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Bug 1045 - (Leica_SP2) Fiji does not open leica SP2 files (.lei)
(Leica_SP2)
Fiji does not open leica SP2 files (.lei)
Status: RESOLVED INVALID
Product: Fiji
Classification: Unclassified
Component: Bio-Formats
unspecified
PC Windows
: P4 critical
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2015-04-01 05:30 CDT by ahernandez
Modified: 2015-04-06 11:27 CDT
3 users (show)

See Also:
Description ahernandez 2015-04-01 05:30:57 CDT 
This is the exception message I get when I try to open a .lei file


(Fiji Is Just) ImageJ 2.0.0-rc-28/1.49q; Java 1.6.0_24 [64-bit]; Windows 7 6.1; 71MB of 2151MB (3%)
 
java.lang.ArithmeticException: / by zero
	at loci.formats.MetadataTools.populatePixelsOnly(MetadataTools.java:276)
	at loci.formats.MetadataTools.populateMetadata(MetadataTools.java:234)
	at loci.formats.MetadataTools.populatePixels(MetadataTools.java:134)
	at loci.formats.MetadataTools.populatePixels(MetadataTools.java:104)
	at loci.formats.in.LeicaReader.initFile(LeicaReader.java:656)
	at loci.formats.FormatReader.setId(FormatReader.java:1395)
	at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:493)
	at loci.plugins.in.ImportProcess.execute(ImportProcess.java:140)
	at loci.plugins.in.Importer.showDialogs(Importer.java:137)
	at loci.plugins.in.Importer.run(Importer.java:75)
	at loci.plugins.LociImporter.run(LociImporter.java:78)
	at ij.IJ.runUserPlugIn(IJ.java:199)
	at ij.IJ.runPlugIn(IJ.java:163)
	at ij.IJ.runPlugIn(IJ.java:152)
	at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:447)
	at HandleExtraFileTypes.run(HandleExtraFileTypes.java:66)
	at ij.IJ.runUserPlugIn(IJ.java:199)
	at ij.IJ.runPlugIn(IJ.java:163)
	at ij.IJ.runPlugIn(IJ.java:152)
	at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:486)
	at ij.io.Opener.openImage(Opener.java:360)
	at ij.io.Opener.openImage(Opener.java:239)
	at ij.io.Opener.open(Opener.java:106)
	at ij.io.Opener.openAndAddToRecent(Opener.java:288)
	at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:176)
	at ij.plugin.DragAndDrop.run(DragAndDrop.java:152)
	at java.lang.Thread.run(Thread.java:662)

Information about your version of Java:

  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: REMIND_LATER

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: C:\Fiji.app/java/win64/jdk1.6.0_24//jre
  imagej.dir => C:\Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20150328055348)
Fiji: http://fiji.sc/update/ (last check:20150325042333)
Bio-Formats: http://sites.imagej.net/Bio-Formats/ (last check:20150401032649)
LOCI: http://sites.imagej.net/LOCI/ (last check:20141210205338)
Comment 1 Mark Hiner 2015-04-01 08:00:35 CDT 
The .lei extension is handled by Bio-Formats. With the Bio-Formats update site enabled you're using the 5.1 development version.

I actually get much better results with .lei data when using Bio-Formats 5.1, but it may be worth disabling the Bio-Formats update site to test with the stable  5.0 line.

In any case, you should report this bug to the OME development team that maintains Bio-Formats:
https://www.openmicroscopy.org/site/support/bio-formats5.0/about/bug-reporting.html

They will likely want you to upload a sample dataset with this problem, as when I tested locally with .lei files I was able to open them successfully.

Thanks for the report! Let us know if you have any questions, and if this issue gets resolved in Bio-Formats.
Comment 2 Curtis Rueden 2015-04-06 11:27:57 CDT 
As Mark suggests, please report this bug to the Bio-Formats development team:

  http://openmicroscopy.org/site/support/bio-formats/about/bug-reporting.html