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Bug 784 - Closing the ImageJ toolbar stopped closing TrakEM2
Closing the ImageJ toolbar stopped closing TrakEM2
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Linux
: P4 normal
Assigned To: Curtis Rueden
Depends on:
Blocks:
 
Reported: 2014-06-12 14:29 CDT by Stephan Saalfeld
Modified: 2014-07-14 12:05 CDT
4 users (show)

See Also:

Description Stephan Saalfeld 2014-06-12 14:29:22 CDT
Freshly updated Fiji stopped closing TrakEM2.  Closing the then standalone TrakEM2 does not close Fiji which remains running without UI.  No output in the terminal.

Information about your version of Java:

  os.arch => amd64
  os.name => Linux
  os.version => 3.2.0-64-generic
  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.X11GraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => gnome
  file.separator => /

The up-to-date check says: REMIND_LATER

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: /groups/saalfeld/home/saalfelds/packages/Fiji.app/java/linux-amd64/jdk1.6.0_24//jre
  imagej.dir => /groups/saalfeld/home/saalfelds/packages/Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20140611133802)

Files not up-to-date:
  7c30c48a (MODIFIED) 20131109081822 Contents/Info.plist
  92d974dd 20131109085215 fiji-linux64
  a02d5340 (MODIFIED) 20131109081823 images/icon.png
  0543a785 (LOCAL_ONLY) 20131109081825 jars/Fiji.jar
  91ece67d (LOCAL_ONLY) 20140610185424 jars/JWlz-1.4.0.jar
  c3f8675e (LOCAL_ONLY) 20131109081825 jars/Jama.jar
  2665fff0 (LOCAL_ONLY) 20140418143956 jars/T2-NIT-1.0-SNAPSHOT.jar
  97e95d02 (LOCAL_ONLY) 20140418144000 jars/T2-TreelineGraph-0.1-SNAPSHOT.jar
  ad44ab73 (LOCAL_ONLY) 20140610185426 jars/VIB-lib-2.0.0-SNAPSHOT.jar
  bd573380 (LOCAL_ONLY) 20131109081826 jars/VectorString.jar
  8e160955 (LOCAL_ONLY) 20131109081828 jars/ant-junit.jar
  4124ed0d (LOCAL_ONLY) 20131109081828 jars/ant-launcher.jar
  b18659ff (LOCAL_ONLY) 20131109081832 jars/ant-nodeps.jar
  70c12cd3 (LOCAL_ONLY) 20131109081839 jars/ant.jar
  a70a2d61 (LOCAL_ONLY) 20140610185428 jars/args4j-2.0.25.jar
  ff131d48 (LOCAL_ONLY) 20131109081840 jars/autocomplete.jar
  5a0c7964 (LOCAL_ONLY) 20140418143946 jars/batik-1.8.jar
  060376e4 (LOCAL_ONLY) 20140610185420 jars/bio-formats/formats-api-5.0.2.jar
  95823b1e (LOCAL_ONLY) 20140610185421 jars/bio-formats/formats-bsd-5.0.2.jar
  06e364df (LOCAL_ONLY) 20140610185422 jars/bio-formats/formats-common-5.0.2.jar
  8f8c6819 (LOCAL_ONLY) 20140610185422 jars/bio-formats/formats-gpl-5.0.2.jar
  3d2962d3 (LOCAL_ONLY) 20140610185423 jars/bio-formats/jai_imageio-5.0.2.jar
  e8d453ec (LOCAL_ONLY) 20140610185423 jars/bio-formats/mdbtools-java-5.0.2.jar
  70e68706 (LOCAL_ONLY) 20140610185423 jars/bio-formats/metakit-5.0.2.jar
  096abf51 (LOCAL_ONLY) 20140610185423 jars/bio-formats/ome-poi-5.0.2.jar
  429311fd (LOCAL_ONLY) 20140610185423 jars/bio-formats/ome-xml-5.0.2.jar
  1deeabc9 (LOCAL_ONLY) 20140610185424 jars/bio-formats/specification-5.0.2.jar
  d879d232 (LOCAL_ONLY) 20140610185424 jars/bio-formats/turbojpeg-5.0.2.jar
  8eb3709e (LOCAL_ONLY) 20131109081952 jars/commons-logging-1.1.1.jar
  f9509b47 (LOCAL_ONLY) 20140418143946 jars/commons-math3-3.2.jar
  b6bf3817 (LOCAL_ONLY) 20131109082006 jars/edu_mines_jtk.jar
  efcc8eb3 (LOCAL_ONLY) 20131109082744 jars/fake-2.0.0-SNAPSHOT.jar
  5f4f0bcc (LOCAL_ONLY) 20140610185424 jars/fiji-compat-2.0.0-SNAPSHOT.jar
  5d038ddb (LOCAL_ONLY) 20140610185424 jars/fiji-lib-2.0.0-SNAPSHOT.jar
  7c5dc207 (LOCAL_ONLY) 20131109082447 jars/fiji-scripting-2.0.0-SNAPSHOT.jar
  c4caa696 (LOCAL_ONLY) 20140418143946 jars/formats-api-5.0.0.jar
  8406c407 (LOCAL_ONLY) 20140418143946 jars/formats-bsd-5.0.0.jar
  be9b3c4c (LOCAL_ONLY) 20140418143946 jars/formats-common-5.0.0.jar
  be2287e8 (LOCAL_ONLY) 20131109082012 jars/imagescience-2.4.1.jar
  780fae40 (LOCAL_ONLY) 20131109082014 jars/imageware.jar
  12c313a8 (MODIFIED) 20140612132330 jars/imglib2-2.0.0-SNAPSHOT.jar
  6e22d9dd (MODIFIED) 20140610185416 jars/imglib2-2.0.0-beta-26.jar
  ce6460d3 (LOCAL_ONLY) 20140610185424 jars/imglib2-algorithms-gpl-2.0.0-beta-26.jar
  673fae25 (LOCAL_ONLY) 20140610185424 jars/imglib2-algorithms-legacy-2.0.0-beta-26.jar
  bb62b52f (MODIFIED) 20140610185418 jars/imglib2-ij-2.0.0-beta-26.jar
  9abf1894 (MODIFIED) 20140605115606 jars/imglib2-ij-2.0.0-beta-27-SNAPSHOT.jar
  93b97ced (MODIFIED) 20140605115611 jars/imglib2-realtransform-2.0.0-SNAPSHOT.jar
  ba955d64 (MODIFIED) 20140610185419 jars/imglib2-realtransform-2.0.0-beta-26.jar
  9a8590f0 (LOCAL_ONLY) 20140612121031 jars/intensity-transform-0.0.1-SNAPSHOT.jar
  c4258671 (LOCAL_ONLY) 20131109082028 jars/itextpdf.jar
  a6c1d188 (LOCAL_ONLY) 20140418143945 jars/j3d-core-1.5.2.jar
  0dccf163 (LOCAL_ONLY) 20131109082031 jars/jacl.jar
  3d81473f (LOCAL_ONLY) 20140418143945 jars/jai-codec-1.1.3.jar
  5f7f32e2 (LOCAL_ONLY) 20140418143945 jars/jai-core-1.1.3.jar
  8c636e50 (LOCAL_ONLY) 20131109082034 jars/jai_codec.jar
  717dd8e0 (LOCAL_ONLY) 20131109082043 jars/jai_core.jar
  e4ac596e (LOCAL_ONLY) 20131109082449 jars/java-cup-0.11a.jar
  15f34947 (LOCAL_ONLY) 20131109082051 jars/javac.jar
  c295a4c5 (LOCAL_ONLY) 20131109082420 jars/jdom-2.0.2.jar
  64241209 (LOCAL_ONLY) 20131109082059 jars/jdom-contrib.jar
  166036ab (LOCAL_ONLY) 20131109082102 jars/jep.jar
  b5efe893 (LOCAL_ONLY) 20140610185428 jars/jgoodies-common-1.7.0.jar
  5198aba1 (LOCAL_ONLY) 20140610185428 jars/jgoodies-forms-1.7.2.jar
  0e15c072 (LOCAL_ONLY) 20131109082422 jars/jgrapht-0.8.3.jar
  0b768690 (LOCAL_ONLY) 20131109082418 jars/jgraphx-1.10.4.1.jar
  90915f54 (LOCAL_ONLY) 20131109082128 jars/jna.jar
  4c09d41c (LOCAL_ONLY) 20140418143946 jars/joda-time-2.2.jar
  1ad3be0d (LOCAL_ONLY) 20131109082136 jars/jpedalSTD.jar
  65f86378 (LOCAL_ONLY) 20131109082203 jars/js.jar
  24d47d70 (LOCAL_ONLY) 20131109082205 jars/junit-4.8.1.jar
  5ce5840c (LOCAL_ONLY) 20131109082252 jars/jzlib-1.0.7.jar
  5a6f6f25 (LOCAL_ONLY) 20140610185424 jars/legacy-imglib1-2.0.0-SNAPSHOT.jar
  7a02f3e7 (LOCAL_ONLY) 20140610185425 jars/logback-classic-1.0.9.jar
  d9d80652 (LOCAL_ONLY) 20140418143946 jars/logback-core-1.0.9.jar
  e9d48f1d (LOCAL_ONLY) 20140418143945 jars/mpicbg-0.6.1.jar
  9c8395f1 (LOCAL_ONLY) 20140612121037 jars/mpicbg-0.6.2-SNAPSHOT.jar
  a51a31db (LOCAL_ONLY) 20140610185426 jars/netcdf-4.3.19.jar
  e0088259 (LOCAL_ONLY) 20131109082257 jars/pal-optimization.jar
  82577709 (LOCAL_ONLY) 20131109082450 jars/pentaho-package-manager-1.0.0.jar
  c586a356 (LOCAL_ONLY) 20140610185426 jars/postgresql.jar
  e6380596 (LOCAL_ONLY) 20140610185426 jars/scifio-bf-compat-1.7.3.jar
  c544d657 (LOCAL_ONLY) 20140610185426 jars/scifio-lifesci-0.5.0.jar
  e5e6a28d (LOCAL_ONLY) 20140610185426 jars/scifio-ome-xml-0.9.0.jar
  a8fe5231 (LOCAL_ONLY) 20140610185429 jars/scifio-tools-0.14.0.jar
  16686f95 (LOCAL_ONLY) 20140418143946 jars/specification-5.0.0.jar
  40da943b (LOCAL_ONLY) 20131109082011 jars/volume_renderer.jar
  7d5ba6c5 (LOCAL_ONLY) 20131109082412 jars/wavelets.jar
  b94bc93f (LOCAL_ONLY) 20140610185427 jars/weave_jy2java-2.0.0-SNAPSHOT.jar
  9a71e194 (LOCAL_ONLY) 20131109082523 jars/weka-dev-3.7.6.jar
  c432f64b (LOCAL_ONLY) 20131109084650 luts/16_colors.lut
  89419f99 (LOCAL_ONLY) 20131109084651 luts/5_ramps.lut
  dc3a1bdd (LOCAL_ONLY) 20131109084652 luts/6_shades.lut
  0b3bbb6c (LOCAL_ONLY) 20131109084652 luts/Cyan Hot.lut
  7a26c39a (LOCAL_ONLY) 20131109084647 luts/GoldenAngle.lut
  655b55e6 (LOCAL_ONLY) 20131109084653 luts/Green Fire Blue.lut
  2918f6d3 (LOCAL_ONLY) 20131109084654 luts/HiLo.lut
  a3312d3f (LOCAL_ONLY) 20131109084655 luts/ICA.lut
  db5bf8a4 (LOCAL_ONLY) 20131109084655 luts/ICA2.lut
  9f7dd167 (LOCAL_ONLY) 20131109084656 luts/ICA3.lut
  697dd3a4 (LOCAL_ONLY) 20131109084657 luts/Magenta Hot.lut
  524604de (LOCAL_ONLY) 20131109084657 luts/Orange Hot.lut
  9c9a56c2 (LOCAL_ONLY) 20131109084659 luts/Rainbow RGB.lut
  4e686ec6 (LOCAL_ONLY) 20131109084700 luts/Red Hot.lut
  2fdb7c96 (LOCAL_ONLY) 20131109084702 luts/Thermal.lut
  32157491 (LOCAL_ONLY) 20131109084703 luts/Yellow Hot.lut
