diff --git a/CMakeExternals/ITK.cmake b/CMakeExternals/ITK.cmake
index 424b6f944e..0bf8235b6e 100644
--- a/CMakeExternals/ITK.cmake
+++ b/CMakeExternals/ITK.cmake
@@ -1,78 +1,82 @@
 #-----------------------------------------------------------------------------
 # ITK
 #-----------------------------------------------------------------------------
 
 # Sanity checks
 if(DEFINED ITK_DIR AND NOT EXISTS ${ITK_DIR})
   message(FATAL_ERROR "ITK_DIR variable is defined but corresponds to non-existing directory")
 endif()
 
 set(proj ITK)
 set(proj_DEPENDENCIES GDCM)
 if(MITK_USE_Python)
   list(APPEND proj_DEPENDENCIES CableSwig)
 endif()
 
 set(ITK_DEPENDS ${proj})
 
 if(NOT DEFINED ITK_DIR)
 
   set(additional_cmake_args )
   if(MINGW)
     set(additional_cmake_args
         -DCMAKE_USE_WIN32_THREADS:BOOL=ON
         -DCMAKE_USE_PTHREADS:BOOL=OFF)
   endif()
 
   if(MITK_USE_Python)
+
     list(APPEND additional_cmake_args
          -DUSE_WRAP_ITK:BOOL=ON
          -DITK_USE_REVIEW:BOOL=ON
-         -DPYTHON_DEBUG_LIBRARY:FILEPATH=${PYTHON_DEBUG_LIBRARY}
-         -DPYTHON_INCLUDE_DIR:PATH=${PYTHON_INCLUDE_DIR}
-         -DPYTHON_LIBRARY:FILEPATH=${PYTHON_LIBRARY}
+         #-DPYTHON_EXECUTABLE=${PYTHON_EXECUTABLE}
+         #-DPYTHON_DEBUG_LIBRARY=${PYTHON_DEBUG_LIBRARY}
+         #-DPYTHON_INCLUDE_DIR=${PYTHON_INCLUDE_DIR}
+         #-DPYTHON_LIBRARY=${MITK_PYTHON_PLAIN_LIBRARY}
+         #-DPYTHON_LIBRARIES=${PYTHON_LIBRARY}
+         #-DPYTHON_DEBUG_LIBRARIES=${PYTHON_DEBUG_LIBRARIES}
          -DCableSwig_DIR:PATH=${CableSwig_DIR}
          -DWRAP_ITK_JAVA:BOOL=OFF
          -DWRAP_ITK_TCL:BOOL=OFF
          -DWRAP_unsigned_char:BOOL=ON
          #-DWRAP_double:BOOL=ON
          -DWRAP_rgb_unsigned_char:BOOL=ON
          #-DWRAP_rgba_unsigned_char:BOOL=ON
          -DWRAP_signed_char:BOOL=ON
          #-DWRAP_signed_long:BOOL=ON
          -DWRAP_signed_short:BOOL=ON
          -DWRAP_short:BOOL=ON
          -DWRAP_unsigned_long:BOOL=ON
         )
   endif()
 
   if(GDCM_IS_2_0_18)
     set(ITK_PATCH_COMMAND ${CMAKE_COMMAND} -DTEMPLATE_FILE:FILEPATH=${MITK_SOURCE_DIR}/CMakeExternals/EmptyFileForPatching.dummy -P ${MITK_SOURCE_DIR}/CMakeExternals/PatchITK-3.20.cmake)
   endif()
 
   ExternalProject_Add(${proj}
      SOURCE_DIR ${CMAKE_BINARY_DIR}/${proj}-src
      BINARY_DIR ${proj}-build
      PREFIX ${proj}-cmake
      URL ${MITK_THIRDPARTY_DOWNLOAD_PREFIX_URL}/InsightToolkit-3.20.1.tar.gz
      URL_MD5 90342ffa78bd88ae48b3f62866fbf050
      INSTALL_COMMAND ""
      PATCH_COMMAND ${ITK_PATCH_COMMAND}
      CMAKE_GENERATOR ${gen}
      CMAKE_ARGS
        ${ep_common_args}
        ${additional_cmake_args}
        -DBUILD_TESTING:BOOL=OFF
        -DBUILD_EXAMPLES:BOOL=OFF
        -DITK_USE_SYSTEM_GDCM:BOOL=ON
        -DGDCM_DIR:PATH=${GDCM_DIR}
      DEPENDS ${proj_DEPENDENCIES}
     )
 
   set(ITK_DIR ${CMAKE_CURRENT_BINARY_DIR}/${proj}-build)
 
 else()
 
   mitkMacroEmptyExternalProject(${proj} "${proj_DEPENDENCIES}")
 
 endif()
diff --git a/CMakeExternals/OpenCV.cmake b/CMakeExternals/OpenCV.cmake
index a443a6c3c2..5bf9699c43 100644
--- a/CMakeExternals/OpenCV.cmake
+++ b/CMakeExternals/OpenCV.cmake
@@ -1,69 +1,72 @@
 #-----------------------------------------------------------------------------
 # OpenCV
 #-----------------------------------------------------------------------------
 
 if(MITK_USE_OpenCV)
 
   # Sanity checks
   if(DEFINED OpenCV_DIR AND NOT EXISTS ${OpenCV_DIR})
     message(FATAL_ERROR "OpenCV_DIR variable is defined but corresponds to non-existing directory")
   endif()
 
   set(proj OpenCV)
   set(proj_DEPENDENCIES)
   set(OpenCV_DEPENDS ${proj})
 
   if(NOT DEFINED OpenCV_DIR)
 
     set(additional_cmake_args )
     if(MITK_USE_Python)
       list(APPEND additional_cmake_args
          -DBUILD_opencv_python:BOOL=ON
          -DBUILD_NEW_PYTHON_SUPPORT:BOOL=ON
-         -DPYTHON_DEBUG_LIBRARY:FILEPATH=${PYTHON_DEBUG_LIBRARY}
-         -DPYTHON_INCLUDE_DIR:PATH=${PYTHON_INCLUDE_DIR}
-         -DPYTHON_LIBRARY:FILEPATH=${PYTHON_LIBRARY}
+         #-DPYTHON_EXECUTABLE=${PYTHON_EXECUTABLE}
+         #-DPYTHON_DEBUG_LIBRARY=${PYTHON_DEBUG_LIBRARY}
+         #-DPYTHON_INCLUDE_DIR=${PYTHON_INCLUDE_DIR}
+         #-DPYTHON_LIBRARY=${MITK_PYTHON_PLAIN_LIBRARY}
+         #-DPYTHON_LIBRARIES=${PYTHON_LIBRARY}
+         #-DPYTHON_DEBUG_LIBRARIES=${PYTHON_DEBUG_LIBRARIES}
           )
     endif()
 
     # 12-05-02, muellerm, added QT usage by OpenCV if QT is used in MITK
     # 12-09-11, muellerm, removed automatic usage again, since this will struggle with the MITK Qt application object
     if(MITK_USE_QT)
       list(APPEND additional_cmake_args
            -DWITH_QT:BOOL=OFF
            -DWITH_QT_OPENGL:BOOL=OFF
            -DQT_QMAKE_EXECUTABLE:FILEPATH=${QT_QMAKE_EXECUTABLE}
           )
     endif()
 
     set(opencv_url ${MITK_THIRDPARTY_DOWNLOAD_PREFIX_URL}/OpenCV-2.4.2.tar.bz2)
     set(opencv_url_md5 d5d13c4a65dc96cdfaad54767e428215)
 
