nwb-linkml/nwb_linkml/schema/core.nwb.ecephys.yaml

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