Confocal Microscopy List

Advice for offline image analysis computer

Classic

List

Threaded

24 messages Options

lechristophe

Advice for offline image analysis computer

Dear listers,

I have to buy a new computer for our team that will be used as for offline image analysis. The software required (ImageJ, Metamorph, Matlab) require to build a Windows/Vista machine. The cost would be around $5,000 / 5000€. The job would be processing (a lot) and rendering. My questions are :
- Should I go for a "traditionnal" computer, I mean a 32-bits, dual core, XP computer with maxed RAM (I guess it is 3GB or so) ? Is it usefull to go to more fancy stuff like 64 bits, 4 or 8 core, 8 to 16GB RAM machine ? Would ImageJ/Metamorph/Matlab really benefit from it (I would love to have an answer from the Metamorph/Matlab people) ?
- What about graphic cards and GPU ? What is the best choice ? I've heard about new strategies to speed up processing by making the GPU churn data as well as graphics, but I don't think it is really commercially available now or implemented in commercial software yet.

Thanks for your advices !

Christophe

Shalin Mehta

Re: Advice for offline image analysis computer

Dear Christophe,

In MATLAB, I particularly found parfor loop useful. It can be used instead of standard for-loop if iterations in the loop are independent of each other (e.g. when batch processing a set of images in the same way). If you have sufficient memory, using parfor loop should give speed up close to the number of cores. I use MATLAB 2007b, but MATLAB has since introduced other features for multi-threading. A good analysis of what functions should benefit from multi-threading is here:
http://www.mathworks.com/support/solutions/data/1-4PG4AN.html?solution=1-4PG4AN

So buying a 64 bit, quad-core, 16 GB computer may be worthwhile.
best
shalin

On Mon, Sep 22, 2008 at 4:33 PM, Christophe Leterrier <[hidden email]> wrote:

Dear listers,

I have to buy a new computer for our team that will be used as for offline image analysis. The software required (ImageJ, Metamorph, Matlab) require to build a Windows/Vista machine. The cost would be around $5,000 / 5000€. The job would be processing (a lot) and rendering. My questions are :
- Should I go for a "traditionnal" computer, I mean a 32-bits, dual core, XP computer with maxed RAM (I guess it is 3GB or so) ? Is it usefull to go to more fancy stuff like 64 bits, 4 or 8 core, 8 to 16GB RAM machine ? Would ImageJ/Metamorph/Matlab really benefit from it (I would love to have an answer from the Metamorph/Matlab people) ?
- What about graphic cards and GPU ? What is the best choice ? I've heard about new strategies to speed up processing by making the GPU churn data as well as graphics, but I don't think it is really commercially available now or implemented in commercial software yet.

Thanks for your advices !

Christophe

Jean-Yves Tinevez

Re: Advice for offline image analysis computer

In reply to this post by lechristophe

> Dear listers,
>
> I have to buy a new computer for our team that will be used as for offline
> image analysis. The software required (ImageJ, Metamorph, Matlab) require
> to
> build a Windows/Vista machine. The cost would be around $5,000 / 5000.
> The
> job would be processing (a lot) and rendering. My questions are :
> - Should I go for a "traditionnal" computer, I mean a 32-bits, dual core,
> XP
> computer with maxed RAM (I guess it is 3GB or so) ? Is it usefull to go to
> more fancy stuff like 64 bits, 4 or 8 core, 8 to 16GB RAM machine ? Would
> ImageJ/Metamorph/Matlab really benefit from it (I would love to have an
> answer from the Metamorph/Matlab people) ?
> - What about graphic cards and GPU ? What is the best choice ? I've heard
> about new strategies to speed up processing by making the GPU churn data
> as
> well as graphics, but I don't think it is really commercially available
> now
> or implemented in commercial software yet.
>

Salut Christophe, je te fais une reponse off-liste histoire de causer
frenchie. Le software que je connais le mieux est Matlab, voila ce que je
peux t'en dire.

Sous windows, le support par Matlab des architectures 64 bits est pour
tres bientot (soit la fin de l'annee soit debut 2009 au pire). Il y a
beaucoup de benefices a y trouver:
- Matlab bosse presque uniquement avec des nombres 'double' qui prennent
64 bits. Avec une architecture 64 bit, chaque operation sur eux prend un
tic et non pas deux comme maintenant.
- Matlab est tres gourmand en memoire (il la gere assez mal), avec un
system 64 bit tu peux te payer 16Go de RAM.
- Certaines operations de Matlab prennent avantages du multi coeur
nativement (multiplication de matrices etc...), mais autrement et pour la
grande majorite de ce qui va t'interesser, un simple coeur suffit. Aller
au dela de 4 coeurs est inutile dans ton cas je pense.
- Il existe des version d'ImageJ qui travaille en 64bit. Dans mon groupe
un type bosse dessus (va voir sur la page notre projet
http://pacific.mpi-cbg.de/wiki/index.php/Main_Page, c'est encore le
bordel, ne t'attend a rien de magique). C'est tres utile, parce que la
aussi on a vite fait de bouffer toute la memoire.

Je sais que Imaris et Volocity utilisent les GPU a fond, et en dependent
meme pour la visualisation 3D/4D (acceleration materielle et tout et
tout). Pour Matlab et Metamorph (ce dernier etant quand meme bien en
retard..) j'en doute.

