[ome-users] opening .lif file in Fiji

[Stephanie Swarbreck]

Thank you very much for your suggestion. All I needed to do was un-thick the ‘Group files with similar names’ option!
Stephanie

Hi Stephanie,

This error would relate to the specific File Grouping options you have used during the import in Fiji.
I have been unable to recreate the same error message while testing.
Would you be able to provide the File Stitching options you were using with an example of the type of File Pattern you had selected?

With Thanks,
David Gault

> On 19 Jul 2016, at 16:13, Stephanie Swarbreck <ss2062 at cam.ac.uk <http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users>> wrote:
>
> Hello,
>
> I am having trouble opening .lif files using Fiji. The error message I get is pasted below. I have the newest version of Bioformat and Fiji…
> Any suggestion?
> Thanks,
> Stephanie
>
>
> (Fiji Is Just) ImageJ 2.0.0-rc-49/1.51d; Java 1.8.0_66 [64-bit]; Mac OS X 10.11.5; 106MB of 9047MB (1%)
>
> java.lang.NumberFormatException: Zero length BigInteger
> at java.math.BigInteger.<init>(BigInteger.java:411)
> at loci.formats.FilePatternBlock.explode(FilePatternBlock.java:144)
> at loci.formats.FilePatternBlock.<init>(FilePatternBlock.java:75)
> at loci.formats.FilePattern.<init>(FilePattern.java:163)
> at loci.formats.FilePattern.findSeriesPatterns(FilePattern.java:513)
> at loci.formats.FilePattern.findSeriesPatterns(FilePattern.java:487)
> at loci.formats.FileStitcher.findPatterns(FileStitcher.java:267)
> at loci.formats.FileStitcher.initFile(FileStitcher.java:916)
> at loci.formats.FileStitcher.setId(FileStitcher.java:872)
> at loci.plugins.in.ImportProcess.initializeStack(ImportProcess.java:520)
> at loci.plugins.in.ImportProcess.execute(ImportProcess.java:147)
> at loci.plugins.in.Importer.showDialogs(Importer.java:140)
> at loci.plugins.in.Importer.run(Importer.java:76)
> at loci.plugins.LociImporter.run(LociImporter.java:78)
> at ij.IJ.runUserPlugIn(IJ.java:216)
> at ij.IJ.runPlugIn(IJ.java:180)
> at ij.IJ.runPlugIn(IJ.java:169)
> at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:499)
> at HandleExtraFileTypes.run(HandleExtraFileTypes.java:72)
> at ij.IJ.runUserPlugIn(IJ.java:216)
> at ij.IJ.runPlugIn(IJ.java:180)
> at ij.IJ.runPlugIn(IJ.java:169)
> at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:515)
> at ij.io.Opener.openImage(Opener.java:369)
> at ij.io.Opener.openImage(Opener.java:243)
> at ij.io.Opener.open(Opener.java:110)
> at ij.io.Opener.openAndAddToRecent(Opener.java:292)
> at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:192)
> at ij.plugin.DragAndDrop.run(DragAndDrop.java:159)
> at java.lang.Thread.run(Thread.java:745)
>
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