This is a Matlab implementation of the procedure described in the Robust Depth Estimation for Light Field Microscopy paper. (it is submitted and yet to be accepted)

It combines vision cues (correspondence, defocus) to estimate accurate and robust depth maps from light field microscopy images. Images are acquired with FiMic microscope or created with Blender.

The FiMic microscope allows to capture light field in a single shot. For further information regarding FiMic Fourier Integral Microscope, refer to the paper FIMic: design for ultimate 3D-integral microscopy of in-vivo biological samples

About implementation, the code is all in Matlab and it makes use of MEX files. It uses other toolboxes, but they are already present in the github folders.

The dependencies are a C++ compiler for the MEX code (if you are using gcc, supported version is 4.7; however until 6.x is working and Matlab just gives a warning, from 7.0 it may cause some problems. If on Linux systems, use of alternatives can help about this read more here)

For further information, please contact me at: lpa@informatik.uni-kiel.de