For each component in ema-tracker, fit-model, and model-builder, run cmake cmake inside that component's directory.
You will need CMake and a standard GCC or LLVM toolchain installed. In addition, the following dependencies are required:
On OSX with Homebrew, install these dependencies with
$ brew install armadillo ann jsoncpp asio yaml-cpp insighttoolkit vtk
On Ubuntu, install these dependencies with
$ sudo apt-get install libarmadillo-dev libann-dev libjsoncpp-dev libasio-dev libyaml-cpp-dev libinsighttoolkit4-dev