This code was used to produce the results presented in Sætra et al., Neurophotonics, 7(3), 035008 (2020): Spatially resolved estimation of metabolic oxygen consumption from optical measurements in cortex.
If you want to reproduce Figures 7 and 8, navigate to the top directory of the repo and enter the following command in the terminal:
python3 setup.py installFigures 7 and 8 also require FEniCS.
Other requirements are given in requirements.txt and can be installed by the following command:
pip install -r requirements.txtThe remaining figures require Matlab (R2017b).
The code was run with Ubuntu 18.04.3.
All data can be downloaded from the data folder or be reproduced by running the script run_all.sh. This might run for a few days on a normal computer.
To plot and save the figures, run plot_all.sh in the figure folder.
Note that some of the figures have been edited in Inkscape for publication purposes.