Spatial networks: Pyramidal cells and interneurons

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Create two populations of pyramidal cells and two populations of interneurons on a 30x30 grid. Connect with two projections, one pyr->pyr, one pyr->in, and visualize.

BCCN Tutorial @ CNS*09 Hans Ekkehard Plesser, UMB

import matplotlib.pyplot as plt
import nest
import numpy as np

nest.ResetKernel()
nest.set_verbosity("M_WARNING")

nest.CopyModel("iaf_psc_alpha", "pyr")
nest.CopyModel("iaf_psc_alpha", "in")

same positions for all populations

pos = nest.spatial.grid(shape=[30, 30], extent=[3.0, 3.0])

a_pyr = nest.Create("pyr", positions=pos)
a_in = nest.Create("in", positions=pos)

b_pyr = nest.Create("pyr", positions=pos)
b_in = nest.Create("in", positions=pos)

nest.Connect(a_pyr, b_pyr, {"rule": "pairwise_bernoulli", "p": 0.5, "mask": {"circular": {"radius": 0.5}}})

nest.Connect(a_pyr, b_in, {"rule": "pairwise_bernoulli", "p": 0.2, "mask": {"circular": {"radius": 1.0}}})

plt.clf()

plot targets of neurons in different grid locations obtain node id for center: pick first node of composite

ctr_index = 30 * 15 + 15
ctr_id = a_pyr[ctr_index : ctr_index + 1]

# get all projection targets of center neuron
conn = nest.GetConnections(ctr_id)
tgts = conn.get("target")

tpyr = nest.GetTargetPositions(ctr_id, b_pyr)[0]
tin = nest.GetTargetPositions(ctr_id, b_in)[0]

tpyr_x = np.array([x for x, y in tpyr])
tpyr_y = np.array([y for x, y in tpyr])
tin_x = np.array([x for x, y in tin])
tin_y = np.array([y for x, y in tin])

# scatter-plot
plt.scatter(tpyr_x - 0.02, tpyr_y - 0.02, 20, "b", zorder=10)
plt.scatter(tin_x + 0.02, tin_y + 0.02, 20, "r", zorder=10)

# mark locations with background grey circle
plt.plot(
    tpyr_x, tpyr_y, "o", markerfacecolor=(0.7, 0.7, 0.7), markersize=10, markeredgewidth=0, zorder=1, label="_nolegend_"
)
plt.plot(
    tin_x, tin_y, "o", markerfacecolor=(0.7, 0.7, 0.7), markersize=10, markeredgewidth=0, zorder=1, label="_nolegend_"
)

# mark sender position with transparent red circle
ctrpos = nest.GetPosition(ctr_id)
plt.gca().add_patch(plt.Circle(ctrpos, radius=0.15, zorder=99, fc="r", alpha=0.4, ec="none"))

# mark mask positions with open red/blue circles
plt.gca().add_patch(plt.Circle(ctrpos, radius=0.5, zorder=2, fc="none", ec="b", lw=3))
plt.gca().add_patch(plt.Circle(ctrpos, radius=1.0, zorder=2, fc="none", ec="r", lw=3))

# mark layer edge
plt.gca().add_patch(plt.Rectangle((-1.5, -1.5), 3.0, 3.0, zorder=1, fc="none", ec="k", lw=3))

# beautify
plt.axes().set_xticks(np.arange(-1.5, 1.55, 0.5))
plt.axes().set_yticks(np.arange(-1.5, 1.55, 0.5))
plt.grid(True)
plt.axis([-1.6, 1.6, -1.6, 1.6])
plt.axes().set_aspect("equal", "box")
plt.show()