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<div>Hi John</div>
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<div>What version of Java are you using? We've come across a similar error before on our daily test servers but it seemed to fix itself after we updated to Java 1.7.0_51:</div>
<div><a href="http://trac.openmicroscopy.org.uk/ome/ticket/11081">http://trac.openmicroscopy.org.uk/ome/ticket/11081</a></div>
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<div>Balaji's just done some testing today on importing large numbers of images, he managed to reproduce your error with 1.7.0_11-b21 but not with 1.7.0_51-b13.</div>
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<div>Thanks</div>
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<div>Simon<br>
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<div>On 26 Mar 2014, at 09:10, "John Webber (NBI)" <<a href="mailto:John.Webber@nbi.ac.uk">John.Webber@nbi.ac.uk</a>></div>
<div> wrote:</div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">Hi Simon,<o:p></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "><br>
Thanks for the quick response.<o:p></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "> </span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">My problem is that I have a bulk upload to perform and the omero.cli is now consistently failing! I can upload 60+ images to Omero before I see this error, so switching
debug on might be omerous! However, I do have the cli.err from an example of this fail – I have attached it to this email.<o:p></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "> </span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; ">
<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">I have also amended my code to work around this issue so that, if it sees this error, it attempts the upload again before crashing out:<o:p></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "> </span></div>
<div style="margin: 0cm 0cm 0.0001pt 36pt; font-size: 12pt; font-family: 'Times New Roman', serif; ">
<span style="font-size: 9pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "> try:<o:p></o:p></span></div>
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<span style="font-size: 9pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "> cli.invoke(import_args, strict=True)<o:p></o:p></span></div>
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<span style="font-size: 9pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "> </span></div>
<div style="margin: 0cm 0cm 0.0001pt 36pt; font-size: 12pt; font-family: 'Times New Roman', serif; ">
<span style="font-size: 9pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "> except omero.cli.NonZeroReturnCode, err:<o:p></o:p></span></div>
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<span style="font-size: 9pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "> logging.warning('%s: Omero CLI has had a NonZeroReturnCode, trying again' % (self))<o:p></o:p></span></div>
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<span style="font-size: 9pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "> </span></div>
<div style="margin: 0cm 0cm 0.0001pt 36pt; font-size: 12pt; font-family: 'Times New Roman', serif; ">
<span style="font-size: 9pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "> try:<o:p></o:p></span></div>
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<span style="font-size: 9pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "> cli.invoke(import_args, strict=True)<o:p></o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt 36pt; font-size: 12pt; font-family: 'Times New Roman', serif; ">
<span style="font-size: 9pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "> </span></div>
<div style="margin: 0cm 0cm 0.0001pt 36pt; font-size: 12pt; font-family: 'Times New Roman', serif; ">
<span style="font-size: 9pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "> except:<o:p></o:p></span></div>
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<span style="font-size: 9pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "> logging.error('%s: Omero CLI has failed twice - exiting.' % (self))<o:p></o:p></span></div>
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<span style="font-size: 9pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "> sys.exit(7)<o:p></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "> </span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">Not a particularly elegant work around – but it works.<o:p></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "> </span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">Thanks<o:p></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">John<o:p></o:p></span></div>
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<b><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif; ">From:</span></b><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif; "><span class="Apple-converted-space"> </span>Simon Li [mailto:s.p.li@<a href="http://dundee.ac.uk">dundee.ac.uk</a>]<span class="Apple-converted-space"> </span><br>
<b>Sent:</b><span class="Apple-converted-space"> </span>25 March 2014 16:40<br>
<b>To:</b><span class="Apple-converted-space"> </span>John Webber (NBI)<br>
