# LGN-Retinal Filter II

Now that we know how to crate a filter is time to use it to calculate how an LGN neuron would react to an incoming stimulus.
In this entry we will create a white noise stimulus in order to see how an LGN neuron reacts to it, this approach has the advantage that we can then
recover the filter by

In the same spirit of the last post, we will define the spatial and time parameters that determine the lengths and resolutions in those dimensions:

#Time parameters dt = 1.0 # resolution of the response (in milliseconds) dt_kernel = 5.0 # resolution of the kernel (in milliseconds) dt_stimuli = 10.0 # resolution of the stimuli (in milliseconds) kernel_size = 25 # The size of the kernel T_simulation = 2 * 10 ** 2.0 # Total time of the simulation in ms Nt_simulation = int(T_simulation / dt) #Simulation points N_stimuli = int(T_simulation / dt_stimuli) #Number of stimuli # Space parameters dx = 1.0 Lx = 20.0 Nx = int(Lx / dx) dy = 1.0 Ly = 20.0 Ny = int(Ly / dy )

Now, we call our kernel which we have wrapped-up as a function from the work in the last post:

# Call the kernel # Size of center area in the center-surround profile sigma_center = 15 # Size of surround area in the center-surround profile sigma_surround = 3 kernel = create_kernel(dx, Lx, dy, Ly, sigma_surround, sigma_center, dt_kernel, kernel_size)

With this in our hand we can use the numpy random functions to create our white noise stimuli, we use here the realization of white noise call ternary noise which consists on values of -1, 0 and 1 assigned randomly to each pixel in our stimuli:

# Call the stimuli stimuli = np.random.randint(-1, 2, size=(N_stimuli, Nx, Ny))

Before we can proceed to calculate the convolution we need to do some preliminary work. The convolution problem involves three time scales with different resolutions. We have first the resolution of the response * dt *, the resolution of the kernel * dt_kernel * and finally the resolution of the stimulus * dt_stimuli*.Operations with the kernel involve jumping from one scale to another constantly so we need a mechanism to keep track of that. In short, we would like to have a mechanism that transforms from some coordinates to the others in one specific place and not scatter all over the place.

Furthermore, in the convolution the kernel is multiplied by a specific point of images for each point in time. For the sake of efficiency we would like to have a mechanism that does this for once. With this in mind I have built a set of indexes for each scale that allow us to associate each element on the indexes of the response to its respective set of images. Also, we have a vector that associates every possible delay time in the kernel to the set of indexes in the response. We illustrate the mechanisms in the next figure

We can appreciate the three different times scales in the image. Furthermore, we have a set of indexes called delay indexes that maps each response to its respective image and also other set of indexes called delay indexes that map each of the delays to his respective response. We can create this set of indexes with the following code:

# Scale factors input_to_image = dt / dt_stimuli # Transforms input to image kernel_to_input = dt_kernel / dt # Transforms kernel to input input_to_kernel = dt / dt_kernel # Transforms input to kernel working_indexes = np.arange(Nt_simulation).astype(int) # From here we remove the start at put the ones remove_start = int(kernel_size * kernel_to_input) signal_indexes = np.arange(remove_start, Nt_simulation).astype(int) # Calculate kernel kernel_times = np.arange(kernel_size) kernel_times = kernel_times.astype(int) # Delay indexes delay_indexes = np.floor(kernel_times * kernel_to_input) delay_indexes = delay_indexes.astype(int) # Image Indexes stimuli_indexes = np.zeros(working_indexes.size) stimuli_indexes = np.floor(working_indexes * input_to_image) stimuli_indexes = stimuli_indexes.astype(int)

Now, we can calculate the response of a neuron with a center-surround receptive field by performing the convolution between its filter and the stimuli. We also plot the stimuli to see how it looks:

for index in signal_indexes: delay = stimuli_indexes[index - delay_indexes] # Do the calculation signal[index] = np.sum(kernel[kernel_times,...] * stimuli[delay,...]) t = np.arange(remove_start*dt, T_simulation, dt) plt.plot(t, signal[signal_indexes], '-', label='Kernel convoluted with noise') plt.legend() plt.xlabel('Time (ms)') plt.ylabel('Convolution') plt.grid() plt.show()

We can see that the resolution of the response is as good as the resolution of the filter and this explains the discontinuities in the figure above.

As a sanity check we can calculate a voltage triggered average to recover the sta:

## Calculate the STA kernel_size = kernel_times.size Nside = np.shape(stimuli)[2] sta = np.zeros((kernel_size ,Nside, Nside)) for tau, delay_index in zip(kernel_times, delay_indexes): # For every tau we calculate the possible delay # and take the appropriate image index delay = stimuli_indexes[signal_indexes - delay_index] # Now we multiply the voltage for the appropriate images weighted_stimuli = np.sum( signal[signal_indexes, np.newaxis, np.newaxis] * stimuli[delay,...], axis=0) # Finally we divide for the sample size sta[tau,...] = weighted_stimuli / signal_indexes.size

Which we can plot in a convenient way with the following set of instructions:

## Visualize the STA closest_square_to_kernel = int(np.sqrt(kernel_size)) ** 2 # Define the color map cdict1 = {'red': ((0.0, 0.0, 0.0), (0.5, 0.0, 0.1), (1.0, 1.0, 1.0)), 'green': ((0.0, 0.0, 0.0), (1.0, 0.0, 0.0)), 'blue': ((0.0, 0.0, 1.0), (0.5, 0.1, 0.0), (1.0, 0.0, 0.0)) } from matplotlib.colors import LinearSegmentedColormap blue_red1 = LinearSegmentedColormap('BlueRed1', cdict1) n = int( np.sqrt(closest_square_to_kernel)) # Plot the filters for i in range(closest_square_to_kernel): plt.subplot(n,n,i + 1) plt.imshow(sta[i,:,:], interpolation='bilinear', cmap=blue_red1) plt.colorbar() plt.show()

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