PC requirements

[Owens, Peter]

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Dear listers,

I am looking into purchasing a high end image processing PC , that will be capable of processing large multidimensional data sets up to 1 TB in size.
Does anyone have any recommendations on a PC configuration that would be suitable?
Do people build custom PCs or buy off the shelf?
Are high spec gaming PCs up to this task?

thanks for any advice on this .

all the best

Peter


Peter Owens
Centre for Microscopy and Imaging,
National University of Ireland Galway.
P: [phone] m: [phone]
W: www.imaging.nuigalway.ie e: [hidden email]


 



-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Oliver Biehlmaier
Sent: 15 January 2018 10:17
To: [hidden email]
Subject: Re: Cleaning of CSU W1 spinning disk scan head

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Dear all, dear Pascal,

This is indeed very annoying!
As some of you might remember from the conversation that Kai started last year asking about the experiences with current spinning disk systems, the reports on dust problems on the W1 were by far the most frequent.
I wonder how the manufacturer can get away with such a problem without being obliged to replace or at least fix those dust collecting systems?!

Pascal, I thought that your system already was “fixed” with the magic tape solution…. So apparently this did not help. Is that correct?

Did anyone of you guys purchase a new W1 within the past 6 months? According to the manufacturer and the local distributers the dust problem should be fixed on those recently sold W1 systems. Can anyone confirm this?

Concerning the problem described I would really try to ask the distributer to solve this, in particular if the system is still under warranty.
I have no idea how to clean the disk but the system should clearly only be opened and cleaned in a clean room. Otherwise Gabor’s solutions should at least reduce the dust problem.

Best regards,
Oliver



Oliver Biehlmaier, PhD | Head of Imaging Core Facility  | Biozentrum, University of Basel | Klingelbergstrasse 50/70 | CH-4056 Basel
Phone: [phone] | Email: [hidden email]<mailto:[hidden email]> | www.biozentrum.unibas.ch/imcf<http://www.biozentrum.unibas.ch/imcf> | www.microscopynetwork.unibas.ch<http://www.microscopynetwork.unibas.ch>








On 15 Jan 2018, at 09:51, Csúcs Gábor <[hidden email]<mailto:[hidden email]>> wrote:

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Dear All,

Though I fully agree with Ferhan that it would be good if either the manufacturer or the distributor would offer a solution to this dust problem, perhaps I can  make two suggestions that will certainly not eliminate the problem but perhaps make it less frequent (less frequent cleaning required). The first one is reduction of the dust in the room (very obvious). This can be potentially achieved by installing filters in the air-conditioning unit (if possible) and to apply some other "tricks" used in clean environments (sticky floor tapes etc.). The other suggestion: I believe (of course I have no scientific proof for this) that box-type incubators (enclosures) also may help. But again this does not solve the issue....

Greetings Gabor


-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Ferhan A
Sent: Saturday, January 13, 2018 9:58 AM
To: [hidden email]
Subject: Re: Cleaning of CSU W1 spinning disk scan head

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Dear Pascal,

We have exactly the same headache with our dust gathering CSU W1 spinning disk unit which started to produce images resembling the ones in the cover pages of dendrochronology journals. As discussed earlier in this forum, this seems to be a design flaw of W1 system. We will be very happy if the original manufacturer comes up with a no-cost-to-customer fix to this problem and offers free dust cleanup and reimburses us for the aspirins.
Best regards,
Ferhan
-------
Ferhan Ayaydin, Ph.D.
Cellular Imaging Laboratory
Biological Research Center
Hungarian Academy of Sciences
Temesvari krt. 62
6726 Szeged
Hungary


On Jan 12, 2018 16:23, "Pascal Lorentz" <[hidden email]> wrote:

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Dear list

We have a CSU W1 spinning disk scan head and most likely a dust particle on the disk that creates a well defined line in the image.
Please find an image here: https://imgur.com/a/e3NKg Did somebody ever clean the disks successfully? I heard that it is very tricky to do on site in a non dust free environment.
How would I need to proceed if I would like to clean it myself? How can I access the disks and are there any tips and tricks on how to prevent even more dust flying onto the disks. So far I just accessed the emission filter wheels and the dichroic mirrors but did not dare to access the disks. Any manuals would be helpful.

Thanks a lot for your help and best regards

Pascal

[Mel Symeonides]

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Hi Peter,

If you have ever built your own PC, or know someone who has, you can
benefit greatly from building it custom. Off-the-shelf systems can be
upmarked considerably and often use outdated components or skimp on
important things like a good power supply. Of course, the benefit of
that would be presumably a warranty on the whole system, in case you are
not able to diagnose things yourself, but if you build a custom system,
each component will come with its own warranty. It would just be up to
you to determine which component is faulty and claim the warranty on it
yourself.

I recently built such a computer for light sheet data acquisition and
processing/analysis. Here is the configuration:

Motherboard: Asus Z10PE-D16 WS
CPU: Intel Xeon E5-2650 V4 (x2)
CPU cooler: Noctua NH-U12DXi4 (x2)
Memory: Samsung M393A2G40EB1-CRC 16GB DDR4 2400MHz ECC-Reg (x8 = 128 GB
total)
OS drive: Samsung 960 EVO 500GB M.2-2280 SSD (on a PCIE M.2 adapter
because the motherboard runs its onboard M.2 at SATA speed)
Data drive: Samsung 850 EVO 1TB SATA (6 drives in RAID10 configuration)
Video card: GeForce GTX 1080 Ti 11GB
Case: Phanteks Enthoo Primo
Power supply: EVGA SuperNOVA P2 1200W 80+ Platinum

You will obviously also need monitors, keyboard, mouse, Windows license,
and some kind of data server - you should assume that you will not be
storing your data on this computer if you are generating 1TB datasets. I
got a Synology DS1817+ 8-bay NAS with a 10GbE adapter and loaded it with
8 Western Digital Gold 10TB drives (WD101KRYZ), and run them in SHR2
(basically RAID6, for double-parity, i.e. you can lose two drives and
still be able to recover). I also got a 10GbE adapter for the
workstation PC, this allows utilization of the maximum transfer rates
the RAID array is capable of, which is 3-4 times faster than standard
Gigabit Ethernet. This data server is costly but, for light sheet data,
basically necessary if your institute does not provide substantial data
storage.

Another thing to note is that component prices can fluctuate quite a
bit. I bought the video card in the summer for under $740. Right now
they are out of stock everywhere (1080 Ti of any brand), and when they
are in stock, they go for anywhere up to $2,000 (you have bitcoin mining
to thank for that). You can get a Titan Xp for less than that now so the
price/perfomance advantage of the 1080 Ti is no longer there, but look
for the Titans to also disappear off the market really quickly as mining
expands higher up the range.

All told, I spent around $9,000 for the workstation and $4,500 for the
data server. Comparable off-the-shelf workstations cost around $12,000 -
$15,000 (and possibly even more now with the GPU market up in the air
and RAM prices currently rising), and off-the-shelf data servers of
similar capacity would cost much more than that.

Assembly and setup of the PC was not trivial, so you will want someone
with experience to help you. Workstation (Xeon) motherboards can be very
finicky, and the installation manuals for some components can be pretty
incomprehensible. Also be aware that if you need multiple PCIE slots
available for data acquisition cards etc., the GPU only takes one but
actually occludes at least one more slot (my card took up three slots
total) so your choice of case/card should be made carefully. I ended up
cutting a hole in the back panel of the case and mounting the GPU
vertically with a 2-slot PCI bracket and PCIE riser cable, as I needed
every last PCIE slot on the motherboard. Some cases come with vertical
GPU mounting positions, but some of those will block the regular PCIE
slots, or will be incompatible with SSI-EEB format motherboards (which
is what most dual CPU boards will be).

Good luck!


Mel


On 1/15/2018 7:22 AM, Owens, Peter 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 listers,
>
> I am looking into purchasing a high end image processing PC , that will be capable of processing large multidimensional data sets up to 1 TB in size.
> Does anyone have any recommendations on a PC configuration that would be suitable?
> Do people build custom PCs or buy off the shelf?
> Are high spec gaming PCs up to this task?
>
> thanks for any advice on this .
>
> all the best
>
> Peter
>
>
> Peter Owens
> Centre for Microscopy and Imaging,
> National University of Ireland Galway.
> P: [phone] m: [phone]
> W: www.imaging.nuigalway.ie e: [hidden email]
>
>
>  
>
>

--
Menelaos Symeonides
Post-Doctoral Associate, Thali Lab
Department of Microbiology and Molecular Genetics
University of Vermont
318 Stafford Hall
95 Carrigan Dr
Burlington, VT 05405
[hidden email]
Phone: [phone]

[Craig Brideau]

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*****

Comment on the M.2 drives: They are significantly faster than SATA SSDs,
but for full speed the motherboard must support NVMe which is a dedicated
protocol for M.2 drives featuring a dedicated slot on the motherboard.
Annoyingly, most dual-CPU-socket 8-DIMM slot motherboards don't feature
this, so it is not an available option if you also want >64GB of RAM. If
anyone happens to come across an NVMe board that also has 8-DIMM slots
please let me know!
I use an M.2 NVMe for a system at home and it boots absurdly fast with only
an older i5 core.

