name: core.nwb.icephys id: core.nwb.icephys imports: - core.nwb.base - 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: 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: false range: PatchClampSeries_data required: true gain: name: gain description: Gain of the recording, in units Volt/Amp (v-clamp) or Volt/Volt (c-clamp). multivalued: false range: PatchClampSeries_gain required: false PatchClampSeries_data: name: PatchClampSeries_data description: Recorded voltage or current. attributes: unit: name: unit description: Base unit of measurement for working with the data. 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 array: name: array range: PatchClampSeries_data_Array PatchClampSeries_data_Array: name: PatchClampSeries_data_Array is_a: Arraylike attributes: num_times: name: num_times range: numeric required: true PatchClampSeries_gain: name: PatchClampSeries_gain description: Gain of the recording, in units Volt/Amp (v-clamp) or Volt/Volt (c-clamp). 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: 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: CurrentClampSeries_bias_current required: false bridge_balance: name: bridge_balance description: Bridge balance, in ohms. multivalued: false range: CurrentClampSeries_bridge_balance required: false capacitance_compensation: name: capacitance_compensation description: Capacitance compensation, in farads. multivalued: false range: CurrentClampSeries_capacitance_compensation required: false CurrentClampSeries_data: name: CurrentClampSeries_data description: Recorded voltage. attributes: 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 CurrentClampSeries_bias_current: name: CurrentClampSeries_bias_current description: Bias current, in amps. CurrentClampSeries_bridge_balance: name: CurrentClampSeries_bridge_balance description: Bridge balance, in ohms. CurrentClampSeries_capacitance_compensation: name: CurrentClampSeries_capacitance_compensation description: Capacitance compensation, in farads. 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: 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: IZeroClampSeries_bias_current required: true bridge_balance: name: bridge_balance description: Bridge balance, in ohms, fixed to 0.0. multivalued: false range: IZeroClampSeries_bridge_balance required: true capacitance_compensation: name: capacitance_compensation description: Capacitance compensation, in farads, fixed to 0.0. multivalued: false range: IZeroClampSeries_capacitance_compensation required: true IZeroClampSeries_bias_current: name: IZeroClampSeries_bias_current description: Bias current, in amps, fixed to 0.0. IZeroClampSeries_bridge_balance: name: IZeroClampSeries_bridge_balance description: Bridge balance, in ohms, fixed to 0.0. IZeroClampSeries_capacitance_compensation: name: IZeroClampSeries_capacitance_compensation description: Capacitance compensation, in farads, fixed to 0.0. CurrentClampStimulusSeries: name: CurrentClampStimulusSeries description: Stimulus current applied during current clamp recording. is_a: PatchClampSeries attributes: data: name: data description: Stimulus current applied. multivalued: false range: CurrentClampStimulusSeries_data required: true CurrentClampStimulusSeries_data: name: CurrentClampStimulusSeries_data description: Stimulus current applied. attributes: 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 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: 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 VoltageClampSeries_data: name: VoltageClampSeries_data description: Recorded current. attributes: 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 VoltageClampSeries_capacitance_fast: name: VoltageClampSeries_capacitance_fast description: Fast capacitance, in farads. attributes: unit: name: unit description: Unit of measurement for capacitance_fast, which is fixed to 'farads'. range: text VoltageClampSeries_capacitance_slow: name: VoltageClampSeries_capacitance_slow description: Slow capacitance, in farads. attributes: unit: name: unit description: Unit of measurement for capacitance_fast, which is fixed to 'farads'. range: text VoltageClampSeries_resistance_comp_bandwidth: name: VoltageClampSeries_resistance_comp_bandwidth description: Resistance compensation bandwidth, in hertz. attributes: unit: name: unit description: Unit of measurement for resistance_comp_bandwidth, which is fixed to 'hertz'. range: text VoltageClampSeries_resistance_comp_correction: name: VoltageClampSeries_resistance_comp_correction description: Resistance compensation correction, in percent. attributes: unit: name: unit description: Unit of measurement for resistance_comp_correction, which is fixed to 'percent'. range: text VoltageClampSeries_resistance_comp_prediction: name: VoltageClampSeries_resistance_comp_prediction description: Resistance compensation prediction, in percent. attributes: unit: name: unit description: Unit of measurement for resistance_comp_prediction, which is fixed to 'percent'. range: text VoltageClampSeries_whole_cell_capacitance_comp: name: VoltageClampSeries_whole_cell_capacitance_comp description: Whole cell capacitance compensation, in farads. attributes: unit: name: unit description: Unit of measurement for whole_cell_capacitance_comp, which is fixed to 'farads'. range: text VoltageClampSeries_whole_cell_series_resistance_comp: name: VoltageClampSeries_whole_cell_series_resistance_comp description: Whole cell series resistance compensation, in ohms. attributes: unit: name: unit description: Unit of measurement for whole_cell_series_resistance_comp, which is fixed to 'ohms'. range: text VoltageClampStimulusSeries: name: VoltageClampStimulusSeries description: Stimulus voltage applied during a voltage clamp recording. is_a: PatchClampSeries attributes: data: name: data description: Stimulus voltage applied. multivalued: false range: VoltageClampStimulusSeries_data required: true VoltageClampStimulusSeries_data: name: VoltageClampStimulusSeries_data description: Stimulus voltage applied. attributes: 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 IntracellularElectrode: name: IntracellularElectrode description: An intracellular electrode and its metadata. is_a: NWBContainer attributes: cell_id: name: cell_id description: unique ID of the cell multivalued: false range: IntracellularElectrode_cell_id required: false description: name: description description: Description of electrode (e.g., whole-cell, sharp, etc.). multivalued: false range: IntracellularElectrode_description required: true filtering: name: filtering description: Electrode specific filtering. multivalued: false range: IntracellularElectrode_filtering required: false initial_access_resistance: name: initial_access_resistance description: Initial access