Bug 911 – Bio-Formats Importer cannot read new .lif format

Bug 911 - Bio-Formats Importer cannot read new .lif format


Summary:	Bio-Formats Importer cannot read new .lif format

Status:	RESOLVED MOVED

Product:	Fiji
Classification:	Unclassified
Component:	Plugins
Version:	unspecified
Hardware:	PC Windows

Importance:	P4 normal
Assigned To:	ImageJ Bugs Mailing List

URL:

Depends on:
Blocks:

Reported:	2014-08-20 14:29 CDT by Andrea Stout
Modified:	2014-10-08 14:58 CDT
CC List:	3 users (show)

See Also:

Attachments
A single 3-channel image; not a z-stack (2.69 MB, application/octet-stream) 2014-08-20 14:38 CDT, Andrea Stout

Description Andrea Stout 2014-08-20 14:29:15 CDT

Our new Leica STED confocal is running version 4.0.0.11706 of LAS AF.  Fiji is unable to import the resulting .lif files acquired on this system using the Bio-Formats Importer plugin.

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:\Users\Public\Fiji.app/java/win64/jdk1.6.0_24//jre
  imagej.dir => C:\Users\Public\Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20140710135854)
Fiji: http://fiji.sc/update/ (last check:20140709163742)

Files not up-to-date:
  a1a0d20a (MODIFIED) 20140708145824 jars/imagej-common-0.8.0.jar
  e8dfe85e (MODIFIED) 20140820152503 jars/imagej-common-0.8.2.jar
  9654e601 (MODIFIED) 20140731143959 jars/imagej-updater-0.5.0.jar
  04d82cff (MODIFIED) 20140820152503 jars/imagej-updater-0.6.1.jar
  4f9cde52 (MODIFIED) 20140708145908 jars/scifio-0.15.4.jar
  2f8d5769 (MODIFIED) 20140820152502 jars/scifio-0.16.1.jar
  06ac0d2a (MODIFIED) 20140731143959 jars/scijava-common-2.27.0.jar
  1f43a668 (MODIFIED) 20140820152502 jars/scijava-common-2.30.0.jar

Comment 1 Andrea Stout 2014-08-20 14:38:44 CDT

Created attachment 205
A single 3-channel image; not a z-stack

Comment 2 Andrea Stout 2014-08-20 14:40:11 CDT

I did update Fiji to the latest version (on 20 Aug. 2014) after reporting the bug, but the problem persisted.

Comment 3 Curtis Rueden 2014-08-20 15:48:54 CDT

Thanks for the report and sample data! This is a known issue:
http://trac.openmicroscopy.org/ome/ticket/12144

Unfortunately, Leica changed the file format, so it may be some time before Bio-Formats can adapt to the changes.

Let us know if you want to be CCed on that ticket to receive automatic notifications of progress.

Comment 4 Andrea Stout 2014-08-20 16:04:32 CDT

Thanks for the quick response, Curtis! I figured Leica messed with the format but didn't know how many systems out there are running this new version of LAS AF. If you could keep me on the cc list, I'd appreciate it.  Best regards, Andrea

Comment 5 Curtis Rueden 2014-08-20 16:09:24 CDT

Sure thing Andrea, I added you to the CC list!