Craig

On Mon, Jan 15, 2018 at 8:06 AM, Menelaos Symeonides <[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 Peter,
>
> If you have ever built your own PC, or know someone who has, you can
> benefit greatly from building it custom. Off-the-shelf systems can be
> upmarked considerably and often use outdated components or skimp on
> important things like a good power supply. Of course, the benefit of that
> would be presumably a warranty on the whole system, in case you are not
> able to diagnose things yourself, but if you build a custom system, each
> component will come with its own warranty. It would just be up to you to
> determine which component is faulty and claim the warranty on it yourself.
>
> I recently built such a computer for light sheet data acquisition and
> processing/analysis. Here is the configuration:
>
> Motherboard: Asus Z10PE-D16 WS
> CPU: Intel Xeon E5-2650 V4 (x2)
> CPU cooler: Noctua NH-U12DXi4 (x2)
> Memory: Samsung M393A2G40EB1-CRC 16GB DDR4 2400MHz ECC-Reg (x8 = 128 GB
> total)
> OS drive: Samsung 960 EVO 500GB M.2-2280 SSD (on a PCIE M.2 adapter
> because the motherboard runs its onboard M.2 at SATA speed)
> Data drive: Samsung 850 EVO 1TB SATA (6 drives in RAID10 configuration)
> Video card: GeForce GTX 1080 Ti 11GB
> Case: Phanteks Enthoo Primo
> Power supply: EVGA SuperNOVA P2 1200W 80+ Platinum
>
> You will obviously also need monitors, keyboard, mouse, Windows license,
> and some kind of data server - you should assume that you will not be
> storing your data on this computer if you are generating 1TB datasets. I
> got a Synology DS1817+ 8-bay NAS with a 10GbE adapter and loaded it with 8
> Western Digital Gold 10TB drives (WD101KRYZ), and run them in SHR2
> (basically RAID6, for double-parity, i.e. you can lose two drives and still
> be able to recover). I also got a 10GbE adapter for the workstation PC,
> this allows utilization of the maximum transfer rates the RAID array is
> capable of, which is 3-4 times faster than standard Gigabit Ethernet. This
> data server is costly but, for light sheet data, basically necessary if
> your institute does not provide substantial data storage.
>
> Another thing to note is that component prices can fluctuate quite a bit.
> I bought the video card in the summer for under $740. Right now they are
> out of stock everywhere (1080 Ti of any brand), and when they are in stock,
> they go for anywhere up to $2,000 (you have bitcoin mining to thank for
> that). You can get a Titan Xp for less than that now so the
> price/perfomance advantage of the 1080 Ti is no longer there, but look for
> the Titans to also disappear off the market really quickly as mining
> expands higher up the range.
>
> All told, I spent around $9,000 for the workstation and $4,500 for the
> data server. Comparable off-the-shelf workstations cost around $12,000 -
> $15,000 (and possibly even more now with the GPU market up in the air and
> RAM prices currently rising), and off-the-shelf data servers of similar
> capacity would cost much more than that.
>
> Assembly and setup of the PC was not trivial, so you will want someone
> with experience to help you. Workstation (Xeon) motherboards can be very
> finicky, and the installation manuals for some components can be pretty
> incomprehensible. Also be aware that if you need multiple PCIE slots
> available for data acquisition cards etc., the GPU only takes one but
> actually occludes at least one more slot (my card took up three slots
> total) so your choice of case/card should be made carefully. I ended up
> cutting a hole in the back panel of the case and mounting the GPU
> vertically with a 2-slot PCI bracket and PCIE riser cable, as I needed
> every last PCIE slot on the motherboard. Some cases come with vertical GPU
> mounting positions, but some of those will block the regular PCIE slots, or
> will be incompatible with SSI-EEB format motherboards (which is what most
> dual CPU boards will be).
>
> Good luck!
>
>
> Mel
>
>
> On 1/15/2018 7:22 AM, Owens, Peter 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 listers,
>>
>> I am looking into purchasing a high end image processing PC , that will
>> be capable of processing large multidimensional data sets up to 1 TB in
>> size.
>> Does anyone have any recommendations on a PC configuration that would be
>> suitable?
>> Do people build custom PCs or buy off the shelf?
>> Are high spec gaming PCs up to this task?
>>
>> thanks for any advice on this .
>>
>> all the best
>>
>> Peter
>>
>>
>> Peter Owens
>> Centre for Microscopy and Imaging,
>> National University of Ireland Galway.
>> P: [phone] m: [phone]
>> W: www.imaging.nuigalway.ie e: [hidden email]
>>
>>
>>
>>
>> --
> Menelaos Symeonides
> Post-Doctoral Associate, Thali Lab
> Department of Microbiology and Molecular Genetics
> University of Vermont
> 318 Stafford Hall
> 95 Carrigan Dr
> Burlington, VT 05405
> [hidden email]
> Phone: [phone]
>

[Avi Jacob]

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*****

 I just wanted to mention, that not every program knows how to use the GPU
- many modern programs can (e.g. the Huygens version on my Hyvolution
machine (note that it's a separate license for the capability to use CUDA),
ImageJ usually can't - but there are plugins designed for GPUs.)

I  also advocate for self-building high-end stuff.
Avi



On Mon, Jan 15, 2018 at 5:06 PM, Menelaos Symeonides <[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 Peter,
>
> If you have ever built your own PC, or know someone who has, you can
> benefit greatly from building it custom. Off-the-shelf systems can be
> upmarked considerably and often use outdated components or skimp on
> important things like a good power supply. Of course, the benefit of that
> would be presumably a warranty on the whole system, in case you are not
> able to diagnose things yourself, but if you build a custom system, each
> component will come with its own warranty. It would just be up to you to
> determine which component is faulty and claim the warranty on it yourself.
>
> I recently built such a computer for light sheet data acquisition and
> processing/analysis. Here is the configuration:
>

[Satoru Uzawa]

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*****

Dear Craig,

  There are few motherboards which can fill your need.  For example, Tyan S7070 A2NR-M2 has an M.2 slot and 16 DIMM slots with maximum 512GB total RAM.

http://www.tyan.com/Motherboards_S7070_S7070A2NR-M2 <http://www.tyan.com/Motherboards_S7070_S7070A2NR-M2>

   Also, many motherboards for AMD Threadripper has 8 DIMM slots and M.2 socket even though they are single CPU system.  As an example, check

https://www.asus.com/us/Motherboards/ROG-ZENITH-EXTREME/ <https://www.asus.com/us/Motherboards/ROG-ZENITH-EXTREME/>

   The maximum RAM capacity is limited to 128GB but the board can take ECC RAM, which is a must feature (at least for me).  AMD Threadripper offers nice CPU core count with decent floating point performance at a lower price.

Best,

Satoru

> On Jan 15, 2018, at 9:02 AM, Craig Brideau <[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.
> *****
>
> Comment on the M.2 drives: They are significantly faster than SATA SSDs,
> but for full speed the motherboard must support NVMe which is a dedicated
> protocol for M.2 drives featuring a dedicated slot on the motherboard.
> Annoyingly, most dual-CPU-socket 8-DIMM slot motherboards don't feature
> this, so it is not an available option if you also want >64GB of RAM. If
> anyone happens to come across an NVMe board that also has 8-DIMM slots
> please let me know!
> I use an M.2 NVMe for a system at home and it boots absurdly fast with only
> an older i5 core.
>
> Craig
>
> On Mon, Jan 15, 2018 at 8:06 AM, Menelaos Symeonides <[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 Peter,
>>
>> If you have ever built your own PC, or know someone who has, you can
>> benefit greatly from building it custom. Off-the-shelf systems can be
>> upmarked considerably and often use outdated components or skimp on
>> important things like a good power supply. Of course, the benefit of that
>> would be presumably a warranty on the whole system, in case you are not
>> able to diagnose things yourself, but if you build a custom system, each
>> component will come with its own warranty. It would just be up to you to
>> determine which component is faulty and claim the warranty on it yourself.
>>
>> I recently built such a computer for light sheet data acquisition and
>> processing/analysis. Here is the configuration:
>>
>> Motherboard: Asus Z10PE-D16 WS
>> CPU: Intel Xeon E5-2650 V4 (x2)
>> CPU cooler: Noctua NH-U12DXi4 (x2)
>> Memory: Samsung M393A2G40EB1-CRC 16GB DDR4 2400MHz ECC-Reg (x8 = 128 GB
>> total)
>> OS drive: Samsung 960 EVO 500GB M.2-2280 SSD (on a PCIE M.2 adapter
>> because the motherboard runs its onboard M.2 at SATA speed)
>> Data drive: Samsung 850 EVO 1TB SATA (6 drives in RAID10 configuration)
>> Video card: GeForce GTX 1080 Ti 11GB
>> Case: Phanteks Enthoo Primo
>> Power supply: EVGA SuperNOVA P2 1200W 80+ Platinum
>>
>> You will obviously also need monitors, keyboard, mouse, Windows license,
>> and some kind of data server - you should assume that you will not be
>> storing your data on this computer if you are generating 1TB datasets. I
>> got a Synology DS1817+ 8-bay NAS with a 10GbE adapter and loaded it with 8
>> Western Digital Gold 10TB drives (WD101KRYZ), and run them in SHR2
>> (basically RAID6, for double-parity, i.e. you can lose two drives and still
>> be able to recover). I also got a 10GbE adapter for the workstation PC,
>> this allows utilization of the maximum transfer rates the RAID array is
>> capable of, which is 3-4 times faster than standard Gigabit Ethernet. This
>> data server is costly but, for light sheet data, basically necessary if
>> your institute does not provide substantial data storage.
>>
>> Another thing to note is that component prices can fluctuate quite a bit.
>> I bought the video card in the summer for under $740. Right now they are
>> out of stock everywhere (1080 Ti of any brand), and when they are in stock,
>> they go for anywhere up to $2,000 (you have bitcoin mining to thank for
>> that). You can get a Titan Xp for less than that now so the
>> price/perfomance advantage of the 1080 Ti is no longer there, but look for
>> the Titans to also disappear off the market really quickly as mining
>> expands higher up the range.
>>
>> All told, I spent around $9,000 for the workstation and $4,500 for the
>> data server. Comparable off-the-shelf workstations cost around $12,000 -
>> $15,000 (and possibly even more now with the GPU market up in the air and
>> RAM prices currently rising), and off-the-shelf data servers of similar
>> capacity would cost much more than that.
>>
>> Assembly and setup of the PC was not trivial, so you will want someone
>> with experience to help you. Workstation (Xeon) motherboards can be very
>> finicky, and the installation manuals for some components can be pretty
>> incomprehensible. Also be aware that if you need multiple PCIE slots
>> available for data acquisition cards etc., the GPU only takes one but
>> actually occludes at least one more slot (my card took up three slots
>> total) so your choice of case/card should be made carefully. I ended up
>> cutting a hole in the back panel of the case and mounting the GPU
>> vertically with a 2-slot PCI bracket and PCIE riser cable, as I needed
>> every last PCIE slot on the motherboard. Some cases come with vertical GPU
>> mounting positions, but some of those will block the regular PCIE slots, or
>> will be incompatible with SSI-EEB format motherboards (which is what most
>> dual CPU boards will be).
>>
>> Good luck!
>>
>>
>> Mel
>>
>>
>> On 1/15/2018 7:22 AM, Owens, Peter 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 listers,
>>>
>>> I am looking into purchasing a high end image processing PC , that will
>>> be capable of processing large multidimensional data sets up to 1 TB in
>>> size.
>>> Does anyone have any recommendations on a PC configuration that would be
>>> suitable?
>>> Do people build custom PCs or buy off the shelf?
>>> Are high spec gaming PCs up to this task?
>>>
>>> thanks for any advice on this .
>>>
>>> all the best
>>>
>>> Peter
>>>
>>>
>>> Peter Owens
>>> Centre for Microscopy and Imaging,
>>> National University of Ireland Galway.
>>> P: [phone] m: [phone]
>>> W: www.imaging.nuigalway.ie e: [hidden email]
>>>
>>>
>>>
>>>
>>> --
>> Menelaos Symeonides
>> Post-Doctoral Associate, Thali Lab
>> Department of Microbiology and Molecular Genetics
>> University of Vermont
>> 318 Stafford Hall
>> 95 Carrigan Dr
>> Burlington, VT 05405
>> [hidden email]
>> Phone: [phone]
>>

[Johannes Helm]

*****
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*****

Dear Peter and dear list,

might it be an alternative to have a PC with large Graphics memory,
only, and use this PC then solely for display purposes? The image
analysis calculations could well be done on a large mainframe computer
(parallel, vector, or both), which usually is provided and taken care of
by specialized staff in a University's or Research Center's central IT
unit. Often, there will also be qualified staff to implement suitable
image analysis software. In addition, one would need a rapid data line
to transfer the original data to a suitable disk on the mainframe
computer, but all this is cheaper than a "super PC".

