diff --git a/Documentation/Doxygen/3-DeveloperManual/Starting/SettingUpMITK/BuildInstructions.dox b/Documentation/Doxygen/3-DeveloperManual/Starting/SettingUpMITK/BuildInstructions.dox
index ff68800dba..b7032e9920 100644
--- a/Documentation/Doxygen/3-DeveloperManual/Starting/SettingUpMITK/BuildInstructions.dox
+++ b/Documentation/Doxygen/3-DeveloperManual/Starting/SettingUpMITK/BuildInstructions.dox
@@ -1,211 +1,223 @@
 /**
 \page BuildInstructionsPage Build Instructions
 
 \tableofcontents
 
 \section BuildInstructions_Introduction Introduction
 
 The CMake-based build system of MITK supports a "superbuild" process,
 meaning that it will download, configure, and build all required third-party
 libraries (except Qt) automatically. These instructions will show you how to use
 the MITK superbuild.
 
 \note This page explains explicitly how to build MITK itself. If you want to
 create your own project based on MITK, the process described below is completely
 automated. Please see \ref HowToNewProject.
 
 For more advanced users, the last sections explains how to inject custom build
 libraries into the superbuild process.
 
 \section BuildInstructions_Prerequisites Prerequisites
 
 You need:
   -# Git from http://git-scm.com (there are also numerous third-party graphical
      clients available). We recomment using Git, but see below for a way how to
      get the current source code without using it.
   -# <a href="http://www.cmake.org">CMake</a> (version \minimumCMakeVersion or higher)
-  -# <a href="http://qt.io">Qt</a> 5.x if you plan to develop Qt-based
+  -# <a href="http://qt.io">Qt</a> 5.6 or 5.7.1 if you plan to develop Qt-based
      applications
   -# If you are using <b>Mac OS X</b> you need an XCode installation as it
      provides the neccessary compilers and SDKs
 
 \section BuildInstructions_Qt A note about Qt
 
 As we do not provide Qt in the MITK superbuild you need to install Qt manually.
 Installing Qt dramatically improved since Qt 5, as The Qt Company provides
 <a href="http://www.qt.io/download/">sophisticated online installers for all
 supported platforms</a>.
 
-\note Make sure that you select a Qt version which provides the right <b>OpenGL-enabled</b>
-packages for your architecture and compiler.
-
 \section BuildInstructions_Get_Source Get a source tree
 
 Since MITK is under active development we recommend to use Git to check out
 the latest stable release from the homepage. If you decide to use the most
 current nightly release, make sure to get a stable tree: Check the
 <a href="http://cdash.mitk.org/index.php?project=MITK">MITK dashboard</a>
 before checking out. If the build tree is not clean, you can specify an
 older revision for the checkout or get a stable tar ball from
 <a href="http://www.mitk.org">www.mitk.org</a>.
 
-If you don't want to use Git, you may also download a snapshot of the current source code
-(or any other older version) as a <a href="http://mitk.org/git/?p=MITK.git;a=shortlog;h=refs/heads/master">tar.gz package</a>.
-
 To clone MITK's current Git repository do:
 
 \code
-git clone https://phabricator.mitk.org/diffusion/MITK/mitk.git MITK
+git clone https://phabricator.mitk.org/source/mitk.git MITK
 \endcode
 
 \section BuildInstructions_Build_With_CMake Build MITK with CMake
 
 Create a new directory for the superbuild binary tree, change to it and call CMake:
 
 In the shell (assuming your current directory is the same as the one where you
 issued the git clone command):
 \code
 mkdir MITK-superbuild
 cd MITK-superbuild
 ccmake ../MITK
 \endcode
 
 If you use <b>Windows</b> or prefer to use the CMake GUI, start the CMake GUI and enter the
 location of the source tree and binary tree, choose a suitable generator
 and configure the project.
 
