Acquisition and Analysis of Neural Data: Analytical Problem Set 1

Acquisition and Analysis of Neural Data
Bernstein Center for Computational Neuroscience Berlin

Lecturer: Prof. Dr. Richard Kempter
Tutors: Paula Kuokkanen and Tiziano D’Albis
Analytical Problem Set 1 Deadline: Tuesday 28th April, 2020 at 23:55
Please scan and upload your solution on Moodle as a single PDF file by the due date. Each student must submit their
own solution. Do not forget to write your name and to mention if you collaborated with someone. Please specify how
much time you needed to finish the exercise.
Convolution and Dirac delta
The convolution of two functions u(t) and v(t) is defined as

Z ∞
(u ∗ v)(t) = u(t − s)v(s) ds . (1)
−∞
Convolution is used widely in mathematics, physics, and engineering, e.g., in signal processing and linear systems’
analysis. In neuroscience, it could be used to estimate firing rates from discrete spike times. With the following
exercises, you will get an intuitive understanding of the convolution operation.
1. Graphical convolution (3 points)

The response A = x ∗ h of a linear, time invariant, system is given by the convolution of the input signal x(t) and the
system’s impulse response h(t). Here, we perform a “graphical” convolution between x and h, by computing the area
under the product of the two functions. Consider the following functions:
 
0 for t < 0
 0 for t < 0

x(t) = 3 for 0 6 t 6 3 and h(t) = 4 for 0 6 t 6 1
 
0 for t > 3 0 for t > 1 .
 
(a) Sketch x(t − s) and h(s) as a function of s for a fixed, generic value of t. Identify the intervals of t where the
system has a stereotypical response. For each interval, sketch again x(t − s) and h(s) as a function of s.
R∞
(b) Compute the system’s response A(t) = −∞ x(t − s)h(s) ds and sketch the result.
2. Properties of the convolution (3 points)

Prove the following properties of the convolution:
(i) Commutative: (u ∗ v)(t) = (v ∗ u)(t)

(ii) Distributive: (u ∗ (αv + βw))(t) = α (u ∗ v)(t) + β (u ∗ w)(t) for all α, β ∈ R
(iii) Associative: (u ∗ (v ∗ w))(t) = ((u ∗ v) ∗ w)(t)
where ∗ stands for convolution. Hint: use the definition of the convolution and change of variables.
3. The Dirac delta (4 points)

The Dirac delta is often used to describe analytically the spike times of a neuron. This exercise gets you acquainted
with the Dirac delta defined as a limit of functions. First, remember that the derivative of a function is defined as
d x(t + h) − x(t)
x(t) = lim . (2)
dt h→0 h
The Dirac delta δ(t) can be can be constructed from a rectangular function with infinitely small width and infinitely
large height.
(a) Define a rectangle R(t) with width A and height 1/A using a difference of two Heaviside step functions.
(b) Define a new function D(t) as the limit of R(t) when the width A is arbitrarily small. Write out the function D(t)
explicitly.
(c) Show that for D(t) the following properties hold:
(i) D(t) = 0 for t 6= 0
R∞
(ii) −∞ D(t) dt = 1
R∞
(iii) −∞ f (t − s)D(s) ds = f (t) .
For the first property, plot the function D(t) and explain. For the third property, use a change of variables and the
definition of the derivative. The three properties above can be used to define a Dirac delta, i.e., δ(t) := D(t) .
(d) Can you think of other ways of defining a Dirac delta?
Numerical Problem Set 1 Deadline: Tuesday 28th April, 2020 at 23:55
Please upload your solution on Moodle by the due date. Return both a Python code file (or notebook) and a PDF file
including figures and code. Please use clear, descriptive variable names and comments. Each student must submit
their own files. Do not forget to write your name and to mention if you cooperated with someone. Please also indicate
how much time you needed to complete the exercise.
Estimating firing rates from spike data
1. Firing rate estimation and convolution (10 points)

