3DImageToolkit: a framework for Medical Image Segmentation and Filtering

A C++ library to perform basic image filtering and a semi-automatic segmentation through the Connected Component Localization of the Region-Scalable Fitting Energy.

The theory behind this segmentation method can be found in details in the following publication:

Fedele, M., Faggiano, E., Barbarotta, L., Cremonesi, F., Formaggia, L., & Perotto, S. (2015, September). Semi-automatic three-dimensional vessel segmentation using a connected component localization of the Region-Scalable Fitting Energy. In Image and Signal Processing and Analysis (ISPA), 2015 9th International Symposium on (pp. 72-77). IEEE.

If you use this work, please don't forget to cite this paper.

License

This library is released with the BSD license, see file license.md for all the details.

Authors and Contacts

Marco Fedele: fedele.marco@gmail.com
Elena Faggiano: elena.faggiano@gmail.com
Luca Barbarotta: luca.barbarotta@gmail.com
Francesco Cremonesi: francesco.cremonesi0@gmail.com

Authors acknowledge Prof. Luca Formaggia and Prof. Simona Perotto for supervising the implementation of the segmentation algorithm.

Installation

This library is tested on Linux and exploits the following libraries:

cmake to create the MakeFile
VTK to visualize, to import and to save 3d images
fftw to compute DFT efficiently
GetPot to import parameters from a data file

All these libraries must be installed before starting the installation.

Some notes:

the library needs the fftw version working with openmp (if you compile it, use the option --enable-shared)
GetPot can be download from the website and copied in your path, e.g. /usr/include/
in debian based Linux distribution all the necessary packages (except GetPot) should be available with apt-get

Once installed all this packages you can exploit cmake to compile all the executables:

mkdir build_directory
cd path_to_build_directory
cmake path_to_source_directory
make

Documentaion

To build documentation you need to install doxygen and graphviz and then type:

cmake path_to_source_directory -DBUILD_DOCUMENTATION=ON
make doc

The html guide is in build_directory/doc/html/

Usage

Launch an executable without any option to see its helper.

3dimagetoolkit

Install / Use

README