Category: Neural signal processing

• Reading Plexon files in Linux or Mac

  Updates (12/10 /2011): Plexon now offers a mex extension for Matlab which compiles on Linux and Mac. I have a Python .plx file reader available, and Huang Xin has a better one based on ctypes, part of RealTimeElectrophy. Plexon hardware is meant to interface with Windows-only tools (including recording software). I think that for such…

  September 7, 2011

• Matching Pursuit for one-dimensional signals: Matlab code

  Matching Pursuit (MP) is a greedy algorithm to obtain a sparse representation for a signal in terms of elements of a dictionary. I’ve seen it used from time to time in neuroscience. For example, Smith and Lewicki (2006) use it as part of their demonstration that a sparse code for natural sounds matches the properties…

  August 5, 2011

• Estimating a PSTH with Bayesian splines (BARS)

  The PSTH (post-stimulus time histogram) summarizes the timing of neuronal spikes following a stimulus. When few trials are available, or the neuron being recorded seldom fires, the PSTH can be quite noisy. Thus, the PSTH is frequently smoothed with a Gaussian kernel — for example, to reliably estimate the latency of the response. It is…

  July 30, 2011

• Wideband monitor for Plexon hardware

  Plexon has a Matlab API that can be used to stream wideband, LFP and spike data for real-time processing. It’s available in the Downloads section of the Plexon website under the name “Matlab client development kit”. They include several sample applications with the API, including a real-time LFP monitor. However, it’s missing a few features…

  July 20, 2011

• Baudline software for viewing long neural recordings on Linux

  Viewing the frequency spectrum of a wideband or LFP signal is important to detect noise issues, whether line noise, monitor refresh noise, reward artifacts or other anomalies. Removing artifacts is critical not only to obtain clean LFPs and wideband signals, but also to sort spikes in low SNR scenarios, for example with multi-electrode arrays. We…

  May 25, 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