The goal of this exercise is to learn how to estimate firing rates from spike train data. To start, you need to download
ExampleSpikeTimes1.dat from the Moodle course page.
This .dat-file can be loaded in Python with the numpy function loadtxt(). The file contains a variable named Spike-
Times, which is a vector of spike times ti (in ms) with i = 1, 2, . . . , n in response to a stimulus with a duration of
T = 4000 ms. The temporal resolution of the spike times is 0.1 ms. Hint: it is convenient to convert the data in
seconds. Here, as in all other exercises, use numpy arrays and avoid loops as much as possible.
Your task is to estimate the firing rate with different methods. Hint: Your plots should be organized similar to Fig. 1.4
on page 12 of the Dayan and Abbott book.
(a) (1 point) Plot the raw spike train. Have a look at the pyplot function eventplot. You may need to set the axes
limits manually for correct visualization.
(b) (3 points) Construct spike-count histograms with non-overlapping bins of widths ∆t = 20, 50 and 150 ms, and
normalize them to obtain a firing rate in spikes/s. Hint: Have a look at the pyplot function hist and the weights
parameter.
(c) (5 points) Use the window functions defined below to estimate an approximate firing rate
n Z T
rapprox (t) = ∑ w(t − ti ) = dτ w(t − τ)ρ(τ)
i=1 0
where ρ(t) := ∑ni=1 δ(t − ti ) is the neural response function and T is the trial length. Hint: Have a look at
the analytical exercises on the convolution and the Dirac delta on this sheet. You can use the numpy function
convolve. Make sure you understand the differences between the convolution modes full and same, particularly
regarding time offsets and boundary effects. You could plot the spikes on top of the rates to check that you
obtained the correct time offset. Firing rates shall be plotted in units of spikes/s.
(i.) Estimate the rate with a rectangular window
(
1/∆t if − ∆t/2 ≤ τ < ∆t/2
w(τ) =
0 otherwise
with widths of ∆t = 20, 50 and 150 ms. The rectangular window is centered at each spike, i.e., the filtering
is non causal.
(ii.) Estimate the rate with a Gaussian window
τ2

1
w(τ) = √ exp − 2
2πσw 2σw
with σw = 10, 20 and 50 ms. Here the Gaussian is centered at each spike (non causal filtering).
(iii.) Estimate the rate with an alpha function
w(τ) = α2 τ exp(−ατ) +

where 1/α is a time scale and [x]+ is the half-wave rectification function. Use 1/α = 10, 20 and 50 ms.
Here the rate starts rising only after a spike is emitted, i.e., the filter is causal. Why would one want to use
a causal rather than a non-causal filter?
n 1 RT
(d) (1 point) Calculate the spike count-rate r = T = T 0 dt ρ(t) .
2. Extra: estimation of firing rate and trial averaging (3 extra points)
(a) (1 extra point) Estimate firing rates for the spike data in ExampleSpikeTimes2.dat to see if your code is flexible
enough to handle it. Spike timings are in milliseconds, the trial length is T = 10 s, and the resolution is 0.1 ms.
(b) (2 extra points) Download ExampleSpikeTimes3.dat and calculate first the trial-averaged neural response and
then the trial-averaged firing rate (only one convolution). You can use a filter of your choice. Load the data using
the numpy function loadtxt() with the keyword parameter delimiter=’;’. The file contains a matrix of spike times
in milliseconds. The dimensions are [m x n, where m=100 is the maximum spike-time index and n=1000 is the
number of trials. Note: each trial has a different number of spikes, the remaining entries are filled with nan. The
trial length is T = 1 s, the resolution is 0.1 ms.
Paula Kuokkanen Phone: 2093 98407 Email: paula.kuokkanen at hu-berlin.de Office: Haus 4, Room 107
Tiziano D’Albis Phone: 2093-98413 Email: tiziano.dalbis at hu-berlin.de Office: Haus 4, Room 013

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Acquisition and Analysis of Neural Data

Bernstein Center for Computational Neuroscience Berlin

Analytical Problem Set 1 Deadline: Tuesday 28th April, 2020 at 23:55

Convolution and Dirac delta

The convolution of two functions u(t) and v(t) is defined as

1. Graphical convolution (3 points)

2. Properties of the convolution (3 points)

(i) Commutative: (u ∗ v)(t) = (v ∗ u)(t)

3. The Dirac delta (4 points)

Numerical Problem Set 1 Deadline: Tuesday 28th April, 2020 at 23:55

Estimating firing rates from spike data

1. Firing rate estimation and convolution (10 points)

2. Extra: estimation of firing rate and trial averaging (3 extra points)

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