Open Microscopy Environment

Posted: **Mon Jun 29, 2015 9:26 am**

I am using the Matlab tools of ome for several years now to read zvi and czi files.
The code uses loci_tools.jar from around 2013. Very likely Version 4.x

If I now execute the same code it fails with an exception:

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:1178)

at loci.formats.ImageReader.setId(ImageReader.java:727)

at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:529)

at loci.formats.ChannelFiller.setId(ChannelFiller.java:263)

at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:529)

at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:274)

How can I further debug this problem?

Posted: **Mon Jun 29, 2015 11:27 am**

Hi,

looking at your stack trace, the Bio-Formats version indeed looks like version 4.4.4 or similar.

Many code changes have been included into Bio-Formats to handle errors similar to the one you reported while opening CZI files (see here for example). These changes should be available in the most recent versions of Bio-Formats. Note also that the 4.4.x line is no longer supported.

Would it be possible for you to upgrade your MATLAB Bio-Formats toolbox either to 5.0.x or even preferably to the latest 5.1.x version and see if that fixes your error while opening the CZI file?

Best,
Sebastien

Open Microscopy Environment

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