_state_drives
I use one of these in our image acquisition computers tied to one of our
microscopes. It makes file writes for large image stacks go much faster
than a mechanical drive.
Craig
On Sun, Mar 10, 2013 at 12:28 AM, Oliver Biehlmaier <
[log in to unmask]> wrote:
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Yes, that is the correct order. At least for the software that we are
> using the CPU speed is the most important.
> The SSD for the OS and swapping (eg in Imaris) is also an important point
> for speed.
> Cheers,
> Oliver
>
> >
> >
> > ------------------------------
> >
> > Date: Sat, 9 Mar 2013 05:56:27 -0500
> > From: "Watkins, Simon C" <[log in to unmask]>
> > Subject: Re: Subject: Computer for image analysis
> >
> > *****
> > To join, leave or search the confocal microscopy listserv, go to:
> > http://lists.umn.edu/cgi-bin/wa?A0=3Dconfocalmicroscopy
> > *****
> >
> > So Oliver, what you are saying is that the ultimate bottleneck is the CPU
> > speed, followed by RAM, followed by CPU core count and finally graphics
> > card capabilities?
> >
> > Simon Watkins Ph.D
> >
> > Professor and Vice Chair Cell Biology
> > Professor Immunology
> > Director Center for Biologic Imaging
> > University of Pittsburgh
> > Bsts 225 3550 terrace st
> > Pittsburgh PA 15261
> > Www.cbi.pitt.edu <http://Www.cbi.pitt.edu/>
> > 412-352-2277
> >
> >
> >
> >
> >
> >
> > On 3/9/13 3:39 AM, "Oliver Biehlmaier" <[log in to unmask]>
> wrote:
> >
> >> Dear Arvydas,
> >> I equipped an entire image analysis room with new Image analysis
> machines
> >> about 1.5 years ago. During the evaluation, our main focus was on the
> >> system's performance using software such as Imaris, Volocity, Huygens,
> >> Fiji, etc.
> >> As already posted in other replies to your email it turns out that GPU
> is
> >> important, but bottlenecks are CPU, RAM, and the speed of the HDD.
> >> As our institute's IT asked us to go for a Dell-solution, we evaluated
> >> several possibilities from Dell. We ended up buying 2 Dell Precision
> with
> >> 3GB-GPU, XEON-processors and between 24 to 48GB of RAM, and many
> "pimped"
> >> Optiplex systems where we installed 3GB-GPU, the max. RAM (16GB), an SSD
> >> for the OS and swapping and a fast 500GB-HDD for saving the data.
> >> Price wise the Optiplex systems sum up to a third of the price of the
> >> precision.
> >> The main reason for the Optiplex was the i7 processor which is capable
> to
> >> do overclocking which is not possible on the XEON systems. We expected
> >> this to be a key advantage in comparison to our expensive Precision
> >> systems.
> >> Now, after 1,5 years of usage I can confirm that this fully worked out.
> >> As many programs (especially Imaris) are still mainly relying on only
> one
> >> but definitely not on all cores, the overclocking feature of the i7
> >> system usually keeps them at the same level or even outperforms the
> >> Precision systems. Only the 48GB-RAM system is a bit faster on the rare
> >> occasions when it can fully profit from the large RAM (large time lapse
> >> or stitching tasks). But even then the fast swapping onto the SDDs on
> the
> >> Optiplex keeps them almost at the same level of performance.
> >> Only recently we ran into some minor problems with our ATI graphics
> cards
> >> which could have been prevented by using NVIDIA cards, thus I would
> >> recommend the latter. There is definitely no need to go for Quadra
> cards,
> >> they are super expensive and receive less updates and patches than the
> >> gaming cards.
> >> I hope this helps you in your decision for your new systems.
> >> Best,
> >> Oliver
> >>
> >>
> >> ----------------------------------------------------------------
> >> Oliver Biehlmaier, PhD
> >> Head of Imaging Core Facility
> >> Biozentrum, University of Basel
> >> Klingelbergstrasse 50/70
> >> 4056 Basel
> >> Switzerland
> >>
> >> Tel: +41 (61) 267 20 73
> >> Email: [log in to unmask]<mailto:
> [log in to unmask]>
> >> http://www.biozentrum.unibas.ch/imcf
> >> ----------------------------------------------------------------
> >>
> >> _________________
> >> From: Arvydas Matiukas <[log in to unmask]<mailto:
> [log in to unmask]>>
> >> To:=20
> >> [log in to unmask]<mailto:
> [log in to unmask]>=
> > =3D
> >> 20
> >> Sent: Friday, March 8, 2013 12:24 PM
> >> Subject: Computer for image analysis
> >>
> >> *****
> >> To join, leave or search the confocal microscopy listserv, go to:
> >> http://lists.umn.edu/cgi-bin/wa?A0=3D3Dconfocalmicroscopy
> >> *****
> >>
> >> Dear listers/microscopists,
> >>
> >> I assume there is good time to update new trends in
> >> image analysis hardware. The last discussions on image
> >> analysis computer were in 2006-8. Though the basic
> >> principles of CPU, RAM, hard drive, video card, monitor
> >> selection still hold some new types of hardware became
> >> popular/available, e.g. SSD drives, APU, water cooling.
> >> Now a decent gaming computer (~$1k) has the processing power
> >> of a 2006 expensive workstation (~$20K). I was suprised that
> >> I was able to completely overhaul my 8 year old ATX case
> >> to a quad core 2GHz APU, 8GB 1600MHz RAM, 160GB SATA-2
> >> SSD, water cooling, USB3 and SATA3 Gigabyte motherboard,
> >> and 4 monitor 1GB video card.
> >> for under $300 (online, after rebates).
> >>
> >> Now I am wiling to upgrade/overhaul my work computer which
> >> is used to run ImageJ, Fiji, Deconvolution (Autoquant, Huygens),
> >> Matlab, PV-Vawe, Labview, Origin. Please advice/share you thoughts
> >> what best configuration is possible to buy for $2-3k (monitor
> >> excluded).
> >> My first choice would be to go with a fast gaming computer, e.g.
> >> Dell-Alienware Aurora=3D20
> >> Windows* 7 Ultimate, 64Bit, English
> >> 2nd Generation Intel* Core* i7-3820 (10M Cache, Overclocked up to 4.1
> >> GHz)
> >> 16GB (4 X 4GB) Quad Channel DDR3 at 1600MHz
> >> NVIDIA* GeForce* GTX 660 1.5GB GDDR5
> >> 1TB RAID 0 (2x 500GB SATA 6Gb/s) Solid State Hybrid
> >> 19-in-1 Media Card Reader
> >> No Monitor
> >> Integrated 7.1 Channel Audio
> >>
> >> The second choice would be to buy all components online and
> >> build a computer myself (I have done this about 50 times over
> >> 25 years). This option typically saves money or buys better
> >> components,
> >> and provides you full specs of the hardware. The con of this
> >> approach is that it wastes some of your time to debug/make all
> >> the hardware work together and with your software. However,
> >> as the computer is for me not just a box but a tool I am ready
> >> to make this sacrifice.
> >>
> >> BTW, is there any solid preference towards CPU Type (Intel ix/AMD/Intel
> >> Xeon)
> >>
> >> Thanks for your input/advice/thoughts,
> >> Arvydas
> >> --------------------
> >>
> >
> > ------------------------------
> >
> > End of CONFOCALMICROSCOPY Digest - 8 Mar 2013 to 9 Mar 2013 (#2013-58)
> > **********************************************************************
>
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