Scribd
Upload
64 views

Neuron Spiking Code in Python

This Python code simulates a neural network model with excitatory and inhibitory neurons. It initializes parameters for the neurons, sets up the connectivity matrix and inputs. It then runs a simulation over 1000 time steps, tracking the membrane voltages and spikes of each neuron. Finally, it plots the spiking activity of the neurons over time.

Uploaded by

Ankit
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PDF, TXT or read online on Scribd
64 views

Neuron Spiking Code in Python

This Python code simulates a neural network model with excitatory and inhibitory neurons. It initializes parameters for the neurons, sets up the connectivity matrix and inputs. It then runs a simulation over 1000 time steps, tracking the membrane voltages and spikes of each neuron. Finally, it plots the spiking activity of the neurons over time.

Uploaded by

Ankit
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PDF, TXT or read online on Scribd
You are on page 1/ 2

CODE IN PYTHON NAME :- Ankit kumar

import numpy as np

Ne=400 # Excitatory neurons


Ni=200 # Inhibitory neurons
float_type = np.float

re=np.random.rand(Ne).astype(float_type)
ri=np.random.rand(Ni).astype(float_type)

#The parameter "a" describes the time scale of the recovery variable u
a=np.concatenate((0.02*np.ones(Ne),0.02+0.08*ri)).astype(float_type)

#The parameter "b" describes the sensitivity of the recovery variable


# u to the subthreshold fluctuations of the membrane potential v

b=np.concatenate((0.2*np.ones(Ne),0.25-0.05*ri)).astype(float_type)

#parameter c describes the after-spike reset value of the membrane potential v caused by
the fast high-threshold K+ conductance
c=np.concatenate((-65+15*re**2,-65*np.ones(Ni))).astype(float_type)

#The parameter d describes after-spike reset of the recovery variable u caused by slow h
igh-threshold Na+ and K+ conductances
d=np.concatenate((8-6*re**2,2*np.ones(Ni))).astype(float_type)

# Excitatory and Inhibitory weights


S=np.hstack([0.5*np.random.rand(Ne+Ni,Ne),\
-np.random.rand(Ne+Ni,Ni)]).astype(float_type)

# Initial membrane voltage


v=-65*np.ones(Ne+Ni, dtype=float_type)

# State variable (recovery)


u=(b*v)

Nsteps = 1000 # simulation of 1000 ms


step = 0.5 # step 0.5 ms
step_3 = step/3.0

firings_ids=np.empty((Nsteps,Ne+Ni),dtype=float_type)

voltages=np.empty((Nsteps,Ne+Ni),dtype=float_type)
voltages_cropped=np.empty((Nsteps,Ne+Ni),dtype=float_type)

I=np.concatenate((5*np.random.normal(loc=0,scale=1,size=Ne),\
2*np.random.normal(loc=0,scale=1,size=Ni))).astype(float_type) # t
halamic input
C:\Users\ankit\anaconda3\lib\site-packages\ipykernel_launcher.py:5: Deprecation
Warning: `np.float` is a deprecated alias for the builtin `float`. To silence t
his warning, use `float` by itself. Doing this will not modify any behavior and
is safe. If you specifically wanted the numpy scalar type, use `np.float64` her
e.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devd
ocs/release/1.20.0-notes.html#deprecations
"""
for t in range(Nsteps):
I=np.concatenate((5*np.random.normal(loc=0,scale=1,size=Ne),\
2*np.random.normal(loc=0,scale=1,size=Ni))).astype(float_
type) # thalamic noisy input
fired=(v>=30) # finds spiking neurons indices
firings_ids[t,:]=fired
voltages[t,:]=v # I'm saving before the cropping
v[fired]=c[fired]
voltages_cropped[t,:]=v # Here I'm saving after crop

u[fired]=u[fired]+d[fired]
I=I+S[:,fired].sum(axis=1)

# Integration
v+=step*(0.04*v**2+5*v+140-u+I)
u+=step*a*(b*v-u)

ids=np.arange(1,Ne+Ni+1)
pfired = []
tfired = []
for t,fired in zip(range(Nsteps),firings_ids):
res=ids[fired==1]
for fi in res:
pfired.append(fi)
tfired.append(t)
pfired = np.array(pfired)
tfired = np.array(tfired)

import matplotlib.pyplot as plt


%matplotlib inline
plt.plot(tfired*step,pfired,'.')
plt.xlabel("t(ms)")
plt.ylabel("neuron index")
plt.show()

You might also like