[ImageJ-bugs] [Bug 1125] New: Trackmate problems after Mac upgrate to OS X Yosemite

[bugzilla at fiji.sc]

http://fiji.sc/bugzilla/show_bug.cgi?id=1125

            Bug ID: 1125
           Summary: Trackmate problems after Mac upgrate to OS X Yosemite
           Product: Fiji
           Version: unspecified
          Hardware: Macintosh
                OS: Mac OS
            Status: NEW
          Severity: normal
          Priority: P4
         Component: Plugins
          Assignee: imagej-bugs at imagej.net
          Reporter: philip.dusart at scilifelab.se
                CC: philip.dusart at scilifelab.se

I was using Trackmate to track particles, however after upgrading my computer
to Yosemite after months of prompting from apple, the plugin doesn't work as
well as previously. 

-When I open a time lapse AVI image stack, the image behaves as normal and as
before the upgrade, and I can play the video normally at the realtime 15 frames
per second.
-After using trackmate (V2.7.4) to detect the points and create the tracks
successfully, the refresh rate when I try and play the time lapse video with
the tracks slows right down, with visible loading from the top of the image
down of the track overlay. 
-If I uncheck the "display tracks" box in the trackmate interface then the
refresh rate goes back to normal levels.

I did not encounter this problem before I upgraded my computer to Yosemite. 

I have read a previous bug report on bad refresh rates with time lapse in
ImageJ after Yosemite upgrade, not related to Trackmate, but that issue appears
to have been resolved in newer versions of ImageJ. 

That report reccomended removing the Java1.8 and replacing with Java1.6,
however it also says that this is no longer nessecary for newer updates of
ImageJ. Once I managed to do this and re-run my test video, the Trackmate
overlay seemed to work properly again, however it made the Fiji program itself
a pain to find and open and some of the options for opening files appeared to
stop working.

Information about your version of Java:

  os.arch => x86_64
  os.name => Mac OS X
  os.version => 10.10.4
  java.version => 1.8.0_51
  java.vendor => Oracle Corporation
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.8.0_51-b16
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 25.51-b03
  java.vm.vendor => Oracle Corporation
  java.vm.info => mixed mode
  java.awt.graphicsenv => sun.awt.CGraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.8
  sun.cpu.endian => little
  sun.desktop => null
  file.separator => /

The up-to-date check says: OFFLINE

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: /Library/Internet
Plug-Ins/JavaAppletPlugin.plugin/Contents/Home/
  imagej.dir => /Applications/Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20150722045527)
Fiji: http://fiji.sc/update/ (last check:20150724215809)

Files not up-to-date:
  b916ac8e (MODIFIED) 20150728111233 jars/ij-1.49u.jar
  b916ac8e (MODIFIED) 20150728125144 jars/ij-1.50a.jar
  1ad3be0d (LOCAL_ONLY) 20140814180800 jars/jpedalSTD.jar

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