[ome-users] Bioformats and lack of JPX image opening

Fri Sep 27 21:14:54 BST 2013

Melissa, 

Thank you. You are correct. Once FIJI was updated, everything worked as you stated. 

Your help is greatly appreciated!

Dave

-----Original Message-----
From: Melissa Linkert [mailto:melissa.linkert at gmail.com] On Behalf Of Melissa Linkert
Sent: Friday, September 27, 2013 1:05 PM
To: Kline, David D.
Cc: ome-users at lists.openmicroscopy.org.uk
Subject: Re: [ome-users] Bioformats and lack of JPX image opening

Hi Dave,

> I will upload the images now, but this is the error I receive when I use the plugin: 
> 
> Sorry, there was a problem during import.
> 
> 
> The log file shows this: 
> 
> loci.formats.MissingLibraryException: The JAI Image I/O Tools are required to read JPEG-2000 files. Please obtain jai_imageio.jar from http://www.openmicroscopy.org/site/support/bio-formats/developers/java-library.html
> 	at loci.formats.codec.JPEG2000Codec.initialize(JPEG2000Codec.java:314)
> 	at loci.formats.codec.JPEG2000Codec.decompress(JPEG2000Codec.java:241)
> 	at loci.formats.codec.JPEG2000Codec.decompress(JPEG2000Codec.java:228)
> 	at loci.formats.in.JPXReader.openBytes(JPXReader.java:170)

Thank you for uploading the files and providing the error message.

I have been able to open both files; the error message suggests that there is a problem with how Bio-Formats is installed in Fiji, and not a problem in Bio-Formats itself.  Could you please try running the Fiji updater ("Help > Update Fiji"), and verify that the "jars/bio-formats/jai_imageio.jar"
entry is installed (after clicking the "Advanced Mode" button)?  I would expect the files to open once that is installed and Fiji is restarted.