J'espere que c'est utile
A bientot
jy

--
Jean-Yves Tinevez, PhD
Image Processing Facility head
Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstr. 108, 01307 Dresden
Germany
tel +49 (0)351 210 2889
fax +49 (0)351 210 1489
e-mail: [hidden email]

mahogny

Re: Advice for offline image analysis computer

In reply to this post by lechristophe

Christophe Leterrier wrote:
> Dear listers,
>
> I have to buy a new computer for our team that will be used as for
> offline image analysis. The software required (ImageJ, Metamorph,
> Matlab) require to build a Windows/Vista machine. The cost would be
> around $5,000 / 5000€. The job would be processing (a lot) and
> rendering. My questions are :
this sounds like a lot to me if it just includes the hardware
> - Should I go for a "traditionnal" computer, I mean a 32-bits, dual
> core, XP computer with maxed RAM (I guess it is 3GB or so) ? Is it
> usefull to go to more fancy stuff like 64 bits, 4 or 8 core, 8 to 16GB
> RAM machine ? Would ImageJ/Metamorph/Matlab really benefit from it (I
> would love to have an answer from the Metamorph/Matlab people) ?
with 32-bit, there is little/no point in more than 4gb (of which 3gb is
available for your program).
imagej can use the full 64-bit as it is java. I think matlab exist in
64bit edition. I can not say anything about metamorph. endrov makes full
use of 64-bit. expect all maintained software to at some point support
full 64-bit, legacy software will not improve (recompilation needed).
but remember that more ram only speeds up the computer if your software
actually will use all of it. this depends on your application. I would
buy 4gb for rather heavy normal use, more if you have a special purpose.

cores: matlab has essentially no use of them (but you can buy a toolbox
for it), imagej has limited use, endrov full use, no idea about
metamorph. they will become more important in the future but require
special programming. 2 cores are always useful, the OS can use one. get
at least 2-4 cores. I doubt 8 cores will be fully useful in a while,
speed-up is not linear.

> - What about graphic cards and GPU ? What is the best choice ? I've
> heard about new strategies to speed up processing by making the GPU
> churn data as well as graphics, but I don't think it is really
> commercially available now or implemented in commercial software yet.
you need the card for 3d rendering. recent cards support GPU calc as
well with no extra cost.

some rather obscure software can do GPU calc but GPU programming is
still taking a lot of effort. expect this to be a hit in 2-4 years,
earlier if you are doing something really intensive (deconvolution would
benefit). the nv8-series is a rather safe bet, can do CUDA, and nvidia
has rather good linux support if you need to upgrade your software later.

--
------------------------------------------------
Johan Henriksson
MSc Engineering
PhD student, Karolinska Institutet
http://mahogny.areta.org http://www.endrov.net

Nowell, Cameron

Re: Advice for offline image analysis computer

In reply to this post by lechristophe

Hi Christophe,
The software package is not the only thing you should consider. The type (and size) of the data sets you will be analysing will govern what to buy. We run MetaMorph, ImageJ, Imaris, Volicty and FluoView on our systems. The systems we have range from older P4 desktops and laptops up to newer 2 x 4 Core Xeon Workstations with 16 or 32 GB of RAM in them.

The most basic of our systems will run metamorph for basic functions such as intensity mersurments, percentage stain and simple cell tracking. The higher end systems are for larger live cell experiments (>200GB) and 3D/4D/5D rendering of data.

$5000 will buy you a high end gaming system that i woudl assume woudl meet most of your needs. The more memory you can fit in the better it will all run. Processing power will help things along a bit but if you don't have enough memory the dastest CPU in the world won't help you.

If you are going to go over 3GB of RAM then you need to goto 64bit Windows. While XP and Vista 32 bit can theoretically support 4GB of RAM, the GB between 3 and 4 is mostly wasted shadowing the video RAM

GPU power is only important if you want to do heavy 3D modeling. There have been posts on graphics cards recently on this list, have a search through the archives and you should be able to find them

Cheers

Cam

Cameron Nowell
Research and Microscopy Core Facility
Peter MacCallum Cancer Centre

________________________________

From: Confocal Microscopy List on behalf of Christophe Leterrier
Sent: Mon 22/09/2008 6:33 PM
To: [hidden email]
Subject: Advice for offline image analysis computer

Dear listers,

I have to buy a new computer for our team that will be used as for offline image analysis. The software required (ImageJ, Metamorph, Matlab) require to build a Windows/Vista machine. The cost would be around $5,000 / 5000EUR. The job would be processing (a lot) and rendering. My questions are :
- Should I go for a "traditionnal" computer, I mean a 32-bits, dual core, XP computer with maxed RAM (I guess it is 3GB or so) ? Is it usefull to go to more fancy stuff like 64 bits, 4 or 8 core, 8 to 16GB RAM machine ? Would ImageJ/Metamorph/Matlab really benefit from it (I would love to have an answer from the Metamorph/Matlab people) ?
- What about graphic cards and GPU ? What is the best choice ? I've heard about new strategies to speed up processing by making the GPU churn data as well as graphics, but I don't think it is really commercially available now or implemented in commercial software yet.

Thanks for your advices !

Christophe

This email (including any attachments or links) may contain
confidential and/or legally privileged information and is
intended only to be read or used by the addressee. If you
are not the intended addressee, any use, distribution,
disclosure or copying of this email is strictly
prohibited.
Confidentiality and legal privilege attached to this email
(including any attachments) are not waived or lost by
reason of its mistaken delivery to you.
If you have received this email in error, please delete it
and notify us immediately by telephone or email. Peter
MacCallum Cancer Centre provides no guarantee that this
transmission is free of virus or that it has not been
intercepted or altered and will not be liable for any delay
in its receipt.

Michael Weber-4

Re: Advice for offline image analysis computer

In reply to this post by lechristophe

Christophe,

from your list I don't see the need for advanced 3D support, or am I wrong?

I would suggest a Quad-Core machine (still useful for multi-tasking, i.e.
calculations in the background) with 8 or 16 GB RAM, fast harddrives (at
least boot disc + data disc), two nice screens with high resolution and
good color reproduction, good keyboard and mouse.

