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Bug 754 - Trackmate doesn't find particles
Trackmate doesn't find particles
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
All Mac OS
: P4 normal
Assigned To: Jean-Yves Tinevez
Depends on:
Blocks:
 
Reported: 2014-05-28 16:52 CDT by Jay Nadeau
Modified: 2014-06-02 15:48 CDT
2 users (show)

See Also:
Description Jay Nadeau 2014-05-28 16:52:15 CDT 
Version 2.0 of trackmate was able to find particles accurately, but the tracking was inaccurate. In order to take advantage of the updates, I installed Version 2.2 by running the Update Fiji updater. Since that time, Trackmate has been unable to find particles in any image, including the test image provided with Trackmate.

Information about your version of Java:

  os.arch => x86_64
  os.name => Mac OS X
  os.version => 10.7.5
  java.version => 1.6.0_45
  java.vendor => Apple Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_45-b06-451-11M4406
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 20.45-b01-451
  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:20140520094735)
Fiji: http://fiji.sc/update/ (last check:20140523143021)

Files not up-to-date:
  0cd08829 (LOCAL_ONLY) 20140523164145 Contents/Info.plist
  9eef97db (LOCAL_ONLY) 20140523111842 Contents/MacOS/ImageJ-macosx
  d50b993b (LOCAL_ONLY) 20140523111842 Contents/MacOS/ImageJ-tiger
  6b82c620 (LOCAL_ONLY) 20130715035116 Contents/Resources/Fiji.icns
  992807f6 (LOCAL_ONLY) 20130715035116 Contents/Resources/ImageJ.icns
  1faaeed6 (LOCAL_ONLY) 20130715035116 images/icon-flat.png
  a02d5340 (LOCAL_ONLY) 20130715035116 images/icon.png
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  d2b52892 (LOCAL_ONLY) 20130715035116 jars/bcprov-jdk14-138.jar
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  7c24e995 (LOCAL_ONLY) 20140523111936 jars/bio-formats/formats-common-5.0.1.jar
  31f6516f (LOCAL_ONLY) 20140523111937 jars/bio-formats/formats-gpl-5.0.1.jar
  3d2962d3 (LOCAL_ONLY) 20140523111939 jars/bio-formats/jai_imageio-5.0.1.jar
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  70e68706 (LOCAL_ONLY) 20140523111939 jars/bio-formats/metakit-5.0.1.jar
  096abf51 (LOCAL_ONLY) 20140523111940 jars/bio-formats/ome-poi-5.0.1.jar
  429311fd (LOCAL_ONLY) 20140523111941 jars/bio-formats/ome-xml-5.0.1.jar
  1deeabc9 (LOCAL_ONLY) 20140523111941 jars/bio-formats/specification-5.0.1.jar
  d879d232 (LOCAL_ONLY) 20140523111943 jars/bio-formats/turbojpeg-5.0.1.jar
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  a3312d3f (LOCAL_ONLY) 20130715035116 luts/ICA.lut
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Comment 1 Jean-Yves Tinevez 2014-05-29 06:36:38 CDT 
I confirm the occurrence of the bug on PC Windows 7.

Another user contacted me via email and reported the same issue on MacOSX. On this platform, there is nothing logged on the console. So no error message.


It seems to be triggered after an update, maybe to imblib2-beta26. 
I will investigate.
Comment 2 Jean-Yves Tinevez 2014-06-02 03:01:14 CDT 
After a quick investigation, I have found that the bug is indeed fueled by a recent change in imglib2. Here is what the console says upon detecting spots:

02/06/14 10:04:05,022 [0x0-0x71071].org.fiji: java.lang.NoSuchMethodError: net.imglib2.algorithm.localextrema.LocalExtrema.findLocalExtrema(Lnet/imglib2/RandomAccessibleInterval;Lnet/imglib2/algorithm/localextrema/LocalExtrema$LocalNeighborhoodCheck;I)Ljava/util/ArrayList;
02/06/14 10:04:05,022 [0x0-0x71071].org.fiji: 	at fiji.plugin.trackmate.detection.DetectionUtils.findLocalMaxima(DetectionUtils.java:189)
02/06/14 10:04:05,022 [0x0-0x71071].org.fiji: 	at fiji.plugin.trackmate.detection.LogDetector.process(LogDetector.java:141)
02/06/14 10:04:05,022 [0x0-0x71071].org.fiji: 	at fiji.plugin.trackmate.TrackMate$1.run(TrackMate.java:433)
Comment 3 Jean-Yves Tinevez 2014-06-02 03:18:59 CDT 
Well I think I cannot fix it simply by patching the current version, so I will have to do a release...
Comment 4 Jean-Yves Tinevez 2014-06-02 04:23:50 CDT 
Ok, so I just uploaded v2.3.0 that fixes the problem.
@Jay, can you update and tell me if it works?
Comment 5 Jean-Yves Tinevez 2014-06-02 15:47:01 CDT 
Mail received from Jay:

"Yes, it's working now--thanks! "

I also tested it by myself on windows 7 and MacOSX Lion.