  a4cec22b (LOCAL_ONLY) 20131109084704 luts/blue_orange_icb.lut
  c9e396a3 (LOCAL_ONLY) 20131109084706 luts/brgbcmyw.lut
  60f85e63 (LOCAL_ONLY) 20131109084707 luts/cool.lut
  ba88e5f3 (LOCAL_ONLY) 20131109084708 luts/edges.lut
  0a4dce83 (LOCAL_ONLY) 20131109084710 luts/gem.lut
  c616e765 (LOCAL_ONLY) 20131109084711 luts/glasbey.lut
  325c01f3 (LOCAL_ONLY) 20131109084718 luts/glow.lut
  1f99f07e (LOCAL_ONLY) 20131109084712 luts/phase.lut
  52a3c399 (LOCAL_ONLY) 20131109084713 luts/physics.lut
  49f5e48a (LOCAL_ONLY) 20131109084714 luts/royal.lut
  898954dd (LOCAL_ONLY) 20131109084715 luts/sepia.lut
  ebd4ed6b (LOCAL_ONLY) 20131109084715 luts/smart.lut
  36e7ca9e (LOCAL_ONLY) 20131109084716 luts/thal.lut
  940b38f9 (LOCAL_ONLY) 20131109084717 luts/thallium.lut
  17243681 (LOCAL_ONLY) 20131109084717 luts/unionjack.lut
  25abcd0c (LOCAL_ONLY) 20131109084723 macros/StartupMacros.fiji.ijm
  a97e1da9 (LOCAL_ONLY) 20131109084722 macros/listManagement.txt
  1785bbbf (LOCAL_ONLY) 20131109084720 macros/toolsets/Clear Custom Tools.txt
  54200f47 (LOCAL_ONLY) 20131109084720 macros/toolsets/Drawing Tools.txt
  9bd39ac4 (LOCAL_ONLY) 20131109084721 macros/toolsets/Lookup Tables.txt
  f7efa1b3 (LOCAL_ONLY) 20131109084724 misc/headless.jar
  8fbab9f6 (LOCAL_ONLY) 20131109084945 plugins/3D_Blob_Segmentation-2.0.0-SNAPSHOT.jar
  d5c84beb (LOCAL_ONLY) 20131109085019 plugins/3D_Objects_Counter-2.0.0-SNAPSHOT.jar
  f42bdae5 (LOCAL_ONLY) 20131109084840 plugins/3D_Viewer.jar
  68175df5 (LOCAL_ONLY) 20131109084841 plugins/Algorithm_Launcher.jar
  9274f337 (LOCAL_ONLY) 20131109084726 plugins/Analyze/Dynamic_ROI_Profiler.clj
  7acae667 (LOCAL_ONLY) 20131109084726 plugins/Analyze/Measure_RGB.txt
  8e49d0ca (LOCAL_ONLY) 20140610185427 plugins/AnalyzeSkeleton_-2.0.0-SNAPSHOT.jar
  263158a7 (LOCAL_ONLY) 20131109084907 plugins/Analyze_Reader_Writer-2.0.0-SNAPSHOT.jar
  645ccb4c (LOCAL_ONLY) 20131109085000 plugins/Anisotropic_Diffusion_2D-2.0.0-SNAPSHOT.jar
  295ba57e (LOCAL_ONLY) 20131109085031 plugins/Arrow_-2.0.0-SNAPSHOT.jar
  04478f7a (LOCAL_ONLY) 20140203133609 plugins/Auto_Threshold-1.16-SNAPSHOT.jar
  fd9b13d9 (LOCAL_ONLY) 20131109085028 plugins/BalloonSegmentation_-2.0.0-SNAPSHOT.jar
  75529242 (LOCAL_ONLY) 20131109085024 plugins/BeanShell_Interpreter-2.0.0-SNAPSHOT.jar
  5ac8c6e3 (LOCAL_ONLY) 20140610185427 plugins/Bug_Submitter-2.0.0-SNAPSHOT.jar
  69972944 (LOCAL_ONLY) 20131109085047 plugins/CLI_-2.0.0-SNAPSHOT.jar
  3e4163b4 (LOCAL_ONLY) 20131109084947 plugins/CPU_Meter-2.0.0-SNAPSHOT.jar
  8c102cb9 (LOCAL_ONLY) 20131109084949 plugins/Calculator_Plus-2.0.0-SNAPSHOT.jar
  e2235578 (LOCAL_ONLY) 20131109084942 plugins/Clojure_Interpreter-2.0.0-SNAPSHOT.jar
  8a9baa41 (LOCAL_ONLY) 20140610185427 plugins/Colocalisation_Analysis-2.0.0-SNAPSHOT.jar
  a99306b3 (LOCAL_ONLY) 20131109085003 plugins/Color_Histogram-2.0.6-SNAPSHOT.jar
  3bac3fbe (LOCAL_ONLY) 20131109085046 plugins/Color_Inspector_3D-2.3-SNAPSHOT.jar
  1902ce83 (LOCAL_ONLY) 20131109084950 plugins/Colour_Deconvolution-2.0.0-SNAPSHOT.jar
  fa6063d9 (LOCAL_ONLY) 20131109085002 plugins/CorrectBleach_-2.0.0-SNAPSHOT.jar
  2a722593 (LOCAL_ONLY) 20131109084857 plugins/Descriptor_based_registration-2.0.0-SNAPSHOT.jar
  4d6319b8 (LOCAL_ONLY) 20131109085051 plugins/Dichromacy_-2.0.0-SNAPSHOT.jar
  96b64b9e (LOCAL_ONLY) 20131109085014 plugins/Differentials_-2.0.0-SNAPSHOT.jar
  eb283f44 (LOCAL_ONLY) 20131109084958 plugins/Directionality_-2.0.1-SNAPSHOT.jar
  83caa3df (LOCAL_ONLY) 20131109084740 plugins/Examples/Add_Popup_Split_Channels.bsh
  f6fcfac7 (LOCAL_ONLY) 20131109084741 plugins/Examples/Anaglyph_for_Red_Cyan_glasses.rb
  5dcd79ab (LOCAL_ONLY) 20131109084741 plugins/Examples/Blobs_Demo_in_Ruby.rb
  73eff736 (LOCAL_ONLY) 20131109084729 plugins/Examples/Command_Launchers/Command_Launcher_BeanShell.bsh
  95549b2f (LOCAL_ONLY) 20131109084730 plugins/Examples/Command_Launchers/Command_Launcher_Clojure.clj
  dceba709 (LOCAL_ONLY) 20131109084731 plugins/Examples/Command_Launchers/Command_Launcher_Javascript.js
  e4954eac (LOCAL_ONLY) 20131109084732 plugins/Examples/Command_Launchers/Command_Launcher_Python.py
  f5111212 (LOCAL_ONLY) 20131109084733 plugins/Examples/Command_Launchers/Command_Launcher_Ruby.rb
  6076ad74 (LOCAL_ONLY) 20131109084735 plugins/Examples/CoverMaker/Cover_Maker.py
  eabbed47 (LOCAL_ONLY) 20131109084734 plugins/Examples/CoverMaker/Prepare_Cover_Maker_Database.py
  77c7bef5 (LOCAL_ONLY) 20131109084742 plugins/Examples/Delayed_Snapshot.py
  5536e038 (LOCAL_ONLY) 20131109084743 plugins/Examples/Delayed_Snapshot_Window.bsh
  4164c08c (LOCAL_ONLY) 20131109084743 plugins/Examples/Edit_LUT_As_Text.py
  398744e6 (LOCAL_ONLY) 20131109084728 plugins/Examples/Example6c.class
  780e948e (LOCAL_ONLY) 20131109084744 plugins/Examples/Extended_Profile_Plot.bsh
  b8881af2 (LOCAL_ONLY) 20131109084745 plugins/Examples/Fiji_Cube.ijm
  3687a018 (LOCAL_ONLY) 20131109084745 plugins/Examples/Fiji_Logo_3D.js
  998cb717 (LOCAL_ONLY) 20131109084747 plugins/Examples/Find_Dimension_of_Raw_Image.py
  66cf50fd (LOCAL_ONLY) 20131109084747 plugins/Examples/Image_To_Tool_Icon.bsh
  ccccc81e (LOCAL_ONLY) 20131109084748 plugins/Examples/Multithreaded_Image_Processing.clj
  720c237b (LOCAL_ONLY) 20131109084749 plugins/Examples/Multithreaded_Image_Processing_in_Javascript.js
  92ce736d (LOCAL_ONLY) 20131109084750 plugins/Examples/Plasma_Cloud.rb
  9efb2292 (LOCAL_ONLY) 20131109084750 plugins/Examples/Same_Slice_in_Multiple_Images.rb
  206a0bbd (LOCAL_ONLY) 20131109084751 plugins/Examples/The_Hue_Game.bsh
  1b6eee3a (LOCAL_ONLY) 20131109084736 plugins/Examples/TrakEM2_Example_Scripts/Homogenize_Ball_Radius.py
  940f6500 (LOCAL_ONLY) 20131109084737 plugins/Examples/TrakEM2_Example_Scripts/Measure_AreaLists.py
  3f4bba61 (LOCAL_ONLY) 20131109084737 plugins/Examples/TrakEM2_Example_Scripts/T2_Select_All.py
  72f00949 (LOCAL_ONLY) 20131109084738 plugins/Examples/TrakEM2_Example_Scripts/T2_set_all_transforms_to_identity.py
  89ef0307 (LOCAL_ONLY) 20131109084739 plugins/Examples/TrakEM2_Example_Scripts/extract_stack_under_arealist.py
  f8479f84 (LOCAL_ONLY) 20131109084753 plugins/Examples/blend_two_images.clj
  0989cf74 (LOCAL_ONLY) 20131109084754 plugins/Examples/celsius_to_fahrenheit.clj
  ff3b9902 (LOCAL_ONLY) 20131109084755 plugins/Examples/chess_.py
  69838e21 (LOCAL_ONLY) 20131109084756 plugins/Examples/compose_rgb-stacks.bsh
  4193ae7c (LOCAL_ONLY) 20131109084756 plugins/Examples/downsample_.js
  66a204d6 (LOCAL_ONLY) 20131109084757 plugins/Examples/list_all_threads.py
  ff4099b9 (LOCAL_ONLY) 20131109084758 plugins/Examples/random_noise_example.clj
  56600961 (LOCAL_ONLY) 20131109085005 plugins/Extended_Depth_Field-2.0.0-SNAPSHOT.jar
  ff0e4481 (LOCAL_ONLY) 20131109084943 plugins/FeatureJ_-1.6.1-SNAPSHOT.jar
  4ea625bc (LOCAL_ONLY) 20131109085027 plugins/Feature_Detection-2.0.0-SNAPSHOT.jar
  c02a1e2c (LOCAL_ONLY) 20140610185427 plugins/Fiji_Developer-2.0.0-SNAPSHOT.jar
  82601384 (LOCAL_ONLY) 20140610185427 plugins/Fiji_Package_Maker-2.0.0-SNAPSHOT.jar
  e19c9416 (LOCAL_ONLY) 20140610185427 plugins/Fiji_Plugins-2.0.0-SNAPSHOT.jar
  6189de52 (LOCAL_ONLY) 20140610185427 plugins/Fiji_Updater.jar
  ce69e79a (LOCAL_ONLY) 20131109085049 plugins/FlowJ_-1.29.1-SNAPSHOT.jar
  f942a886 (LOCAL_ONLY) 20131109085010 plugins/Graph_Cut-0.1.1-SNAPSHOT.jar
  bf032087 (LOCAL_ONLY) 20131109084952 plugins/Gray_Morphology-2.3.2-SNAPSHOT.jar
  f48de7ae (LOCAL_ONLY) 20131109084954 plugins/Helmholtz_Analysis-2.0.1-SNAPSHOT.jar
  dc5df090 (LOCAL_ONLY) 20131109084954 plugins/IJ_Robot-2.0.0-SNAPSHOT.jar
  eb581ab4 (LOCAL_ONLY) 20131109084911 plugins/IO_-2.0.0-SNAPSHOT.jar
  8b85c6b0 (LOCAL_ONLY) 20131109084849 plugins/Image_5D.jar
  dc5e4695 (LOCAL_ONLY) 20131109085001 plugins/Image_Expression_Parser-2.0.0-SNAPSHOT.jar
  65b42030 (LOCAL_ONLY) 20131109084941 plugins/Interactive_3D_Surface_Plot-2.31.1-SNAPSHOT.jar
  b483961e (LOCAL_ONLY) 20131109085023 plugins/IsoData_Classifier-2.0.0-SNAPSHOT.jar
  28582f55 (LOCAL_ONLY) 20131109084759 plugins/JRuby/imagej.rb
  9a5d6894 (LOCAL_ONLY) 20131109085021 plugins/JRuby_Interpreter-2.0.0-SNAPSHOT.jar