Besides being considerably cheaper than putting a lot of money into a
de-centralized unit, which still will be slower than a large main frame
computer, one can avoid having to take care about any expensive damage,
which sooner or later will materialize on the PC. Also, the IT unit will
take care of software, hardware and firmware updates on the main frame
computer.

The disadvantages might be a somewhat reduced flexibility and that
someone in the lab would have to learn at least some UNIX.

I had, during the late 80s and early 90s, been in a lab in Heidelberg,
FRG, where one of the old Sarastro Phoibos IV systems had been installed
and in use. It was one of the earliest CLSMs, and it was a very fine
one. The software was run on a Personal Iris by Silicon Graphics. Once
the scanned data volumes became larger and larger, we asked for and got
access to the source codes for the 3D reconstruction software, and a
master student vectorized the source code, which then was installed and
run on a Convex C210, then one of the fastest mainframe computer systems
available. When initial problems with process swapping had been
resolved, the speed of data processing increased roughly "by and order
of magnitude", i.e. processing large data sets consumed about 1/10 of
the time, which had been required before on the small frame Personal
Iris.

Best wishes,

Johannes



On 2018-01-15 13:22, Owens, Peter 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 listers,
>
> I am looking into purchasing a high end image processing PC , that
> will be capable of processing large multidimensional data sets up to 1
> TB in size.
> Does anyone have any recommendations on a PC configuration that would
> be suitable?
> Do people build custom PCs or buy off the shelf?
> Are high spec gaming PCs up to this task?
>
> thanks for any advice on this .
>
> all the best
>
> Peter
>
>
> Peter Owens
> Centre for Microscopy and Imaging,
> National University of Ireland Galway.
> P: [phone] m: [phone]
> W: www.imaging.nuigalway.ie e: [hidden email]
>
>
>

--
P. Johannes Helm, M.Sc. PhD
Seniorengineer
University of Oslo
Institute of Basic Medical Sciences
Department of Molecular Medicine
Division of Physiology
P. O. Box 1103 - Blindern
NO-0317 Oslo
Norway

Voice: [phone]
Fax: [phone]

WWW: folk.uio.no/jhelm

[Michael Giacomelli]

*****
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 Craig,

You can buy M.2. NVME to PCIe adapters for a few dollars on Amazon.
They're pure passive (they just route the PCIe pins to the M.2. connector)
and work well for adding M.2. to motherboards that don't support it.  You
lose an x4 PCIe slot, but usually there is at least one extra on a full
size motherboard.

Otherwise we usually just use Intel's single socket HEDT platform
(currently X299-based) which supports up to 18 cores and 8 DIMMs (128GB of
RAM).  These typically come with 2x M.2. slots for NVME storage.  Dual
socket would allow more than 20 cores, but the value is lower due to the
cost of the Xeon platform.

Mike

On Mon, Jan 15, 2018 at 12:02 PM, Craig Brideau <[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.
> *****
>
> Comment on the M.2 drives: They are significantly faster than SATA SSDs,
> but for full speed the motherboard must support NVMe which is a dedicated
> protocol for M.2 drives featuring a dedicated slot on the motherboard.
> Annoyingly, most dual-CPU-socket 8-DIMM slot motherboards don't feature
> this, so it is not an available option if you also want >64GB of RAM. If
> anyone happens to come across an NVMe board that also has 8-DIMM slots
> please let me know!
> I use an M.2 NVMe for a system at home and it boots absurdly fast with only
> an older i5 core.
>
> Craig
>
> On Mon, Jan 15, 2018 at 8:06 AM, Menelaos Symeonides <[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 Peter,
> >
> > If you have ever built your own PC, or know someone who has, you can
> > benefit greatly from building it custom. Off-the-shelf systems can be
> > upmarked considerably and often use outdated components or skimp on
> > important things like a good power supply. Of course, the benefit of that
> > would be presumably a warranty on the whole system, in case you are not
> > able to diagnose things yourself, but if you build a custom system, each
> > component will come with its own warranty. It would just be up to you to
> > determine which component is faulty and claim the warranty on it
> yourself.
> >
> > I recently built such a computer for light sheet data acquisition and
> > processing/analysis. Here is the configuration:
> >
> > Motherboard: Asus Z10PE-D16 WS
> > CPU: Intel Xeon E5-2650 V4 (x2)
> > CPU cooler: Noctua NH-U12DXi4 (x2)
> > Memory: Samsung M393A2G40EB1-CRC 16GB DDR4 2400MHz ECC-Reg (x8 = 128 GB
> > total)
> > OS drive: Samsung 960 EVO 500GB M.2-2280 SSD (on a PCIE M.2 adapter
> > because the motherboard runs its onboard M.2 at SATA speed)
> > Data drive: Samsung 850 EVO 1TB SATA (6 drives in RAID10 configuration)
> > Video card: GeForce GTX 1080 Ti 11GB
> > Case: Phanteks Enthoo Primo
> > Power supply: EVGA SuperNOVA P2 1200W 80+ Platinum
> >
> > You will obviously also need monitors, keyboard, mouse, Windows license,
> > and some kind of data server - you should assume that you will not be
> > storing your data on this computer if you are generating 1TB datasets. I
> > got a Synology DS1817+ 8-bay NAS with a 10GbE adapter and loaded it with
> 8
> > Western Digital Gold 10TB drives (WD101KRYZ), and run them in SHR2
> > (basically RAID6, for double-parity, i.e. you can lose two drives and
> still
> > be able to recover). I also got a 10GbE adapter for the workstation PC,
> > this allows utilization of the maximum transfer rates the RAID array is
> > capable of, which is 3-4 times faster than standard Gigabit Ethernet.
> This
> > data server is costly but, for light sheet data, basically necessary if
> > your institute does not provide substantial data storage.
> >
> > Another thing to note is that component prices can fluctuate quite a bit.
> > I bought the video card in the summer for under $740. Right now they are
> > out of stock everywhere (1080 Ti of any brand), and when they are in
> stock,
> > they go for anywhere up to $2,000 (you have bitcoin mining to thank for
> > that). You can get a Titan Xp for less than that now so the
> > price/perfomance advantage of the 1080 Ti is no longer there, but look
> for
> > the Titans to also disappear off the market really quickly as mining
> > expands higher up the range.
> >
> > All told, I spent around $9,000 for the workstation and $4,500 for the
> > data server. Comparable off-the-shelf workstations cost around $12,000 -
> > $15,000 (and possibly even more now with the GPU market up in the air and
> > RAM prices currently rising), and off-the-shelf data servers of similar
> > capacity would cost much more than that.
> >
> > Assembly and setup of the PC was not trivial, so you will want someone
> > with experience to help you. Workstation (Xeon) motherboards can be very
> > finicky, and the installation manuals for some components can be pretty
> > incomprehensible. Also be aware that if you need multiple PCIE slots
> > available for data acquisition cards etc., the GPU only takes one but
> > actually occludes at least one more slot (my card took up three slots
> > total) so your choice of case/card should be made carefully. I ended up
> > cutting a hole in the back panel of the case and mounting the GPU
> > vertically with a 2-slot PCI bracket and PCIE riser cable, as I needed
> > every last PCIE slot on the motherboard. Some cases come with vertical
> GPU
> > mounting positions, but some of those will block the regular PCIE slots,
> or
> > will be incompatible with SSI-EEB format motherboards (which is what most
> > dual CPU boards will be).
> >
> > Good luck!
> >
> >
> > Mel
> >
> >
> > On 1/15/2018 7:22 AM, Owens, Peter 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 listers,
> >>
> >> I am looking into purchasing a high end image processing PC , that will
> >> be capable of processing large multidimensional data sets up to 1 TB in
> >> size.
> >> Does anyone have any recommendations on a PC configuration that would be
> >> suitable?
> >> Do people build custom PCs or buy off the shelf?
> >> Are high spec gaming PCs up to this task?
> >>
> >> thanks for any advice on this .
> >>
> >> all the best
> >>
> >> Peter
> >>
> >>
> >> Peter Owens
> >> Centre for Microscopy and Imaging,
> >> National University of Ireland Galway.
> >> P: [phone] m: [phone]
> >> W: www.imaging.nuigalway.ie e: [hidden email]
> >>
> >>
> >>
> >>
> >> --
> > Menelaos Symeonides
> > Post-Doctoral Associate, Thali Lab
> > Department of Microbiology and Molecular Genetics
> > University of Vermont
> > 318 Stafford Hall
> > 95 Carrigan Dr
> > Burlington, VT 05405
> > [hidden email]
> > Phone: [phone]
> >
>

[Mel Symeonides]

*****
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 Johannes,

Thanks for your input, I appreciate it and have some comments. While
mainframe computers/clusters are in principle much faster than any
reasonable custom built PC, as per your experience at Heidelberg it can
be a challenge to actually run your analysis pipeline on it and you will
need someone on staff who can code to get it done. If you don't have
that knowledge in your immediate group, and if you are at a smaller
institute where such support is unavailable or stretched very thin and
always busy, the custom PC could get the job done in very reasonable
time (It took me about 3.5 hours to deskew a light sheet stage scan
dataset of 500 planes x 2000 timepoints x 2 colors at 512x512
resolution) with readily available and optimized programs like ImageJ or
commercial turnkey packages.

I don't think $9,000 is a prohibitive cost for a computer when the
instrument that generates the data can cost 20x - 100x more than that.
The Hamamatsu sCMOS camera we bought cost more than the workstation and
data server combined. Besides all that, as you mentioned data transfer
speed can be a big issue, and I don't think it's cheap at all. I'm sure
many institutes do not have the network infrastructure to support
transferring 1 TB datasets within any reasonable timeframe (you are
lucky if you have Cat5 wiring if you are in an older building), so
farming out processing of such datasets to a mainframe may end up
actually being much slower than doing it locally if you include the data
transfer time, that is IF they even give you enough server disk space
for a whole dataset. Rewiring a building for faster networking can be a
very costly project for a university, i.e. one that will likely never be
done (the typical answer is: "What's the problem? We installed 802.11n
WiFi for you.")

Lastly, a powerful computer like that can be useful not just for
processing raw data (which a mainframe could in theory do faster) but
also to prepare data for presentation, e.g. composing flythrough 3D
movies, annotation etc., which cannot be farmed out. Such functions
require a powerful workstation PC and the fastest possible access to
your dataset (i.e. local).

