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Kwik format

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Cyrille Rossant edited this page Jun 10, 2014 · 36 revisions

File format specification

Warning: the following specification concerns v0.3+ of the KlustaSuite.

Quick info

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

To read the spike times and cluster numbers, open the .kwik file and do:

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 in HDF5.

  • The data are 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 spiking data: features, masks, waveforms
    • the KWD files contain the raw/filtered recordings

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

  • All files contain a version number in / (kwik_version attribute), which is an integer equal to 2 now.

  • There can be other HDF5 .kwd files with similar structures, containing more specific information related to particular experiments and protocols. This should make possible the compatibility with Open Ephys.

  • The input files the user provides to the programs to generate these data are:

    • the raw data coming out from the acquisition system, in any proprietary format (NS5, etc.)
    • processing parameters (PRM file) and description of the probe (PRB file)

  • There's support for multiple clusterings. By default, there are two clusterings: main (manual) and original (output of KlustaKwik). More clusterings can be added.

  • The mapping between the columns in the raw data array (old .dat file, or new .kwd file), and the channels (defined in the probe file), is trivial. In other words, column #i in the raw data array corresponds to channel #i. Channels have absolute indices spanning all shanks.

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*
        ...
/user_data
/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
        user_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
                    klustaviewa
                    spikedetekt
                user_data
        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)
                    application_data
                        klustaviewa
                            color*
                    cluster_group*
                    mean_waveform_raw*
                    mean_waveform_filtered*
                    quality_measures
                        isolation_distance*
                        matrix_isolation*
                        refractory_violation*
                        amplitude*
                    user_data
                        ...
        cluster_groups
            [clustering_name]
                [X]  # Cluster number from 0 to Nclusters-1 (unique within a given channel group & clustering name)
                    name*
                    application_data
                        klustaviewa
                            color*
                    user_data
/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']
        user_data
/event_types
    [X]  # The name of the event type.
        user_data
        application_data
            klustaviewa
                color*
        events
            time_samples* [N-long EArray of UInt64]
            recording* [N-long EArray of UInt16]
            user_data [group or EArray]

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]
        waveforms_raw* [(N x NWAVESAMPLES x NCHANNELS) EArray of Int16]
        waveforms_filtered* [(N x NWAVESAMPLES x NCHANNELS) EArray of Int16]

KWD

The KWD files contain the original recordings (raw and filtered). Each file among the .raw, .high and .low contains:

/kwik_version* [=2]
/recordings
    [X]
        data* [(Nsamples x Nchannels) EArray of Int16]
        filter
            name*
            param1*
        downsample_factor*

        # The following metadata fields are duplicated from the .kwik files
        # and are here for convenience only. The KWIK programs will not read
        # them, they are only there for other programs.
        name
        start_time
        start_sample
        sample_rate
        bit_depth

        application_data
            band_high
            band_low

User files

PRB

This Python script describes the probe used for the experiment: its geometry and topology. It must define a channel_groups variable, which is a list where each item is a dictionary with the following keys:

  • channels
  • graph
  • geometry

Example:

channel_groups = {
            "0": {
                "channels": [0, 1, 2, 3],  # list of channels to keep
                "graph": [[0, 1], [2, 3], ...],  # list of pairs of connected (nearby) channels
                "geometry": {0: [0.1, 0.2], 1: [0.3, 0.4], ...}  # (x,y) coordinates of each channel (for visualization purposes only)
                },
            "1": {
                "channels": [4, 5, 6, 7],
                "graph": [[4, 5], [6, 7], ...],
                "geometry": {4: [0.1, 0.2], 5: [0.3, 0.4], ...}
                }
        }

PRM

This Python script defines all parameters necessary for the programs to process, open and display the data.

EXPERIMENT_NAME = 'myexperiment'
RAW_DATA_FILES = ['n6mab041109blahblah1.dat', 'n6mab041109blahblah2.dat']
PRB_FILE = 'buzsaki32.probe'
NCHANNELS = 32
SAMPLE_RATE = 20000.
NBITS = 16
VOLTAGE_GAIN = 10.
WAVEFORMS_NSAMPLES = 20  # or a dictionary {channel_group: nsamples}
NFEATURES_PER_CHANNEL = 3  # or a dictionary {channel_group: fetdim}
# ...

# SpikeDetekt parameters
# ...


# KlustaKwik parameters
# ...
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