pynwb.icephys module

class pynwb.icephys.CurrentClampSeries(name, source, data, unit, electrode, gain, bias_current, bridge_balance, capacitance_compensation, 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 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 (list or ndarray or TimeSeries or Iterable) – 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
  • 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 (list or ndarray or TimeSeries or Iterable) – 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
bridge_balance
capacitance_compensation
class pynwb.icephys.CurrentClampStimulusSeries(name, source, data, unit, electrode, gain, 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 (list or ndarray or TimeSeries or Iterable) – 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)
  • 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 (list or ndarray or TimeSeries or Iterable) – 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
class pynwb.icephys.IZeroClampSeries(name, source, data, unit, electrode, gain, 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 (list or ndarray or TimeSeries or Iterable) – 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
  • 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 (list or ndarray or TimeSeries or Iterable) – 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
class pynwb.icephys.IntracellularElectrode(name, source, slice, seal, description, location, resistance, filtering, initial_access_resistance, device)

Bases: pynwb.core.NWBContainer

Parameters:
  • name (str) – the name of this electrode
  • source (str) – the source of the data
  • slice (str) – Information about slice used for recording.
  • seal (str) – Information about seal used for recording.
  • description (str) – Recording description, description of electrode (e.g., whole-cell, sharp, etc)COMMENT: Free-form text (can be from Methods)
  • 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.
  • device (str) – Name(s) of devices in general/devices.
description
device
filtering
initial_access_resistance
location
resistance
seal
slice
class pynwb.icephys.PatchClampSeries(name, source, data, unit, electrode, gain, 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 (list or ndarray or TimeSeries or Iterable) – 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)
  • 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 (list or ndarray or TimeSeries or Iterable) – 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
gain
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, 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 (list or ndarray or TimeSeries or Iterable) – 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
  • 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 (list or ndarray or TimeSeries or Iterable) – 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
capacitance_slow
resistance_comp_bandwidth
resistance_comp_correction
resistance_comp_prediction
whole_cell_capacitance_comp
whole_cell_series_resistance_comp
class pynwb.icephys.VoltageClampStimulusSeries(name, source, data, unit, electrode, gain, 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 (list or ndarray or TimeSeries or Iterable) – 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)
  • 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 (list or ndarray or TimeSeries or Iterable) – 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