radiens_core.models.spikes

Spike sorting and neural recording domain models.

CLASS	DESCRIPTION
ChannelSpikeData	Spike timestamps and neuron labels for a single recording channel.
NeuronInfo	Descriptive statistics for one sorted neuron, as recorded on one site.
NeuronSpikeData	Spike timestamps for a single sorted neuron.
NeuronsResult	Neuron descriptors organized by recording channel.
SpikesSiteSpec	Spike-detection settings for a single recording site.
SpikesSpec	Metadata of a spikes fileset.
Unit	One sorted cell, merged from the per-site listings in NeuronsResult.

Classes

ChannelSpikeData

Bases: BaseModel

Spike timestamps and neuron labels for a single recording channel.

ATTRIBUTE	DESCRIPTION
ntv_chan_idx	Native channel index. TYPE: int
timestamps	Spike timestamps in seconds, shape (N,). TYPE: NDArray[float64]
labels	Integer neuron label per spike, shape (N,), matching the label get_neurons() reports. 0 marks a spike the sorter did not assign to a neuron. None when waveforms were not requested; labels and waveforms are always present or absent together. TYPE: NDArray[int32] | None
waveforms	Spike waveforms in µV, shape (N, n_sites, waveform_n_points), or None if waveforms were not requested. Each spike is kept on the site that detected it, the one with the largest peak among its neighbors. Site 0 is this channel and the rest are its detection neighborhood at the same moment. TYPE: NDArray[float32] | None
site_ntv_chan_idx	The channel each entry of the waveform site axis was recorded on, length n_sites, with element 0 equal to ntv_chan_idx. Neighbors are ordered by distance from the detecting site rather than by position on the probe, so this cannot be inferred from geometry. None when waveforms were not requested or the server did not report the neighborhood. TYPE: list[int] | None

NeuronInfo

Bases: BaseModel

Descriptive statistics for one sorted neuron, as recorded on one site.

ATTRIBUTE	DESCRIPTION
neuron_id	Unique neuron identifier string. TYPE: str
site_ntv_chan_idx	Native channel index of the site this listing is for. TYPE: int
spike_label	Neuron label as a string (e.g. "1", "2"). TYPE: str
spike_count	Spikes of this neuron on this site. TYPE: int
spike_rate	Mean spike rate in Hz. TYPE: float
mean_abs_peak_wfm	Mean absolute peak waveform amplitude. TYPE: float
snr	Signal-to-noise ratio. TYPE: float
pos_probe	Probe coordinate [x, y, z] in microns. TYPE: list[float]
pos_tissue	Tissue coordinate [x, y, z] in microns. TYPE: list[float]

NeuronSpikeData

Bases: BaseModel

Spike timestamps for a single sorted neuron.

ATTRIBUTE	DESCRIPTION
label	Integer neuron label. Correlates with NeuronInfo.spike_label (string) from get_neurons(). TYPE: int
ntv_chan_idx	Native channel index of the primary recording site for this neuron. -1 if the channel could not be determined from the spike spec. TYPE: int
timestamps	Spike timestamps in seconds, shape (N,). TYPE: NDArray[float64]
waveforms	The neuron's spike waveforms in µV, shape (N, n_sites, waveform_n_points), row i being timestamps[i], or None if waveforms were not requested. Every row is on the same sites, site_ntv_chan_idx. A spike is kept only on the neighborhood of the site that detected it, so each row is NaN on the sites the spike was not recorded on; no recorded site is dropped. TYPE: NDArray[float32] | None
site_ntv_chan_idx	The channel each entry of the waveform site axis was recorded on, length n_sites: every site any of these spikes was recorded on. The neighborhood of the channel that detected most of them comes first, starting with that channel; the other sites follow by how many spikes recorded them. None when waveforms were not requested. TYPE: list[int] | None
detect_ntv_chan_idx	The channel that detected each spike, shape (N,). None when waveforms were not requested. TYPE: NDArray[int32] | None

NeuronsResult

Bases: BaseModel

Neuron descriptors organized by recording channel.

ATTRIBUTE	DESCRIPTION
neurons_by_channel	Map from native channel index to a list of neuron descriptors detected on that channel. TYPE: dict[int, list[NeuronInfo]]

SpikesSiteSpec

Bases: BaseModel

Spike-detection settings for a single recording site.

A threshold is None when spike detection is not active on that polarity.

ATTRIBUTE	DESCRIPTION
ntv_chan_idx	Native channel index of the site. TYPE: int
pos_threshold_uv	Positive detection threshold in microvolts. TYPE: float | None
pos_threshold_sd	Positive detection threshold in noise standard deviations. TYPE: float | None
neg_threshold_uv	Negative detection threshold in microvolts. TYPE: float | None
neg_threshold_sd	Negative detection threshold in noise standard deviations. TYPE: float | None
neighbor_ntv_chan_idx	Native channel indices of this site's detection neighborhood, ordered by distance from it. This is the order the site axis of a spike waveform follows after its own row, so it is how a waveform row is attributed to a channel. TYPE: list[int]
neighbor_distance_um	Distance to each neighbor in microns, parallel to neighbor_ntv_chan_idx. TYPE: list[float]
neighbor_radius_um	Radius the neighborhood was selected within, in microns. TYPE: float

SpikesSpec

Bases: BaseModel

Metadata of a spikes fileset.

Reports the detection settings the spike fileset was produced with, so a caller holding an on-disk .spikes fileset can tell how it was generated.

ATTRIBUTE	DESCRIPTION
biointerface_id	ID of the spikes fileset. TYPE: str
dataset_uid	UID of the dataset the fileset was sorted from. TYPE: str
num_neurons	Number of distinct neuron labels across all sites, not counting unclustered spikes. TYPE: int
num_sites	Number of amplifier channels in the dataset. TYPE: int
enabled_channel_indices	Native channel indices of enabled recording sites, sorted in ascending order. TYPE: list[int]
time_range	Full time range of the recording in seconds (start, end). TYPE: tuple[float, float]
spike_time_range	Time range over which spike data is available in seconds (start, end). TYPE: tuple[float, float]
req_num_neighbors	Largest number of neighbors any site's detection neighborhood holds. TYPE: int
neighborhood_radius_um	Detection neighborhood radius in microns. TYPE: float
sites	Per-site detection thresholds, in the dataset's channel order. TYPE: list[SpikesSiteSpec]

Unit

Bases: BaseModel

One sorted cell, merged from the per-site listings in NeuronsResult.

get_neurons() lists a cell under every site that recorded it, each listing with that site's share of the spikes. spike_count and spike_rate are summed over the listings; site_ntv_chan_idx, snr and probe_y come from the listing with the most spikes. Unclustered spikes (label 0) and clusters marked bad or delete are not units.

ATTRIBUTE	DESCRIPTION
label	The sorter's integer label, which spike trains and rasters are keyed by. Unique within a probe; on a multi-probe recording two units can share it. TYPE: int
neuron_id	Unique across the fileset and stable across the per-site listings. TYPE: str
site_ntv_chan_idx	Native index of the site that saw the most spikes. TYPE: int
spike_count	Spikes summed over the cell's listings. TYPE: int
spike_rate	Mean rate in Hz summed over the cell's listings. TYPE: float
snr	SNR at site_ntv_chan_idx. TYPE: float
probe_y	Depth coordinate of site_ntv_chan_idx in microns; nan if the sorter reported no position. TYPE: float