Performs filtering, common-average-referencing (CAR), spike detection, waveform and feature extraction for a given memory block of raw traces. This function is called by file2spk_(), which loads a recording file to RAM in multiple loading cycles permitted by an available system memory.

Spike waveforms are extracted (mn2tn_wav_()) which is centered at the peak site, and coincident weaker spikes are removed (spikeMerge_(). Features are extracted from given spike waveforms (trWav2Fet_()) according to the specified feature (P.vcFet). Default feature is P.vcFet='gpca' with P.nPcPerChan=1, which is recommended for high-density probes such as Neuropixels probes.

Syntax

• [tnWav_raw, tnWav_spk, trFet_spk, miSite_spk, viTime_spk, vnAmp_spk, vnThresh_site, fGpu] = wav2spk_(mnWav1, vrWav_mean1, P, viTime_spk, viSite_spk, mnWav1_pre, mnWav1_post)

Input

• mnWav1: Raw recording traces (nSamples_load x nSites: int16)
• vrWav_mean1: Averaged raw trace across all recording sites (unused, default: [])
• P: Parameters struct (P)
• viTime_spk: Optional spike peak timing, used for importing spiking data from previous sorting output (default: [])
• viSite_spk: Optional spike center sites, used for importing spiking data from previous sorting output (default: [])
• mnWav1_pre: Raw traces preceding the current block (mnWav1), used for edge-safe filtering operation
• mnWav1_post: Raw traces following the current block (mnWav1), used for edge-safe filtering operation

Output

• tnWav_raw: raw spike waveforms
• tnWav_spk: filtered spike waveforms
• trFet_spk: spike features
• miSite_spk: sites centered at the (nPositions x nSpikes: int32)
• viTime_spk: spike time
• `vnAmp_spk: peak spike amplitude at the peak site
• vnThresh_site: spike detection threshold per site (nSites x 1: int16)
• fGpu: flag for GPU usage. 0 if GPU use is disabled or failed.

Operations performed

• fft_clean(): Perform adaptive notch filter in the frequency domain if P.[[fft_thresh] > 0.
• filt_car_(): Filter (P.vcFilter) and apply common average referencing (P.vcCommonRef).
• car_reject_(): Reject spike detection if average across sites exceeds certain threshold (P.blank_thresh).
• detect_spikes_(): Detect spikes using a detection threshold (P.qqFactor).
  • spikeDetectSingle_fast_(): Perform spike detection for each site using GPU (if P.fGpu==1)
  • spikeMerge_(): Merge spikes detected at multiple neighboring sites using multiple CPU cores. P.spkRefrac_ms and P.maxDist_site_um parameters define the spatiotemporal limit. If larger spikes are detected within the limit, weaker spikes are removed.
• mn2tn_wav_(): Extract event waveforms from a list of specified site (viSite_spk) and time (viTime_spk)
• trWav2fet_(): Extract event features from the supplied spike waveforms (see P.vcFet)

See also

file2spk_(), detect_()