  7d22f08d (LOCAL_ONLY) 20131109084959 plugins/Javascript_-2.0.0-SNAPSHOT.jar
  a7edca68 (LOCAL_ONLY) 20131109084857 plugins/Jython_Interpreter-2.0.0-SNAPSHOT.jar
  542ef100 (LOCAL_ONLY) 20131109084849 plugins/LSM_Reader.jar
  6566ced8 (LOCAL_ONLY) 20131109084852 plugins/LSM_Toolbox.jar
  5830f8ee (LOCAL_ONLY) 20140610185427 plugins/Lasso_and_Blow_Tool-2.0.0-SNAPSHOT.jar
  c10ee505 (LOCAL_ONLY) 20131109084956 plugins/Linear_Kuwahara-2.0.0-SNAPSHOT.jar
  cf4ad6ab (LOCAL_ONLY) 20131109085033 plugins/LocalThickness_-3.1.1-SNAPSHOT.jar
  587c9f4b (LOCAL_ONLY) 20131109085012 plugins/MTrack2_-2.0.0-SNAPSHOT.jar
  f6a6a497 (LOCAL_ONLY) 20131109085006 plugins/MTrackJ_-1.5.1-SNAPSHOT.jar
  64ccfd05 (LOCAL_ONLY) 20131109085018 plugins/M_I_P-2.0.0-SNAPSHOT.jar
  65a2dd78 (LOCAL_ONLY) 20131109084802 plugins/Macros/About_Plugin_Macros.txt
  dff5642d (LOCAL_ONLY) 20131109084803 plugins/Macros/Bulls_Eye.txt
  e7ffe8ba (LOCAL_ONLY) 20131109084804 plugins/Macros/Polygon_.txt
  39f7ffcd (LOCAL_ONLY) 20131109084804 plugins/Macros/RGB_Histogram.txt
  3ee0edfa (LOCAL_ONLY) 20131109084805 plugins/Macros/batch_convert_any_to_tif.txt
  55f5b6a0 (LOCAL_ONLY) 20131109085007 plugins/Manual_Tracking-2.0.0-SNAPSHOT.jar
  9c541ad9 (LOCAL_ONLY) 20131109084957 plugins/MosaicJ_-2.0.0-SNAPSHOT.jar
  04a4a5c1 (LOCAL_ONLY) 20131109085004 plugins/PIV_analyser-1.1.1-SNAPSHOT.jar
  19181db3 (LOCAL_ONLY) 20131109085009 plugins/PointPicker_-2.0.0-SNAPSHOT.jar
  964d054a (LOCAL_ONLY) 20131109085016 plugins/QuickPALM_-1.1.1-SNAPSHOT.jar
  9fb03125 (LOCAL_ONLY) 20131109084946 plugins/RATS_-2.0.0-SNAPSHOT.jar
  5c7f3968 (LOCAL_ONLY) 20131109084949 plugins/RandomJ_-1.5.1-SNAPSHOT.jar
  7d1ad162 (LOCAL_ONLY) 20131109084852 plugins/Reconstruct_Reader.jar
  8bc6c355 (LOCAL_ONLY) 20140610185427 plugins/Refresh_Javas-2.0.0-SNAPSHOT.jar
  4ddf620c (LOCAL_ONLY) 20131109084854 plugins/SPIM_Opener.jar
  5b5857d2 (LOCAL_ONLY) 20140203133609 plugins/SPIM_Registration-2.0.0-SNAPSHOT.jar
  b9076c0a (LOCAL_ONLY) 20131109084951 plugins/Samples_-2.0.0-SNAPSHOT.jar
  b307010c (LOCAL_ONLY) 20140610185427 plugins/Scripts/File/Make_Screencast.bsh
  c70b2e6f (LOCAL_ONLY) 20131109084807 plugins/Scripts/File/Open_Samples/Adelsons_Squares.ijm
  60df5674 (LOCAL_ONLY) 20131109084808 plugins/Scripts/File/Open_Samples/Spirals_.ijm
  a3edd6db (LOCAL_ONLY) 20131109084810 plugins/Scripts/Image/Adjust/Scale_to_DPI.js
  209aed52 (LOCAL_ONLY) 20131109084811 plugins/Scripts/Image/Color/Set_Color_By_Wavelength.ijm
  1de6c712 (LOCAL_ONLY) 20131109084812 plugins/Scripts/Image/Hyperstacks/Temporal-Color_Code.ijm
  af064f17 (LOCAL_ONLY) 20131109084814 plugins/Scripts/Plugins/Registration/Correct_3D_drift.py
  a6e496fc (LOCAL_ONLY) 20131109084818 plugins/Scripts/Plugins/Utilities/Create_Desktop_Icon.bsh
  b5ee58a2 (LOCAL_ONLY) 20131109084817 plugins/Scripts/Plugins/Utilities/Find_Jar_For_Class.bsh
  fc46bd40 (LOCAL_ONLY) 20131109084815 plugins/Scripts/Plugins/Utilities/Record_Desktop.py
  9d4d012a (LOCAL_ONLY) 20131109084816 plugins/Scripts/Plugins/Utilities/Record_Window.py
  8cb22fe2 (LOCAL_ONLY) 20140610185427 plugins/Series_Labeler-2.0.0-SNAPSHOT.jar
  7c62b5c5 (LOCAL_ONLY) 20131109085052 plugins/SheppLogan_-2.0.0-SNAPSHOT.jar
  332f6608 (LOCAL_ONLY) 20140610185427 plugins/Sholl_Analysis-3.4.1.jar
  95dc5b19 (LOCAL_ONLY) 20140610185427 plugins/Simple_Neurite_Tracer-2.0.2-SNAPSHOT.jar
  0bd5f179 (LOCAL_ONLY) 20131109085022 plugins/Siox_Segmentation-1.0.1-SNAPSHOT.jar
  52fecf09 (LOCAL_ONLY) 20140610185427 plugins/Skeletonize3D_-1.0.1-SNAPSHOT.jar
  b0820703 (LOCAL_ONLY) 20131109085040 plugins/Snakuscule_-2.0.0-SNAPSHOT.jar
  33b6af85 (LOCAL_ONLY) 20140203133610 plugins/SplineDeformationGenerator_-2.0.0-SNAPSHOT.jar
  27de591e (LOCAL_ONLY) 20131109084953 plugins/StackReg_-2.0.0-SNAPSHOT.jar
  736bb192 (LOCAL_ONLY) 20131109085011 plugins/Stack_Manipulation-2.0.0-SNAPSHOT.jar
  59f36299 (LOCAL_ONLY) 20131109085032 plugins/Statistical_Region_Merging-2.0.0-SNAPSHOT.jar
  6880141e (LOCAL_ONLY) 20140610185427 plugins/Stitching_-2.0.0-SNAPSHOT.jar
  30100de7 (LOCAL_ONLY) 20131109084944 plugins/Sync_Win-1.7-fiji2-SNAPSHOT.jar
  685ca9dc (LOCAL_ONLY) 20131109085025 plugins/Thread_Killer-2.0.0-SNAPSHOT.jar
  2cee6c37 (LOCAL_ONLY) 20131109084944 plugins/Threshold_Colour-2.0.1-SNAPSHOT.jar
  d822b123 (LOCAL_ONLY) 20131109084908 plugins/Time_Stamper-2.0.0-SNAPSHOT.jar
  584cb5b9 (LOCAL_ONLY) 20131109085055 plugins/ToAST_-25.0.1-SNAPSHOT.jar
  4cf59217 (LOCAL_ONLY) 20131109085033 plugins/TopoJ_-2.0.0-SNAPSHOT.jar
  6008b366 (LOCAL_ONLY) 20140610185428 plugins/TrackMate_-2.3.0.jar
  e3cd0654 (LOCAL_ONLY) 20140610185428 plugins/Trainable_Segmentation-2.1.0-SNAPSHOT.jar
  fcd67c78 (LOCAL_ONLY) 20140606164517 plugins/TrakEM2_-1.0b-SNAPSHOT.jar
  8e7f3b79 (LOCAL_ONLY) 20131109084948 plugins/TransformJ_-2.8.1-SNAPSHOT.jar
  c4e87a76 (LOCAL_ONLY) 20131109085027 plugins/TurboReg_-2.0.0-SNAPSHOT.jar
  9558400d (LOCAL_ONLY) 20131109084902 plugins/UnwarpJ_.jar
  a32dfe46 (LOCAL_ONLY) 20131109084820 plugins/Utilities/Close_All_Without_Saving.txt
  253c6df4 (LOCAL_ONLY) 20140610185428 plugins/VIB_-2.0.0-SNAPSHOT.jar
  baa78901 (LOCAL_ONLY) 20131109084853 plugins/Vaa3d_Reader-2.0.0-SNAPSHOT.jar
  81279d21 (LOCAL_ONLY) 20131109084955 plugins/Video_Editing-2.0.0-SNAPSHOT.jar
  73396eef (LOCAL_ONLY) 20131109085020 plugins/View5D_-1.3.1-SNAPSHOT.jar
  980c0ed9 (LOCAL_ONLY) 20131109085056 plugins/Volume_Calculator-1.0.1-SNAPSHOT.jar
  2ef6f1eb (LOCAL_ONLY) 20140610185428 plugins/Volume_Viewer-2.01.1-SNAPSHOT.jar
  2079ca32 (LOCAL_ONLY) 20131109085030 plugins/bUnwarpJ_-2.6.1-SNAPSHOT.jar
  1d01fcfb (LOCAL_ONLY) 20140610185427 plugins/bio-formats_plugins-5.0.2.jar
  0307564a (LOCAL_ONLY) 20131109084900 plugins/blockmatching_-2.0.0-SNAPSHOT.jar
  95ff2656 (LOCAL_ONLY) 20131109084835 plugins/contrast_adjustment.jar
  659ad6a3 (LOCAL_ONLY) 20131109084903 plugins/ij-ImageIO_.jar
  fc868626 (LOCAL_ONLY) 20140610185118 plugins/jars/Jython.jar
  82f900ac (LOCAL_ONLY) 20131109085038 plugins/level_sets-1.0.1-SNAPSHOT.jar
  df2af815 (LOCAL_ONLY) 20140610185427 plugins/mpicbg_-0.6.1-SNAPSHOT.jar
  a9db180f (LOCAL_ONLY) 20140605115613 plugins/mpicbg_-0.6.2-SNAPSHOT.jar
  5e32d936 (LOCAL_ONLY) 20131109084905 plugins/panorama_.jar
  4bd07822 (LOCAL_ONLY) 20140610185427 plugins/register_virtual_stack_slices-2.0.0-SNAPSHOT.jar
  16012d5a (LOCAL_ONLY) 20131109085053 plugins/registration_3d-2.0.0-SNAPSHOT.jar
  4889514d (LOCAL_ONLY) 20131109084906 plugins/saalfeld_experiments-2.0.0-SNAPSHOT.jar
  34b7341d (LOCAL_ONLY) 20131109085144 retro/backport-util-concurrent-3.1.jar
  8759ba20 (LOCAL_ONLY) 20131109085148 retro/retrotranslator-runtime-1.2.9.jar
  a6d5a3b2 (LOCAL_ONLY) 20131109085149 retro/retrotranslator-transformer-1.2.9.jar
  d7160d38 (LOCAL_ONLY) 20131109085151 scripts/InstallJava3D.m
  05a92a3c (LOCAL_ONLY) 20131109085152 scripts/IsJava3DInstalled.m
  ff34d026 (LOCAL_ONLY) 20131109085152 scripts/Matlab3DViewerDemo_1.m
  25be149f (LOCAL_ONLY) 20131109085153 scripts/Matlab3DViewerDemo_2.m
  cb529b6c (LOCAL_ONLY) 20131109085154 scripts/Matlab3DViewerDemo_3.m
  53d2da73 (LOCAL_ONLY) 20131109085155 scripts/Matlab3DViewerIntroduction.m
  4bb342fa (LOCAL_ONLY) 20131109085156 scripts/Miji.m
  868cd434 (LOCAL_ONLY) 20131109085157 scripts/Miji_Test.m
  d3260180 (LOCAL_ONLY) 20131109085158 scripts/Record_Desktop.py
  0ea7f8fc (LOCAL_ONLY) 20131109085158 scripts/Record_Window.py
  dc94c3a3 (LOCAL_ONLY) 20131109085159 scripts/bfopen.m
  a77cab39 (LOCAL_ONLY) 20131109085200 scripts/importTrackMateTracks.m
Comment 1 Curtis Rueden 2014-06-12 16:31:12 CDT
Hmm, at this point I think we're fighting a losing battle by trying to avoid calling System.exit(0); from the legacy ImageJ UI. We should just bite the bullet and make that call, since so many plugins, including flagship core Fiji plugins like TrakEM2, do not bother to clean up after themselves as would be needed to avoid an explicit shutdown.
Comment 2 Johannes Schindelin 2014-06-13 10:19:17 CDT
> 0543a785 (LOCAL_ONLY) 20131109081825 jars/Fiji.jar

