NOTICE! This is a static HTML version of a legacy Fiji BugZilla bug.

The Fiji project now uses GitHub Issues for issue tracking.

Please file all new issues there.

Bug 887 - Error - lif files LAS 4.0
Error - lif files LAS 4.0
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Bio-Formats
unspecified
Macintosh Mac OS
: P2 major
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2014-08-07 18:39 CDT by Paula Sampaio
Modified: 2014-11-06 13:07 CST
4 users (show)

See Also:


Attachments
Image test aquired with LAS AF 4.0.0 that can't be open in Fiji (1.07 MB, application/octet-stream)
2014-08-08 10:52 CDT, Paula Sampaio

Description Paula Sampaio 2014-08-07 18:39:43 CDT
Error when try lif files generated by Leica LAS AF 4.0. 
When I tried to open it appears a box saing that file is not in a suported format. 
Open via Bioformats I get the following log:
loci.formats.FormatException: Invalid Memory Block: found magic bytes 0, expected 112
This appens in Mac OS X and Linux. Windows not tested.

Thank you very much.

Paula Sampaio

Information about your version of Java:

  os.arch => x86_64
  os.name => Mac OS X
  os.version => 10.6.8
  java.version => 1.6.0_65
  java.vendor => Apple Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_65-b14-462-10M4609
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 20.65-b04-462
  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: REMIND_LATER

Information relevant to JAVA_HOME related problems:

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

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20140802165300)
Fiji: http://fiji.sc/update/ (last check:20140730200634)
3D ImageJ Suite: http://sites.imagej.net/Tboudier/ (last check:20140604070506)
BAR: http://sites.imagej.net/Tiago/ (last check:20140714042313)
Bio-Formats: http://sites.imagej.net/Bio-Formats/ (last check:20140806022639)
Biomedgroup: http://sites.imagej.net/Biomedgroup/ (last check:20140720121812)
BioVoxxel: http://sites.imagej.net/BioVoxxel/ (last check:20140730091642)
Cookbook: http://sites.imagej.net/Cookbook/ (last check:20131220231857)
CMCI-EMBL: http://sites.imagej.net/Miura/ (last check:20140718150940)
CMP-BIA tools: http://sites.imagej.net/CMP-BIA/ (last check:20140423153817)
IBMP-CNRS: http://www-ibmp.u-strasbg.fr/fijiupdates/ (last check:20140526154644)
IMCF Uni Basel: http://sites.imagej.net/UniBas-IMCF/ (last check:20140802222144)
MOSAIC ToolSuite: http://mosaic.mpi-cbg.de/Downloads/update/Fiji/MosaicToolsuite/ (last check:20140801103045)
PHANTAST: http://sites.imagej.net/Nicjac/ (last check:20140224225450)
PTBIOP: http://biop.epfl.ch/Fiji-Update/ (last check:20140730103856)
ScientiFig: http://sites.imagej.net/Aigouy/ (last check:20140806152638)

