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<p class=MsoNormal>multi-image-pixels.ome.tif submitted as QA Bug | 1008.<o:p></o:p></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
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<p class=MsoNormal><b><span lang=EN-US style='font-size:10.0pt;font-family:
"Tahoma","sans-serif"'>From:</span></b><span lang=EN-US style='font-size:10.0pt;
font-family:"Tahoma","sans-serif"'> Jason Swedlow
[mailto:jason@lifesci.dundee.ac.uk] <br>
<b>Sent:</b> 22 October 2009 23:58<br>
<b>To:</b> Woodbridge, Mark R<br>
<b>Cc:</b> David Gutman; ome-users@lists.openmicroscopy.org.uk<br>
<b>Subject:</b> Re: [ome-users] Problematic OME-TIFF file<o:p></o:p></span></p>
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<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Hi All-<o:p></o:p></p>
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<p class=MsoNormal><o:p> </o:p></p>
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<p class=MsoNormal>Thanks for this feedback.<o:p></o:p></p>
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<p class=MsoNormal><o:p> </o:p></p>
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<p class=MsoNormal>From our experience, this size should cause a problem.
In our testing, we imported multi-plane OME-TIFF's that were much larger,
with no problem.<o:p></o:p></p>
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<p class=MsoNormal><o:p> </o:p></p>
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<p class=MsoNormal>The best bet is to use qa.openmicroscopy.org.uk, and we'll
take a look at the file.<o:p></o:p></p>
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<p class=MsoNormal><o:p> </o:p></p>
</div>
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<p class=MsoNormal>Cheers,<o:p></o:p></p>
</div>
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<p class=MsoNormal><o:p> </o:p></p>
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<p class=MsoNormal>Jason<o:p></o:p></p>
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<p class=MsoNormal><o:p> </o:p></p>
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<p class=MsoNormal><o:p> </o:p></p>
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<p class=MsoNormal>On 22 Oct 2009, at 22:26, Woodbridge, Mark R wrote:<o:p></o:p></p>
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<p class=MsoNormal><br>
<br>
<o:p></o:p></p>
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<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>It’s about 100MB, but same problem seems to affect upload of
(for example) multi-image-pixels.ome.tif from<span class=apple-converted-space> </span><a
href="http://www.loci.wisc.edu/ome/ome-tiff-data.html">http://www.loci.wisc.edu/ome/ome-tiff-data.html</a><span
class=apple-converted-space> </span>which is about 10MB so looks like a
more general problem with some types of OME-TIFF.</span><span style='color:
black'><o:p></o:p></span></p>
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<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'> </span><span style='color:black'><o:p></o:p></span></p>
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<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>But, more generally, Beta4.1 is looking good – many thanks to
the OMERO developers! All our other file formats have uploaded successfully,
including some which have only been supported since this new release. Other
large files haven’t presented a problem either.</span><span style='color:black'><o:p></o:p></span></p>
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<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'> </span><span style='color:black'><o:p></o:p></span></p>
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<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Mark.</span><span style='color:black'><o:p></o:p></span></p>
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<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'> </span><span style='color:black'><o:p></o:p></span></p>
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<p class=MsoNormal><b><span lang=EN-US style='font-size:10.0pt;font-family:
"Tahoma","sans-serif";color:black'>From:</span></b><span
class=apple-converted-space><span lang=EN-US style='font-size:10.0pt;
font-family:"Tahoma","sans-serif";color:black'> </span></span><span
lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif";
color:black'>David Gutman [<a href="mailto:dagutman@gmail.com">mailto:dagutman@gmail.com</a>]<span
class=apple-converted-space> </span><br>
<b>Sent:</b><span class=apple-converted-space> </span>22 October 2009
21:16<br>
<b>To:</b><span class=apple-converted-space> </span>Woodbridge, Mark R<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]
Problematic OME-TIFF file</span><span style='color:black'><o:p></o:p></span></p>
</div>
</div>
<div>
<p class=MsoNormal><span style='color:black'> <o:p></o:p></span></p>
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<p class=MsoNormal style='margin-bottom:12.0pt'><span style='color:black'>Mark
how big is the image? I haven't updated to the newer version of OME yet
(that's next week's goal) but I would have some images work, and others die
depending on file size-- often I would get an error related to ICE timing out,
etc...<br>
<br>
<br>
dg<o:p></o:p></span></p>
<div>
<div>
<p class=MsoNormal><span style='color:black'>On Thu, Oct 22, 2009 at 3:47 PM,
Woodbridge, Mark R <<a href="mailto:m.woodbridge@imperial.ac.uk">m.woodbridge@imperial.ac.uk</a>>
wrote:<o:p></o:p></span></p>
</div>
<div>
<div>
<div>
<p class=MsoNormal><span style='color:black'>Hi,<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='color:black'> <o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='color:black'>I’ve just been trying to upload a
set of files to Beta4.1 using the importer. One file causes the Importer to get
stuck in a loop where it just says ‘analysing’ until I cancel the import:<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='color:black'> <o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='color:black'><a
href="http://cisbic.bioinformatics.ic.ac.uk/20090422bead20x_C1.ome.tif"
target="_blank">http://cisbic.bioinformatics.ic.ac.uk/20090422bead20x_C1.ome.tif</a><o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='color:black'> <o:p></o:p></span></p>
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<div>
<p class=MsoNormal><span style='color:black'>The importer previously refused to
import the file. I’m not sure whether this was correct, as the OME-TIFF
