OMERO set-up and use
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ============================================================ Hi All, My wife and I are setting up a new lab and would really like to start off right with archiving of imaging data for easy access. It seems from going through the open microscopy site that using the OMERO server/client software would be a great a way to organize and access our microscopy data. However, I am wondering about people's experience with setting up and running this package. We have essentially no experience with setting up and maintaining a server, so I must admit to being a bit scared of this endeavor. Any feedback that the community can provide would be great. Thanks, Sean Speese Research Assistant Professor OHSU/Junger's Center Portland, OR [hidden email] |
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ============================================================ I recently gave the problem to my very knowledgable computer support guy to try to set up for our facility. He tried to install it and got very frustrated with the challenges and so I stopped the attempt. So I conclude that it is definitely not trivial and I don't intend to try again until they get a better installation system. Dave On Sep 16, 2010, at 8:04 PM, Sean Speese wrote: > ============================================================ > To join, leave or search the confocal microscopy listserv, go to: > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > ============================================================ > > Hi All, > My wife and I are setting up a new lab and would really like to start off > right with archiving of imaging data for easy access. It seems from going > through the open microscopy site that using the OMERO server/client software > would be a great a way to organize and access our microscopy data. However, > I am wondering about people's experience with setting up and running this > package. We have essentially no experience with setting up and maintaining > a server, so I must admit to being a bit scared of this endeavor. Any > feedback that the community can provide would be great. > > Thanks, > Sean Speese > > Research Assistant Professor > OHSU/Junger's Center > Portland, OR > [hidden email] Dr. David Knecht Department of Molecular and Cell Biology Co-head Flow Cytometry and Confocal Microscopy Facility U-3125 91 N. Eagleville Rd. University of Connecticut Storrs, CT 06269 860-486-2200 860-486-4331 (fax) |
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To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
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The bioinformatics team on our institute got OMERO up and running here and asked for "beta testers" before deploying it as an institute-wide service. I got to try it and I must say I was a bit disappointed. We had very large confocal files with large z-stacks, multichannels, timepoints and combinations of those and OMERO was very slow in handling those files. A problem with it being a networked service, is that it will be bottleneckled by your infrastructure. Even so, while I can transfer gigabytes through our network at a speedy pace, OMERO was very slow loading any file. While browsing through the z's and channels of the files it was also quite slow, since if it was trying to load the correct frame on every change of z, t or c.
Maybe it's gotten better since (it's been a year since I tried it again) and maybe it was an issue specific to our network, but we ended up sticking to obsessively detailed filenames on each file since it was faster to browse... Hope this helps you. Pedro Almada Microscopy Technician Gulbenkian Institute of Science Oeiras, Portugal On 17 September 2010 02:13, David Knecht charter <[hidden email]> wrote:
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In reply to this post by Sean Speese-2
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ============================================================ Posted on behalf of Jason Swedlow as his submissions to the list are currently being rejected: Hi Sean- Indeed, OMERO is rather complex. It isn't a simple 'download and click' install, specifically because of this extensive functionality. OMERO.server contains a number of pieces of software, that must be installed, so it does take some time. However, there are over 1800 OMERO installs worldwide, so we don't think it is impossible. We've had roughly 50 people write to our lists (see http://www.openmicroscopy.org/community/) and ask for help on installation, so that's not a bad ratio. That doesn't mean that we think this is OK-- we're preparing completely built packages, with sample data, using Ubuntu virtual machines. We hope to have these ready for use in the next few weeks. David recently wrote to the list, and to us directly, commenting on the difficulty that he and a colleague were having with the install. This is certainly frustrating for all of us. Using the confocal list is certainly fine, but as Colin Rickman pointed out (and we did as well, directly to David), using the OME lists or Forums might be a better idea. There's a community there that helps one another, and some info might be all that is required. Unfortunately, we've never heard from anyone at UConn. If we can't get any info, we can't help at all. This is important as we often find that the details of what someone is doing might make install harder-- often a small thing stands between success and frustration. One thing you might try is to use our demo server, based in Germany. Performance to the US won't be great, but at least you'll have a server you don't have to install or administer, and some idea whether the functionality justifies contacting the OME lists and figuring out what's going wrong. If you're interested, see openmicroscopy.org-- the link is on the front page. Hope that helps. Cheers, Jason |
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