[ome-users] Slide book files not opening

Amanda Balaban nabalab90 at gmail.com
Mon Mar 27 14:08:52 BST 2017 

Hi Sebasien,

I have enabled the SSlidebook site, but still am getting error messages.  Like the one below:

java.lang.ArrayIndexOutOfBoundsException: 0
	at loci.formats.in.SlidebookReader.initFile(SlidebookReader.java:634)
	at loci.formats.FormatReader.setId(FormatReader.java:1426)
	at loci.formats.ImageReader.setId(ImageReader.java:835)
	at io.scif.bf.BioFormatsFormat$Parser.typedParse(BioFormatsFormat.java:424)
	at io.scif.bf.BioFormatsFormat$Parser.typedParse(BioFormatsFormat.java:406)
	at io.scif.AbstractParser.parse(AbstractParser.java:253)
	at io.scif.AbstractParser.parse(AbstractParser.java:336)
	at io.scif.AbstractParser.parse(AbstractParser.java:52)
	at io.scif.AbstractReader.setSource(AbstractReader.java:270)
	at io.scif.services.DefaultInitializeService.initializeReader(DefaultInitializeService.java:90)
	at io.scif.img.ImgOpener.createReader(ImgOpener.java:562)
	at io.scif.img.ImgOpener.openImgs(ImgOpener.java:145)



or 

Finding offsets to pixel data
Determining dimensions
[ERROR] Exception during event handling:
	[Event] org.scijava.platform.event.AppOpenFilesEvent
	context = org.scijava.Context at 61361166
	consumed = false
	[Subscriber] net.imagej.legacy.IJ1Helper$LegacyEventDelegator at 73386d72
	[Method] private void net.imagej.legacy.IJ1Helper$LegacyEventDelegator.onEvent(org.scijava.platform.event.AppOpenFilesEvent)
java.lang.ArrayIndexOutOfBoundsException: 0
	at loci.formats.in.SlidebookReader.initFile(SlidebookReader.java:634)
	at loci.formats.FormatReader.setId(FormatReader.java:1426)
	at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:505)
	at loci.plugins.in.ImportProcess.execute(ImportProcess.java:143)
	at loci.plugins.in.Importer.showDialogs(Importer.java:140)
	at loci.plugins.in.Importer.run(Importer.java:76)
	at loci.plugins.LociImporter.run(LociImporter.java:78)
	at ij.IJ.runUserPlugIn(IJ.java:217)
	at ij.IJ.runPlugIn(IJ.java:181)
	at ij.IJ.runPlugIn(IJ.java:170)
	at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:499)
	at HandleExtraFileTypes.run(HandleExtraFileTypes.java:72)
	at ij.IJ.runUserPlugIn(IJ.java:217)
	at ij.IJ.runPlugIn(IJ.java:181)
	at ij.IJ.runPlugIn(IJ.java:170)
	at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:515)
	at ij.io.Opener.openImage(Opener.java:369)
	at ij.io.Opener.openImage(Opener.java:243)
	at ij.io.Opener.open(Opener.java:110)
	at ij.io.Opener.openAndAddToRecent(Opener.java:292)
	at net.imagej.legacy.IJ1Helper.openAndAddToRecent(IJ1Helper.java:465)
	at net.imagej.legacy.IJ1Helper$LegacyEventDelegator.onEvent(IJ1Helper.java:591)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.scijava.event.DefaultEventService$ProxySubscriber.onEvent(DefaultEventService.java:302)
	at org.scijava.event.DefaultEventService$ProxySubscriber.onEvent(DefaultEventService.java:276)
	at org.bushe.swing.event.ThreadSafeEventService.publish(ThreadSafeEventService.java:971)
	at org.scijava.event.DefaultEventBus.access$101(DefaultEventBus.java:56)
	at org.scijava.event.DefaultEventBus$1.run(DefaultEventBus.java:190)
	at org.scijava.thread.DefaultThreadService.invoke(DefaultThreadService.java:107)
	at org.scijava.event.DefaultEventBus.publishNow(DefaultEventBus.java:184)
	at org.scijava.event.DefaultEventBus.publishNow(DefaultEventBus.java:75)
	at org.scijava.event.DefaultEventService.publish(DefaultEventService.java:104)
	at org.scijava.plugins.platforms.osx.OSXAppEventDispatcher.openFiles(OSXAppEventDispatcher.java:205)
	at com.apple.eawt._AppEventHandler$_OpenFileDispatcher.performUsing(_AppEventHandler.java:361)
	at com.apple.eawt._AppEventHandler$_OpenFileDispatcher.performUsing(_AppEventHandler.java:352)
	at com.apple.eawt._AppEventHandler$_AppEventDispatcher$1.run(_AppEventHandler.java:516)
	at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)
	at java.awt.EventQueue.access$500(EventQueue.java:97)
	at java.awt.EventQueue$3.run(EventQueue.java:709)
	at java.awt.EventQueue$3.run(EventQueue.java:703)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:726)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
	at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)