Wow, blast from the past.

It also means that your Fiji update site is not checked.

> Hmm, at this point I think we're fighting a losing battle by trying to avoid calling System.exit(0); from the legacy ImageJ UI.

What with TrakEM2 being an official part of Fiji, I think we can expect it to do better. I would agree for other plugins, but not for TrakEM2.

> We should just bite the bullet and make that call, since so many plugins, including flagship core Fiji plugins like TrakEM2, do not bother to clean up after themselves as would be needed to avoid an explicit shutdown.

Well, if flagship core Fiji plugins do not bother to register themselves properly, how can we *hope* to ask others to register properly?

I guess you're right... :-(
Comment 3 Stephan Saalfeld 2014-06-13 15:48:48 CDT
I just noticed that a running Beanshell script (in the Beanshell Interpreter) does not quit either.  The Beanshell Interpreter window remains open while the rest of ImageJ is gone.  After the script finished, I could close the Beanshell window but the JVM kept running.  While the movement is new to me (has it been communicated to anybody before?), I understand the motivation to not kill the JVM on exit but nicely depend on everybody shutting down properly.  However, this takes away the opportunity to kill things in the middle that got trapped.  ImageJ is, beyond being a fantastic drawing tool ;), a platform for developing macros, scripts and pipelines.  Doing so will lead to the oocasional deadlock or infinite loop that one wishes to escape by killing the platform.  Earlier, I could always do so by shutting donw ImageJ.  Now, I have to be more experienced and know about processes or shut down the operating system.  That's bad in my opinion.  Ideas?
Comment 4 Stephan Saalfeld 2014-06-16 09:58:59 CDT
Adding more observations: I just ran the updater, it updated and asked me to close and restart ImageJ.  I closed it and guess what: Fiji keeps running.  Seems like some core in-house components are affected too ;).
Comment 5 Curtis Rueden 2014-06-16 10:11:51 CDT
Stephan, it would be very helpful if you could generate a thread dump whenever that happens. Otherwise, as you know, it is very difficult to diagnose what caused the issue after the fact.
Comment 6 Curtis Rueden 2014-06-16 12:08:09 CDT
Stephan Saalfeld wrote:
> Curtis, help me out how.  JVisualVM?  Will try next time.  I thought you
> already had an idea.

See this page:
http://fiji.sc/Debugging#Debugging_JVM_hangs

Fiji also now ships with a "Dump Stack" plugin that can be run via Ctrl+\ to dump the stack to a new UI window -- but this may or may not work after ImageJ gets stuck trying to shut down. So doing it from the console (also Ctrl+\) is still your best bet.

> Sorry that I cannot quickly reproduce the updater
> issue as Fiji is updated now.  Next time.

If you think it is a problem with the Updater UI having run at all, you can just delete a small non-critical JAR file and run the Updater to redownload it.
Comment 7 Stephan Saalfeld 2014-06-17 10:40:37 CDT
Here is an incomplete Thread dump (exceeds the size of my terminal) with Ctrl+\ from the terminal in which I had Fiji started.  The remaining open window that does not close with Fiji this time is the 3DViewer:

[...]

"repainter-21" daemon prio=10 tid=0x00007f585c11f800 nid=0x1da5 waiting on condition [0x00007f57997d6000]
   java.lang.Thread.State: WAITING (parking)
	at sun.misc.Unsafe.park(Native Method)
	- parking to wait for  <0x00007f5969eb8e88> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1987)
	at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:399)
	at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:947)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
	at java.lang.Thread.run(Thread.java:662)

"regenerator-4" daemon prio=10 tid=0x00007f5834008800 nid=0x1da4 waiting on condition [0x00007f5877049000]
   java.lang.Thread.State: WAITING (parking)
	at sun.misc.Unsafe.park(Native Method)
	- parking to wait for  <0x00007f596aa8fe80> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1987)
	at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:399)
	at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:947)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
	at java.lang.Thread.run(Thread.java:662)

"mipmap remover-4" daemon prio=10 tid=0x00007f5834007800 nid=0x1da3 waiting on condition [0x00007f579bffe000]
   java.lang.Thread.State: WAITING (parking)
	at sun.misc.Unsafe.park(Native Method)
	- parking to wait for  <0x00007f596a819d08> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1987)
	at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:399)
	at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:947)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
	at java.lang.Thread.run(Thread.java:662)

"repainter-20" daemon prio=10 tid=0x00007f585c11e800 nid=0x1da2 waiting on condition [0x00007f5874e87000]
   java.lang.Thread.State: WAITING (parking)
	at sun.misc.Unsafe.park(Native Method)
	- parking to wait for  <0x00007f5969eb8e88> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1987)
	at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:399)
	at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:947)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
	at java.lang.Thread.run(Thread.java:662)

"regenerator-3" daemon prio=10 tid=0x00007f5834006800 nid=0x1da1 waiting on condition [0x00007f5799bda000]
   java.lang.Thread.State: WAITING (parking)
	at sun.misc.Unsafe.park(Native Method)
	- parking to wait for  <0x00007f596aa8fe80> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1987)
	at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:399)
	at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:947)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
	at java.lang.Thread.run(Thread.java:662)

"mipmap remover-3" daemon prio=10 tid=0x00007f5834005800 nid=0x1da0 waiting on condition [0x00007f5875891000]
   java.lang.Thread.State: WAITING (parking)
	at sun.misc.Unsafe.park(Native Method)
	- parking to wait for  <0x00007f596a819d08> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1987)
	at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:399)
	at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:947)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
	at java.lang.Thread.run(Thread.java:662)

"repainter-19" daemon prio=10 tid=0x00007f585c11e000 nid=0x1d9f waiting on condition [0x00007f5875a93000]
   java.lang.Thread.State: WAITING (parking)
	at sun.misc.Unsafe.park(Native Method)
	- parking to wait for  <0x00007f5969eb8e88> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1987)
	at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:399)
	at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:947)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
	at java.lang.Thread.run(Thread.java:662)