Regarding the operating system, probably XP 64 would be the best
compromise. Not sure about the Vista x64 support of the programs you
mentioned.

One option would be an Apple Mac Pro, Mac OS on a separate drive would
offer additional features.

Michael

Jean-Christophe Olaya

Re: Advice for offline image analysis computer

In reply to this post by Jean-Yves Tinevez

[hidden email] schrieb:

>> Dear listers,
>>
>> I have to buy a new computer for our team that will be used as for offline
>> image analysis. The software required (ImageJ, Metamorph, Matlab) require
>> to
>> build a Windows/Vista machine. The cost would be around $5,000 / 5000€.
>> The
>> job would be processing (a lot) and rendering. My questions are :
>> - Should I go for a "traditionnal" computer, I mean a 32-bits, dual core,
>> XP
>> computer with maxed RAM (I guess it is 3GB or so) ? Is it usefull to go to
>> more fancy stuff like 64 bits, 4 or 8 core, 8 to 16GB RAM machine ? Would
>> ImageJ/Metamorph/Matlab really benefit from it (I would love to have an
>> answer from the Metamorph/Matlab people) ?
>> - What about graphic cards and GPU ? What is the best choice ? I've heard
>> about new strategies to speed up processing by making the GPU churn data
>> as
>> well as graphics, but I don't think it is really commercially available
>> now
>> or implemented in commercial software yet.
>>
>>
>
> Salut Christophe, je te fais une reponse off-liste histoire de causer
> frenchie. Le software que je connais le mieux est Matlab, voila ce que je
> peux t'en dire.
>
>
> Sous windows, le support par Matlab des architectures 64 bits est pour
> tres bientot (soit la fin de l'annee soit debut 2009 au pire). Il y a
> beaucoup de benefices a y trouver:
> - Matlab bosse presque uniquement avec des nombres 'double' qui prennent
> 64 bits. Avec une architecture 64 bit, chaque operation sur eux prend un
> tic et non pas deux comme maintenant.
> - Matlab est tres gourmand en memoire (il la gere assez mal), avec un
> system 64 bit tu peux te payer 16Go de RAM.
> - Certaines operations de Matlab prennent avantages du multi coeur
> nativement (multiplication de matrices etc...), mais autrement et pour la
> grande majorite de ce qui va t'interesser, un simple coeur suffit. Aller
> au dela de 4 coeurs est inutile dans ton cas je pense.
> - Il existe des version d'ImageJ qui travaille en 64bit. Dans mon groupe
> un type bosse dessus (va voir sur la page notre projet
> http://pacific.mpi-cbg.de/wiki/index.php/Main_Page, c'est encore le
> bordel, ne t'attend a rien de magique). C'est tres utile, parce que la
> aussi on a vite fait de bouffer toute la memoire.
>
>
> Je sais que Imaris et Volocity utilisent les GPU a fond, et en dependent
> meme pour la visualisation 3D/4D (acceleration materielle et tout et
> tout). Pour Matlab et Metamorph (ce dernier etant quand meme bien en
> retard..) j'en doute.
>
> J'espere que c'est utile
> A bientot
> jy
>
>
>
>
> --
> Jean-Yves Tinevez, PhD
> Image Processing Facility head
> Max Planck Institute of Molecular Cell Biology and Genetics
> Pfotenhauerstr. 108, 01307 Dresden
> Germany
> tel +49 (0)351 210 2889
> fax +49 (0)351 210 1489
> e-mail: [hidden email]
>

...pas si "horts liste", ta réponse ;-)

JC

--
Jean-Christophe Olaya
Biotechnologisches Zentrum der TU Dresden
Light Microscopy Facility
Tatzberg 47-51
01307 Dresden
Germany
email: [hidden email]
Tel: +49 351 463-40230
Fax: +49 351 463-40038

Jean-Yves Tinevez

Re: Advice for offline image analysis computer

>>
> ...pas si "horts liste", ta réponse ;-)

Je veux mourir....
Enfin bon, la tienne non plus est pas hors liste du tout :)
on fait un mail commun d'excuses pbuliques ?
bises
jy

Hu Xian

Re: Advice for offline image analysis computer

In reply to this post by Jean-Christophe Olaya

Hi there,

Well, generally, I would prefer 64 bits over 32 bits operation system.

But the details of operation system greatly depends on the software you want to use.

For instance, we know the ImageJ works much better on Leopard than Vista 64 bits. If I'm not wrong, you can allocate around 1.5G memory for ImageJ on Vista before it starts to crash, whereas on leopard it can take upto 10Gb of memory.

And some of the software might not be stable on certain operation, velocity isn't very stable on vista 64 bits yet. Imaris is better in stability, but it does not supply multicore system yet(hence our 2.8G 8-core doesnot work nearly as well as 3.2G single core)

I'm not very familiar with matlab and metamorph.
But a computer with more ram and computing power will definitely helps accelerate rendering process a lot.

$5000 is a lot of money. Not sure about European market, but should be too far off. You should be able to get a 64bits operation system with 64GB, 8 core. Disc space is not that critical as long as you are not using the computer as data storage.

We were trying to purchase an image processing workstation around the same price from Dell, I can send you the quote for your reference(no commercial interest).

