pynwb.icephys module

class pynwb.icephys.IntracellularElectrode(name, device, source, description, slice=None, seal=None, location=None, resistance=None, filtering=None, initial_access_resistance=None)

Bases: pynwb.core.NWBContainer

Parameters:
  • name (str) – the name of this electrode
  • device (Device) – the device that was used to record from this electrode
  • source (str) – the source of the data
  • description (str) – Recording description, description of electrode (e.g., whole-cell, sharp, etc) COMMENT: Free-form text (can be from Methods)
  • slice (str) – Information about slice used for recording.
  • seal (str) – Information about seal used for recording.
  • location (str) – Area, layer, comments on estimation, stereotaxis coordinates (if in vivo, etc).
  • resistance (str) – Electrode resistance COMMENT: unit: Ohm.
  • filtering (str) – Electrode specific filtering.
  • initial_access_resistance (str) – Initial access resistance.
slice

Information about slice used for recording.

seal

Information about seal used for recording.

description

Recording description, description of electrode (e.g., whole-cell, sharp, etc) COMMENT – Free-form text (can be from Methods)

location

Area, layer, comments on estimation, stereotaxis coordinates (if in vivo, etc).

resistance

**Electrode resistance COMMENT* – unit* – Ohm.

filtering

Electrode specific filtering.

initial_access_resistance

Initial access resistance.

device

the device that was used to record from this electrode

namespace = 'core'
neurodata_type = 'IntracellularElectrode'
class pynwb.icephys.PatchClampSeries(name, source, data, unit, electrode, gain, stimulus_description='NA', resolution=0.0, conversion=1.0, timestamps=None, starting_time=None, rate=None, comments='no comments', description='no description', control=None, control_description=None, parent=None)

Bases: pynwb.base.TimeSeries

Stores stimulus or response current or voltage. Superclass definition for patch-clamp data (this class should not be instantiated directly).

Parameters:
  • name (str) – The name of this TimeSeries dataset
  • source (str) – Name of TimeSeries or Modules that serve as the source for the data contained here. It can also be the name of a device, for stimulus or acquisition data
  • data (ndarray or list or tuple or Dataset or AbstractDataChunkIterator or DataIO or FORMDataset or TimeSeries) – The data this TimeSeries dataset stores. Can also store binary data e.g. image frames
  • unit (str) – The base unit of measurement (should be SI unit)
  • electrode (IntracellularElectrode) – IntracellularElectrode group that describes the electrode that was used to apply or record this data.
  • gain (float) – Units: Volt/Amp (v-clamp) or Volt/Volt (c-clamp)
  • stimulus_description (str) – the stimulus name/protocol
  • resolution (float) – The smallest meaningful difference (in specified unit) between values in data
  • conversion (float) – Scalar to multiply each element by to conver to volts
  • timestamps (ndarray or list or tuple or Dataset or AbstractDataChunkIterator or DataIO or FORMDataset or TimeSeries) – Timestamps for samples stored in data
  • starting_time (float) – The timestamp of the first sample
  • rate (float) – Sampling rate in Hz
  • comments (str) – Human-readable comments about this TimeSeries dataset
  • description (str) – Description of this TimeSeries dataset
  • control (Iterable) – Numerical labels that apply to each element in data
  • control_description (Iterable) – Description of each control value
  • parent (NWBContainer) – The parent NWBContainer for this NWBContainer
electrode

IntracellularElectrode group that describes the electrode that was used to apply or record this data.

gain

Units – Volt/Amp (v-clamp) or Volt/Volt (c-clamp)

stimulus_description

the stimulus name/protocol

namespace = 'core'
neurodata_type = 'PatchClampSeries'
class pynwb.icephys.CurrentClampSeries(name, source, data, unit, electrode, gain, bias_current, bridge_balance, capacitance_compensation, stimulus_description='NA', resolution=0.0, conversion=1.0, timestamps=None, timestamps=None, starting_time=None, rate=None, comments='no comments', description='no description', control=None, control_description=None, parent=None)

Bases: pynwb.icephys.PatchClampSeries

Stores voltage data recorded from intracellular current-clamp recordings. A corresponding CurrentClampStimulusSeries (stored separately as a stimulus) is used to store the current injected.

Parameters:
  • name (str) – The name of this TimeSeries dataset
  • source (str) – Name of TimeSeries or Modules that serve as the source for the data contained here. It can also be the name of a device, for stimulus or acquisition data
  • data (ndarray or list or tuple or Dataset or AbstractDataChunkIterator or DataIO or FORMDataset or TimeSeries) – The data this TimeSeries dataset stores. Can also store binary data e.g. image frames
  • unit (str) – The base unit of measurement (should be SI unit)
  • electrode (IntracellularElectrode) – IntracellularElectrode group that describes the electrode that was used to apply or record this data.
  • gain (float) – Units: Volt/Amp (v-clamp) or Volt/Volt (c-clamp)
  • bias_current (float) – Unit: Amp
  • bridge_balance (float) – Unit: Ohm
  • capacitance_compensation (float) – Unit: Farad
  • stimulus_description (str) – the stimulus name/protocol
  • resolution (float) – The smallest meaningful difference (in specified unit) between values in data
  • conversion (float) – Scalar to multiply each element by to conver to volts
  • timestamps (ndarray or list or tuple or Dataset or AbstractDataChunkIterator or DataIO or FORMDataset or TimeSeries) – Timestamps for samples stored in data
  • timestamps – Timestamps for samples stored in data
  • starting_time (float) – The timestamp of the first sample
  • rate (float) – Sampling rate in Hz
  • comments (str) – Human-readable comments about this TimeSeries dataset
  • description (str) – Description of this TimeSeries dataset
  • control (Iterable) – Numerical labels that apply to each element in data
  • control_description (Iterable) – Description of each control value
  • parent (NWBContainer) – The parent NWBContainer for this NWBContainer
bias_current

