In addition to the primary objective of making OCT imaging systems accessible for researchers CBORT has also developed reconstruction software, white papers, manuals, signal processing, and data management tools.

Please acknowledge support from the Center for Biomedical OCT Research and Translation (National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health Award P41 EB015903) when using these resources.

Github Repository

Reconstruction Software
Open Source Python package for reconstructing raw OCT/OFDI data.

SIPS reconstruction
Open Source Python package for reconstructing tissue birefringence from a single input state

White papers and manuals

Wavelength-swept laser sources based on Fabry-Perot filters
Detailed manual and component list for building simple, low cost, and high performance wavelength swept lasers for OCT.

Plugins and toolboxes

Synchronous Viewer 
This ImageJ plug-in offers synchronous reviewing of multiple volumes and generates cross-sectional views through the synchronized cursor position. Synchronization of the cursor, the window location and the magnification is provided. Users are allowed to open at most three stacks.

PMD Compensation
Signal processing algorithms implemented in Matlab for PS-OCT imaging using Jones formalism: 1) Conventional method ignoring polarization mode dispersion (PMD) and 2) PMD compensation method, based on three calibration signals.

Spectral binning
Spectral binning mitigates polarization mode dispersion in PS-OCT without calibration signals. The signal processing algorithms provided here are implemented in Matlab and use the Stokes formalism to reconstruct the local retardation and the degree of polarization (DOP).

Toolbox for signal processing and volume projection of OCT-based angiography implemented in Matlab.

Matlab class of managing volumetric OCT data
The tifStack class enables to load a gray scale volumetric tif-stack, and generate different views of the volumetric data without physically rearranging the memory. It is designed to support and visualize multiple channels typically arising in functional OCT applications or polarization sensitive PS-OCT, and can also directly map data from cylindrical to Cartesian coordinates.

Robust wavenumber and dispersion calibration
Matlab functions, exemplary usage and example calibration data for an automated strategy to compute the wavenumber and dispersion calibration required for Fourier-Domain Optical Coherence Tomography.