     ExternalProject_Add(${proj}
       SOURCE_DIR ${CMAKE_BINARY_DIR}/${proj}-src
       BINARY_DIR ${proj}-build
       PREFIX ${proj}-cmake
       URL ${opencv_url}
       URL_MD5 ${opencv_url_md5}
       INSTALL_COMMAND ""
       CMAKE_GENERATOR ${gen}
       CMAKE_ARGS
         ${ep_common_args}
         -DBUILD_DOCS:BOOL=OFF
         -DBUILD_TESTS:BOOL=OFF
         -DBUILD_EXAMPLES:BOOL=OFF
         -DBUILD_DOXYGEN_DOCS:BOOL=OFF
         -DWITH_CUDA:BOOL=ON
         ${additional_cmake_args}
       DEPENDS ${proj_DEPENDENCIES}
     )
 
     set(OpenCV_DIR ${CMAKE_CURRENT_BINARY_DIR}/${proj}-build)
 
   else()
 
     mitkMacroEmptyExternalProject(${proj} "${proj_DEPENDENCIES}")
 
   endif()
 
 endif()
diff --git a/CMakeExternals/VTK.cmake b/CMakeExternals/VTK.cmake
index fd16c17ea8..7c54e9203c 100644
--- a/CMakeExternals/VTK.cmake
+++ b/CMakeExternals/VTK.cmake
@@ -1,91 +1,94 @@
 #-----------------------------------------------------------------------------
 # VTK
 #-----------------------------------------------------------------------------
 
 if(WIN32)
   option(VTK_USE_SYSTEM_FREETYPE OFF)
 else(WIN32)
   option(VTK_USE_SYSTEM_FREETYPE ON)
 endif(WIN32)
 
 # Sanity checks
 if(DEFINED VTK_DIR AND NOT EXISTS ${VTK_DIR})
   message(FATAL_ERROR "VTK_DIR variable is defined but corresponds to non-existing directory")
 endif()
 
 set(proj VTK)
 set(proj_DEPENDENCIES )
 set(VTK_DEPENDS ${proj})
 
 if(NOT DEFINED VTK_DIR)
 
   set(additional_cmake_args )
   if(MINGW)
     set(additional_cmake_args
         -DCMAKE_USE_WIN32_THREADS:BOOL=ON
         -DCMAKE_USE_PTHREADS:BOOL=OFF
         -DVTK_USE_VIDEO4WINDOWS:BOOL=OFF # no header files provided by MinGW
         )
   endif()
 
   if(MITK_USE_Python)
     list(APPEND additional_cmake_args
          -DVTK_WRAP_PYTHON:BOOL=ON
          -DVTK_USE_TK:BOOL=OFF
          -DVTK_WINDOWS_PYTHON_DEBUGGABLE:BOOL=OFF
-         -DPYTHON_DEBUG_LIBRARY:FILEPATH=${PYTHON_DEBUG_LIBRARY}
-         -DPYTHON_INCLUDE_DIR:PATH=${PYTHON_INCLUDE_DIR}
-         -DPYTHON_LIBRARY:FILEPATH=${PYTHON_LIBRARY}
+         #-DPYTHON_DEBUG_LIBRARY=${PYTHON_DEBUG_LIBRARY}
+         #-DPYTHON_INCLUDE_DIR=${PYTHON_INCLUDE_DIR}
+         #-DPYTHON_LIBRARY=${MITK_PYTHON_PLAIN_LIBRARY}
+         #-DPYTHON_EXECUTABLE=${PYTHON_EXECUTABLE}
+         #-DPYTHON_LIBRARIES=${PYTHON_LIBRARY}
+         #-DPYTHON_DEBUG_LIBRARIES=${PYTHON_DEBUG_LIBRARIES}
         )
   endif()
 
   if(MITK_USE_QT)
     list(APPEND additional_cmake_args
         -DDESIRED_QT_VERSION:STRING=4
         -DVTK_USE_GUISUPPORT:BOOL=ON
         -DVTK_USE_QVTK_QTOPENGL:BOOL=OFF
         -DVTK_USE_QT:BOOL=ON
         -DQT_QMAKE_EXECUTABLE:FILEPATH=${QT_QMAKE_EXECUTABLE}
      )
   endif()
 
   set(VTK_URL ${MITK_THIRDPARTY_DOWNLOAD_PREFIX_URL}/vtk-5.10.0.tar.gz)
   set(VTK_URL_MD5 a0363f78910f466ba8f1bd5ab5437cb9)
 
   if(APPLE)
     set(VTK_PATCH_COMMAND ${CMAKE_COMMAND} -DTEMPLATE_FILE:FILEPATH=${MITK_SOURCE_DIR}/CMakeExternals/EmptyFileForPatching.dummy -P ${MITK_SOURCE_DIR}/CMakeExternals/PatchVTK-5.10-Mac.cmake)
   endif()
 
     ExternalProject_Add(${proj}
     SOURCE_DIR ${CMAKE_BINARY_DIR}/${proj}-src
     BINARY_DIR ${proj}-build
     PREFIX ${proj}-cmake
     URL ${VTK_URL}
     URL_MD5 ${VTK_URL_MD5}
     INSTALL_COMMAND ""
     PATCH_COMMAND ${VTK_PATCH_COMMAND}
     CMAKE_GENERATOR ${gen}
     CMAKE_ARGS
         ${ep_common_args}
         -DVTK_WRAP_TCL:BOOL=OFF
         -DVTK_WRAP_PYTHON:BOOL=OFF
         -DVTK_WRAP_JAVA:BOOL=OFF
         -DBUILD_SHARED_LIBS:BOOL=ON
         -DVTK_USE_PARALLEL:BOOL=ON
         -DVTK_USE_CHARTS:BOOL=OFF
         -DVTK_USE_QTCHARTS:BOOL=ON
         -DVTK_USE_GEOVIS:BOOL=OFF
         -DVTK_USE_SYSTEM_FREETYPE:BOOL=${VTK_USE_SYSTEM_FREETYPE}
         -DVTK_USE_QVTK_QTOPENGL:BOOL=OFF
         -DVTK_LEGACY_REMOVE:BOOL=ON
         ${additional_cmake_args}
      DEPENDS ${proj_DEPENDENCIES}
     )
 
   set(VTK_DIR ${CMAKE_CURRENT_BINARY_DIR}/${proj}-build)
 
 else()
 
   mitkMacroEmptyExternalProject(${proj} "${proj_DEPENDENCIES}")
 
 endif()
diff --git a/CMakeLists.txt b/CMakeLists.txt
index e6b167b703..865e03165d 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -1,943 +1,961 @@
 if(APPLE)
   # With XCode 4.3, the SDK location changed. Older CMake
   # versions are not able to find it.
   cmake_minimum_required(VERSION 2.8.8)
 else()
   cmake_minimum_required(VERSION 2.8.4)
 endif()
 
 #-----------------------------------------------------------------------------
 # Set a default build type if none was specified
 #-----------------------------------------------------------------------------
 
 if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES)
   message(STATUS "Setting build type to 'Debug' as none was specified.")
   set(CMAKE_BUILD_TYPE Debug CACHE STRING "Choose the type of build." FORCE)
 
   # Set the possible values of build type for cmake-gui
   set_property(CACHE CMAKE_BUILD_TYPE PROPERTY
                STRINGS "Debug" "Release" "MinSizeRel" "RelWithDebInfo")
 endif()
 
 #-----------------------------------------------------------------------------
 # Superbuild Option - Enabled by default
 #-----------------------------------------------------------------------------
 
 option(MITK_USE_SUPERBUILD "Build MITK and the projects it depends on via SuperBuild.cmake." ON)
 
 if(MITK_USE_SUPERBUILD)
   project(MITK-superbuild)
   set(MITK_SOURCE_DIR ${PROJECT_SOURCE_DIR})
   set(MITK_BINARY_DIR ${PROJECT_BINARY_DIR})
 else()
   project(MITK)
 endif()
 
