Reconstruction and Spectral Analysis for Optical Coherence Tomography

A code for reconstruction and spectral analysis of spectral domain OCT images.

MATLAB code for reconstruction and spectral analysis of spectral domain OCT images. This code can be used as part of a platform for molecular imaging with OCT, which we call MOZART.
This code was created to read raw interferograms from Thorlabs OCTs (SW version 4 works best, but version 3 is also supported with a few changes). It reconstructs the raw interferograms into OCT images, and supports both 2D, 3D and speckle variance. In addition to reconstructing the images this code:
Calculates the normalized spcekle variance (useful for detecting blood vessels)
Calculates dispersion compensation
Calculates a map of spectral contras, based on dual-band spectral analysis
Calculates spectral-depth compensation
Creates images that combine the OCT image, spectral analysis and speckle variance.
and more features...
This code was used to create images and analysis for: "Contrast-enhanced optical coherence tomography with picomolar sensitivity for functional in vivo imaging" O Liba, ED SoRelle, D Sen, A de La Zerda - Scientific reports, 2016.
Please cite our paper if you use our code.