Category: Selected articles

• An alternative method for spike-triggered covariance

  Spike-triggered covariance (STC) is a method of estimating receptive fields with quadratic or more generally symmetric nonlinearities in stimulus space. The basis idea behind spike-triggered covariance is that the ensemble of stimuli which drive a cell has different statistical properties than the ensemble of all stimuli that are presented to a neuron. In particular if…

  June 2, 2011

• Quartz clock accuracy matters in RF estimation

  To estimate visual receptive fields accurately with reverse correlation or other inference techniques, you need to know the exact timing of each stimulus and spike (give or take 10 ms). In my more naive days, I thought that I could use the nominal frame rate of the computer screen to figure out when each frame…

  May 17, 2011

• 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…

  May 12, 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…

  May 7, 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,…

  April 18, 2011

• Forwarding spikes in a Plexon system to some other computer over IP

  We have a 96-channel MAP Plexon system in the lab, which we use to record from an array implanted in V4. Originally we ran open-loop experiments (mapping stimuli and such), but soon we decided to perform closed loop experiments. Recording at 10kHz per channel sucks up a lot of CPU and thus the presentation software…

  March 9, 2011