#openephys

A python library and scripts for loading and converting data saved by the Open Ephys GUI.

Python 2/3 compatible.

More info on the Open Ephys data format can be found at https://open-ephys.atlassian.net/wiki/display/OEW/Data+format

More info on the Kwik data format (implemented in the GUI as of October 2014) can be found at https://github.com/klusta-team/kwiklib/wiki/Kwik-format

install

git clone https://github.com/kylerbrown/openephys.git
pip install -e openephys

scripts

• kwik2arf.py: converts .kwd files to .arf
• kwik2dat.py: converts .kwd files to raw binary, which is used by programs such as phy, neuroscope.
• kwik2wav.py: converts a selected channel to a .wav file for acoustic analysis.

For Python:

• use the 'OpenEphys.py' module for .continuous files, .spikes, and .events files
• use the 'kwik.py' module for .kwd files

Spike sorting with Spyking Circus

• Obtain source code from here. Follow the install instructions. Spyking circus has good documentation, so you may want to spend some time reading through it.

• Convert raw.kwd file to a raw binary, for example: kwik2dat.py experiment1_100.raw.kwd. If only some channels contain neural data, run kwik2dat.py experiement1_100.raw.kwd -c 6 7 8, where 6 7 8 are the zero indexed channel numbers. (You can use h5ls -r experiement1_100.raw.kwd to see the total number of recorded channels. Or you can export all the channels by leaving out the -c flag and view the raw data first in neuroscope)

• Run spyking-circus *.dat, spyking circus will ask if you want to create a parameter file. Say yes. [y ENTER]

• edit the .params file. At a minimum you must change these lines:

    data_offset    = 0                    # Length of the header ('MCS' is auto for MCS file)
    mapping        = probe_map.prb     # Mapping of the electrode (see http://spyking-circus.rtfd.ord)
    data_dtype     = int16                 # Type of the data
    sampling_rate  = 30000                  # Sampling rate of the data [Hz]
  

• Here the file probe_map.prb is an example probe file for 3 independent electrodes. You're going to want to use a different .prb file, one that matches your array. Here's the contents of file, placed in the same directory:

    total_nb_channels = 3
    radius = 00
    channel_groups = {
        0: {
            "channels": [0, 1, 2],
            "graph" : [[0, 1],[1, 2], [0, 2]],
            "geometry": {
                0: [0, 0],
                1: [0, 200],
                2: [200, 200],
            }
        }
    }
  

Note that the channel names are now 0, 1 and 2, instead of 6, 7, 8, as extracted from the .kwd file. For more information on designing a .prb file see the spyking circus documentation.

• finally, re-run spyking-circus *.dat.
• Make coffee ☕