"regenerator-2" daemon prio=10 tid=0x00007f5834004800 nid=0x1d9e waiting on condition [0x00007f579a5e4000]
   java.lang.Thread.State: WAITING (parking)
	at sun.misc.Unsafe.park(Native Method)
	- parking to wait for  <0x00007f596aa8fe80> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1987)
	at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:399)
	at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:947)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
	at java.lang.Thread.run(Thread.java:662)

"repainter-18" daemon prio=10 tid=0x00007f585c11d000 nid=0x1d9d waiting on condition [0x00007f57993d2000]
   java.lang.Thread.State: WAITING (parking)
	at sun.misc.Unsafe.park(Native Method)
	- parking to wait for  <0x00007f5969eb8e88> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1987)
	at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:399)
	at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:947)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
	at java.lang.Thread.run(Thread.java:662)

"mipmap remover-2" daemon prio=10 tid=0x00007f5834003800 nid=0x1d9c waiting on condition [0x00007f5798dcc000]
   java.lang.Thread.State: WAITING (parking)
	at sun.misc.Unsafe.park(Native Method)
	- parking to wait for  <0x00007f596a819d08> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1987)
	at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:399)
	at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:947)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
	at java.lang.Thread.run(Thread.java:662)

"regenerator-1" daemon prio=10 tid=0x00007f5834002800 nid=0x1d9b waiting on condition [0x00007f587619a000]
   java.lang.Thread.State: WAITING (parking)
	at sun.misc.Unsafe.park(Native Method)
	- parking to wait for  <0x00007f596aa8fe80> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1987)
	at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:399)
	at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:947)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
	at java.lang.Thread.run(Thread.java:662)

"repainter-17" daemon prio=10 tid=0x00007f585c11c000 nid=0x1d9a waiting on condition [0x00007f579a7e6000]
   java.lang.Thread.State: WAITING (parking)
	at sun.misc.Unsafe.park(Native Method)
	- parking to wait for  <0x00007f5969eb8e88> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1987)
	at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:399)
	at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:947)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
	at java.lang.Thread.run(Thread.java:662)

"repainter-16" daemon prio=10 tid=0x00007f585c11b000 nid=0x1d99 waiting on condition [0x00007f5874f88000]
   java.lang.Thread.State: WAITING (parking)
	at sun.misc.Unsafe.park(Native Method)
	- parking to wait for  <0x00007f5969eb8e88> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1987)
	at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:399)
	at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:947)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
	at java.lang.Thread.run(Thread.java:662)

"mipmap remover-1" daemon prio=10 tid=0x00007f5834001800 nid=0x1d98 waiting on condition [0x00007f579a3e2000]
   java.lang.Thread.State: WAITING (parking)
	at sun.misc.Unsafe.park(Native Method)
	- parking to wait for  <0x00007f596a819d08> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1987)
	at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:399)
	at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:947)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
	at java.lang.Thread.run(Thread.java:662)

"repainter-15" daemon prio=10 tid=0x00007f585c11a800 nid=0x1d97 waiting on condition [0x00007f5798ccb000]
   java.lang.Thread.State: WAITING (parking)
	at sun.misc.Unsafe.park(Native Method)
	- parking to wait for  <0x00007f5969eb8e88> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1987)
	at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:399)
	at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:947)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
	at java.lang.Thread.run(Thread.java:662)

"repainter-14" daemon prio=10 tid=0x00007f585c114000 nid=0x1d94 waiting on condition [0x00007f579b8f7000]
   java.lang.Thread.State: WAITING (parking)
	at sun.misc.Unsafe.park(Native Method)
	- parking to wait for  <0x00007f5969eb8e88> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1987)
	at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:399)
	at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:947)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
	at java.lang.Thread.run(Thread.java:662)

"repainter-13" daemon prio=10 tid=0x00007f585c113000 nid=0x1d93 waiting on condition [0x00007f587568f000]
   java.lang.Thread.State: WAITING (parking)
	at sun.misc.Unsafe.park(Native Method)
	- parking to wait for  <0x00007f5969eb8e88> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1987)
	at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:399)
	at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:947)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
	at java.lang.Thread.run(Thread.java:662)

"repainter-12" daemon prio=10 tid=0x00007f585c112000 nid=0x1d92 waiting on condition [0x00007f587518a000]
   java.lang.Thread.State: WAITING (parking)
	at sun.misc.Unsafe.park(Native Method)
	- parking to wait for  <0x00007f5969eb8e88> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1987)
	at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:399)
	at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:947)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
	at java.lang.Thread.run(Thread.java:662)

"repainter-11" daemon prio=10 tid=0x00007f585c111000 nid=0x1d91 waiting on condition [0x00007f579a9e8000]
   java.lang.Thread.State: WAITING (parking)
	at sun.misc.Unsafe.park(Native Method)
	- parking to wait for  <0x00007f5969eb8e88> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1987)
	at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:399)
	at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:947)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
	at java.lang.Thread.run(Thread.java:662)

"repainter-10" daemon prio=10 tid=0x00007f585c110000 nid=0x1d90 waiting on condition [0x00007f5793ffe000]
   java.lang.Thread.State: WAITING (parking)
	at sun.misc.Unsafe.park(Native Method)
	- parking to wait for  <0x00007f5969eb8e88> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1987)
	at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:399)
	at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:947)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
	at java.lang.Thread.run(Thread.java:662)

"repainter-9" daemon prio=10 tid=0x00007f585c10f000 nid=0x1d8f waiting on condition [0x00007f579abea000]
   java.lang.Thread.State: WAITING (parking)
	at sun.misc.Unsafe.park(Native Method)
	- parking to wait for  <0x00007f5969eb8e88> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1987)
	at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:399)
	at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:947)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
	at java.lang.Thread.run(Thread.java:662)

"repainter-8" daemon prio=10 tid=0x00007f585c10e800 nid=0x1d8e waiting on condition [0x00007f57995d4000]
   java.lang.Thread.State: WAITING (parking)
	at sun.misc.Unsafe.park(Native Method)
	- parking to wait for  <0x00007f5969eb8e88> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1987)
	at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:399)
	at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:947)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
	at java.lang.Thread.run(Thread.java:662)

"repainter-7" daemon prio=10 tid=0x00007f585c10c800 nid=0x1d8d waiting on condition [0x00007f5798bca000]
   java.lang.Thread.State: WAITING (parking)
	at sun.misc.Unsafe.park(Native Method)
	- parking to wait for  <0x00007f5969eb8e88> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1987)
	at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:399)
	at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:947)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
	at java.lang.Thread.run(Thread.java:662)

"repainter-6" daemon prio=10 tid=0x00007f585c10b800 nid=0x1d8c waiting on condition [0x00007f5799ddc000]
   java.lang.Thread.State: WAITING (parking)
	at sun.misc.Unsafe.park(Native Method)
	- parking to wait for  <0x00007f5969eb8e88> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1987)
	at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:399)
	at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:947)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
	at java.lang.Thread.run(Thread.java:662)

"repainter-5" daemon prio=10 tid=0x00007f585c10a800 nid=0x1d8b waiting on condition [0x00007f587548d000]
   java.lang.Thread.State: WAITING (parking)
	at sun.misc.Unsafe.park(Native Method)
	- parking to wait for  <0x00007f5969eb8e88> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1987)
	at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:399)
	at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:947)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
	at java.lang.Thread.run(Thread.java:662)

"repainter-4" daemon prio=10 tid=0x00007f585c10a000 nid=0x1d8a waiting on condition [0x00007f5798fce000]
   java.lang.Thread.State: WAITING (parking)
	at sun.misc.Unsafe.park(Native Method)
	- parking to wait for  <0x00007f5969eb8e88> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1987)
	at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:399)
	at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:947)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
	at java.lang.Thread.run(Thread.java:662)

"repainter-3" daemon prio=10 tid=0x00007f585c109000 nid=0x1d89 waiting on condition [0x00007f587427b000]
   java.lang.Thread.State: WAITING (parking)
	at sun.misc.Unsafe.park(Native Method)
	- parking to wait for  <0x00007f5969eb8e88> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1987)
	at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:399)
	at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:947)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
	at java.lang.Thread.run(Thread.java:662)

"repainter-2" daemon prio=10 tid=0x00007f585c108800 nid=0x1d88 waiting on condition [0x00007f579a1e0000]
   java.lang.Thread.State: WAITING (parking)
	at sun.misc.Unsafe.park(Native Method)
	- parking to wait for  <0x00007f5969eb8e88> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1987)
	at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:399)
	at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:947)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
	at java.lang.Thread.run(Thread.java:662)

"repainter-1" daemon prio=10 tid=0x00007f585c106000 nid=0x1d87 waiting on condition [0x00007f5799fde000]
   java.lang.Thread.State: WAITING (parking)
	at sun.misc.Unsafe.park(Native Method)
	- parking to wait for  <0x00007f5969eb8e88> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1987)
	at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:399)
	at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:947)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
	at java.lang.Thread.run(Thread.java:662)

"TimerQueue" daemon prio=10 tid=0x00007f585c01f000 nid=0x1d05 in Object.wait() [0x00007f587714a000]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
	at java.lang.Object.wait(Native Method)
	at javax.swing.TimerQueue.run(TimerQueue.java:232)
	- locked <0x00007f596aa7c690> (a javax.swing.TimerQueue)
	at java.lang.Thread.run(Thread.java:662)

"DestroyJavaVM" prio=10 tid=0x0000000001a8e800 nid=0x1cbd waiting on condition [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"Timer-0" daemon prio=10 tid=0x0000000002df8000 nid=0x1cfc in Object.wait() [0x00007f58779ea000]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
	at java.lang.Object.wait(Native Method)
	at java.util.TimerThread.mainLoop(Timer.java:509)
	- locked <0x00007f5969f15540> (a java.util.TaskQueue)
	at java.util.TimerThread.run(Timer.java:462)

"AWT-EventQueue-0" prio=10 tid=0x0000000002ded800 nid=0x1cfb in Object.wait() [0x00007f5877aeb000]
   java.lang.Thread.State: WAITING (on object monitor)
	at java.lang.Object.wait(Native Method)
	at java.lang.Object.wait(Object.java:485)
	at java.awt.EventQueue.getNextEvent(EventQueue.java:485)
	- locked <0x00007f596a28e428> (a java.awt.EventQueue)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:236)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)
	at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)

"AWT-Shutdown" prio=10 tid=0x0000000002dd2000 nid=0x1cfa in Object.wait() [0x00007f5877bec000]
   java.lang.Thread.State: WAITING (on object monitor)
	at java.lang.Object.wait(Native Method)
	at java.lang.Object.wait(Object.java:485)
	at sun.awt.AWTAutoShutdown.run(AWTAutoShutdown.java:265)
	- locked <0x00007f5969e09778> (a java.lang.Object)
	at java.lang.Thread.run(Thread.java:662)

"AWT-XAWT" daemon prio=10 tid=0x0000000002da2800 nid=0x1cf8 runnable [0x00007f5877ced000]
   java.lang.Thread.State: RUNNABLE
	at sun.awt.X11.XToolkit.waitForEvents(Native Method)
	at sun.awt.X11.XToolkit.run(XToolkit.java:579)
	at sun.awt.X11.XToolkit.run(XToolkit.java:543)
	at java.lang.Thread.run(Thread.java:662)

