Category: Selected articles
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GLMs and Hidden Markov models for single neurons
I posted recently about modeling neurons with continuous state-space dynamics. It’s also possible to model neurons with Hidden Markov models (HMMs), which are state-space models with discrete rather than continuous states. In this post I’m going to focus on the application of HMMs to single neuron data. Single neurons with simple states Suppose that a…
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State-space GLMs for neural data: a simple example
State space methods are a very broad class of methods to analyze temporal data. At its most basic, you assume that your temporal data is generated by a model with underlying parameters. The parameters are time-varying, and usually it’s assumed that the temporal variation is generated through Markovian dynamics. That is, at every time-step, the…
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Removing line noise from LFPs, wideband signals
…Trail of papers had a recent post on standard analyses in neuroscience, which reminded me that I’ve meaning to post about signal preprocessing for a while now. If there’s too much line noise (electrical noise at multiples of 60Hz in North America and 50Hz in Europe) in a signal, this will render the signal unusable.…
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Using the SVD to estimate receptive fields
Spatio-temporal receptive fields can be hard to visualize. They can also be quite noisy. Thus, it’s desirable to find a low-dimensional approximation to the RF that is both easier to visualize and less noisy. The SVD is frequently used in neurophysiology for this purpose. Reading the Wikipedia page on the SVD, you might have trouble…
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Spikes trigger LFP waves – not so fast
There’s been a lot of buzz at recent conferences around a controversial new paper in J. Neurosci. from Ray and Maunsell on LFP traveling waves. It’s a pretty direct, and rather convincing rebuttal of an influential Nature Neuroscience paper by Nauhaus et al. published a couple of years ago. Initial findings Nauhaus found what seemed…
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Reading .plx files in Mac/Linux: a Python script
Update (12/10/2011): Huang Xin has written better Python script based on ctypes, part of RealTimeElectrophy. I posted a few days ago on solutions for reading .plx files on Mac/Linux, and was kind of bummed out that in spite of doing a thorough background search I couldn’t find a really satisfying solution to the problem. So…
xcorr: AI & neuro 