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Bug 1165 - Trackmate XML output reports pixelated y displacement values but not x or z
Trackmate XML output reports pixelated y displacement values but not x or z
Product: ImageJ
Classification: Unclassified
Component: Common
PC Windows
: P5 enhancement
Assigned To: Curtis Rueden
Depends on:
Reported: 2015-09-28 16:35 CDT by Leanna Owen
Modified: 2015-10-13 11:02 CDT
1 user (show)

See Also:

Description Leanna Owen 2015-09-28 16:35:43 CDT
When using Trackmate to track fluorescent particles, the output results sent to XML do not make sense, despite being checked over several raw fluorescence datasets. The displacements between timepoints for the X and Z components of the tracks appear approximately gaussian-distributed, as I would expect, but the Y components are concentrated in small peaks centered on integral pixel displacements. Is it possible to make sure that the particle detection and output generation for these two components are the same? 

My pixel dimensions are isotropic, I am using the LoG detector option (no median filtering, subpixel localization=on), and the LAP tracker (no gap closing). 
I have run this with the same result on both processed and unprocessed image stacks, so I know this is not an artifact of the image processing. 

Information about your version of Java:

  os.arch => amd64 => Windows 7
  os.version => 6.1
  java.version => 1.6.0_24
  java.vendor => Sun Microsystems Inc. => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_24-b07 => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 19.1-b02
  java.vm.vendor => Sun Microsystems Inc. => mixed mode
  java.awt.graphicsenv => sun.awt.Win32GraphicsEnvironment => 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\Leanna\Desktop\
  imagej.dir => C:\Users\Leanna\Desktop\

Information about the version of each plugin:

Activated update sites:
ImageJ: (last check:20140916081414)
Fiji: (last check:20140925082044)

Files not up-to-date:
  fdaccfea (LOCAL_ONLY) 20130528165028 macros/BatchMacro.ijm
  d89be7db (LOCAL_ONLY) 20140914142458 plugins/Correct_3D_drift.txt
  e8692561 (LOCAL_ONLY) 20140120155254 plugins/Iterative_Deconvolve_3D.class
  19a2caaf (LOCAL_ONLY) 20140120153814 plugins/ParallelIterativeDeconvolution3D.txt
  616e3252 (MODIFIED) 20130919195651 plugins/StackReg_.jar
  240bc793 (LOCAL_ONLY) 20130919200249 plugins/turboRegDialog$15.class
  48404114 (LOCAL_ONLY) 20130919200250 plugins/turboRegDialog$16.class
Comment 1 Curtis Rueden 2015-10-13 11:02:15 CDT
Migrated to the TrackMate GitHub issues, to increase visibility of this issue: