<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Mark,<div><br></div><div>That's the error you should be getting from trying to import a multi-image-pixels ome.tif so I doubt your database has any issues. Lets try to delete your history database (you can use the 'wipe history' button on the history tab) - maybe your history file is corrupt.</div><div><br></div><div>Cheers,</div><div><br></div><div>Brian</div><div><br><div><div>On 23 Oct 2009, at 11:21, Woodbridge, Mark R wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div lang="EN-GB" link="blue" vlink="purple" style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div class="Section1"><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">Yes, Beta4.1 final for both server and client.<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "><o:p> </o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">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></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "><o:p> </o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">Mark.<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "><o:p> </o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "><o:p> </o:p></span></div><div><div style="border-right-style: none; border-bottom-style: none; border-left-style: none; border-width: initial; border-color: initial; border-top-style: solid; border-top-color: rgb(181, 196, 223); border-top-width: 1pt; padding-top: 3pt; padding-right: 0cm; padding-bottom: 0cm; padding-left: 0cm; "><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><b><span lang="EN-US" style="font-size: 10pt; font-family: Tahoma, sans-serif; ">From:</span></b><span lang="EN-US" style="font-size: 10pt; font-family: Tahoma, sans-serif; "><span class="Apple-converted-space"> </span>Brian Loranger [<a href="mailto:brian.loranger@lifesci.dundee.ac.uk" style="color: blue; text-decoration: underline; ">mailto:brian.loranger@lifesci.dundee.ac.uk</a>]<span class="Apple-converted-space"> </span><br><b>Sent:</b><span class="Apple-converted-space"> </span>23 October 2009 11:11<br><b>To:</b><span class="Apple-converted-space"> </span>Woodbridge, Mark R<br><b>Cc:</b><span class="Apple-converted-space"> </span>David Gutman;<span class="Apple-converted-space"> </span><a href="mailto:ome-users@lists.openmicroscopy.org.uk" style="color: blue; text-decoration: underline; ">ome-users@lists.openmicroscopy.org.uk</a><br><b>Subject:</b><span class="Apple-converted-space"> </span>Re: [ome-users] Problematic OME-TIFF file<o:p></o:p></span></div></div></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><o:p> </o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; ">Hi Mark,<o:p></o:p></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><o:p> </o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; ">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></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><o:p> </o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; ">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></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><o:p> </o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; ">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></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><o:p> </o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; ">Thanks for the feedback Mark,<o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><o:p> </o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; ">Brian<o:p></o:p></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><o:p> </o:p></div><div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; ">On 22 Oct 2009, at 22:26, Woodbridge, Mark R wrote:<o:p></o:p></div></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><br><br><o:p></o:p></div><div><div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">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" style="color: blue; text-decoration: underline; ">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></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "> </span><span style="color: black; "><o:p></o:p></span></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">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></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "> </span><span style="color: black; "><o:p></o:p></span></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">Mark.</span><span style="color: black; "><o:p></o:p></span></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "> </span><span style="color: black; "><o:p></o:p></span></div></div><div style="border-right-style: none; border-bottom-style: none; border-left-style: none; border-width: initial; border-color: initial; border-top-style: solid; padding-top: 3pt; padding-right: 0cm; padding-bottom: 0cm; padding-left: 0cm; border-width: initial; border-color: initial; z-index: auto; "><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><b><span lang="EN-US" style="font-size: 10pt; font-family: Tahoma, sans-serif; color: black; ">From:</span></b><span class="apple-converted-space"><span lang="EN-US" style="font-size: 10pt; font-family: Tahoma, sans-serif; color: black; "> </span></span><span lang="EN-US" style="font-size: 10pt; font-family: Tahoma, sans-serif; color: black; ">David Gutman [<a href="mailto:dagutman@gmail.com" style="color: blue; text-decoration: underline; ">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" style="color: blue; text-decoration: underline; ">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></div></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="color: black; "> <o:p></o:p></span></div></div><p class="MsoNormal" style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 12pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><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><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="color: black; ">On Thu, Oct 22, 2009 at 3:47 PM, Woodbridge, Mark R <<a href="mailto:m.woodbridge@imperial.ac.uk" style="color: blue; text-decoration: underline; ">m.woodbridge@imperial.ac.uk</a>> wrote:<o:p></o:p></span></div></div><div><div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="color: black; ">Hi,<o:p></o:p></span></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="color: black; "> <o:p></o:p></span></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><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></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="color: black; "> <o:p></o:p></span></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="color: black; "><a href="http://cisbic.bioinformatics.ic.ac.uk/20090422bead20x_C1.ome.tif" target="_blank" style="color: blue; text-decoration: underline; ">http://cisbic.bioinformatics.ic.ac.uk/20090422bead20x_C1.ome.tif</a><o:p></o:p></span></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="color: black; "> <o:p></o:p></span></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><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></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="color: black; "> <o:p></o:p></span></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="color: black; ">Tested with Importer running on Windows and Linux.<o:p></o:p></span></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="color: black; "> <o:p></o:p></span></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="color: rgb(136, 136, 136); ">Mark.</span><span style="color: black; "><o:p></o:p></span></div></div></div></div><p class="MsoNormal" style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 12pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="color: black; "><br>_______________________________________________<br>ome-users mailing list<br><a href="mailto:ome-users@lists.openmicroscopy.org.uk" style="color: blue; text-decoration: underline; ">ome-users@lists.openmicroscopy.org.uk</a><br><a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users" target="_blank" style="color: blue; text-decoration: underline; ">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a><o:p></o:p></span></p></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><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></div></div></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><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" style="color: blue; text-decoration: underline; ">ome-users@lists.openmicroscopy.org.uk</a><br><a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users" style="color: blue; text-decoration: underline; ">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a><o:p></o:p></span></div></div></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><o:p> </o:p></div><div><div><div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 9pt; font-family: Helvetica, sans-serif; color: black; ">Brian Loranger<o:p></o:p></span></div></div><div><div><div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 9pt; font-family: Helvetica, sans-serif; color: black; ">Software Developer, Open Microscopy Environment<o:p></o:p></span></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 9pt; font-family: Helvetica, sans-serif; color: black; ">Division of Gene Regulation and Expression<o:p></o:p></span></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 9pt; font-family: Helvetica, sans-serif; color: black; ">University of Dundee<o:p></o:p></span></div></div><div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 9pt; font-family: Helvetica, sans-serif; color: black; ">(The University of Dundee is a registered Scottish charity, No: SC015096)<o:p></o:p></span></div></div></div></div></div></div></div></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman', serif; "><o:p> </o:p></div></div><span><Blitz-0.log></span></div></div></span></blockquote></div><br><div> <span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>Brian Loranger</div><div><div><div><div>Software Developer, Open Microscopy Environment</div><div>Division of Gene Regulation and Expression</div><div>University of Dundee</div><div>(The University of Dundee is a registered Scottish charity, No: SC015096)</div></div></div></div></div></div></span> </div><br></div></body></html>