Best,
Mel


On 1/15/2018 12:23 PM, P. Johannes Helm 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 Peter and dear list,
>
> might it be an alternative to have a PC with large Graphics memory,
> only, and use this PC then solely for display purposes? The image
> analysis calculations could well be done on a large mainframe computer
> (parallel, vector, or both), which usually is provided and taken care
> of by specialized staff in a University's or Research Center's central
> IT unit. Often, there will also be qualified staff to implement
> suitable image analysis software. In addition, one would need a rapid
> data line to transfer the original data to a suitable disk on the
> mainframe computer, but all this is cheaper than a "super PC".
>
> Besides being considerably cheaper than putting a lot of money into a
> de-centralized unit, which still will be slower than a large main
> frame computer, one can avoid having to take care about any expensive
> damage, which sooner or later will materialize on the PC. Also, the IT
> unit will take care of software, hardware and firmware updates on the
> main frame computer.
>
> The disadvantages might be a somewhat reduced flexibility and that
> someone in the lab would have to learn at least some UNIX.
>
> I had, during the late 80s and early 90s, been in a lab in Heidelberg,
> FRG, where one of the old Sarastro Phoibos IV systems had been
> installed and in use. It was one of the earliest CLSMs, and it was a
> very fine one. The software was run on a Personal Iris by Silicon
> Graphics. Once the scanned data volumes became larger and larger, we
> asked for and got access to the source codes for the 3D reconstruction
> software, and a master student vectorized the source code, which then
> was installed and run on a Convex C210, then one of the fastest
> mainframe computer systems available. When initial problems with
> process swapping had been resolved, the speed of data processing
> increased roughly "by and order of magnitude", i.e. processing large
> data sets consumed about 1/10 of the time, which had been required
> before on the small frame Personal Iris.
>
> Best wishes,
>
> Johannes
>
>
>
> On 2018-01-15 13:22, Owens, Peter 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 listers,
>>
>> I am looking into purchasing a high end image processing PC , that
>> will be capable of processing large multidimensional data sets up to 1
>> TB in size.
>> Does anyone have any recommendations on a PC configuration that would
>> be suitable?
>> Do people build custom PCs or buy off the shelf?
>> Are high spec gaming PCs up to this task?
>>
>> thanks for any advice on this .
>>
>> all the best
>>
>> Peter
>>
>>
>> Peter Owens
>> Centre for Microscopy and Imaging,
>> National University of Ireland Galway.
>> P: [phone] m: [phone]
>> W: www.imaging.nuigalway.ie e: [hidden email]
>>
>>
>>
>

[Craig Brideau]

*****
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.
*****

Should have clarified: PCIe is only part of the attachment process. The
motherboard must also support the NVMe standard via PCIe to achieve maximum
performance. Most motherboards that support the latest NVMe protocol have a
dedicated M.2 slot (or two) specifically for mounting M.2 NVMe compatible
drives. (Some also are backwards compatible with SATA, this is slot
dependent!) You *can* attach such drives via PCIe adapter cards but this
depends on if the motherboard supports NVMe through the standard PCIe
slots. The drives will still work in a PCIe slot, but you really only get
the full potential out of them with the NVMe protocol implemented on the
motherboard.

Craig

On Mon, Jan 15, 2018 at 11:04 AM, Michael Giacomelli <[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 Craig,
>
> You can buy M.2. NVME to PCIe adapters for a few dollars on Amazon.
> They're pure passive (they just route the PCIe pins to the M.2. connector)
> and work well for adding M.2. to motherboards that don't support it.  You
> lose an x4 PCIe slot, but usually there is at least one extra on a full
> size motherboard.
>
> Otherwise we usually just use Intel's single socket HEDT platform
> (currently X299-based) which supports up to 18 cores and 8 DIMMs (128GB of
> RAM).  These typically come with 2x M.2. slots for NVME storage.  Dual
> socket would allow more than 20 cores, but the value is lower due to the
> cost of the Xeon platform.
>
> Mike
>
> On Mon, Jan 15, 2018 at 12:02 PM, Craig Brideau <[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.
> > *****
> >
> > Comment on the M.2 drives: They are significantly faster than SATA SSDs,
> > but for full speed the motherboard must support NVMe which is a dedicated
> > protocol for M.2 drives featuring a dedicated slot on the motherboard.
> > Annoyingly, most dual-CPU-socket 8-DIMM slot motherboards don't feature
> > this, so it is not an available option if you also want >64GB of RAM. If
> > anyone happens to come across an NVMe board that also has 8-DIMM slots
> > please let me know!
> > I use an M.2 NVMe for a system at home and it boots absurdly fast with
> only
> > an older i5 core.
> >
> > Craig
> >
> > On Mon, Jan 15, 2018 at 8:06 AM, Menelaos Symeonides <[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 Peter,
> > >
> > > If you have ever built your own PC, or know someone who has, you can
> > > benefit greatly from building it custom. Off-the-shelf systems can be
> > > upmarked considerably and often use outdated components or skimp on
> > > important things like a good power supply. Of course, the benefit of
> that
> > > would be presumably a warranty on the whole system, in case you are not
> > > able to diagnose things yourself, but if you build a custom system,
> each
> > > component will come with its own warranty. It would just be up to you
> to
> > > determine which component is faulty and claim the warranty on it
> > yourself.
> > >
> > > I recently built such a computer for light sheet data acquisition and
> > > processing/analysis. Here is the configuration:
> > >
> > > Motherboard: Asus Z10PE-D16 WS
> > > CPU: Intel Xeon E5-2650 V4 (x2)
> > > CPU cooler: Noctua NH-U12DXi4 (x2)
> > > Memory: Samsung M393A2G40EB1-CRC 16GB DDR4 2400MHz ECC-Reg (x8 = 128 GB
> > > total)
> > > OS drive: Samsung 960 EVO 500GB M.2-2280 SSD (on a PCIE M.2 adapter
> > > because the motherboard runs its onboard M.2 at SATA speed)
> > > Data drive: Samsung 850 EVO 1TB SATA (6 drives in RAID10 configuration)
> > > Video card: GeForce GTX 1080 Ti 11GB
> > > Case: Phanteks Enthoo Primo
> > > Power supply: EVGA SuperNOVA P2 1200W 80+ Platinum
> > >
> > > You will obviously also need monitors, keyboard, mouse, Windows
> license,
> > > and some kind of data server - you should assume that you will not be
> > > storing your data on this computer if you are generating 1TB datasets.
> I
> > > got a Synology DS1817+ 8-bay NAS with a 10GbE adapter and loaded it
> with
> > 8
> > > Western Digital Gold 10TB drives (WD101KRYZ), and run them in SHR2
> > > (basically RAID6, for double-parity, i.e. you can lose two drives and
> > still
> > > be able to recover). I also got a 10GbE adapter for the workstation PC,
> > > this allows utilization of the maximum transfer rates the RAID array is
> > > capable of, which is 3-4 times faster than standard Gigabit Ethernet.
> > This
> > > data server is costly but, for light sheet data, basically necessary if
> > > your institute does not provide substantial data storage.
> > >
> > > Another thing to note is that component prices can fluctuate quite a
> bit.
> > > I bought the video card in the summer for under $740. Right now they
> are
> > > out of stock everywhere (1080 Ti of any brand), and when they are in
> > stock,
> > > they go for anywhere up to $2,000 (you have bitcoin mining to thank for
> > > that). You can get a Titan Xp for less than that now so the
> > > price/perfomance advantage of the 1080 Ti is no longer there, but look
> > for
> > > the Titans to also disappear off the market really quickly as mining
> > > expands higher up the range.
> > >
> > > All told, I spent around $9,000 for the workstation and $4,500 for the
> > > data server. Comparable off-the-shelf workstations cost around $12,000
> -
> > > $15,000 (and possibly even more now with the GPU market up in the air
> and
> > > RAM prices currently rising), and off-the-shelf data servers of similar
> > > capacity would cost much more than that.
> > >
> > > Assembly and setup of the PC was not trivial, so you will want someone
> > > with experience to help you. Workstation (Xeon) motherboards can be
> very
> > > finicky, and the installation manuals for some components can be pretty
> > > incomprehensible. Also be aware that if you need multiple PCIE slots
> > > available for data acquisition cards etc., the GPU only takes one but
> > > actually occludes at least one more slot (my card took up three slots
> > > total) so your choice of case/card should be made carefully. I ended up
> > > cutting a hole in the back panel of the case and mounting the GPU
> > > vertically with a 2-slot PCI bracket and PCIE riser cable, as I needed
> > > every last PCIE slot on the motherboard. Some cases come with vertical
> > GPU
> > > mounting positions, but some of those will block the regular PCIE
> slots,
> > or
> > > will be incompatible with SSI-EEB format motherboards (which is what
> most
> > > dual CPU boards will be).
> > >
> > > Good luck!
> > >
> > >
> > > Mel
> > >
> > >
> > > On 1/15/2018 7:22 AM, Owens, Peter 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 listers,
> > >>
> > >> I am looking into purchasing a high end image processing PC , that
> will
> > >> be capable of processing large multidimensional data sets up to 1 TB
> in
> > >> size.
> > >> Does anyone have any recommendations on a PC configuration that would
> be
> > >> suitable?
> > >> Do people build custom PCs or buy off the shelf?
> > >> Are high spec gaming PCs up to this task?
> > >>
> > >> thanks for any advice on this .
> > >>
> > >> all the best
> > >>
> > >> Peter
> > >>
> > >>
> > >> Peter Owens
> > >> Centre for Microscopy and Imaging,
> > >> National University of Ireland Galway.
> > >> P: [phone] m: [phone]
> > >> W: www.imaging.nuigalway.ie e: [hidden email]
> > >>
> > >>
> > >>
> > >>
> > >> --
> > > Menelaos Symeonides
> > > Post-Doctoral Associate, Thali Lab
> > > Department of Microbiology and Molecular Genetics
> > > University of Vermont
> > > 318 Stafford Hall
> > > 95 Carrigan Dr
> > > Burlington, VT 05405
> > > [hidden email]
> > > Phone: [phone]
> > >
> >
>

[Michael Giacomelli]

*****
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 Craig,

It is actually more simple than that.  Motherboard support is required if
you want to boot an OS like Windows from the NVMe device because the UEFI
ROM has to have an NVME driver to actually read the OS into memory during
boot.  That is all motherboard support means.

Once the computer boots the motherboard's UEFI ROM is no longer used, and
you use the OS's driver instead.  You can use NVMe storage at full speed on
any PCIe 3.0 device regardless of motherboard support for booting or the
presence of M.2. sockets on the board so long as your OS has a driver.
PCIe 2.0 devices will be a slower due to the lower transfer rate (2GB/s),
but will also work.  You can actually use NVMe devices with 10+ year old
computers if you really want to, but you will need a second ATA device to
boot from.

