graphic cards
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An alternative CUDA is OpenCL. Interestingly, OpenCL will be implemented in the next major upgrade of MacOS X, Snow Leopard, and how easily imaging apps can utilize OpenCL depends on how it is implemented. Hopefully, Snow Leopard has an OpenCL frame work which makes it so much easier for any apps to take advantage of GPGPU. There is one thing though. I wonder how hot my MBP will be when it is fully utilizing GPU.
Aki Hoji University of Pittsburgh On Aug 14, 2008, at 6:26 PM, Nowell, Cameron wrote: Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal |
 
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Scott.Young |
Re: question for Leica SP5 users - followup
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In reply to this post by Aryeh Weiss
I would like to provide what Leica Microsystems recommends to its confocal
users regarding networking and third party software: Computers used by multiple users or with connections to the internet are often targeted by viruses and other harmful exploits from intruders. The installation and regular update of virus scanners, firewalls and operating system upgrades and hotfixes is a good practice to avoid system damages and loss or corruption of data. The confocal software, LAS AF, installed from Leica Microsystems does not require any particular protection software. Although we do not recommend installation of third party software, the confocal software will run with most of the commonly available antivirus and third party software products. The variety of third party software is large and updates and hotfixes for the third party software are provided regularly. A guarantee that each available update, virus scanner or firewall will be compatible with software from Leica Microsystems cannot be given and we therefore recommend the following: The confocal workstation is designed and built to drive the confocal hardware attached. It is not designed to be a personal PC. We recommend that you do not connect to the Internet (WWW) with the confocal system workstation. However, the system can be networked to allow data transfer from the workstation to peripheral workstations. Networks vary with regard to structure and configuration. If you need further information on networking your confocal system workstation please contact your network administrator. We do not recommend installation of third party software on the confocal workstation. We can not test the compatibility of all third party software and updates of hotfixes with the software driving the confocal system. From Leica Microsystems CMS GmbH there will be the recommendation to install all available updates and hotfixes from Microsoft. Upgrades like “Service Packs” should only be installed after confirmation from Leica Microsystems. Virus scanners and firewalls must be tried out; we have no special recommendation for preference. The confocal system is guaranteed to perform to specifications only in the original state it was delivered and installed. If third party software (image analysis, antivirus, etc) is required we can not guarantee that the system will perform to specifications. In case of unacceptable results to the confocal system after installation of a third party software we recommend removal of the software or update/hotfix separately to restore functionality to the system. All antivirus software installed must be prevented from “Live” scanning the confocal system working directories: Firewalls must allow full access for the confocal system network connection. If you have further questions regarding networking or third party software installation, please contact your local Leica Microsystems Sales or Service Representative. ____________________________________________ Scott Young Product Manager SP5 Confocal Systems Leica Microsystems CMS GmbH Am Friedensplatz 3 | 68165 Mannheim (Germany) Phone : +49 621 7028 1151 | Fax : +49 621 7028 2780 Cell: +49 172 729 34 17 Leica Microsystems CMS GmbH | GmbH mit Sitz in Wetzlar | Amtsgericht Wetzlar HRB 2432 Geschäftsführer : Dr. Stefan Traeger | Dr. David R. Martyr | Colin Davis | Dr. Wolf-Otto Reuter E-Mail: [hidden email] Confocal Microscopy List <[hidden email]> wrote on 15.08.2008 09:29:13: > Search the CONFOCAL archive at > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal > > I have received many replies to this -- most of them off list. So > first, thank > you to the many Leica users who replied. There are too many (and > more coming > in, to reply personally to everyone who wrote, but it is greatly appreciated. > > The consensus of the replies (so far about a dozen replies) is that one must > exercise care, but most everyone who wrote has added something to > their system > (usually