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Bug 110 - Can't open Olympus oib files in Fiji
Can't open Olympus oib files in Fiji
Status: RESOLVED WORKSFORME
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Windows
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2009-11-30 09:44 CST by Jack Fransen
Modified: 2010-01-11 10:35 CST
1 user (show)

See Also:
Description Jack Fransen 2009-11-30 09:44:04 CST 
In fiji we encountered the problem that we cannot open Olympus .oib files anymore. In ImageJ we still can open them. Both have the latest versions of LOCI. See below the exception we get.
Hope you can help us

java.lang.NullPointerException
	at java.util.Hashtable.get(Hashtable.java:334)
	at loci.formats.POITools.getFileSize(POITools.java:109)
	at loci.formats.POITools.getDocumentStream(POITools.java:82)
	at loci.formats.in.FV1000Reader.getFile(FV1000Reader.java:1264)
	at loci.formats.in.FV1000Reader.openBytes(FV1000Reader.java:210)
	at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:273)
	at loci.formats.DimensionSwapper.openBytes(DimensionSwapper.java:255)
	at loci.formats.FileStitcher.openBytes(FileStitcher.java:461)
	at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:191)
	at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:157)
	at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:261)
	at loci.formats.DimensionSwapper.openBytes(DimensionSwapper.java:239)
	at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:261)
	at loci.plugins.util.ImagePlusReader.openProcessors(ImagePlusReader.java:167)
	at loci.plugins.util.ImagePlusReader.openProcessors(ImagePlusReader.java:144)
	at loci.plugins.util.ImageProcessorSource.getObject(ImageProcessorSource.java:72)
	at loci.formats.cache.Cache.recache(Cache.java:199)
	at loci.formats.cache.Cache.recache(Cache.java:219)
	at loci.formats.cache.Cache.<init>(Cache.java:83)
	at loci.plugins.util.BFVirtualStack.<init>(BFVirtualStack.java:114)
	at loci.plugins.importer.Importer.run(Importer.java:610)
	at loci.plugins.LociImporter.run(LociImporter.java:77)
	at ij.IJ.runUserPlugIn(IJ.java:184)
	at ij.IJ.runPlugIn(IJ.java:151)
	at ij.IJ.runPlugIn(IJ.java:140)
	at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:300)
	at HandleExtraFileTypes.run(HandleExtraFileTypes.java:38)
	at ij.IJ.runUserPlugIn(IJ.java:184)
	at ij.IJ.runPlugIn(IJ.java:151)
	at ij.IJ.runPlugIn(IJ.java:140)
	at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:386)
	at ij.io.Opener.openImage(Opener.java:280)
	at ij.io.Opener.openImage(Opener.java:303)
	at ij.io.Opener.open(Opener.java:140)
	at ij.io.Opener.open(Opener.java:68)
	at ij.plugin.Commands.run(Commands.java:23)
	at ij.IJ.runPlugIn(IJ.java:157)
	at ij.Executer.runCommand(Executer.java:145)
	at ij.Executer.run(Executer.java:76)
	at java.lang.Thread.run(Thread.java:619)


Information about your version of Java - this information is useful for the Fiji developers:
  os.arch => x86
  os.name => Windows XP
  os.version => 5.1
  java.version => 1.6.0_16
  java.vendor => Sun Microsystems Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_16-b01
  java.vm.name => Java HotSpot(TM) Client VM
  java.vm.version => 14.2-b01
  java.vm.vendor => Sun Microsystems Inc.
  java.vm.info => mixed mode
  java.awt.graphicsenv => sun.awt.Win32GraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => windows
  file.separator => \
Comment 1 Greg Jefferis 2009-11-30 14:25:16 CST 
Just a couple of thoughts

1) Have you actually tried updating loci using Plugins ... Loci ... Update Loci Plugins?
2) Does it make any difference if you open images directly using Plugins ... Loci ... Bio-Formats Importer rather than File ... Open

Best,

Greg.
Comment 2 Jack Fransen 2009-12-02 09:19:24 CST 
Dear Greg

Yes we updated the LOCI plugin and I just checked it again with the latest version. It also happens when we try to open them via the LOCI data browser or bio-formats importer.
In the mean time we can work since we open them in the olympus software and save them afterwards in the other olympus format .oif

Hope you can use this info

Best wishes
Jack

(In reply to comment #1)
> Just a couple of thoughts
> 
> 1) Have you actually tried updating loci using Plugins ... Loci ... Update Loci
> Plugins?
> 2) Does it make any difference if you open images directly using Plugins ...
> Loci ... Bio-Formats Importer rather than File ... Open
> 
> Best,
> 
> Greg.
>
Comment 3 Curtis Rueden 2010-01-08 20:01:31 CST 
I was unable to duplicate this issue with the latest version of Fiji on my Mac OS X 10.6 system. Do OIB files still fail for anyone, and if so, is it all OIBs, or only specific ones? If specific ones, could someone provide a sample non-working dataset?
Comment 4 Jean-Yves Tinevez 2010-01-11 10:35:24 CST 
(In reply to comment #3)
> I was unable to duplicate this issue with the latest version of Fiji on my Mac
> OS X 10.6 system. Do OIB files still fail for anyone, and if so, is it all
> OIBs, or only specific ones? If specific ones, could someone provide a sample
> non-working dataset?
> 

It works on all the oib files I have (1-3 channels, 100-500 time points, 2 series). I am unable to provide a data set for which LOCI fails.