Thanks,

Edna, HU Xian

-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Jean-Christophe Olaya
Sent: Monday, September 22, 2008 5:57 PM
To: [hidden email]
Subject: Re: Advice for offline image analysis computer

[hidden email] schrieb:

mahogny

Re: Advice for offline image analysis computer

Hu Xian wrote:
> Hi there,
>
> Well, generally, I would prefer 64 bits over 32 bits operation system.
>
> But the details of operation system greatly depends on the software you want to use.
>
> For instance, we know the ImageJ works much better on Leopard than Vista 64 bits. If I'm not wrong, you can allocate around 1.5G memory for ImageJ on Vista before it starts to crash, whereas on leopard it can take upto 10Gb of memory.
>
I think this is problem with the java environment on windows. on 32bit
it can actually never grow past 2gb. how well the 64bit works I do not know.
> $5000 is a lot of money. Not sure about European market, but should be too far off. You should be able to get a 64bits operation system with 64GB, 8 core. Disc space is not that critical as long as you are not using the computer as data storage.
>
however, you might want to have a look at the bandwidth to whatever
storage you have. the disk is a bottleneck to take into consideration.
you want gigabit if you have a network, and maybe even RAID if you run
locally. at the same time, make sure you use good a image format. some
sort of compression is a requirement, lossless at minimum.

--
--
------------------------------------------------
Johan Henriksson
MSc Engineering
PhD student, Karolinska Institutet
http://mahogny.areta.org http://www.endrov.net

Jon Ekman-2

Re: Advice for offline image analysis computer

In reply to this post by lechristophe

I would recommend the Vista 64bit, 8 core with an Open GL “workstation grade” video card and 16GB of RAM. Eventually the software you use will grow into multi-core processing. Ignore the GPU options they are mainly for 3D graphics and games.

As for Video, Nvidia Quadro cards and ATI Fire GL cards are the way to go with 256MB-512MB of RAM for a new science imaging analysis workstation. We build all our own workstations here with Quadros (FX 1500 and FX 3450s mainly) and use RAID striped drives 2-4 disks (500GB to 1TB each disk) we place 4GB RAM (XP) -16GB RAM (Vista). We also use Intel boards for our single processor systems(2-4core) and Supermicro boards for our dual processor machines (4-8cores). We stopped using AMD CPUs about 3 years ago in favor of Intel. We also use 600W to 800W power supplies to feed these systems.

Hope this helps.

Cheers,

Jonathan M. Ekman

Imaging Technology Group

Beckman Institute for Advanced Science and Technology

University of Illinois at Urbana-Champaign

405 N. Mathews Avenue

Urbana, IL 61801 USA

Tel: 217-244-6292

Fax: 217-244-6219

From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Christophe Leterrier
Sent: Monday, September 22, 2008 3:33 AM
To: [hidden email]
Subject: Advice for offline image analysis computer

Craig Brideau

Re: Advice for offline image analysis computer

We use Mac Pros with eight cores. Mine dual-boots into WinXP and in this mode it works quite beautifully with Matlab, ImageJ, and Zemax (an optical modeling program). We also have a few in-house utilities for Mac (works with Tiger or Leopard) called ImageTrak and MasterlabDB for image analysis (ala ImageJ but better for our use) and Database management. Again these run quite well on the Mac Pro. Leopard is 64 bit native, but I'm using XP32 at the moment. If I get more RAM in my machine (current only 4GB) then I'd need to switch to XP64, or hopefully Windows 7 when it eventually comes out will be native 64 bit.

Craig

On Mon, Sep 22, 2008 at 9:42 AM, Jon Ekman <[hidden email]> wrote:

I would recommend the Vista 64bit, 8 core with an Open GL "workstation grade" video card and 16GB of RAM. Eventually the software you use will grow into multi-core processing. Ignore the GPU options they are mainly for 3D graphics and games.

As for Video, Nvidia Quadro cards and ATI Fire GL cards are the way to go with 256MB-512MB of RAM for a new science imaging analysis workstation. We build all our own workstations here with Quadros (FX 1500 and FX 3450s mainly) and use RAID striped drives 2-4 disks (500GB to 1TB each disk) we place 4GB RAM (XP) -16GB RAM (Vista). We also use Intel boards for our single processor systems(2-4core) and Supermicro boards for our dual processor machines (4-8cores). We stopped using AMD CPUs about 3 years ago in favor of Intel. We also use 600W to 800W power supplies to feed these systems.

Hope this helps.

Cheers,

Jonathan M. Ekman

Imaging Technology Group

Beckman Institute for Advanced Science and Technology

University of Illinois at Urbana-Champaign

405 N. Mathews Avenue

Urbana, IL 61801 USA

Tel: 217-244-6292

Fax: 217-244-6219

From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Christophe Leterrier
Sent: Monday, September 22, 2008 3:33 AM

To: [hidden email]

Subject: Advice for offline image analysis computer

Dear listers,

I have to buy a new computer for our team that will be used as for offline image analysis. The software required (ImageJ, Metamorph, Matlab) require to build a Windows/Vista machine. The cost would be around $5,000 / 5000€. The job would be processing (a lot) and rendering. My questions are :
- Should I go for a "traditionnal" computer, I mean a 32-bits, dual core, XP computer with maxed RAM (I guess it is 3GB or so) ? Is it usefull to go to more fancy stuff like 64 bits, 4 or 8 core, 8 to 16GB RAM machine ? Would ImageJ/Metamorph/Matlab really benefit from it (I would love to have an answer from the Metamorph/Matlab people) ?
- What about graphic cards and GPU ? What is the best choice ? I've heard about new strategies to speed up processing by making the GPU churn data as well as graphics, but I don't think it is really commercially available now or implemented in commercial software yet.

Thanks for your advices !

Christophe

Gabriel Lapointe

Re: Advice for offline image analysis computer

In reply to this post by Jon Ekman-2

Personnally, I would go for a 64bit OS (Linux, OSX, XP64) but I would avoid Vista at all cost. The system requirement for Vista is too high for an efficient image analysis station. Remember that the 2 gig of ram required for Vista to run semi-smoothly will not be available for image processing. A high end Mac could also be a good machine, with bootcamp for the windows only software, but (unless things changed in recent years) they are not upgradable so forget about adding a new hard-drive or adding more memory afterward.

