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Bug 664 - Trackmate does not go to the initial thresholding panel
Trackmate does not go to the initial thresholding panel
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Windows
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2013-09-22 18:42 CDT by Lily
Modified: 2014-06-16 16:21 CDT
4 users (show)

See Also:
Description Lily 2013-09-22 18:42:39 CDT 
I want to track image sequence of 1860 images with trackmate. After selecting Log Detector, it shows that detection done in 106.8s. But the next button is not enabled to click, which means it always shows this panel but cannot go to the next panel "Initial Thresholding".

Information about your version of Java:

  os.arch => amd64
  os.name => Windows 7
  os.version => 6.1
  java.version => 1.6.0_24
  java.vendor => Sun Microsystems Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_24-b07
  java.vm.name => Java HotSpot(TM) 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.Win32GraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => windows
  file.separator => \

The up-to-date check says: REMIND_LATER

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: C:\Users\liyanl\Desktop\Fiji.app/java/win64/jdk1.6.0_24//jre
  ij.dir => C:\Users\liyanl\Desktop\Fiji.app

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Comment 1 Johannes Schindelin 2013-09-22 19:14:02 CDT 
Thanks for the report! Could you please upload the sample image via Help>Upload Sample Image and tell us the parameters you chose so we can try to reproduce?
Comment 2 Jean-Yves Tinevez 2013-09-23 03:26:56 CDT 
Hi all

I fear that the bug with imglib2-meta is still interfering. 
On the Fiji app, freshly updated, TrackMate still segments for each frame all the frames of a movie as if they were Z-slices. 

Uploading a new imglib2 made from the master fixes this.
Comment 3 Johannes Schindelin 2013-09-23 11:58:39 CDT 
Oh, I see... Lily, could you please start the updater via Help>Update Fiji, click on "Manage Update Sites" and enable the "TrackMate-dev" site? That should get you going again until we fix things with the default installation of Fiji. Thanks!
Comment 4 Lily 2013-09-23 18:59:33 CDT 
Thank you so much. I will try again.
Comment 5 Jean-Yves Tinevez 2013-10-16 02:37:37 CDT 
Hi Lily.
Any news from this issue? Most of the problem that recently popped up with TrackMate are actually related to a dependency problem with imglib2. 
If the workaround worked for you I would like to close this bug.
Best
jy
Comment 6 Lily 2013-10-16 03:38:24 CDT 
Yes, I think it's the imglib2 problems. But the problem is still existing.
Comment 7 Jean-Yves Tinevez 2013-10-16 04:01:24 CDT 
Can you upload the faulty image?
Comment 8 Johannes Schindelin 2013-10-16 08:54:55 CDT 
What J-Y refers to is: in the main Fiji window, call Help>Upload Sample Image, choose your sample file, and after it uploaded successfully, post the name here so that we know something arrived.

If uploading does *not* work, please let us know, too.
Comment 9 Curtis Rueden 2014-06-16 14:57:53 CDT 
I checked the list of incoming files, but didn't see anything from 2013-10-16 through the end of 2013 that could possibly be the dataset in question (i.e., 1860 image planes).

Lily, did you ever upload anything? If so, what is the name of the file?

J-Y: Do you expect that this issue might still be present in the last code? Or can we mark this bug as resolved?
Comment 10 Jean-Yves Tinevez 2014-06-16 16:20:47 CDT 
I think we can close it. I forgot to do it sorry.
Lili's problem was with generating a hugen number of spots with little RAM, which caused Java to die. 
The fix was to use a threshold value at the detection level to forbid generating spurious spots.