http://imagej.273.s1.nabble.com/Problem-uploading-Leica-format-image-stacks-tp3687179p3687181.html
pointing it out to me as it solved the problem. I really appreciate it.
> Hi Waldemar,
>
> This exact problem was mentioned in a previous post to the list:
>
>
http://imagej.588099.n2.nabble.com/Java-Exceptions-Thrown-When-a-Leica-Confocal-Stack-is-Opened-td5035883.html>
> The solution is to update to the latest stable release or trunk build of
> Bio-Formats, which can be done by following the instructions here:
>
>
http://loci.wisc.edu/bio-formats/imagej>
> Regards,
> -Melissa
>
> On Tue, Aug 24, 2010 at 01:14:27AM -0700, Caricas wrote:
>> 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
>>
>>
>> -----------------------------------------------------------------------------------------------
>> 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)
>> --
>> View this message in context:
>>
http://imagej.588099.n2.nabble.com/Problem-uploading-Leica-format-image-stacks-tp5455936p5455936.html>> Sent from the ImageJ mailing list archive at Nabble.com.
>
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