[ome-users] Error message help using Bio-Formats 5.1.3 in (Fiji is Just)ImageJ 64-bit

[Melissa Linkert]

Hi Anna,

> When I attempt to open my .lif files (I cannot attach them, they are too large) taken on a Leica Scanning Confocal Microscope, in the Bio-Formats Importer, I get the following error message:
> 
> (Fiji Is Just) ImageJ 2.0.0-rc-34/1.50a; Java 1.6.0_24 [64-bit]; Windows 7 6.1; 58MB of 6079MB (<1%)
> java.lang.ArrayIndexOutOfBoundsException: 0
>                 at loci.formats.FileStitcher.initFile(FileStitcher.java:892)
>                 at loci.formats.FileStitcher.setId(FileStitcher.java:872)
>                 at loci.plugins.in.ImportProcess.initializeStack(ImportProcess.java:522)
>                 at loci.plugins.in.ImportProcess.execute(ImportProcess.java:147)
>                 at loci.plugins.in.Importer.showDialogs(Importer.java:137)
>                 at loci.plugins.in.Importer.run(Importer.java:75)
>                 at loci.plugins.LociImporter.run(LociImporter.java:78)
>                 at ij.IJ.runUserPlugIn(IJ.java:212)
>                 at ij.IJ.runPlugIn(IJ.java:176)
>                 at ij.Executer.runCommand(Executer.java:132)
>                 at ij.Executer.run(Executer.java:65)
>                 at java.lang.Thread.run(Thread.java:662)
> 
> I used to be able to open all of my .lif files, but starting last week this was no longer possible. What do I need to do to work around this message and open my files again?

Is the "Group files with similar names" option checked in the
"Bio-Formats Import Options" windows?  If so, does unchecking that
option solve the problem?

If that doesn't work, could you please send the name of the file, and
the names of any other files that are in the same folder?  We don't need
the actual files yet, just the complete file names.

Regards,
-Melissa

On Mon, Aug 17, 2015 at 03:18:21PM +0000, Boudoures, Anna wrote:
> To whom it may concern -
> 
> When I attempt to open my .lif files (I cannot attach them, they are too large) taken on a Leica Scanning Confocal Microscope, in the Bio-Formats Importer, I get the following error message:
> 
> (Fiji Is Just) ImageJ 2.0.0-rc-34/1.50a; Java 1.6.0_24 [64-bit]; Windows 7 6.1; 58MB of 6079MB (<1%)
> java.lang.ArrayIndexOutOfBoundsException: 0
>                 at loci.formats.FileStitcher.initFile(FileStitcher.java:892)
>                 at loci.formats.FileStitcher.setId(FileStitcher.java:872)
>                 at loci.plugins.in.ImportProcess.initializeStack(ImportProcess.java:522)
>                 at loci.plugins.in.ImportProcess.execute(ImportProcess.java:147)
>                 at loci.plugins.in.Importer.showDialogs(Importer.java:137)
>                 at loci.plugins.in.Importer.run(Importer.java:75)
>                 at loci.plugins.LociImporter.run(LociImporter.java:78)
>                 at ij.IJ.runUserPlugIn(IJ.java:212)
>                 at ij.IJ.runPlugIn(IJ.java:176)
>                 at ij.Executer.runCommand(Executer.java:132)
>                 at ij.Executer.run(Executer.java:65)
>                 at java.lang.Thread.run(Thread.java:662)
> 
> I used to be able to open all of my .lif files, but starting last week this was no longer possible. What do I need to do to work around this message and open my files again?
> 
> Anna

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