"Java2D Disposer" daemon prio=10 tid=0x0000000002d41800 nid=0x1cf7 in Object.wait() [0x00007f5877dee000]
   java.lang.Thread.State: WAITING (on object monitor)
	at java.lang.Object.wait(Native Method)
	at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:118)
	- locked <0x00007f596a143cc0> (a java.lang.ref.ReferenceQueue$Lock)
	at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:134)
	at sun.java2d.Disposer.run(Disposer.java:127)
	at java.lang.Thread.run(Thread.java:662)

"Low Memory Detector" daemon prio=10 tid=0x0000000001f09800 nid=0x1cf1 runnable [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"CompilerThread1" daemon prio=10 tid=0x0000000001f07000 nid=0x1cf0 waiting on condition [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"CompilerThread0" daemon prio=10 tid=0x0000000001f04800 nid=0x1cef waiting on condition [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"Signal Dispatcher" daemon prio=10 tid=0x0000000001f02800 nid=0x1cee waiting on condition [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"Surrogate Locker Thread (CMS)" daemon prio=10 tid=0x0000000001f00800 nid=0x1ced waiting on condition [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"Finalizer" daemon prio=10 tid=0x0000000001ee5000 nid=0x1cec in Object.wait() [0x00007f589d4b8000]
   java.lang.Thread.State: WAITING (on object monitor)
	at java.lang.Object.wait(Native Method)
	at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:118)
	- locked <0x00007f5968ea52b0> (a java.lang.ref.ReferenceQueue$Lock)
	at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:134)
	at java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:159)

"Reference Handler" daemon prio=10 tid=0x0000000001ee3000 nid=0x1ceb in Object.wait() [0x00007f589d5b9000]
   java.lang.Thread.State: WAITING (on object monitor)
	at java.lang.Object.wait(Native Method)
	at java.lang.Object.wait(Object.java:485)
	at java.lang.ref.Reference$ReferenceHandler.run(Reference.java:116)
	- locked <0x00007f5968ebde20> (a java.lang.ref.Reference$Lock)

"VM Thread" prio=10 tid=0x0000000001edc000 nid=0x1cea runnable 

"Gang worker#0 (Parallel GC Threads)" prio=10 tid=0x0000000001aa3000 nid=0x1cbf runnable 

"Gang worker#1 (Parallel GC Threads)" prio=10 tid=0x0000000001aa4800 nid=0x1cc0 runnable 

"Gang worker#2 (Parallel GC Threads)" prio=10 tid=0x0000000001aa6800 nid=0x1cc1 runnable 

"Gang worker#3 (Parallel GC Threads)" prio=10 tid=0x0000000001aa8800 nid=0x1cc2 runnable 

"Gang worker#4 (Parallel GC Threads)" prio=10 tid=0x0000000001aaa000 nid=0x1cc3 runnable 

"Gang worker#5 (Parallel GC Threads)" prio=10 tid=0x0000000001aac000 nid=0x1cc4 runnable 

"Gang worker#6 (Parallel GC Threads)" prio=10 tid=0x0000000001aad800 nid=0x1cc5 runnable 

"Gang worker#7 (Parallel GC Threads)" prio=10 tid=0x0000000001aaf800 nid=0x1cc6 runnable 

"Gang worker#8 (Parallel GC Threads)" prio=10 tid=0x0000000001ab1800 nid=0x1cc7 runnable 

"Gang worker#9 (Parallel GC Threads)" prio=10 tid=0x0000000001ab3000 nid=0x1cc8 runnable 

"Gang worker#10 (Parallel GC Threads)" prio=10 tid=0x0000000001ab5000 nid=0x1cc9 runnable 

"Gang worker#11 (Parallel GC Threads)" prio=10 tid=0x0000000001ab7000 nid=0x1cca runnable 

"Gang worker#12 (Parallel GC Threads)" prio=10 tid=0x0000000001ab8800 nid=0x1ccb runnable 

"Gang worker#13 (Parallel GC Threads)" prio=10 tid=0x0000000001aba800 nid=0x1ccc runnable 

"Gang worker#14 (Parallel GC Threads)" prio=10 tid=0x0000000001abc800 nid=0x1ccd runnable 

"Gang worker#15 (Parallel GC Threads)" prio=10 tid=0x0000000001abe000 nid=0x1cce runnable 

"Gang worker#16 (Parallel GC Threads)" prio=10 tid=0x0000000001ac0000 nid=0x1ccf runnable 

"Gang worker#17 (Parallel GC Threads)" prio=10 tid=0x0000000001ac1800 nid=0x1cd0 runnable 

"Gang worker#18 (Parallel GC Threads)" prio=10 tid=0x0000000001ac3800 nid=0x1cd1 runnable 

"Gang worker#19 (Parallel GC Threads)" prio=10 tid=0x0000000001ac5800 nid=0x1cd2 runnable 

"Gang worker#20 (Parallel GC Threads)" prio=10 tid=0x0000000001ac7000 nid=0x1cd3 runnable 

"Gang worker#21 (Parallel GC Threads)" prio=10 tid=0x0000000001ac9000 nid=0x1cd4 runnable 

"Gang worker#22 (Parallel GC Threads)" prio=10 tid=0x0000000001acb000 nid=0x1cd5 runnable 

"Gang worker#23 (Parallel GC Threads)" prio=10 tid=0x0000000001acc800 nid=0x1cd6 runnable 

"Gang worker#24 (Parallel GC Threads)" prio=10 tid=0x0000000001ace800 nid=0x1cd7 runnable 

"Gang worker#25 (Parallel GC Threads)" prio=10 tid=0x0000000001ad0000 nid=0x1cd8 runnable 

"Gang worker#26 (Parallel GC Threads)" prio=10 tid=0x0000000001ad2000 nid=0x1cd9 runnable 

"Gang worker#27 (Parallel GC Threads)" prio=10 tid=0x0000000001ad4000 nid=0x1cda runnable 

"Gang worker#28 (Parallel GC Threads)" prio=10 tid=0x0000000001ad5800 nid=0x1cdb runnable 

"Gang worker#29 (Parallel GC Threads)" prio=10 tid=0x0000000001ad7800 nid=0x1cdc runnable 

"Gang worker#30 (Parallel GC Threads)" prio=10 tid=0x0000000001ad9800 nid=0x1cdd runnable 

"Gang worker#31 (Parallel GC Threads)" prio=10 tid=0x0000000001adb000 nid=0x1cde runnable 

"Gang worker#32 (Parallel GC Threads)" prio=10 tid=0x0000000001add000 nid=0x1cdf runnable 

"Concurrent Mark-Sweep GC Thread" prio=10 tid=0x0000000001e3b000 nid=0x1ce9 runnable 
"Gang worker#0 (Parallel CMS Threads)" prio=10 tid=0x0000000001e29800 nid=0x1ce0 runnable 

"Gang worker#1 (Parallel CMS Threads)" prio=10 tid=0x0000000001e2b800 nid=0x1ce1 runnable 

"Gang worker#2 (Parallel CMS Threads)" prio=10 tid=0x0000000001e2d000 nid=0x1ce2 runnable 

"Gang worker#3 (Parallel CMS Threads)" prio=10 tid=0x0000000001e2f000 nid=0x1ce3 runnable 

"Gang worker#4 (Parallel CMS Threads)" prio=10 tid=0x0000000001e30800 nid=0x1ce4 runnable 

"Gang worker#5 (Parallel CMS Threads)" prio=10 tid=0x0000000001e32800 nid=0x1ce5 runnable 

"Gang worker#6 (Parallel CMS Threads)" prio=10 tid=0x0000000001e34800 nid=0x1ce6 runnable 

"Gang worker#7 (Parallel CMS Threads)" prio=10 tid=0x0000000001e36000 nid=0x1ce7 runnable 

"Gang worker#8 (Parallel CMS Threads)" prio=10 tid=0x0000000001e38000 nid=0x1ce8 runnable 

"VM Periodic Task Thread" prio=10 tid=0x0000000001f14800 nid=0x1cf2 waiting on condition 

JNI global references: 3590

Heap
 par new generation   total 383488K, used 337431K [0x00007f593e000000, 0x00007f5958010000, 0x00007f5968e60000)
  eden space 340928K,  93% used [0x00007f593e000000, 0x00007f59518c7ad8, 0x00007f5952cf0000)
  from space 42560K,  40% used [0x00007f5955680000, 0x00007f595673e460, 0x00007f5958010000)
  to   space 42560K,   0% used [0x00007f5952cf0000, 0x00007f5952cf0000, 0x00007f5955680000)
 concurrent mark-sweep generation total 9490680K, used 5931204K [0x00007f5968e60000, 0x00007f5bac29e000, 0x00007f71a8000000)
 concurrent-mark-sweep perm gen total 131072K, used 55204K [0x00007f71a8000000, 0x00007f71b0000000, 0x00007f71b0000000)
Comment 8 Stephan Saalfeld 2014-06-17 10:43:32 CDT
And here another incomplete dump after I have closed the 3DViewer window and Fiji kept running in the terminal:

[...]

"repainter-21" daemon prio=10 tid=0x00007f585c11f800 nid=0x1da5 waiting on condition [0x00007f57997d6000]
   java.lang.Thread.State: WAITING (parking)
	at sun.misc.Unsafe.park(Native Method)
	- parking to wait for  <0x00007f5969eb8e88> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1987)
	at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:399)
	at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:947)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
	at java.lang.Thread.run(Thread.java:662)

"regenerator-4" daemon prio=10 tid=0x00007f5834008800 nid=0x1da4 waiting on condition [0x00007f5877049000]
   java.lang.Thread.State: WAITING (parking)
	at sun.misc.Unsafe.park(Native Method)
	- parking to wait for  <0x00007f596aa8fe80> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1987)
	at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:399)
	at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:947)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
	at java.lang.Thread.run(Thread.java:662)

"mipmap remover-4" daemon prio=10 tid=0x00007f5834007800 nid=0x1da3 waiting on condition [0x00007f579bffe000]
   java.lang.Thread.State: WAITING (parking)
	at sun.misc.Unsafe.park(Native Method)
	- parking to wait for  <0x00007f596a819d08> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1987)
	at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:399)
	at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:947)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
	at java.lang.Thread.run(Thread.java:662)

"repainter-20" daemon prio=10 tid=0x00007f585c11e800 nid=0x1da2 waiting on condition [0x00007f5874e87000]
   java.lang.Thread.State: WAITING (parking)
	at sun.misc.Unsafe.park(Native Method)
	- parking to wait for  <0x00007f5969eb8e88> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1987)
	at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:399)
	at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:947)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
	at java.lang.Thread.run(Thread.java:662)

"regenerator-3" daemon prio=10 tid=0x00007f5834006800 nid=0x1da1 waiting on condition [0x00007f5799bda000]
   java.lang.Thread.State: WAITING (parking)
	at sun.misc.Unsafe.park(Native Method)
	- parking to wait for  <0x00007f596aa8fe80> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1987)
	at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:399)
	at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:947)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
	at java.lang.Thread.run(Thread.java:662)

