This is the README file for running simulations associated with: Newton, A.J.H, McDougal, R.A., Hines, M.L. and Lytton, W.W., 2018. Using NEURON for reaction-diffusion modeling of extracellular dynamics. Frontiers in neuroinformatics, 12. This code was contributed by AJH Newton and questions should be addressed to adam.newton"at"yale.edu There are two examples included here, the trivial example used for validations (figure 4) and the spreading depression simulation (figures 1 and 2). Run trivial.py, it will display the plot shown in figure 4 (with dx = 1) and create a 'trivial_1.00.npy' file with the results. To get the other relative errors shown in 4C modify the dx parameter (line 19). spreading_depression.py accepts command line arguments to switch between the 4 different model combinations. To run it first compile the NEURON mod files. An error in the original model where multiple dendrite segments were used has been corrected leading to quantitatively but not qualitatively different results from those report in the paper. usage: spreading_depression.py [-h] [--edema] [--buffer] [--tstop [TSTOP]] dir Run the spreading depression simulation positional arguments: dir a directory to save the figures and data optional arguments: -h, --help show this help message and exit --edema Use inhomogeneous tortuosity and volume fraction to simulate edema --buffer Use a reaction to model astrocytic buffering --tstop [TSTOP] duration of the simulation in ms (defaults to 200ms) The spreading depression simulations are computationally demanding, a demo version with fewer larger neurons and larger extracellular voxels is included spreading_depression_demo.py