[ome-users] Exception when opening .czi files

[Lorenz Maier]

Hi all,

the current release of LOCI Tools (4.4.2) seems to have a problem opening my Zeiss (.czi) files.

I attached an example which has 49x49 pixels, 2 z-stacks, and 1 time point. It fails on both Linux and Windows with recent versions of Java, within Fiji and within Matlab / bfopen.

Using bfopen, I get the following exception:

>> bfopen('exceptionalize.czi')
log4j:WARN No appenders could be found for logger (loci.common.services.ServiceFactory).
log4j:WARN Please initialize the log4j system properly.
Unknown MicroscopeType value 'null' will be stored as "Other"
Unknown Correction value 'null' will be stored as "Other"
Error using loci.formats.ChannelSeparator/setId
Java exception occurred:
java.lang.NullPointerException
                at
        loci.formats.in.ZeissCZIReader.translateInformation(ZeissCZIReader.java:1066)
                at loci.formats.in.ZeissCZIReader.translateMetadata(ZeissCZIReader.java:758)
                at loci.formats.in.ZeissCZIReader.initFile(ZeissCZIReader.java:444)
                at loci.formats.FormatReader.setId(FormatReader.java:1105)
                at loci.formats.ImageReader.setId(ImageReader.java:695)
                at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:505)
                at loci.formats.ChannelFiller.setId(ChannelFiller.java:263)
                at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:505)
                at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:274)

Error in bfopen (line 138)
r.setId(id);


Could you please have a look on that?

Best regards,
Lorenz
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