SepOsiriXSegmentation

Chair for Computer Aided Medical Procedures & Augmented Reality
Lehrstuhl für Informatikanwendungen in der Medizin & Augmented Reality

Sep OsiriX Segmentation plugin

student: Brian Jensen
Advisor: Prof. Dr. Nassir Navab
Supervision by: Ralph Bundschuh

Abstract

Osirix PNG

OsiriX is an open source DICOM image viewer for Mac OS X offering advanced image visualization capabilities. The goal of this project was to create a plugin for the OsiriX DICOM viewer in order to add support for semi automatic segmentation of tumors in fused PET / CT images. After accepting the selection from a user the plugin offers the ability to perform several different kinds of region growing algorithms. The plugin can perform the segmentation on the image itself, or optionally on a registered image, such as a PET image in CT/ PET fused image setup, after which the segmented volume is then mapped back onto the main image. The plugin also provides methods simple integration with other image processing frameworks.

This project was conducted as a cooperation between the Chair for Computer Aided Medical Procedures and Augmented Reality at the TU München, and Department of Nuclear Medicine at the Univserity Hospital Rechts der Isar, TU München.

Methods

ITK logo Xcode Logo

OsiriX is a native Mac OS X application and as such is mainly written in objective-c. The main image processing framework used in the plugin is the Insight Segmentation and Registration Toolkit (ITK) which is written using C++. Because of these constraints most of the plugin was written in objective-c++ (the interface and OsiriX interaction), and the segmentation code was written in pure C++. In addition a shell script was written for the automatic refactoring of the ITK namespace.

The user interface has support for three standard ITK region growing algorithms: connected threshold, neighborhood connected threshold and confidence connected. A fourth algorithm was developed using the ITK framework, gradient threshold. This custom threshold algorithm operates on image gradient magnitudes in the image, segmenting voxels whose gradient magnitude falls below a certain ratio starting with from a seed point.

PDF icon Plugin Documentation: NMSegmentation Documentation.pdf

Project Configuration Guide: ProjectConfiguration.pdf


powerpoint icon Final Presentation: Presentation.pdf

Download

Latest release: 14.07.09

Osirix plugin icon NMSegmention 1.01 binary (x86_64, i386, ppc)

Plugin project icon NMSegmentation 1.0.1 Source code

Results

Here are some screenshots of the OsiriX plugin NMSegmentation in action.

Plugin Screenshot 1


Plugin Screenshot 2Plugin Screenshot 3Plugin Screenshot 4


This screenshot shows the results after performing a connected threshold segmentation on the region of interest

Plugin Screenshot 5


This screenshot shows the results using the gradient magnitude threshold segmentation algorithm on the same region

Plugin Screenshot 6

This screenshot shows the results of the gradient threshold segmentation algorithm on a different lesion type Plugin Screenshot 7

Students.ProjectForm
Title: Development of an OsiriX Segmentation plugin
Abstract: OsiriX is an open source DICOM image viewer for Mac OS X offering advanced image visualization capabilities. The goal of this project is to create a plugin for the segmentation of tumors in fused PET / CT image. The plugin should provide methods for integrating with external image procesing libraries, so that additional segmentation can be easily added.
Student: Brian Jensen
Director: Nassir Navab
Supervisor: Ralph Bundschuh
Type: SEP
Area: Segmentation, Medical Imaging, Molecular Imaging
Status: finished
Start: 05/2008
Finish: 06/2009


Edit | Attach | Refresh | Diffs | More | Revision r1.18 - 21 Oct 2009 - 09:21 - BrianJensen