http://confocal-microscopy-list.275.s1.nabble.com/Ratiometric-FRET-on-Fluoview-tp7579865p7579928.html
host computer. This lets us get away with smaller and cheaper SSD's (or
secure storage after the fact. I agree with George that you shouldn't
leave anything on them long term. That said, some high-end servers use
frequently. They get around the potential reliability issue by using RAID
arrays of SSD's. This is pricey, but very efficient for critical
> *****
> To join, leave or search the confocal microscopy listserv, go to:
>
http://lists.umn.edu/cgi-bin/**wa?A0=confocalmicroscopy<
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy>
> *****
>
> I second Craig's comment on SSD PCI-e card speed. I have several such
> cards in my core's PC's, also some of their SSD SATA drives. One problem
> with all SSD's is when they die, that's it" everything is lost. Back it up
> or expect to lose it. Don't count on achieving the specifications provided
> by OCZ (or any other vendor) - operating system driver performance may be
> limiting.
>
>
>
> On 3/10/2013 2:30 PM, Craig Brideau wrote:
>
>> *****
>> To join, leave or search the confocal microscopy listserv, go to:
>>
http://lists.umn.edu/cgi-bin/**wa?A0=confocalmicroscopy<
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy>
>> *****
>>
>> 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<
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<
>>
[hidden email]> wrote:
>>
>>
>>
>>> *****
>>> To join, leave or search the confocal microscopy listserv, go to:
>>>
http://lists.umn.edu/cgi-bin/**wa?A0=confocalmicroscopy<
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"<
[hidden email]>
>>>> 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<
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/ <
http://Www.cbi.pitt.edu/>>
>>>> 412-352-2277
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> On 3/9/13 3:39 AM, "Oliver Biehlmaier"<oliver.biehlmaier@**UNIBAS.CH<
[hidden email]>
>>>> >
>>>>
>>>>
>>> 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:
[hidden email]<**mailto:
>>>>>
>>>>>
>>>>
[hidden email]>
>>>
>>>
>>>>
http://www.biozentrum.unibas.**ch/imcf<
http://www.biozentrum.unibas.ch/imcf>
>>>>> ------------------------------**------------------------------**----
>>>>>
>>>>> _________________
>>>>> From: Arvydas Matiukas<
[hidden email]<**mailto:
>>>>>
>>>>>
>>>>
[hidden email]>>
>>>
>>>
>>>> To:=20
>>>>>
[hidden email].**EDU <
[hidden email]>
>>>>> <mailto:
>>>>>
>>>>>
>>>>
[hidden email].**EDU <
[hidden email]>>=
>>>
>>>
>>>> =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<
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)
>>>> ****************************************************************
>>>> **********
>>>>
>>>>
>>>
>>>
>>
>>
>