Problem opening multi-scene .czi images with fiji/bioformats

Hi all,

I have some images taken on a Zeiss Elyra microscope. essentially, I have single snapshots taken at different locations. The .czi format saves information on this as an additional dimension (dimensions are XYCZTSB, S is series, not sure what B is). When I try to open multi-scene czi images with bioformats, it fails to open the file and kicks up the following error:

java.lang.NumberFormatException: null
	at java.lang.Integer.parseInt(Integer.java:542)
	at java.lang.Integer.parseInt(Integer.java:615)
	at loci.formats.in.ZeissCZIReader.translateExperiment(ZeissCZIReader.java:2268)
	at loci.formats.in.ZeissCZIReader.translateMetadata(ZeissCZIReader.java:1329)
	at loci.formats.in.ZeissCZIReader.initFile(ZeissCZIReader.java:731)
	at loci.formats.FormatReader.setId(FormatReader.java:1426)
	at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:505)
	at loci.plugins.in.ImportProcess.execute(ImportProcess.java:143)
	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.Executer.runCommand(Executer.java:137)
	at ij.Executer.run(Executer.java:66)
	at java.lang.Thread.run(Thread.java:745)

This doesn’t happen with single scene images, stacks or videos which have no header data beyond the five dimensions that bioformats uses - XYCZT

If I split the scenes, the output files still have S and B fields, each with a value of 1 in all images and they still refuse to open in FIJI.

Can anyone help me with this?

Thanks,

O

Thanks for the report, @Oliver. FYI, some members of the OME team do monitor this forum, but the most surefire way to report Bio-Formats bugs is via the OME bug reporting mechanisms. So if you don’t hear back within some days, that would be your best bet.

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