xcorr: AI & neuro

by Patrick Mineault

LFPs above 50Hz: is it all garbage?

There’s a recent paper by the Maunsell lab in PLoS Biology that examines the origins of local field potentials in the low-gamma (30-80Hz) and high-gamma ranges (> 80 Hz) ranges. The paper uses a clever experimental paradigm that allows one to dissociate LFPs and spike activity through the phenomenon of surround suppression. Basically, in surround
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May 12, 2011
Plexon C++ API on 64-bit Linux

Plexon has a C++ SDK which I was toying around with because all Plexon software including the Matlab API is Windows only, and all of our analyses run on 64-bit Ubuntu. So I figured the command line version of the .plx reader could be modified to run on Linux and suit our needs. Surprisingly, this
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May 11, 2011
Is it practical to train an HMM for spike sorting with Baum-Welch?

*The short version: at the end of the post there’s some fast code (Matlab with MEX) for training an HMM for spike sorting* Earlier, we evaluated different solutions for sorting spikes for our 96-electrode array. One solution we looked at was spike sorting with HMMs (Hidden Markov Model). While most spike sorters first detect spikes
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May 7, 2011
MEX file generator

I just posted a script in Matlab Central that generates a .c file that can be compiled with mex based on a snippet of (purely numeric) C code and a definition of the arguments to the function. In the file description I show how to write a recursive (IIR) filter in 3 lines of C
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May 3, 2011
Hierarchical Bayes and WinBUGS for tracking receptive fields

I’ve been reading Bayesian Modeling Using WinBUGS: An introduction. It’s a really nice intro to fitting complex Bayesian models with WinBUGS (aka OpenBUGS), which is a program that can sample from the posterior distribution of a Bayesian model’s parameters using MCMC methods (the GS in BUGS stands for Gibbs sampling). MCMC methods are very general,
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April 18, 2011
Faster median in Matlab

There are O(n) algorithms for finding a median, yet Matlab uses an O(n log n) algo (sorting an entire list, then taking the middle element). Here is a nicely written mex file that performs medians faster (on my computer, about 3x faster).
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April 5, 2011