name: core.nwb.icephys id: core.nwb.icephys imports: - core.nwb.base - core.nwb.device - hdmf-common.table - nwb.language 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 CurrentClampSeries__data: name: CurrentClampSeries__data description: Recorded voltage. 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. which 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' and add 'offset'. range: text value: name: value range: AnyType required: 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 CurrentClampStimulusSeries__data: name: CurrentClampStimulusSeries__data description: Stimulus current applied. 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. which is fixed to 'amperes'. Actual stored values are not necessarily stored in these units. To access the data in these units, multiply 'data' by 'conversion' and add 'offset'. range: text value: name: value range: AnyType required: 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 VoltageClampSeries__data: name: VoltageClampSeries__data description: Recorded current. 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. which is fixed to 'amperes'. Actual stored values are not necessarily stored in these units. To access the data in these units, multiply 'data' by 'conversion' and add 'offset'. range: text value: name: value range: AnyType required: true VoltageClampSeries__capacitance_fast: name: VoltageClampSeries__capacitance_fast description: Fast capacitance, in farads. attributes: name: name: name ifabsent: string(capacitance_fast) range: string required: true equals_string: capacitance_fast unit: name: unit description: Unit of measurement for capacitance_fast, which is fixed to 'farads'. range: text value: name: value range: float32 required: true VoltageClampSeries__capacitance_slow: name: VoltageClampSeries__capacitance_slow description: Slow capacitance, in farads. attributes: name: name: name ifabsent: string(capacitance_slow) range: string required: true equals_string: capacitance_slow unit: name: unit description: Unit of measurement for capacitance_fast, which is fixed to 'farads'. range: text value: name: value range: float32 required: true VoltageClampSeries__resistance_comp_bandwidth: name: VoltageClampSeries__resistance_comp_bandwidth description: Resistance compensation bandwidth, in hertz. attributes: name: name: name ifabsent: string(resistance_comp_bandwidth) range: string required: true equals_string: resistance_comp_bandwidth unit: name: unit description: Unit of measurement for resistance_comp_bandwidth, which is fixed to 'hertz'. range: text value: name: value range: float32 required: true VoltageClampSeries__resistance_comp_correction: name: VoltageClampSeries__resistance_comp_correction description: Resistance compensation correction, in percent. attributes: name: name: name ifabsent: string(resistance_comp_correction) range: string required: true equals_string: resistance_comp_correction unit: name: unit description: Unit of measurement for resistance_comp_correction, which is fixed to 'percent'. range: text value: name: value range: float32 required: true VoltageClampSeries__resistance_comp_prediction: name: VoltageClampSeries__resistance_comp_prediction description: Resistance compensation prediction, in percent. attributes: name: name: name ifabsent: string(resistance_comp_prediction) range: string required: true equals_string: resistance_comp_prediction unit: name: unit description: Unit of measurement for resistance_comp_prediction, which is fixed to 'percent'. range: text value: name: value range: float32 required: true VoltageClampSeries__whole_cell_capacitance_comp: name: VoltageClampSeries__whole_cell_capacitance_comp description: Whole cell capacitance compensation, in farads. attributes: name: name: name ifabsent: string(whole_cell_capacitance_comp) range: string required: true equals_string: whole_cell_capacitance_comp unit: name: unit description: Unit of measurement for whole_cell_capacitance_comp, which is fixed to 'farads'. range: text value: name: value range: float32 required: true VoltageClampSeries__whole_cell_series_resistance_comp: name: VoltageClampSeries__whole_cell_series_resistance_comp description: Whole cell series resistance compensation, in ohms. attributes: name: name: name ifabsent: string(whole_cell_series_resistance_comp) range: string required: true equals_string: whole_cell_series_resistance_comp unit: name: unit description: Unit of measurement for whole_cell_series_resistance_comp, which is fixed to 'ohms'. range: text value: name: value range: float32 required: 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 VoltageClampStimulusSeries__data: name: VoltageClampStimulusSeries__data description: Stimulus voltage applied. 