mirror of
https://github.com/p2p-ld/nwb-linkml.git
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sneakers-the-rat
be21325123
- split off generated subclasses into "include" files, not sure if that's good, but in any case we have them separable now. - more work on cleanly un-nesting scalar and 1D-vector data into attributes and lists, respectively - brought the pydantic generator in-repo to do a bunch of overrides
425 lines
16 KiB
YAML
425 lines
16 KiB
YAML
name: core.nwb.icephys
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id: core.nwb.icephys
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imports:
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- core.nwb.base
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- core.nwb.device
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- hdmf-common.table
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- nwb.language
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- core.nwb.icephys.include
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- core.nwb.icephys
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default_prefix: core.nwb.icephys/
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classes:
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PatchClampSeries:
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name: PatchClampSeries
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description: An abstract base class for patch-clamp data - stimulus or response,
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current or voltage.
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is_a: TimeSeries
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attributes:
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stimulus_description:
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name: stimulus_description
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description: Protocol/stimulus name for this patch-clamp dataset.
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range: text
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sweep_number:
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name: sweep_number
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description: Sweep number, allows to group different PatchClampSeries together.
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range: uint32
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data:
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name: data
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description: Recorded voltage or current.
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multivalued: false
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range: PatchClampSeries__data
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required: true
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gain:
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name: gain
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description: Gain of the recording, in units Volt/Amp (v-clamp) or Volt/Volt
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(c-clamp).
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multivalued: false
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range: float32
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required: false
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CurrentClampSeries:
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name: CurrentClampSeries
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description: Voltage data from an intracellular current-clamp recording. A corresponding
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CurrentClampStimulusSeries (stored separately as a stimulus) is used to store
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the current injected.
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is_a: PatchClampSeries
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attributes:
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data:
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name: data
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description: Recorded voltage.
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multivalued: false
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range: CurrentClampSeries__data
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required: true
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bias_current:
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name: bias_current
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description: Bias current, in amps.
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multivalued: false
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range: float32
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required: false
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bridge_balance:
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name: bridge_balance
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description: Bridge balance, in ohms.
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multivalued: false
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range: float32
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required: false
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capacitance_compensation:
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name: capacitance_compensation
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description: Capacitance compensation, in farads.
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multivalued: false
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range: float32
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required: false
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IZeroClampSeries:
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name: IZeroClampSeries
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description: Voltage data from an intracellular recording when all current and
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amplifier settings are off (i.e., CurrentClampSeries fields will be zero). There
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is no CurrentClampStimulusSeries associated with an IZero series because the
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amplifier is disconnected and no stimulus can reach the cell.
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is_a: CurrentClampSeries
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attributes:
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stimulus_description:
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name: stimulus_description
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description: An IZeroClampSeries has no stimulus, so this attribute is automatically
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set to "N/A"
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range: text
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bias_current:
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name: bias_current
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description: Bias current, in amps, fixed to 0.0.
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multivalued: false
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range: float32
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required: true
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bridge_balance:
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name: bridge_balance
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description: Bridge balance, in ohms, fixed to 0.0.
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multivalued: false
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range: float32
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required: true
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capacitance_compensation:
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name: capacitance_compensation
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description: Capacitance compensation, in farads, fixed to 0.0.
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multivalued: false
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range: float32
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required: true
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CurrentClampStimulusSeries:
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name: CurrentClampStimulusSeries
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description: Stimulus current applied during current clamp recording.
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is_a: PatchClampSeries
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attributes:
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data:
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name: data
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description: Stimulus current applied.
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multivalued: false
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range: CurrentClampStimulusSeries__data
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required: true
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VoltageClampSeries:
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name: VoltageClampSeries
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description: Current data from an intracellular voltage-clamp recording. A corresponding
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VoltageClampStimulusSeries (stored separately as a stimulus) is used to store
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the voltage injected.
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is_a: PatchClampSeries
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attributes:
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data:
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name: data
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description: Recorded current.
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multivalued: false
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range: VoltageClampSeries__data
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required: true
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capacitance_fast:
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name: capacitance_fast
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description: Fast capacitance, in farads.
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multivalued: false
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range: VoltageClampSeries__capacitance_fast
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required: false
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capacitance_slow:
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name: capacitance_slow
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description: Slow capacitance, in farads.
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multivalued: false
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range: VoltageClampSeries__capacitance_slow
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required: false
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resistance_comp_bandwidth:
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name: resistance_comp_bandwidth
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description: Resistance compensation bandwidth, in hertz.