Mike

On Mon, Jan 15, 2018 at 5:35 PM, Craig Brideau <[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.
> *****
>
> Should have clarified: PCIe is only part of the attachment process. The
> motherboard must also support the NVMe standard via PCIe to achieve maximum
> performance. Most motherboards that support the latest NVMe protocol have a
> dedicated M.2 slot (or two) specifically for mounting M.2 NVMe compatible
> drives. (Some also are backwards compatible with SATA, this is slot
> dependent!) You *can* attach such drives via PCIe adapter cards but this
> depends on if the motherboard supports NVMe through the standard PCIe
> slots. The drives will still work in a PCIe slot, but you really only get
> the full potential out of them with the NVMe protocol implemented on the
> motherboard.
>
> Craig
>
> On Mon, Jan 15, 2018 at 11:04 AM, Michael Giacomelli <[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 Craig,
> >
> > You can buy M.2. NVME to PCIe adapters for a few dollars on Amazon.
> > They're pure passive (they just route the PCIe pins to the M.2.
> connector)
> > and work well for adding M.2. to motherboards that don't support it.  You
> > lose an x4 PCIe slot, but usually there is at least one extra on a full
> > size motherboard.
> >
> > Otherwise we usually just use Intel's single socket HEDT platform
> > (currently X299-based) which supports up to 18 cores and 8 DIMMs (128GB
> of
> > RAM).  These typically come with 2x M.2. slots for NVME storage.  Dual
> > socket would allow more than 20 cores, but the value is lower due to the
> > cost of the Xeon platform.
> >
> > Mike
> >
> > On Mon, Jan 15, 2018 at 12:02 PM, Craig Brideau <[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.
> > > *****
> > >
> > > Comment on the M.2 drives: They are significantly faster than SATA
> SSDs,
> > > but for full speed the motherboard must support NVMe which is a
> dedicated
> > > protocol for M.2 drives featuring a dedicated slot on the motherboard.
> > > Annoyingly, most dual-CPU-socket 8-DIMM slot motherboards don't feature
> > > this, so it is not an available option if you also want >64GB of RAM.
> If
> > > anyone happens to come across an NVMe board that also has 8-DIMM slots
> > > please let me know!
> > > I use an M.2 NVMe for a system at home and it boots absurdly fast with
> > only
> > > an older i5 core.
> > >
> > > Craig
> > >
> > > On Mon, Jan 15, 2018 at 8:06 AM, Menelaos Symeonides <[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 Peter,
> > > >
> > > > If you have ever built your own PC, or know someone who has, you can
> > > > benefit greatly from building it custom. Off-the-shelf systems can be
> > > > upmarked considerably and often use outdated components or skimp on
> > > > important things like a good power supply. Of course, the benefit of
> > that
> > > > would be presumably a warranty on the whole system, in case you are
> not
> > > > able to diagnose things yourself, but if you build a custom system,
> > each
> > > > component will come with its own warranty. It would just be up to you
> > to
> > > > determine which component is faulty and claim the warranty on it
> > > yourself.
> > > >
> > > > I recently built such a computer for light sheet data acquisition and
> > > > processing/analysis. Here is the configuration:
> > > >
> > > > Motherboard: Asus Z10PE-D16 WS
> > > > CPU: Intel Xeon E5-2650 V4 (x2)
> > > > CPU cooler: Noctua NH-U12DXi4 (x2)
> > > > Memory: Samsung M393A2G40EB1-CRC 16GB DDR4 2400MHz ECC-Reg (x8 = 128
> GB
> > > > total)
> > > > OS drive: Samsung 960 EVO 500GB M.2-2280 SSD (on a PCIE M.2 adapter
> > > > because the motherboard runs its onboard M.2 at SATA speed)
> > > > Data drive: Samsung 850 EVO 1TB SATA (6 drives in RAID10
> configuration)
> > > > Video card: GeForce GTX 1080 Ti 11GB
> > > > Case: Phanteks Enthoo Primo
> > > > Power supply: EVGA SuperNOVA P2 1200W 80+ Platinum
> > > >
> > > > You will obviously also need monitors, keyboard, mouse, Windows
> > license,
> > > > and some kind of data server - you should assume that you will not be
> > > > storing your data on this computer if you are generating 1TB
> datasets.
> > I
> > > > got a Synology DS1817+ 8-bay NAS with a 10GbE adapter and loaded it
> > with
> > > 8
> > > > Western Digital Gold 10TB drives (WD101KRYZ), and run them in SHR2
> > > > (basically RAID6, for double-parity, i.e. you can lose two drives and
> > > still
> > > > be able to recover). I also got a 10GbE adapter for the workstation
> PC,
> > > > this allows utilization of the maximum transfer rates the RAID array
> is
> > > > capable of, which is 3-4 times faster than standard Gigabit Ethernet.
> > > This
> > > > data server is costly but, for light sheet data, basically necessary
> if
> > > > your institute does not provide substantial data storage.
> > > >
> > > > Another thing to note is that component prices can fluctuate quite a
> > bit.
> > > > I bought the video card in the summer for under $740. Right now they
> > are
> > > > out of stock everywhere (1080 Ti of any brand), and when they are in
> > > stock,
> > > > they go for anywhere up to $2,000 (you have bitcoin mining to thank
> for
> > > > that). You can get a Titan Xp for less than that now so the
> > > > price/perfomance advantage of the 1080 Ti is no longer there, but
> look
> > > for
> > > > the Titans to also disappear off the market really quickly as mining
> > > > expands higher up the range.
> > > >
> > > > All told, I spent around $9,000 for the workstation and $4,500 for
> the
> > > > data server. Comparable off-the-shelf workstations cost around
> $12,000
> > -
> > > > $15,000 (and possibly even more now with the GPU market up in the air
> > and
> > > > RAM prices currently rising), and off-the-shelf data servers of
> similar
> > > > capacity would cost much more than that.
> > > >
> > > > Assembly and setup of the PC was not trivial, so you will want
> someone
> > > > with experience to help you. Workstation (Xeon) motherboards can be
> > very
> > > > finicky, and the installation manuals for some components can be
> pretty
> > > > incomprehensible. Also be aware that if you need multiple PCIE slots
> > > > available for data acquisition cards etc., the GPU only takes one but
> > > > actually occludes at least one more slot (my card took up three slots
> > > > total) so your choice of case/card should be made carefully. I ended
> up
> > > > cutting a hole in the back panel of the case and mounting the GPU
> > > > vertically with a 2-slot PCI bracket and PCIE riser cable, as I
> needed
> > > > every last PCIE slot on the motherboard. Some cases come with
> vertical
> > > GPU
> > > > mounting positions, but some of those will block the regular PCIE
> > slots,
> > > or
> > > > will be incompatible with SSI-EEB format motherboards (which is what
> > most
> > > > dual CPU boards will be).
> > > >
> > > > Good luck!
> > > >
> > > >
> > > > Mel
> > > >
> > > >
> > > > On 1/15/2018 7:22 AM, Owens, Peter 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 listers,
> > > >>
> > > >> I am looking into purchasing a high end image processing PC , that
> > will
> > > >> be capable of processing large multidimensional data sets up to 1 TB
> > in
> > > >> size.
> > > >> Does anyone have any recommendations on a PC configuration that
> would
> > be
> > > >> suitable?
> > > >> Do people build custom PCs or buy off the shelf?
> > > >> Are high spec gaming PCs up to this task?
> > > >>
> > > >> thanks for any advice on this .
> > > >>
> > > >> all the best
> > > >>
> > > >> Peter
> > > >>
> > > >>
> > > >> Peter Owens
> > > >> Centre for Microscopy and Imaging,
> > > >> National University of Ireland Galway.
> > > >> P: [phone] m: [phone]
> > > >> W: www.imaging.nuigalway.ie e: [hidden email]
> > > >>
> > > >>
> > > >>
> > > >>
> > > >> --
> > > > Menelaos Symeonides
> > > > Post-Doctoral Associate, Thali Lab
> > > > Department of Microbiology and Molecular Genetics
> > > > University of Vermont
> > > > 318 Stafford Hall
> > > > 95 Carrigan Dr
> > > > Burlington, VT 05405
> > > > [hidden email]
> > > > Phone: [phone]
> > > >
> > >
> >
>

[Craig Brideau]

*****
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.
*****

Thanks for the tip Mike! I had not realized that the driver was at OS level
which definitely makes things easier. I'll have to tinker around with this
at some point.

