Problem uploading Leica format image stacks

[Caricas]

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)

[Melissa Linkert-2]

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.

[Caricas]

Hi Melissa,

thanks a lot for your email! I hadn't seen the post so thanks for  
pointing it out to me as it solved the problem. I really appreciate it.

regards,
Waldemar



Quoting Melissa Linkert <[hidden email]>:

> 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.
>

Waldemar Ockert
Faculty of Life Sciences
University of Manchester
G.006 AV Hill building,
Oxford Road,
Manchester
M13 9PT
e-mail [hidden email]
Tel. [phone]