 #-----------------------------------------------------------------------------
 # Warn if source or build path is too long
 #-----------------------------------------------------------------------------
 
 if(WIN32)
   set(_src_dir_length_max 50)
   set(_bin_dir_length_max 50)
   if(MITK_USE_SUPERBUILD)
     set(_src_dir_length_max 43) # _src_dir_length_max - strlen(ITK-src)
     set(_bin_dir_length_max 40) # _bin_dir_length_max - strlen(MITK-build)
   endif()
 
   string(LENGTH "${MITK_SOURCE_DIR}" _src_n)
   string(LENGTH "${MITK_BINARY_DIR}" _bin_n)
 
   # The warnings should be converted to errors
   if(_src_n GREATER _src_dir_length_max)
     message(WARNING "MITK source code directory path length is too long (${_src_n} > ${_src_dir_length_max})."
                     "Please move the MITK source code directory to a directory with a shorter path." )
   endif()
   if(_bin_n GREATER _bin_dir_length_max)
     message(WARNING "MITK build directory path length is too long (${_bin_n} > ${_bin_dir_length_max})."
                     "Please move the MITK build directory to a directory with a shorter path." )
   endif()
 endif()
 
 #-----------------------------------------------------------------------------
 # See http://cmake.org/cmake/help/cmake-2-8-docs.html#section_Policies for details
 #-----------------------------------------------------------------------------
 
 set(project_policies
   CMP0001 # NEW: CMAKE_BACKWARDS_COMPATIBILITY should no longer be used.
   CMP0002 # NEW: Logical target names must be globally unique.
   CMP0003 # NEW: Libraries linked via full path no longer produce linker search paths.
   CMP0004 # NEW: Libraries linked may NOT have leading or trailing whitespace.
   CMP0005 # NEW: Preprocessor definition values are now escaped automatically.
   CMP0006 # NEW: Installing MACOSX_BUNDLE targets requires a BUNDLE DESTINATION.
   CMP0007 # NEW: List command no longer ignores empty elements.
   CMP0008 # NEW: Libraries linked by full-path must have a valid library file name.
   CMP0009 # NEW: FILE GLOB_RECURSE calls should not follow symlinks by default.
   CMP0010 # NEW: Bad variable reference syntax is an error.
   CMP0011 # NEW: Included scripts do automatic cmake_policy PUSH and POP.
   CMP0012 # NEW: if() recognizes numbers and boolean constants.
   CMP0013 # NEW: Duplicate binary directories are not allowed.
   CMP0014 # NEW: Input directories must have CMakeLists.txt
   )
 foreach(policy ${project_policies})
   if(POLICY ${policy})
     cmake_policy(SET ${policy} NEW)
   endif()
 endforeach()
 
 #-----------------------------------------------------------------------------
 # Update CMake module path
 #------------------------------------------------------------------------------
 
 set(CMAKE_MODULE_PATH
   ${MITK_SOURCE_DIR}/CMake
   ${CMAKE_MODULE_PATH}
   )
 
 #-----------------------------------------------------------------------------
 # CMake function(s) and macro(s)
 #-----------------------------------------------------------------------------
 
 include(mitkMacroEmptyExternalProject)
 include(mitkFunctionGenerateProjectXml)
 include(mitkFunctionSuppressWarnings)
 
 SUPPRESS_VC_DEPRECATED_WARNINGS()
 
 #-----------------------------------------------------------------------------
 # Output directories.
 #-----------------------------------------------------------------------------
 
 foreach(type LIBRARY RUNTIME ARCHIVE)
   # Make sure the directory exists
   if(DEFINED MITK_CMAKE_${type}_OUTPUT_DIRECTORY
      AND NOT EXISTS ${MITK_CMAKE_${type}_OUTPUT_DIRECTORY})
     message("Creating directory MITK_CMAKE_${type}_OUTPUT_DIRECTORY: ${MITK_CMAKE_${type}_OUTPUT_DIRECTORY}")
     file(MAKE_DIRECTORY "${MITK_CMAKE_${type}_OUTPUT_DIRECTORY}")
   endif()
 
   if(MITK_USE_SUPERBUILD)
     set(output_dir ${MITK_BINARY_DIR}/bin)
     if(NOT DEFINED MITK_CMAKE_${type}_OUTPUT_DIRECTORY)
       set(MITK_CMAKE_${type}_OUTPUT_DIRECTORY ${MITK_BINARY_DIR}/MITK-build/bin)
     endif()
   else()
     if(NOT DEFINED MITK_CMAKE_${type}_OUTPUT_DIRECTORY)
       set(output_dir ${MITK_BINARY_DIR}/bin)
     else()
       set(output_dir ${MITK_CMAKE_${type}_OUTPUT_DIRECTORY})
     endif()
   endif()
   set(CMAKE_${type}_OUTPUT_DIRECTORY ${output_dir} CACHE INTERNAL "Single output directory for building all libraries.")
   mark_as_advanced(CMAKE_${type}_OUTPUT_DIRECTORY)
 endforeach()
 
 #-----------------------------------------------------------------------------
 # Additional MITK Options (also shown during superbuild)
 #-----------------------------------------------------------------------------
 
 option(BUILD_SHARED_LIBS "Build MITK with shared libraries" ON)
 option(WITH_COVERAGE "Enable/Disable coverage" OFF)
 option(BUILD_TESTING "Test the project" ON)
 
 option(MITK_BUILD_ALL_APPS "Build all MITK applications" OFF)
 set(MITK_BUILD_TUTORIAL OFF CACHE INTERNAL "Deprecated! Use MITK_BUILD_EXAMPLES instead!")
 option(MITK_BUILD_EXAMPLES "Build the MITK Examples" ${MITK_BUILD_TUTORIAL})
 option(MITK_USE_Boost "Use the Boost C++ library" OFF)
 option(MITK_USE_BLUEBERRY "Build the BlueBerry platform" ON)
 option(MITK_USE_CTK "Use CTK in MITK" ${MITK_USE_BLUEBERRY})
 option(MITK_USE_QT "Use Nokia's Qt library" ${MITK_USE_CTK})
 option(MITK_USE_DCMTK "EXPERIMENTAL, superbuild only: Use DCMTK in MITK" ${MITK_USE_CTK})
 option(MITK_DCMTK_BUILD_SHARED_LIBS "EXPERIMENTAL, superbuild only: build DCMTK as shared libs" OFF)
 option(MITK_USE_OpenCV "Use Intel's OpenCV library" OFF)
 option(MITK_USE_OpenCL "Use OpenCL GPU-Computing library" OFF)
 option(MITK_USE_Python "Use Python wrapping in MITK" OFF)
 set(MITK_USE_CableSwig ${MITK_USE_Python})
 if(MITK_USE_Python)
-  include("${CMAKE_CURRENT_SOURCE_DIR}/Cmake/PackageDepends/MITK_PythonLibs_Config.cmake")
+  #FIND_PACKAGE(PythonLibs REQUIRED)
+  #set(PYTHON_LIBRARY "" CACHE FILEPATH "Specify where to find the Python library for the superbuild")
+
+  #FIND_PACKAGE(PythonInterp REQUIRED)
+  #FIND_PACKAGE(PythonLibs REQUIRED)
+  #list(LENGTH PYTHON_LIBRARY pythLibsListLength)
+  # on windows PYTHON_LIBRARY is "optimized;C:/Python27/libs/python27.lib;debug;C:/Python27/libs/python27_d.lib"
+  # this struggles with passing the var through the superbuild
+  #SET(MITK_PYTHON_NO_OPTIMIZED_LIBRARY ${PYTHON_LIBRARY})
+  #if( pythLibsListLength EQUAL 4 )
+    #list(GET PYTHON_LIBRARY 1 MITK_PYTHON_NO_OPTIMIZED_LIBRARY)
+  #endif()
+  #message("PYTHON_LIBRARY ${PYTHON_LIBRARY}")
+  #message("MITK_PYTHON_PLAIN_LIBRARY ${MITK_PYTHON_NO_OPTIMIZED_LIBRARY}")
+  #message("PYTHON_INCLUDE_DIR ${PYTHON_INCLUDE_DIR}")
+  #message("PYTHON_DEBUG_LIBRARY ${PYTHON_DEBUG_LIBRARY}")
+  #message("PYTHON_EXECUTABLE ${PYTHON_EXECUTABLE}")
+  #message("PYTHON_LIBRARIES ${PYTHON_LIBRARIES}")
+  #message("PYTHON_DEBUG_LIBRARIES ${PYTHON_DEBUG_LIBRARIES}")
 endif()
 
