<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Mark,<div><br></div><div>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). </div><div><br></div><div>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).</div><div><br></div><div>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.</div><div><br></div><div>Thanks for the feedback Mark,</div><div><br></div><div>Brian</div><div><br><div><div>On 22 Oct 2009, at 22:26, 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"><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); ">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.<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); ">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.<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="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; position: static; z-index: auto; "><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>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<o:p></o:p></span></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><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; ">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></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; ">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></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; ">Hi,<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; "> <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; ">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></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; "><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></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; ">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></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; ">Tested with Importer running on Windows and Linux.<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; "> <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; "><span style="color: rgb(136, 136, 136); ">Mark.<o:p></o:p></span></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; "><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></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; "><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></div></div>_______________________________________________<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><br></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>