Open Microscopy Environment

Hello again,

Some of our users are encoutering some problems when they try to open ".czi" files (from Zen 2011).
You will find some openable files in "EXP12 1 CD31 A.czi" ; "EXP12 1 CD31 B.czi" and some files that cause an error ("EXP12 14 CD31 A.czi" ; "EXP12 14 DAPI A.czi"):

Code: Select all

java.lang.reflect.InvocationTargetException
   at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
   at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
   at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
   at java.lang.reflect.Method.invoke(Method.java:597)
   at ij.Command.runPlugIn(Command.java:146)
   at ij.Command.runCommand(Command.java:95)
   at ij.Executer.run(Executer.java:64)
   at java.lang.Thread.run(Thread.java:662)
Caused by: java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
   at java.util.ArrayList.RangeCheck(ArrayList.java:547)
   at java.util.ArrayList.get(ArrayList.java:322)
   at loci.formats.in.ZeissCZIReader.initFile(ZeissCZIReader.java:489)
   at loci.formats.FormatReader.setId(FormatReader.java:1178)
   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:185)
   at ij.IJ.runPlugIn(IJ.java:152)
   ... 8 more


You can download the files from your SFTP Server under the folder "PTBIOP CZI Problems"

Best!

Oli

Thanks Oli.

This was fortunately quite easy to fix; the fix is here:

https://github.com/melissalinkert/biofo ... fb70d73396

...and will be included in the upcoming 4.4.5 version of Bio-Formats.

-Melissa