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Bug 544 - Fiji cannot open images acquired with 2 optical configurations in NIS 4.11
Fiji cannot open images acquired with 2 optical configurations in NIS 4.11
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Windows
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2013-01-07 10:14 CST by sylvie le guyader
Modified: 2013-03-09 22:27 CST
2 users (show)

See Also:
Description sylvie le guyader 2013-01-07 10:14:53 CST 
NIS ND acquisition can acquire images in multiple xy,z, time points and also multiple optical configuration (system set up). I can open images acquired with NIS4.11 but only if they were acquired with 1 optical configuration. If I acquire 2 optical configurations and I try to open the file with fiji, I get this error:

java.lang.ArrayIndexOutOfBoundsException: 1175
	at loci.formats.in.NativeND2Reader.initFile(NativeND2Reader.java:516)
	at loci.formats.FormatReader.setId(FormatReader.java:1238)
	at loci.formats.DelegateReader.setId(DelegateReader.java:266)
	at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:482)
	at loci.plugins.in.ImportProcess.execute(ImportProcess.java:146)
	at loci.plugins.in.Importer.showDialogs(Importer.java:141)
	at loci.plugins.in.Importer.run(Importer.java:79)
	at loci.plugins.LociImporter.run(LociImporter.java:81)
	at ij.IJ.runUserPlugIn(IJ.java:184)
	at ij.IJ.runPlugIn(IJ.java:151)
	at ij.IJ.runPlugIn(IJ.java:140)
	at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:405)
	at HandleExtraFileTypes.run(HandleExtraFileTypes.java:57)
	at ij.IJ.runUserPlugIn(IJ.java:184)
	at ij.IJ.runPlugIn(IJ.java:151)
	at ij.IJ.runPlugIn(IJ.java:140)
	at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:430)
	at ij.io.Opener.openImage(Opener.java:304)
	at ij.io.Opener.openImage(Opener.java:325)
	at ij.io.Opener.open(Opener.java:140)
	at ij.io.Opener.openAndAddToRecent(Opener.java:240)
	at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:176)
	at ij.plugin.DragAndDrop.run(DragAndDrop.java:152)
	at java.lang.Thread.run(Thread.java:662)


Sylvie

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

  os.arch => amd64
  os.name => Windows 7
  os.version => 6.1
  java.version => 1.6.0_24
  java.vendor => Sun Microsystems Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_24-b07
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 19.1-b02
  java.vm.vendor => Sun Microsystems Inc.
  java.vm.info => mixed mode
  java.awt.graphicsenv => sun.awt.Win32GraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => windows
  file.separator => \

The up-to-date check says: UP_TO_DATE

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: C:\Users\Public\DOCUME~1\FIJI-W~1\Fiji.app/java/win64/jdk1.6.0_24/jre/
  ij.dir => C:\Users\Public\DOCUME~1\FIJI-W~1\Fiji.app

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Comment 1 Melissa Linkert 2013-01-07 22:20:57 CST 
Could you please upload one of the files that does not open using "Help > Upload Sample Image"?
Comment 2 sylvie le guyader 2013-01-14 12:33:22 CST 
Hi Melissa

I have now uploaded the 2 files.
One was acquired using 2 optical configurations (green/red channels + only green) and the second one only no change in optical configuration(green/red channels). 

I just realized that I actually have the expected number of channels (3 in the file with 2 OC and 2 in the second file) but the 3rd channel got wrongly assigned a blue LUT instead of green so I did not notice that there was a third channel. 

So I can manually change the LUT of the 3rd channel but it would be great if we could get Fiji to read the LUT properly.

thanks

Sylvie
Comment 3 Melissa Linkert 2013-03-09 22:27:22 CST 
This has been fixed; the version of Bio-Formats currently in Fiji assigns the correct channel colors for both uploaded files.