ImageJ, Mathlab, Huygens and BioimageXD all run natively on Linux. (which has minimal system requirement less than 128 meg of ram), thus leaving plenty of room to work with those big stack. 64 bit Linux is also more stable than XP64 and it is easier to find drivers. Methamorph, Imaris and Volocity, could then be used either with a virtual machine or dual boot when required.

I would say that the importance of RAM > CPU > GPU = HD.

More and more high end software can make use of those extra CPU core so don't be shy to buy a quad core (or more) if you can but I would take those with the biggest L1 cache, it will become a bottleneck faster than the clock for big data set.

RAM should be numerous and fast (800MHz) and get a high bus speed.

Gabriel

Jon Ekman wrote:

I would recommend the Vista 64bit, 8 core with an Open GL “workstation grade” video card and 16GB of RAM. Eventually the software you use will grow into multi-core processing. Ignore the GPU options they are mainly for 3D graphics and games.

As for Video, Nvidia Quadro cards and ATI Fire GL cards are the way to go with 256MB-512MB of RAM for a new science imaging analysis workstation. We build all our own workstations here with Quadros (FX 1500 and FX 3450s mainly) and use RAID striped drives 2-4 disks (500GB to 1TB each disk) we place 4GB RAM (XP) -16GB RAM (Vista). We also use Intel boards for our single processor systems(2-4core) and Supermicro boards for our dual processor machines (4-8cores). We stopped using AMD CPUs about 3 years ago in favor of Intel. We also use 600W to 800W power supplies to feed these systems.

Hope this helps.

Cheers,

Jonathan M. Ekman

Imaging Technology Group

Beckman Institute for Advanced Science and Technology

University of Illinois at Urbana-Champaign

405 N. Mathews Avenue

Urbana, IL 61801 USA

Tel: 217-244-6292

Fax: 217-244-6219

From: Confocal Microscopy List [[hidden email]] On Behalf Of Christophe Leterrier
Sent: Monday, September 22, 2008 3:33 AM
To: [hidden email]
Subject: Advice for offline image analysis computer

Dear listers,

I have to buy a new computer for our team that will be used as for offline image analysis. The software required (ImageJ, Metamorph, Matlab) require to build a Windows/Vista machine. The cost would be around $5,000 / 5000€. The job would be processing (a lot) and rendering. My questions are :
- Should I go for a "traditionnal" computer, I mean a 32-bits, dual core, XP computer with maxed RAM (I guess it is 3GB or so) ? Is it usefull to go to more fancy stuff like 64 bits, 4 or 8 core, 8 to 16GB RAM machine ? Would ImageJ/Metamorph/Matlab really benefit from it (I would love to have an answer from the Metamorph/Matlab people) ?
- What about graphic cards and GPU ? What is the best choice ? I've heard about new strategies to speed up processing by making the GPU churn data as well as graphics, but I don't think it is really commercially available now or implemented in commercial software yet.

Thanks for your advices !

Christophe

mahogny

Re: Advice for offline image analysis computer

Gabriel Lapointe wrote:

> Personnally, I would go for a 64bit OS (Linux, OSX, XP64) but I would
> avoid Vista at all cost. The system requirement for Vista is too high
> for an efficient image analysis station. Remember that the 2 gig of ram
> required for Vista to run semi-smoothly will not be available for image
> processing. A high end Mac could also be a good machine, with bootcamp
> for the windows only software, but (unless things changed in recent
> years) they are not upgradable so forget about adding a new hard-drive
> or adding more memory afterward.
>
> ImageJ, Mathlab, Huygens and BioimageXD all run natively on Linux.
> (which has minimal system requirement less than 128 meg of ram
> <http://www.debian.org/releases/stable/amd64/ch03s04.html.en>), thus
> leaving plenty of room to work with those big stack. 64 bit Linux is
> also more stable than XP64 and it is easier to find drivers. Methamorph,
> Imaris and Volocity, could then be used either with a virtual machine or
> dual boot when required.
>

I second the linux recommendation as well. I have upgraded osx machines
(G4 & intel) and seen
noticeable speed-ups. for example it is now possible to play modern
movies on the g4. the amount
windows and osx waste by just sitting there is just crazy.

you can run both windows, linux & osx on a mac machine but they cost
insanely and you can barely
upgrade them. only advantage is that you can be sure they work well (the
hardware that is, not osx).

/Johan

Rosemary.White

Re: Advice for offline image analysis computer

In reply to this post by Craig Brideau

Hi Craig,
So, no compromises on performance running WinXP on the MacPro?
thanks,
Rosemary

-----Original Message-----
From: Confocal Microscopy List on behalf of Craig Brideau
Sent: Tue 9/23/2008 3:56 AM
To: [hidden email]
Cc:
Subject: Re: Advice for offline image analysis computer

We use Mac Pros with eight cores. Mine dual-boots into WinXP and in this
mode it works quite beautifully with Matlab, ImageJ, and Zemax (an optical
modeling program). We also have a few in-house utilities for Mac (works
with Tiger or Leopard) called ImageTrak and MasterlabDB for image analysis
(ala ImageJ but better for our use) and Database management. Again these
run quite well on the Mac Pro. Leopard is 64 bit native, but I'm using XP32
at the moment. If I get more RAM in my machine (current only 4GB) then I'd
need to switch to XP64, or hopefully Windows 7 when it eventually comes out
will be native 64 bit.

