Photoacoustic and ultrasound tomography images of phantom and in-vivo data aquired with the PAM3 scanner and corresponding visualization scripts

Overview

This repository contains most of the photoacoustic tomography (PAT) reconstructions and speed-of-sound (SOS) reconstructions shown in the article:

"Hybrid three-dimensional full-view multi-wavelength photoacoustic and ultrasound breast tomography" by Dantuma et al., published in Photoacoustics, 2026  

(also available on [arXiv:2308.06754]). It also contains the Matlab scripts to visualize the reconstructions and produce the figures used in the article. 

Usage

• The folder `reconstructions` contains the reconstructed volumes as `.mat` files.
• The folder `figure 3` contains the Matlab script `plot_figure_3_bottom.m`, which reproduces Figures 3d - 3f. Running it will save the sub figures as `.fig` and/or `.png` files in the subfolder `fig_png` . The Matlab script `validate_reference_SOS_model.m` illustrates how the reference SOS image was constructed that was used to validate the reconstructions of the SOS test object.
• The folder `figure 4` contains the Matlab scripts `plot_figure_4_top.m` and `plot_figure_4_bottom.m`, which reproduces all subfigures from Figure 4.
• The folder `figure 5` contains the Matlab script `plot_figure_5.m` which reproduces Figures 5a, 5b, 5c, 5e.
• The folder `figure appendix volunteers` contains Matlab scripts `plot_all_volunteers_PA.m` and `plot_all_volunteers_SOS.m`, which reproduces Appendix Figure A4.
• The folder `figure appendix SOS test object` contains the Matlab script `plot_figure_appendix_sos_test_object.m` , which reproduces Appendix Figure A6.
• The folder `figure appendix image processing` contains the Matlab script `plot_figure_image_processing.m` , which reproduces Appendix Figure A7.
• The folder `cups` contains segmentations of the region of interest inside the breast cup and image volumes that list the distance of each voxel from the cup surface. These are used by the PA visulizations routines, see, e.g., `figure 4/plot_figure_4_top.m`   
• The folder `matlab functions` contains `.m` and `.mex` functions used by the visulization scripts. Note that the `.mex` files may need to be (re)compiled for your system.