Supported Preprocessing Steps

In spikewrap, all preprocessing is performed using SpikeInterface under the hood.

In the majority of cases, preprocessing settings in the configuration dictionary map 1:1 with spikeinterface function names and their arguments.

In a few cases (highlighted below) this is not possible, and these functions are documented below. In time, the aim will be to transfer all preprocessing into SpikeInterface.

As a reminder, an example configuration dictionary is strictured like:

pp_steps = {
    "1": ["phase_shift", {}],
    "2": ["bandpass_filter", {"freq_min": 300, "freq_max": 6000}],
    "3": ["remove_bad_channels", {"detect_bad_channel_kwargs": {"chunk_duration_s": 0.5}}],
    "4": ["common_reference", {"operator": "median"}],
}

(see the the Managing Configs tutorials for details).

Steps that directly map SpikeInterface

phase_shift

The name and arguments map directly to SpikeInterface’s phase_shift function.

bandpass_filter:

The name and arguments map directly to SpikeInterface’s bandpass_filter function.

common_reference:

The name and arguments map directly to SpikeInterface’s common_reference function.

whiten:

The name and arguments map directly to SpikeInterface’s whiten function.

Steps that do not directly map SpikeInterface

While these steps use SpikeInterface under the hood, they do not map 1:1 to the SpikeInterface API.

For reference, their implementations are in spikewrap.process._preprocessing (however, they should not be called directly, instead use the config_dict as above).

Note

Currently, bad-channel detection is performed per-run (if not concatenated). In some cases it is useful to remove the union of all bad channels (across runs from each run). This is not currently implemented in spikewrap, but if you would like to use this, please get in contact.

Warning

Bad-channel detection is performed at the spikewrap.Session.preprocess stage, and so may slow down this call. This is in contract to other preprocessing steps which are lazy.

remove_bad_channels

This function removes bad channels from the recording. Under the hood it uses SpikeInterface’s detect_bad_channels and remove_channels functions. The default settings use the International Brain Laboratory’s (IBLs) detect bad channels approach. It’s parameters are:

• labels_to_remove: Set the bad-channel labels to remove. During bad channel detection, channels are labelled "good", "out" (of brain), "noise" and "dead"". This argument removes channels that have the passed labels. e.g. ["noise", "dead"] will remove only dead and noisy channels, but out of brain and good channels will be retained.

• detect_bad_channel_kwargs: A dictionary of arguments that will be passed to SpikeInterface’s detect_bad_channels.

interpolate_bad_channels

This function interpolates (Kriging) bad channels in the recording. Under the hood it uses SpikeInterface’s detect_bad_channels and interpolate_bad_channels function. Note that the spikeinterface interpolate_bad_channels only interpolates a given list of channels, rather than the detect-and-interpolate performed in spikewrap. The default method uses the International Brain Laboratory’s (IBLs) detect bad channels approach

• labels_to_remove: Set the bad-channel labels to interpolate. During bad channel detection, channels are labelled "good", "out" (of brain), "noise" and "dead"". This argument interpolates channels that have the passed labels. e.g. ["noise", "dead"] will interpolate only dead and noisy channels, but out of brain and good channels will be retained.

• detect_bad_channel_kwargs: A dictionary of arguments that will be passed to SpikeInterface’s detect_bad_channels.

• interpolate_bad_channel_kwargs: A dictionary of kwargs that will be passed to SpikeInterface’s interpolate_bad_channels function that performs the interpolation (but not detection).

remove_channels

This function to remove a given list of channels from the recording. Uses SpikeInterface’s whiten function.

• channel_ids: A list of channel ids to remove from the recording.

interpolate_channels

This function to interpolate (Kriging) a given list of channels in the recording. Uses SpikeInterface’s interpolate_bad_channels function.

• channel_ids: A list of channel ids to interpolate.

• interpolate_bad_channel_kwargs: A dictionary of kwargs that will be passed to SpikeInterface’s interpolate_bad_channels function that performs the interpolation (but not detection).