Plotting Neural Events With Spike Raster Plot Using Python Matplotlib

Overview:

  • A Spike raster plot is a plot used in neuroscience to study the neural responses.

 

  • Neurons generate spikes or action potentials in response to various stimuli.

 

  • The Spike raster plot marks the neural activity - either a spike or an action potential from a neuron at a specified position.

 

  • The Y-axis of the spike raster plot can represent either a neuron or a trial number of the experiment on a specific neuron.

 

  • The X-axis of the spike raster plot represents the spike.

 

  • The eventplot() function matplotlib.pyplot module marks lines at specified locations.

 

  • If the orientation of the plot is horizontal the lines drawn are vertical lines.

 

  • If the orientation of the plot is vertical the lines drawn are horizontal lines.

 

  • The line drawn extends to both sides of the Y-axis or the X-axis (when orientation of the plot is vertical) with equal height or width.

 

  • The size of the line is controlled by the linelengths parameter.

 

Example:

import matplotlib.pyplot as plot

import numpy as np

 

# Set the random seed for data generation

np.random.seed(2)

 

# Create rows of random data with 50 data points simulating rows of spike trains

neuralData = np.random.random([8, 50])

 

# Set different colors for each neuron

colorCodes = np.array([[0, 0, 0],

                        [1, 0, 0],

                        [0, 1, 0],

                        [0, 0, 1],

                        [1, 1, 0],

                        [1, 0, 1],

                        [0, 1, 1],

                        [1, 0, 1]])

                       

# Set spike colors for each neuron

lineSize = [0.4, 0.3, 0.2, 0.8, 0.5, 0.6, 0.7, 0.9]                                  

        

# Draw a spike raster plot

plot.eventplot(neuralData, color=colorCodes, linelengths = lineSize)     

 

# Provide the title for the spike raster plot

plot.title('Spike raster plot')

 

# Give x axis label for the spike raster plot

plot.xlabel('Neuron')

 

# Give y axis label for the spike raster plot

plot.ylabel('Spike')

 

# Display the spike raster plot

plot.show()

 

Output:

Spike Raster Plot used in neuroscience drawn using Python Matplotlib


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