<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi Sebastien,<div class=""><br class=""></div><div class="">Seems the Java site was the problem! Thank you so much for your help!!!!!</div><div class=""><br class=""></div><div class="">Amanda</div><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Mar 27, 2017, at 10:06 AM, Sebastien Besson (Staff) <<a href="mailto:s.besson@dundee.ac.uk" class="">s.besson@dundee.ac.uk</a>> wrote:</div><br class="Apple-interchange-newline"><div class="">
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii" class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
HI Amanda,
<div class=""><br class="">
</div>
<div class="">It looks like the legacy reader is still chosen and fails to open the file.</div>
<div class=""><br class="">
</div>
<div class="">One additional check/question: can you tell us which update sites are enabled in your</div>
<div class="">Fiji distribution? The new Slidebook reader is only available since Bio-Formats 5.2.0 and</div>
<div class="">currently requires the Java8 update site to be enabled.</div>
<div class=""><br class="">
</div>
<div class="">
<div class="">If your sample file size is lower than 2GB, you should be able to upload it at this URL [1].</div>
</div>
<div class=""><br class="">
</div>
<div class="">Best,</div>
<div class="">Sebastien</div>
<div class=""><br class="">
</div>
<div class="">[1] <a href="http://qa.openmicroscopy.org.uk/qa/upload/" class="">http://qa.openmicroscopy.org.uk/qa/upload/</a></div>
<div class=""><br class="">
</div>
<div class=""><br class="">
<div class="">
<div class="">
<blockquote type="cite" class="">
<div class="">On 27 Mar 2017, at 14:08, Amanda Balaban <<a href="mailto:nabalab90@gmail.com" class="">nabalab90@gmail.com</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
Hi Sebasien,
<div class=""><br class="">
</div>
<div class="">I have enabled the SSlidebook site, but still am getting error messages. Like the one below:</div>
<div class=""><br class="">
</div>
<div class="">
<div class="">java.lang.ArrayIndexOutOfBoundsException: 0</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at loci.formats.in.SlidebookReader.initFile(SlidebookReader.java:634)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at loci.formats.FormatReader.setId(FormatReader.java:1426)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at loci.formats.ImageReader.setId(ImageReader.java:835)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at io.scif.bf.BioFormatsFormat$Parser.typedParse(BioFormatsFormat.java:424)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at io.scif.bf.BioFormatsFormat$Parser.typedParse(BioFormatsFormat.java:406)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at io.scif.AbstractParser.parse(AbstractParser.java:253)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at io.scif.AbstractParser.parse(AbstractParser.java:336)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at io.scif.AbstractParser.parse(AbstractParser.java:52)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at io.scif.AbstractReader.setSource(AbstractReader.java:270)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at io.scif.services.DefaultInitializeService.initializeReader(DefaultInitializeService.java:90)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at io.scif.img.ImgOpener.createReader(ImgOpener.java:562)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at io.scif.img.ImgOpener.openImgs(ImgOpener.java:145)</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">or </div>
<div class=""><br class="">
</div>
<div class="">
<div class="">Finding offsets to pixel data</div>
<div class="">Determining dimensions</div>
<div class="">[ERROR] Exception during event handling:</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>[Event] org.scijava.platform.event.AppOpenFilesEvent</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>context = org.scijava.Context@61361166</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>consumed = false</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>[Subscriber] net.imagej.legacy.IJ1Helper$LegacyEventDelegator@73386d72</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>[Method] private void net.imagej.legacy.IJ1Helper$LegacyEventDelegator.onEvent(org.scijava.platform.event.AppOpenFilesEvent)</div>
<div class="">java.lang.ArrayIndexOutOfBoundsException: 0</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at loci.formats.in.SlidebookReader.initFile(SlidebookReader.java:634)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at loci.formats.FormatReader.setId(FormatReader.java:1426)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:505)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at loci.plugins.in.ImportProcess.execute(ImportProcess.java:143)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at loci.plugins.in.Importer.showDialogs(Importer.java:140)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at loci.plugins.in.Importer.run(Importer.java:76)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at loci.plugins.LociImporter.run(LociImporter.java:78)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at ij.IJ.runUserPlugIn(IJ.java:217)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at ij.IJ.runPlugIn(IJ.java:181)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at ij.IJ.runPlugIn(IJ.java:170)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:499)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at HandleExtraFileTypes.run(HandleExtraFileTypes.java:72)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at ij.IJ.runUserPlugIn(IJ.java:217)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at ij.IJ.runPlugIn(IJ.java:181)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at ij.IJ.runPlugIn(IJ.java:170)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:515)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at ij.io.Opener.openImage(Opener.java:369)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at ij.io.Opener.openImage(Opener.java:243)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at ij.io.Opener.open(Opener.java:110)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at ij.io.Opener.openAndAddToRecent(Opener.java:292)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at net.imagej.legacy.IJ1Helper.openAndAddToRecent(IJ1Helper.java:465)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at net.imagej.legacy.IJ1Helper$LegacyEventDelegator.onEvent(IJ1Helper.java:591)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at java.lang.reflect.Method.invoke(Method.java:498)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at