 mark_as_advanced(MITK_BUILD_ALL_APPS
                  MITK_USE_CTK
                  MITK_USE_DCMTK
                 )
 
 
 if(MITK_USE_Boost)
   option(MITK_USE_SYSTEM_Boost "Use the system Boost" OFF)
   set(MITK_USE_Boost_LIBRARIES "" CACHE STRING "A semi-colon separated list of required Boost libraries")
 endif()
 
 if(MITK_USE_BLUEBERRY)
   option(MITK_BUILD_ALL_PLUGINS "Build all MITK plugins" OFF)
   mark_as_advanced(MITK_BUILD_ALL_PLUGINS)
 
   if(NOT MITK_USE_CTK)
     message("Forcing MITK_USE_CTK to ON because of MITK_USE_BLUEBERRY")
     set(MITK_USE_CTK ON CACHE BOOL "Use CTK in MITK" FORCE)
   endif()
 endif()
 
 if(MITK_USE_CTK)
   if(NOT MITK_USE_QT)
     message("Forcing MITK_USE_QT to ON because of MITK_USE_CTK")
     set(MITK_USE_QT ON CACHE BOOL "Use Nokia's Qt library in MITK" FORCE)
   endif()
   if(NOT MITK_USE_DCMTK)
     message("Setting MITK_USE_DCMTK to ON because DCMTK needs to be build for CTK")
     set(MITK_USE_DCMTK ON CACHE BOOL "Use DCMTK in MITK" FORCE)
   endif()
 endif()
 
 if(MITK_USE_QT)
   # find the package at the very beginning, so that QT4_FOUND is available
   find_package(Qt4 4.6.2 REQUIRED)
 endif()
 
 
 # Customize the default pixel types for multiplex macros
 
 set(MITK_ACCESSBYITK_INTEGRAL_PIXEL_TYPES
     "int, unsigned int, short, unsigned short, char, unsigned char"
     CACHE STRING "List of integral pixel types used in AccessByItk and InstantiateAccessFunction macros")
 
 set(MITK_ACCESSBYITK_FLOATING_PIXEL_TYPES
     "double, float"
     CACHE STRING "List of floating pixel types used in AccessByItk and InstantiateAccessFunction macros")
 
 set(MITK_ACCESSBYITK_COMPOSITE_PIXEL_TYPES
     "itk::RGBPixel<unsigned char>, itk::RGBAPixel<unsigned char>"
     CACHE STRING "List of composite pixel types used in AccessByItk and InstantiateAccessFunction macros")
 
 set(MITK_ACCESSBYITK_DIMENSIONS
     "2,3"
     CACHE STRING "List of dimensions used in AccessByItk and InstantiateAccessFunction macros")
 
 mark_as_advanced(MITK_ACCESSBYITK_INTEGRAL_PIXEL_TYPES
                  MITK_ACCESSBYITK_FLOATING_PIXEL_TYPES
                  MITK_ACCESSBYITK_COMPOSITE_PIXEL_TYPES
                  MITK_ACCESSBYITK_DIMENSIONS
                 )
 
 # consistency checks
 
 if(NOT MITK_ACCESSBYITK_INTEGRAL_PIXEL_TYPES)
   set(MITK_ACCESSBYITK_INTEGRAL_PIXEL_TYPES
       "int, unsigned int, short, unsigned short, char, unsigned char"
       CACHE STRING "List of integral pixel types used in AccessByItk and InstantiateAccessFunction macros" FORCE)
 endif()
 
 if(NOT MITK_ACCESSBYITK_FLOATING_PIXEL_TYPES)
   set(MITK_ACCESSBYITK_FLOATING_PIXEL_TYPES
       "double, float"
       CACHE STRING "List of floating pixel types used in AccessByItk and InstantiateAccessFunction macros" FORCE)
 endif()
 
 if(NOT MITK_ACCESSBYITK_COMPOSITE_PIXEL_TYPES)
   set(MITK_ACCESSBYITK_COMPOSITE_PIXEL_TYPES
     "itk::RGBPixel<unsigned char>, itk::RGBAPixel<unsigned char>"
     CACHE STRING "List of composite pixel types used in AccessByItk and InstantiateAccessFunction macros" FORCE)
 endif()
 
 if(NOT MITK_ACCESSBYITK_DIMENSIONS)
   set(MITK_ACCESSBYITK_DIMENSIONS
       "2,3"
       CACHE STRING "List of dimensions used in AccessByItk and InstantiateAccessFunction macros")
 endif()
 
 #-----------------------------------------------------------------------------
 # Additional CXX/C Flags
 #-----------------------------------------------------------------------------
 
 set(ADDITIONAL_C_FLAGS "" CACHE STRING "Additional C Flags")
 mark_as_advanced(ADDITIONAL_C_FLAGS)
 set(ADDITIONAL_CXX_FLAGS "" CACHE STRING "Additional CXX Flags")
 mark_as_advanced(ADDITIONAL_CXX_FLAGS)
 
 #-----------------------------------------------------------------------------
 # Project.xml
 #-----------------------------------------------------------------------------
 
 # A list of topologically ordered targets
 set(CTEST_PROJECT_SUBPROJECTS)
 if(MITK_USE_BLUEBERRY)
   list(APPEND CTEST_PROJECT_SUBPROJECTS BlueBerry)
 endif()
 
 list(APPEND CTEST_PROJECT_SUBPROJECTS
   MITK-Core
   MITK-CoreUI
   MITK-IGT
   MITK-ToF
   MITK-DTI
   MITK-Registration
   MITK-Modules # all modules not contained in a specific subproject
   MITK-Plugins # all plugins not contained in a specific subproject
   MITK-Examples
   Unlabeled # special "subproject" catching all unlabeled targets and tests
   )
 
 # Configure CTestConfigSubProject.cmake that could be used by CTest scripts
 configure_file(${MITK_SOURCE_DIR}/CTestConfigSubProject.cmake.in
                ${MITK_BINARY_DIR}/CTestConfigSubProject.cmake)
 
 if(CTEST_PROJECT_ADDITIONAL_TARGETS)
   # those targets will be executed at the end of the ctest driver script
   # and they also get their own subproject label
   set(subproject_list "${CTEST_PROJECT_SUBPROJECTS};${CTEST_PROJECT_ADDITIONAL_TARGETS}")
 else()
   set(subproject_list "${CTEST_PROJECT_SUBPROJECTS}")
 endif()
 
 # Generate Project.xml file expected by the CTest driver script
 mitkFunctionGenerateProjectXml(${MITK_BINARY_DIR} MITK "${subproject_list}" ${MITK_USE_SUPERBUILD})
 
