Stimulus estimation in Python
As I mentioned previously I’ve been working on translating my code from Matlab into Python and I was having some trouble with stimulus estimation (aka signal reconstruction). Well, my problems are no more. Fortunately, there is a whole library in Python called Scipy which includes a set of functions called Signal and will cover most of your needs for signal processing in Python. I’ve been using this library extensively and I’ve found so far that it is excellent for scientific programming or at least for my work. It definitely eases the transition from Matlab to Python.
Using this library I can build a Wiener-Kolmogorov filter which allows me to estimate the input that was presented to a spiking neuron model given only the neural response. Below is a picture of what the WK filter looks like and an example of stimulus estimation using this filter.
This is what a Wiener-Kolmogrov filter looks like (left) and stimulus estimation (right) using that same filter.
As you can see it works pretty well. There is even a very good way to quantify how well it works but I won’t go into that right now. This was the hardest part so far and I think I can safely say that I am now almost as proficient with Python as I am with Matlab at least as far as scientific programming goes.
So, to help others that may need it and maybe to feel a bit proud of myself and my work, here is a simple function for stimulus estimation/reconstruction in a neural system using a Wiener-Kolmogorov filter.
