[ome-users] .czi files from Ziess 880 confocal won't open

[Sebastien Besson (Staff)]

Hi Michael,

can you confirm the exact version of Bio-Formats you are using? The error stack trace
does not look like you are using the latest Bio-Formats 5.1.x. Furthermore your issue
looks very similar to the one reported in this thread [1] and fixed in [2].

Could you try installing the 5.1.8 version of Bio-Formats [3] and see if the error persists?

Best regards,
Sebastien

[1] http://lists.openmicroscopy.org.uk/pipermail/ome-users/2015-January/004988.html
[2] https://github.com/openmicroscopy/bioformats/pull/1531
[3] http://downloads.openmicroscopy.org/bio-formats/5.1.8/

On 16 Mar 2016, at 17:04, Cammer, Michael <Michael.Cammer at med.nyu.edu<mailto:Michael.Cammer at med.nyu.edu>> wrote:

.czi files from the Zeiss 880 will not open.  This includes both raw and processed data.

I was using a daily build version of LOCI BioFormats plugins from two weeks ago and just upgraded to daily build.

Please let me know if you’d like me to upload a dataset.  We have examples from two different Ziess 880s, one here and one from a neighboring institution.

Thank you!!
-Michael


Example error:
ImageJ 1.50g18; Java 1.6.0_20 [64-bit]; Windows 7 6.1; 23MB of 12000MB (<1%)
java.lang.NumberFormatException: null
                at java.lang.Integer.parseInt(Integer.java:417)
                at java.lang.Integer.parseInt(Integer.java:499)
                at loci.formats.in.ZeissCZIReader.translateExperiment(ZeissCZIReader.java:2151)
                at loci.formats.in.ZeissCZIReader.translateMetadata(ZeissCZIReader.java:1214)
                at loci.formats.in.ZeissCZIReader.initFile(ZeissCZIReader.java:699)
                at loci.formats.FormatReader.setId(FormatReader.java:1317)
                at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:494)
                at loci.plugins.in.ImportProcess.execute(ImportProcess.java:144)
                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:212)
                at ij.IJ.runPlugIn(IJ.java:176)
                at ij.IJ.runPlugIn(IJ.java:165)
                at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:258)
                at HandleExtraFileTypes.run(HandleExtraFileTypes.java:37)
                at ij.IJ.runUserPlugIn(IJ.java:212)
                at ij.IJ.runPlugIn(IJ.java:176)
                at ij.IJ.runPlugIn(IJ.java:165)
                at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:503)
                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:186)
                at ij.plugin.DragAndDrop.run(DragAndDrop.java:153)
                at java.lang.Thread.run(Thread.java:619)

=========================================================================
Michael Cammer, Microscopy Core & Skirball Institute, NYU Langone Medical Center
                      Cell:  914-309-3270     ** Office: Skirball 2nd Floor main office, back right **
          http://ocs.med.nyu.edu/microscopy & http://microscopynotes.com/


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