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

name: core.nwb.icephys
id: core.nwb.icephys
imports:
- core.nwb.base
- core.nwb.device
- hdmf-common.table
- nwb.language
- core.nwb.icephys.include
- core.nwb.icephys
prefixes:
  core.nwb.icephys:
    prefix_prefix: core.nwb.icephys
    prefix_reference: https://example.com/core.nwb.icephys/
default_prefix: core.nwb.icephys
classes:
  PatchClampSeries:
    name: PatchClampSeries
    description: An abstract base class for patch-clamp data - stimulus or response,
      current or voltage.
    is_a: TimeSeries
    attributes:
      name:
        name: name
        range: string
        required: true
      stimulus_description:
        name: stimulus_description
        description: Protocol/stimulus name for this patch-clamp dataset.
        range: text
      sweep_number:
        name: sweep_number
        description: Sweep number, allows to group different PatchClampSeries together.
        range: uint32
      data:
        name: data
        description: Recorded voltage or current.
        multivalued: true
        range: numeric
        required: true
      gain:
        name: gain
        description: Gain of the recording, in units Volt/Amp (v-clamp) or Volt/Volt
          (c-clamp).
        multivalued: false
        range: float32
        required: false
    tree_root: true
  CurrentClampSeries:
    name: CurrentClampSeries
    description: Voltage data from an intracellular current-clamp recording. A corresponding
      CurrentClampStimulusSeries (stored separately as a stimulus) is used to store
      the current injected.
    is_a: PatchClampSeries
    attributes:
      name:
        name: name
        range: string
        required: true
      data:
        name: data
        description: Recorded voltage.
        multivalued: false
        range: CurrentClampSeries__data
        required: true
      bias_current:
        name: bias_current
        description: Bias current, in amps.
        multivalued: false
        range: float32
        required: false
      bridge_balance:
        name: bridge_balance
        description: Bridge balance, in ohms.
        multivalued: false
        range: float32
        required: false
      capacitance_compensation:
        name: capacitance_compensation
        description: Capacitance compensation, in farads.
        multivalued: false
        range: float32
        required: false
    tree_root: true
  IZeroClampSeries:
    name: IZeroClampSeries
    description: Voltage data from an intracellular recording when all current and
      amplifier settings are off (i.e., CurrentClampSeries fields will be zero). There
      is no CurrentClampStimulusSeries associated with an IZero series because the
      amplifier is disconnected and no stimulus can reach the cell.
    is_a: CurrentClampSeries
    attributes:
      name:
        name: name
        range: string
        required: true
      stimulus_description:
        name: stimulus_description
        description: An IZeroClampSeries has no stimulus, so this attribute is automatically
          set to "N/A"
        range: text
      bias_current:
        name: bias_current
        description: Bias current, in amps, fixed to 0.0.
        multivalued: false
        range: float32
        required: true
      bridge_balance:
        name: bridge_balance
        description: Bridge balance, in ohms, fixed to 0.0.
        multivalued: false
        range: float32
        required: true
      capacitance_compensation:
        name: capacitance_compensation
        description: Capacitance compensation, in farads, fixed to 0.0.
        multivalued: false
        range: float32
        required: true
    tree_root: true
  CurrentClampStimulusSeries:
    name: CurrentClampStimulusSeries
    description: Stimulus current applied during current clamp recording.
    is_a: PatchClampSeries
    attributes:
      name:
        name: name
        range: string
        required: true
      data:
        name: data
        description: Stimulus current applied.
        multivalued: false
        range: CurrentClampStimulusSeries__data
        required: true
    tree_root: true
  VoltageClampSeries:
    name: VoltageClampSeries
    description: Current data from an intracellular voltage-clamp recording. A corresponding
      VoltageClampStimulusSeries (stored separately as a stimulus) is used to store
      the voltage injected.
    is_a: PatchClampSeries
    attributes:
      name:
        name: name
        range: string
        required: true
      data:
        name: data
        description: Recorded current.
        multivalued: false
        range: VoltageClampSeries__data
        required: true
      capacitance_fast:
        name: capacitance_fast
        description: Fast capacitance, in farads.
        multivalued: false
        range: VoltageClampSeries__capacitance_fast
        required: false
      capacitance_slow:
        name: capacitance_slow
        description: Slow capacitance, in farads.
        multivalued: false
        range: VoltageClampSeries__capacitance_slow
        required: false
      resistance_comp_bandwidth:
        name: resistance_comp_bandwidth
        description: Resistance compensation bandwidth, in hertz.
        multivalued: false
        range: VoltageClampSeries__resistance_comp_bandwidth
        required: false
      resistance_comp_correction:
        name: resistance_comp_correction
        description: Resistance compensation correction, in percent.
        multivalued: false
        range: VoltageClampSeries__resistance_comp_correction
        required: false
      resistance_comp_prediction:
        name: resistance_comp_prediction
        description: Resistance compensation prediction, in percent.