Unit – Amp

bridge_balance

Unit – Ohm

capacitance_compensation

Unit – Farad

namespace = 'core'
neurodata_type = 'CurrentClampSeries'
class pynwb.icephys.IZeroClampSeries(name, source, data, unit, electrode, gain, stimulus_description='NA', bias_current=0.0, bridge_balance=0.0, capacitance_compensation=0.0, resolution=0.0, conversion=1.0, timestamps=None, starting_time=None, rate=None, comments='no comments', description='no description', control=None, control_description=None, parent=None)

Bases: pynwb.icephys.CurrentClampSeries

Stores recorded voltage data from intracellular recordings 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.

Parameters:
  • name (str) – The name of this TimeSeries dataset
  • source (str) – Name of TimeSeries or Modules that serve as the source for the data contained here. It can also be the name of a device, for stimulus or acquisition data
  • data (ndarray or list or tuple or Dataset or AbstractDataChunkIterator or DataIO or FORMDataset or TimeSeries) – The data this TimeSeries dataset stores. Can also store binary data e.g. image frames
  • unit (str) – The base unit of measurement (should be SI unit)
  • electrode (IntracellularElectrode) – IntracellularElectrode group that describes the electrode that was used to apply or record this data.
  • gain (float) – Units: Volt/Amp (v-clamp) or Volt/Volt (c-clamp)
  • stimulus_description (str) – the stimulus name/protocol
  • bias_current (float) – Unit: Amp
  • bridge_balance (float) – Unit: Ohm
  • capacitance_compensation (float) – Unit: Farad
  • resolution (float) – The smallest meaningful difference (in specified unit) between values in data
  • conversion (float) – Scalar to multiply each element by to conver to volts
  • timestamps (ndarray or list or tuple or Dataset or AbstractDataChunkIterator or DataIO or FORMDataset or TimeSeries) – Timestamps for samples stored in data
  • starting_time (float) – The timestamp of the first sample
  • rate (float) – Sampling rate in Hz
  • comments (str) – Human-readable comments about this TimeSeries dataset
  • description (str) – Description of this TimeSeries dataset
  • control (Iterable) – Numerical labels that apply to each element in data
  • control_description (Iterable) – Description of each control value
  • parent (NWBContainer) – The parent NWBContainer for this NWBContainer
namespace = 'core'
neurodata_type = 'IZeroClampSeries'
class pynwb.icephys.CurrentClampStimulusSeries(name, source, data, unit, electrode, gain, stimulus_description='NA', resolution=0.0, conversion=1.0, timestamps=None, starting_time=None, rate=None, comments='no comments', description='no description', control=None, control_description=None, parent=None)

Bases: pynwb.icephys.PatchClampSeries

Aliases to standard PatchClampSeries. Its functionality is to better tag PatchClampSeries for machine (and human) readability of the file.

Parameters:
  • name (str) – The name of this TimeSeries dataset
  • source (str) – Name of TimeSeries or Modules that serve as the source for the data contained here. It can also be the name of a device, for stimulus or acquisition data
  • data (ndarray or list or tuple or Dataset or AbstractDataChunkIterator or DataIO or FORMDataset or TimeSeries) – The data this TimeSeries dataset stores. Can also store binary data e.g. image frames
  • unit (str) – The base unit of measurement (should be SI unit)
  • electrode (IntracellularElectrode) – IntracellularElectrode group that describes the electrode that was used to apply or record this data.
  • gain (float) – Units: Volt/Amp (v-clamp) or Volt/Volt (c-clamp)
  • stimulus_description (str) – the stimulus name/protocol
  • resolution (float) – The smallest meaningful difference (in specified unit) between values in data
  • conversion (float) – Scalar to multiply each element by to conver to volts
  • timestamps (ndarray or list or tuple or Dataset or AbstractDataChunkIterator or DataIO or FORMDataset or TimeSeries) – Timestamps for samples stored in data
  • starting_time (float) – The timestamp of the first sample
  • rate (float) – Sampling rate in Hz
  • comments (str) – Human-readable comments about this TimeSeries dataset
  • description (str) – Description of this TimeSeries dataset
  • control (Iterable) – Numerical labels that apply to each element in data
  • control_description (Iterable) – Description of each control value
  • parent (NWBContainer) – The parent NWBContainer for this NWBContainer
namespace = 'core'
neurodata_type = 'CurrentClampStimulusSeries'
class pynwb.icephys.VoltageClampSeries(name, source, data, unit, electrode, gain, capacitance_fast, capacitance_slow, resistance_comp_bandwidth, resistance_comp_correction, resistance_comp_prediction, whole_cell_capacitance_comp, whole_cell_series_resistance_comp, stimulus_description='NA', resolution=0.0, conversion=1.0, timestamps=None, starting_time=None, rate=None, comments='no comments', description='no description', control=None, control_description=None, parent=None)