<b>Cc:</b><span class="Apple-converted-space"> </span><a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a><br>
<b>Subject:</b><span class="Apple-converted-space"> </span>Re: [ome-users] omero.cli error<o:p></o:p></span></div>
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<o:p> </o:p></div>
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Hi John<o:p></o:p></div>
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<o:p> </o:p></div>
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Could you try adding --debug DEBUG to your import command, and see if it gives any more information? If that doesn't help could you send us cli.err and cli.out?<o:p></o:p></div>
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<o:p> </o:p></div>
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Many thanks<o:p></o:p></div>
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<o:p> </o:p></div>
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Simon<o:p></o:p></div>
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<o:p> </o:p></div>
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On 25 Mar 2014, at 15:46, "John Webber (NBI)" <<a href="mailto:John.Webber@nbi.ac.uk" style="color: purple; text-decoration: underline; ">John.Webber@nbi.ac.uk</a>><o:p></o:p></div>
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wrote:<o:p></o:p></div>
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<o:p></o:p></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; ">Hi,<o:p></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; "> <o:p></o:p></span></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; ">
<span style="font-size: 11pt; font-family: Calibri, sans-serif; ">I’m currently experiencing an issue with a bulk upload of images to Omero. This is being run from the command line.<o:p></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; "> <o:p></o:p></span></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; ">
<span style="font-size: 11pt; font-family: Calibri, sans-serif; ">I am seeing the following errors, and my bulk upload fails:<o:p></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; "> <o:p></o:p></span></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; ">
<span style="font-size: 9pt; font-family: Calibri, sans-serif; "> cli.invoke(import_args, strict=True)</span><span style="font-size: 11pt; font-family: Calibri, sans-serif; "><o:p></o:p></span></div>
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<span style="font-size: 9pt; font-family: Calibri, sans-serif; "> File "/opt/OMERO.server-4.4.8p1-ice33-b304/lib/python/omero/cli.py", line 749, in invoke</span><span style="font-size: 11pt; font-family: Calibri, sans-serif; "><o:p></o:p></span></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; ">
<span style="font-size: 9pt; font-family: Calibri, sans-serif; "> self.assertRC()</span><span style="font-size: 11pt; font-family: Calibri, sans-serif; "><o:p></o:p></span></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; ">
<span style="font-size: 9pt; font-family: Calibri, sans-serif; "> File "/opt/OMERO.server-4.4.8p1-ice33-b304/lib/python/omero/cli.py", line 738, in assertRC</span><span style="font-size: 11pt; font-family: Calibri, sans-serif; "><o:p></o:p></span></div>
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<span style="font-size: 9pt; font-family: Calibri, sans-serif; "> raise NonZeroReturnCode(self.rv, "assert failed")</span><span style="font-size: 11pt; font-family: Calibri, sans-serif; "><o:p></o:p></span></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; ">
<span style="font-size: 9pt; font-family: Calibri, sans-serif; ">omero.cli.NonZeroReturnCode: assert failed</span><span style="font-size: 11pt; font-family: Calibri, sans-serif; "><o:p></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; "> <o:p></o:p></span></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; ">
<span style="font-size: 11pt; font-family: Calibri, sans-serif; ">The bulk upload failed while writing an image, with the following arguments:<o:p></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; "> <o:p></o:p></span></div>
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<span style="font-size: 9pt; font-family: Calibri, sans-serif; ">['import', '-s', 'localhost', '-u', 'upload', '-w', '<password removed>', '-p', '4064', '-d', '1687', '-n', '11_03_14_krp4_1130_b1_boundaries.inr.gz', '---errs=cli.err', '---file=cli.out', '--',
'/tmp/tmpB3u1Gn/11_03_14_krp4_1130_b1/11_03_14_krp4_1130_b1_boundaries.inr.gz']</span><span style="font-size: 11pt; font-family: Calibri, sans-serif; "><o:p></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; "> <o:p></o:p></span></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; ">
<span style="font-size: 11pt; font-family: Calibri, sans-serif; ">When I try to run the upload again, it fails for a different image – it does not fail on the same one upload time!<o:p></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; "> <o:p></o:p></span></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; ">
