Experiments

The experiments directory contains scripts allowing to reproduce the results presented in our publications.

Each folder corresponds to a specific publication and contains explanations on the experiments and how to run them.

OVC_2021

This directory contains scripts to reproduce results published in

Marelli, F. and Liebling, M. “Optics versus computation: influence of illumination and reconstruction model accuracy in Focal-plane-scanning optical projection tomography.” 2021 IEEE 18th International Symposium on Biomedical Imaging (ISBI). IEEE, 2021.

To run the experiments, first set the following environment variables:

• OVC_PATH: full path to the directory in which you want the experiments to run (must be writable, 90G free space required)

• OVC_PYTHON: full path to the python executable that will be used for the experiments

The script setup.sh creates the directory layout and generates the simulation datasets (phantom, PSF, light sheet illumination).

The script run_fpsopt.sh simulates FPS-OPT imaging, deconvolution and reconstruction with multiple PSF models (incorrect NA, approximate model).

The script run_fssopt.sh simulates FSS-OPT and X-ray imaging, and reconstruction it can be run in parallel to the previous one.

The script run_results.sh gathers the simulations and computes PSNR and generates the graphs. It requires matplotlib_scalebar to be installed.

Final results are stored in the folder $OVC_PATH/graph. The json files contain the computed PSNR.

The simulations benefit greatly from running on multithreaded machines.