The Medical Image Segmentation Tool Set (iSEG) is a fully integrated segmentation (including pre- and postprocessing) toolbox for the efficient, fast, and flexible generation of anatomical models from various types of imaging data. iSEG includes a variety of semi-automatic segmentation methods. The key strengths of iSEG are a) a powerful set of tools for manual segmentation (correction), b) support for massive image sizes, c) suport for segmenting complex models with a large number of tissues. iSEG features a plugin mechanism, which allows users to easily extend the application with custom widgets. The development of iSEG has been driven by the Virtual Population project at the IT'IS Foundation, due to a lack of alternatives amongst open source and commercial tools.

A defined set of 3rd party libraries are required in order to compile iSEG. Instructions as to how these libraries must be installed and compiled are provided below.

The application below must be installed on the system in order to compile iSEG and its dependencies.

• CMake: v3 minimum
• Visual Studio 2015 with x64 C++ compiler
• Git

The libraries below are required to be compiled and installed on the system in order to compile iSEG. Instructions for each library follows hereafter.

• Boost, Boost license
• HDF5, BSD-like license
• zlib, ZLIB license
• ITK, Apache 2.0 license
• VTK, BSD license
• Qt 4.8, GPL3 and LGPL2.1 license

• GraphCut, LGPL license. This library is compiled depending on the CMake configuration (plugin selection).

• Boost installer: boost_1_64_0-msvc-14.0, or newer

  1. Download the installer boost_1_64_0_msvc-14.0-64.exe
  2. Run the installer and follow the default instructions

• HDF5 installer: v1.8.18, or newer

  1. Download the installer hdf5-1.8.18-win64-vs2013-shared.zip
  2. Unzip the installer
  3. Run the installer and follow the default instructions

• ITK source code: v4.12.2, or newer

  1. Download and unzip the ITK folder
  2. CMake (source ITK folder, build in separate folder), press Configure
  3. Press configure and select VS Studio 14 2015 Win64
  4. Press Advanced checkbox and select BUILD_SHARED_LIBS , press configure again (CMake will find the ZLib library installed with the HDF5 package above)
  5. Press Generate
  6. Press Open Project and build the solution in Debug and Release

• VTK source code: v7.1.0, or newer

  1. Download and unzip the VTK folder
  2. CMake (source VTK folder, build in separate folder), press Configure
  3. Set ISEG_VTK_OPENGL2 depending on the value of VTK_RENDERING_BACKEND (OpenGL or OpenGL2)
  4. Press Generate
  5. Press Open Project and build the solution in Debug and Release

• Qt: v4.8.7 (min 4.8.6)

  1. Download and unzip the Qt folder
  2. Apply the patch located in the repo root folder(02-fix_build_with_msvc2015-45e8f4ee.diff) (based on these instructions)
  3. Open a VisualStudio 2015 x64 prompt
  4. Go to downloaded Qt folder (cd %QTFOLDER%)
  5. Input set Path=%PATH%;%QTFOLDER%\bin
  6. Input configure -debug-and-release -opensource -confirm-license opengl desktop -nomake examples -nomake tests in the command window
  7. Compile Qt by inputing nmake

1. Clone the repository
2. CMake (source root folder, build in separate folder), press Configure
3. Define BOOST_ROOT as the folder where Boost library was installed (e.g. c:\boost_1_64_0), press Configure
4. Define HDF5_ROOT as the folder where HDF5 was installed (e.g. C:\Program Files\HDF_Group\HDF5\1.8.18), press Configure
5. Define ITK_DIR as the folder where ITK was built (e.g. ITK_BUILD_DIR), press Configure
6. Define QT_QMAKE_EXECUTABLE by selecting qmake.exe in the folder where Qt was compiled/Installed (e.g. QT_DIR/bin/qmake.exe), press Configure
7. Define VTK_DIR as the folder where VTK was built (e.g. VTK_BUILD_DIR), press Configure
8. Press Generate, then Open Project
9. In Visual Studio, build the solution (Debug/Release)