xcorr: AI & neuro

by Patrick Mineault

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
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September 7, 2011
Update to Gaussian surface fitting function: Gabors

I’ve updated my automatic 2d Gaussian surface fitting function, available in Matlab Central, to add a function to fit Gabors to noisy data. As I’ve discussed previously, fitting a parametric surface to noisy data is pretty trivial whether it’s a Gabor, Gaussian, or otherwise — it’s a straightforward application of numerical optimization that can be
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September 5, 2011
Obscure Matlab features #3: progress reports with publish

Neurophysiology experiments can generate tons of data. In the initial stages of a project, you can easily become overwhelmed with the results of preliminary analyses. It’s a good idea to collect together the results of these analyses into a single document. This can make it easier to peruse the results with others in your lab,
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September 4, 2011
The joy of object-oriented programming in Matlab

Matlab has had support for full object oriented programming (OOP) since 2008a. Those with an OOP background (say, in Java, C# or Python) will find Matlab’s OOP features to be fairly complete. These include: Pass-by-reference semantics via subclassing the handle class Instance methods and static methods Full selection of access control for methods, properties (public,
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August 21, 2011
B-splines: Matlab code

B-splines are mathematical curves with convenient properties. The B in B-spline means basis. A curve y(t) is defined in terms of weights w and knots k, such that . Each basis function is a piecewise polynomial with compact support determined by the position of the knots. The order of the polynomial is determined by the
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August 13, 2011
Temporal precision in the LGN

There’s a new paper just out in J Neurosci by Dan Butts et al. (2011) that offers some key insights into temporal precision in the lateral geniculate nucleus (LGN). The spike trains of LGN cells are remarkably regular; while a Poisson train has Fano factor (variance to mean ratio) of 1, and cortical neurons in
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August 10, 2011