name: core.nwb.ecephys id: core.nwb.ecephys imports: - core.nwb.base - hdmf-common.table - nwb.language default_prefix: core.nwb.ecephys/ classes: ElectricalSeries: name: ElectricalSeries description: A time series of acquired voltage data from extracellular recordings. The data field is an int or float array storing data in volts. The first dimension should always represent time. The second dimension, if present, should represent channels. is_a: TimeSeries attributes: filtering: name: filtering description: Filtering applied to all channels of the data. For example, if this ElectricalSeries represents high-pass-filtered data (also known as AP Band), then this value could be "High-pass 4-pole Bessel filter at 500 Hz". If this ElectricalSeries represents low-pass-filtered LFP data and the type of filter is unknown, then this value could be "Low-pass filter at 300 Hz". If a non-standard filter type is used, provide as much detail about the filter properties as possible. range: text data: name: data description: Recorded voltage data. multivalued: false range: ElectricalSeries_data required: true electrodes: name: electrodes description: DynamicTableRegion pointer to the electrodes that this time series was generated from. multivalued: false range: ElectricalSeries_electrodes required: true channel_conversion: name: channel_conversion description: Channel-specific conversion factor. Multiply the data in the 'data' dataset by these values along the channel axis (as indicated by axis attribute) AND by the global conversion factor in the 'conversion' attribute of 'data' to get the data values in Volts, i.e, data in Volts = data * data.conversion * channel_conversion. This approach allows for both global and per-channel data conversion factors needed to support the storage of electrical recordings as native values generated by data acquisition systems. If this dataset is not present, then there is no channel-specific conversion factor, i.e. it is 1 for all channels. multivalued: false range: ElectricalSeries_channel_conversion required: false ElectricalSeries_data: name: ElectricalSeries_data description: Recorded voltage data. attributes: unit: name: unit description: Base unit of measurement for working with the data. This value is fixed to 'volts'. Actual stored values are not necessarily stored in these units. To access the data in these units, multiply 'data' by 'conversion', followed by 'channel_conversion' (if present), and then add 'offset'. range: text array: name: array range: ElectricalSeries_data_Array ElectricalSeries_data_Array: name: ElectricalSeries_data_Array is_a: Arraylike attributes: num_times: name: num_times range: numeric required: true num_channels: name: num_channels range: numeric required: false num_samples: name: num_samples range: numeric required: false ElectricalSeries_electrodes: name: ElectricalSeries_electrodes description: DynamicTableRegion pointer to the electrodes that this time series was generated from. is_a: DynamicTableRegion ElectricalSeries_channel_conversion: name: ElectricalSeries_channel_conversion description: Channel-specific conversion factor. Multiply the data in the 'data' dataset by these values along the channel axis (as indicated by axis attribute) AND by the global conversion factor in the 'conversion' attribute of 'data' to get the data values in Volts, i.e, data in Volts = data * data.conversion * channel_conversion. This approach allows for both global and per-channel data conversion factors needed to support the storage of electrical recordings as native values generated by data acquisition systems. If this dataset is not present, then there is no channel-specific conversion factor, i.e. it is 1 for all channels. attributes: axis: name: axis description: The zero-indexed axis of the 'data' dataset that the channel-specific conversion factor corresponds to. This value is fixed to 1. range: int32 array: name: array range: ElectricalSeries_channel_conversion_Array ElectricalSeries_channel_conversion_Array: name: ElectricalSeries_channel_conversion_Array is_a: Arraylike attributes: num_channels: name: num_channels range: float32 required: true SpikeEventSeries: name: SpikeEventSeries description: 'Stores snapshots/snippets of recorded spike events (i.e., threshold crossings). This may also be raw data, as reported by ephys hardware. If so, the TimeSeries::description field should describe how events were detected. All SpikeEventSeries should reside in a module (under EventWaveform interface) even if the spikes were reported