Multi-slice beam propagation scattering model for 3D refractive-index reconstruction of multiple-scattering objects
Please cite the following paper when using the code:
High-resolution 3D refractive index microscopy of multiple-scattering samples from intensity images
Shwetadwip Chowdhury, Michael Chen, Regina Eckert, David Ren, Fan Wu, Nicole Repina, and Laura Waller
Data can be found at this link: 3D Intensity-based ODT data
README.txt contains information about the organization of the data in the C. elegans data folders.
- Clone this repo:
git clone https://github.berkeley.edu/Waller-Lab/multi-slice.git - Download the UNLocBoX regularization toolbox, an extensive open-source compilation of several optimizers utilizing proximity operators. Make sure to put this toolbox into your download path. This toolbox can be found at this link: UNLocBoX toolbox.
- Downlod the data (from above) into your download path.
- Run main_phantom.m to run MSBP forward-model and inverse recontruction on simulated phantom
- Run main_data.m to run MSBP inverse recontruction on C. elegan data
Python implementation of Multi-slice as well Multi-layer Born scattering models can be found here.
08/27/2020:
- Added first public version of code to repo. This is an updated version compared to what is used in the paper.