ImageJ, admin utilities, and similar). Most have their computer > networked, with some antivirus. None appear to have been ordered by > Leica not to > put anything on their machine, but Leica did recommend (at least > to some)that > other programs not be added. > > One responder asked why we would want to add anything. We of course do > intend to turn this into a general use computer, but there are some additions > that I consider important. I should add that we have not yet received the > machine -- the rep had visited to inspect the installation site, and > apparently > he wanted to "lay down the law". So I am not sure exactly what it included in > the Leica software installation. > > 1. A compression utility, such as WINZIP. Last time I saw the Leica image > format, it was uncompressed. Lossless LZW compression can save > 30-50%, depending > on the images, and even more if you have two channels stored in > uncompressed RGB > (becasue the third channel is identically zero). The datasets can be very > large, and transferring compressed files can save time. > > 2. ImageJ + bioformats plugin. We prefer this to the utilities that the > manufacturers sometimes provide to read their special formats. We often put > ImageJ+appropriate plugins onto data DVDs that we burn. It saves > time because > the users have something with which they can read their files. We > can tell them > to install ImageJ at their end until we are blue in the face -- it > is easier to > just give them a working copy. > > 3. Network -- I prefer to leave a machine which is dedicated to > running hardware > off of the network. However, if Leica is anyway going to make us > connect it to > the network, then I want to use that to transfer intermediate sized data > (too small to justify burning a DVD, too large for a flashdisk). I > know DVDs are > cheap, but there are ecological considerations... BTW -- a few responses > mentioned that they are running antivirus software without problems. > > 4. Someone warned against installing Microscoft office on the system. I would > extend this warning any Microsoft software. They apparently believe > that it is > ok for software to fiddle with system files, drivers, whatever. However, > OpenOffice would be nice, mainly for being able to conveniently make > notes about > the system or the experiment. > > 5. Finally, we may want to put some tracking or auditing software on > the system. > > Someone asked if we were talking about an SPE, because that system has real > restrictions on its OS. I can assure you all that are talking about an SP5. > > --aryeh > -- > Aryeh Weiss > School of Engineering > Bar Ilan University > Ramat Gan 52900 Israel > > Ph: 972-3-5317638 > FAX: 972-3-7384050 ______________________________________________________________________ This email has been scanned by the MessageLabs Email Security System. For more information please visit http://www.messagelabs.com/email ______________________________________________________________________ |
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In reply to this post by Marc Thibault
Search the CONFOCAL archive at
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OK, maybe I'm iggerant, but what on earth is 'folding at
home'?
Guy
Optical Imaging Techniques in Cell Biology From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of aki hoji Sent: Saturday, 16 August 2008 12:45 AM To: [hidden email] Subject: Re: graphic cards Aki Hoji
University of Pittsburgh
On Aug 14, 2008, at 6:26 PM, Nowell, Cameron wrote: Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal No virus found in this incoming message. No virus found in this outgoing message. |
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Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Folding at home (http://folding.stanford.edu/) is a drisributed computing system that is used to study protein folding. Each user signs up and installs a client on their PC. Then when their PC is inactive the client crunchs through downloaded datasets. They have just released a client that now uses the extra power of the graphics card to crunch the data. Cheers Cam ________________________________ From: Confocal Microscopy List on behalf of Guy Cox Sent: Sat 16/08/2008 5:09 AM To: [hidden email] Subject: Re: graphic cards Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal OK, maybe I'm iggerant, but what on earth is 'folding at home'? Guy Optical Imaging Techniques in Cell Biology by Guy Cox CRC Press / Taylor & Francis http://www.guycox.com/optical.htm ______________________________________________ Associate Professor Guy Cox, MA, DPhil(Oxon) Electron Microscope Unit, Madsen Building F09, University of Sydney, NSW 2006 ______________________________________________ Phone +61 2 9351 3176 Fax +61 2 9351 7682 Mobile 0413 281 861 ______________________________________________ http://www.guycox.net <http://www.guycox.net/> ________________________________ From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of aki hoji Sent: Saturday, 16 August 2008 12:45 AM To: [hidden email] Subject: Re: graphic cards Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal An alternative CUDA is OpenCL. Interestingly, OpenCL will be implemented in the next major upgrade of MacOS X, Snow Leopard, and how easily imaging apps can utilize OpenCL depends on how it is implemented. Hopefully, Snow Leopard has an OpenCL frame work which makes it so much easier for any apps to take advantage of GPGPU. There is one thing though. I wonder how hot my MBP will be when it is fully utilizing GPU. Aki Hoji University of Pittsburgh On Aug 14, 2008, at 6:26 PM, Nowell, Cameron wrote: Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal You are spot on. The only software i know of that uses a GPU for analysis is the GPU client for the folding at home project. Now this raises a very interesting issue. Folding at home uses the Nvidia CUDA language to run applications on the GPU. The GPU has a much faster floating point unit so therefore can crunch raw data more efficently. For example when running the CPU version of the folding at home client on my dual core 2.8Ghz 12MB cache CPU i get around 100 iterations per second, but when i change over to the GPU version runnign through 2 512MB 8800GTX nvidia cards i get around 2000 iterations per second. So GPU are great for crunching data if the program is written for them. Sadly though there are no imaging apps yet that take advantage of this, in the future i am sure there will be. Cheers Cam ________________________________ From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Craig Brideau Sent: Friday, 15 August 2008 5:46 AM To: [hidden email] Subject: Re: graphic cards Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal CPU speeds is something that could vary a lot even with the same application. It will depend on what you are doing. If you are just throwing around a pretty 3D model, the GPU will be doing the majority of the work. But if you start doing some analysis of that 3D model you will start to ramp up your CPU usage. The speed of your CPU will only affect how fast a set of data can be crunched, the amount of RAM in your machine will govern how big that data set can be. So if you are happy to wait a little, a low end CPU with lots of RAM would be a better combination. I was thinking mainly of analysis when I made my earlier comment that the GPU might not be used as much. So in terms of displaying the data, the GPU is king, but in performing actual statistics or the like on an image it's mainly the CPU that's doing the work, correct? Are you aware of software that uses the GPU for the actual analysis? Craig I am sure you can hit a bottleneck (CPU or GPU becoming the limit) with analysis software if you give it enough data. But as long as you have a decent mid to high range CPU, and while i have been an AMD fan boy for years that CPU should be a dual core Intel chip (something from the 9000 series with large cache memory would be good). Couple that with a good GPU board and you will be fine. Oh i guess one other thing is make sure the mother board is using the newer Intel P35 chipset as well. Really it comes down to how much money you have to spend and what you are trying to model/analyse. Cheers Cam From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Craig Brideau Sent: Thursday, 14 August 2008 1:03 PM To: [hidden email] Subject: Re: graphic cards Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal I wasn't aware of that the Olympus and Leica systems actually took advantage of GPUs. Any thoughts as to what sort of crunching they use them for? Given the tremendous variety of video cards, how would one go about matching optimal card to optimal software? At what point do you have to worry about basic CPU speeds as well? (i.e. GPU vs CPU mismatch...?) Craig On Wed, Aug 13, 2008 at 8:59 PM, Michael C. Wussow <[hidden email]> wrote: Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Hello, I have to completely agree with Cam. His comments are spot on and what we at Bitplane recommend to our customers. However, it is recommend that you check with the company that you are getting the software from just to make sure there are no incompatibilities between the software and the graphics card. If you want specific recommendations don't hesitate to contact us offline. Mike Bitplane Inc. Michael C. Wussow Vice President and General Manager Bitplane Inc. Cell Phone: 651-336-4600 Fax: 866-691-9112 Toll Free: 1-888-3D-BITPX (332-4879) Visit Our Web Site At: www.bitplane.com <http://www.bitplane.com/> -----Original Message----- From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Nowell, Cameron Sent: Wednesday, August 13, 2008 3:45 PM To: [hidden email] Subject: Re: graphic cards Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Hi List, I owuld like to disagree with Craig. There are now quite a few programs that use the graphics card to process 3D data in real time now. MetaMorph, Imaris, Volocity, 3D Studio, Olympus FV1000, Leica LAS AF just to name a few. There is an enourmous ammount of choice out there in the graphics card market, but my recomendation (and the recomendation of many other people) is to buy the best GAMING card you can afford. While each graphics card manuafacturer has "Workstation" class cards that cost a heap of money, these cards oare not really any better than a good gaming card. So avoid things like the Nvidia Quadro, ATI FirePro or Wildcat Studio type of cards. So you are going to need something like an Nvidia Geforce 280GTX or an ATI Radeon HD 4870. You will need at least 512MB of RAM on the card as well. Also these cards cost in the order of $500-600 US dollars. Now slapping a highend card in a lower end computer is not going to fix things either. To match the card you will need to have a good CPU (dual coe is fine, there are very, very few programs coded for more than 2 cores currently) and the more system RAM the better. If you are playing with large data sets (eg 2000 images per 3D stack) you will need to go beyond the maximum 4GB of RAM in a 32 bit system and go for a 64Bit system and put 16 or 32 GB RAM into it. Fast hardrives will always help a little bit but not too much. Also don't worry about going for a two graphics cards running togther (Nvidia SLI or ATI CrossFire), as far as i know there are no modeling programs out there yet that can leaverage both cards. Hope that helps you out, if you need any more help just let me know. Cheers Cam Cameron Nowell Research and Microscopy Imaging Core Peter MacCallum Cancer Centre Melbourne, Australia ________________________________ From: Confocal Microscopy List on behalf of Craig Brideau Sent: Thu 14/08/2008 6:16 AM To: [hidden email] Subject: Re: graphic cards Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Actually most image display and manipulation software uses your CPU rather than your GPU. The CPU does all the number crunching then hands the resulting data off to the GPU (video card) to display it. There are a handful of programs that will actually use the GPU instead, but they are few and far between as they require special programming. What sort of processor, video card, and how much RAM do you have in your computer? Craig On Wed, Aug 13, 2008 at 2:04 PM, Marc Thibault <[hidden email]> wrote: Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Hi all, I would like to know what are the best graphic cards to add in your PC for microscopic 3D image analysis and manipulation. Mine is currently not up to the task. Thanks Marc 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. No virus found in this incoming message. Checked by AVG - http://www.avg.com <http://www.avg.com/> Version: 8.0.138 / Virus Database: 270.6.2/1609 - Release Date: 13/08/2008 6:43 AM 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. 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. No virus found in this incoming message. Checked by AVG. Version: 7.5.526 / Virus Database: 270.6.3/1612 - Release Date: 14/08/2008 6:03 PM No virus found in this outgoing message. Checked by AVG. Version: 7.5.526 / Virus Database: 270.6.3/1612 - Release Date: 14/08/2008 6:03 PM 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. |
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In reply to this post by Guy Cox
Search the CONFOCAL archive at
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I believe the folding at home project is akin to
that of the SETI (search for extraterrestial life) project way back in the
90's/2000's? Basically whenever your computer is idle your computer takes the
time to fold a bit of some protein. I'm not too sure about the details and it
might need a graphics card to do so. The ATI card on my laptop appears to have
that function to do my bit for protein folding science. I must admit I've never
taken up the offer. Too many TSR programs on my computer as it is.
Elijah
Research Engineer
Optical BioImaging Group
Division of BioEngineering
National University of Singapore
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In reply to this post by Larry Tague
Search the CONFOCAL archive at
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I know that when working for both Nikon and Leica dealerships we were always told to use plain old purple Sparkle for lens cleaning by the respective factories.