validator says it’s ok, but previous investigations suggested that the channel
order metadata may be wrong. Anyway, it should probably either succeed or fail
rather than getting stuck ;-)<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='color:black'> <o:p></o:p></span></p>
</div>
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<p class=MsoNormal><span style='color:black'>Tested with Importer running on
Windows and Linux.<o:p></o:p></span></p>
</div>
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<p class=MsoNormal><span style='color:black'> <o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='color:#888888'>Mark.</span><span
style='color:black'><o:p></o:p></span></p>
</div>
</div>
</div>
<p class=MsoNormal style='margin-bottom:12.0pt'><span style='color:black'><br>
_______________________________________________<br>
ome-users mailing list<br>
<a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a><br>
<a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users"
target="_blank">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a><o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='color:black'><br>
<br clear=all>
<br>
--<span class=apple-converted-space> </span><br>
David A Gutman, M.D. Ph.D.<br>
Center for Comprehensive Informatics<br>
Emory University School of Medicine<o:p></o:p></span></p>
</div>
</div>
<p class=MsoNormal><span style='font-size:13.5pt;font-family:"Helvetica","sans-serif";
color:black'>_______________________________________________<br>
ome-users mailing list<br>
<a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a><br>
<a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a><o:p></o:p></span></p>
</div>
</div>
<p class=MsoNormal><o:p> </o:p></p>
<div>
<div>
<p class=MsoNormal style='margin-bottom:12.0pt'><span style='font-size:9.0pt;
font-family:"Helvetica","sans-serif";color:black'><o:p> </o:p></span></p>
</div>
<div>
<p class=MsoNormal><span class=apple-style-span><span style='font-size:9.0pt;
font-family:"Helvetica","sans-serif";color:black'>**************************</span></span><span
style='font-size:9.0pt;font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:9.0pt;font-family:"Arial","sans-serif";
color:black'>Wellcome Trust Centre for Gene Regulation & Expression</span><span
style='font-size:9.0pt;font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:9.0pt;font-family:"Arial","sans-serif";
color:black'>College of Life Sciences</span><span style='font-size:9.0pt;
font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:9.0pt;font-family:"Arial","sans-serif";
color:black'>MSI/WTB/JBC Complex</span><span style='font-size:9.0pt;font-family:
"Helvetica","sans-serif";color:black'><o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span class=apple-style-span><span style='font-size:9.0pt;
font-family:"Helvetica","sans-serif";color:black'>University of Dundee</span></span><span
style='font-size:9.0pt;font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span class=apple-style-span><span style='font-size:9.0pt;
font-family:"Helvetica","sans-serif";color:black'>Dow Street</span></span><span
style='font-size:9.0pt;font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span class=apple-style-span><span style='font-size:9.0pt;
font-family:"Helvetica","sans-serif";color:black'>Dundee DD1 5EH</span></span><span
style='font-size:9.0pt;font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p>
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<p class=MsoNormal><span class=apple-style-span><span style='font-size:9.0pt;
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style='font-size:9.0pt;font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p>
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<p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif";
color:black'><o:p> </o:p></span></p>
</div>
<div>
<p class=MsoNormal><span class=apple-style-span><span style='font-size:9.0pt;
font-family:"Helvetica","sans-serif";color:black'>phone (01382) 385819</span></span><span
style='font-size:9.0pt;font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span class=apple-style-span><span style='font-size:9.0pt;
font-family:"Helvetica","sans-serif";color:black'>Intl phone: 44 1382
385819 </span></span><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif";
color:black'><o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span class=apple-style-span><span style='font-size:9.0pt;
font-family:"Helvetica","sans-serif";color:black'>FAX (01382)
388072 </span></span><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif";
color:black'><o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span class=apple-style-span><span style='font-size:9.0pt;
font-family:"Helvetica","sans-serif";color:black'>email: <a
href="mailto:jason@lifesci.dundee.ac.uk">jason@lifesci.dundee.ac.uk</a></span></span><span
style='font-size:9.0pt;font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p>
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color:black'><o:p> </o:p></span></p>
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<p class=MsoNormal><span class=apple-style-span><span style='font-size:9.0pt;
font-family:"Helvetica","sans-serif";color:black'>Lab Page: <a
href="http://www.dundee.ac.uk/lifesciences/swedlow/">http://www.dundee.ac.uk/lifesciences/swedlow/</a></span></span><span
style='font-size:9.0pt;font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p>
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<p class=MsoNormal><span class=apple-style-span><span style='font-size:9.0pt;
font-family:"Helvetica","sans-serif";color:black'>Open Microscopy Environment: <a
href="http://openmicroscopy.org">http://openmicroscopy.org</a></span></span><span
style='font-size:9.0pt;font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p>
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<p class=MsoNormal><span class=apple-style-span><span style='font-size:9.0pt;
font-family:"Helvetica","sans-serif";color:black'>**************************</span></span><span
style='font-size:9.0pt;font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p>
</div>
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<p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif";
color:black'><o:p> </o:p></span></p>
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<div>
<p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif";
color:black'>The University of Dundee is a Scottish Registered Charity, No.
SC015096.<o:p></o:p></span></p>
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