 #-----------------------------------------------------------------------------
 # Superbuild script
 #-----------------------------------------------------------------------------
 
 if(MITK_USE_SUPERBUILD)
   include("${CMAKE_CURRENT_SOURCE_DIR}/SuperBuild.cmake")
   return()
 endif()
 
 #*****************************************************************************
 #****************************  END OF SUPERBUILD  ****************************
 #*****************************************************************************
 
 #-----------------------------------------------------------------------------
 # CMake function(s) and macro(s)
 #-----------------------------------------------------------------------------
 
 include(CheckCXXSourceCompiles)
 include(mitkFunctionCheckCompilerFlags)
 include(mitkFunctionGetGccVersion)
 include(MacroParseArguments)
 include(mitkFunctionSuppressWarnings) # includes several functions
 include(mitkFunctionOrganizeSources)
 include(mitkFunctionGetVersion)
 include(mitkFunctionGetVersionDescription)
 include(mitkFunctionCreateWindowsBatchScript)
 include(mitkFunctionInstallProvisioningFiles)
 include(mitkFunctionInstallAutoLoadModules)
 include(mitkFunctionCompileSnippets)
 include(mitkMacroCreateModuleConf)
 include(mitkMacroCreateModule)
 include(mitkMacroCheckModule)
 include(mitkMacroCreateModuleTests)
 include(mitkFunctionAddCustomModuleTest)
 include(mitkMacroUseModule)
 include(mitkMacroMultiplexPicType)
 include(mitkMacroInstall)
 include(mitkMacroInstallHelperApp)
 include(mitkMacroInstallTargets)
 include(mitkMacroGenerateToolsLibrary)
 include(mitkMacroGetLinuxDistribution)
 
 #-----------------------------------------------------------------------------
 # Prerequesites
 #-----------------------------------------------------------------------------
 
 find_package(ITK REQUIRED)
 find_package(VTK REQUIRED)
 
 if(ITK_USE_SYSTEM_GDCM)
   find_package(GDCM PATHS ${ITK_GDCM_DIR} REQUIRED)
 endif()
 
 #-----------------------------------------------------------------------------
 # Set MITK specific options and variables (NOT available during superbuild)
 #-----------------------------------------------------------------------------
 
 # ASK THE USER TO SHOW THE CONSOLE WINDOW FOR CoreApp and mitkWorkbench
 option(MITK_SHOW_CONSOLE_WINDOW "Use this to enable or disable the console window when starting MITK GUI Applications" ON)
 mark_as_advanced(MITK_SHOW_CONSOLE_WINDOW)
 
 # TODO: check if necessary
 option(USE_ITKZLIB "Use the ITK zlib for pic compression." ON)
 mark_as_advanced(USE_ITKZLIB)
 
 if(NOT MITK_FAST_TESTING)
   if(DEFINED MITK_CTEST_SCRIPT_MODE
       AND (MITK_CTEST_SCRIPT_MODE STREQUAL "continuous" OR MITK_CTEST_SCRIPT_MODE STREQUAL "experimental") )
     set(MITK_FAST_TESTING 1)
   endif()
 endif()
 
 #-----------------------------------------------------------------------------
 # Get MITK version info
 #-----------------------------------------------------------------------------
 
 mitkFunctionGetVersion(${MITK_SOURCE_DIR} MITK)
 mitkFunctionGetVersionDescription(${MITK_SOURCE_DIR} MITK)
 
 #-----------------------------------------------------------------------------
 # Installation preparation
 #
 # These should be set before any MITK install macros are used
 #-----------------------------------------------------------------------------
 
 # on Mac OSX all BlueBerry plugins get copied into every
 # application bundle (.app directory) specified here
 if(MITK_USE_BLUEBERRY AND APPLE)
 
   include("${CMAKE_CURRENT_SOURCE_DIR}/Applications/AppList.cmake")
 
   foreach(mitk_app ${MITK_APPS})
     # extract option_name
     string(REPLACE "^^" "\\;" target_info ${mitk_app})
     set(target_info_list ${target_info})
     list(GET target_info_list 1 option_name)
     list(GET target_info_list 0 app_name)
     # check if the application is enabled
     if(${option_name} OR MITK_BUILD_ALL_APPS)
       set(MACOSX_BUNDLE_NAMES ${MACOSX_BUNDLE_NAMES} ${app_name})
     endif()
   endforeach()
 
 endif()
 
 #-----------------------------------------------------------------------------
 # Set symbol visibility Flags
 #-----------------------------------------------------------------------------
 
 # MinGW does not export all symbols automatically, so no need to set flags
 if(CMAKE_COMPILER_IS_GNUCXX AND NOT MINGW)
   set(VISIBILITY_CXX_FLAGS ) #"-fvisibility=hidden -fvisibility-inlines-hidden")
 endif()
 
 #-----------------------------------------------------------------------------
 # Set coverage Flags
 #-----------------------------------------------------------------------------
 
 if(WITH_COVERAGE)
   if("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
     set(coverage_flags "-g -fprofile-arcs -ftest-coverage -O0 -DNDEBUG")
     set(COVERAGE_CXX_FLAGS ${coverage_flags})
     set(COVERAGE_C_FLAGS ${coverage_flags})
   endif()
 endif()
 
 #-----------------------------------------------------------------------------
 # MITK C/CXX Flags
 #-----------------------------------------------------------------------------
 
 set(MITK_C_FLAGS "${COVERAGE_C_FLAGS} ${ADDITIONAL_C_FLAGS}")
 set(MITK_CXX_FLAGS "${VISIBILITY_CXX_FLAGS} ${COVERAGE_CXX_FLAGS} ${ADDITIONAL_CXX_FLAGS}")
 
 include(mitkSetupC++0xVariables)
 
 set(cflags )
 if(WIN32)
   set(cflags "${cflags} -DPOCO_NO_UNWINDOWS -DWIN32_LEAN_AND_MEAN")
 endif()
 
 if(CMAKE_COMPILER_IS_GNUCXX)
   set(cflags "${cflags} -Wall -Wextra -Wpointer-arith -Winvalid-pch -Wcast-align -Wwrite-strings")
 
   mitkFunctionCheckCompilerFlags("-fdiagnostics-show-option" cflags)
   mitkFunctionCheckCompilerFlags("-Wl,--no-undefined" cflags)
   mitkFunctionCheckCompilerFlags("-Wl,--as-needed" cflags)
 
   if(MITK_USE_C++0x)
     mitkFunctionCheckCompilerFlags("-std=c++0x" MITK_CXX_FLAGS)
   endif()
 
   mitkFunctionGetGccVersion(${CMAKE_CXX_COMPILER} GCC_VERSION)
   # With older version of gcc supporting the flag -fstack-protector-all, an extra dependency to libssp.so
   # is introduced. If gcc is smaller than 4.4.0 and the build type is Release let's not include the flag.
   # Doing so should allow to build package made for distribution using older linux distro.
   if(${GCC_VERSION} VERSION_GREATER "4.4.0" OR (CMAKE_BUILD_TYPE STREQUAL "Debug" AND ${GCC_VERSION} VERSION_LESS "4.4.0"))
     mitkFunctionCheckCompilerFlags("-fstack-protector-all" cflags)
   endif()
   if(MINGW)
     # suppress warnings about auto imported symbols
     set(MITK_CXX_FLAGS "-Wl,--enable-auto-import ${MITK_CXX_FLAGS}")
     # we need to define a Windows version
     set(MITK_CXX_FLAGS "-D_WIN32_WINNT=0x0500 ${MITK_CXX_FLAGS}")
   endif()
 
