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Bug 629 - incorrect voxel size for Leica LAS *.lif files
incorrect voxel size for Leica LAS *.lif files
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Bio-Formats
unspecified
PC Windows
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2013-07-10 14:47 CDT by Andrea Stout
Modified: 2013-08-15 15:58 CDT
4 users (show)

See Also:

Description Andrea Stout 2013-07-10 14:47:04 CDT
LOCI Importer does not correctly identify the z-interval in 3D Leica .lif files (z-stacks) acquired using LAS AF (version 3.1.0 on a TCS SP8 confocal).  No matter what z-interval was used during acquisition, the voxel depth is always read in as 1 micron.

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: UP_TO_DATE

Information relevant to JAVA_HOME related problems:

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

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Comment 1 Johannes Schindelin 2013-07-10 19:31:50 CDT
Hey Andrea, how about uploading a small example to reproduce the issue easily via Help>Upload Sample Image?
Comment 2 Andrea Stout 2013-07-11 09:23:30 CDT
Hi Johannes,

I just uploaded a .lif file called "FijiBug_Stout.lif".  It's a single z-stack with 2 channels, 512 x 512 pixels. The z-interval during acquisition was 0.5 microns (x-y pixel size = 0.216 microns).  

If you look at the metadata for the file, you can see that DimensionDescriptionLength 2 (which is the total thickness of the z-stack) = 3.02 microns.  The NumberOfElements for this dimension is 7, so you can calculate the z-interval from that (3 divided by (7-1) = 0.5).

Let me know if the upload didn't take.   Thanks!

Andrea
Comment 3 Johannes Schindelin 2013-07-11 09:48:17 CDT
The upload worked! Now let's hope that the Bio-Formats developer(s) will have time soon to look into this and work with you to get your problem resolved.
Comment 4 Melissa Linkert 2013-07-11 22:16:07 CDT
Thank you for uploading an example file.  This problem was recently fixed in Bio-Formats (see https://github.com/openmicroscopy/bioformats/pull/521); the next stable version will include the fix.
Comment 5 Johannes Schindelin 2013-07-11 22:57:20 CDT
I reopen this because in Fiji we try to close bug reports only when the fix reached the reporter... ;-)
Comment 6 Andrea Stout 2013-08-07 15:37:07 CDT
This LOCI error reading the correct z-spacing in Leica .lif files still occurs with the most recent version of Fiji (updated on August 7, 2013). I tried to update LOCI independently but that caused problems with Fiji (I could no longer open .lif files at all!)  Will the corrected LOCI be updated in Fiji anytime soon? Thanks!  Andrea
Comment 7 Curtis Rueden 2013-08-14 16:19:23 CDT
The Bio-Formats team plans to release version 4.4.9 within a few weeks. Releasing Bio-Formats more often is currently a primary goal of the project. There has been a lot of work this summer on making the release process more automated, so hopefully we will see faster releases moving forward.

Until then, if you need the latest bugfixes for your work, you can download the latest build of loci_tools.jar from:

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

Drop it into the "plugins" folder, and delete all the following files:

jars/bio-formats/scifio-4.4.9-SNAPSHOT.jar
jars/bio-formats-4.4.9-SNAPSHOT.jar
jars/jruby.jar
jars/loci-common-4.4.9-SNAPSHOT.jar
jars/mdbtools-java-4.4.9-SNAPSHOT.jar
jars/metakit-4.4.4.jar
jars/ome-xml-4.4.8.jar
jars/poi-loci-4.4.9-SNAPSHOT.jar
plugins/loci_plugins-4.4.9-SNAPSHOT.jar

Then when you start Fiji after that, you should have the latest Bio-Formats installed and working.

I am sorry the process is not easier. Hopefully that will change soon.
Comment 8 Andrea Stout 2013-08-15 09:22:09 CDT
Thanks for your response, Curtis, I really appreciate it, and I look forward to the next release of Bio-Formats. My facility has quite a few computers running Fiji, so your proposed fix for LOCI isn't terribly practical. I may try it on my own computer, though, just to see if it solves the problem.   Thanks again!
Comment 9 Curtis Rueden 2013-08-15 15:10:18 CDT
Thanks for the feedback, Andrea. I completely agree that the process I outlined earlier is burdensome, and not scalable to many installations.

To remedy that, I finally set up something we have been wanting for a long time now: a dedicated Bio-Formats update site for daily builds.

To use it:

* Help > Update Fiji
* Click "Manage update sites"
* Check "Bio-Formats daily builds"
* Click "Close"

Five files should appear on the list with "Status/Action" of "Update it".

* Click "Apply changes"
* Restart Fiji
* Help > About Plugins > LOCI Plugins...

The dialog should now show a build date of "14 August 2013" or later.

Please let us know how it works for you!

Now that you can use this update site to access Bio-Formats bug fixes, we can close this bug as fixed!
Comment 10 Andrea Stout 2013-08-15 15:17:33 CDT
Hey it worked!  Thanks, Curtis -- that was really easy!!
Comment 11 Johannes Schindelin 2013-08-15 15:58:33 CDT
Thank you, Curtis, for fulfilling the mission of Fiji!