[ImageJ-bugs] [Bug 1165] New: Trackmate XML output reports pixelated y displacement values but not x or z

[bugzilla at fiji.sc]

http://fiji.sc/bugzilla/show_bug.cgi?id=1165

            Bug ID: 1165
           Summary: Trackmate XML output reports pixelated y displacement
                    values but not x or z
           Product: ImageJ
           Version: unspecified
          Hardware: PC
                OS: Windows
            Status: NEW
          Severity: enhancement
          Priority: P5
         Component: Common
          Assignee: ctrueden at wisc.edu
          Reporter: leannao at stanford.edu
                CC: imagej-bugs at imagej.net

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
  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\Leanna\Desktop\Fiji.app/java/win64/jdk1.6.0_24//jre
  imagej.dir => C:\Users\Leanna\Desktop\Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20140916081414)
Fiji: http://fiji.sc/update/ (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

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