graphic cards
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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 |
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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 |
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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. |
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I've learned that imaging software may be optimized for particular hardware, so the "best" specifications may not necessarily make your program run the fastest. I'd call the manufacturer of the application and ask them what their recommended CPU and graphics card configuration is.
-Esteban
On Wed, Aug 13, 2008 at 3:44 PM, Nowell, Cameron <[hidden email]> wrote: Search the CONFOCAL archive at -- G. Esteban Fernandez, Ph.D. Associate Director Molecular Cytology Core Facility University of Missouri 120 Bond Life Sciences Center Columbia, MO 65211 http://www.biotech.missouri.edu/mcc/ 573-882-4895 573-884-9395 fax |
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In reply to this post by Nowell, Cameron
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http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal On 14/08/2008, at 4:44 AM, Nowell, Cameron wrote: > 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. Here is a recent "value" analysis of gaming cards... http://www.dansdata.com/askdan00034.htm Adrian |
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In reply to this post by Nowell, Cameron
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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 -----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. |
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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: Hello, |
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The Olympus and Leica software only leverage the graphics card
for the 3D modelling part of their software. All other parts rely on the CPU
and RAM. While there are a large array of graphics cards out there, they
can basically be broken down into two groups Nvida GeForce and ATI Radeon.
There are heaps of variations of each of these but in the end they are all built
around the same core GPU unit. Some may be clocked slower, have less memory,
have slower memory or have parts of the GPU disabled, but they are essentially
all the same. Some software will work better on an ATI card vs Nvidia and visa
versa, but mostly it will just be a speed difference. You would be pretty unlucky
to get a bit of software that would crash constantly on one brand of card. 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 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 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? On Wed, Aug 13, 2008 at 8:59 PM, Michael C. Wussow <[hidden email]> wrote: Search the CONFOCAL archive at Hello,
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Search the CONFOCAL archive at
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Hello all -
A Coworker came to me today looking for a protocol for
tissue processing dsRED labeled leukocytes.
What fixatives are compatible with
dsRED? If we are only interested in the dsRED cells
do we need to fix the tissue?
Can we simply freeze fresh tissue in OCT and section?
Thank you for your time.
-Lars
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In reply to this post by Nowell, Cameron
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal This may be old news to everyone, but A.J. Funk has released an Optical Microscope Lens Cleaner version of Sparkle. http://www.bestcleaningproducts.com/shop/product.asp?prodID=3779 I am guessing it is the same thing as the purple Sparkle but without the dye that can leave a fluorescent residue. No commercial interest. Tom |
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In reply to this post by Nowell, Cameron
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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
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Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal We have been told by the Leica rep here that we may put no program on the SP5 computer -- not ImageJ, not Winzip, nothing. We were also told that the computer may not be connected to the network, except when they want to do service. To more exact, we were told that if we want anything on the machine, we need to ask Leica to do it (and to pay for it to be done). Is this how all the SP5 users out there are using their systems? Aside from the obvious reasons that this policy bothers us, we have a problem because the IT people in the university will not permit a computer to be connected to the network unless they have installed their approved anti-virus program personally. If the issue is delicate, perhaps you may prefer to reply off list. --aryeh -- Aryeh Weiss School of Engineering Bar Ilan University Ramat Gan 52900 Israel Ph: 972-3-5317638 FAX: 972-3-7384050 |
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http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal I think there is some confusion here. I think you are talking about the low-cost SPE, which runs a really cut-down OS. I don't think any of this applies to the SP5. 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 -----Original Message----- From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Aryeh Weiss Sent: Friday, 15 August 2008 6:17 AM To: [hidden email] Subject: question for Leica SP5 users Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal We have been told by the Leica rep here that we may put no program on the SP5 computer -- not ImageJ, not Winzip, nothing. We were also told that the computer may not be connected to the network, except when they want to do service. To more exact, we were told that if we want anything on the machine, we need to ask Leica to do it (and to pay for it to be done). Is this how all the SP5 users out there are using their systems? Aside from the obvious reasons that this policy bothers us, we have a problem because the IT people in the university will not permit a computer to be connected to the network unless they have installed their approved anti-virus program personally. If the issue is delicate, perhaps you may prefer to reply off list. --aryeh -- Aryeh Weiss School of Engineering Bar Ilan University Ramat Gan 52900 Israel Ph: 972-3-5317638 FAX: 972-3-7384050 No virus found in this incoming message. Checked by AVG. Version: 7.5.526 / Virus Database: 270.6.3/1610 - Release Date: 13/08/2008 4:14 PM No virus found in this outgoing message. Checked by AVG. Version: 7.5.526 / Virus Database: 270.6.3/1610 - Release Date: 13/08/2008 4:14 PM |
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In reply to this post by Craig Brideau
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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
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
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In reply to this post by Donnelly, Tom
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Yea, I saw the Funk new microscope objective cleaner, but we have been using the purple stuff for a long time on Zeiss and Nikon objectives with no problems.... of course I do dilute it 1 part Sparkle to 3 parts distilled water. I understand if you don't like the color, you can leave it in the sun for a day or so and it turns clear. Never tried that... not needed in my opinion. Larry Donnelly, Tom wrote: > Search the CONFOCAL archive at > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal > > This may be old news to everyone, but A.J. Funk has released an Optical Microscope Lens Cleaner version of Sparkle. http://www.bestcleaningproducts.com/shop/product.asp?prodID=3779 > > I am guessing it is the same thing as the purple Sparkle but without the dye that can leave a fluorescent residue. > > No commercial interest. > > Tom > -- Larry Tague Co-Investigator BBHSL* Co-Director of MECCA** Research Associate (Dept. of Physiology) University of Tennessee Health Science Center 894 Union Ave. Memphis, TN 38163 Phone Bus.: 901-448-7152 Phone FAX: 901-448-7126 e-mail:[hidden email] or [hidden email] *BBHSL "Building Bridges to Health Science Literacy" URL: http://bbhsl.mecca.org, a Science Education Partnership Award (SEPA). Supported by the National Center of Research Resources (NCRR) of the National Institutes of Health (NIH). **MECCA (Memphis Educational Computer Connectivity Alliance) URL: http://www.mecca.org/. Originally support by the National Science Foundation's "Networking Infrastructure or Education" program. CONFIDENTIALITY NOTICE: This email and any files transmitted with it are confidential and are intended solely for the use of the individual or entity to whom they are addressed. This communication may contain protected health information, or other legally privileged, confidential, or proprietary information. If you are not the intended recipient or the individual responsible for delivering the email to the recipient, please be advised that you have received this email in error and that any use, dissemination, forwarding, printing, or copying of this email is strictly prohibited. If you have received this email in error, please immediately notify the sender, disregard the foregoing message, and delete the message. We apologize for any inconvenience this may have caused. IMPORTANT NOTE: Confidential health information is protected by state and federal law, including, but not limited to, the Health Insurance Portability and Accountability Act of 1996 and related regulations. |
 
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Nowell, Cameron |
Re: question for Leica SP5 users
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In reply to this post by Guy Cox
