<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=Windows-1252">
</head>
<body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
Hi Mubarik,
<div class=""><br class="">
</div>
<div class="">Thank you for uploading the sample file for testing. I was able to reproduce the same error that you encountered.</div>
<div class=""><br class="">
</div>
<div class="">This is caused by a bug in the Dimension Swap Dialog for the Bio-Formats plugin. </div>
<div class="">When an image has different dimensions for each series then the dimension swapping dialog was incorrectly displaying and expecting the dimension sizes for the last series in the image. </div>
<div class=""><br class="">
</div>
<div class="">I have opened a Bio-Formats PR with a proposed fix for this issue:</div>
<div class=""><a href="https://github.com/openmicroscopy/bioformats/pull/2546" class="">https://github.com/openmicroscopy/bioformats/pull/2546</a></div>
<div class=""><br class="">
</div>
<div class="">With Thanks,</div>
<div class="">David Gault</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
<div>
<blockquote type="cite" class="">
<div class="">On 24 Aug 2016, at 10:16, Burki, Mubarik <<a href="mailto:z.burki.12@ucl.ac.uk" class="">z.burki.12@ucl.ac.uk</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div id="divtagdefaultwrapper" style="font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; font-size: 12pt; background-color: rgb(255, 255, 255); font-family: Calibri, Arial, Helvetica, sans-serif;" class="">
<div style="margin-top: 0px; margin-bottom: 0px;" class="">Dear David,</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class="">
</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class="">I have the 5.2.0 version for Bio-Formats.</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class="">
</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class="">I will upload a sample now. </div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class="">
</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class="">Best wishes,</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class="">
</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class="">Mubarik </div>
<br class="">
<br class="">
<div style="" class="">
<hr tabindex="-1" style="display: inline-block; width: 821.234375px;" class="">
<div id="divRplyFwdMsg" dir="ltr" class=""><font face="Calibri, sans-serif" style="font-size: 11pt;" class=""><b class="">From:</b><span class="Apple-converted-space"> </span>ome-users <<a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk" class="">ome-users-bounces@lists.openmicroscopy.org.uk</a>>
on behalf of David Gault (Staff) <<a href="mailto:d.gault@dundee.ac.uk" class="">d.gault@dundee.ac.uk</a>><br class="">
<b class="">Sent:</b><span class="Apple-converted-space"> </span>24 August 2016 10:06<br class="">
<b class="">To:</b><span class="Apple-converted-space"> </span>OME User Support List<br class="">
<b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [ome-users] Fiji error!</font>
<div class=""> </div>
</div>
<div class="">Hi Mubarik,
<div class=""><br class="">
</div>
<div class="">Could you tell us which version of Bio-Formats you are currently using? </div>
<div class="">You can find out by going to Help -> About Plugins -> Bio-Formats Plugins, the version will be listed beside ‘Release’.</div>
<div class=""><br class="">
</div>
<div class="">Also if it is possible would you be able to upload a sample file for testing to:</div>
<div class=""><a href="https://www.openmicroscopy.org/qa2/qa/upload/" class="" id="LPlnk116592">https://www.openmicroscopy.org/qa2/qa/upload/</a></div>
<div id="LPBorder_GT_14720300941540.8592265471816063" style="margin-bottom: 20px; overflow: auto; width: 838px; text-indent: 0px;" class="">
<table id="LPContainer_14720300941520.8616939368657768" cellspacing="0" style="width: 754px; background-color: rgb(255, 255, 255); position: relative; overflow: auto; padding-top: 20px; padding-bottom: 20px; margin-top: 20px; border-top-width: 1px; border-top-style: dotted; border-top-color: rgb(200, 200, 200); border-bottom-width: 1px; border-bottom-style: dotted; border-bottom-color: rgb(200, 200, 200);" class="">
<tbody class="">
<tr valign="top" style="border-spacing: 0px;" class="">
<td id="TextCell_14720300941520.7301436278503388" colspan="2" style="vertical-align: top; position: relative; padding: 0px; display: table-cell;" class="">
<div id="LPRemovePreviewContainer_14720300941520.1792336127255112" class=""></div>
<div id="LPTitle_14720300941520.9197075986303389" style="top: 0px; color: rgb(0, 120, 215); font-weight: normal; font-size: 21px; font-family: wf_segoe-ui_light, 'Segoe UI Light', 'Segoe WP Light', 'Segoe UI', 'Segoe WP', Tahoma, Arial, sans-serif; line-height: 21px;" class="">
<a id="LPUrlAnchor_14720300941530.5425667546223849" href="https://www.openmicroscopy.org/qa2/qa/upload/" target="_blank" style="text-decoration: none;" class="">OMERO.qa - Open Microscopy Environment</a></div>
<div id="LPMetadata_14720300941530.7827748493291438" style="margin: 10px 0px 16px; color: rgb(102, 102, 102); font-weight: normal; font-family: wf_segoe-ui_normal, 'Segoe UI', 'Segoe WP', Tahoma, Arial, sans-serif; font-size: 14px; line-height: 14px;" class="">
<a href="http://www.openmicroscopy.org/" class="">www.openmicroscopy.org</a></div>
<div id="LPDescription_14720300941530.8432480660267174" style="display: block; color: rgb(102, 102, 102); font-weight: normal; font-family: wf_segoe-ui_normal, 'Segoe UI', 'Segoe WP', Tahoma, Arial, sans-serif; font-size: 14px; line-height: 20px; max-height: 100px; overflow: hidden;" class="">
Uploading sample images. OMERO uses Bio-Formats to help with importing files. Any files listed as a supported format should import into OMERO.</div>
</td>
</tr>
</tbody>
</table>
</div>
<br class="">
<div class=""><br class="">
</div>
<div class="">With Thanks,</div>
<div class="">David Gault</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
<div class="">
<blockquote type="cite" class="">
<div class="">On 23 Aug 2016, at 14:42, Burki, Mubarik <<a href="mailto:z.burki.12@ucl.ac.uk" class="">z.burki.12@ucl.ac.uk</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div id="divtagdefaultwrapper" class="" style="font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; font-size: 12pt; background-color: rgb(255, 255, 255); font-family: Calibri, Arial, Helvetica, sans-serif;">
<div class="" style="margin-top: 0px; margin-bottom: 0px;">Dear All,</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;"><br class="">
