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<div style="font-size: 14px; font-family: Calibri, sans-serif;">Hi James,</div>
<div style="font-size: 14px; font-family: Calibri, sans-serif;"><br>
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<div style="font-size: 14px; font-family: Calibri, sans-serif;">We tried checking the validity of ome-xml and found that the ome-xml is invalid in this file.</div>
<div style="font-size: 14px; font-family: Calibri, sans-serif;">This suggests that the ome-tiff was not written properly, by the acquisition software.</div>
<div style="font-size: 14px; font-family: Calibri, sans-serif;"><br>
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<div style="font-size: 14px; font-family: Calibri, sans-serif;">And if you had opened the file as Curtis suggested: then Fiji reads the file as a regular multi-page TIFF, and thus treats it as a time series.</div>
<div style="font-size: 14px; font-family: Calibri, sans-serif;"><br>
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<div style="font-size: 14px; font-family: Calibri, sans-serif;">Stack trace for ./xmlvalid (from bftools):</div>
<div style="font-size: 14px; font-family: Calibri, sans-serif;">*****************************************************************************************************************************************************</div>
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<p style="font-size: 11px; font-family: Menlo; margin: 0px; line-height: normal;">
<span style="font-variant-ligatures: no-common-ligatures">ls29010:bftools bramalingam$ ./xmlvalid /Volumes/ome/apache_repo/17373/Z_Time.tif </span></p>
<p style="font-size: 11px; font-family: Menlo; margin: 0px; line-height: normal;">
<span style="font-variant-ligatures: no-common-ligatures">Parsing schema path</span></p>
<p style="font-size: 11px; font-family: Menlo; margin: 0px; line-height: normal;">
<span style="font-variant-ligatures: no-common-ligatures">http://www.openmicroscopy.org/XMLschemas/OME/FC/ome.xsd</span></p>
<p style="font-size: 11px; font-family: Menlo; margin: 0px; line-height: normal;">
<span style="font-variant-ligatures: no-common-ligatures">Validating /Volumes/ome/apache_repo/17373/Z_Time.tif</span></p>
<p style="font-size: 11px; font-family: Menlo; margin: 0px; line-height: normal;">
<span style="font-variant-ligatures: no-common-ligatures">cvc-pattern-valid: Value 'ome.bitplane.com:ChannelInfo:{82ae6204-0013-4563-9990-949cf96235ee}' is not facet-valid with respect to pattern '(urn:lsid:)?(\S+\.\S+)+(:LogicalChannel)(:\S+)' for type 'LogicalChannelID'.</span></p>
<p style="font-size: 11px; font-family: Menlo; margin: 0px; line-height: normal;">
<span style="font-variant-ligatures: no-common-ligatures">cvc-attribute.3: The value 'ome.bitplane.com:ChannelInfo:{82ae6204-0013-4563-9990-949cf96235ee}' of attribute 'ID' on element 'ChannelInfo' is not valid with respect to its type, 'LogicalChannelID'.</span></p>
<p style="font-size: 11px; font-family: Menlo; margin: 0px; line-height: normal;">
<span style="font-variant-ligatures: no-common-ligatures">cvc-complex-type.3.2.2: Attribute 'Description' is not allowed to appear in element 'ChannelInfo'.</span></p>
<p style="font-size: 11px; font-family: Menlo; margin: 0px; line-height: normal;">
<span style="font-variant-ligatures: no-common-ligatures">cvc-datatype-valid.1.2.1: '600 nm' is not a valid value for 'integer'.</span></p>
<p style="font-size: 11px; font-family: Menlo; margin: 0px; line-height: normal;">
<span style="font-variant-ligatures: no-common-ligatures">cvc-attribute.3: The value '600 nm' of attribute 'EmWave' on element 'ChannelInfo' is not valid with respect to its type, 'positiveInteger'.</span></p>
<p style="font-size: 11px; font-family: Menlo; margin: 0px; line-height: normal;">
<span style="font-variant-ligatures: no-common-ligatures">cvc-datatype-valid.1.2.1: 'unknown nm' is not a valid value for 'integer'.</span></p>
<p style="font-size: 11px; font-family: Menlo; margin: 0px; line-height: normal;">
<span style="font-variant-ligatures: no-common-ligatures">cvc-attribute.3: The value 'unknown nm' of attribute 'ExWave' on element 'ChannelInfo' is not valid with respect to its type, 'positiveInteger'.</span></p>