"mipmap remover-3" daemon prio=10 tid=0x00007f5834005800 nid=0x1da0 waiting on condition [0x00007f5875891000]
   java.lang.Thread.State: WAITING (parking)
	at sun.misc.Unsafe.park(Native Method)
	- parking to wait for  <0x00007f596a819d08> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1987)
	at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:399)
	at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:947)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
	at java.lang.Thread.run(Thread.java:662)

"repainter-19" daemon prio=10 tid=0x00007f585c11e000 nid=0x1d9f waiting on condition [0x00007f5875a93000]
   java.lang.Thread.State: WAITING (parking)
	at sun.misc.Unsafe.park(Native Method)
	- parking to wait for  <0x00007f5969eb8e88> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1987)
	at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:399)
	at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:947)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
	at java.lang.Thread.run(Thread.java:662)

"regenerator-2" daemon prio=10 tid=0x00007f5834004800 nid=0x1d9e waiting on condition [0x00007f579a5e4000]
   java.lang.Thread.State: WAITING (parking)
	at sun.misc.Unsafe.park(Native Method)
	- parking to wait for  <0x00007f596aa8fe80> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1987)
	at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:399)
	at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:947)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
	at java.lang.Thread.run(Thread.java:662)

"repainter-18" daemon prio=10 tid=0x00007f585c11d000 nid=0x1d9d waiting on condition [0x00007f57993d2000]
   java.lang.Thread.State: WAITING (parking)
	at sun.misc.Unsafe.park(Native Method)
	- parking to wait for  <0x00007f5969eb8e88> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1987)
	at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:399)
	at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:947)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
	at java.lang.Thread.run(Thread.java:662)

"mipmap remover-2" daemon prio=10 tid=0x00007f5834003800 nid=0x1d9c waiting on condition [0x00007f5798dcc000]
   java.lang.Thread.State: WAITING (parking)
	at sun.misc.Unsafe.park(Native Method)
	- parking to wait for  <0x00007f596a819d08> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1987)
	at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:399)
	at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:947)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
	at java.lang.Thread.run(Thread.java:662)

"regenerator-1" daemon prio=10 tid=0x00007f5834002800 nid=0x1d9b waiting on condition [0x00007f587619a000]
   java.lang.Thread.State: WAITING (parking)
	at sun.misc.Unsafe.park(Native Method)
	- parking to wait for  <0x00007f596aa8fe80> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1987)
	at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:399)
	at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:947)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
	at java.lang.Thread.run(Thread.java:662)

"repainter-17" daemon prio=10 tid=0x00007f585c11c000 nid=0x1d9a waiting on condition [0x00007f579a7e6000]
   java.lang.Thread.State: WAITING (parking)
	at sun.misc.Unsafe.park(Native Method)
	- parking to wait for  <0x00007f5969eb8e88> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1987)
	at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:399)
	at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:947)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
	at java.lang.Thread.run(Thread.java:662)

"repainter-16" daemon prio=10 tid=0x00007f585c11b000 nid=0x1d99 waiting on condition [0x00007f5874f88000]
   java.lang.Thread.State: WAITING (parking)
	at sun.misc.Unsafe.park(Native Method)
	- parking to wait for  <0x00007f5969eb8e88> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1987)
	at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:399)
	at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:947)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
	at java.lang.Thread.run(Thread.java:662)

"mipmap remover-1" daemon prio=10 tid=0x00007f5834001800 nid=0x1d98 waiting on condition [0x00007f579a3e2000]
   java.lang.Thread.State: WAITING (parking)
	at sun.misc.Unsafe.park(Native Method)
	- parking to wait for  <0x00007f596a819d08> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1987)
	at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:399)
	at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:947)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
	at java.lang.Thread.run(Thread.java:662)

"repainter-15" daemon prio=10 tid=0x00007f585c11a800 nid=0x1d97 waiting on condition [0x00007f5798ccb000]
   java.lang.Thread.State: WAITING (parking)
	at sun.misc.Unsafe.park(Native Method)
	- parking to wait for  <0x00007f5969eb8e88> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1987)
	at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:399)
	at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:947)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
	at java.lang.Thread.run(Thread.java:662)

"repainter-14" daemon prio=10 tid=0x00007f585c114000 nid=0x1d94 waiting on condition [0x00007f579b8f7000]
   java.lang.Thread.State: WAITING (parking)
	at sun.misc.Unsafe.park(Native Method)
	- parking to wait for  <0x00007f5969eb8e88> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1987)
	at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:399)
	at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:947)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
	at java.lang.Thread.run(Thread.java:662)

"repainter-13" daemon prio=10 tid=0x00007f585c113000 nid=0x1d93 waiting on condition [0x00007f587568f000]
   java.lang.Thread.State: WAITING (parking)
	at sun.misc.Unsafe.park(Native Method)
	- parking to wait for  <0x00007f5969eb8e88> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1987)
	at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:399)
	at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:947)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
	at java.lang.Thread.run(Thread.java:662)

"repainter-12" daemon prio=10 tid=0x00007f585c112000 nid=0x1d92 waiting on condition [0x00007f587518a000]
   java.lang.Thread.State: WAITING (parking)
	at sun.misc.Unsafe.park(Native Method)
	- parking to wait for  <0x00007f5969eb8e88> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1987)
	at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:399)
	at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:947)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
	at java.lang.Thread.run(Thread.java:662)

"repainter-11" daemon prio=10 tid=0x00007f585c111000 nid=0x1d91 waiting on condition [0x00007f579a9e8000]
   java.lang.Thread.State: WAITING (parking)
	at sun.misc.Unsafe.park(Native Method)
	- parking to wait for  <0x00007f5969eb8e88> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1987)
	at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:399)
	at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:947)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
	at java.lang.Thread.run(Thread.java:662)

"repainter-10" daemon prio=10 tid=0x00007f585c110000 nid=0x1d90 waiting on condition [0x00007f5793ffe000]
   java.lang.Thread.State: WAITING (parking)
	at sun.misc.Unsafe.park(Native Method)
	- parking to wait for  <0x00007f5969eb8e88> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1987)
	at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:399)
	at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:947)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
	at java.lang.Thread.run(Thread.java:662)

"repainter-9" daemon prio=10 tid=0x00007f585c10f000 nid=0x1d8f waiting on condition [0x00007f579abea000]
   java.lang.Thread.State: WAITING (parking)
	at sun.misc.Unsafe.park(Native Method)
	- parking to wait for  <0x00007f5969eb8e88> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1987)
	at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:399)
	at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:947)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
	at java.lang.Thread.run(Thread.java:662)

"repainter-8" daemon prio=10 tid=0x00007f585c10e800 nid=0x1d8e waiting on condition [0x00007f57995d4000]
   java.lang.Thread.State: WAITING (parking)
	at sun.misc.Unsafe.park(Native Method)
	- parking to wait for  <0x00007f5969eb8e88> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1987)
	at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:399)
	at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:947)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
	at java.lang.Thread.run(Thread.java:662)

"repainter-7" daemon prio=10 tid=0x00007f585c10c800 nid=0x1d8d waiting on condition [0x00007f5798bca000]
   java.lang.Thread.State: WAITING (parking)
	at sun.misc.Unsafe.park(Native Method)
	- parking to wait for  <0x00007f5969eb8e88> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1987)
	at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:399)
	at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:947)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
	at java.lang.Thread.run(Thread.java:662)

"repainter-6" daemon prio=10 tid=0x00007f585c10b800 nid=0x1d8c waiting on condition [0x00007f5799ddc000]
   java.lang.Thread.State: WAITING (parking)
	at sun.misc.Unsafe.park(Native Method)
	- parking to wait for  <0x00007f5969eb8e88> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1987)
	at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:399)
	at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:947)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
	at java.lang.Thread.run(Thread.java:662)

"repainter-5" daemon prio=10 tid=0x00007f585c10a800 nid=0x1d8b waiting on condition [0x00007f587548d000]
   java.lang.Thread.State: WAITING (parking)
	at sun.misc.Unsafe.park(Native Method)
	- parking to wait for  <0x00007f5969eb8e88> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1987)
	at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:399)
	at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:947)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
	at java.lang.Thread.run(Thread.java:662)

"repainter-4" daemon prio=10 tid=0x00007f585c10a000 nid=0x1d8a waiting on condition [0x00007f5798fce000]
   java.lang.Thread.State: WAITING (parking)
	at sun.misc.Unsafe.park(Native Method)
	- parking to wait for  <0x00007f5969eb8e88> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1987)
	at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:399)
	at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:947)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
	at java.lang.Thread.run(Thread.java:662)

"repainter-3" daemon prio=10 tid=0x00007f585c109000 nid=0x1d89 waiting on condition [0x00007f587427b000]
   java.lang.Thread.State: WAITING (parking)
	at sun.misc.Unsafe.park(Native Method)
	- parking to wait for  <0x00007f5969eb8e88> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1987)
	at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:399)
	at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:947)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
	at java.lang.Thread.run(Thread.java:662)

"repainter-2" daemon prio=10 tid=0x00007f585c108800 nid=0x1d88 waiting on condition [0x00007f579a1e0000]
   java.lang.Thread.State: WAITING (parking)
	at sun.misc.Unsafe.park(Native Method)
	- parking to wait for  <0x00007f5969eb8e88> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1987)
	at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:399)
	at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:947)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
	at java.lang.Thread.run(Thread.java:662)

"repainter-1" daemon prio=10 tid=0x00007f585c106000 nid=0x1d87 waiting on condition [0x00007f5799fde000]
   java.lang.Thread.State: WAITING (parking)
	at sun.misc.Unsafe.park(Native Method)
	- parking to wait for  <0x00007f5969eb8e88> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.park(LockSupport.java:158)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1987)
	at java.util.concurrent.LinkedBlockingQueue.take(LinkedBlockingQueue.java:399)
	at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:947)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
	at java.lang.Thread.run(Thread.java:662)

"TimerQueue" daemon prio=10 tid=0x00007f585c01f000 nid=0x1d05 in Object.wait() [0x00007f587714a000]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
	at java.lang.Object.wait(Native Method)
	at javax.swing.TimerQueue.run(TimerQueue.java:232)
	- locked <0x00007f596aa7c690> (a javax.swing.TimerQueue)
	at java.lang.Thread.run(Thread.java:662)

"DestroyJavaVM" prio=10 tid=0x0000000001a8e800 nid=0x1cbd waiting on condition [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"Timer-0" daemon prio=10 tid=0x0000000002df8000 nid=0x1cfc in Object.wait() [0x00007f58779ea000]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
	at java.lang.Object.wait(Native Method)
	at java.util.TimerThread.mainLoop(Timer.java:509)
	- locked <0x00007f5969f15540> (a java.util.TaskQueue)
	at java.util.TimerThread.run(Timer.java:462)

