Difference between revisions of "User:Haehn"

From NAMIC Wiki
Jump to: navigation, search
Line 13: Line 13:
 
'''Project goal:''' Implementing a vessel/tube segmentation module in Slicer3<br>
 
'''Project goal:''' Implementing a vessel/tube segmentation module in Slicer3<br>
 
'''Kick-Off:''' 10/15/2008
 
'''Kick-Off:''' 10/15/2008
 +
'''Final Milestone:''' 03/31/2009
  
−
=== Task 1: Module for Slicer3 based on old version ===
+
=== VMTK Level-Set Segmentation in 3D Slicer ===
  
−
In Slicer2 exists a module called '''vtkExtractAirway'''. This module is based on a centerline approach documented in the following paper: "Aylward, S.: Initialization, Noise, Singularities, and Scale in Height Ridge Traversal for Tubular Object Centerline Extraction (available http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.18.8435)".<br>
+
The NITRC project page including a SVN repository with the latest code: http://www.nitrc.org/projects/slicervmtklvlst/
−
 
 
−
Since the algorithm is not fully implemented yet, the idea is to port the Slicer2 module to Slicer3 and finalize it to be used as a semi-interactive way to segment vessel or other tube shaped ROI.<br>
 
−
 
 
−
The semi-interactive way should work like the following that a user clicks into a path of a ROI and then the algorithm computes all the connected tubes and highlights them.<br>
 
−
 
 
−
=== Task 2: an interface to VMTK in Slicer3 ===
 
  
 
More recent news on this project: http://www.na-mic.org/Wiki/index.php/2009_Winter_Project_Week_Slicer_VMTK
 
More recent news on this project: http://www.na-mic.org/Wiki/index.php/2009_Winter_Project_Week_Slicer_VMTK
Line 28: Line 23:
 
VMTK is the Vascular Modeling Toolkit (http://vmtk.org) and offers interesting techniques for segmentation of vessels or tube-shapes.<br>
 
VMTK is the Vascular Modeling Toolkit (http://vmtk.org) and offers interesting techniques for segmentation of vessels or tube-shapes.<br>
  
−
It should be very interesting to offer such techniques in Slicer3. So the plan is to make a python scripted module that connects to VMTK pipes and provides even the possibility of user interaction.<br>
+
The downloadable scripted module provides VMTK techniques like Colliding Fronts, Fast Marching, Thresholding, Iso-Surface and Seeds to segment vessels and tubular structures in 3D Slicer.<br>
  
−
This task is scheduled for the NAMIC project week 2009. Luca Antiga and me planned to develop it in an "extreme programming"-way. Until then I will focus on the ground work for making an interactive slicer module and on building VMTK pipes.
+
This work is done in conjunction with Luca Antiga (Medical Imaging Unit, Bioengineering Department, Mario Negri Institute, Bergamo, Italy).

Revision as of 15:16, 20 March 2009

Daniel Haehn's Page

Info
Daniel Hähn
Student of Medical Informatics
University of Heidelberg, Germany
E-Mail: haehn@bwh.harvard.edu or haehn@urz.uni-heidelberg.de
Expected Graduation: Summer 2009
Haehn.jpg

Vessel Segmentation in Slicer3

Project goal: Implementing a vessel/tube segmentation module in Slicer3
Kick-Off: 10/15/2008 Final Milestone: 03/31/2009

VMTK Level-Set Segmentation in 3D Slicer

The NITRC project page including a SVN repository with the latest code: http://www.nitrc.org/projects/slicervmtklvlst/

More recent news on this project: http://www.na-mic.org/Wiki/index.php/2009_Winter_Project_Week_Slicer_VMTK

VMTK is the Vascular Modeling Toolkit (http://vmtk.org) and offers interesting techniques for segmentation of vessels or tube-shapes.

The downloadable scripted module provides VMTK techniques like Colliding Fronts, Fast Marching, Thresholding, Iso-Surface and Seeds to segment vessels and tubular structures in 3D Slicer.

This work is done in conjunction with Luca Antiga (Medical Imaging Unit, Bioengineering Department, Mario Negri Institute, Bergamo, Italy).

Retrieved from "https://www.na-mic.org/w/index.php?title=User:Haehn&oldid=35751"