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http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal We have an SP5 in our facility and the only thing we have been told by leica we can't do is connect it to a network, which is fine for us as the network here is notoriously unstable. We run our own anti-virus software and defrag utilities on it, as well as a few admin apps to track data usage etc. Cheers Cam Cameron Nowell Research and Microscopy Imaging Core Peter MacCallum Cancer Centre Melbourne, Australia -----Original Message----- From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Guy Cox Sent: Friday, 15 August 2008 8:10 AM To: [hidden email] Subject: Re: question for Leica SP5 users Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal I think there is some confusion here. I think you are talking about the low-cost SPE, which runs a really cut-down OS. I don't think any of this applies to the SP5. 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 -----Original Message----- From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Aryeh Weiss Sent: Friday, 15 August 2008 6:17 AM To: [hidden email] Subject: question for Leica SP5 users Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal We have been told by the Leica rep here that we may put no program on the SP5 computer -- not ImageJ, not Winzip, nothing. We were also told that the computer may not be connected to the network, except when they want to do service. To more exact, we were told that if we want anything on the machine, we need to ask Leica to do it (and to pay for it to be done). Is this how all the SP5 users out there are using their systems? Aside from the obvious reasons that this policy bothers us, we have a problem because the IT people in the university will not permit a computer to be connected to the network unless they have installed their approved anti-virus program personally. If the issue is delicate, perhaps you may prefer to reply off list. --aryeh -- Aryeh Weiss School of Engineering Bar Ilan University Ramat Gan 52900 Israel Ph: 972-3-5317638 FAX: 972-3-7384050 No virus found in this incoming message. Checked by AVG. Version: 7.5.526 / Virus Database: 270.6.3/1610 - Release Date: 13/08/2008 4:14 PM No virus found in this outgoing message. Checked by AVG. Version: 7.5.526 / Virus Database: 270.6.3/1610 - Release Date: 13/08/2008 4:14 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 Aryeh Weiss
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http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal I haven't checked with Leica but I find this hard to believe. There's no way we could use any system that could not be networked (since we run a central server for all digital images) and I would reckon that the same would apply for more than 90% of all facilities that would buy a high-end confocal. Maybe Leica can reply to this? 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 -----Original Message----- From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Nowell, Cameron Sent: Friday, 15 August 2008 8:30 AM To: [hidden email] Subject: Re: question for Leica SP5 users Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal We have an SP5 in our facility and the only thing we have been told by leica we can't do is connect it to a network, which is fine for us as the network here is notoriously unstable. We run our own anti-virus software and defrag utilities on it, as well as a few admin apps to track data usage etc. Cheers Cam Cameron Nowell Research and Microscopy Imaging Core Peter MacCallum Cancer Centre Melbourne, Australia -----Original Message----- From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Guy Cox Sent: Friday, 15 August 2008 8:10 AM To: [hidden email] Subject: Re: question for Leica SP5 users Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal I think there is some confusion here. I think you are talking about the low-cost SPE, which runs a really cut-down OS. I don't think any of this applies to the SP5. 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 -----Original Message----- From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Aryeh Weiss Sent: Friday, 15 August 2008 6:17 AM To: [hidden email] Subject: question for Leica SP5 users Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal We have been told by the Leica rep here that we may put no program on the SP5 computer -- not ImageJ, not Winzip, nothing. We were also told that the computer may not be connected to the network, except when they want to do service. To more exact, we were told that if we want anything on the machine, we need to ask Leica to do it (and to pay for it to be done). Is this how all the SP5 users out there are using their systems? Aside from the obvious reasons that this policy bothers us, we have a problem because the IT people in the university will not permit a computer to be connected to the network unless they have installed their approved anti-virus program personally. If the issue is delicate, perhaps you may prefer to reply off list. --aryeh -- Aryeh Weiss School of Engineering Bar Ilan University Ramat Gan 52900 Israel Ph: 972-3-5317638 FAX: 972-3-7384050 No virus found in this incoming message. Checked by AVG. Version: 7.5.526 / Virus Database: 270.6.3/1610 - Release Date: 13/08/2008 4:14 PM No virus found in this outgoing message. Checked by AVG. Version: 7.5.526 / Virus Database: 270.6.3/1610 - Release Date: 13/08/2008 4:14 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. No virus found in this incoming message. Checked by AVG. Version: 7.5.526 / Virus Database: 270.6.3/1610 - Release Date: 13/08/2008 4:14 PM No virus found in this outgoing message. Checked by AVG. Version: 7.5.526 / Virus Database: 270.6.3/1610 - Release Date: 13/08/2008 4:14 PM |
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Lenaldo Rocha |
Re: question for Leica SP5 users
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In reply to this post by Nowell, Cameron
Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Our SP5 is connected to our network. I even installed a vnc server on it and used to live broadcast over the internet the images captured during a course. Lenaldo On 14/08/2008, at 19:29, Nowell, Cameron wrote: > Search the CONFOCAL archive at > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal > > We have an SP5 in our facility and the only thing we have been told by > leica we can't do is connect it to a network, which is fine for us as > the network here is notoriously unstable. > > We run our own anti-virus software and defrag utilities on it, as well > as a few admin apps to track data usage etc. > > > Cheers > > > Cam > > > Cameron Nowell > Research and Microscopy Imaging Core > Peter MacCallum Cancer Centre > Melbourne, Australia > > > > -----Original Message----- > From: Confocal Microscopy List > [mailto:[hidden email]] On > Behalf Of Guy Cox > Sent: Friday, 15 August 2008 8:10 AM > To: [hidden email] > Subject: Re: question for Leica SP5 users > > > Search the CONFOCAL archive at > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal > > I think there is some confusion here. I think you are talking about > the > low-cost SPE, which runs a really cut-down OS. I don't think any of > this applies to the SP5. > > 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 > -----Original Message----- > From: Confocal Microscopy List > [mailto:[hidden email]] On > Behalf Of Aryeh Weiss > Sent: Friday, 15 August 2008 6:17 AM > To: [hidden email] > Subject: question for Leica SP5 users > > Search the CONFOCAL archive at > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal > > We have been told by the Leica rep here that we may put no program on > the SP5 computer -- not ImageJ, not Winzip, nothing. We were also told > that the computer may not be connected to the network, except when > they > want to do service. > To more exact, we were told that if we want anything on the machine, > we > need to ask Leica to do it (and to pay for it to be done). > > > Is this how all the SP5 users out there are using their systems? > > Aside from the obvious reasons that this policy bothers us, we have a > problem because the IT people in the university will not permit a > computer to be connected to the network unless they have installed > their > approved anti-virus program personally. > > If the issue is delicate, perhaps you may prefer to reply off list. > > --aryeh > -- > Aryeh Weiss > School of Engineering > Bar Ilan University > Ramat Gan 52900 Israel > > Ph: 972-3-5317638 > FAX: 972-3-7384050 > > No virus found in this incoming message. > Checked by AVG. > Version: 7.5.526 / Virus Database: 270.6.3/1610 - Release Date: > 13/08/2008 4:14 PM > > > No virus found in this outgoing message. > Checked by AVG. > Version: 7.5.526 / Virus Database: 270.6.3/1610 - Release Date: > 13/08/2008 4:14 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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Aryeh Weiss |
Re: question for Leica SP5 users - followup
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In reply to this post by Guy Cox
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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 |
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Oshel, Philip Eugene |
Re: Objective cleaning solution
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In reply to this post by Larry Tague
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http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal 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. As near as I can tell, the new lens cleaner version is just non-purple Sparkle at ~13X the price ($30/0.75 L vs $3/1 L). Guess they're aiming at the hospital market. I've used Sparkly clear and purple for years now on fluorescence microscopes, and haven't noticed any residue problems. Phil >Search the CONFOCAL archive at >http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal > >Yea, I saw the Funk new microscope objective cleaner, but we have >been using the purple stuff for a long time on Zeiss and Nikon >objectives with no problems.... of course I do dilute it 1 part >Sparkle to 3 parts distilled water. I understand if you don't like >the color, you can leave it in the sun for a day or so and it turns >clear. Never tried that... not needed in my opinion. > >Larry > >Donnelly, Tom wrote: >> Search the CONFOCAL archive at >> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal >> >> This may be old news to everyone, but A.J. Funk has released an >>Optical Microscope Lens Cleaner version of Sparkle. >>http://www.bestcleaningproducts.com/shop/product.asp?prodID=3779 >> >> I am guessing it is the same thing as the purple Sparkle but >>without the dye that can leave a fluorescent residue. >> No commercial interest. >> Tom >> > >-- >Larry Tague >Co-Investigator BBHSL* >Co-Director of MECCA** >Research Associate (Dept. of Physiology) >University of Tennessee Health Science Center >894 Union Ave. >Memphis, TN 38163 >Phone Bus.: 901-448-7152 >Phone FAX: 901-448-7126 >e-mail:[hidden email] or > [hidden email] Philip Oshel Microscopy Facility Supervisor Biology Department 024C Brooks Hall Central Michigan University Mt. Pleasant, MI 48859 (989) 774-3576 |
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