Error Starting Desktop (java.lang​​.NullPoin​t​erExcept​io​n)

I'm running Matlab_R2015b on OS X 10.11. After running ImageJ through Matlab and installing Java3D I started getting the following error:

java.lang.NullPointerException
  at net.imagej.updater.util.AvailableSites.getAvailableSites(AvailableSites.java:66)
  at net.imagej.updater.util.AvailableSites.initializeSites(AvailableSites.java:138)
  at net.imagej.updater.util.AvailableSites.initializeAndAddSites(AvailableSites.java:187)
  at net.imagej.ui.swing.updater.ImageJUpdater.run(ImageJUpdater.java:107)
  at org.scijava.command.CommandModule.run(CommandModule.java:201)
  at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167)
  at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126)
  at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65)
  at org.scijava.thread.DefaultThreadService$2.call(DefaultThreadService.java:191)
  at java.util.concurrent.FutureTask.run(FutureTask.java:262)
  at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
  at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
  at java.lang.Thread.run(Thread.java:745)
[ERROR] Module threw error
java.lang.Error: The markup in the document preceding the root element must be well-formed.

Public ID: None, System ID: None,
Line number: 2, Column number: 2
  at net.imagej.updater.XMLFileErrorHandler.throwError(XMLFileErrorHandler.java:61)
  at net.imagej.updater.XMLFileErrorHandler.fatalError(XMLFileErrorHandler.java:52)
  at org.apache.xerces.util.ErrorHandlerWrapper.fatalError(Unknown Source)
  at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
  at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
  at org.apache.xerces.impl.XMLScanner.reportFatalError(Unknown Source)
  at org.apache.xerces.impl.XMLDocumentScannerImpl$PrologDispatcher.dispatch(Unknown Source)
  at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)
  at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
  at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
  at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
  at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
  at org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source)
  at net.imagej.updater.XMLFileReader.read(XMLFileReader.java:135)
  at net.imagej.updater.XMLFileReader.read(XMLFileReader.java:111)
  at net.imagej.updater.FilesCollection.read(FilesCollection.java:424)
  at net.imagej.updater.FilesCollection.read(FilesCollection.java:418)
  at net.imagej.updater.FilesCollection.read(FilesCollection.java:412)
  at net.imagej.updater.FilesCollection.downloadIndexAndChecksum(FilesCollection.java:1128)
  at net.imagej.ui.swing.updater.ImageJUpdater.run(ImageJUpdater.java:140)
  at org.scijava.command.CommandModule.run(CommandModule.java:201)
  at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167)
  at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126)
  at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65)
  at org.scijava.thread.DefaultThreadService$2.call(DefaultThreadService.java:191)
  at java.util.concurrent.FutureTask.run(FutureTask.java:262)
  at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
  at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
  at java.lang.Thread.run(Thread.java:745)

Does anybody know how to solve this issue? Thanks.

[Walter Roberson]

What are the circumstances that trigger that?

[Usha Duddu]

How are you calling imagej from MATLAB? Are you calling ImageJ classes through MATLAB JAVA interface? Are you adding any particular ImageJ specific jar files to static or dynamic JAVA classpath path in MATLAB? Please note that as of now MATLAB does not have any specific interface for ImageJ.

More Information about how exactly you are calling the ImageJ classes from MATLAB will be helpful to troubleshoot further.