resistance. multivalued: false range: IntracellularElectrode_initial_access_resistance 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: IntracellularElectrode_location required: false resistance: name: resistance description: Electrode resistance, in ohms. multivalued: false range: IntracellularElectrode_resistance required: false seal: name: seal description: Information about seal used for recording. multivalued: false range: IntracellularElectrode_seal required: false slice: name: slice description: Information about slice used for recording. multivalued: false range: IntracellularElectrode_slice required: false IntracellularElectrode_cell_id: name: IntracellularElectrode_cell_id description: unique ID of the cell IntracellularElectrode_description: name: IntracellularElectrode_description description: Description of electrode (e.g., whole-cell, sharp, etc.). IntracellularElectrode_filtering: name: IntracellularElectrode_filtering description: Electrode specific filtering. IntracellularElectrode_initial_access_resistance: name: IntracellularElectrode_initial_access_resistance description: Initial access resistance. IntracellularElectrode_location: name: IntracellularElectrode_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. IntracellularElectrode_resistance: name: IntracellularElectrode_resistance description: Electrode resistance, in ohms. IntracellularElectrode_seal: name: IntracellularElectrode_seal description: Information about seal used for recording. IntracellularElectrode_slice: name: IntracellularElectrode_slice description: Information about slice used for recording. 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: sweep_number: name: sweep_number description: Sweep number of the PatchClampSeries in that row. multivalued: false range: SweepTable_sweep_number required: true series: name: series description: The PatchClampSeries with the sweep number in that row. multivalued: false range: SweepTable_series required: true series_index: name: series_index description: Index for series. multivalued: false range: SweepTable_series_index required: true SweepTable_sweep_number: name: SweepTable_sweep_number description: Sweep number of the PatchClampSeries in that row. is_a: VectorData SweepTable_series: name: SweepTable_series description: The PatchClampSeries with the sweep number in that row. is_a: VectorData SweepTable_series_index: name: SweepTable_series_index description: Index for series. is_a: VectorIndex IntracellularElectrodesTable: name: IntracellularElectrodesTable description: Table for storing intracellular electrode related metadata. is_a: DynamicTable attributes: 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: false range: IntracellularElectrodesTable_electrode required: true IntracellularElectrodesTable_electrode: name: IntracellularElectrodesTable_electrode description: Column for storing the reference to the intracellular electrode. is_a: VectorData IntracellularStimuliTable: name: IntracellularStimuliTable description: Table for storing intracellular stimulus related metadata. is_a: DynamicTable attributes: 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 IntracellularStimuliTable_stimulus: name: IntracellularStimuliTable_stimulus description: Column storing the reference to the recorded stimulus for the recording (rows). is_a: TimeSeriesReferenceVectorData IntracellularResponsesTable: name: IntracellularResponsesTable description: Table for storing intracellular response related metadata. is_a: DynamicTable attributes: 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 IntracellularResponsesTable_response: name: IntracellularResponsesTable_response description: Column storing the reference to the recorded response for the recording (rows) is_a: TimeSeriesReferenceVectorData 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: 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: IntracellularRecordingsTable_electrodes required: true stimuli: name: stimuli description: Table for storing intracellular stimulus related metadata. multivalued: false range: IntracellularRecordingsTable_stimuli required: true responses: name: responses description: Table for storing intracellular response related metadata. multivalued: false range: IntracellularRecordingsTable_responses required: true IntracellularRecordingsTable_electrodes: name: IntracellularRecordingsTable_electrodes description: Table for storing intracellular electrode related metadata. is_a: IntracellularElectrodesTable IntracellularRecordingsTable_stimuli: name: IntracellularRecordingsTable_stimuli description: Table for storing intracellular stimulus related metadata. is_a: IntracellularStimuliTable IntracellularRecordingsTable_responses: name: IntracellularRecordingsTable_responses description: Table for storing intracellular response related metadata. is_a: IntracellularResponsesTable 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: 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 SimultaneousRecordingsTable_recordings: name: SimultaneousRecordingsTable_recordings description: A reference to one or more rows in the IntracellularRecordingsTable table. is_a: DynamicTableRegion attributes: 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 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: 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: false range: SequentialRecordingsTable_stimulus_type required: true SequentialRecordingsTable_simultaneous_recordings: name: SequentialRecordingsTable_simultaneous_recordings description: A reference to one or more rows in the SimultaneousRecordingsTable table. is_a: DynamicTableRegion attributes: 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 SequentialRecordingsTable_stimulus_type: name: SequentialRecordingsTable_stimulus_type description: The type of stimulus used for the sequential recording. is_a: VectorData 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: 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 RepetitionsTable_sequential_recordings: name: RepetitionsTable_sequential_recordings description: A reference to one or more rows in the SequentialRecordingsTable table. is_a: DynamicTableRegion attributes: 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 ExperimentalConditionsTable: name: ExperimentalConditionsTable description: A table for grouping different intracellular recording repetitions together that belong to the same experimental condition. is_a: DynamicTable attributes: 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 ExperimentalConditionsTable_repetitions: name: ExperimentalConditionsTable_repetitions description: A reference to one or more rows in the RepetitionsTable table. is_a: DynamicTableRegion attributes: 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