        multivalued: false
        range: VoltageClampSeries__resistance_comp_prediction
        required: false
      whole_cell_capacitance_comp:
        name: whole_cell_capacitance_comp
        description: Whole cell capacitance compensation, in farads.
        multivalued: false
        range: VoltageClampSeries__whole_cell_capacitance_comp
        required: false
      whole_cell_series_resistance_comp:
        name: whole_cell_series_resistance_comp
        description: Whole cell series resistance compensation, in ohms.
        multivalued: false
        range: VoltageClampSeries__whole_cell_series_resistance_comp
        required: false
    tree_root: true
  VoltageClampStimulusSeries:
    name: VoltageClampStimulusSeries
    description: Stimulus voltage applied during a voltage clamp recording.
    is_a: PatchClampSeries
    attributes:
      name:
        name: name
        range: string
        required: true
      data:
        name: data
        description: Stimulus voltage applied.
        multivalued: false
        range: VoltageClampStimulusSeries__data
        required: true
    tree_root: true
  IntracellularElectrode:
    name: IntracellularElectrode
    description: An intracellular electrode and its metadata.
    is_a: NWBContainer
    attributes:
      name:
        name: name
        range: string
        required: true
      cell_id:
        name: cell_id
        description: unique ID of the cell
        multivalued: false
        range: text
        required: false
      description:
        name: description
        description: Description of electrode (e.g.,  whole-cell, sharp, etc.).
        multivalued: false
        range: text
        required: true
      filtering:
        name: filtering
        description: Electrode specific filtering.
        multivalued: false
        range: text
        required: false
      initial_access_resistance:
        name: initial_access_resistance
        description: Initial access resistance.
        multivalued: false
        range: text
        required: false
      location:
        name: location
        description: Location of the electrode. Specify the area, layer, comments
          on estimation of area/layer, stereotaxic coordinates if in vivo, etc. Use
          standard atlas names for anatomical regions when possible.
        multivalued: false
        range: text
        required: false
      resistance:
        name: resistance
        description: Electrode resistance, in ohms.
        multivalued: false
        range: text
        required: false
      seal:
        name: seal
        description: Information about seal used for recording.
        multivalued: false
        range: text
        required: false
      slice:
        name: slice
        description: Information about slice used for recording.
        multivalued: false
        range: text
        required: false
    tree_root: true
  SweepTable:
    name: SweepTable
    description: '[DEPRECATED] Table used to group different PatchClampSeries. SweepTable
      is being replaced by IntracellularRecordingsTable and SimultaneousRecordingsTable
      tables. Additional SequentialRecordingsTable, RepetitionsTable, and ExperimentalConditions
      tables provide enhanced support for experiment metadata.'
    is_a: DynamicTable
    attributes:
      name:
        name: name
        range: string
        required: true
      sweep_number:
        name: sweep_number
        description: Sweep number of the PatchClampSeries in that row.
        multivalued: true
        range: uint32
      series:
        name: series
        description: The PatchClampSeries with the sweep number in that row.
        multivalued: true
        range: PatchClampSeries
      series_index:
        name: series_index
        description: Index for series.
        multivalued: false
        range: SweepTable__series_index
        required: true
    tree_root: true
  IntracellularElectrodesTable:
    name: IntracellularElectrodesTable
    description: Table for storing intracellular electrode related metadata.
    is_a: DynamicTable
    attributes:
      name:
        name: name
        range: string
        required: true
      description:
        name: description
        description: Description of what is in this dynamic table.
        range: text
      electrode:
        name: electrode
        description: Column for storing the reference to the intracellular electrode.
        multivalued: true
        range: IntracellularElectrode
    tree_root: true
  IntracellularStimuliTable:
    name: IntracellularStimuliTable
    description: Table for storing intracellular stimulus related metadata.
    is_a: DynamicTable
    attributes:
      name:
        name: name
        range: string
        required: true
      description:
        name: description
        description: Description of what is in this dynamic table.
        range: text
      stimulus:
        name: stimulus
        description: Column storing the reference to the recorded stimulus for the
          recording (rows).
        multivalued: false
        range: IntracellularStimuliTable__stimulus
        required: true
    tree_root: true
  IntracellularResponsesTable:
    name: IntracellularResponsesTable
    description: Table for storing intracellular response related metadata.
    is_a: DynamicTable
    attributes:
      name:
        name: name
        range: string
        required: true
      description:
        name: description
        description: Description of what is in this dynamic table.
        range: text
      response:
        name: response
        description: Column storing the reference to the recorded response for the
          recording (rows)
        multivalued: false
        range: IntracellularResponsesTable__response
        required: true
    tree_root: true
  IntracellularRecordingsTable:
    name: IntracellularRecordingsTable
    description: A table to group together a stimulus and response from a single electrode
      and a single simultaneous recording. Each row in the table represents a single
      recording consisting typically of a stimulus and a corresponding response. In
      some cases, however, only a stimulus or a response is recorded as part of an
      experiment. In this case, both the stimulus and response will point to the same
      TimeSeries while the idx_start and count of the invalid column will be set to
      -1, thus, indicating that no values have been recorded for the stimulus or response,
      respectively. Note, a recording MUST contain at least a stimulus or a response.