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. which 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' and add 'offset'. range: text value: name: value range: AnyType required: 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 SweepTable__series_index: name: SweepTable__series_index description: Index for series. is_a: VectorIndex attributes: name: name: name ifabsent: string(series_index) range: string required: true equals_string: series_index 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 IntracellularStimuliTable__stimulus: name: IntracellularStimuliTable__stimulus description: Column storing the reference to the recorded stimulus for the recording (rows). is_a: TimeSeriesReferenceVectorData attributes: name: name: name ifabsent: string(stimulus) range: string required: true equals_string: stimulus 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 IntracellularResponsesTable__response: name: IntracellularResponsesTable__response description: Column storing the reference to the recorded response for the recording (rows) is_a: TimeSeriesReferenceVectorData attributes: name: name: name ifabsent: string(response) range: string required: true equals_string: response 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 SimultaneousRecordingsTable__recordings: name: SimultaneousRecordingsTable__recordings description: A reference to one or more rows in the IntracellularRecordingsTable table. is_a: DynamicTableRegion attributes: name: name: name ifabsent: string(recordings) range: string required: true equals_string: recordings table: name: table description: Reference to the IntracellularRecordingsTable table that this table region applies to. This specializes the attribute inherited from DynamicTableRegion to fix the type of table that can be referenced here. range: IntracellularRecordingsTable SimultaneousRecordingsTable__recordings_index: name: SimultaneousRecordingsTable__recordings_index description: Index dataset for the recordings column. is_a: VectorIndex attributes: name: name: name ifabsent: string(recordings_index) range: string required: true equals_string: recordings_index 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 SequentialRecordingsTable__simultaneous_recordings: name: SequentialRecordingsTable__simultaneous_recordings description: A reference to one or more rows in the SimultaneousRecordingsTable table. is_a: DynamicTableRegion attributes: name: name: name ifabsent: string(simultaneous_recordings) range: string required: true equals_string: simultaneous_recordings table: name: table description: Reference to the SimultaneousRecordingsTable table that this table region applies to. This specializes the attribute inherited from DynamicTableRegion to fix the type of table that can be referenced here. range: SimultaneousRecordingsTable SequentialRecordingsTable__simultaneous_recordings_index: name: SequentialRecordingsTable__simultaneous_recordings_index description: Index dataset for the simultaneous_recordings column. is_a: VectorIndex attributes: name: name: name ifabsent: string(simultaneous_recordings_index) range: string required: true equals_string: simultaneous_recordings_index 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 RepetitionsTable__sequential_recordings: name: RepetitionsTable__sequential_recordings description: A reference to one or more rows in the SequentialRecordingsTable table. is_a: DynamicTableRegion attributes: name: name: name ifabsent: string(sequential_recordings) range: string required: true equals_string: sequential_recordings table: name: table description: Reference to the SequentialRecordingsTable table that this table region applies to. This specializes the attribute inherited from DynamicTableRegion to fix the type of table that can be referenced here. range: SequentialRecordingsTable RepetitionsTable__sequential_recordings_index: name: RepetitionsTable__sequential_recordings_index description: Index dataset for the sequential_recordings column. is_a: VectorIndex attributes: name: name: name ifabsent: string(sequential_recordings_index) range: string required: true equals_string: sequential_recordings_index 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 ExperimentalConditionsTable__repetitions: name: ExperimentalConditionsTable__repetitions description: A reference to one or more rows in the RepetitionsTable table. is_a: DynamicTableRegion attributes: name: name: name ifabsent: string(repetitions) range: string required: true equals_string: repetitions table: name: table description: Reference to the RepetitionsTable table that this table region applies to. This specializes the attribute inherited from DynamicTableRegion to fix the type of table that can be referenced here. range: RepetitionsTable ExperimentalConditionsTable__repetitions_index: name: ExperimentalConditionsTable__repetitions_index description: Index dataset for the repetitions column. is_a: VectorIndex attributes: name: name: name ifabsent: string(repetitions_index) range: string required: true equals_string: repetitions_index