Slidebook File Opening Failed

bio-formats
Tags: #<Tag:0x00007fb87d769a48>

#1

Hello,

I am trying to open a slidebook file in fiji. I have updated/redownloaded fiji as well as java. the file is approx. 200 MB and I am using a Mac. When I try to open the file, the following error message appears:

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 have opened these files before in fiji so I am not sure what has changed. Any help appreciated!

Thank you!


#2

See if the slidebook update site is enabled in the Fiji updater. The needed functionality was split a while back into native libraries provided and managed separately by 3i.


#3

You can find information on how to follow an update site at https://imagej.net/Following_an_update_site. The one you are looking for is called SlideBook.


#4

All the updates have been performed. I think it is a bug in the software.


#5

Your language here is imprecise. Are you saying that you do have the SlideBook update site enabled?


#6

Quick update on this post from a recent ome-users thread.

As mentioned by @mabruce, the 3i Slidebook reader is managed separately since Bio-Formats 5.2.0. The Slidebook update site requires the Java8 update site to be enabled in order to use a recent version of Bio-Formats compatible with the reader maintained by 3i.