Craig

On Mon, Jan 15, 2018 at 4:31 PM, Michael Giacomelli <[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 Craig,
>
> It is actually more simple than that.  Motherboard support is required if
> you want to boot an OS like Windows from the NVMe device because the UEFI
> ROM has to have an NVME driver to actually read the OS into memory during
> boot.  That is all motherboard support means.
>
> Once the computer boots the motherboard's UEFI ROM is no longer used, and
> you use the OS's driver instead.  You can use NVMe storage at full speed on
> any PCIe 3.0 device regardless of motherboard support for booting or the
> presence of M.2. sockets on the board so long as your OS has a driver.
> PCIe 2.0 devices will be a slower due to the lower transfer rate (2GB/s),
> but will also work.  You can actually use NVMe devices with 10+ year old
> computers if you really want to, but you will need a second ATA device to
> boot from.
>
> Mike
>
> On Mon, Jan 15, 2018 at 5:35 PM, Craig Brideau <[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.
> > *****
> >
> > Should have clarified: PCIe is only part of the attachment process. The
> > motherboard must also support the NVMe standard via PCIe to achieve
> maximum
> > performance. Most motherboards that support the latest NVMe protocol
> have a
> > dedicated M.2 slot (or two) specifically for mounting M.2 NVMe compatible
> > drives. (Some also are backwards compatible with SATA, this is slot
> > dependent!) You *can* attach such drives via PCIe adapter cards but this
> > depends on if the motherboard supports NVMe through the standard PCIe
> > slots. The drives will still work in a PCIe slot, but you really only get
> > the full potential out of them with the NVMe protocol implemented on the
> > motherboard.
> >
> > Craig
> >
> > On Mon, Jan 15, 2018 at 11:04 AM, Michael Giacomelli <[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 Craig,
> > >
> > > You can buy M.2. NVME to PCIe adapters for a few dollars on Amazon.
> > > They're pure passive (they just route the PCIe pins to the M.2.
> > connector)
> > > and work well for adding M.2. to motherboards that don't support it.
> You
> > > lose an x4 PCIe slot, but usually there is at least one extra on a full
> > > size motherboard.
> > >
> > > Otherwise we usually just use Intel's single socket HEDT platform
> > > (currently X299-based) which supports up to 18 cores and 8 DIMMs (128GB
> > of
> > > RAM).  These typically come with 2x M.2. slots for NVME storage.  Dual
> > > socket would allow more than 20 cores, but the value is lower due to
> the
> > > cost of the Xeon platform.
> > >
> > > Mike
> > >
> > > On Mon, Jan 15, 2018 at 12:02 PM, Craig Brideau <
> [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.
> > > > *****
> > > >
> > > > Comment on the M.2 drives: They are significantly faster than SATA
> > SSDs,
> > > > but for full speed the motherboard must support NVMe which is a
> > dedicated
> > > > protocol for M.2 drives featuring a dedicated slot on the
> motherboard.
> > > > Annoyingly, most dual-CPU-socket 8-DIMM slot motherboards don't
> feature
> > > > this, so it is not an available option if you also want >64GB of RAM.
> > If
> > > > anyone happens to come across an NVMe board that also has 8-DIMM
> slots
> > > > please let me know!
> > > > I use an M.2 NVMe for a system at home and it boots absurdly fast
> with
> > > only
> > > > an older i5 core.
> > > >
> > > > Craig
> > > >
> > > > On Mon, Jan 15, 2018 at 8:06 AM, Menelaos Symeonides <
> [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 Peter,
> > > > >
> > > > > If you have ever built your own PC, or know someone who has, you
> can
> > > > > benefit greatly from building it custom. Off-the-shelf systems can
> be
> > > > > upmarked considerably and often use outdated components or skimp on
> > > > > important things like a good power supply. Of course, the benefit
> of
> > > that
> > > > > would be presumably a warranty on the whole system, in case you are
> > not
> > > > > able to diagnose things yourself, but if you build a custom system,
> > > each
> > > > > component will come with its own warranty. It would just be up to
> you
> > > to
> > > > > determine which component is faulty and claim the warranty on it
> > > > yourself.
> > > > >
> > > > > I recently built such a computer for light sheet data acquisition
> and
> > > > > processing/analysis. Here is the configuration:
> > > > >
> > > > > Motherboard: Asus Z10PE-D16 WS
> > > > > CPU: Intel Xeon E5-2650 V4 (x2)
> > > > > CPU cooler: Noctua NH-U12DXi4 (x2)
> > > > > Memory: Samsung M393A2G40EB1-CRC 16GB DDR4 2400MHz ECC-Reg (x8 =
> 128
> > GB
> > > > > total)
> > > > > OS drive: Samsung 960 EVO 500GB M.2-2280 SSD (on a PCIE M.2 adapter
> > > > > because the motherboard runs its onboard M.2 at SATA speed)
> > > > > Data drive: Samsung 850 EVO 1TB SATA (6 drives in RAID10
> > configuration)
> > > > > Video card: GeForce GTX 1080 Ti 11GB
> > > > > Case: Phanteks Enthoo Primo
> > > > > Power supply: EVGA SuperNOVA P2 1200W 80+ Platinum
> > > > >
> > > > > You will obviously also need monitors, keyboard, mouse, Windows
> > > license,
> > > > > and some kind of data server - you should assume that you will not
> be
> > > > > storing your data on this computer if you are generating 1TB
> > datasets.
> > > I
> > > > > got a Synology DS1817+ 8-bay NAS with a 10GbE adapter and loaded it
> > > with
> > > > 8
> > > > > Western Digital Gold 10TB drives (WD101KRYZ), and run them in SHR2
> > > > > (basically RAID6, for double-parity, i.e. you can lose two drives
> and
> > > > still
> > > > > be able to recover). I also got a 10GbE adapter for the workstation
> > PC,
> > > > > this allows utilization of the maximum transfer rates the RAID
> array
> > is
> > > > > capable of, which is 3-4 times faster than standard Gigabit
> Ethernet.
> > > > This
> > > > > data server is costly but, for light sheet data, basically
> necessary
> > if
> > > > > your institute does not provide substantial data storage.
> > > > >
> > > > > Another thing to note is that component prices can fluctuate quite
> a
> > > bit.
> > > > > I bought the video card in the summer for under $740. Right now
> they
> > > are
> > > > > out of stock everywhere (1080 Ti of any brand), and when they are
> in
> > > > stock,
> > > > > they go for anywhere up to $2,000 (you have bitcoin mining to thank
> > for
> > > > > that). You can get a Titan Xp for less than that now so the
> > > > > price/perfomance advantage of the 1080 Ti is no longer there, but
> > look
> > > > for
> > > > > the Titans to also disappear off the market really quickly as
> mining
> > > > > expands higher up the range.
> > > > >
> > > > > All told, I spent around $9,000 for the workstation and $4,500 for
> > the
> > > > > data server. Comparable off-the-shelf workstations cost around
> > $12,000
> > > -
> > > > > $15,000 (and possibly even more now with the GPU market up in the
> air
> > > and
> > > > > RAM prices currently rising), and off-the-shelf data servers of
> > similar
> > > > > capacity would cost much more than that.
> > > > >
> > > > > Assembly and setup of the PC was not trivial, so you will want
> > someone
> > > > > with experience to help you. Workstation (Xeon) motherboards can be
> > > very
> > > > > finicky, and the installation manuals for some components can be
> > pretty
> > > > > incomprehensible. Also be aware that if you need multiple PCIE
> slots
> > > > > available for data acquisition cards etc., the GPU only takes one
> but
> > > > > actually occludes at least one more slot (my card took up three
> slots
> > > > > total) so your choice of case/card should be made carefully. I
> ended
> > up
> > > > > cutting a hole in the back panel of the case and mounting the GPU
> > > > > vertically with a 2-slot PCI bracket and PCIE riser cable, as I
> > needed
> > > > > every last PCIE slot on the motherboard. Some cases come with
> > vertical
> > > > GPU
> > > > > mounting positions, but some of those will block the regular PCIE
> > > slots,
> > > > or
> > > > > will be incompatible with SSI-EEB format motherboards (which is
> what
> > > most
> > > > > dual CPU boards will be).
> > > > >
> > > > > Good luck!
> > > > >
> > > > >
> > > > > Mel
> > > > >
> > > > >
> > > > > On 1/15/2018 7:22 AM, Owens, Peter 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 listers,
> > > > >>
> > > > >> I am looking into purchasing a high end image processing PC , that
> > > will
> > > > >> be capable of processing large multidimensional data sets up to 1
> TB
> > > in
> > > > >> size.
> > > > >> Does anyone have any recommendations on a PC configuration that
> > would
> > > be
> > > > >> suitable?
> > > > >> Do people build custom PCs or buy off the shelf?
> > > > >> Are high spec gaming PCs up to this task?
> > > > >>
> > > > >> thanks for any advice on this .
> > > > >>
> > > > >> all the best
> > > > >>
> > > > >> Peter
> > > > >>
> > > > >>
> > > > >> Peter Owens
> > > > >> Centre for Microscopy and Imaging,
> > > > >> National University of Ireland Galway.
> > > > >> P: [phone] m: [phone]
> > > > >> W: www.imaging.nuigalway.ie e: [hidden email]
> > > > >>
> > > > >>
> > > > >>
> > > > >>
> > > > >> --
> > > > > Menelaos Symeonides
> > > > > Post-Doctoral Associate, Thali Lab
> > > > > Department of Microbiology and Molecular Genetics
> > > > > University of Vermont
> > > > > 318 Stafford Hall
> > > > > 95 Carrigan Dr
> > > > > Burlington, VT 05405
> > > > > [hidden email]
> > > > > Phone: [phone]
> > > > >
> > > >
> > >
> >
>

[Michael Giacomelli]

*****
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.
*****

No problem.

I suppose vendors don't make this clear because they're hoping people will
replace their systems rather than just upgrade the storage.