and stored by hardware. All events span the same recording channels and store snapshots of equal duration. TimeSeries::data array structure: [num events] [num channels] [num samples] (or [num events] [num samples] for single electrode).' is_a: ElectricalSeries attributes: data: name: data description: Spike waveforms. multivalued: false range: SpikeEventSeries_data required: true timestamps: name: timestamps description: Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time. Timestamps are required for the events. Unlike for TimeSeries, timestamps are required for SpikeEventSeries and are thus re-specified here. multivalued: false range: SpikeEventSeries_timestamps required: true SpikeEventSeries_data: name: SpikeEventSeries_data description: Spike waveforms. attributes: unit: name: unit description: Unit of measurement for waveforms, which is fixed to 'volts'. range: text array: name: array range: SpikeEventSeries_data_Array SpikeEventSeries_data_Array: name: SpikeEventSeries_data_Array is_a: Arraylike attributes: num_events: name: num_events range: numeric required: true num_samples: name: num_samples range: numeric required: true num_channels: name: num_channels range: numeric required: false SpikeEventSeries_timestamps: name: SpikeEventSeries_timestamps description: Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time. Timestamps are required for the events. Unlike for TimeSeries, timestamps are required for SpikeEventSeries and are thus re-specified here. attributes: interval: name: interval description: Value is '1' range: int32 unit: name: unit description: Unit of measurement for timestamps, which is fixed to 'seconds'. range: text array: name: array range: SpikeEventSeries_timestamps_Array SpikeEventSeries_timestamps_Array: name: SpikeEventSeries_timestamps_Array is_a: Arraylike attributes: num_times: name: num_times range: float64 required: true FeatureExtraction: name: FeatureExtraction description: Features, such as PC1 and PC2, that are extracted from signals stored in a SpikeEventSeries or other source. is_a: NWBDataInterface attributes: description: name: description description: Description of features (eg, ''PC1'') for each of the extracted features. multivalued: false range: FeatureExtraction_description required: true features: name: features description: Multi-dimensional array of features extracted from each event. multivalued: false range: FeatureExtraction_features required: true times: name: times description: Times of events that features correspond to (can be a link). multivalued: false range: FeatureExtraction_times required: true electrodes: name: electrodes description: DynamicTableRegion pointer to the electrodes that this time series was generated from. multivalued: false range: FeatureExtraction_electrodes required: true FeatureExtraction_description: name: FeatureExtraction_description description: Description of features (eg, ''PC1'') for each of the extracted features. attributes: array: name: array range: FeatureExtraction_description_Array FeatureExtraction_description_Array: name: FeatureExtraction_description_Array is_a: Arraylike attributes: num_features: name: num_features range: text required: true FeatureExtraction_features: name: FeatureExtraction_features description: Multi-dimensional array of features extracted from each event. attributes: array: name: array range: FeatureExtraction_features_Array FeatureExtraction_features_Array: name: FeatureExtraction_features_Array is_a: Arraylike attributes: num_events: name: num_events range: float32 required: false num_channels: name: num_channels range: float32 required: false num_features: name: num_features range: float32 required: false FeatureExtraction_times: name: FeatureExtraction_times description: Times of events that features correspond to (can be a link). attributes: array: name: array range: FeatureExtraction_times_Array FeatureExtraction_times_Array: name: FeatureExtraction_times_Array is_a: Arraylike attributes: num_events: name: num_events range: float64 required: true FeatureExtraction_electrodes: name: FeatureExtraction_electrodes description: DynamicTableRegion pointer to the electrodes that this time series was generated from. is_a: DynamicTableRegion EventDetection: name: EventDetection description: Detected spike events from voltage trace(s). is_a: NWBDataInterface attributes: detection_method: name: detection_method description: Description of how events were detected, such as voltage threshold, or dV/dT threshold, as well as relevant values. multivalued: false