Craig

On Mon, Sep 22, 2008 at 9:42 AM, Jon Ekman <[hidden email]> wrote:

> I would recommend the Vista 64bit, 8 core with an Open GL "workstation
> grade" video card and 16GB of RAM. Eventually the software you use will grow
> into multi-core processing. Ignore the GPU options they are mainly for 3D
> graphics and games.
>
>
>
> As for Video, Nvidia Quadro cards and ATI Fire GL cards are the way to go
> with 256MB-512MB of RAM for a new science imaging analysis workstation. We
> build all our own workstations here with Quadros (FX 1500 and FX 3450s
> mainly) and use RAID striped drives 2-4 disks (500GB to 1TB each disk) we
> place 4GB RAM (XP) -16GB RAM (Vista). We also use Intel boards for our
> single processor systems(2-4core) and Supermicro boards for our dual
> processor machines (4-8cores). We stopped using AMD CPUs about 3 years ago
> in favor of Intel. We also use 600W to 800W power supplies to feed these
> systems.
>
>
>
> Hope this helps.
>
>
>
> Cheers,
>
>
>
> Jonathan M. Ekman
>
> Imaging Technology Group
>
> Beckman Institute for Advanced Science and Technology
>
> University of Illinois at Urbana-Champaign
>
> 405 N. Mathews Avenue
>
> Urbana, IL 61801 USA
>
> Tel: 217-244-6292
>
> Fax: 217-244-6219
>
>
>
>
>
> *From:* Confocal Microscopy List [mailto:[hidden email]]
> *On Behalf Of *Christophe Leterrier
> *Sent:* Monday, September 22, 2008 3:33 AM
> *To:* [hidden email]
> *Subject:* Advice for offline image analysis computer
>
>
>
> Dear listers,
>
> I have to buy a new computer for our team that will be used as for offline
> image analysis. The software required (ImageJ, Metamorph, Matlab) require to
> build a Windows/Vista machine. The cost would be around $5,000 / 5000€. The
> job would be processing (a lot) and rendering. My questions are :
> - Should I go for a "traditionnal" computer, I mean a 32-bits, dual core,
> XP computer with maxed RAM (I guess it is 3GB or so) ? Is it usefull to go
> to more fancy stuff like 64 bits, 4 or 8 core, 8 to 16GB RAM machine ? Would
> ImageJ/Metamorph/Matlab really benefit from it (I would love to have an
> answer from the Metamorph/Matlab people) ?
> - What about graphic cards and GPU ? What is the best choice ? I've heard
> about new strategies to speed up processing by making the GPU churn data as
> well as graphics, but I don't think it is really commercially available now
> or implemented in commercial software yet.
>
> Thanks for your advices !
>
> Christophe
>

Craig Brideau

Re: Advice for offline image analysis computer

No performance slowdown whatsoever; Mac has gone with Intel processors now, so XP runs natively even though it's 'mac' hardware. A little driver CD comes with the machine to help you install XP:

Step 1, make sure you have the driver CD (comes with your mac)
Step 2, make sure you have a copy of windows XP (32 or 64 bit -pick one)
Step 3, run bootcamp (either comes with your mac under utilities somewhere or you can download it from the mac site)
Step 4, Install windows XP; this is where you need that driver CD. When the 'found new hardware wizard' comes up looking for motherboard and video card drivers just point it at this driver CD. It even installs a function so that your mac keyboard and mouse will work properly with all the buttons enabled. (This is important since the DVD drive eject button is only on the keyboard!)

During the Bootcamp install the system will let you partition your HD into Leopard and Windows partitions (default is a 50/50 split but you can change this during setup).
Once you're done with bootcamp and have installed windows on the new partition you can choose to boot into either Windows or Leopard. When you boot, hold down the 'option' key and a screen appears which lets you select what partition you want to boot from; one Windows, the other Leopard. It's also possible to add Linux, although there's a couple other steps to get this to work. Check around on the web first for Linux tips if you choose to go that route.

I strongly suggest printing out the help document that comes with bootcamp before you do the install. It has a step-by-step procedure in it you should follow closely.

Craig

On Mon, Sep 22, 2008 at 4:19 PM, <[hidden email]> wrote:

Hi Craig,
So, no compromises on performance running WinXP on the MacPro?
thanks,
Rosemary

-----Original Message-----
From: Confocal Microscopy List on behalf of Craig Brideau
Sent: Tue 9/23/2008 3:56 AM
To: [hidden email]

Cc:
Subject: Re: Advice for offline image analysis computer

We use Mac Pros with eight cores. Mine dual-boots into WinXP and in this
mode it works quite beautifully with Matlab, ImageJ, and Zemax (an optical
modeling program). We also have a few in-house utilities for Mac (works
with Tiger or Leopard) called ImageTrak and MasterlabDB for image analysis
(ala ImageJ but better for our use) and Database management. Again these
run quite well on the Mac Pro. Leopard is 64 bit native, but I'm using XP32
at the moment. If I get more RAM in my machine (current only 4GB) then I'd
need to switch to XP64, or hopefully Windows 7 when it eventually comes out
will be native 64 bit.

Craig

On Mon, Sep 22, 2008 at 9:42 AM, Jon Ekman <[hidden email]> wrote:

