Visualize NEURON model#

import navis
import neuron

import navis.interfaces.neuron as nrn

# Load one of the example neurons (a Drosophila projection neuron from the hemibrain connectome)
# Note the conversion to microns!
n = navis.example_neurons(1).convert_units("um")

# Here we manually corrected the soma
n.soma = 20

# Reroot to the soma
n.reroot(n.soma, inplace=True)

# Create the compartment model
cmp = nrn.CompartmentModel(n, res=10)

# Set the specific axial resistivity for the entire neuron in Ohm cm
cmp.Ra = 266.1

# Set the specific membran capacitance in mF / cm**2
cmp.cm = 0.8

# Add passive membran properties for the entire neuron
cmp.insert(
    "pas",
    g=1
    / 20800,  # specific leakage conductance = 1/Rm; Rm = specific membran resistance in Ohm cm**2
    e=-60,  # leakage reverse potential
)

# Label axon/dendrite
navis.split_axon_dendrite(n, label_only=True, cellbodyfiber="soma")

# Collect axon nodes
axon_nodes = n.nodes.loc[n.nodes.compartment.isin(["axon", "linker"]), "node_id"].values

# Get the sections for the given nodes
axon_secs = list(set(cmp.get_node_section(axon_nodes)))

# Insert HH mechanism at the given sections
cmp.insert("hh", subset=axon_secs)

cmp.add_voltage_record(n.nodes.node_id.values)

# Get dendritic postsynapses
post = n.postsynapses[n.postsynapses.compartment == "dendrite"]

# Add synaptic input to the first 10 postsynapses after 2 ms
cmp.add_synaptic_current(where=post.node_id.unique()[0:10], start=2, max_syn_cond=0.1, rev_pot=-10)

# This is equivalent to neuron.h.finitialize + neuron.h.continuerun
cmp.run_simulation(100, v_init=-60)

import numpy as np
import pandas as pd

# Collect the voltage recordings at each node
records = pd.DataFrame(np.vstack([r.as_numpy() for r in cmp.records['v'].values()]), index=list(cmp.records['v'].keys()))

# Reindex to make sure it matches the node table
records = records.reindex(n.nodes.node_id)

records.head()

# The interval for each step is 0.025ms by default
print(neuron.h.dt)

n.nodes['v'] = records.loc[:, int(5 / 0.025)].values

# Plot
fig, ax = navis.plot2d(
    n,
    method="2d",
    color_by="v",  # color by the voltage column
    palette="viridis",
    vmin = -70,
    vmax = 10,
    view=('x', '-y')
)

# Manually add a colorbar
import matplotlib.pyplot as plt
from matplotlib.cm import ScalarMappable
sm = ScalarMappable(norm=plt.Normalize(vmin=-70, vmax=10), cmap='viridis')
_ = fig.colorbar(sm, ax=ax, fraction=0.075, shrink=0.5, label="V")

# Convert our skeleton to a mesh for nicer visualization
mesh = navis.conversion.tree2meshneuron(n, warn_missing_radii=False)

# Plot the neuron
fig, ax = navis.plot2d(mesh, method='2d',color='k', view=('x','-y'))

sm = ScalarMappable(norm=plt.Normalize(vmin=-70, vmax=10), cmap='viridis')
_ = fig.colorbar(sm, ax=ax, fraction=0.075, shrink=0.5, label="V")

# Add a text in the top right for the timestamp
t = ax.text(0.02, 0.95, 'ms', ha='left', va='top', transform=ax.transAxes, color='r')

# Get the collection representing our neuron
c = ax.collections[0]
c.set_cmap('viridis')
c.set_norm(plt.Normalize(vmin=-70, vmax=10))

# This function updates the voltages according to the frame
def animate(i):
    # We need to map the voltages at individual nodes to faces in the mesh
    # First nodes to vertices
    vert_voltage = records[i].values[mesh.vertex_map]
    # Then vertices to faces
    face_voltage = vert_voltage[mesh.faces].mean(axis=1)
    # Set the values
    c.set_array(face_voltage)
    # Also update the timestamp
    t.set_text(f'{i * 0.025:.2f} ms')
    return (c, t)

import matplotlib.animation as animation
ani = animation.FuncAnimation(fig, animate, interval=40, blit=True, repeat=True, frames=400)