Files not up-to-date:
  bc774937 (MODIFIED) 20140611224841 Contents/Info.plist
  4f6e4a5e (LOCAL_ONLY) 20140414120839 macros/Metadata.ijm
  0bd63441 (LOCAL_ONLY) 20140622203309 macros/Pedro.ijm
  a72820a7 (LOCAL_ONLY) 20140617031214 macros/on wor.ijm
  2f47077b (LOCAL_ONLY) 20140617143621 macros/on wor.txt
  9f80d875 (LOCAL_ONLY) 20080611153812 macros/toolsets/3D measure Tools.txt
  399e67af (LOCAL_ONLY) 20050406100906 macros/toolsets/3D-Distance-Tool.txt
  25640c70 (LOCAL_ONLY) 20090622130806 macros/toolsets/ColourProfiler Tools.txt
  bd7bc5d1 (LOCAL_ONLY) 20140410001925 plugins/ActionBar/Shared Bars/BIOP_MultiManualSelect.ijm
  c271b415 (LOCAL_ONLY) 20140510010455 plugins/ActionBar/Shared Bars/BIOP_PSF_Quality.ijm
  08afb731 (LOCAL_ONLY) 20140410001925 plugins/ActionBar/Shared Bars/BIOP_VSI_Reader.ijm
  4edb1d6f (LOCAL_ONLY) 20140410001925 plugins/ActionBar/Shared Bars/Common_Tools.ijm
  db280c9c (LOCAL_ONLY) 20140410001926 plugins/ActionBar/Shared Bars/JaCoP_Tools.ijm
  b0398adb (LOCAL_ONLY) 20140212164320 plugins/DeconvolutionLab/DeconvolutionLab_.jar
  85178932 (LOCAL_ONLY) 20130319101304 plugins/PSF_Generator.jar
  a67c844f (LOCAL_ONLY) 20140703232429 plugins/ScientiFig/ScientiFigPrefs.txt
  3bec3288 (LOCAL_ONLY) 20140410235319 plugins/gdsc_.jar
Comment 1 Paula Sampaio 2014-08-07 18:45:47 CDT
loci.formats.FormatException: Invalid Memory Block: found magic bytes 0, expected 112
	at loci.formats.in.LIFReader.initFile(LIFReader.java:416)
	at loci.formats.FormatReader.setId(FormatReader.java:1317)
	at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:494)
	at loci.plugins.in.ImportProcess.execute(ImportProcess.java:144)
	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:202)
	at ij.IJ.runPlugIn(IJ.java:166)
	at ij.Executer.runCommand(Executer.java:131)
	at ij.Executer.run(Executer.java:64)
	at java.lang.Thread.run(Thread.java:695)
Comment 2 Paula Sampaio 2014-08-08 10:52:37 CDT
Created attachment 192
Image test aquired with LAS AF 4.0.0 that can't be open in Fiji

The attachement is an exemple of a .lif file aquired with LAS AF 4.0.0 that can't be open by Fiji even when via Bioformats plugin.
It has two channels.
Comment 3 Mark Hiner 2014-08-08 11:50:15 CDT
Hi Paula,

 Since you are using the Bio-Formats importer directly and it's failing to open your dataset, this is actually a bug with Bio-Formats itself and not Fiji.

 This page: http://www.openmicroscopy.org/site/support/bio-formats5/about/bug-reporting.html has instructions for submitting Bio-Formats bug reports to the OME Users mailing list (http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users).

Thanks for taking the time to report your issue,
Mark
Comment 4 Tecedor 2014-11-06 10:28:25 CST
I'm having the same problem than Paula Sampaio (same log window message than she wrote in comment 1). I found this problem in Mac and PC
Comment 5 Curtis Rueden 2014-11-06 10:35:29 CST
Tecedor: This issue was being tracked on the OME bug tracker:

https://trac.openmicroscopy.org.uk/ome/ticket/12144

The issue is now fixed, and the changes merged:

https://github.com/openmicroscopy/bioformats/pull/1399

So you should be able to receive the fix by enabling the Bio-Formats update site as described at:

http://imagej.net/Bio-Formats#Daily_builds
Comment 6 Tecedor 2014-11-06 12:38:47 CST
Hi Curtis,

I really appreciate your fast answer.

Unfortunately, Bio-formats plugin for imageJ is still not opening .lif files LAS 4.0 for me (it does for .lsm and .dm3 files). I updated to version 5.0.5 before submit the bug in bugzilla. Now, I update to version 5.1.0-m1 and still doesn’t work.

* If I try to open a .lif file dragging and dropping the file directly to ImageJ, a window with:

File is not in a supported format, a reader plugin is not available, or it was not found 

* If I try to open a .lif file using the  bio-formats importer, a window with:

Sorry, there was a problem during import


 and then other window with:


loci.formats.FormatException: Invalid Memory Block: found magic bytes 0, expected 112
	at loci.formats.in.LIFReader.initFile(LIFReader.java:416)
	at loci.formats.FormatReader.setId(FormatReader.java:1317)
	at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:494)
	at loci.plugins.in.ImportProcess.execute(ImportProcess.java:144)
	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:202)
	at ij.IJ.runPlugIn(IJ.java:166)
	at ij.Executer.runCommand(Executer.java:131)
	at ij.Executer.run(Executer.java:64)
	at java.lang.Thread.run(Thread.java:695)


Any suggestion?

Thanks a lot.

Luis
Comment 7 Curtis Rueden 2014-11-06 13:07:58 CST
If you are sure you have the Bio-Formats update site enabled, then I suggest reporting the bug to the OME developers:

https://www.openmicroscopy.org/site/support/bio-formats5/about/bug-reporting.html