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Bug 1125 - Trackmate problems after Mac upgrate to OS X Yosemite
Trackmate problems after Mac upgrate to OS X Yosemite
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
Macintosh Mac OS
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2015-07-28 08:36 CDT by philip.dusart
Modified: 2015-10-20 11:04 CDT
2 users (show)

See Also:

Description philip.dusart 2015-07-28 08:36:01 CDT
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
Comment 1 Jean-Yves Tinevez 2015-10-18 10:32:25 CDT
Hi Philip

I confirm that TrackMate painting has become extremely slow using recent version of MacOSX Yosemite. The problem is not present on Windows platforms.

I tested Java 1.6 and 1.8, and the bug is still the same. Unfortunately, I have no clue on how to fix this, as the bug seems to come from Java directly. 

I'll investigate and keep this page updated.
Comment 2 Jean-Yves Tinevez 2015-10-20 11:03:54 CDT
I made some changes in TrackMate that should help to tame the problem. However, it does not fix the core of the problem.
Check this:
https://github.com/fiji/TrackMate/commit/4d1fe92e11a8ad43b8ef8f072b74601c41748425
I am closing this bug for now.