org.scijava.event.DefaultEventService$ProxySubscriber.onEvent(DefaultEventService.java:302)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at org.scijava.event.DefaultEventService$ProxySubscriber.onEvent(DefaultEventService.java:276)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at org.bushe.swing.event.ThreadSafeEventService.publish(ThreadSafeEventService.java:971)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at org.scijava.event.DefaultEventBus.access$101(DefaultEventBus.java:56)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at org.scijava.event.DefaultEventBus$1.run(DefaultEventBus.java:190)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at org.scijava.thread.DefaultThreadService.invoke(DefaultThreadService.java:107)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at org.scijava.event.DefaultEventBus.publishNow(DefaultEventBus.java:184)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at org.scijava.event.DefaultEventBus.publishNow(DefaultEventBus.java:75)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at org.scijava.event.DefaultEventService.publish(DefaultEventService.java:104)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at org.scijava.plugins.platforms.osx.OSXAppEventDispatcher.openFiles(OSXAppEventDispatcher.java:205)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at com.apple.eawt._AppEventHandler$_OpenFileDispatcher.performUsing(_AppEventHandler.java:361)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at com.apple.eawt._AppEventHandler$_OpenFileDispatcher.performUsing(_AppEventHandler.java:352)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at com.apple.eawt._AppEventHandler$_AppEventDispatcher$1.run(_AppEventHandler.java:516)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at java.awt.EventQueue.access$500(EventQueue.java:97)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at java.awt.EventQueue$3.run(EventQueue.java:709)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at java.awt.EventQueue$3.run(EventQueue.java:703)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at java.security.AccessController.doPrivileged(Native Method)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at java.awt.EventQueue.dispatchEvent(EventQueue.java:726)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)</div>
</div>
<div class=""><br class="">
</div>
<div class="">My files are too large to send over email. Do you have another mechanism by which I cans end you an example data set?</div>
<div class=""><br class="">
</div>
<div class="">Thank you for your help!!!</div>
<div class=""><br class="">
</div>
<div class="">Amanda</div>
<div class=""><br class="">
</div>
<div class="">
<blockquote type="cite" class="">
<div class="">On Mar 24, 2017, at 4:21 AM, Sebastien Besson (Staff) <<a href="mailto:s.besson@dundee.ac.uk" class="">s.besson@dundee.ac.uk</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
Hi Amanda,</div>
</div>
</blockquote>
<blockquote type="cite" class="">
<div class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
<div class=""><br class="">
</div>
<div class="">thanks for contacting us. </div>
<div class=""><br class="">
</div>
<div class="">As mentioned in a related ImageJ forum thread [1], modern Slidebook files now require</div>
<div class="">the enabling of the 3i Slidebook update site to open in Fiji - see their instructions [2].</div>
<div class=""><br class="">
</div>
<div class="">Can you check whether this update site is enabled and the images still fail to open? If this</div>
<div class="">remains the case, we might need a failing sample file before engaging with 3i to discuss the</div>
<div class="">issue.</div>
<div class=""><br class="">
</div>
<div class="">Best,</div>
<div class="">Sebastien</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">[1] <a href="http://forum.imagej.net/t/slidebook-file-opening-failed/4533" class="">http://forum.imagej.net/t/slidebook-file-opening-failed/4533</a></div>
<div class="">[2] <a href="https://support.intelligent-imaging.com/techanswers.php#SLDinFiji" class="">https://support.intelligent-imaging.com/techanswers.php#SLDinFiji</a> </div>
<div class=""><br class="">
</div>
<div class="">
<div class="">
<blockquote type="cite" class="">
<div class="">On 23 Mar 2017, at 16:27, Amanda Balaban <<a href="mailto:nabalab90@gmail.com" class="">nabalab90@gmail.com</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">Hello,<br class="">
<br class="">
Hello. I have been receiving an error message when attempting to open a slide book file in fiji.<br class="">
<br class="">
Exception in thread "DrawAndDrop" java.lang.ArrayIndexOutOfBoundsException: 0<br class="">
at loci.formats.in.SlidebookReader.initFile(SlidebookReader.java:634)<br class="">
at loci.formats.FormatReader.setId(FormatReader.java:1399)<br class="">
at loci.formats.ImageReader.setId(ImageReader.java:839)<br class="">
at io.scif.bf.BioFormatsFormat$Parser.typedParse(BioFormatsFormat.java:431)<br class="">
at io.scif.bf.BioFormatsFormat$Parser.typedParse(BioFormatsFormat.java:413)<br class="">
at io.scif.AbstractParser.parse(AbstractParser.java:253)<br class="">
at io.scif.AbstractParser.parse(AbstractParser.java:336)<br class="">
at io.scif.AbstractParser.parse(AbstractParser.java:52)<br class="">
at io.scif.AbstractReader.setSource(AbstractReader.java:270)<br class="">
at io.scif.services.DefaultInitializeService.initializeReader(DefaultInitializeService.java:90)<br class="">
at io.scif.img.ImgOpener.createReader(ImgOpener.java:562)<br class="">
at io.scif.img.ImgOpener.openImgs(ImgOpener.java:145)<br class="">
at io.scif.services.DefaultDatasetIOService.open(DefaultDatasetIOService.java:126)<br class="">
at io.scif.services.DefaultDatasetIOService.open(DefaultDatasetIOService.java:111)<br class="">
at io.scif.io.DatasetIOPlugin.open(DatasetIOPlugin.java:75)<br class="">
at io.scif.io.DatasetIOPlugin.open(DatasetIOPlugin.java:50)<br class="">
at net.imagej.legacy.plugin.DefaultLegacyOpener.open(DefaultLegacyOpener.java:135)<br class="">
at net.imagej.legacy.DefaultLegacyHooks.interceptDragAndDropFile(DefaultLegacyHooks.java:363)<br class="">
at ij.plugin.DragAndDrop.openFile(DragAndDrop.java)<br class="">
at ij.plugin.DragAndDrop.run(DragAndDrop.java:159)<br class="">
at java.lang.Thread.run(Thread.java:745)<br class="">
<br class="">
<br class="">
I am running this on a Mac. Have updated/reinstalled the latest version of fiji and java. I have also tried this on other computers/fiji downloads witht he same result.<br class="">
<br class="">
Thank you,<br class="">
<br class="">
Amanda<br class="">
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