That implies you have a set of JAR mismatches Oli and is not a bug with the reader. Do you still have loci_tools.jar in your Fiji plugins folder?
For now the solution that has worked is as follows.
1. Get a new Fiji and update to latest version of everything using the built-in updater.
a. This still generates the error I had sent on the first post
2. Use LOCI->Update LOCI Plugins->Stable Build (4.3)
Rename loci_plugins-4.4-SNAPSHOT.jar to some other extension
Use the old loci-tools.jar
So far using the latest build is troublesome and until I can know where this is coming from I cannot update the LOCI plugins for our machines.
Let me know if you managed to replicate this error. It happens with every VSI file for us.
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 ij.Command.runPlugIn(Command.java:146)
at ij.Command.runCommand(Command.java:95)
at ij.Executer.run(Executer.java:64)
at java.lang.Thread.run(Thread.java:662)
Caused by: java.lang.NoSuchMethodError: loci.common.Region.intersects(Lloci/common/Region;)Z
at loci.formats.in.CellSensReader.openBytes(CellSensReader.java:250)
at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:197)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:226)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:318)
at loci.formats.DimensionSwapper.openBytes(DimensionSwapper.java:255)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:318)
at loci.formats.MinMaxCalculator.openBytes(MinMaxCalculator.java:273)
at loci.formats.MinMaxCalculator.openBytes(MinMaxCalculator.java:265)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:306)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:306)
at loci.plugins.util.ImageProcessorReader.openProcessors(ImageProcessorReader.java:190)
at loci.plugins.in.ImagePlusReader.readProcessors(ImagePlusReader.java:416)
at loci.plugins.in.ImagePlusReader.readPlanes(ImagePlusReader.java:380)
at loci.plugins.in.ImagePlusReader.readImage(ImagePlusReader.java:277)
at loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:238)
at loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:216)
at loci.plugins.in.ImagePlusReader.openImagePlus(ImagePlusReader.java:114)
at loci.plugins.in.Importer.readPixels(Importer.java:150)
at loci.plugins.in.Importer.run(Importer.java:89)
at loci.plugins.LociImporter.run(LociImporter.java:81)
at ij.IJ.runUserPlugIn(IJ.java:184)
at ij.IJ.runPlugIn(IJ.java:151)
... 8 more
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:4020)
at ij.macro.Functions.getStringFunction(Functions.java:260)
at ij.macro.Interpreter.getStringTerm(Interpreter.java:1209)
at ij.macro.Interpreter.getString(Interpreter.java:1188)
at ij.macro.Interpreter.doStatement(Interpreter.java:264)
at ij.macro.Interpreter.doStatements(Interpreter.java:207)
at ij.macro.Interpreter.run(Interpreter.java:104)
at ij.macro.Interpreter.run(Interpreter.java:74)
at ij.macro.MacroRunner.run(MacroRunner.java:130)
at java.lang.Thread.run(Thread.java:662)
Caused by: loci.common.enumeration.EnumException: Unable to find TiffCompresssion with code: 34712
at loci.formats.tiff.TiffCompression.get(TiffCompression.java:220)
at loci.formats.tiff.IFD.getCompression(IFD.java:664)
at loci.formats.tiff.IFD.getSamplesPerPixel(IFD.java:638)
at loci.formats.in.CellSensReader.initFile(CellSensReader.java:435)
at loci.formats.FormatReader.setId(FormatReader.java:1238)
at loci.formats.ImageReader.setId(ImageReader.java:742)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:552)
at loci.formats.DimensionSwapper.setId(DimensionSwapper.java:285)
at loci.formats.FileStitcher.initFile(FileStitcher.java:839)
at loci.formats.FileStitcher.setId(FileStitcher.java:803)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:552)
at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:274)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:552)
at loci.plugins.macro.LociFunctions.setId(LociFunctions.java:398)
... 16 more
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