2017-04-24-Poisson-firing-basic


Poisson firing with a gaussian preference (Basic place cell)


In [1]:
%pylab inline --no-import-all
import numpy as np

# Gaussian function
def sum_of_gaussians(a, positions, c):        
    f = lambda x: sum(a * np.exp( -(x-b)**2 / (2 * c**2)) for b in positions)
    return f

def poisson_firing(ratefn, time):
    """
    ratefn describes the prescribed rate for each point in time t. 
    (Try to use a lambda function for the ratefn input)
    Time can be in seconds or milliseconds
    
    Assumption:
    Assuming only one spike can happen in a second (reasonable assumption)
    Effective refractive period for continuous firing is 1 ms 
    (i.e max firing = 1000 Hz)
    Good enough assumption as long as a rate function with an insane firing
    rate is used
    """
    
    dt = time[1]-time[0]
    spiketimes = []    
    
    for t in time:
        P = np.exp(-1 * dt * ratefn(t))
        rand = np.random.random()
        if np.random.random() > P:
            spiketimes.append(t)

    return spiketimes


Populating the interactive namespace from numpy and matplotlib

In [2]:
# 1-D line
vel = 1    # 1 unit per sec
t = np.arange(0, 30, 0.001)
x = lambda t: vel * t

# Preference distribution of neurons (tuning curve) - max firing - 50 Hz
neuron1_preference = sum_of_gaussians(50, [10], 5)
neuron2_preference = sum_of_gaussians(50, [15], 5)
neuron3_preference = sum_of_gaussians(50, [20], 5)

# Plot preference
pylab.plot(x(t), neuron1_preference(x(t)))
pylab.plot(x(t), neuron2_preference(x(t)))
pylab.plot(x(t), neuron3_preference(x(t)))


Out[2]:
[<matplotlib.lines.Line2D at 0x7fc78c90aed0>]

In [5]:
# Obtain poisson based firing rates of each (place cell) neuron
trials = 10

neuron1_firing = []
neuron2_firing = []
neuron3_firing = []

for _ in range(trials):
    neuron1_firing.append(poisson_firing(lambda t: neuron1_preference(vel * t), t))
    neuron2_firing.append(poisson_firing(lambda t: neuron2_preference(vel * t), t))
    neuron3_firing.append(poisson_firing(lambda t: neuron3_preference(vel * t), t))

In [6]:
# Raster plot each of the three neurons
for i in range(trials):
    pylab.plot(neuron1_firing[i], (5 * i + 1) * np.ones(len(neuron1_firing[i])), '|b')
    pylab.plot(neuron2_firing[i], (5 * i + 2) * np.ones(len(neuron2_firing[i])), '|g')
    pylab.plot(neuron3_firing[i], (5 * i + 3) * np.ones(len(neuron3_firing[i])), '|r')

# beautify
pylab.axes().set_xticks(np.arange(0,30+1,5))
pylab.axes().set_yticks(np.arange(0,trials*2,3))


Out[6]:
[<matplotlib.axis.YTick at 0x7fc78c882b90>,
 <matplotlib.axis.YTick at 0x7fc78c8a1350>,
 <matplotlib.axis.YTick at 0x7fc78b976790>,
 <matplotlib.axis.YTick at 0x7fc78b976cd0>,
 <matplotlib.axis.YTick at 0x7fc78b97d2d0>,
 <matplotlib.axis.YTick at 0x7fc78b97da10>,
 <matplotlib.axis.YTick at 0x7fc78b986190>]