A Python package written by Martin Spacek for visualizing, navigating, and spike sorting our high-density multichannel extracellular waveform data.
The latest version, along with its entire history, is now available on GitHub. It’s now developed in Linux and has fewer dependencies than before.
sample data
Here is 20 sec of 54 channel 25 kHz spontaneous extracellular data in .srf format. You can use this for testing spyke:
- ptc15_tr7c_r87_spont_20sec.zip (52 MB)
old version
Here’s a very old (as of 2010-03-26) revision, rev761:
- source distribution, in tar.gz format: spyke-0.2.rev761.tar.gz
Here are the dependencies for rev761:
- Python 2.6
- NumPy
- SciPy
- matplotlib
- wxPython
- Mayavi (see below)
- Cython
- PyWavelets
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 https://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.