[ome-users] Slide book files not opening

Mon Mar 27 15:30:15 BST 2017

Hi Amanda,

glad enabling the update site fixed the problem for you. Could you also update the
ImageJ forum thread to let them know the issue is resolved?

Best,
Sebastien

On 27 Mar 2017, at 15:23, Amanda Balaban <nabalab90 at gmail.com<mailto:nabalab90 at gmail.com>> wrote:

Hi Sebastien,

Seems the Java site was the problem!  Thank you so much for your help!!!!!

Amanda

On Mar 27, 2017, at 10:06 AM, Sebastien Besson (Staff) <s.besson at dundee.ac.uk<mailto:s.besson at dundee.ac.uk>> wrote:

HI Amanda,

It looks like the legacy reader is still chosen and fails to open the file.

One additional check/question: can you tell us which update sites are enabled in your
Fiji distribution? The new Slidebook reader is only available since Bio-Formats 5.2.0 and
currently requires the Java8 update site to be enabled.

If your sample file size is lower than 2GB, you should be able to upload it at this URL [1].

Best,
Sebastien

[1] http://qa.openmicroscopy.org.uk/qa/upload/

On 27 Mar 2017, at 14:08, Amanda Balaban <nabalab90 at gmail.com<mailto:nabalab90 at gmail.com>> wrote:

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<mailto: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
[2] 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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