name: core.nwb.ecephys id: core.nwb.ecephys imports: - core.nwb.base - hdmf-common.table - core.nwb.device - 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: name: name: name range: string required: true 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: true range: float32 required: false tree_root: true ElectricalSeries__data: name: ElectricalSeries__data description: Recorded voltage data. attributes: name: name: name ifabsent: string(data) range: string required: true equals_string: data 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 attributes: name: name: name ifabsent: string(electrodes) range: string required: true equals_string: electrodes 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: name: name: name range: string required: true 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: true range: float64 required: true tree_root: true SpikeEventSeries__data: name: SpikeEventSeries__data description: Spike waveforms. attributes: name: name: name ifabsent: string(data) range: string required: true equals_string: data 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 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: name: name: name range: string required: true description: name: description description: Description of features (eg, ''PC1'') for each of the extracted features. multivalued: true range: text 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: true range: float64 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 tree_root: true FeatureExtraction__features: name: FeatureExtraction__features description: Multi-dimensional array of features extracted from each event. attributes: name: name: name ifabsent: string(features) range: string required: true equals_string: features 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: true num_channels: name: num_channels range: float32 required: true num_features: name: num_features range: float32 required: true FeatureExtraction__electrodes: name: FeatureExtraction__electrodes description: DynamicTableRegion pointer to the electrodes that this time series was generated from. is_a: DynamicTableRegion attributes: name: name: name ifabsent: string(electrodes) range: string required: true equals_string: electrodes EventDetection: name: EventDetection description: Detected spike events from voltage trace(s). is_a: NWBDataInterface attributes: name: name: name range: string required: true 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: text 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: true range: int32 required: true times: name: times description: Timestamps of events, in seconds. multivalued: true range: float64 required: true tree_root: 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: name: name: name range: string required: true spike_event_series: name: spike_event_series description: SpikeEventSeries object(s) containing detected spike event waveforms. multivalued: true range: SpikeEventSeries required: false tree_root: true 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: name: name: name range: string required: true electrical_series: name: electrical_series description: ElectricalSeries object(s) containing filtered electrophysiology data. multivalued: true range: ElectricalSeries required: true tree_root: 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: name: name: name range: string required: true electrical_series: name: electrical_series description: ElectricalSeries object(s) containing LFP data for one or more channels. multivalued: true range: ElectricalSeries required: true tree_root: true ElectrodeGroup: name: ElectrodeGroup description: A physical grouping of electrodes, e.g. a shank of an array. is_a: NWBContainer attributes: name: name: name range: string required: true 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: AnyType required: false tree_root: true 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: name: name: name range: string required: true waveform_filtering: name: waveform_filtering description: Filtering applied to data before generating mean/sd multivalued: false range: text 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 tree_root: true 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: name: name: name ifabsent: string(waveform_mean) range: string required: true equals_string: waveform_mean 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: true num_samples: name: num_samples range: float32 required: true ClusterWaveforms__waveform_sd: name: ClusterWaveforms__waveform_sd description: Stdev of waveforms for each cluster, using the same indices as in mean attributes: name: name: name ifabsent: string(waveform_sd) range: string required: true equals_string: waveform_sd 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: true num_samples: name: num_samples range: float32 required: true 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: name: name: name range: string required: true description: name: description description: Description of clusters or clustering, (e.g. cluster 0 is noise, clusters curated using Klusters, etc) multivalued: false range: text required: true num: name: num description: Cluster number of each event multivalued: true range: int32 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: true range: float32 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: true range: float64 required: true tree_root: true