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Bug 416 - Zeiss czi. format nor implemented into Bio-Formats yet??
Zeiss czi. format nor implemented into Bio-Formats yet??
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Bio-Formats
unspecified
Macintosh Mac OS
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2012-03-22 09:31 CDT by Silke White
Modified: 2012-04-24 22:50 CDT
2 users (show)

See Also:

Description Silke White 2012-03-22 09:31:51 CDT
tried to open a Zeiss .czi file over the Bio-Format-Importer. Got the following exception:

java.lang.NullPointerException
	at loci.formats.in.ZeissCZIReader.translateExperiment(ZeissCZIReader.java:1250)
	at loci.formats.in.ZeissCZIReader.translateMetadata(ZeissCZIReader.java:662)
	at loci.formats.in.ZeissCZIReader.initFile(ZeissCZIReader.java:372)
	at loci.formats.FormatReader.setId(FormatReader.java:1087)
	at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:480)
	at loci.plugins.in.ImportProcess.execute(ImportProcess.java:144)
	at loci.plugins.in.Importer.showDialogs(Importer.java:139)
	at loci.plugins.in.Importer.run(Importer.java:77)
	at loci.plugins.LociImporter.run(LociImporter.java:79)
	at ij.IJ.runUserPlugIn(IJ.java:183)
	at ij.IJ.runPlugIn(IJ.java:150)
	at ij.IJ.runPlugIn(IJ.java:139)
	at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:375)
	at HandleExtraFileTypes.run(HandleExtraFileTypes.java:53)
	at ij.IJ.runUserPlugIn(IJ.java:183)
	at ij.IJ.runPlugIn(IJ.java:150)
	at ij.IJ.runPlugIn(IJ.java:139)
	at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:411)
	at ij.io.Opener.openImage(Opener.java:288)
	at ij.io.Opener.openImage(Opener.java:307)
	at ij.io.Opener.open(Opener.java:138)
	at ij.io.Opener.openAndAddToRecent(Opener.java:224)
	at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:176)
	at ij.plugin.DragAndDrop.run(DragAndDrop.java:152)
	at java.lang.Thread.run(Thread.java:680)


Information about your version of Java - this information is useful for the Fiji developers:

  os.arch => x86_64
  os.name => Mac OS X
  os.version => 10.7.3
  java.version => 1.6.0_29
  java.vendor => Apple Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_29-b11-402-11M3527
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 20.4-b02-402
  java.vm.vendor => Apple Inc.
  java.vm.info => mixed mode
  java.awt.graphicsenv => apple.awt.CGraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => null
  file.separator => /

The up-to-date check says: Up-to-date

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: null
  ij.dir => /Applications/Fiji.app

Information about the version of each plugin:

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Comment 1 Melissa Linkert 2012-03-22 18:57:22 CDT
I would suggest first trying the very latest trunk build of Bio-Formats:

http://hudson.openmicroscopy.org.uk/view/Bio-Formats/job/BIOFORMATS-trunk/lastSuccessfulBuild/artifact/artifacts/loci_tools.jar

If you still see an error message when using that build, then it would be very helpful if you could send one of the problematic files (by selecting "Help > Upload Sample Image" in Fiji).  .czi files are supported in Bio-Formats, but only relatively recently, and so have not been extensively tested.
Comment 2 Silke White 2012-03-26 14:15:37 CDT
Hi,

the new loci_tools build solved the problem for files from all systems but one.

Files from that one system still give an error (below). I uploaded an example file (white-574.czi) into the fiji uploader.

java.lang.NullPointerException
	at sun.misc.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:989)
	at java.lang.Double.valueOf(Double.java:475)
	at java.lang.Double.<init>(Double.java:567)
	at loci.formats.in.ZeissCZIReader.translateInformation(ZeissCZIReader.java:890)
	at loci.formats.in.ZeissCZIReader.translateMetadata(ZeissCZIReader.java:670)
	at loci.formats.in.ZeissCZIReader.initFile(ZeissCZIReader.java:373)
	at loci.formats.FormatReader.setId(FormatReader.java:1091)
	at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:480)
	at loci.plugins.in.ImportProcess.execute(ImportProcess.java:144)
	at loci.plugins.in.Importer.showDialogs(Importer.java:139)
	at loci.plugins.in.Importer.run(Importer.java:77)
	at loci.plugins.LociImporter.run(LociImporter.java:79)
	at ij.IJ.runUserPlugIn(IJ.java:183)
	at ij.IJ.runPlugIn(IJ.java:150)
	at ij.IJ.runPlugIn(IJ.java:139)
	at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:375)
	at HandleExtraFileTypes.run(HandleExtraFileTypes.java:53)
	at ij.IJ.runUserPlugIn(IJ.java:183)
	at ij.IJ.runPlugIn(IJ.java:150)
	at ij.IJ.runPlugIn(IJ.java:139)
	at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:411)
	at ij.io.Opener.openImage(Opener.java:288)
	at ij.io.Opener.openImage(Opener.java:307)
	at ij.io.Opener.open(Opener.java:138)
	at ij.io.Opener.openAndAddToRecent(Opener.java:224)
	at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:176)
	at ij.plugin.DragAndDrop.run(DragAndDrop.java:152)
	at java.lang.Thread.run(Thread.java:680)


Thanks for your help!

Silke
Comment 3 Melissa Linkert 2012-04-09 19:10:53 CDT
Thank you for uploading an example file.

The very latest build of Bio-Formats:

http://hudson.openmicroscopy.org.uk/view/Bio-Formats/job/BIOFORMATS-trunk/lastSuccessfulBuild/artifact/artifacts/loci_tools.jar

should allow white-574.czi to open as well. 
Comment 4 Johannes Schindelin 2012-04-20 23:25:26 CDT
Silke, you should be able to drag 'n drop the link in this webpage directly onto your Fiji window. After that, the new Bio-Formats should be used by Fiji even without restarting.

Can you please test? Thanks!
Comment 5 Silke White 2012-04-23 11:53:01 CDT
(In reply to comment #4)
> Silke, you should be able to drag 'n drop the link in this webpage directly
> onto your Fiji window. After that, the new Bio-Formats should be used by Fiji
> even without restarting.
> 
> Can you please test? Thanks!
> 

Hi Johannes and Melissa,
thanks a lot for your help! My Bio Formats Importer now works flawless for czi-files from all of my available systems!
Me happy!! ;-)
best,
Silke
Comment 6 Curtis Rueden 2012-04-24 22:50:28 CDT
I've uploaded the new version of Bio-Formats to the updater, so this bug is closed!