range: EventDetection_detection_method required: true source_idx: name: source_idx description: Indices (zero-based) into source ElectricalSeries::data array corresponding to time of event. ''description'' should define what is meant by time of event (e.g., .25 ms before action potential peak, zero-crossing time, etc). The index points to each event from the raw data. multivalued: false range: EventDetection_source_idx required: true times: name: times description: Timestamps of events, in seconds. multivalued: false range: EventDetection_times required: true EventDetection_detection_method: name: EventDetection_detection_method description: Description of how events were detected, such as voltage threshold, or dV/dT threshold, as well as relevant values. EventDetection_source_idx: name: EventDetection_source_idx description: Indices (zero-based) into source ElectricalSeries::data array corresponding to time of event. ''description'' should define what is meant by time of event (e.g., .25 ms before action potential peak, zero-crossing time, etc). The index points to each event from the raw data. attributes: array: name: array range: EventDetection_source_idx_Array EventDetection_source_idx_Array: name: EventDetection_source_idx_Array is_a: Arraylike attributes: num_events: name: num_events range: int32 required: true EventDetection_times: name: EventDetection_times description: Timestamps of events, in seconds. attributes: unit: name: unit description: Unit of measurement for event times, which is fixed to 'seconds'. range: text array: name: array range: EventDetection_times_Array EventDetection_times_Array: name: EventDetection_times_Array is_a: Arraylike attributes: num_events: name: num_events range: float64 required: true EventWaveform: name: EventWaveform description: Represents either the waveforms of detected events, as extracted from a raw data trace in /acquisition, or the event waveforms that were stored during experiment acquisition. is_a: NWBDataInterface attributes: SpikeEventSeries: name: SpikeEventSeries description: SpikeEventSeries object(s) containing detected spike event waveforms. multivalued: true range: SpikeEventSeries required: false FilteredEphys: name: FilteredEphys description: Electrophysiology data from one or more channels that has been subjected to filtering. Examples of filtered data include Theta and Gamma (LFP has its own interface). FilteredEphys modules publish an ElectricalSeries for each filtered channel or set of channels. The name of each ElectricalSeries is arbitrary but should be informative. The source of the filtered data, whether this is from analysis of another time series or as acquired by hardware, should be noted in each's TimeSeries::description field. There is no assumed 1::1 correspondence between filtered ephys signals and electrodes, as a single signal can apply to many nearby electrodes, and one electrode may have different filtered (e.g., theta and/or gamma) signals represented. Filter properties should be noted in the ElectricalSeries 'filtering' attribute. is_a: NWBDataInterface attributes: ElectricalSeries: name: ElectricalSeries description: ElectricalSeries object(s) containing filtered electrophysiology data. multivalued: true range: ElectricalSeries required: true LFP: name: LFP description: LFP data from one or more channels. The electrode map in each published ElectricalSeries will identify which channels are providing LFP data. Filter properties should be noted in the ElectricalSeries 'filtering' attribute. is_a: NWBDataInterface attributes: ElectricalSeries: name: ElectricalSeries description: ElectricalSeries object(s) containing LFP data for one or more channels. multivalued: true range: ElectricalSeries required: true ElectrodeGroup: name: ElectrodeGroup description: A physical grouping of electrodes, e.g. a shank of an array. is_a: NWBContainer attributes: description: name: description description: Description of this electrode group. range: text location: name: location description: Location of electrode group. Specify the area, layer, comments on estimation of area/layer, etc. Use standard atlas names for anatomical regions when possible. range: text position: name: position description: stereotaxic or common framework coordinates multivalued: false range: ElectrodeGroup_position required: false ElectrodeGroup_position: name: ElectrodeGroup_position description: stereotaxic or common framework coordinates ClusterWaveforms: name: ClusterWaveforms description: DEPRECATED The mean waveform shape, including