spyke

spyke is a Python package for visualization, navigation, and spike sorting of our extracellular waveform data.

download

Here's a recent (as of 2010-03-26) revision, rev761:

Note that this code is currently in a state of flux.

Here are its current dependencies:

There may be some others that I've forgotten about. Let me know if you need help.

If installing on win32, you'll also need the free MinGW compiler. See http://wiki.cython.org/InstallingOnWindows.

If you're running 64 bit windows, you can install 64 bit versions of all of these dependencies, and gain the benefit of almost unlimited virtual memory on your 64 bit machine. Christoph Gohlke has put together a vast collection of recent versions of various 32 and 64 bit Python packages for windows, including all those listed above. These are otherwise hard to find and difficult to build yourself.

Mayavi is part of the Enthought Tool Suite, and is easiest to install from Christoph Gohlke's page.

If installing on win64, unfortunately you'll need Microsoft Visual Studio 2008 to build the scipy.weave code and the Cython code included in spyke. There isn't a working 64 bit compiler in MinGW as far as I know.

wxPython has some bugs running in linux unfortunately. I may try working around them at some point, or I may switch to Qt instead.

sample data

Here's 1 sec of spontaneous extracellular waveform data in .srf format. You can use this for testing spyke:

SwindaleLab: spyke (last edited 2010-03-26 14:54:04 by MartinSpacek)