      Typically the stimulus and response are PatchClampSeries. However, the use of
      AD/DA channels that are not associated to an electrode is also common in intracellular
      electrophysiology, in which case other TimeSeries may be used.
    is_a: AlignedDynamicTable
    attributes:
      name:
        name: name
        ifabsent: string(intracellular_recordings)
        range: string
        required: true
        equals_string: intracellular_recordings
      description:
        name: description
        description: Description of the contents of this table. Inherited from AlignedDynamicTable
          and overwritten here to fix the value of the attribute.
        range: text
      electrodes:
        name: electrodes
        description: Table for storing intracellular electrode related metadata.
        multivalued: false
        range: IntracellularElectrodesTable
        required: true
      stimuli:
        name: stimuli
        description: Table for storing intracellular stimulus related metadata.
        multivalued: false
        range: IntracellularStimuliTable
        required: true
      responses:
        name: responses
        description: Table for storing intracellular response related metadata.
        multivalued: false
        range: IntracellularResponsesTable
        required: true
    tree_root: true
  SimultaneousRecordingsTable:
    name: SimultaneousRecordingsTable
    description: A table for grouping different intracellular recordings from the
      IntracellularRecordingsTable table together that were recorded simultaneously
      from different electrodes.
    is_a: DynamicTable
    attributes:
      name:
        name: name
        ifabsent: string(simultaneous_recordings)
        range: string
        required: true
        equals_string: simultaneous_recordings
      recordings:
        name: recordings
        description: A reference to one or more rows in the IntracellularRecordingsTable
          table.
        multivalued: false
        range: SimultaneousRecordingsTable__recordings
        required: true
      recordings_index:
        name: recordings_index
        description: Index dataset for the recordings column.
        multivalued: false
        range: SimultaneousRecordingsTable__recordings_index
        required: true
    tree_root: true
  SequentialRecordingsTable:
    name: SequentialRecordingsTable
    description: A table for grouping different sequential recordings from the SimultaneousRecordingsTable
      table together. This is typically used to group together sequential recordings
      where a sequence of stimuli of the same type with varying parameters have been
      presented in a sequence.
    is_a: DynamicTable
    attributes:
      name:
        name: name
        ifabsent: string(sequential_recordings)
        range: string
        required: true
        equals_string: sequential_recordings
      simultaneous_recordings:
        name: simultaneous_recordings
        description: A reference to one or more rows in the SimultaneousRecordingsTable
          table.
        multivalued: false
        range: SequentialRecordingsTable__simultaneous_recordings
        required: true
      simultaneous_recordings_index:
        name: simultaneous_recordings_index
        description: Index dataset for the simultaneous_recordings column.
        multivalued: false
        range: SequentialRecordingsTable__simultaneous_recordings_index
        required: true
      stimulus_type:
        name: stimulus_type
        description: The type of stimulus used for the sequential recording.
        multivalued: true
        range: text
    tree_root: true
  RepetitionsTable:
    name: RepetitionsTable
    description: A table for grouping different sequential intracellular recordings
      together. With each SequentialRecording typically representing a particular
      type of stimulus, the RepetitionsTable table is typically used to group sets
      of stimuli applied in sequence.
    is_a: DynamicTable
    attributes:
      name:
        name: name
        ifabsent: string(repetitions)
        range: string
        required: true
        equals_string: repetitions
      sequential_recordings:
        name: sequential_recordings
        description: A reference to one or more rows in the SequentialRecordingsTable
          table.
        multivalued: false
        range: RepetitionsTable__sequential_recordings
        required: true
      sequential_recordings_index:
        name: sequential_recordings_index
        description: Index dataset for the sequential_recordings column.
        multivalued: false
        range: RepetitionsTable__sequential_recordings_index
        required: true
    tree_root: true
  ExperimentalConditionsTable:
    name: ExperimentalConditionsTable
    description: A table for grouping different intracellular recording repetitions
      together that belong to the same experimental condition.
    is_a: DynamicTable
    attributes:
      name:
        name: name
        ifabsent: string(experimental_conditions)
        range: string
        required: true
        equals_string: experimental_conditions
      repetitions:
        name: repetitions
        description: A reference to one or more rows in the RepetitionsTable table.
        multivalued: false
        range: ExperimentalConditionsTable__repetitions
        required: true
      repetitions_index:
        name: repetitions_index
        description: Index dataset for the repetitions column.
        multivalued: false
        range: ExperimentalConditionsTable__repetitions_index
        required: true
    tree_root: true