<span style="font-size: 11pt; font-family: Calibri, sans-serif; ">I am unable to see much additional information: I have checked in the omero logs, (/opt/Omero/var/log), but am not able to see any additional logging. I have checked filesystem sizes, and nothing
seems to have filled up!<o:p></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; "> <o:p></o:p></span></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; ">
<span style="font-size: 11pt; font-family: Calibri, sans-serif; ">Please can you point me in the right direction as to how I can debug this issue further?<o:p></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; "><br>
Thanks<o:p></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; ">John<o:p></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; "> <o:p></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; "> <o:p></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; "> <o:p></o:p></span></div>
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<b><span style="font-size: 10pt; font-family: Arial, sans-serif; color: rgb(79, 129, 189); ">-------------------------------------------------------------------------------------------------------------------------------------------- </span></b><span style="font-size: 11pt; font-family: Calibri, sans-serif; "><o:p></o:p></span></div>
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<b><span style="font-size: 11pt; font-family: Arial, sans-serif; color: rgb(84, 141, 212); ">John Webber<br>
</span></b><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">Computing and Information Services</span><span style="font-size: 11pt; font-family: Calibri, sans-serif; "><o:p></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">NBI Partnership Ltd</span><span style="font-size: 11pt; font-family: Calibri, sans-serif; "><o:p></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">Norwich Research park</span><span style="font-size: 11pt; font-family: Calibri, sans-serif; "><o:p></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">Colney Lane</span><span style="font-size: 11pt; font-family: Calibri, sans-serif; "><o:p></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">Norwich</span><span style="font-size: 11pt; font-family: Calibri, sans-serif; "><o:p></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">E-Mail:</span><span style="font-size: 11pt; font-family: Calibri, sans-serif; "> </span><a href="mailto:john.webber@nbi.ac.uk" style="color: purple; text-decoration: underline; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; ">john.webber@nbi.ac.uk</span></a><span style="font-size: 11pt; font-family: Calibri, sans-serif; "><o:p></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">Tel:</span><span style="font-size: 11pt; font-family: Calibri, sans-serif; "> <span style="color: rgb(31, 73, 125); "> +44(0)1603 450 818</span><o:p></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">Helpdesk (Tel): 1234</span><span style="font-size: 11pt; font-family: Calibri, sans-serif; "> <span style="color: rgb(31, 73, 125); "> HPC Support (Web):</span> <span style="color: rgb(31, 73, 125); "> <span class="apple-converted-space"> </span></span></span><a href="http://hpc.nbi.ac.uk/" style="color: purple; text-decoration: underline; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; ">http://hpc.nbi.ac.uk</span></a><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "> HPC Support (Tel):</span><span style="font-size: 11pt; font-family: Calibri, sans-serif; "> <span style="color: rgb(31, 73, 125); ">
2003 (NBI internal)</span><o:p></o:p></span></div>
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<i><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">The NBI Partnership Ltd provides non-scientific services to the Institute of Food Research, the John Innes Centre, The Genome Analysis Centre and The Sainsbury Laboratory</span></i><span style="font-size: 11pt; font-family: Calibri, sans-serif; "><o:p></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; "> <o:p></o:p></span></div>
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<span style="font-size: 13.5pt; font-family: Helvetica, sans-serif; ">_______________________________________________<br>
ome-users mailing list<br>
</span><a href="mailto:ome-users@lists.openmicroscopy.org.uk" style="color: purple; text-decoration: underline; "><span style="font-size: 13.5pt; font-family: Helvetica, sans-serif; color: rgb(149, 79, 114); ">ome-users@lists.openmicroscopy.org.uk</span></a><span style="font-size: 13.5pt; font-family: Helvetica, sans-serif; "><br>
</span><a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users" style="color: purple; text-decoration: underline; "><span style="font-size: 13.5pt; font-family: Helvetica, sans-serif; color: rgb(149, 79, 114); ">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</span></a><span style="font-size: 13.5pt; font-family: Helvetica, sans-serif; "><o:p></o:p></span></div>
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<span style="font-size: 10pt; ">The University of Dundee is a registered Scottish Charity, No: SC015096</span><o:p></o:p></div>
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<span style="font-size:10pt;">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
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