</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;">I am trying to open some files using Fiji that I have previously opened several times. However, I am now unable to open my lif files and <span class="" style="font-size: 12pt;">the following error
comes up:</span></div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;"><br class="">
</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;"><br class="">
</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;"><b class=""> (Fiji Is Just) ImageJ 2.0.0-rc-49/1.51f; Java 1.8.0_66 [64-bit]; Mac OS X 10.9.5; 37MB of 1682MB (2%)</b></div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;"><b class=""> </b></div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;"><b class="">java.lang.IllegalArgumentException: order is unexpected length (4)</b></div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;"><b class=""><span class="Apple-tab-span" style="white-space: pre;"></span>at loci.formats.DimensionSwapper.swapDimensions(DimensionSwapper.java:91)</b></div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;"><b class=""><span class="Apple-tab-span" style="white-space: pre;"></span>at loci.plugins.in.ImportProcess.initializeDimOrder(ImportProcess.java:575)</b></div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;"><b class=""><span class="Apple-tab-span" style="white-space: pre;"></span>at loci.plugins.in.ImportProcess.execute(ImportProcess.java:155)</b></div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;"><b class=""><span class="Apple-tab-span" style="white-space: pre;"></span>at loci.plugins.in.Importer.showDialogs(Importer.java:140)</b></div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;"><b class=""><span class="Apple-tab-span" style="white-space: pre;"></span>at loci.plugins.in.Importer.run(Importer.java:76)</b></div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;"><b class=""><span class="Apple-tab-span" style="white-space: pre;"></span>at loci.plugins.LociImporter.run(LociImporter.java:78)</b></div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;"><b class=""><span class="Apple-tab-span" style="white-space: pre;"></span>at ij.IJ.runUserPlugIn(IJ.java:217)</b></div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;"><b class=""><span class="Apple-tab-span" style="white-space: pre;"></span>at ij.IJ.runPlugIn(IJ.java:181)</b></div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;"><b class=""><span class="Apple-tab-span" style="white-space: pre;"></span>at ij.IJ.runPlugIn(IJ.java:170)</b></div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;"><b class=""><span class="Apple-tab-span" style="white-space: pre;"></span>at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:499)</b></div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;"><b class=""><span class="Apple-tab-span" style="white-space: pre;"></span>at HandleExtraFileTypes.run(HandleExtraFileTypes.java:72)</b></div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;"><b class=""><span class="Apple-tab-span" style="white-space: pre;"></span>at ij.IJ.runUserPlugIn(IJ.java:217)</b></div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;"><b class=""><span class="Apple-tab-span" style="white-space: pre;"></span>at ij.IJ.runPlugIn(IJ.java:181)</b></div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;"><b class=""><span class="Apple-tab-span" style="white-space: pre;"></span>at ij.IJ.runPlugIn(IJ.java:170)</b></div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;"><b class=""><span class="Apple-tab-span" style="white-space: pre;"></span>at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:515)</b></div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;"><b class=""><span class="Apple-tab-span" style="white-space: pre;"></span>at ij.io.Opener.openImage(Opener.java:369)</b></div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;"><b class=""><span class="Apple-tab-span" style="white-space: pre;"></span>at ij.io.Opener.openImage(Opener.java:243)</b></div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;"><b class=""><span class="Apple-tab-span" style="white-space: pre;"></span>at ij.io.Opener.open(Opener.java:110)</b></div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;"><b class=""><span class="Apple-tab-span" style="white-space: pre;"></span>at ij.io.Opener.openAndAddToRecent(Opener.java:292)</b></div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;"><b class=""><span class="Apple-tab-span" style="white-space: pre;"></span>at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:192)</b></div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;"><b class=""><span class="Apple-tab-span" style="white-space: pre;"></span>at ij.plugin.DragAndDrop.run(DragAndDrop.java:159)</b></div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;"><b class=""><span class="Apple-tab-span" style="white-space: pre;"></span>at java.lang.Thread.run(Thread.java:745)</b></div>
<div class=""><br class="">
</div>
<div class="">I have tried updating FIJI and reinstalling it. Nothing seems to work. </div>
<div class=""><br class="">
</div>
<div class="">Please help!</div>
</div>
<span class="" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; float: none; display: inline !important;">_______________________________________________</span><br class="" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px;">
<span class="" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; float: none; display: inline !important;">ome-users
mailing list</span><br class="" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px;">
<a href="mailto:ome-users@lists.openmicroscopy.org.uk" class="" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px;">ome-users@lists.openmicroscopy.org.uk</a><br class="" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px;">
<a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users" class="" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px;">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a></div>
</blockquote>
</div>
<br class="">
</div>
<br class="">
<span style="font-size: 10pt;" class="">The University of Dundee is a registered Scottish Charity, No: SC015096</span></div>
</div>
</div>
<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">_______________________________________________</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">ome-users
mailing list</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<a href="mailto:ome-users@lists.openmicroscopy.org.uk" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">ome-users@lists.openmicroscopy.org.uk</a><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
</div>
</blockquote>
</div>
<br class="">
</div>
<br>
<span style="font-size:10pt;">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
</body>
</html>