NegativeArraySizeException when opening Metamorph nd or stk files

Dear @OMETeam,

in addition to various issues we had with bio-formats and the Metamorph format in the past, I now encountered a new bug that prevents opening a valid nd/stk dataset written with VisiView.

Opening the dataset with Plugins > Bio-Formats > Bio-Formats Importer (or dragging the .nd file onto Fiji) will throw the following exception:

(Fiji Is Just) ImageJ 2.0.0-rc-69/1.52p; Java 1.8.0_172 [64-bit]; Windows 10 10.0; 191MB of 98056MB (<1%)
 
java.lang.NegativeArraySizeException
	at loci.common.RandomAccessInputStream.readString(RandomAccessInputStream.java:632)
	at loci.formats.in.MetamorphReader.readPlaneData(MetamorphReader.java:2063)
	at loci.formats.in.MetamorphReader.parseUIC1Tags(MetamorphReader.java:1936)
	at loci.formats.in.MetamorphReader.initStandardMetadata(MetamorphReader.java:1244)
	at loci.formats.in.BaseTiffReader.initMetadata(BaseTiffReader.java:97)
	at loci.formats.in.BaseTiffReader.initFile(BaseTiffReader.java:586)
	at loci.formats.in.MetamorphReader.initFile(MetamorphReader.java:410)
	at loci.formats.FormatReader.setId(FormatReader.java:1389)
	at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:499)
	at loci.plugins.in.ImportProcess.execute(ImportProcess.java:142)
	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:230)
	at ij.IJ.runPlugIn(IJ.java:193)
	at ij.Executer.runCommand(Executer.java:137)
	at ij.Executer.run(Executer.java:66)
	at java.lang.Thread.run(Thread.java:748)

Relevant component versions:

  • formats-gpl-6.5.0.jar
  • ome-common-6.0.4.jar

I can share a dataset (23 GB) privately if you tell me where to upload.

Thank you for reporting the issue @imagejan . I have opened an initial GitHub Issue at https://github.com/ome/bioformats/issues/3578

For transferring such a large dataset, if you send me a DM on here with an email address that I can use to set up ftp credentials for you

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