> I would recommend the Vista 64bit, 8 core with an Open GL "workstation
> grade" video card and 16GB of RAM. Eventually the software you use will grow
> into multi-core processing. Ignore the GPU options they are mainly for 3D
> graphics and games.
>
>
>
> As for Video, Nvidia Quadro cards and ATI Fire GL cards are the way to go
> with 256MB-512MB of RAM for a new science imaging analysis workstation. We
> build all our own workstations here with Quadros (FX 1500 and FX 3450s
> mainly) and use RAID striped drives 2-4 disks (500GB to 1TB each disk) we
> place 4GB RAM (XP) -16GB RAM (Vista). We also use Intel boards for our
> single processor systems(2-4core) and Supermicro boards for our dual
> processor machines (4-8cores). We stopped using AMD CPUs about 3 years ago
> in favor of Intel. We also use 600W to 800W power supplies to feed these
> systems.
>
>
>
> Hope this helps.
>
>
>
> Cheers,
>
>
>
> Jonathan M. Ekman
>
> Imaging Technology Group
>
> Beckman Institute for Advanced Science and Technology
>
> University of Illinois at Urbana-Champaign
>
> 405 N. Mathews Avenue
>
> Urbana, IL 61801 USA
>
> Tel: 217-244-6292
>
> Fax: 217-244-6219
>
>
>
>
>
> *From:* Confocal Microscopy List [mailto:[hidden email]]
> *On Behalf Of *Christophe Leterrier
> *Sent:* Monday, September 22, 2008 3:33 AM
> *To:* [hidden email]
> *Subject:* Advice for offline image analysis computer
>
>
>
> Dear listers,
>
> I have to buy a new computer for our team that will be used as for offline
> image analysis. The software required (ImageJ, Metamorph, Matlab) require to
> build a Windows/Vista machine. The cost would be around $5,000 / 5000€. The
> job would be processing (a lot) and rendering. My questions are :
> - Should I go for a "traditionnal" computer, I mean a 32-bits, dual core,
> XP computer with maxed RAM (I guess it is 3GB or so) ? Is it usefull to go
> to more fancy stuff like 64 bits, 4 or 8 core, 8 to 16GB RAM machine ? Would
> ImageJ/Metamorph/Matlab really benefit from it (I would love to have an
> answer from the Metamorph/Matlab people) ?
> - What about graphic cards and GPU ? What is the best choice ? I've heard
> about new strategies to speed up processing by making the GPU churn data as
> well as graphics, but I don't think it is really commercially available now
> or implemented in commercial software yet.
>
> Thanks for your advices !
>
> Christophe
>

Craig Brideau

Re: Advice for offline image analysis computer

Oh, just remembered something regarding step 4; don't use 'found new hardware wizard'; the driver cd should pop up an installer when you put the disk in so use that.
Also, you might be wondering how you can open the CD drive to put in the driver disk for the CD drive opening button on the keyboard... In 'My Computer' right click on the DVD drive and choose 'eject' from the drop down menu to open the drive. @:-)

Craig

On Mon, Sep 22, 2008 at 5:26 PM, Craig Brideau <[hidden email]> wrote:

No performance slowdown whatsoever; Mac has gone with Intel processors now, so XP runs natively even though it's 'mac' hardware. A little driver CD comes with the machine to help you install XP:

Step 1, make sure you have the driver CD (comes with your mac)
Step 2, make sure you have a copy of windows XP (32 or 64 bit -pick one)
Step 3, run bootcamp (either comes with your mac under utilities somewhere or you can download it from the mac site)
Step 4, Install windows XP; this is where you need that driver CD. When the 'found new hardware wizard' comes up looking for motherboard and video card drivers just point it at this driver CD. It even installs a function so that your mac keyboard and mouse will work properly with all the buttons enabled. (This is important since the DVD drive eject button is only on the keyboard!)

During the Bootcamp install the system will let you partition your HD into Leopard and Windows partitions (default is a 50/50 split but you can change this during setup).
Once you're done with bootcamp and have installed windows on the new partition you can choose to boot into either Windows or Leopard. When you boot, hold down the 'option' key and a screen appears which lets you select what partition you want to boot from; one Windows, the other Leopard. It's also possible to add Linux, although there's a couple other steps to get this to work. Check around on the web first for Linux tips if you choose to go that route.

I strongly suggest printing out the help document that comes with bootcamp before you do the install. It has a step-by-step procedure in it you should follow closely.

Craig

On Mon, Sep 22, 2008 at 4:19 PM, <[hidden email]> wrote:
Hi Craig,
So, no compromises on performance running WinXP on the MacPro?
thanks,
Rosemary

-----Original Message-----
From: Confocal Microscopy List on behalf of Craig Brideau
Sent: Tue 9/23/2008 3:56 AM
To: [hidden email]

Cc:
Subject: Re: Advice for offline image analysis computer

We use Mac Pros with eight cores. Mine dual-boots into WinXP and in this
mode it works quite beautifully with Matlab, ImageJ, and Zemax (an optical
modeling program). We also have a few in-house utilities for Mac (works
with Tiger or Leopard) called ImageTrak and MasterlabDB for image analysis
(ala ImageJ but better for our use) and Database management. Again these
run quite well on the Mac Pro. Leopard is 64 bit native, but I'm using XP32
at the moment. If I get more RAM in my machine (current only 4GB) then I'd
need to switch to XP64, or hopefully Windows 7 when it eventually comes out
will be native 64 bit.

Craig

On Mon, Sep 22, 2008 at 9:42 AM, Jon Ekman <[hidden email]> wrote:

