Unable to open .czi file through Bioformats

bio-formats
Tags: #<Tag:0x00007fb87bf164c8>

#1

Hi all, I’m getting an error message when I try to open .czi files on FIJI. I’ve included a screenshot of the error message below. (If it doesn’t display, it reads “Sorry, there was a problem constructing the OME-XML metadata store”)

This isn’t an issue with the file(s) since I’m also unable to open older .czi’s that I used to be able to open. Maybe I’m missing some line of code with my new update/install? Any help would be much appreciated!

Here is the log:

Unable to retrieve constructor for class loci.formats.services.OMEXMLServiceImpl
at loci.common.services.ServiceFactory.getConstructor(ServiceFactory.java:190)
at loci.common.services.ServiceFactory.getInstance(ServiceFactory.java:161)
at loci.plugins.in.ImportProcess.createBaseReader(ImportProcess.java:652)
at loci.plugins.in.ImportProcess.initializeReader(ImportProcess.java:484)
at loci.plugins.in.ImportProcess.execute(ImportProcess.java:137)
at loci.plugins.in.Importer.showDialogs(Importer.java:140)
at loci.plugins.in.Importer.run(Importer.java:76)
at loci.plugins.LociImporter.run(LociImporter.java:78)
at ij.IJ.runUserPlugIn(IJ.java:217)
at ij.IJ.runPlugIn(IJ.java:181)
at ij.IJ.runPlugIn(IJ.java:170)
at loci.plugins.shortcut.ShortcutPanel$1.run(ShortcutPanel.java:189)
Caused by: java.lang.NoClassDefFoundError: loci/common/xml/XMLTools$SchemaReader
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:264)
at loci.common.services.ServiceFactory.getConstructor(ServiceFactory.java:185)
... 11 more
Caused by: java.lang.ClassNotFoundException: loci.common.xml.XMLTools$SchemaReader
	at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
	... 14 more
loci.formats.FormatException: Unable to retrieve constructor for class loci.formats.services.OMEXMLServiceImpl
	at loci.plugins.in.ImportProcess.createBaseReader(ImportProcess.java:661)
	at loci.plugins.in.ImportProcess.initializeReader(ImportProcess.java:484)
	at loci.plugins.in.ImportProcess.execute(ImportProcess.java:137)
	at loci.plugins.in.Importer.showDialogs(Importer.java:140)
	at loci.plugins.in.Importer.run(Importer.java:76)
	at loci.plugins.LociImporter.run(LociImporter.java:78)
	at ij.IJ.runUserPlugIn(IJ.java:217)
	at ij.IJ.runPlugIn(IJ.java:181)
	at ij.IJ.runPlugIn(IJ.java:170)
	at loci.plugins.shortcut.ShortcutPanel$1.run(ShortcutPanel.java:189)
Caused by: Unable to retrieve constructor for class loci.formats.services.OMEXMLServiceImpl
	at loci.common.services.ServiceFactory.getConstructor(ServiceFactory.java:190)
	at loci.common.services.ServiceFactory.getInstance(ServiceFactory.java:161)
	at loci.plugins.in.ImportProcess.createBaseReader(ImportProcess.java:652)
	... 9 more
Caused by: java.lang.NoClassDefFoundError: loci/common/xml/XMLTools$SchemaReader
	at java.lang.Class.forName0(Native Method)
	at java.lang.Class.forName(Class.java:264)
	at loci.common.services.ServiceFactory.getConstructor(ServiceFactory.java:185)
	... 11 more
Caused by: java.lang.ClassNotFoundException: loci.common.xml.XMLTools$SchemaReader
	at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
	... 14 more

#2

Hi @PatrickD,

  • Can you replicate the issue with a fresh installation of Fiji?
  • Did you update your installation yesterday to the new Bio-Formats version 5.5.2? (see release announcement)?

Best,
Stefan


#3

The problem predated the update and continued afterwards, so that wasn’t it. Fresh install fixed the issue. Thanks!