Regards,
-Melissa

On Thu, Sep 26, 2013 at 07:28:01PM +0000, Kline, David D. wrote:
> Melissa,
> 
> I will upload the images now, but this is the error I receive when I use the plugin: 
> 
> Sorry, there was a problem during import.
> 
> 
> The log file shows this: 
> 
> loci.formats.MissingLibraryException: The JAI Image I/O Tools are required to read JPEG-2000 files. Please obtain jai_imageio.jar from http://www.openmicroscopy.org/site/support/bio-formats/developers/java-library.html
> 	at loci.formats.codec.JPEG2000Codec.initialize(JPEG2000Codec.java:314)
> 	at loci.formats.codec.JPEG2000Codec.decompress(JPEG2000Codec.java:241)
> 	at loci.formats.codec.JPEG2000Codec.decompress(JPEG2000Codec.java:228)
> 	at loci.formats.in.JPXReader.openBytes(JPXReader.java:170)
> 	at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:197)
> 	at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:226)
> 	at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:159)
> 	at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:305)
> 	at loci.formats.DimensionSwapper.openBytes(DimensionSwapper.java:248)
> 	at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:305)
> 	at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:305)
> 	at loci.plugins.util.ImageProcessorReader.openProcessors(ImageProcessorReader.java:190)
> 	at loci.plugins.in.ImagePlusReader.readProcessors(ImagePlusReader.java:416)
> 	at loci.plugins.in.ImagePlusReader.readPlanes(ImagePlusReader.java:380)
> 	at loci.plugins.in.ImagePlusReader.readImage(ImagePlusReader.java:277)
> 	at loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:238)
> 	at loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:216)
> 	at loci.plugins.in.ImagePlusReader.openImagePlus(ImagePlusReader.java:114)
> 	at loci.plugins.in.Importer.readPixels(Importer.java:150)
> 	at loci.plugins.in.Importer.run(Importer.java:89)
> 	at loci.plugins.LociImporter.run(LociImporter.java:81)
> 	at ij.IJ.runUserPlugIn(IJ.java:196)
> 	at ij.IJ.runPlugIn(IJ.java:160)
> 	at ij.Executer.runCommand(Executer.java:128)
> 	at ij.Executer.run(Executer.java:64)
> 	at java.lang.Thread.run(Thread.java:662)
> Caused by: Unable to retrieve constructor for class loci.formats.services.JAIIIOServiceImpl
> 	at loci.common.services.ServiceFactory.getConstructor(ServiceFactory.java:198)
> 	at loci.common.services.ServiceFactory.getInstance(ServiceFactory.java:169)
> 	at loci.formats.codec.JPEG2000Codec.initialize(JPEG2000Codec.java:311)
> 	... 25 more
> Caused by: java.lang.NoClassDefFoundError: com/sun/media/imageio/plugins/jpeg2000/J2KImageReadParam
> 	at java.lang.Class.forName0(Native Method)
> 	at java.lang.Class.forName(Class.java:169)
> 	at loci.common.services.ServiceFactory.getConstructor(ServiceFactory.java:193)
> 	... 27 more
> Caused by: java.lang.ClassNotFoundException: com.sun.media.imageio.plugins.jpeg2000.J2KImageReadParam
> 	at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
> 	at java.security.AccessController.doPrivileged(Native Method)
> 	at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
> 	at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
> 	at java.lang.ClassLoader.loadClass(ClassLoader.java:248)
> 	... 30 more
> 
> 
> -----Original Message-----
> From: Melissa Linkert [mailto:melissa.linkert at gmail.com] On Behalf Of 
> Melissa Linkert
> Sent: Thursday, September 26, 2013 12:19 PM
> To: Kline, David D.
> Cc: ome-users at lists.openmicroscopy.org.uk
> Subject: Re: [ome-users] Bioformats and lack of JPX image opening
> 
> Hi Dave,
> 
> > Thanks for the prompt response. Here are the requested details: 
> > 
> > Version: revision 34f3393, built 7 May 2013, Release: 4.4.9-DEV
> > Error: File is not in a supported format, a reader plugin is not available, or it was not found. 
> 
> Do you see the same error if you open the file by clicking "Plugins > LOCI > Bio-Formats Importer Plugin"?  If you aren't able to open the file that way, then it would be helpful if you could send one of the files that cannot be opened so that we can duplicate the problem.
> Files can be uploaded to:
> 
> http://qa.openmicroscopy.org.uk/qa/upload/
> 
> Regards,
> -Melissa
> 
> On Thu, Sep 26, 2013 at 04:41:07PM +0000, Kline, David D. wrote:
> > Melissa-
> > 
> > Thanks for the prompt response. Here are the requested details: 
> > 
> > Version: revision 34f3393, built 7 May 2013, Release: 4.4.9-DEV
> > Error: File is not in a supported format, a reader plugin is not available, or it was not found. 
> > 
> > Best,
> > Dave
> > 
> > 
> > -----Original Message-----
> > From: Melissa Linkert [mailto:melissa.linkert at gmail.com] On Behalf 
> > Of Melissa Linkert
> > Sent: Wednesday, September 25, 2013 5:04 PM
> > To: Kline, David D.
> > Cc: 'ome-users at lists.openmicroscopy.org.uk'
> > Subject: Re: [ome-users] Bioformats and lack of JPX image opening
> > 
> > Hi Dave,
> > 
> > > Greetings. I have JPX images generated by Neurolucida that I cannot open using Bioformats and Image J (FIJI package). Any help would be greatly appreciated.
> > 
> > Which version of Bio-Formats are you using (see "Help > About Plugins > LOCI Plugins" in Fiji)?  Do you see an error message when you open the files?
> > If so, what is it?
> > 
> > Regards,
> > -Melissa
> > 
> > On Wed, Sep 25, 2013 at 04:55:21PM +0000, Kline, David D. wrote:
> > > Greetings. I have JPX images generated by Neurolucida that I cannot open using Bioformats and Image J (FIJI package). Any help would be greatly appreciated.
> > > 
> > > Thanks,
> > > Dave
> > 
> > > _______________________________________________
> > > ome-users mailing list
> > > ome-users at lists.openmicroscopy.org.uk
> > > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
> > 