This is the readme for the model associated with the paper:
Lopez-Jury L, Meza RC, Brown MTC, Henny P, Canavier CC (2018)
Morphological and biophysical determinants of the intracellular and
extracellular waveforms in nigral dopaminergic neurons: A
computational study. J Neurosci
This model was contributed by L Lopez-Jury and requires NEURON which is freely available from https://www.neuron.yale.eduUsage
about the extracellular simulations, a ShapePlot with the neuron morphology and two windows showing the somatic intracellular membrane potential (top) and the extracellular potential recorded close to the soma (bottom). You may zoom-in to note the waveform of the extracellular spike.
To check how AIS length modify the shape of the action potential use "L" NEURON parameter by typing: ais.L Original reconstruction length is 41.45 microns, try changing it to 10 or 100 microns to see the effect on the waveform. From our results, the range of AIS length of 16 dopaminergic neuron reconstructions is from 19 to 58 microns.
To better visualize the effect of the AIS length on the intracellular shape of action potential you may calculate the first derivative of membrane potential or generate a phase plane plot of the spike. The effect on the extracellular waveform is clearly visible.
To change from 2-domain model to 3-domain model, open "parameters.hoc" file and change the sodium and delayed rectifier potassium conductance densities to 200 and 100 respectively. As indicated in the comments. This will change the conductance only in the soma section, dendrites keep their conductances fix.
Also, you may change the neuron 3D reconstruction by changing the second line in "parameters.hoc" file. We have included two different reconstructions: one from a mouse and the other from a rat. Both neuron models reproduce the extracellular waveform obtained by experimental recordings without changing any parameter.