**8. Simulation techniques**

The simulation software for modeling diffuse optical tomography is CULA, NIRFAST NETGEN and MIMICS. CULA is GPU Accelerated Linear Algebra which has a parallel computing architecture to dramatically improve the computation speed of sophisticated mathematics and also contains routines for systems solvers, singular value decompositions and Eigen problems. For reconstruction in diffuse optical tomography it facilitates singular value decomposition, matrix multiplication, matrix inversion etc.

NIRFAST is Near Infrared Fluorescence and Spectroscopy Tomography [33, 34] which is an FEM based software package designed for modeling Near Infrared Frequency domain [35] light transport in tissue.

NETGEN [36] is an automatic 3D tetrahedral mesh generator which accepts input from Constructive Solid Geometry (CSG) or Boundary Representation (BR) from the STL (Stereo Lithography) file format. It contains modules for mesh optimization and hierarchical mesh refinement and it is also open-source software available for Unix/Linux and Windows.

MIMICS is software specially developed for medical image processing. The ROI (Region of Interest) is selected in the segmentation process which is converted to a 3D surface model using an adapted marching cubes algorithm that takes the partial volume effect into account, leading to very accurate 3D model. The 3D files are represented in the STL format.