 CMake will present you a couple of options, these are the most important ones:
 
- - <tt><b>CMAKE_PREFIX_PATH</b></tt> The path to your Qt installation, e.g., <i>C:/Qt/5.4/msvc2013_64_opengl</i> or <i>/home/user/Qt/5.4/gcc_64</i>
+ - <tt><b>CMAKE_PREFIX_PATH</b></tt> The path to your Qt installation, e.g., <i>C:/Qt/5.6/msvc2013_64</i> or <i>/home/user/Qt/5.6/gcc_64</i>
  - <tt><b>MITK_USE_ACVD</b></tt> Build MITK code which depends on ACVD (this
    will download and build ACVD)
  - <tt><b>MITK_USE_BLUEBERRY</b></tt> Build the BlueBerry application framework
  - <tt><b>MITK_USE_Boost_LIBRARIES</b></tt> If you need binary Boost libraries,
    specify them here.
  - <tt><b>MITK_USE_OpenCV</b></tt> Build MITK code which depends on OpenCV (this
    will download and build OpenCV 2.4)
  - <tt><b>MITK_USE_Python</b></tt> Enables Python wrapping in MITK. This will also
    configure ITK, VTK, and OpenCV (if enabled) to build Python wrappers.
- - <tt><b>MITK_USE_QT</b></tt> Build MITK code which depends on Qt
+ - <tt><b>MITK_USE_QT5</b></tt> Build MITK code which depends on Qt
  - <tt><b>MITK_USE_SOFA</b></tt> Build MITK code which depends on SOFA (this will
    download and build SOFA)
- - <tt><b>CMAKE_PREFIX_PATH</b></tt> If Qt5 is not found automatically, set
-   this variable to the base directory of your Qt5 installation.
 
 If you are satisfied with the configuration of your MITK superbuild, generate
 the project files with CMake by pressing "Generate".
 
 <b>Linux</b> and <b>Mac OS X</b> users usually just enter "make" (optionally
 supplying the number threads to be used for a parallel build):
 \code
 make -j6
 \endcode
 
 <b>Windows</b> users using Visual Studio can open the generated
 <tt>MITK-superbuild.sln</tt> solution file in the <tt>MITK-superbuild</tt>
 directory and start the build by building the <tt>BUILD_ALL</tt> project.
 
 \section BuildInstructions_Customize Customize your MITK superbuild
 
 The MITK superbuild configures MITK as well as all external libraries. The
 build directories of these libraries, and of MITK itself are located inside
 the <tt>MITK-superbuild</tt> directory. For example, the directory layout may
 look like:
 
 \code
 MITK-superbuild
  |- ep "external projects"
     |-bin
     |-lib
     |-include
     |-src
  |- MITK-build
 \endcode
 
 To change the configuration of the MITK build itself, choose the MITK-build directory
 as the binary directory in the CMake GUI (not the MITK-superbuild directory).
 After generating the project files, build the MITK project by either issuing "make"
 in the MITK-build directory (Linux, Mac OS X), or by opening MITK-build/MITK.sln (Windows).
 
 You may also change the configuration of any project configured via the
 superbuild process. Make sure to also build the changed project and also the
 projects which depend on it.
 
 \section BuildInstructions_Running Running Applications
 
 On Linux, just execute the application you want to run. MITK executables are
 located in <tt>MITK-superbuild/MITK-build/bin</tt>
 
 On Windows, the <tt>PATH</tt> environment variable must contain the directories
-containing the third-party libraries. The MITK build system generated <b>Windows batch
-files</b> in the <tt>MITK-build</tt> directory set up a correct environment
-and opens the appropriate Visual Studio solution file. Use these batch files to be able
-to start and debug MITK applications from inside Visual Studio.
+containing the third-party libraries. This is automatically done from Visual Studio.
+For running the applications directly use the generated batch files in the
+<tt>MITK-superbuild/MITK-build/bin</tt>.
 
 \section BuildInstructions_Documentation Documentation
 
 If you have the <a href="http://www.doxygen.org">Doxygen</a> documentation tool
 installed, you get a new project (Visual Studio) or "make" target named "doc".
 You can build this to generate the HTML documentation of MITK in the
 Documentation/Doxygen directory of your MITK-build binary tree or in the
 <tt>MITK_DOXYGEN_OUTPUT_DIR</tt> CMake variable (if specified).
 
 \section BuildInstructions_Extending Extend MITK on your own (using the application framework BlueBerry)
 
 Please see \ref NewPluginPage
 
 \section BuildInstructions_As_Toolkit Use MITK in your own project (as a toolkit)
 
 To use MITK in your external project, add the CMake command
 <code>find_package(MITK REQUIRED)</code> to your CMakeLists.txt and make use of
 the CMake macros <code>mitk_create_module()</code> and
 <code>mitk_create_executable()</code> provided by MITK.
 
