Spatially resolved estimation of metabolic oxygen consumption from optical measurements in cortex

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.

Requirements

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 install

Figures 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.txt

The remaining figures require Matlab (R2017b).

The code was run with Ubuntu 18.04.3.

Reproducing the results of the paper

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.