In silico tomography with Finite-Difference Time-Domain (FDTD) simulations
This is a collection of Meep scripts and Python wrappers to generate tomographic scattering data of artificial cell phantoms, to reconstruct the refractive index (RI) from these scattering data, and to analyze the quality of the reconstructed RI in dependence of cell phantom properties and used reconstruction algorithm.
- examples: Example usages of the Python wrapper
- meep_tomo: Python wrapper for the C++ scripts located in
- phantoms_meep: Meep C++ scripts of 2D and 3D cell phantoms
I used these scripts for the 2015 publication ODTbrain: a Python library for full-view, dense diffraction tomography (Müller et al.) BMC Bioinformatics. Please cite this paper if you are using them in a scientific publication.