"AWT-EventQueue-0" prio=10 tid=0x0000000002ded800 nid=0x1cfb in Object.wait() [0x00007f5877aeb000]
   java.lang.Thread.State: WAITING (on object monitor)
	at java.lang.Object.wait(Native Method)
	at java.lang.Object.wait(Object.java:485)
	at java.awt.EventQueue.getNextEvent(EventQueue.java:485)
	- locked <0x00007f596a28e428> (a java.awt.EventQueue)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:236)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)
	at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)

"AWT-Shutdown" prio=10 tid=0x0000000002dd2000 nid=0x1cfa in Object.wait() [0x00007f5877bec000]
   java.lang.Thread.State: WAITING (on object monitor)
	at java.lang.Object.wait(Native Method)
	at java.lang.Object.wait(Object.java:485)
	at sun.awt.AWTAutoShutdown.run(AWTAutoShutdown.java:265)
	- locked <0x00007f5969e09778> (a java.lang.Object)
	at java.lang.Thread.run(Thread.java:662)

"AWT-XAWT" daemon prio=10 tid=0x0000000002da2800 nid=0x1cf8 runnable [0x00007f5877ced000]
   java.lang.Thread.State: RUNNABLE
	at sun.awt.X11.XToolkit.waitForEvents(Native Method)
	at sun.awt.X11.XToolkit.run(XToolkit.java:579)
	at sun.awt.X11.XToolkit.run(XToolkit.java:543)
	at java.lang.Thread.run(Thread.java:662)

"Java2D Disposer" daemon prio=10 tid=0x0000000002d41800 nid=0x1cf7 in Object.wait() [0x00007f5877dee000]
   java.lang.Thread.State: WAITING (on object monitor)
	at java.lang.Object.wait(Native Method)
	at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:118)
	- locked <0x00007f596a143cc0> (a java.lang.ref.ReferenceQueue$Lock)
	at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:134)
	at sun.java2d.Disposer.run(Disposer.java:127)
	at java.lang.Thread.run(Thread.java:662)

"Low Memory Detector" daemon prio=10 tid=0x0000000001f09800 nid=0x1cf1 runnable [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"CompilerThread1" daemon prio=10 tid=0x0000000001f07000 nid=0x1cf0 waiting on condition [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"CompilerThread0" daemon prio=10 tid=0x0000000001f04800 nid=0x1cef waiting on condition [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"Signal Dispatcher" daemon prio=10 tid=0x0000000001f02800 nid=0x1cee waiting on condition [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"Surrogate Locker Thread (CMS)" daemon prio=10 tid=0x0000000001f00800 nid=0x1ced waiting on condition [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

"Finalizer" daemon prio=10 tid=0x0000000001ee5000 nid=0x1cec in Object.wait() [0x00007f589d4b8000]
   java.lang.Thread.State: WAITING (on object monitor)
	at java.lang.Object.wait(Native Method)
	at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:118)
	- locked <0x00007f5968ea52b0> (a java.lang.ref.ReferenceQueue$Lock)
	at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:134)
	at java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:159)

"Reference Handler" daemon prio=10 tid=0x0000000001ee3000 nid=0x1ceb in Object.wait() [0x00007f589d5b9000]
   java.lang.Thread.State: WAITING (on object monitor)
	at java.lang.Object.wait(Native Method)
	at java.lang.Object.wait(Object.java:485)
	at java.lang.ref.Reference$ReferenceHandler.run(Reference.java:116)
	- locked <0x00007f5968ebde20> (a java.lang.ref.Reference$Lock)

"VM Thread" prio=10 tid=0x0000000001edc000 nid=0x1cea runnable 

"Gang worker#0 (Parallel GC Threads)" prio=10 tid=0x0000000001aa3000 nid=0x1cbf runnable 

"Gang worker#1 (Parallel GC Threads)" prio=10 tid=0x0000000001aa4800 nid=0x1cc0 runnable 

"Gang worker#2 (Parallel GC Threads)" prio=10 tid=0x0000000001aa6800 nid=0x1cc1 runnable 

"Gang worker#3 (Parallel GC Threads)" prio=10 tid=0x0000000001aa8800 nid=0x1cc2 runnable 

"Gang worker#4 (Parallel GC Threads)" prio=10 tid=0x0000000001aaa000 nid=0x1cc3 runnable 

"Gang worker#5 (Parallel GC Threads)" prio=10 tid=0x0000000001aac000 nid=0x1cc4 runnable 

"Gang worker#6 (Parallel GC Threads)" prio=10 tid=0x0000000001aad800 nid=0x1cc5 runnable 

"Gang worker#7 (Parallel GC Threads)" prio=10 tid=0x0000000001aaf800 nid=0x1cc6 runnable 

"Gang worker#8 (Parallel GC Threads)" prio=10 tid=0x0000000001ab1800 nid=0x1cc7 runnable 

"Gang worker#9 (Parallel GC Threads)" prio=10 tid=0x0000000001ab3000 nid=0x1cc8 runnable 

"Gang worker#10 (Parallel GC Threads)" prio=10 tid=0x0000000001ab5000 nid=0x1cc9 runnable 

"Gang worker#11 (Parallel GC Threads)" prio=10 tid=0x0000000001ab7000 nid=0x1cca runnable 

"Gang worker#12 (Parallel GC Threads)" prio=10 tid=0x0000000001ab8800 nid=0x1ccb runnable 

"Gang worker#13 (Parallel GC Threads)" prio=10 tid=0x0000000001aba800 nid=0x1ccc runnable 

"Gang worker#14 (Parallel GC Threads)" prio=10 tid=0x0000000001abc800 nid=0x1ccd runnable 

"Gang worker#15 (Parallel GC Threads)" prio=10 tid=0x0000000001abe000 nid=0x1cce runnable 

"Gang worker#16 (Parallel GC Threads)" prio=10 tid=0x0000000001ac0000 nid=0x1ccf runnable 

"Gang worker#17 (Parallel GC Threads)" prio=10 tid=0x0000000001ac1800 nid=0x1cd0 runnable 

"Gang worker#18 (Parallel GC Threads)" prio=10 tid=0x0000000001ac3800 nid=0x1cd1 runnable 

"Gang worker#19 (Parallel GC Threads)" prio=10 tid=0x0000000001ac5800 nid=0x1cd2 runnable 

"Gang worker#20 (Parallel GC Threads)" prio=10 tid=0x0000000001ac7000 nid=0x1cd3 runnable 

"Gang worker#21 (Parallel GC Threads)" prio=10 tid=0x0000000001ac9000 nid=0x1cd4 runnable 

"Gang worker#22 (Parallel GC Threads)" prio=10 tid=0x0000000001acb000 nid=0x1cd5 runnable 

"Gang worker#23 (Parallel GC Threads)" prio=10 tid=0x0000000001acc800 nid=0x1cd6 runnable 

"Gang worker#24 (Parallel GC Threads)" prio=10 tid=0x0000000001ace800 nid=0x1cd7 runnable 

"Gang worker#25 (Parallel GC Threads)" prio=10 tid=0x0000000001ad0000 nid=0x1cd8 runnable 

"Gang worker#26 (Parallel GC Threads)" prio=10 tid=0x0000000001ad2000 nid=0x1cd9 runnable 

"Gang worker#27 (Parallel GC Threads)" prio=10 tid=0x0000000001ad4000 nid=0x1cda runnable 

"Gang worker#28 (Parallel GC Threads)" prio=10 tid=0x0000000001ad5800 nid=0x1cdb runnable 

"Gang worker#29 (Parallel GC Threads)" prio=10 tid=0x0000000001ad7800 nid=0x1cdc runnable 

"Gang worker#30 (Parallel GC Threads)" prio=10 tid=0x0000000001ad9800 nid=0x1cdd runnable 

"Gang worker#31 (Parallel GC Threads)" prio=10 tid=0x0000000001adb000 nid=0x1cde runnable 

"Gang worker#32 (Parallel GC Threads)" prio=10 tid=0x0000000001add000 nid=0x1cdf runnable 

"Concurrent Mark-Sweep GC Thread" prio=10 tid=0x0000000001e3b000 nid=0x1ce9 runnable 
"Gang worker#0 (Parallel CMS Threads)" prio=10 tid=0x0000000001e29800 nid=0x1ce0 runnable 

"Gang worker#1 (Parallel CMS Threads)" prio=10 tid=0x0000000001e2b800 nid=0x1ce1 runnable 

"Gang worker#2 (Parallel CMS Threads)" prio=10 tid=0x0000000001e2d000 nid=0x1ce2 runnable 

"Gang worker#3 (Parallel CMS Threads)" prio=10 tid=0x0000000001e2f000 nid=0x1ce3 runnable 

"Gang worker#4 (Parallel CMS Threads)" prio=10 tid=0x0000000001e30800 nid=0x1ce4 runnable 

"Gang worker#5 (Parallel CMS Threads)" prio=10 tid=0x0000000001e32800 nid=0x1ce5 runnable 

"Gang worker#6 (Parallel CMS Threads)" prio=10 tid=0x0000000001e34800 nid=0x1ce6 runnable 

"Gang worker#7 (Parallel CMS Threads)" prio=10 tid=0x0000000001e36000 nid=0x1ce7 runnable 

"Gang worker#8 (Parallel CMS Threads)" prio=10 tid=0x0000000001e38000 nid=0x1ce8 runnable 

"VM Periodic Task Thread" prio=10 tid=0x0000000001f14800 nid=0x1cf2 waiting on condition 

JNI global references: 3612

Heap
 par new generation   total 383488K, used 30574K [0x00007f593e000000, 0x00007f5958010000, 0x00007f5968e60000)
  eden space 340928K,   4% used [0x00007f593e000000, 0x00007f593ed96c48, 0x00007f5952cf0000)
  from space 42560K,  39% used [0x00007f5952cf0000, 0x00007f5953d34d98, 0x00007f5955680000)
  to   space 42560K,   0% used [0x00007f5955680000, 0x00007f5955680000, 0x00007f5958010000)
 concurrent mark-sweep generation total 9490680K, used 5931204K [0x00007f5968e60000, 0x00007f5bac29e000, 0x00007f71a8000000)
 concurrent-mark-sweep perm gen total 131072K, used 55227K [0x00007f71a8000000, 0x00007f71b0000000, 0x00007f71b0000000)
Comment 9 Curtis Rueden 2014-06-23 16:41:18 CDT
Thanks, Stephan. I am going to work on a general solution to the "Fiji won't quit" problem over the next couple of days. See also http://fiji.sc/bugzilla/﷒0
Comment 10 Curtis Rueden 2014-07-10 13:07:32 CDT
I believe the quitting problems have been resolved. Can you please retest TrakEM2 and see if this problem is also fixed?
Comment 11 Curtis Rueden 2014-07-14 12:05:08 CDT
I attempted to reproduce on my OS X 10.9 system with a fully updated Fiji. Clicking the X on the ImageJ main window closes down TrakEM2 (with prompts to save). So I think this bug is resolved.

Strangely, after TrakEM2 is gone, the ImageJ main window does _not_ close. You have to close it again to quit the program. But I think this is OK for now -- not a critical/blocking issue.

Please reopen if you can reproduce some behavior worse than that.