Problem uploading Leica format image stacks

Posted by Caricas on Aug 24, 2010; 8:14am
URL: http://imagej.273.s1.nabble.com/Problem-uploading-Leica-format-image-stacks-tp3687179.html

Hi,

I am having difficulties uploading Leica confocal files with MBP Image J to work with. Only some of the files cannot be opened either in the LOCI opening options or with the standard open file and I get an error message (pasted below).

I've checked the web to see, if anyone has experienced a similar problem, but haven't found anything related to it.
I would greatly appreciate, if someone could help.

regards,
Waldemar


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java.lang.ArrayIndexOutOfBoundsException: -1
        at java.util.Vector.get(Vector.java:696)
        at loci.formats.ome.OMEXML200809Metadata.getImageNode(OMEXML200809Metadata.java:5675)
        at loci.formats.ome.OMEXML200809Metadata.setImageCreationDate(OMEXML200809Metadata.java:3409)
        at loci.formats.meta.FilterMetadata.setImageCreationDate(FilterMetadata.java:643)
        at loci.formats.in.LeicaHandler.startElement(LeicaHandler.java:715)
        at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.startElement(AbstractSAXParser.java:501)
        at com.sun.org.apache.xerces.internal.parsers.AbstractXMLDocumentParser.emptyElement(AbstractXMLDocumentParser.java:179)
        at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanStartElement(XMLDocumentFragmentScannerImpl.java:1339)
        at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl$FragmentContentDriver.next(XMLDocumentFragmentScannerImpl.java:2747)
        at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:648)
        at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:510)
        at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:807)
        at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:737)
        at com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:107)
        at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1205)
        at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(SAXParserImpl.java:522)
        at javax.xml.parsers.SAXParser.parse(SAXParser.java:395)
        at javax.xml.parsers.SAXParser.parse(SAXParser.java:198)
        at loci.common.XMLTools.parseXML(XMLTools.java:277)
        at loci.common.XMLTools.parseXML(XMLTools.java:252)
        at loci.formats.in.LIFReader.initMetadata(LIFReader.java:383)
        at loci.formats.in.LIFReader.initFile(LIFReader.java:315)
        at loci.formats.FormatReader.setId(FormatReader.java:901)
        at loci.plugins.importer.Importer.run(Importer.java:267)
        at loci.plugins.LociImporter.run(LociImporter.java:77)
        at ij.IJ.runUserPlugIn(IJ.java:180)
        at ij.IJ.runPlugIn(IJ.java:147)
        at ij.IJ.runPlugIn(IJ.java:136)
        at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:229)
        at HandleExtraFileTypes.run(HandleExtraFileTypes.java:37)
        at ij.IJ.runUserPlugIn(IJ.java:180)
        at ij.IJ.runPlugIn(IJ.java:147)
        at ij.IJ.runPlugIn(IJ.java:136)
        at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:384)
        at ij.io.Opener.openImage(Opener.java:278)
        at ij.io.Opener.openImage(Opener.java:301)
        at ij.io.Opener.open(Opener.java:137)
        at ij.io.Opener.openMultiple(Opener.java:106)
        at ij.plugin.Commands.run(Commands.java:21)
        at ij.IJ.runPlugIn(IJ.java:153)
        at ij.Executer.runCommand(Executer.java:122)
        at ij.Executer.run(Executer.java:59)
        at java.lang.Thread.run(Thread.java:619)