<p style="font-size: 11px; font-family: Menlo; margin: 0px; line-height: normal;">
<span style="font-variant-ligatures: no-common-ligatures">cvc-minInclusive-valid: Value '0' is not facet-valid with respect to minInclusive '1' for type 'positiveInteger'.</span></p>
<p style="font-size: 11px; font-family: Menlo; margin: 0px; line-height: normal;">
<span style="font-variant-ligatures: no-common-ligatures">cvc-attribute.3: The value '0' of attribute 'PinholeSize' on element 'ChannelInfo' is not valid with respect to its type, 'positiveInteger'.</span></p>
<p style="font-size: 11px; font-family: Menlo; margin: 0px; line-height: normal;">
<span style="font-variant-ligatures: no-common-ligatures"><b>Error validating document: 9 errors found</b></span></p>
<p style="font-size: 11px; font-family: Menlo; margin: 0px; line-height: normal;">
<span style="font-variant-ligatures: no-common-ligatures"><b>*************************************************************************************************************************************************************</b></span></p>
<p style="font-size: 11px; font-family: Menlo; margin: 0px; line-height: normal;">
<br>
</p>
<p style="margin: 0px; line-height: normal;"><font face="Calibri">Hope that helps.</font></p>
<p style="margin: 0px; line-height: normal;"><font face="Calibri"><br>
</font></p>
<p style="margin: 0px; line-height: normal;"><font face="Calibri">Best,</font></p>
<p style="margin: 0px; line-height: normal;"><font face="Calibri">Balaji</font></p>
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<div style="color: rgb(40, 40, 40);"><span style="background-color: rgb(255, 255, 255);">__________________</span></div>
<div style="color: rgb(40, 40, 40);">
<p style="margin-top: 0px; margin-bottom: 0px;">Mr Balaji Ramalingam</p>
<p style="margin-top: 0px; margin-bottom: 0px;">Software Developer<br>
</p>
<p style="margin-top: 0px; margin-bottom: 0px;">OME Team</p>
<p style="margin-top: 0px; margin-bottom: 0px;">School of Life Sciences</p>
<p style="margin-top: 0px; margin-bottom: 0px;">University of Dundee</p>
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<span style="font-weight:bold">From: </span>ome-users <<a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk">ome-users-bounces@lists.openmicroscopy.org.uk</a>> on behalf of Curtis Rueden <<a href="mailto:ctrueden@wisc.edu">ctrueden@wisc.edu</a>><br>
<span style="font-weight:bold">Reply-To: </span>OME User Support List <<a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a>><br>
<span style="font-weight:bold">Date: </span>Wednesday, 12 October 2016 at 16:36<br>
<span style="font-weight:bold">To: </span>OME User Support List <<a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a>><br>
<span style="font-weight:bold">Subject: </span>Re: [ome-users] FW: OMERO.qa - new feedback for QA Bug<br>
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<div dir="ltr">Hi James,
<div><br>
</div>
<div>Did you open the file using File > Import > Bio-Formats? If you used File > Open, and you don't have the SCIFIO option enabled (in Edit > Options > ImageJ2), then Bio-Formats will not be used, and the fact that the file is an OME-TIFF will not be detected.</div>
<div><br>
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<div>Regards,</div>
<div>Curtis</div>
</div>
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<div><span style="font-size:12.8px">--</span></div>
<div><span style="font-size:12.8px">Curtis Rueden</span><br>
</div>
<div><span style="font-size:12.8px">LOCI software architect - <a href="http://loci.wisc.edu/software" target="_blank">
http://loci.wisc.edu/software</a></span></div>
<div>ImageJ2 lead, Fiji maintainer - <span style="font-size:12.8px"><a href="http://imagej.net/User:Rueden" target="_blank">http://imagej.net/User:Rueden</a></span></div>
<div>Did you know ImageJ has a forum? <a href="http://forum.imagej.net/" target="_blank">
http://forum.imagej.net/</a></div>
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<div class="gmail_quote">On Wed, Oct 12, 2016 at 5:21 AM, WAINWRIGHT James <span dir="ltr">