Bases: pynwb.icephys.PatchClampSeries

Stores current data recorded from intracellular voltage-clamp recordings. A corresponding VoltageClampStimulusSeries (stored separately as a stimulus) is used to store the voltage injected.

Parameters:
  • name (str) – The name of this TimeSeries dataset
  • source (str) – Name of TimeSeries or Modules that serve as the source for the data contained here. It can also be the name of a device, for stimulus or acquisition data
  • data (ndarray or list or tuple or Dataset or AbstractDataChunkIterator or DataIO or FORMDataset or TimeSeries) – The data this TimeSeries dataset stores. Can also store binary data e.g. image frames
  • unit (str) – The base unit of measurement (should be SI unit)
  • electrode (IntracellularElectrode) – IntracellularElectrode group that describes the electrode that was used to apply or record this data.
  • gain (float) – Units: Volt/Amp (v-clamp) or Volt/Volt (c-clamp)
  • capacitance_fast (float) – Unit: Farad
  • capacitance_slow (float) – Unit: Farad
  • resistance_comp_bandwidth (float) – Unit: Hz
  • resistance_comp_correction (float) – Unit: %
  • resistance_comp_prediction (float) – Unit: %
  • whole_cell_capacitance_comp (float) – Unit: Farad
  • whole_cell_series_resistance_comp (float) – Unit: Ohm
  • stimulus_description (str) – the stimulus name/protocol
  • resolution (float) – The smallest meaningful difference (in specified unit) between values in data
  • conversion (float) – Scalar to multiply each element by to conver to volts
  • timestamps (ndarray or list or tuple or Dataset or AbstractDataChunkIterator or DataIO or FORMDataset or TimeSeries) – Timestamps for samples stored in data
  • starting_time (float) – The timestamp of the first sample
  • rate (float) – Sampling rate in Hz
  • comments (str) – Human-readable comments about this TimeSeries dataset
  • description (str) – Description of this TimeSeries dataset
  • control (Iterable) – Numerical labels that apply to each element in data
  • control_description (Iterable) – Description of each control value
  • parent (NWBContainer) – The parent NWBContainer for this NWBContainer
capacitance_fast

Unit – Farad

capacitance_slow

Unit – Farad

resistance_comp_bandwidth

Unit – Hz

resistance_comp_correction

Unit – %

resistance_comp_prediction

Unit – %

whole_cell_capacitance_comp

Unit – Farad

whole_cell_series_resistance_comp

Unit – Ohm

namespace = 'core'
neurodata_type = 'VoltageClampSeries'
class pynwb.icephys.VoltageClampStimulusSeries(name, source, data, unit, electrode, gain, stimulus_description='NA', resolution=0.0, conversion=1.0, timestamps=None, starting_time=None, rate=None, comments='no comments', description='no description', control=None, control_description=None, parent=None)

Bases: pynwb.icephys.PatchClampSeries

Aliases to standard PatchClampSeries. Its functionality is to better tag PatchClampSeries for machine (and human) readability of the file.

Parameters:
  • name (str) – The name of this TimeSeries dataset
  • source (str) – Name of TimeSeries or Modules that serve as the source for the data contained here. It can also be the name of a device, for stimulus or acquisition data
  • data (ndarray or list or tuple or Dataset or AbstractDataChunkIterator or DataIO or FORMDataset or TimeSeries) – The data this TimeSeries dataset stores. Can also store binary data e.g. image frames
  • unit (str) – The base unit of measurement (should be SI unit)
  • electrode (IntracellularElectrode) – IntracellularElectrode group that describes the electrode that was used to apply or record this data.
  • gain (float) – Units: Volt/Amp (v-clamp) or Volt/Volt (c-clamp)
  • stimulus_description (str) – the stimulus name/protocol
  • resolution (float) – The smallest meaningful difference (in specified unit) between values in data
  • conversion (float) – Scalar to multiply each element by to conver to volts
  • timestamps (ndarray or list or tuple or Dataset or AbstractDataChunkIterator or DataIO or FORMDataset or TimeSeries) – Timestamps for samples stored in data
  • starting_time (float) – The timestamp of the first sample
  • rate (float) – Sampling rate in Hz
  • comments (str) – Human-readable comments about this TimeSeries dataset
  • description (str) – Description of this TimeSeries dataset
  • control (Iterable) – Numerical labels that apply to each element in data
  • control_description (Iterable) – Description of each control value
  • parent (NWBContainer) – The parent NWBContainer for this NWBContainer
namespace = 'core'
neurodata_type = 'VoltageClampStimulusSeries'