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Bug 1083 - Unable to open Deltavision (.DV) files using Bioformats importer
Unable to open Deltavision (.DV) files using Bioformats importer
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Bio-Formats
unspecified
PC Windows
: P4 normal
Assigned To: Jean-Yves Tinevez
Depends on:
Blocks:
 
Reported: 2015-06-11 04:33 CDT by Andrew Porter
Modified: 2015-10-20 11:04 CDT
3 users (show)

See Also:

Description Andrew Porter 2015-06-11 04:33:55 CDT
I am unable to open .DV files generated by our Deltavision microscope.

I have previously (over the last 6 months) been able to drag-and-drop, and these files have opened; or I can use the File-Import-Bioformats dialogue box to open them.

Now when I try either of these messages (and I have tried this for multiple files).

I have recently been using TrackMate, and I notice that this seems to have some Bioformats plugins associated with it; and I don't think I've tried opening .DV files since I added TrackMate to my update list - so I wonder if this might be the issue?

-> I have tried updating FIJI using the Help-Update FIJI option
-> I tried uninstalling Bioformats and reloading it using the Advanced Options under the Manage Sites dialogue
-> I have tried opening files from different folders/locations
-> I manually installed the Deltavision Opener Plugin from here (http://rsb.info.nih.gov/ij/plugins/track/delta.html) and can use this to open the files, but it doesn't provide the Bioformats functionality (splitting channels, autoscale) which are really useful

Any help gratefully received!

Andrew

Information about your version of Java:

  os.arch => x86
  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) Client 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\aporter\DOCUME~1\FIJI\FIJI-W~1\Fiji.app/java/win32/jdk1.6.0_24//jre
  imagej.dir => C:\Users\aporter\DOCUME~1\FIJI\FIJI-W~1\Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20150602025708)
Fiji: http://fiji.sc/update/ (last check:20150605140752)
BAR: http://sites.imagej.net/Tiago/ (last check:20150604154025)
Bio-Formats: http://sites.imagej.net/Bio-Formats/ (last check:20150609022639)
CellMotility: http://sites.imagej.net/CellMotility/ (last check:20150514151923)
LOCI: http://sites.imagej.net/LOCI/ (last check:20150428225912)
Morphology: http://sites.imagej.net/Landini/ (last check:20140723155558)
NucleusJ: http://sites.imagej.net/PouletAxel/ (last check:20141101093602)
ScientiFig: http://sites.imagej.net/Aigouy/ (last check:20150326113209)
TrackMate-dev: http://sites.imagej.net/TrackMate-dev/ (last check:20150330132557)
New:  (last check:0)

Files not up-to-date:
  1ad3be0d (LOCAL_ONLY) 20141025210334 jars/jpedalSTD.jar
  27211db7 (LOCAL_ONLY) 20090403141332 macros/StartupMacros.txt
  54a8746b (LOCAL_ONLY) 20141031160322 macros/toolsets/FibrilTool.txt
  1a200546 (LOCAL_ONLY) 20141031133346 macros/toolsets/PeakFinderTool.txt
  6bcba459 (LOCAL_ONLY) 20141031141921 macros/toolsets/aporter's Toolset.txt
  bc887d8f (LOCAL_ONLY) 20150116090502 plugins/3D_measure.txt
  29ebdb9a (LOCAL_ONLY) 20150611095857 plugins/Deltavision_Opener.jar
  66b8f8d1 (LOCAL_ONLY) 20150325155510 plugins/Macros/3DAngleTool.txt
  7a4e24bc (LOCAL_ONLY) 20150325152512 plugins/Macros/3Dangle.txt
  48f196e3 (LOCAL_ONLY) 20141031141714 plugins/PeakFinderTool.txt
  f61fbfec (LOCAL_ONLY) 20141031141653 plugins/Tools/PeakFinder_Tool.ijm
Comment 1 Andrew Porter 2015-06-11 04:37:20 CDT
I forgot to say - I get the normal Bio-Formats import options box, click OK, and then get this error message:

(Fiji Is Just) ImageJ 2.0.0-rc-25/1.49p; Java 1.6.0_24 [32-bit]; Windows 7 6.1; 99MB of 1529MB (6%)
 
java.lang.NoClassDefFoundError: ome/units/quantity/Length
	at loci.formats.in.DeltavisionReader$DVExtHdrFields.<init>(DeltavisionReader.java:2383)
	at loci.formats.in.DeltavisionReader$DVExtHdrFields.<init>(DeltavisionReader.java:2282)
	at loci.formats.in.DeltavisionReader.initPixels(DeltavisionReader.java:417)
	at loci.formats.in.DeltavisionReader.initFile(DeltavisionReader.java:276)
	at loci.formats.FormatReader.setId(FormatReader.java:1319)
	at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:505)
	at loci.plugins.in.ImportProcess.execute(ImportProcess.java:143)
	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.Executer.runCommand(Executer.java:131)
	at ij.Executer.run(Executer.java:64)
	at java.lang.Thread.run(Thread.java:662)
Comment 2 Mark Hiner 2015-06-11 06:58:13 CDT
Hi Andrew,

>NoClassDefFoundError

 This error comes up when there is a skew in the dependencies. In this case the problem is that Fiji ships Bio-Formats 5.1.2, and TrackMate-dev ships its own version of 5.0 - without fully removing/overriding all the .jars in 5.1.2. This mixes 5.1 jars with 5.0 jars, which causes the NoClassDefFoundError you saw.

Assigned to Jean-Yves, since TrackMate-dev lists you as the maintainer. My suggestion would be to simply not ship Bio-Formats with the TrackMate-dev update site, since Bio-Formats a) ships with core Fiji and b) has its own update site - so you have at least two opportunities for conflict like this.

Andrew - you should be able to work around this issue by disabling the TrackMate-dev update site for now.
Comment 3 Jean-Yves Tinevez 2015-06-11 07:02:14 CDT
> Assigned to Jean-Yves, since TrackMate-dev lists you as the maintainer. My
> suggestion would be to simply not ship Bio-Formats with the TrackMate-dev
> update site, since Bio-Formats a) ships with core Fiji and b) has its own
> update site - so you have at least two opportunities for conflict like this.

Understood, will do.
Comment 4 Andrew Porter 2015-06-11 08:28:55 CDT
Thank you very much Jean-Yves Tinevez; I did a clean install of FIJI, and I can use both the BioFormats Importer and TrackMate; I just haven't activated the TrackMate update site this time!

Thanks again for the help!

Andrew
Comment 5 Jean-Yves Tinevez 2015-06-22 06:40:35 CDT
@Mark: Bad news: I tried to remove dependencies BioFormats from TrackMate-dev update site, but this breaks Fiji. It does not launch after trying to update TrackMate-dev.

In my humble opinion, one should simply nuke the TrackMate-dev site. Development is now slower, and we are reaching a 'stable' mode.
Comment 6 Jean-Yves Tinevez 2015-10-20 11:04:37 CDT
Thanks to @hinerm, this is done.