<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi All-<div><br></div><div>Thanks for this feedback.</div><div><br></div><div>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.</div><div><br></div><div>The best bet is to use qa.openmicroscopy.org.uk, and we'll take a look at the file.</div><div><br></div><div>Cheers,</div><div><br></div><div>Jason</div><div><br></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<span class="Apple-converted-space"> </span><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; "><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; 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