pySpikeSorter

• A(nother) spike sorting utility capable of helping in the analisis of extracelullar action potential recordings.
• It is inspired by some of the features of the offline sorter software from plexon.
• It is intended to be a completely "Manual" solution for spike sorting (old school neurophysiologists don't like automated stuf, although there is some work to provide and/or interface with automatic clustering algorithms.
• It is far from being complete, but at this moment it is functional.
• I'm not a programmer, so I think there are lots of things that can be improved, that is why any comments aiming at improving it are welcome.

Installation Instructions:

Requirements:

• Numpy
• Scipy
• Matplotlib
• PyQt4
• pyopengl
• guidata
• pyqtgraph
• pytables
• optional: Klustakwik

To meet all the requirements is important to have a working python installation.

In Debian based linux distributions i.e. ubuntu you can do:

sudo apt-get install python-numpy python-scipy python-tables python-guidata python-matplotlib
sudo apt-get install python-opengl python-qt4-gl
sudo pip install pyqtgraph

In Windows it is recomemnded to install a python bundle, for example PythonXY.

Under MacOS it is recommended to install the Enthought package, which bundles most of the requirements. If you do not want to install enthought, there are guides that can be used to succesfully install python in MAC: link1 , link2

Running pySpikeSorter:

There is no installation needed. Just download the files to a known location, and from the command line run:

cd /folder/that/contains/the/files
ipython -i pySpikeSorter.py

Notes:

• It is not required to use ipython, but is more convenient if one wants to explore and intereact with the Spyke Sorter object.

Tutorial:

• A "test.h5" file is provided, which can be loaded in the appplication clicking on the green button.
• It should display an overview of the channels
• By clicking a particular channel it gets selected. Clicking the "Plot Chan" button plots the data in a specific Tab.
• Under that tab there are aeveral analisys and tools that can be used to sort the data.

Video Tutorial:

in progress ...

Screenshots:

##H5File Definition: pySpikeSorter allows to sort spike events saved in an H5File. The package Neo, makes possible to read data in various formats and transform those into an h5file. The excellent package Pytables provides a convenient way to create and manipulate these files.

To facilitate the process, a sample h5file with the basic structure is provided. You can examine the internal structure of the files using the viTables application. The h5file basic structure is as follows:

• A group or folder called 'Spikes' (capital 'S')
• Inside, one grou/folder named 'Chan_000', where the zeros are replaced by the channel number. Note that the script asumes there are three integers.
• Inside each channel folder a:
  • 'Waveforms' numpy array, with the shape (events, points)
  • 'Unsorted': numpy array containing the indices of the unsorted events.
  • 'isMultiunit': boolean
  • 'TimeStamp': a numpy vector containing the timestamps (in milliseconds) of the neural events.
  • 'isTrash': Boolean.

To do List:

• Tetrodes implementation.