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<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Yes, Beta4.1 final for both server and client.<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Had a closer look at the server log file when importing the ome-tiff
sample from the loci webpage. Looks like an exception is occurring... could my
database be corrupt? Log attached.<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Mark.<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></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"'> Brian Loranger
[mailto:brian.loranger@lifesci.dundee.ac.uk] <br>
<b>Sent:</b> 23 October 2009 11:11<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 Mark,<o:p></o:p></p>
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<p class=MsoNormal><o:p> </o:p></p>
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<div>
<p class=MsoNormal>Melissa and I had a look over this file this morning. The
problem here is that the ome.tiff contains 2 channels, but the tiff actually
only contains one. While this is a valid ome tiff, that setup is not supported
in the OMERO data model (hence the reason you can open it in bio-formats but
not in OMERO). <o:p></o:p></p>
</div>
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<p class=MsoNormal><o:p> </o:p></p>
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<div>
<p class=MsoNormal>I was a bit surprised you got into a permanent analyze loop
with this. I have tried importing this file on mac and windows so far and in
both cases it failed 'properly' (adding the file to the QA report tab of the
importer). We will probably need to provide better feedback or some workaround
for both of your problem file types (the 2 to 1 channel and the
multi-image-pixels ones you're having trouble with).<o:p></o:p></p>
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<p class=MsoNormal><o:p> </o:p></p>
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<p class=MsoNormal>I'll keep trying to duplicate your endless analysis loop
problem here. In the meantime can you double check for me you're using the
latest server and client releases (from the download page) - just so we're all
on the same page.<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 the feedback Mark,<o:p></o:p></p>
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<p class=MsoNormal><o:p> </o:p></p>
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<p class=MsoNormal>Brian<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<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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<div>
<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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<div>
<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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<div>
<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>
</div>
<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>
</div>
<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>
<div>
<p class=MsoNormal><span style='color:black'>Tested with Importer running on
Windows and Linux.<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:#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>
<div>
<div>
<p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif";
color:black'>Brian Loranger<o:p></o:p></span></p>
</div>
<div>
<div>
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<div>
<p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif";
color:black'>Software Developer, Open Microscopy Environment<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif";
color:black'>Division of Gene Regulation and Expression<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif";
color:black'>University of Dundee<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif";
color:black'>(The University of Dundee is a registered Scottish charity, No:
SC015096)<o:p></o:p></span></p>
</div>
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<p class=MsoNormal><o:p> </o:p></p>
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