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multivalued: false
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range: VoltageClampSeries__resistance_comp_bandwidth
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required: false
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resistance_comp_correction:
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name: resistance_comp_correction
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description: Resistance compensation correction, in percent.
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multivalued: false
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range: VoltageClampSeries__resistance_comp_correction
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required: false
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resistance_comp_prediction:
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name: resistance_comp_prediction
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description: Resistance compensation prediction, in percent.
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multivalued: false
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range: VoltageClampSeries__resistance_comp_prediction
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required: false
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whole_cell_capacitance_comp:
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name: whole_cell_capacitance_comp
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description: Whole cell capacitance compensation, in farads.
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multivalued: false
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range: VoltageClampSeries__whole_cell_capacitance_comp
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required: false
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whole_cell_series_resistance_comp:
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name: whole_cell_series_resistance_comp
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description: Whole cell series resistance compensation, in ohms.
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multivalued: false
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range: VoltageClampSeries__whole_cell_series_resistance_comp
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required: false
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VoltageClampStimulusSeries:
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name: VoltageClampStimulusSeries
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description: Stimulus voltage applied during a voltage clamp recording.
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is_a: PatchClampSeries
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attributes:
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data:
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name: data
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description: Stimulus voltage applied.
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multivalued: false
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range: VoltageClampStimulusSeries__data
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required: true
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IntracellularElectrode:
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name: IntracellularElectrode
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description: An intracellular electrode and its metadata.
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is_a: NWBContainer
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attributes:
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cell_id:
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name: cell_id
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description: unique ID of the cell
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multivalued: false
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range: text
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required: false
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description:
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name: description
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description: Description of electrode (e.g., whole-cell, sharp, etc.).
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multivalued: false
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range: text
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required: true
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filtering:
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name: filtering
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description: Electrode specific filtering.
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multivalued: false
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range: text
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required: false
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initial_access_resistance:
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name: initial_access_resistance
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description: Initial access resistance.
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multivalued: false
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range: text
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required: false
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location:
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name: location
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description: Location of the electrode. Specify the area, layer, comments
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on estimation of area/layer, stereotaxic coordinates if in vivo, etc. Use
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standard atlas names for anatomical regions when possible.
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multivalued: false
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range: text
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required: false
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resistance:
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name: resistance
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description: Electrode resistance, in ohms.
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multivalued: false
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range: text
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required: false
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seal:
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name: seal
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description: Information about seal used for recording.
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multivalued: false
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range: text
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required: false
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slice:
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name: slice
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description: Information about slice used for recording.
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multivalued: false
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range: text
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required: false
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SweepTable:
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name: SweepTable
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description: '[DEPRECATED] Table used to group different PatchClampSeries. SweepTable
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is being replaced by IntracellularRecordingsTable and SimultaneousRecordingsTable
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tables. Additional SequentialRecordingsTable, RepetitionsTable, and ExperimentalConditions
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tables provide enhanced support for experiment metadata.'
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is_a: DynamicTable
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attributes:
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sweep_number:
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name: sweep_number
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description: Sweep number of the PatchClampSeries in that row.
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multivalued: true
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range: uint32
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series:
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name: series
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description: The PatchClampSeries with the sweep number in that row.
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multivalued: true
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range: PatchClampSeries
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series_index:
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name: series_index
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description: Index for series.
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multivalued: false
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range: SweepTable__series_index
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required: true
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IntracellularElectrodesTable:
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name: IntracellularElectrodesTable
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description: Table for storing intracellular electrode related metadata.
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is_a: DynamicTable
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attributes:
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description:
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name: description
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description: Description of what is in this dynamic table.
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range: text
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electrode:
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name: electrode
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description: Column for storing the reference to the intracellular electrode.
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multivalued: true
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range: IntracellularElectrode
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IntracellularStimuliTable:
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name: IntracellularStimuliTable
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description: Table for storing intracellular stimulus related metadata.
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is_a: DynamicTable
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attributes:
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description:
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name: description
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description: Description of what is in this dynamic table.
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range: text
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stimulus:
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name: stimulus
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description: Column storing the reference to the recorded stimulus for the
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recording (rows).
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multivalued: false
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range: IntracellularStimuliTable__stimulus
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required: true
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IntracellularResponsesTable:
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name: IntracellularResponsesTable
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description: Table for storing intracellular response related metadata.
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is_a: DynamicTable
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attributes:
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description:
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name: description
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description: Description of what is in this dynamic table.
