allensdk.brain_observatory.ecephys.probes module

class allensdk.brain_observatory.ecephys.probes.Probes

Bases: DataObject, JsonReadableInterface, NwbReadableInterface, NwbWritableInterface

classmethod from_json(probes: List[Dict[str, Any]], skip_probes: List[str] | None = None) → Probes

Parameters:

probes

skip_probes: Names of probes to exclude (due to known bad data

for example)

Returns

——-

`Probes` instance

classmethod from_nwb(nwbfile: NWBFile, probe_lfp_meta_map: Dict[str, ProbeWithLFPMeta] | None = None) → Probes

Parameters:

nwbfile

probe_lfp_meta_map

See description in BehaviorEcephysSession.from_nwb

Returns:

NWBFile with probes added

get_units_table(filter_by_validity: bool = True, filter_out_of_brain_units: bool = True, amplitude_cutoff_maximum: float | None = None, presence_ratio_minimum: float | None = None, isi_violations_maximum: float | None = None) → DataFrame

Gets a dataframe representing all units detected by all probes

Parameters:

filter_by_validity

Whether to filter out units in channels with valid_data==False

filter_out_of_brain_units

Whether to filter out units with missing ecephys_structure_acronym

amplitude_cutoff_maximum

Filter units by this upper bound

presence_ratio_minimum

Filter units by this lower bound

isi_violations_maximum

Filter units by this upper bound

Returns

——-

Dataframe containing all units detected by probes

Columns:

• properties of allensdk.ecephys._unit.Unit

except for ‘spike_times’, ‘spike_amplitudes’, ‘mean_waveforms’ which are returned separately

property mean_waveforms: Dict[int, ndarray]

Returns:

Dictionary mapping unit id to mean_waveforms for all probes

property probes

property spike_amplitudes: Dict[int, ndarray]

Returns:

Dictionary mapping unit id to spike_amplitudes for all probes

property spike_times: Dict[int, ndarray]

Returns:

Dictionary mapping unit id to spike_times for all probes

to_dataframe()

to_nwb(nwbfile: NWBFile) → Tuple[NWBFile, Dict[str, NWBFile | None]]

Adds probes to NWBFile instance

Parameters:

nwbfile

Returns:

(session NWBFile instance,

mapping from probe name to optional probe NWBFile instance. Contains LFP and CSD data if it exists)

Notes

We return a map from probe name to nwb file separately, since the LFP data is large, and we want this written separately from the session nwb file