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Hi Susan-<div><br><div><div>On 24 Sep 2008, at 21:54, Curtis Rueden wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div dir="ltr">Hi Susan,<br><div class="gmail_quote"><br></div><div class="gmail_quote"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div style=""> <div>I downloaded the latest trunk build of the loci_tools.jar and placed it in the plugins folder and re-ran ImageJ. The LOCI Bioformats Importer gives the same error on that zvi file that OMERO.insight does.</div></div></blockquote></div><br>Strange; I checked the source code and it should not be generating this error. Would you be willing to send us the problematic file for us to use for debugging? Once we have the problem solved in Bio-Formats, the next version of OMERO.importer will also incorporate the fix -- or I can provide you with instructions on how to update your existing version of OMERO.importer if you like.<br> <br></div></blockquote><div><br></div><div>Can you let us know which version of Zeiss software produced the file. We test .zvi files before every release, but our testing is only as good and as up-to-date as our test files, so knowing which versions are giving us problems is very helpful.</div><div><br></div><div>Thanks!</div><div><br></div><div>Cheers,</div><div><br></div><div>Jason</div><div><br></div><br><blockquote type="cite"><div dir="ltr">-Curtis<br><br><div class="gmail_quote">On Wed, Sep 24, 2008 at 3:48 PM, Susan Wilson <span dir="ltr"><<a href="mailto:smwilson@hpc.unm.edu">smwilson@hpc.unm.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"> <div style="">Hi again,<div><br></div><div>I downloaded the latest trunk build of the loci_tools.jar and placed it in the plugins folder and re-ran ImageJ. The LOCI Bioformats Importer gives the same error on that zvi file that OMERO.insight does.</div> <div><br></div><div>Susan</div><div><br><div><div class="Ih2E3d"><div>On Sep 24, 2008, at 2:20 PM, Curtis Rueden wrote:</div><br></div><div><div></div><div class="Wj3C7c"><blockquote type="cite"><div dir="ltr">Hi Susan,<br> <br>That exception looks like a bug in Bio-Formats to me. Are you able to import the ZVI file into ImageJ using the Bio-Formats Importer plugin (<a href="http://www.loci.wisc.edu/ome/formats-imagej.html" target="_blank">http://www.loci.wisc.edu/ome/formats-imagej.html</a>) with the latest trunk build (<a href="http://www.loci.wisc.edu/ome/formats-download.html" target="_blank">http://www.loci.wisc.edu/ome/formats-download.html</a>)?<br> <br>-Curtis<br><br><div class="gmail_quote">On Wed, Sep 24, 2008 at 3:09 PM, Susan Wilson <span dir="ltr"><<a href="mailto:smwilson@hpc.unm.edu" target="_blank">smwilson@hpc.unm.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"> Hi,<br> <br> Runniing Beta3.0.1 all around. This is the error I get when I attempt<br> to import a .zvi file:<br> <br> java.lang.NumberFormatException: For input string: "9/17/2008 7:05:39<br> PM"<br> at<br> java<br> .lang.NumberFormatException.forInputString(NumberFormatException.java:<br> 48)<br> at java.lang.Long.parseLong(Long.java:412)<br> at java.lang.Long.parseLong(Long.java:461)<br> at loci.formats.in.ZeissZVIReader.initMetadata(ZeissZVIReader.java:623)<br> at loci.formats.in.ZeissZVIReader.initFile(ZeissZVIReader.java:513)<br> at loci.formats.FormatReader.setId(FormatReader.java:216)<br> at loci.formats.ImageReader.setId(ImageReader.java:565)<br> at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:71)<br> at loci.formats.ChannelFiller.setId(ChannelFiller.java:186)<br> at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:71)<br> at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:61)<br> at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:71)<br> at ome.formats.importer.ImportLibrary.open(ImportLibrary.java:181)<br> at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:<br> 355)<br> at ome.formats.importer.ImportHandler.importImages(ImportHandler.java:<br> 172)<br> at ome.formats.importer.ImportHandler.access$0(ImportHandler.java:106)<br> at ome.formats.importer.ImportHandler$1.run(ImportHandler.java:87)<br> <br> Also, I may be crazy, but the documentation for OMERO.insight does not<br> match what I am seeing. This error is on my MAC to OMERO.server on<br> debian. I downloaded and ran both (linux) importer and insight on the<br> localhost debian host and got the same importer error and the same<br> insight application. Help/About shows Beta3.0.1, which is the server<br> I am running, but insight has no categories, no "Browse Button"...<br> And importer won't import the zvi on either platform.<br> <br> Thanks.<br> Susan<br> _______________________________________________<br> ome-users mailing list<br> <a href="mailto:ome-users@lists.openmicroscopy.org.uk" target="_blank">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><br> </blockquote></div><br></div></blockquote></div></div></div><br></div></div></blockquote></div><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">_______________________________________________</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">ome-users mailing list</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a></div> </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="font-family: Helvetica; "><br class="Apple-interchange-newline"><br class="khtml-block-placeholder"></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">**************************</span></div><div style="font-family: Helvetica; "><font class="Apple-style-span" face="Arial">Wellcome Trust Centre for Gene Regulation & Expression</font></div><div style="font-family: Helvetica; "><font class="Apple-style-span" face="Arial">College of Life Sciences</font></div><div style="font-family: Helvetica; "><font class="Apple-style-span" face="Arial">MSI/WTB/JBC Complex</font></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">University of Dundee</span></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">Dow Street</span></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">Dundee DD1 5EH</span></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">United Kingdom</span></div><div style="font-family: Helvetica; "><br style="font-family: Helvetica; "></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">phone (01382) 385819</span></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">Intl phone: 44 1382 385819 </span></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">FAX (01382) 388072 </span></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">email: <a href="mailto:jason@lifesci.dundee.ac.uk">jason@lifesci.dundee.ac.uk</a></span></div><div style="font-family: Helvetica; "><br style="font-family: Helvetica; "></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">Lab Page: <a href="http://www.dundee.ac.uk/lifesciences/swedlow/">http://www.dundee.ac.uk/lifesciences/swedlow/</a></span></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">Open Microscopy Environment: <a href="http://openmicroscopy.org">http://openmicroscopy.org</a></span></div><div style="font-family: Helvetica; "><span class="Apple-style-span" style="font-family: Helvetica; ">**************************</span></div><div style="font-family: Helvetica; "><br class="webkit-block-placeholder"></div><div style="font-family: Helvetica; "><div>The University of Dundee is a Scottish Registered Charity, No. SC015096.</div></div><br class="Apple-interchange-newline"></span><br class="Apple-interchange-newline"> </div><br></div></body></html>