Kwik format

This page describe the Kwik format.

Quick start with MATLAB

You can open Kwik files in recent versions of MATLAB (they have native support for HDF5).

To read the spike times and cluster numbers, type (filename is the .kwik file):

hdf5read(filename, '/channel_groups/0/spikes/time_samples');
hdf5read(filename, '/channel_groups/0/spikes/clusters/main');

The channel_group number is the shank number (indexing starts at 0).

Data files

All files are HDF5 files.

• The data is stored in the following files:

  • the KWIK file is the main file, it contains:
    • all metadata
    • spike times
    • clusters
    • recording for each spike time
    • probe-related information
    • information about channels
    • information about cluster groups
    • events, event_types
    • aesthetic information, user data, application data
  • the KWX file contains the masks and features of every spike

• Once spike sorting is finished, one can discard the KWX file and just keep the KWIK file for subsequent analysis (where spike sorting information like masks and features are not necessary).

KWIK

Below is the structure of the KWIK file.Everything is a group, except fields with a star (*) which are either leaves (datasets: arrays or tables) or attributes of their parents.

[X] is 0, 1, 2...

/kwik_version* [=2]
/name*
/application_data
    spikedetekt
        MY_SPIKEDETEKT_PARAM*
        ...
/channel_groups
    [X]  # Absolute channel group index from 0 to Nchannelgroups-1
        name*
        channel_order*  # ordered list of channels, as specified in the PRB file
        adjacency_graph* [Kx2 array of integers]
        application_data
        channels
            [X]  # Relative channel index from 0 to shanksize-1
                name*
                ignored*
                position* (a pair (x, y) in microns relative to the whole multishank probe)
                voltage_gain* (a float32 number, in microvolts)
                display_threshold*
                application_data
                    spikedetekt
        spikes
            time_samples* [N-long EArray of UInt64]
            time_fractional* [N-long EArray of UInt8]
            recording* [N-long EArray of UInt16]
            clusters
                main* [N-long EArray of UInt32]
                original* [N-long EArray of UInt32]
            features_masks
                hdf5_path* [='{kwx}/channel_groups/X/features_masks']
            waveforms_raw
                hdf5_path* [='{kwx}/channel_groups/X/waveforms_raw']
            waveforms_filtered
                hdf5_path* [='{kwx}/channel_groups/X/waveforms_filtered']
        clusters
            [clustering_name]
                [X]  # Cluster number from 0 to Nclusters-1 (unique within a given channel group & clustering name)
                    cluster_group*
                    mean_waveform_raw*
                    mean_waveform_filtered*
                    quality_measures
                        isolation_distance*
                        matrix_isolation*
                        refractory_violation*
                        amplitude*
                        ...
        cluster_groups
            [clustering_name]
                [X]  # Cluster group number
                    name*
/recordings
    [X]  # Recording index from 0 to Nrecordings-1
        name*
        start_time*
        start_sample*
        sample_rate*
        bit_depth*
        band_high*
        band_low*
        raw
            hdf5_path* [='{raw.kwd}/recordings/X']
        high
            hdf5_path* [='{high.kwd}/recordings/X']
        low
            hdf5_path* [='{low.kwd}/recordings/X']

KWX

The KWX file contains spike-sorting-related information.

/kwik_version* [=2]
/channel_groups
    [X]
        features_masks* [(N x NFEATURES x 2) EArray of Float32]