<<a href="mailto:J.Wainwright@andor.com" target="_blank">J.Wainwright@andor.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div lang="EN-GB" link="blue" vlink="purple">
<div class="m_8677963326046548805WordSection1">
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Hi there!<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">I seem to have problems opening OME TIFF with Bio-Formats, but I can’t tell if it’s the file or Bio-Formats at fault.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">I’ve uploaded an example dataset as per the below. It has 4 Z and 3 time, but appears in FIJI as 12 time points.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Let me know if I can provide any more information.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Thanks!<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">James<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><u></u> <u></u></span></p>
<div>
<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1c2674">James Wainwright<u></u><u></u></span></b></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1c2674">Global Applications Specialist - Microscopy Systems<br>
<br>
<u></u><u></u></span></p>
<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1c2674">Tel:
</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1c2674"><a href="tel:%2B44%20%280%29%202890%20237%20126%20ext.%202130" value="+442890237126" target="_blank">+44 (0) 2890 237 126 ext. 2130</a><u></u><u></u></span></p>
<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1c2674">Skype:
</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1c2674">andor.j.wainwright
<u></u><u></u></span></p>
<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1c2674">Mob:
</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1c2674"><a href="tel:%2B44%20%280%29%207834%20710%20834" value="+447834710834" target="_blank">+44 (0) 7834 710 834</a><br>
<b>Web:</b> <a href="https://www.andor.com/microscopy-systems" target="_blank">
https://www.andor.com/<wbr>microscopy-systems</a><u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Arial",sans-serif;color:#1f497d"><br>
</span><span style="font-size:11.0pt;color:#1f497d"><img border="0" width="128" height="38" style="width:1.3333in;height:.3958in" id="m_8677963326046548805Picture_x0020_1" src="cid:image001.jpg@01D22479.F2D31C10" alt="logo"></span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><u></u> <u></u></span></p>
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<div style="border:none;border-top:solid #e1e1e1 1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal"><b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif"><a href="mailto:qa@openmicroscopy.org.uk" target="_blank">qa@openmicroscopy.org.uk</a>
[mailto:<a href="mailto:qa@openmicroscopy.org.uk" target="_blank">qa@openmicroscopy.org.<wbr>uk</a>]
<br>
<b>Sent:</b> 12 October 2016 11:09<br>
<b>To:</b> WAINWRIGHT James <<a href="mailto:J.Wainwright@andor.com" target="_blank">J.Wainwright@andor.com</a>><br>
<b>Subject:</b> OMERO.qa - new feedback for QA Bug <u></u><u></u></span></p>
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<p class="MsoNormal"><u></u> <u></u></p>
<p><b>EXTERNAL EMAIL</b><u></u><u></u></p>
<div>
<p><b>ATTACHMENT ADVISORY</b><u></u><u></u></p>
<div>
<p>Hi OMERO user!<u></u><u></u></p>
<p>Thank you for your feedback. Please follow the status of the feedback on: <a href="https://www.openmicroscopy.org/qa2/qa/feedback/17373/?token=5490784af0b469ef70e473c0fe33b7ba" target="_blank">
https://www.openmicroscopy.<wbr>org/qa2/qa/feedback/17373/?<wbr>token=<wbr>5490784af0b469ef70e473c0fe33b7<wbr>ba</a><u></u><u></u></p>
<p>OMERO team<u></u><u></u></p>
<p>Please do not reply to this e-mail as the mailbox doesn't accept incoming messages. If you have any comments or queries please use the link above, we can only be contacted via our website.<u></u><u></u></p>
<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="background:white"><u></u> <u></u></span></p>
<p align="center" style="text-align:center"><span style="background:white">Click <a href="https://www.mailcontrol.com/sr/MZbqvYs5QwJvpeaetUwhCQ==" target="_blank">
here</a> to report this email as spam.<u></u><u></u></span></p>
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