My files are too large to send over email.  Do you have another mechanism by which I cans end you an example data set?

Thank you for your help!!!

Amanda

> On Mar 24, 2017, at 4:21 AM, Sebastien Besson (Staff) <s.besson at dundee.ac.uk> wrote:
> 
> Hi Amanda,
> 
> thanks for contacting us. 
> 
> As mentioned in a related ImageJ forum thread [1], modern Slidebook files now require
> the enabling of the 3i Slidebook update site to open in Fiji - see their instructions [2].
> 
> Can you check whether this update site is enabled and the images still fail to open? If this
> remains the case, we might need a failing sample file before engaging with 3i to discuss the
> issue.
> 
> Best,
> Sebastien
> 
> 
> [1] http://forum.imagej.net/t/slidebook-file-opening-failed/4533 <http://forum.imagej.net/t/slidebook-file-opening-failed/4533>
> [2] https://support.intelligent-imaging.com/techanswers.php#SLDinFiji <https://support.intelligent-imaging.com/techanswers.php#SLDinFiji> 
> 
>> On 23 Mar 2017, at 16:27, Amanda Balaban <nabalab90 at gmail.com <mailto:nabalab90 at gmail.com>> wrote:
>> 
>> Hello,
>> 
>> Hello. I have been receiving an error message when attempting to open a slide book file in fiji.
>> 
>> Exception in thread "DrawAndDrop" java.lang.ArrayIndexOutOfBoundsException: 0
>> at loci.formats.in.SlidebookReader.initFile(SlidebookReader.java:634)
>> at loci.formats.FormatReader.setId(FormatReader.java:1399)
>> at loci.formats.ImageReader.setId(ImageReader.java:839)
>> at io.scif.bf.BioFormatsFormat$Parser.typedParse(BioFormatsFormat.java:431)
>> at io.scif.bf.BioFormatsFormat$Parser.typedParse(BioFormatsFormat.java:413)
>> at io.scif.AbstractParser.parse(AbstractParser.java:253)
>> at io.scif.AbstractParser.parse(AbstractParser.java:336)
>> at io.scif.AbstractParser.parse(AbstractParser.java:52)
>> at io.scif.AbstractReader.setSource(AbstractReader.java:270)
>> at io.scif.services.DefaultInitializeService.initializeReader(DefaultInitializeService.java:90)
>> at io.scif.img.ImgOpener.createReader(ImgOpener.java:562)
>> at io.scif.img.ImgOpener.openImgs(ImgOpener.java:145)
>> at io.scif.services.DefaultDatasetIOService.open(DefaultDatasetIOService.java:126)
>> at io.scif.services.DefaultDatasetIOService.open(DefaultDatasetIOService.java:111)
>> at io.scif.io.DatasetIOPlugin.open(DatasetIOPlugin.java:75)
>> at io.scif.io.DatasetIOPlugin.open(DatasetIOPlugin.java:50)
>> at net.imagej.legacy.plugin.DefaultLegacyOpener.open(DefaultLegacyOpener.java:135)
>> at net.imagej.legacy.DefaultLegacyHooks.interceptDragAndDropFile(DefaultLegacyHooks.java:363)
>> at ij.plugin.DragAndDrop.openFile(DragAndDrop.java)
>> at ij.plugin.DragAndDrop.run(DragAndDrop.java:159)
>> at java.lang.Thread.run(Thread.java:745)
>> 
>> 
>> 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.
>> 
>> Thank you,
>> 
>> Amanda
>> _______________________________________________
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>> ome-users at lists.openmicroscopy.org.uk <mailto:ome-users at lists.openmicroscopy.org.uk>
>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
> 
> 
> The University of Dundee is a registered Scottish Charity, No: SC015096
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