-Here is an example CMakeLists.txt (from the Examples/QtAppExample/ directory)
-which allows you to create a Qt-based application using MITK to display an image.
-\include QtAppExample/CMakeLists.txt
+Here is a very basic example CMakeLists.txt including MITK as a project:
+\code
+cmake_minimum_required(VERSION 3.5 FATAL_ERROR)
+
+project(MyProject)
+
+find_package(MITK 2016.11 REQUIRED)
+
+add_executable(MyApp main.cpp)
+
+target_link_libraries(MyApp MitkCore)
+\endcode
+
+with the main.ccp being
+\code
+#include <iostream>
+#include <mitkLogMacros.h>
+
+int main()
+{
+  MITK_INFO << "Hello world!";
+  return 0;
+}
+\endcode
 
 \section BuildInstructions_Advanced_Customization Superbuild customization
 
 You can inject pre-build third-party libraries into the MITK superbuild by
 setting certain CMake variables before the first configure step. MITK will
 then use these third-party libraries instead of downloading and building them
 by itself. Note that you must take care of configuring those libraries with all options
 MITK requires.
 
 The variables listed below are provided for injecting third-party libraries.
 Their occurrence in the CMake GUI or in ccmake may depend on specific
 MITK_USE_* options set to ON. You may also use the variable names below without
 the <tt>EXTERNAL_</tt> prefix, for example when providing their values on a
 command line call to CMake.
 
  - <tt><b>EXTERNAL_BOOST_ROOT</b></tt> Set this variable to your custom Boost
    installation
  - <tt><b>EXTERNAL_CTK_DIR</b></tt> Set this variable to your CTK binary tree
    (the directory containing the CTKConfig.cmake file)
  - <tt><b>EXTERNAL_CableSwig_DIR</b></tt> Set this variable to your CableSwig
    binary tree for Python wrapping (the directory containing the
    CableSwigConfig.cmake file)
  - <tt><b>EXTERNAL_DCMTK_DIR</b></tt> Set this variable to your DCMTK binary
    tree (the directory containing the DCMTKConfig.cmake file)
  - <tt><b>EXTERNAL_GDCM_DIR</b></tt> Set this variable to your GDCM binary
    tree (the directory containing the GDCMConfig.cmake file)
  - <tt><b>EXTERNAL_ITK_DIR</b></tt> Set this variable to your ITK binary tree
    (the directory containing the ITKConfig.cmake file)
  - <tt><b>EXTERNAL_OpenCV_DIR</b></tt> Set this variable to your OpenCV binary
    tree (the directory containing the OpenCVConfig.cmake file)
  - <tt><b>EXTERNAL_VTK_DIR</b></tt> Set this variable to your VTK binary tree
    (the directory containing the VTKConfig.cmake file)
 
 To set CMake options before the first configure step is invoked, supply them
 on the command line, i.e.
 
 \code
 ccmake -DITK_DIR:PATH=/opt/ITK-release ../MITK
 \endcode
 
 See the following link for more information about how to configure third-party
 libraries:
 \subpage BuildToolkits "How to build ITK, VTK and Qt"
 
 */
diff --git a/Documentation/Doxygen/4-API/Pages.dox b/Documentation/Doxygen/4-API/Pages.dox
index 9fe46d1779..d29909ecc2 100644
--- a/Documentation/Doxygen/4-API/Pages.dox
+++ b/Documentation/Doxygen/4-API/Pages.dox
@@ -1,30 +1,33 @@
 /**
 
 
 \defgroup MITKDeprecatedAPI Deprecated
 
 \page deprecatedSince2012_09 Deprecated as of 2012.09
 \ingroup MITKDeprecatedAPI
 
 \page deprecatedSince2013_03 Deprecated as of 2013.03
 \ingroup MITKDeprecatedAPI
 
 \page deprecatedSince2013_06 Deprecated as of 2013.06
 \ingroup MITKDeprecatedAPI
 
 \page deprecatedSince2013_09 Deprecated as of 2013.09
 \ingroup MITKDeprecatedAPI
 
 \page deprecatedSince2014_03 Deprecated as of 2014.03
 \ingroup MITKDeprecatedAPI
 
 \page deprecatedSince2014_10 Deprecated as of 2014.10
 \ingroup MITKDeprecatedAPI
 
 \page deprecatedSince2015_05 Deprecated as of 2015.05
 \ingroup MITKDeprecatedAPI
 
 \page deprecatedSince2016_03 Deprecated as of 2016.03
 \ingroup MITKDeprecatedAPI
 
+\page deprecatedSince2016_11 Deprecated as of 2016.11
+\ingroup MITKDeprecatedAPI
+
 */