   #set(MITK_CXX_FLAGS "-Woverloaded-virtual -Wold-style-cast -Wstrict-null-sentinel -Wsign-promo ${MITK_CXX_FLAGS}")
   set(MITK_CXX_FLAGS "-Woverloaded-virtual -Wstrict-null-sentinel ${MITK_CXX_FLAGS}")
   set(MITK_CXX_FLAGS_RELEASE "-D_FORTIFY_SOURCE=2 ${MITK_CXX_FLAGS_RELEASE}")
 
 endif()
 
 set(MITK_C_FLAGS "${cflags} ${MITK_C_FLAGS}")
 set(MITK_CXX_FLAGS "${cflags} ${MITK_CXX_FLAGS}")
 
 #-----------------------------------------------------------------------------
 # MITK Packages
 #-----------------------------------------------------------------------------
 
 set(MITK_MODULES_PACKAGE_DEPENDS_DIR ${MITK_SOURCE_DIR}/CMake/PackageDepends)
 set(MODULES_PACKAGE_DEPENDS_DIRS ${MITK_MODULES_PACKAGE_DEPENDS_DIR})
 
 #-----------------------------------------------------------------------------
 # Testing
 #-----------------------------------------------------------------------------
 
 if(BUILD_TESTING)
   enable_testing()
   include(CTest)
   mark_as_advanced(TCL_TCLSH DART_ROOT)
 
   option(MITK_ENABLE_GUI_TESTING OFF "Enable the MITK GUI tests")
 
   # Setup file for setting custom ctest vars
   configure_file(
     CMake/CTestCustom.cmake.in
     ${MITK_BINARY_DIR}/CTestCustom.cmake
     @ONLY
     )
 
   # Configuration for the CMake-generated test driver
   set(CMAKE_TESTDRIVER_EXTRA_INCLUDES "#include <stdexcept>")
   set(CMAKE_TESTDRIVER_BEFORE_TESTMAIN "
     try
       {")
   set(CMAKE_TESTDRIVER_AFTER_TESTMAIN "    }
       catch( std::exception & excp )
         {
         fprintf(stderr,\"%s\\n\",excp.what());
         return EXIT_FAILURE;
         }
       catch( ... )
         {
         printf(\"Exception caught in the test driver\\n\");
         return EXIT_FAILURE;
         }
       ")
 
   set(MITK_TEST_OUTPUT_DIR "${MITK_BINARY_DIR}/test_output")
   if(NOT EXISTS ${MITK_TEST_OUTPUT_DIR})
     file(MAKE_DIRECTORY ${MITK_TEST_OUTPUT_DIR})
   endif()
 
   # Test the external project template
   if(MITK_USE_BLUEBERRY)
     include(mitkTestProjectTemplate)
   endif()
 
   # Test the package target
   include(mitkPackageTest)
 endif()
 
 configure_file(mitkTestingConfig.h.in ${MITK_BINARY_DIR}/mitkTestingConfig.h)
 
 #-----------------------------------------------------------------------------
 # MITK_SUPERBUILD_BINARY_DIR
 #-----------------------------------------------------------------------------
 
 # If MITK_SUPERBUILD_BINARY_DIR isn't defined, it means MITK is *NOT* build using Superbuild.
 # In that specific case, MITK_SUPERBUILD_BINARY_DIR should default to MITK_BINARY_DIR
 if(NOT DEFINED MITK_SUPERBUILD_BINARY_DIR)
   set(MITK_SUPERBUILD_BINARY_DIR ${MITK_BINARY_DIR})
 endif()
 
 #-----------------------------------------------------------------------------
 # Compile Utilities and set-up MITK variables
 #-----------------------------------------------------------------------------
 
 include(mitkSetupVariables)
 
   #-----------------------------------------------------------------------------
   # Cleanup
   #-----------------------------------------------------------------------------
 
   file(GLOB _MODULES_CONF_FILES ${PROJECT_BINARY_DIR}/${MODULES_CONF_DIRNAME}/*.cmake)
   if(_MODULES_CONF_FILES)
     file(REMOVE ${_MODULES_CONF_FILES})
   endif()
 
 add_subdirectory(Utilities)
 
 if(MITK_USE_BLUEBERRY)
 
   # We need to hack a little bit because MITK applications may need
   # to enable certain BlueBerry plug-ins. However, these plug-ins
   # are validated separately from the MITK plug-ins and know nothing
   # about potential MITK plug-in dependencies of the applications. Hence
   # we cannot pass the MITK application list to the BlueBerry
   # ctkMacroSetupPlugins call but need to extract the BlueBerry dependencies
   # from the applications and set them explicitly.
 
   include("${CMAKE_CURRENT_SOURCE_DIR}/Applications/AppList.cmake")
 
   foreach(mitk_app ${MITK_APPS})
     # extract target_dir and option_name
     string(REPLACE "^^" "\\;" target_info ${mitk_app})
     set(target_info_list ${target_info})
     list(GET target_info_list 0 target_dir)
     list(GET target_info_list 1 option_name)
     # check if the application is enabled and if target_libraries.cmake exists
     if((${option_name} OR MITK_BUILD_ALL_APPS) AND EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/Applications/${target_dir}/target_libraries.cmake")
       include("${CMAKE_CURRENT_SOURCE_DIR}/Applications/${target_dir}/target_libraries.cmake")
       foreach(_target_dep ${target_libraries})
         if(_target_dep MATCHES org_blueberry_)
           string(REPLACE _ . _app_bb_dep ${_target_dep})
           # explicitly set the build option for the BlueBerry plug-in
           set(BLUEBERRY_BUILD_${_app_bb_dep} ON CACHE BOOL "Build the ${_app_bb_dep} plug-in")
         endif()
       endforeach()
     endif()
   endforeach()
 
   set(mbilog_DIR "${mbilog_BINARY_DIR}")
 
   if(MITK_BUILD_ALL_PLUGINS)
     set(BLUEBERRY_BUILD_ALL_PLUGINS ON)
   endif()
 
   add_subdirectory(BlueBerry)
 
   set(BlueBerry_DIR ${CMAKE_CURRENT_BINARY_DIR}/BlueBerry
       CACHE PATH "The directory containing a CMake configuration file for BlueBerry" FORCE)
 
   include(mitkMacroCreateCTKPlugin)
 
 endif()
 
 #-----------------------------------------------------------------------------
 # Set C/CXX Flags for MITK code
 #-----------------------------------------------------------------------------
 
 set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${MITK_CXX_FLAGS}")
 set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} ${MITK_CXX_FLAGS_RELEASE}")
 set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${MITK_C_FLAGS}")
 
 if(MITK_USE_QT)
   add_definitions(-DQWT_DLL)
 endif()
 
 #-----------------------------------------------------------------------------
 # Add custom targets representing CDash subprojects
 #-----------------------------------------------------------------------------
 
 foreach(subproject ${CTEST_PROJECT_SUBPROJECTS})
   if(NOT TARGET ${subproject} AND NOT subproject MATCHES "Unlabeled")
     add_custom_target(${subproject})
   endif()
 endforeach()
 
 #-----------------------------------------------------------------------------
 # Add subdirectories
 #-----------------------------------------------------------------------------
 
 link_directories(${MITK_LINK_DIRECTORIES})
 
 add_subdirectory(Core)
 add_subdirectory(Modules)
 
 if(MITK_USE_BLUEBERRY)
 
   find_package(BlueBerry REQUIRED)
 
   set(MITK_DEFAULT_SUBPROJECTS MITK-Plugins)
 
