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

Contents

1. Data
2. Usage
3. Resources
4. Updates

Data

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.

Usage

0. Clone this repo: git clone https://github.berkeley.edu/Waller-Lab/multi-slice.git
1. 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.
2. Downlod the data (from above) into your download path.
3. Run main_phantom.m to run MSBP forward-model and inverse recontruction on simulated phantom
4. Run main_data.m to run MSBP inverse recontruction on C. elegan data

Resources

Python implementation of Multi-slice as well Multi-layer Born scattering models can be found here.

Updates

08/27/2020:

1. Added first public version of code to repo. This is an updated version compared to what is used in the paper.