Mike

On Mon, Jan 15, 2018 at 6:48 PM, Craig Brideau <[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.
> *****
>
> Thanks for the tip Mike! I had not realized that the driver was at OS level
> which definitely makes things easier. I'll have to tinker around with this
> at some point.
>
> Craig
>
> On Mon, Jan 15, 2018 at 4:31 PM, Michael Giacomelli <[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 Craig,
> >
> > It is actually more simple than that.  Motherboard support is required if
> > you want to boot an OS like Windows from the NVMe device because the UEFI
> > ROM has to have an NVME driver to actually read the OS into memory during
> > boot.  That is all motherboard support means.
> >
> > Once the computer boots the motherboard's UEFI ROM is no longer used, and
> > you use the OS's driver instead.  You can use NVMe storage at full speed
> on
> > any PCIe 3.0 device regardless of motherboard support for booting or the
> > presence of M.2. sockets on the board so long as your OS has a driver.
> > PCIe 2.0 devices will be a slower due to the lower transfer rate (2GB/s),
> > but will also work.  You can actually use NVMe devices with 10+ year old
> > computers if you really want to, but you will need a second ATA device to
> > boot from.
> >
> > Mike
> >
> > On Mon, Jan 15, 2018 at 5:35 PM, Craig Brideau <[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.
> > > *****
> > >
> > > Should have clarified: PCIe is only part of the attachment process. The
> > > motherboard must also support the NVMe standard via PCIe to achieve
> > maximum
> > > performance. Most motherboards that support the latest NVMe protocol
> > have a
> > > dedicated M.2 slot (or two) specifically for mounting M.2 NVMe
> compatible
> > > drives. (Some also are backwards compatible with SATA, this is slot
> > > dependent!) You *can* attach such drives via PCIe adapter cards but
> this
> > > depends on if the motherboard supports NVMe through the standard PCIe
> > > slots. The drives will still work in a PCIe slot, but you really only
> get
> > > the full potential out of them with the NVMe protocol implemented on
> the
> > > motherboard.
> > >
> > > Craig
> > >
> > > On Mon, Jan 15, 2018 at 11:04 AM, Michael Giacomelli <[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 Craig,
> > > >
> > > > You can buy M.2. NVME to PCIe adapters for a few dollars on Amazon.
> > > > They're pure passive (they just route the PCIe pins to the M.2.
> > > connector)
> > > > and work well for adding M.2. to motherboards that don't support it.
> > You
> > > > lose an x4 PCIe slot, but usually there is at least one extra on a
> full
> > > > size motherboard.
> > > >
> > > > Otherwise we usually just use Intel's single socket HEDT platform
> > > > (currently X299-based) which supports up to 18 cores and 8 DIMMs
> (128GB
> > > of
> > > > RAM).  These typically come with 2x M.2. slots for NVME storage.
> Dual
> > > > socket would allow more than 20 cores, but the value is lower due to
> > the
> > > > cost of the Xeon platform.
> > > >
> > > > Mike
> > > >
> > > > On Mon, Jan 15, 2018 at 12:02 PM, Craig Brideau <
> > [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.
> > > > > *****
> > > > >
> > > > > Comment on the M.2 drives: They are significantly faster than SATA
> > > SSDs,
> > > > > but for full speed the motherboard must support NVMe which is a
> > > dedicated
> > > > > protocol for M.2 drives featuring a dedicated slot on the
> > motherboard.
> > > > > Annoyingly, most dual-CPU-socket 8-DIMM slot motherboards don't
> > feature
> > > > > this, so it is not an available option if you also want >64GB of
> RAM.
> > > If
> > > > > anyone happens to come across an NVMe board that also has 8-DIMM
> > slots
> > > > > please let me know!
> > > > > I use an M.2 NVMe for a system at home and it boots absurdly fast
> > with
> > > > only
> > > > > an older i5 core.
> > > > >
> > > > > Craig
> > > > >
> > > > > On Mon, Jan 15, 2018 at 8:06 AM, Menelaos Symeonides <
> > [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 Peter,
> > > > > >
> > > > > > If you have ever built your own PC, or know someone who has, you
> > can
> > > > > > benefit greatly from building it custom. Off-the-shelf systems
> can
> > be
> > > > > > upmarked considerably and often use outdated components or skimp
> on
> > > > > > important things like a good power supply. Of course, the benefit
> > of
> > > > that
> > > > > > would be presumably a warranty on the whole system, in case you
> are
> > > not
> > > > > > able to diagnose things yourself, but if you build a custom
> system,
> > > > each
> > > > > > component will come with its own warranty. It would just be up to
> > you
> > > > to
> > > > > > determine which component is faulty and claim the warranty on it
> > > > > yourself.
> > > > > >
> > > > > > I recently built such a computer for light sheet data acquisition
> > and
> > > > > > processing/analysis. Here is the configuration:
> > > > > >
> > > > > > Motherboard: Asus Z10PE-D16 WS
> > > > > > CPU: Intel Xeon E5-2650 V4 (x2)
> > > > > > CPU cooler: Noctua NH-U12DXi4 (x2)
> > > > > > Memory: Samsung M393A2G40EB1-CRC 16GB DDR4 2400MHz ECC-Reg (x8 =
> > 128
> > > GB
> > > > > > total)
> > > > > > OS drive: Samsung 960 EVO 500GB M.2-2280 SSD (on a PCIE M.2
> adapter
> > > > > > because the motherboard runs its onboard M.2 at SATA speed)
> > > > > > Data drive: Samsung 850 EVO 1TB SATA (6 drives in RAID10
> > > configuration)
> > > > > > Video card: GeForce GTX 1080 Ti 11GB
> > > > > > Case: Phanteks Enthoo Primo
> > > > > > Power supply: EVGA SuperNOVA P2 1200W 80+ Platinum
> > > > > >
> > > > > > You will obviously also need monitors, keyboard, mouse, Windows
> > > > license,
> > > > > > and some kind of data server - you should assume that you will
> not
> > be
> > > > > > storing your data on this computer if you are generating 1TB
> > > datasets.
> > > > I
> > > > > > got a Synology DS1817+ 8-bay NAS with a 10GbE adapter and loaded
> it
> > > > with
> > > > > 8
> > > > > > Western Digital Gold 10TB drives (WD101KRYZ), and run them in
> SHR2
> > > > > > (basically RAID6, for double-parity, i.e. you can lose two drives
> > and
> > > > > still
> > > > > > be able to recover). I also got a 10GbE adapter for the
> workstation
> > > PC,
> > > > > > this allows utilization of the maximum transfer rates the RAID
> > array
> > > is
> > > > > > capable of, which is 3-4 times faster than standard Gigabit
> > Ethernet.
> > > > > This
> > > > > > data server is costly but, for light sheet data, basically
> > necessary
> > > if
> > > > > > your institute does not provide substantial data storage.
> > > > > >
> > > > > > Another thing to note is that component prices can fluctuate
> quite
> > a
> > > > bit.
> > > > > > I bought the video card in the summer for under $740. Right now
> > they
> > > > are
> > > > > > out of stock everywhere (1080 Ti of any brand), and when they are
> > in
> > > > > stock,
> > > > > > they go for anywhere up to $2,000 (you have bitcoin mining to
> thank
> > > for
> > > > > > that). You can get a Titan Xp for less than that now so the
> > > > > > price/perfomance advantage of the 1080 Ti is no longer there, but
> > > look
> > > > > for
> > > > > > the Titans to also disappear off the market really quickly as
> > mining
> > > > > > expands higher up the range.
> > > > > >
> > > > > > All told, I spent around $9,000 for the workstation and $4,500
> for
> > > the
> > > > > > data server. Comparable off-the-shelf workstations cost around
> > > $12,000
> > > > -
> > > > > > $15,000 (and possibly even more now with the GPU market up in the
> > air
> > > > and
> > > > > > RAM prices currently rising), and off-the-shelf data servers of
> > > similar
> > > > > > capacity would cost much more than that.
> > > > > >
> > > > > > Assembly and setup of the PC was not trivial, so you will want
> > > someone
> > > > > > with experience to help you. Workstation (Xeon) motherboards can
> be
> > > > very
> > > > > > finicky, and the installation manuals for some components can be
> > > pretty
> > > > > > incomprehensible. Also be aware that if you need multiple PCIE
> > slots
> > > > > > available for data acquisition cards etc., the GPU only takes one
> > but
> > > > > > actually occludes at least one more slot (my card took up three
> > slots
> > > > > > total) so your choice of case/card should be made carefully. I
> > ended
> > > up
> > > > > > cutting a hole in the back panel of the case and mounting the GPU
> > > > > > vertically with a 2-slot PCI bracket and PCIE riser cable, as I
> > > needed
> > > > > > every last PCIE slot on the motherboard. Some cases come with
> > > vertical
> > > > > GPU
> > > > > > mounting positions, but some of those will block the regular PCIE
> > > > slots,
> > > > > or
> > > > > > will be incompatible with SSI-EEB format motherboards (which is
> > what
> > > > most
> > > > > > dual CPU boards will be).
> > > > > >
> > > > > > Good luck!
> > > > > >
> > > > > >
> > > > > > Mel
> > > > > >
> > > > > >
> > > > > > On 1/15/2018 7:22 AM, Owens, Peter 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 listers,
> > > > > >>
> > > > > >> I am looking into purchasing a high end image processing PC ,
> that
> > > > will
> > > > > >> be capable of processing large multidimensional data sets up to
> 1
> > TB
> > > > in
> > > > > >> size.
> > > > > >> Does anyone have any recommendations on a PC configuration that
> > > would
> > > > be
> > > > > >> suitable?
> > > > > >> Do people build custom PCs or buy off the shelf?
> > > > > >> Are high spec gaming PCs up to this task?
> > > > > >>
> > > > > >> thanks for any advice on this .
> > > > > >>
> > > > > >> all the best
> > > > > >>
> > > > > >> Peter
> > > > > >>
> > > > > >>
> > > > > >> Peter Owens
> > > > > >> Centre for Microscopy and Imaging,
> > > > > >> National University of Ireland Galway.
> > > > > >> P: [phone] m: [phone]
> > > > > >> W: www.imaging.nuigalway.ie e: [hidden email]
> > > > > >>
> > > > > >>
> > > > > >>
> > > > > >>
> > > > > >> --
> > > > > > Menelaos Symeonides
> > > > > > Post-Doctoral Associate, Thali Lab
> > > > > > Department of Microbiology and Molecular Genetics
> > > > > > University of Vermont
> > > > > > 318 Stafford Hall
> > > > > > 95 Carrigan Dr
> > > > > > Burlington, VT 05405
> > > > > > [hidden email]
> > > > > > Phone: [phone]
> > > > > >
> > > > >
> > > >
> > >
> >
>

[Mel Symeonides]

*****
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 Satoru & Peter,

That Tyan motherboard does have an M.2 slot but it will run at SATA
speeds, several times slower than PCIE. The only dual Xeon board I have
seen with onboard M.2 PCIE is from Gigabyte (the MD80-TM0), but it is
pretty poor in terms of standard PCIE slot availability (one x16 and
three x8) and I have read unfavorable opinions on its reliability. I am
pretty happy with the ASUS board I got, if you just take for granted
that you will be down one x8 slot for the PCIE M.2 card, you are still
left with four x16 slots and one x8 slot.

I didn't really properly appreciate the massive benefit of the number of
PCIE lanes you get out of a dual Xeon system, it's probably its biggest
advantage. In terms of CPU power it basically doesn't matter, a
half-decent quad or hexacore single CPU can handle almost anything you
can throw at it now that GPU CUDA cores are utilized so often instead
for the dirty work. If you need multiple add-on cards (and huge amounts
of RAM), however, dual Xeon is a must. If the computer will be doing
acquisition, you're looking at 3 or 4 PCIE slots at the very least for
intermediate or advanced microscopes.

In that sense, one could argue that for a pure data analysis workstation
that won't be doing acquisition, it would be best to go for a single CPU
motherboard that has dual M.2 (PCIE) slots. Use the money saved (by not
needing two very expensive Xeons) on a big SSD RAID array, a good NAS
box with high quality drives and a QSFP interface card, or a better GPU.

Mel


On 1/15/2018 12:18 PM, Satoru Uzawa 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 Craig,
>
>    There are few motherboards which can fill your need.  For example, Tyan S7070 A2NR-M2 has an M.2 slot and 16 DIMM slots with maximum 512GB total RAM.
>
> http://www.tyan.com/Motherboards_S7070_S7070A2NR-M2 <http://www.tyan.com/Motherboards_S7070_S7070A2NR-M2>
>
>     Also, many motherboards for AMD Threadripper has 8 DIMM slots and M.2 socket even though they are single CPU system.  As an example, check
>
> https://www.asus.com/us/Motherboards/ROG-ZENITH-EXTREME/ <https://www.asus.com/us/Motherboards/ROG-ZENITH-EXTREME/>
>
>     The maximum RAM capacity is limited to 128GB but the board can take ECC RAM, which is a must feature (at least for me).  AMD Threadripper offers nice CPU core count with decent floating point performance at a lower price.
>
> Best,
>
> Satoru
>
>> On Jan 15, 2018, at 9:02 AM, Craig Brideau <[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.
>> *****
>>
>> Comment on the M.2 drives: They are significantly faster than SATA SSDs,
>> but for full speed the motherboard must support NVMe which is a dedicated
>> protocol for M.2 drives featuring a dedicated slot on the motherboard.
>> Annoyingly, most dual-CPU-socket 8-DIMM slot motherboards don't feature
>> this, so it is not an available option if you also want >64GB of RAM. If
>> anyone happens to come across an NVMe board that also has 8-DIMM slots
>> please let me know!
>> I use an M.2 NVMe for a system at home and it boots absurdly fast with only
>> an older i5 core.
>>
>> Craig
>>
>> On Mon, Jan 15, 2018 at 8:06 AM, Menelaos Symeonides <[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 Peter,
>>>
>>> If you have ever built your own PC, or know someone who has, you can
>>> benefit greatly from building it custom. Off-the-shelf systems can be
>>> upmarked considerably and often use outdated components or skimp on
>>> important things like a good power supply. Of course, the benefit of that
>>> would be presumably a warranty on the whole system, in case you are not
>>> able to diagnose things yourself, but if you build a custom system, each
>>> component will come with its own warranty. It would just be up to you to
>>> determine which component is faulty and claim the warranty on it yourself.
>>>
>>> I recently built such a computer for light sheet data acquisition and
>>> processing/analysis. Here is the configuration:
>>>
>>> Motherboard: Asus Z10PE-D16 WS
>>> CPU: Intel Xeon E5-2650 V4 (x2)
>>> CPU cooler: Noctua NH-U12DXi4 (x2)
>>> Memory: Samsung M393A2G40EB1-CRC 16GB DDR4 2400MHz ECC-Reg (x8 = 128 GB
>>> total)
>>> OS drive: Samsung 960 EVO 500GB M.2-2280 SSD (on a PCIE M.2 adapter
>>> because the motherboard runs its onboard M.2 at SATA speed)
>>> Data drive: Samsung 850 EVO 1TB SATA (6 drives in RAID10 configuration)
>>> Video card: GeForce GTX 1080 Ti 11GB
>>> Case: Phanteks Enthoo Primo
>>> Power supply: EVGA SuperNOVA P2 1200W 80+ Platinum
>>>
>>> You will obviously also need monitors, keyboard, mouse, Windows license,
>>> and some kind of data server - you should assume that you will not be
>>> storing your data on this computer if you are generating 1TB datasets. I
>>> got a Synology DS1817+ 8-bay NAS with a 10GbE adapter and loaded it with 8
>>> Western Digital Gold 10TB drives (WD101KRYZ), and run them in SHR2
>>> (basically RAID6, for double-parity, i.e. you can lose two drives and still
>>> be able to recover). I also got a 10GbE adapter for the workstation PC,
>>> this allows utilization of the maximum transfer rates the RAID array is
>>> capable of, which is 3-4 times faster than standard Gigabit Ethernet. This
>>> data server is costly but, for light sheet data, basically necessary if
>>> your institute does not provide substantial data storage.
>>>
>>> Another thing to note is that component prices can fluctuate quite a bit.
>>> I bought the video card in the summer for under $740. Right now they are
>>> out of stock everywhere (1080 Ti of any brand), and when they are in stock,
>>> they go for anywhere up to $2,000 (you have bitcoin mining to thank for
>>> that). You can get a Titan Xp for less than that now so the
>>> price/perfomance advantage of the 1080 Ti is no longer there, but look for
>>> the Titans to also disappear off the market really quickly as mining
>>> expands higher up the range.
>>>
>>> All told, I spent around $9,000 for the workstation and $4,500 for the
>>> data server. Comparable off-the-shelf workstations cost around $12,000 -
>>> $15,000 (and possibly even more now with the GPU market up in the air and
>>> RAM prices currently rising), and off-the-shelf data servers of similar
>>> capacity would cost much more than that.
>>>
>>> Assembly and setup of the PC was not trivial, so you will want someone
>>> with experience to help you. Workstation (Xeon) motherboards can be very
>>> finicky, and the installation manuals for some components can be pretty
>>> incomprehensible. Also be aware that if you need multiple PCIE slots
>>> available for data acquisition cards etc., the GPU only takes one but
>>> actually occludes at least one more slot (my card took up three slots
>>> total) so your choice of case/card should be made carefully. I ended up
>>> cutting a hole in the back panel of the case and mounting the GPU
>>> vertically with a 2-slot PCI bracket and PCIE riser cable, as I needed
>>> every last PCIE slot on the motherboard. Some cases come with vertical GPU
>>> mounting positions, but some of those will block the regular PCIE slots, or
>>> will be incompatible with SSI-EEB format motherboards (which is what most
>>> dual CPU boards will be).
>>>
>>> Good luck!
>>>
>>>
>>> Mel
>>>
>>>
>>> On 1/15/2018 7:22 AM, Owens, Peter 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 listers,
>>>>
>>>> I am looking into purchasing a high end image processing PC , that will
>>>> be capable of processing large multidimensional data sets up to 1 TB in
>>>> size.
>>>> Does anyone have any recommendations on a PC configuration that would be
>>>> suitable?
>>>> Do people build custom PCs or buy off the shelf?
>>>> Are high spec gaming PCs up to this task?
>>>>
>>>> thanks for any advice on this .
>>>>
>>>> all the best
>>>>
>>>> Peter
>>>>
>>>>
>>>> Peter Owens
>>>> Centre for Microscopy and Imaging,
>>>> National University of Ireland Galway.
>>>> P: [phone] m: [phone]
>>>> W: www.imaging.nuigalway.ie e: [hidden email]
>>>>
>>>>
>>>>
>>>>
>>>> --
>>> Menelaos Symeonides
>>> Post-Doctoral Associate, Thali Lab
>>> Department of Microbiology and Molecular Genetics
>>> University of Vermont
>>> 318 Stafford Hall
>>> 95 Carrigan Dr
>>> Burlington, VT 05405
>>> [hidden email]
>>> Phone: [phone]
>>>

[Benjamin Smith]

*****
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.
*****

There is no one best solution.  If almost all of your tasks are going to be
multi-threaded on large image sets (such as median filters, etc.) then a
server wins.  However, if the tasks are also going to be single threaded
(such as EDTs and most plugins) then a desktop wins easily.  If you need
just one computer, then I've found a single CPU desktop with as many cores
and as much RAM as you can afford is a great compromise (you can never have
too much or too fast RAM for image processing).  Add on a quality
motherboard to push the data and some nice fans for a bit of over-clocking,
and you'll have a decent enough work-horse.  An M.2 drive is also nice to
keep the system stable in the event of hard faults.

In short, if all tasks can be multi-threaded, go with a server, but for
anything else go with a desktop.  The problem with servers is they can get
profoundly bogged down when distributing single-threaded tasks.  Although,
you can also do what I call a "poor man's" multi-thread and run multiple
different instances of the image processing at the same time. For
suppliers, we've had excellent luck with Puget Systems, good support and
excellent build quality.  No personal interest, just a very happy repeat
customer.  Even better if you have a good in house IT person, but those are
a rare treat.

-Ben Smith



On Mon, Jan 15, 2018 at 4:22 AM, Owens, Peter <[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.
> *****
>
> Dear listers,
>
> I am looking into purchasing a high end image processing PC , that will be
> capable of processing large multidimensional data sets up to 1 TB in size.
> Does anyone have any recommendations on a PC configuration that would be
> suitable?
> Do people build custom PCs or buy off the shelf?
> Are high spec gaming PCs up to this task?
>
> thanks for any advice on this .
>
> all the best
>
> Peter
>
>
> Peter Owens
> Centre for Microscopy and Imaging,
> National University of Ireland Galway.
> P: [phone] m: [phone]
> W: www.imaging.nuigalway.ie e: [hidden email]
>
>
>
>
>
>
> -----Original Message-----
> From: Confocal Microscopy List [mailto:[hidden email]]
> On Behalf Of Oliver Biehlmaier
> Sent: 15 January 2018 10:17
> To: [hidden email]
> Subject: Re: Cleaning of CSU W1 spinning disk scan head
>
> *****
> 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 all, dear Pascal,
>
> This is indeed very annoying!
> As some of you might remember from the conversation that Kai started last
> year asking about the experiences with current spinning disk systems, the
> reports on dust problems on the W1 were by far the most frequent.
> I wonder how the manufacturer can get away with such a problem without
> being obliged to replace or at least fix those dust collecting systems?!
>
> Pascal, I thought that your system already was “fixed” with the magic tape
> solution…. So apparently this did not help. Is that correct?
>
> Did anyone of you guys purchase a new W1 within the past 6 months?
> According to the manufacturer and the local distributers the dust problem
> should be fixed on those recently sold W1 systems. Can anyone confirm this?
>
> Concerning the problem described I would really try to ask the distributer
> to solve this, in particular if the system is still under warranty.
> I have no idea how to clean the disk but the system should clearly only be
> opened and cleaned in a clean room. Otherwise Gabor’s solutions should at
> least reduce the dust problem.
>
> Best regards,
> Oliver
>
>
>
> Oliver Biehlmaier, PhD | Head of Imaging Core Facility  | Biozentrum,
> University of Basel | Klingelbergstrasse 50/70 | CH-4056 Basel
> Phone: [phone] | Email: [hidden email]<mailto:
> [hidden email]> | www.biozentrum.unibas.ch/imcf<
> http://www.biozentrum.unibas.ch/imcf> | www.microscopynetwork.unibas.ch<
> http://www.microscopynetwork.unibas.ch>
>
>
>
>
>
>
>
>
> On 15 Jan 2018, at 09:51, Csúcs Gábor <[hidden email]<mailto:
> [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.
> *****
>
> Dear All,
>
> Though I fully agree with Ferhan that it would be good if either the
> manufacturer or the distributor would offer a solution to this dust
> problem, perhaps I can  make two suggestions that will certainly not
> eliminate the problem but perhaps make it less frequent (less frequent
> cleaning required). The first one is reduction of the dust in the room
> (very obvious). This can be potentially achieved by installing filters in
> the air-conditioning unit (if possible) and to apply some other "tricks"
> used in clean environments (sticky floor tapes etc.). The other suggestion:
> I believe (of course I have no scientific proof for this) that box-type
> incubators (enclosures) also may help. But again this does not solve the
> issue....
>
> Greetings Gabor
>
>
> -----Original Message-----
> From: Confocal Microscopy List [mailto:[hidden email]]
> On Behalf Of Ferhan A
> Sent: Saturday, January 13, 2018 9:58 AM
> To: [hidden email]
> Subject: Re: Cleaning of CSU W1 spinning disk scan head
>
> *****
> 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 Pascal,
>
> We have exactly the same headache with our dust gathering CSU W1 spinning
> disk unit which started to produce images resembling the ones in the cover
> pages of dendrochronology journals. As discussed earlier in this forum,
> this seems to be a design flaw of W1 system. We will be very happy if the
> original manufacturer comes up with a no-cost-to-customer fix to this
> problem and offers free dust cleanup and reimburses us for the aspirins.
> Best regards,
> Ferhan
> -------
> Ferhan Ayaydin, Ph.D.
> Cellular Imaging Laboratory
> Biological Research Center
> Hungarian Academy of Sciences
> Temesvari krt. 62
> 6726 Szeged
> Hungary
>
>
> On Jan 12, 2018 16:23, "Pascal Lorentz" <[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.
> *****
>
> Dear list
>
> We have a CSU W1 spinning disk scan head and most likely a dust particle
> on the disk that creates a well defined line in the image.
> Please find an image here: https://imgur.com/a/e3NKg Did somebody ever
> clean the disks successfully? I heard that it is very tricky to do on site
> in a non dust free environment.
> How would I need to proceed if I would like to clean it myself? How can I
> access the disks and are there any tips and tricks on how to prevent even
> more dust flying onto the disks. So far I just accessed the emission filter
> wheels and the dichroic mirrors but did not dare to access the disks. Any
> manuals would be helpful.
>
> Thanks a lot for your help and best regards
>
> Pascal
>
>
>

--
Benjamin E. Smith, Ph. D.
Imaging Specialist, Vision Science
University of California, Berkeley
195 Life Sciences Addition
Berkeley, CA  94720-3200
Tel  [phone]
Fax [phone]
e-mail: [hidden email]
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