   # Plug-in testing (needs some work to be enabled again)
   if(BUILD_TESTING)
     include(berryTestingHelpers)
 
     set(BLUEBERRY_UI_TEST_APP "${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/CoreApp")
     get_target_property(_is_macosx_bundle CoreApp MACOSX_BUNDLE)
     if(APPLE AND _is_macosx_bundle)
       set(BLUEBERRY_UI_TEST_APP "${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/CoreApp.app/Contents/MacOS/CoreApp")
     endif()
 
     set(BLUEBERRY_TEST_APP_ID "org.mitk.qt.coreapplication")
   endif()
 
   include("${CMAKE_CURRENT_SOURCE_DIR}/Plugins/PluginList.cmake")
   set(mitk_plugins_fullpath )
   foreach(mitk_plugin ${MITK_EXT_PLUGINS})
     list(APPEND mitk_plugins_fullpath Plugins/${mitk_plugin})
   endforeach()
 
   if(EXISTS ${MITK_PRIVATE_MODULES}/PluginList.cmake)
     include(${MITK_PRIVATE_MODULES}/PluginList.cmake)
 
     foreach(mitk_plugin ${MITK_PRIVATE_PLUGINS})
       list(APPEND mitk_plugins_fullpath ${MITK_PRIVATE_MODULES}/${mitk_plugin})
     endforeach()
   endif()
 
   # Specify which plug-ins belong to this project
   macro(GetMyTargetLibraries all_target_libraries varname)
     set(re_ctkplugin_mitk "^org_mitk_[a-zA-Z0-9_]+$")
     set(re_ctkplugin_bb "^org_blueberry_[a-zA-Z0-9_]+$")
     set(_tmp_list)
     list(APPEND _tmp_list ${all_target_libraries})
     ctkMacroListFilter(_tmp_list re_ctkplugin_mitk re_ctkplugin_bb OUTPUT_VARIABLE ${varname})
   endmacro()
 
   # Get infos about application directories and build options
   include("${CMAKE_CURRENT_SOURCE_DIR}/Applications/AppList.cmake")
   set(mitk_apps_fullpath )
   foreach(mitk_app ${MITK_APPS})
     list(APPEND mitk_apps_fullpath "${CMAKE_CURRENT_SOURCE_DIR}/Applications/${mitk_app}")
   endforeach()
 
   ctkMacroSetupPlugins(${mitk_plugins_fullpath}
                        BUILD_OPTION_PREFIX MITK_BUILD_
                        APPS ${mitk_apps_fullpath}
                        BUILD_ALL ${MITK_BUILD_ALL_PLUGINS}
                        COMPACT_OPTIONS)
 
   set(MITK_PLUGIN_USE_FILE "${MITK_BINARY_DIR}/MitkPluginUseFile.cmake")
   if(${PROJECT_NAME}_PLUGIN_LIBRARIES)
     ctkFunctionGeneratePluginUseFile(${MITK_PLUGIN_USE_FILE})
   else()
     file(REMOVE ${MITK_PLUGIN_USE_FILE})
     set(MITK_PLUGIN_USE_FILE )
   endif()
 
 endif()
 
 # Construct a list of paths containing runtime directories
 # for MITK applications on Windows
 set(MITK_RUNTIME_PATH
     "${VTK_LIBRARY_DIRS}/%VS_BUILD_TYPE%;${ITK_LIBRARY_DIRS}/%VS_BUILD_TYPE%;${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/%VS_BUILD_TYPE%"
     )
 
 if(QT4_FOUND)
   set(MITK_RUNTIME_PATH "${MITK_RUNTIME_PATH};${QT_LIBRARY_DIR}/../bin")
 endif()
 
 if(MITK_USE_BLUEBERRY)
   set(MITK_RUNTIME_PATH "${MITK_RUNTIME_PATH};${CTK_RUNTIME_LIBRARY_DIRS}/%VS_BUILD_TYPE%")
   if(DEFINED CTK_PLUGIN_RUNTIME_OUTPUT_DIRECTORY)
     if(IS_ABSOLUTE "${CTK_PLUGIN_RUNTIME_OUTPUT_DIRECTORY}")
       set(MITK_RUNTIME_PATH "${MITK_RUNTIME_PATH};${CTK_PLUGIN_RUNTIME_OUTPUT_DIRECTORY}/%VS_BUILD_TYPE%")
     else()
       set(MITK_RUNTIME_PATH "${MITK_RUNTIME_PATH};${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${CTK_PLUGIN_RUNTIME_OUTPUT_DIRECTORY}/%VS_BUILD_TYPE%")
     endif()
   else()
     set(MITK_RUNTIME_PATH "${MITK_RUNTIME_PATH};${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/plugins/%VS_BUILD_TYPE%")
   endif()
 endif()
 
 if(GDCM_DIR)
   set(MITK_RUNTIME_PATH "${MITK_RUNTIME_PATH};${GDCM_DIR}/bin/%VS_BUILD_TYPE%")
 endif()
 
 if(OpenCV_DIR)
   set(MITK_RUNTIME_PATH "${MITK_RUNTIME_PATH};${OpenCV_DIR}/bin/%VS_BUILD_TYPE%")
 endif()
 
 # DCMTK is statically build
 #if(DCMTK_DIR)
 #  set(MITK_RUNTIME_PATH "${MITK_RUNTIME_PATH};${DCMTK_DIR}/bin/%VS_BUILD_TYPE%")
 #endif()
 
 if(MITK_USE_Boost AND MITK_USE_Boost_LIBRARIES AND NOT MITK_USE_SYSTEM_Boost)
   set(MITK_RUNTIME_PATH "${MITK_RUNTIME_PATH};${Boost_LIBRARY_DIRS}")
 endif()
 
 #-----------------------------------------------------------------------------
 # Python Wrapping
 #-----------------------------------------------------------------------------
 option(MITK_USE_Python "Build Python integration for MITK (requires CableSwig)." OFF)
 
 if(MITK_USE_Python)
   #message(STATUS "CTK_PYTHONQT_INSTALL_DIR: ${CTK_PYTHONQT_INSTALL_DIR}")
   set(MITK_RUNTIME_PATH "${MITK_RUNTIME_PATH};${CTK_PYTHONQT_INSTALL_DIR}/bin")
 endif()
 #-----------------------------------------------------------------------------
 # Documentation
 #-----------------------------------------------------------------------------
 
 add_subdirectory(Documentation)
 
 #-----------------------------------------------------------------------------
 # Installation
 #-----------------------------------------------------------------------------
 
 
 # set MITK cpack variables
 # These are the default variables, which can be overwritten ( see below )
 include(mitkSetupCPack)
 
 set(use_default_config ON)
 
 # MITK_APPS is set in Applications/AppList.cmake (included somewhere above
 # if MITK_USE_BLUEBERRY is set to ON).
 if(MITK_APPS)
 
   set(activated_apps_no 0)
   list(LENGTH MITK_APPS app_count)
 
