[ome-users] Problem opening VSI file

[Filipe De Vadder]

Hello,
I have had some trouble opening VSI files on FIJI. If I try to open them using Bioformats on hyper stack (but the other options are not working either), here is the message that I get: 
(Fiji Is Just) ImageJ 2.0.0-rc-15/1.49k; Java 1.6.0_65 [64-bit]; Mac OS X 10.10; 22MB of 1067MB (2%) 
  
java.lang.IllegalArgumentException: Invalid series: 0 
        at loci.formats.FormatReader.seriesToCoreIndex(FormatReader.java:1198) 
        at loci.formats.FormatReader.setSeries(FormatReader.java:927) 
        at loci.formats.MetadataTools.populatePixels(MetadataTools.java:179) 
        at loci.formats.MetadataTools.populatePixels(MetadataTools.java:97) 
        at loci.formats.in.CellSensReader.initFile(CellSensReader.java:456) 
        at loci.formats.FormatReader.setId(FormatReader.java:1317) 
        at loci.formats.ImageReader.setId(ImageReader.java:753) 
        at io.scif.bf.BioFormatsFormat$Parser.typedParse(BioFormatsFormat.java:406) 
        at io.scif.bf.BioFormatsFormat$Parser.typedParse(BioFormatsFormat.java:388) 
        at io.scif.AbstractParser.parse(AbstractParser.java:252) 
        at io.scif.AbstractParser.parse(AbstractParser.java:335) 
        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:542) 
        at io.scif.img.ImgOpener.openImgs(ImgOpener.java:144) 
        at net.imagej.DefaultDatasetService.open(DefaultDatasetService.java:266) 
        at net.imagej.DefaultDatasetService.open(DefaultDatasetService.java:250) 
        at net.imagej.io.DatasetIOPlugin.open(DatasetIOPlugin.java:78) 
        at net.imagej.io.DatasetIOPlugin.open(DatasetIOPlugin.java:50) 
        at net.imagej.legacy.plugin.DefaultLegacyOpener.open(DefaultLegacyOpener.java:134) 
        at net.imagej.legacy.DefaultLegacyHooks.interceptFileOpen(DefaultLegacyHooks.java:327) 
        at net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:150) 
        at ij.IJ.runPlugIn(IJ.java) 
        at ij.Executer.runCommand(Executer.java:131) 
        at ij.Executer.run(Executer.java:64) 
        at java.lang.Thread.run(Thread.java:695) 

I have tried to open on Windows but still the same message.
If I try to open it using BIOP plugin, I also get a "macro error" message: 
Relative Path, adding Path to Fiji 
Full path to BIOPLib :/Applications/Fiji.app/plugins/BIOP/BIOPLib.ijm 
Empty Library. Adding BIOPLib Library. 
java.lang.reflect.InvocationTargetException 
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) 
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) 
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) 
        at java.lang.reflect.Method.invoke(Method.java:597) 
        at loci.plugins.macro.MacroFunctions.handleExtension(MacroFunctions.java:83) 
        at ij.macro.ExtensionDescriptor.dispatch(ExtensionDescriptor.java:288) 
        at ij.macro.Functions.doExt(Functions.java:4261) 
        at ij.macro.Functions.getStringFunction(Functions.java:267) 
        at ij.macro.Interpreter.getStringTerm(Interpreter.java:1283) 
        at ij.macro.Interpreter.getString(Interpreter.java:1262) 
        at ij.macro.Interpreter.doStatement(Interpreter.java:277) 
        at ij.macro.Interpreter.doBlock(Interpreter.java:598) 
        at ij.macro.Interpreter.runUserFunction(Interpreter.java:307) 
        at ij.macro.Interpreter.doUserFunctionAssignment(Interpreter.java:877) 
        at ij.macro.Interpreter.doAssignment(Interpreter.java:717) 
        at ij.macro.Interpreter.doStatement(Interpreter.java:241) 
        at ij.macro.Interpreter.doStatements(Interpreter.java:214) 
        at ij.macro.Interpreter.run(Interpreter.java:111) 
        at ij.macro.Interpreter.run(Interpreter.java:81) 
        at ij.macro.MacroRunner.run(MacroRunner.java:139) 
        at java.lang.Thread.run(Thread.java:695) 
Caused by: java.lang.IllegalArgumentException: Invalid series: 0 
        at loci.formats.FormatReader.seriesToCoreIndex(FormatReader.java:1198) 
        at loci.formats.FormatReader.setSeries(FormatReader.java:927) 
        at loci.formats.MetadataTools.populatePixels(MetadataTools.java:179) 
        at loci.formats.MetadataTools.populatePixels(MetadataTools.java:97) 
        at loci.formats.in.CellSensReader.initFile(CellSensReader.java:456) 
        at loci.formats.FormatReader.setId(FormatReader.java:1317) 
        at loci.formats.ImageReader.setId(ImageReader.java:753) 
        at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:569) 
        at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:270) 
        at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:569) 
        at loci.plugins.macro.LociFunctions.setId(LociFunctions.java:402) 
        ... 21 more 

I have ticked the updates from both Bioformats, LOCI and BIOP and my software is up to date. I really don't know what is going on. My bioformats version is the latest release.
If you want, you can access the file I am trying to open (and all other files in the same folder) at:  http://dl.free.fr/gNluLSgVz <http://dl.free.fr/gNluLSgVz>
I hope this is enough to know what is going on.
Your help will be very much appreciated. 
Thanks a lot, 
Filipe

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