[ome-users] Multi-part .czi files, again

[Lorenz Maier]

Hi everyone,

I've just uplodaed a multi-file .czi to https://www.openmicroscopy.org/qa2/qa2/qa/feedback/7387/

Opening the ...(2).czi with bioformats-4.5 dev (quite recent version of fiji) returns an empty first scene instead the second image only.
I also have bigger files with more scenes, there ...(8).czi returns 7 empty scenes and then the actual image.

With bioformats-5.0.0 beta 1, I get an exception when opening it:

ImageJ 1.47t; Java 1.7.0_21 [64-bit]; Windows 7 6.1; 52MB of 6400MB (<1%)
 
java.lang.IllegalArgumentException: Invalid T index: 1/1
	at loci.formats.FormatTools.getIndex(FormatTools.java:344)
	at loci.formats.FormatTools.getIndex(FormatTools.java:289)
	at loci.formats.FormatReader.getIndex(FormatReader.java:1044)
	at loci.formats.in.ZeissCZIReader.assignPlaneIndices(ZeissCZIReader.java:929)
	at loci.formats.in.ZeissCZIReader.initFile(ZeissCZIReader.java:562)
	at loci.formats.FormatReader.setId(FormatReader.java:1333)
	at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:482)
	at loci.plugins.in.ImportProcess.execute(ImportProcess.java:146)
	at loci.plugins.in.Importer.showDialogs(Importer.java:141)
	at loci.plugins.in.Importer.run(Importer.java:79)
	at loci.plugins.LociImporter.run(LociImporter.java:81)
	at ij.IJ.runUserPlugIn(IJ.java:194)
	at ij.IJ.runPlugIn(IJ.java:160)
	at ij.IJ.runPlugIn(IJ.java:149)
	at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:258)
	at HandleExtraFileTypes.run(HandleExtraFileTypes.java:37)
	at ij.IJ.runUserPlugIn(IJ.java:194)
	at ij.IJ.runPlugIn(IJ.java:160)
	at ij.IJ.runPlugIn(IJ.java:149)
	at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:438)
	at ij.io.Opener.openImage(Opener.java:310)
	at ij.io.Opener.openImage(Opener.java:333)
	at ij.io.Opener.open(Opener.java:143)
	at ij.io.Opener.open(Opener.java:70)
	at ij.plugin.Commands.run(Commands.java:27)
	at ij.IJ.runPlugIn(IJ.java:166)
	at ij.Executer.runCommand(Executer.java:128)
	at ij.Executer.run(Executer.java:64)
	at java.lang.Thread.run(Unknown Source)

	
Best,
Lorenz