Bug 731 – Treestructure (branches) of tracing in Simple Neurite Tracer are occasionally wrong

Bug 731 - Treestructure (branches) of tracing in Simple Neurite Tracer are occasionally wrong


Summary:	Treestructure (branches) of tracing in Simple Neurite Tracer are occasionally...

Status:	NEW

Product:	Fiji
Classification:	Unclassified
Component:	Plugins
Version:	unspecified
Hardware:	Macintosh Mac OS

Importance:	P4 normal
Assigned To:	ImageJ Bugs Mailing List

URL:

Depends on:
Blocks:

Reported:	2014-04-18 06:36 CDT by olivia.viessmann
Modified:	2014-04-18 06:36 CDT
CC List:	1 user (show)

See Also:

Description olivia.viessmann 2014-04-18 06:36:42 CDT

I used the SNT to segment vessels in MR data. I created a tree structure and exported it as SWC. I loaded the swc file in the trees toolbox (Matlab based) which can calculate for example the angle between the branches. Comparing the angle values with my tree, some angles didn't make sense. By the eye I could tell, that the angle was smaller then 90 degrees, but the trees toolbox gave me , for example 120. In other cases it seemed to match. I then loaded the SWC file in the neuromantic software and took a close look at the branches and saw that for some branches the branch didn't start at the mother path, but crossed it (creating a secon angle, which is 180-true angle). Talking to a friend, he told me he already experienced the same behaviour in the SNT, that sometimes branches do not start correctly at the mother path. I could send you the SWC file if you like. 
Thank you very much and lot's of sunshine,
Olivia

Information about your version of Java:

  os.arch => x86_64
  os.name => Mac OS X
  os.version => 10.9.2
  java.version => 1.6.0_65
  java.vendor => Apple Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_65-b14-462-11M4609
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 20.65-b04-462
  java.vm.vendor => Apple Inc.
  java.vm.info => mixed mode
  java.awt.graphicsenv => apple.awt.CGraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => null
  file.separator => /

The up-to-date check says: REMIND_LATER

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: null
  ij.dir => /Applications/Fiji.app

Information about the version of each plugin:

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