> I would recommend the Vista 64bit, 8 core with an Open GL "workstation
> grade" video card and 16GB of RAM. Eventually the software you use will grow
> into multi-core processing. Ignore the GPU options they are mainly for 3D
> graphics and games.
>
>
>
> As for Video, Nvidia Quadro cards and ATI Fire GL cards are the way to go
> with 256MB-512MB of RAM for a new science imaging analysis workstation. We
> build all our own workstations here with Quadros (FX 1500 and FX 3450s
> mainly) and use RAID striped drives 2-4 disks (500GB to 1TB each disk) we
> place 4GB RAM (XP) -16GB RAM (Vista). We also use Intel boards for our
> single processor systems(2-4core) and Supermicro boards for our dual
> processor machines (4-8cores). We stopped using AMD CPUs about 3 years ago
> in favor of Intel. We also use 600W to 800W power supplies to feed these
> systems.
>
>
>
> Hope this helps.
>
>
>
> Cheers,
>
>
>
> Jonathan M. Ekman
>
> Imaging Technology Group
>
> Beckman Institute for Advanced Science and Technology
>
> University of Illinois at Urbana-Champaign
>
> 405 N. Mathews Avenue
>
> Urbana, IL 61801 USA
>
> Tel: 217-244-6292
>
> Fax: 217-244-6219
>
>
>
>
>
> *From:* Confocal Microscopy List [mailto:[hidden email]]
> *On Behalf Of *Christophe Leterrier
> *Sent:* Monday, September 22, 2008 3:33 AM
> *To:* [hidden email]
> *Subject:* Advice for offline image analysis computer
>
>
>
> Dear listers,
>
> I have to buy a new computer for our team that will be used as for offline
> image analysis. The software required (ImageJ, Metamorph, Matlab) require to
> build a Windows/Vista machine. The cost would be around $5,000 / 5000€. The
> job would be processing (a lot) and rendering. My questions are :
> - Should I go for a "traditionnal" computer, I mean a 32-bits, dual core,
> XP computer with maxed RAM (I guess it is 3GB or so) ? Is it usefull to go
> to more fancy stuff like 64 bits, 4 or 8 core, 8 to 16GB RAM machine ? Would
> ImageJ/Metamorph/Matlab really benefit from it (I would love to have an
> answer from the Metamorph/Matlab people) ?
> - What about graphic cards and GPU ? What is the best choice ? I've heard
> about new strategies to speed up processing by making the GPU churn data as
> well as graphics, but I don't think it is really commercially available now
> or implemented in commercial software yet.
>
> Thanks for your advices !
>
> Christophe
>

Adrian Smith-6

Re: Advice for offline image analysis computer

In reply to this post by Gabriel Lapointe

On 23/09/2008, at 5:38 AM, Gabriel Lapointe wrote:

> A high end Mac could also be a good machine, with bootcamp for the
> windows only software, but (unless things changed in recent years)
> they are not upgradable so forget about adding a new hard-drive or
> adding more memory afterward.

It has long been possible to upgrade "high-end" Macs. Hard-drives and
memory have not been a problem. It is the consumer level machines (eg
iMacs) that are more difficult (and even then you can almost alway add
extra RAM but not necessarily hard drives unless you want to get very
intimate with the service manual or the mod-pages on the web :).

The extent to which you can add extra hardware has varied over the
years and is generally not as extensive as a generic wintel box but it
is certainly been there ( eg G5 PowerMacs could only take two drives
whereas the G4s before then and Mac Pro after can take more (I've got
a processor upgrade, upgraded optical drives, three hard drives and
extra RAM in my c2000 G4)). It has been physically easy to access Mac
"tower" machines for at least 10 years.

Regards,

Adrian Smith
Centenary Institute, Sydney, Australia

Martin Spitaler

Re: Advice for offline image analysis computer

In reply to this post by lechristophe

Dear Christophe,

you got a lot of replies already, just a few details that are still missing:

- WinXP-64 in combination with 16GB RAM really makes the difference between
work and crash if you open seriously large image files, and it even helps
with software that doesn't actually support it (because then Windows puts
the page file in the memory beyond 3GB instead of the harddrive, which is
obviously much faster). But be aware, some software simply doesn't run on
WindXP-64, e.g. ironically the Leica confocal software and Zeiss ZEN (the
old LSM software works fine!!).

- Even if many programs don't support multiple processors, it is extremely
useful as soon as you use more that one program at the same time: Windows
will assign different processors to different programs, so you can easily do
3D rendering or whatever analysis while doing deconvolution in the
background (as long as RAM and harddrive speed are sufficient).

- Don't forget the harddrives, when you handle GBytes of data that becomes
limiting. We use RAID 0 for that, so almost double read / write speed (but
don't store any data there without backup, it also doubles the risk of disk
failure!).

Good luck,

Martin

################################
Martin Spitaler, PhD

FILM - Facility for Imaging by Light Microscopy
- Facility Manager -
Sir Alexander Fleming Building, desk 401
Imperial College London / South Kensington
Exhibition Road
London SW7 2AZ
UK

Tel. +44-(0)20-759-42023
E-mail [hidden email]
Website: http://imperial.ac.uk/imagingfacility

Craig Brideau

Re: Advice for offline image analysis computer

Does anyone use those SAS hard drives in their machines? I'm just using SATA; I was wondering if SAS was a substantial improvement (i.e. worth the extra cost)?

Craig

On Tue, Sep 23, 2008 at 11:34 AM, Martin Spitaler <[hidden email]> wrote:

Dear Christophe,

you got a lot of replies already, just a few details that are still missing:

- WinXP-64 in combination with 16GB RAM really makes the difference between
work and crash if you open seriously large image files, and it even helps
with software that doesn't actually support it (because then Windows puts
the page file in the memory beyond 3GB instead of the harddrive, which is
obviously much faster). But be aware, some software simply doesn't run on
WindXP-64, e.g. ironically the Leica confocal software and Zeiss ZEN (the
old LSM software works fine!!).

- Even if many programs don't support multiple processors, it is extremely
useful as soon as you use more that one program at the same time: Windows
will assign different processors to different programs, so you can easily do
3D rendering or whatever analysis while doing deconvolution in the
background (as long as RAM and harddrive speed are sufficient).

- Don't forget the harddrives, when you handle GBytes of data that becomes
limiting. We use RAID 0 for that, so almost double read / write speed (but
don't store any data there without backup, it also doubles the risk of disk
failure!).

Good luck,

Martin

################################
Martin Spitaler, PhD

FILM - Facility for Imaging by Light Microscopy
- Facility Manager -
Sir Alexander Fleming Building, desk 401
Imperial College London / South Kensington
Exhibition Road
London SW7 2AZ
UK

Tel. +44-(0)20-759-42023
E-mail [hidden email]
Website: http://imperial.ac.uk/imagingfacility