Bio-Formats problem?

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Bio-Formats problem?

TimFeinstein
Hi folks,

Is anyone else having trouble with Bio-Formats?  Suddenly I cannot import either .nd2's from an A1 confocal or .lif's from our DMI6000.  It seems like a general problem with Bio-Formats.  I tried updating ImageJ (1.51h) and Fiji (through the Help menu, some Bio-Formats components updated).  Still no luck.  The error report is below.  The files open with no problem using ImageJ for OSX with Java 1.8 and the files seem to open fine, I just have to shuttle everything over to Fiji as TIFFs to work with my plugins.  

Best,


Tim

Timothy Feinstein, Ph.D.
Research Scientist
University of Pittsburgh Department of Developmental Biology

------------------------------------------------------------





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.Executer.runCommand(Executer.java:137)
        at ij.Executer.run(Executer.java:66)
        at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.NoClassDefFoundError: loci/common/xml/XMLTools$SchemaReader
        at java.lang.Class.forName0(Native Method)
        at java.lang.Class.forName(Class.java:264)
        at loci.common.services.ServiceFactory.getConstructor(ServiceFactory.java:185)
        ... 12 more
Caused by: java.lang.ClassNotFoundException: loci.common.xml.XMLTools$SchemaReader
        at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
        at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
        ... 15 more
loci.formats.FormatException: Unable to retrieve constructor for class loci.formats.services.OMEXMLServiceImpl
        at loci.plugins.in.ImportProcess.createBaseReader(ImportProcess.java:661)
        at loci.plugins.in.ImportProcess.initializeReader(ImportProcess.java:484)
        at loci.plugins.in.ImportProcess.execute(ImportProcess.java:137)
        at loci.plugins.in.Importer.showDialogs(Importer.java:140)
        at loci.plugins.in.Importer.run(Importer.java:76)
        at loci.plugins.LociImporter.run(LociImporter.java:78)
        at ij.IJ.runUserPlugIn(IJ.java:217)
        at ij.IJ.runPlugIn(IJ.java:181)
        at ij.Executer.runCommand(Executer.java:137)
        at ij.Executer.run(Executer.java:66)
        at java.lang.Thread.run(Thread.java:745)
Caused by: Unable to retrieve constructor for class loci.formats.services.OMEXMLServiceImpl
        at loci.common.services.ServiceFactory.getConstructor(ServiceFactory.java:190)
        at loci.common.services.ServiceFactory.getInstance(ServiceFactory.java:161)
        at loci.plugins.in.ImportProcess.createBaseReader(ImportProcess.java:652)
        ... 10 more
Caused by: java.lang.NoClassDefFoundError: loci/common/xml/XMLTools$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)
        ... 12 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)
        ... 15 more



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Re: Bio-Formats problem?

ctrueden
Hi Tim,

Do you have the Bio-Formats update site enabled? If so, try disabling it.
That update site is for the latest unstable and unreleased version of
Bio-Formats (see http://imagej.net/Bio-Formats#Daily_builds) and it is
currently broken.

Regards,
Curtis

--
Curtis Rueden
LOCI software architect - http://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/


On Wed, Jan 11, 2017 at 3:28 PM, Feinstein, Timothy N <[hidden email]> wrote:

> Hi folks,
>
> Is anyone else having trouble with Bio-Formats?  Suddenly I cannot import
> either .nd2's from an A1 confocal or .lif's from our DMI6000.  It seems
> like a general problem with Bio-Formats.  I tried updating ImageJ (1.51h)
> and Fiji (through the Help menu, some Bio-Formats components updated).
> Still no luck.  The error report is below.  The files open with no problem
> using ImageJ for OSX with Java 1.8 and the files seem to open fine, I just
> have to shuttle everything over to Fiji as TIFFs to work with my plugins.
>
> Best,
>
>
> Tim
>
> Timothy Feinstein, Ph.D.
> Research Scientist
> University of Pittsburgh Department of Developmental Biology
>
> ------------------------------------------------------------
>
>
>
>
>
> 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.Executer.runCommand(Executer.java:137)
>         at ij.Executer.run(Executer.java:66)
>         at java.lang.Thread.run(Thread.java:745)
> 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)
>         ... 12 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$AppClassLoader.loadClass(Launcher.java:331)
>         at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
>         ... 15 more
> loci.formats.FormatException: Unable to retrieve constructor for class
> loci.formats.services.OMEXMLServiceImpl
>         at loci.plugins.in.ImportProcess.createBaseReader(
> ImportProcess.java:661)
>         at loci.plugins.in.ImportProcess.initializeReader(
> ImportProcess.java:484)
>         at loci.plugins.in.ImportProcess.execute(ImportProcess.java:137)
>         at loci.plugins.in.Importer.showDialogs(Importer.java:140)
>         at loci.plugins.in.Importer.run(Importer.java:76)
>         at loci.plugins.LociImporter.run(LociImporter.java:78)
>         at ij.IJ.runUserPlugIn(IJ.java:217)
>         at ij.IJ.runPlugIn(IJ.java:181)
>         at ij.Executer.runCommand(Executer.java:137)
>         at ij.Executer.run(Executer.java:66)
>         at java.lang.Thread.run(Thread.java:745)
> Caused by: Unable to retrieve constructor for class loci.formats.services.
> OMEXMLServiceImpl
>         at loci.common.services.ServiceFactory.getConstructor(
> ServiceFactory.java:190)
>         at loci.common.services.ServiceFactory.getInstance(
> ServiceFactory.java:161)
>         at loci.plugins.in.ImportProcess.createBaseReader(
> ImportProcess.java:652)
>         ... 10 more
> Caused by: java.lang.NoClassDefFoundError: loci/common/xml/XMLTools$
> 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)
>         ... 12 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)
>         ... 15 more
>
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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