   # Check how many apps have been enabled
   # If more than one app has been activated, the we use the
   # default CPack configuration. Otherwise that apps configuration
   # will be used, if present.
   foreach(mitk_app ${MITK_APPS})
     # extract option_name
     string(REPLACE "^^" "\\;" target_info ${mitk_app})
     set(target_info_list ${target_info})
     list(GET target_info_list 1 option_name)
     # check if the application is enabled
     if(${option_name} OR MITK_BUILD_ALL_APPS)
       MATH(EXPR activated_apps_no "${activated_apps_no} + 1")
     endif()
   endforeach()
 
   if(app_count EQUAL 1 AND (activated_apps_no EQUAL 1 OR MITK_BUILD_ALL_APPS))
     # Corner case if there is only one app in total
     set(use_project_cpack ON)
   elseif(activated_apps_no EQUAL 1 AND NOT MITK_BUILD_ALL_APPS)
     # Only one app is enabled (no "build all" flag set)
     set(use_project_cpack ON)
   else()
     # Less or more then one app is enabled
     set(use_project_cpack OFF)
   endif()
 
   foreach(mitk_app ${MITK_APPS})
     # extract target_dir and option_name
     string(REPLACE "^^" "\\;" target_info ${mitk_app})
     set(target_info_list ${target_info})
     list(GET target_info_list 0 target_dir)
     list(GET target_info_list 1 option_name)
     # check if the application is enabled
     if(${option_name} OR MITK_BUILD_ALL_APPS)
       # check whether application specific configuration files will be used
       if(use_project_cpack)
         # use files if they exist
         if(EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/Applications/${target_dir}/CPackOptions.cmake")
           include("${CMAKE_CURRENT_SOURCE_DIR}/Applications/${target_dir}/CPackOptions.cmake")
         endif()
 
         if(EXISTS "${PROJECT_SOURCE_DIR}/Applications/${target_dir}/CPackConfig.cmake.in")
           set(CPACK_PROJECT_CONFIG_FILE "${PROJECT_BINARY_DIR}/Applications/${target_dir}/CPackConfig.cmake")
           configure_file(${PROJECT_SOURCE_DIR}/Applications/${target_dir}/CPackConfig.cmake.in
                          ${CPACK_PROJECT_CONFIG_FILE} @ONLY)
           set(use_default_config OFF)
         endif()
       endif()
     # add link to the list
     list(APPEND CPACK_CREATE_DESKTOP_LINKS "${target_dir}")
     endif()
   endforeach()
 
 endif()
 
 # if no application specific configuration file was used, use default
 if(use_default_config)
   configure_file(${MITK_SOURCE_DIR}/MITKCPackOptions.cmake.in
                  ${MITK_BINARY_DIR}/MITKCPackOptions.cmake @ONLY)
   set(CPACK_PROJECT_CONFIG_FILE "${MITK_BINARY_DIR}/MITKCPackOptions.cmake")
 endif()
 
 # include CPack model once all variables are set
 include(CPack)
 
 # Additional installation rules
 include(mitkInstallRules)
 
 #-----------------------------------------------------------------------------
 # Last configuration steps
 #-----------------------------------------------------------------------------
 
 # This is for installation support of external projects depending on
 # MITK plugins and modules. The export file should not be used for linking to MITK
 # libraries without using LINK_DIRECTORIES, since the exports are incomplete
 # yet (depending libraries are not exported).
 
 set(MITK_EXPORTS_FILE "${MITK_BINARY_DIR}/MitkExports.cmake")
 file(REMOVE ${MITK_EXPORTS_FILE})
 
 set(targets_to_export)
 get_property(module_targets GLOBAL PROPERTY MITK_MODULE_TARGETS)
 if(module_targets)
   list(APPEND targets_to_export ${module_targets})
 endif()
 
 if(MITK_USE_BLUEBERRY)
   if(MITK_PLUGIN_LIBRARIES)
     list(APPEND targets_to_export ${MITK_PLUGIN_LIBRARIES})
   endif()
 endif()
 
 export(TARGETS ${targets_to_export} APPEND
        FILE ${MITK_EXPORTS_FILE})
 
 set(MITK_EXPORTED_TARGET_PROPERTIES )
 foreach(target_to_export ${targets_to_export})
   get_target_property(autoload_targets ${target_to_export} MITK_AUTOLOAD_TARGETS)
   if(autoload_targets)
     set(MITK_EXPORTED_TARGET_PROPERTIES "${MITK_EXPORTED_TARGET_PROPERTIES}
 set_target_properties(${target_to_export} PROPERTIES MITK_AUTOLOAD_TARGETS \"${autoload_targets}\")")
   endif()
   get_target_property(autoload_dir ${target_to_export} MITK_AUTOLOAD_DIRECTORY)
   if(autoload_dir)
     set(MITK_EXPORTED_TARGET_PROPERTIES "${MITK_EXPORTED_TARGET_PROPERTIES}
 set_target_properties(${target_to_export} PROPERTIES MITK_AUTOLOAD_DIRECTORY \"${autoload_dir}\")")
   endif()
 endforeach()
 
 configure_file(${MITK_SOURCE_DIR}/CMake/ToolExtensionITKFactory.cpp.in
                ${MITK_BINARY_DIR}/ToolExtensionITKFactory.cpp.in COPYONLY)
 configure_file(${MITK_SOURCE_DIR}/CMake/ToolExtensionITKFactoryLoader.cpp.in
                ${MITK_BINARY_DIR}/ToolExtensionITKFactoryLoader.cpp.in COPYONLY)
 configure_file(${MITK_SOURCE_DIR}/CMake/ToolGUIExtensionITKFactory.cpp.in
                ${MITK_BINARY_DIR}/ToolGUIExtensionITKFactory.cpp.in COPYONLY)
 
 set(VISIBILITY_AVAILABLE 0)
 set(visibility_test_flag "")
 mitkFunctionCheckCompilerFlags("-fvisibility=hidden" visibility_test_flag)
 if(visibility_test_flag)
   # The compiler understands -fvisiblity=hidden (probably gcc >= 4 or Clang)
   set(VISIBILITY_AVAILABLE 1)
 endif()
 configure_file(mitkExportMacros.h.in ${MITK_BINARY_DIR}/mitkExportMacros.h)
 
 configure_file(mitkVersion.h.in ${MITK_BINARY_DIR}/mitkVersion.h)
 configure_file(mitkConfig.h.in ${MITK_BINARY_DIR}/mitkConfig.h)
 
 set(VECMATH_INCLUDE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/Utilities/vecmath)
 set(IPFUNC_INCLUDE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/Utilities/ipFunc)
 set(UTILITIES_DIR ${CMAKE_CURRENT_SOURCE_DIR}/Utilities)
 
 file(GLOB _MODULES_CONF_FILES RELATIVE ${PROJECT_BINARY_DIR}/${MODULES_CONF_DIRNAME} ${PROJECT_BINARY_DIR}/${MODULES_CONF_DIRNAME}/*.cmake)
 set(MITK_MODULE_NAMES)
 foreach(_module ${_MODULES_CONF_FILES})
   string(REPLACE Config.cmake "" _module_name ${_module})
   list(APPEND MITK_MODULE_NAMES ${_module_name})
 endforeach()
 
 configure_file(mitkConfig.h.in ${MITK_BINARY_DIR}/mitkConfig.h)
 configure_file(MITKConfig.cmake.in ${MITK_BINARY_DIR}/MITKConfig.cmake @ONLY)
 
 # If we are under Windows, create two batch files which correctly
 # set up the environment for the application and for Visual Studio
 if(WIN32)
   include(mitkFunctionCreateWindowsBatchScript)
 
   set(VS_SOLUTION_FILE "${PROJECT_BINARY_DIR}/${PROJECT_NAME}.sln")
   foreach(VS_BUILD_TYPE debug release)
     mitkFunctionCreateWindowsBatchScript("${MITK_SOURCE_DIR}/CMake/StartVS.bat.in"
       ${PROJECT_BINARY_DIR}/StartVS_${VS_BUILD_TYPE}.bat
       ${VS_BUILD_TYPE})
   endforeach()
 endif(WIN32)
 
 
 #-----------------------------------------------------------------------------
 # MITK Applications
 #-----------------------------------------------------------------------------
 
 # This must come after MITKConfig.h was generated, since applications
 # might do a find_package(MITK REQUIRED).
 add_subdirectory(Applications)
 
 #-----------------------------------------------------------------------------
 # MITK Examples
 #-----------------------------------------------------------------------------
 
 if(MITK_BUILD_EXAMPLES)
   # This must come after MITKConfig.h was generated, since applications
   # might do a find_package(MITK REQUIRED).
   add_subdirectory(Examples)
 endif()