Chris On Fri, Aug 15, 2008 at 9:08 AM, Philip Oshel <[hidden email]> wrote: Sparkle does indeed bleach if left in the sun. I discovered this accidentally, and the bleaching of the color has no effect on Sparkle's cleaning ability. -- Chris Tully Microscopy and Image Analysis Expert [hidden email] 240-888-1021 http://www.linkedin.com/in/christully |
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Steffen Dietzel |
Re: question for Leica SP5 users - followup
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In reply to this post by Aryeh Weiss
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Hi Aryeh and everybody, what Leica people told us was essentially: "Do what you want but don't blame us if the system dosn't work any more." So, my recommendation is, when the system is coming in, as the very first step, but certainly before hooking it up to the network or installing any third party software, make a complete system backup (e.g. with Acronis) and check that the backup is readable. That way, you can always go back to a stable version if necessary. The system usually comes with a backup-CD but we once had one that had a problem (not readable or different software version, I don't remember) Repeat a backup every time Leica-Software gets updated, so that you don't have to go back all the way if you really should once download an incompatible Windows patch. I know of two SP5s, one is hooked up to the internet with zonealarm and sophos antivir, it runs fine so far (no computer problems, that is). The other is isolated, in the days of affordable 4 GB USB sticks that also works out nicely. Conerning the warning about Microsoft software, I wonder how you are going to keep that up, given the operating system it is running on... :-) Concerning an Office application, you might want to have a look at http://portableapps.com/suite The portable apps are software that runs without (!) installation on the target computer, from a USB stick (name) or some disk directory. They include firefox and OpenOffice. They also have links to individual portable applications, i.e. without the "suite" user interface. Steffen At 09:29 15.08.2008, you wrote: >Search the CONFOCAL archive at >http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal > >I have received many replies to this -- most of >them off list. So first, thank you to the >many Leica users who replied. There are too >many (and more coming in, to reply personally >to everyone who wrote, but it is greatly appreciated. > >The consensus of the replies (so far about a >dozen replies) is that one must exercise care, >but most everyone who wrote has added something >to their system (usually ImageJ, admin >utilities, and similar). Most have their >computer networked, with some antivirus. None >appear to have been ordered by Leica not to put >anything on their machine, but Leica did >recommend (at least to some)that other programs not be added. > >One responder asked why we would want to add >anything. We of course do not intend to turn >this into a general use computer, but there are >some additions that I consider important. I >should add that we have not yet received the >machine -- the rep had visited to inspect the >installation site, and apparently he wanted to >"lay down the law". So I am not sure exactly >what it included in the Leica software installation. > >1. A compression utility, such as WINZIP. Last >time I saw the Leica image format, it was >uncompressed. Lossless LZW compression can save >30-50%, depending on the images, and even more >if you have two channels stored in uncompressed >RGB (becasue the third channel is identically >zero). The datasets can be very large, and >transferring compressed files can save time. > >2. ImageJ + bioformats plugin. We prefer this to >the utilities that the manufacturers sometimes >provide to read their special formats. We often >put ImageJ+appropriate plugins onto data >DVDs that we burn. It saves time because the >users have something with which they can read >their files. We can tell them to install ImageJ >at their end until we are blue in the face -- it >is easier to just give them a working copy. > >3. Network -- I prefer to leave a machine which >is dedicated to running hardware off of the >network. However, if Leica is anyway going to >make us connect it to the network, then I want >to use that to transfer intermediate sized data >sets (too small to justify burning a DVD, too >large for a flashdisk). I know DVDs are cheap, >but there are ecological considerations... BTW >-- a few responses mentioned that they are >running antivirus software without problems. > >4. Someone warned against installing Microscoft >office on the system. I would extend this >warning any Microsoft software. They apparently >believe that it is ok for software to fiddle >with system files, drivers, whatever. However, >OpenOffice would be nice, mainly for being able >to conveniently make notes about the system or the experiment. > >5. Finally, we may want to put some tracking or >auditing software on the system. > >Someone asked if we were talking about an SPE, >because that system has real restrictions on its >OS. I can assure you all that are talking about an SP5. > >--aryeh >-- >Aryeh Weiss >School of Engineering >Bar Ilan University >Ramat Gan 52900 Israel > >Ph: 972-3-5317638 >FAX: 972-3-7384050 -- --------------------------------------------------------------------------------------------------- Steffen Dietzel, PD Dr. rer. nat Ludwig-Maximilians-Universität München Walter-Brendel-Zentrum für experimentelle Medizin (WBex) Head of light microscopy Mail room (for letters etc.): Marchioninistr. 15, D-81377 München Building location and address for courier, parcel services etc: Marchioninistr. 27, D-81377 München (Großhadern) Phone: +49/89/2180-76509 Fax-to-email: +49/89/2180-9976509 skype: steffendietzel e-mail: [hidden email] |
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