standard deviation, of the different clusters. Ideally, the waveform analysis should be performed on data that is only high-pass filtered. This is a separate module because it is expected to require updating. For example, IMEC probes may require different storage requirements to store/display mean waveforms, requiring a new interface or an extension of this one. is_a: NWBDataInterface attributes: waveform_filtering: name: waveform_filtering description: Filtering applied to data before generating mean/sd multivalued: false range: ClusterWaveforms_waveform_filtering required: true waveform_mean: name: waveform_mean description: The mean waveform for each cluster, using the same indices for each wave as cluster numbers in the associated Clustering module (i.e, cluster 3 is in array slot [3]). Waveforms corresponding to gaps in cluster sequence should be empty (e.g., zero- filled) multivalued: false range: ClusterWaveforms_waveform_mean required: true waveform_sd: name: waveform_sd description: Stdev of waveforms for each cluster, using the same indices as in mean multivalued: false range: ClusterWaveforms_waveform_sd required: true ClusterWaveforms_waveform_filtering: name: ClusterWaveforms_waveform_filtering description: Filtering applied to data before generating mean/sd ClusterWaveforms_waveform_mean: name: ClusterWaveforms_waveform_mean description: The mean waveform for each cluster, using the same indices for each wave as cluster numbers in the associated Clustering module (i.e, cluster 3 is in array slot [3]). Waveforms corresponding to gaps in cluster sequence should be empty (e.g., zero- filled) attributes: array: name: array range: ClusterWaveforms_waveform_mean_Array ClusterWaveforms_waveform_mean_Array: name: ClusterWaveforms_waveform_mean_Array is_a: Arraylike attributes: num_clusters: name: num_clusters range: float32 required: false num_samples: name: num_samples range: float32 required: false ClusterWaveforms_waveform_sd: name: ClusterWaveforms_waveform_sd description: Stdev of waveforms for each cluster, using the same indices as in mean attributes: array: name: array range: ClusterWaveforms_waveform_sd_Array ClusterWaveforms_waveform_sd_Array: name: ClusterWaveforms_waveform_sd_Array is_a: Arraylike attributes: num_clusters: name: num_clusters range: float32 required: false num_samples: name: num_samples range: float32 required: false Clustering: name: Clustering description: DEPRECATED Clustered spike data, whether from automatic clustering tools (e.g., klustakwik) or as a result of manual sorting. is_a: NWBDataInterface attributes: description: name: description description: Description of clusters or clustering, (e.g. cluster 0 is noise, clusters curated using Klusters, etc) multivalued: false range: Clustering_description required: true num: name: num description: Cluster number of each event multivalued: false range: Clustering_num required: true peak_over_rms: name: peak_over_rms description: Maximum ratio of waveform peak to RMS on any channel in the cluster (provides a basic clustering metric). multivalued: false range: Clustering_peak_over_rms required: true times: name: times description: Times of clustered events, in seconds. This may be a link to times field in associated FeatureExtraction module. multivalued: false range: Clustering_times required: true Clustering_description: name: Clustering_description description: Description of clusters or clustering, (e.g. cluster 0 is noise, clusters curated using Klusters, etc) Clustering_num: name: Clustering_num description: Cluster number of each event attributes: array: name: array range: Clustering_num_Array Clustering_num_Array: name: Clustering_num_Array is_a: Arraylike attributes: num_events: name: num_events range: int32 required: true Clustering_peak_over_rms: name: Clustering_peak_over_rms description: Maximum ratio of waveform peak to RMS on any channel in the cluster (provides a basic clustering metric). attributes: array: name: array range: Clustering_peak_over_rms_Array Clustering_peak_over_rms_Array: name: Clustering_peak_over_rms_Array is_a: Arraylike attributes: num_clusters: name: num_clusters range: float32 required: true Clustering_times: name: Clustering_times description: Times of clustered events, in seconds. This may be a link to times field in associated FeatureExtraction module. attributes: array: name: array range: Clustering_times_Array Clustering_times_Array: name: Clustering_times_Array is_a: Arraylike attributes: num_events: name: num_events range: float64 required: true