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

[Melissa Linkert]

Hi Lorenz,

> 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.
>

I would not expect opening of individual files from a multi-file dataset
to work as expected, since the dimensions stored in those files are
representative of the entire dataset (not the individual file).  Opening
the master file (Experiment-191.czi in this case) should correctly open
the whole dataset; if you only want a subset of the planes, then the
"Specify range for each series" checkbox in the "Bio-Formats Import
Options" window should help.

Regards,
-Melissa

On Wed, Jun 26, 2013 at 05:17:51PM +0200, Lorenz Maier wrote:
> 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
> 	
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