Analyzing Action Potentials in Axons

This script shows how to use the methods of axon_results-class to detect and analyze action potentials.

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Number of APs detected: 5
APs reached end: False
APs reached end within the timeframe: True
InterAP collision detected: True
AP propagation velocity: 57.5m/s

import nrv
import matplotlib.pyplot as plt

if __name__ == '__main__':
    y = 0
    z = 0
    d = 10
    L = 20000
    #with AP collision
    axon2 = nrv.myelinated(y,z,d,L,dt=0.005,rec='all')
    t_start = 2
    duration = 0.1
    amplitude = 2

    axon2.insert_I_Clamp(0.5, 2.01, duration, amplitude)
    axon2.insert_I_Clamp(0.75, 6.01, duration, amplitude)
    axon2.insert_I_Clamp(0.25, 6.0, duration, amplitude)
    axon2.insert_I_Clamp(0.75, 8.01, duration, amplitude)
    axon2.insert_I_Clamp(0.25, 8.0, duration, amplitude)
    results = axon2.simulate(t_sim=10)

    results.rasterize()
    x_APs,_,t_APs,_ = results.split_APs()

    print(f"Number of APs detected: {results.count_APs()}")
    print(f"APs reached end: {results.APs_reached_end()}")
    print(f"APs reached end within the timeframe: {results.APs_in_timeframe()}")
    print(f"InterAP collision detected: {results.detect_AP_collisions()}")
    if (results.count_APs()):
        print(f"AP propagation velocity: {results.getAPspeed()[0]}m/s")

    fig,ax = plt.subplots(1)
    results.colormap_plot(ax)

    fig,axs = plt.subplots(2)

    results.plot_x_t(axs[0],"V_mem")
    axs[0].set_xlabel('time (ms)')
    axs[0].set_ylabel("x-axis (µm)")
    axs[0].set_xlim(0,results['tstop'])

    results.raster_plot(axs[1],"V_mem")
    for x_AP,t_AP in zip(x_APs,t_APs):
        axs[1].scatter(t_AP,x_AP)
        x_start,t_start = results.get_start_AP(x_AP,t_AP)
        x_max,t_xmax = results.get_xmax_AP(x_AP,t_AP)
        x_min,t_xmin = results.get_xmin_AP(x_AP,t_AP)
        axs[1].scatter(t_start,x_start,s=10,c = 'k')
        axs[1].scatter(t_xmax,x_max,s=10,c = 'g')
        axs[1].scatter(t_xmin,x_min,s=10,c = 'b')

    if results.detect_AP_collisions():
        x_coll,t_coll,_ = results.get_collision_pts()
        axs[1].scatter(t_coll,x_coll,s=50,c = 'r')

    axs[1].set_xlabel('time (ms)')
    axs[1].set_ylabel("x-axis (µm)")
    axs[1].set_xlim(0,results['tstop'])

    fig.tight_layout()
    plt.show()