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range: text
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response:
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name: response
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description: Column storing the reference to the recorded response for the
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recording (rows)
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multivalued: false
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range: IntracellularResponsesTable__response
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required: true
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IntracellularRecordingsTable:
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name: IntracellularRecordingsTable
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description: A table to group together a stimulus and response from a single electrode
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and a single simultaneous recording. Each row in the table represents a single
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recording consisting typically of a stimulus and a corresponding response. In
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some cases, however, only a stimulus or a response is recorded as part of an
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experiment. In this case, both the stimulus and response will point to the same
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TimeSeries while the idx_start and count of the invalid column will be set to
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-1, thus, indicating that no values have been recorded for the stimulus or response,
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respectively. Note, a recording MUST contain at least a stimulus or a response.
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Typically the stimulus and response are PatchClampSeries. However, the use of
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AD/DA channels that are not associated to an electrode is also common in intracellular
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electrophysiology, in which case other TimeSeries may be used.
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is_a: AlignedDynamicTable
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attributes:
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description:
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name: description
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description: Description of the contents of this table. Inherited from AlignedDynamicTable
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and overwritten here to fix the value of the attribute.
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range: text
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electrodes:
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name: electrodes
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description: Table for storing intracellular electrode related metadata.
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multivalued: false
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range: IntracellularRecordingsTable__electrodes
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required: true
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stimuli:
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name: stimuli
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description: Table for storing intracellular stimulus related metadata.
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multivalued: false
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range: IntracellularRecordingsTable__stimuli
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required: true
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responses:
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name: responses
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description: Table for storing intracellular response related metadata.
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multivalued: false
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range: IntracellularRecordingsTable__responses
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required: true
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SimultaneousRecordingsTable:
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name: SimultaneousRecordingsTable
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description: A table for grouping different intracellular recordings from the
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IntracellularRecordingsTable table together that were recorded simultaneously
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from different electrodes.
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is_a: DynamicTable
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attributes:
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recordings:
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name: recordings
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description: A reference to one or more rows in the IntracellularRecordingsTable
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table.
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multivalued: false
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range: SimultaneousRecordingsTable__recordings
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required: true
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recordings_index:
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name: recordings_index
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description: Index dataset for the recordings column.
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multivalued: false
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range: SimultaneousRecordingsTable__recordings_index
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required: true
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SequentialRecordingsTable:
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name: SequentialRecordingsTable
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description: A table for grouping different sequential recordings from the SimultaneousRecordingsTable
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table together. This is typically used to group together sequential recordings
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where a sequence of stimuli of the same type with varying parameters have been
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presented in a sequence.
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is_a: DynamicTable
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attributes:
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simultaneous_recordings:
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name: simultaneous_recordings
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description: A reference to one or more rows in the SimultaneousRecordingsTable
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table.
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multivalued: false
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range: SequentialRecordingsTable__simultaneous_recordings
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required: true
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simultaneous_recordings_index:
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name: simultaneous_recordings_index
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description: Index dataset for the simultaneous_recordings column.
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multivalued: false
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range: SequentialRecordingsTable__simultaneous_recordings_index
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required: true
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stimulus_type:
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name: stimulus_type
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description: The type of stimulus used for the sequential recording.
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multivalued: true
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range: text
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RepetitionsTable:
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name: RepetitionsTable
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description: A table for grouping different sequential intracellular recordings
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together. With each SequentialRecording typically representing a particular
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type of stimulus, the RepetitionsTable table is typically used to group sets
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of stimuli applied in sequence.
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is_a: DynamicTable
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attributes:
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sequential_recordings:
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name: sequential_recordings
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description: A reference to one or more rows in the SequentialRecordingsTable
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table.
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multivalued: false
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range: RepetitionsTable__sequential_recordings
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required: true
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sequential_recordings_index:
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name: sequential_recordings_index
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description: Index dataset for the sequential_recordings column.
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multivalued: false
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range: RepetitionsTable__sequential_recordings_index
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required: true
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ExperimentalConditionsTable:
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name: ExperimentalConditionsTable
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description: A table for grouping different intracellular recording repetitions
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together that belong to the same experimental condition.
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is_a: DynamicTable
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attributes:
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repetitions:
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name: repetitions
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description: A reference to one or more rows in the RepetitionsTable table.
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multivalued: false
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range: ExperimentalConditionsTable__repetitions
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required: true
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repetitions_index:
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name: repetitions_index
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description: Index dataset for the repetitions column.
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multivalued: false
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range: ExperimentalConditionsTable__repetitions_index
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required: true
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