pynwb.icephys module

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

Bases: pynwb.core.NWBContainer

Parameters:
  • name (str) – the name of this electrode
  • device (Device) – the device that was used to record from this electrode
  • 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

Free-form text (can be from Methods)

Type:Recording description, description of electrode (e.g., whole-cell, sharp, etc) COMMENT
location

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

resistance

Ohm.

Type:Electrode resistance COMMENT
Type:unit
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, data, unit, electrode, gain, stimulus_description='NA', resolution=-1.0, conversion=1.0, timestamps=None, starting_time=None, rate=None, comments='no comments', description='no description', control=None, control_description=None, sweep_number=None)[source]

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
  • data (ndarray or list or tuple or Dataset or HDMFDataset or AbstractDataChunkIterator or DataIO or TimeSeries) – The data values. The first dimension must be time.
  • 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 (str or float) – The smallest meaningful difference (in specified unit) between values in data
  • conversion (str or float) – Scalar to multiply each element in data to convert it to the specified unit
  • timestamps (ndarray or list or tuple or Dataset or HDMFDataset or AbstractDataChunkIterator or DataIO 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
  • sweep_number (int or uint32 or uint64) – Sweep number, allows for grouping different PatchClampSeries together via the sweep_table
electrode

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

gain

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

Type:Units
stimulus_description

the stimulus name/protocol

sweep_number

Sweep number, allows for grouping different PatchClampSeries together via the sweep_table

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

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
  • data (ndarray or list or tuple or Dataset or HDMFDataset or AbstractDataChunkIterator or DataIO or TimeSeries) – The data values. The first dimension must be time.
  • electrode (IntracellularElectrode) – IntracellularElectrode group that describes the electrode that was used to apply or record this data.
  • gain (float) – Units: Volt/Volt
  • stimulus_description (str) – the stimulus name/protocol
  • bias_current (float) – Unit: Amp
  • bridge_balance (float) – Unit: Ohm
  • capacitance_compensation (float) – Unit: Farad
  • resolution (str or float) – The smallest meaningful difference (in specified unit) between values in data
  • conversion (str or float) – Scalar to multiply each element in data to convert it to the specified unit
  • timestamps (ndarray or list or tuple or Dataset or HDMFDataset or AbstractDataChunkIterator or DataIO 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
  • sweep_number (int or uint32 or uint64) – Sweep number, allows for grouping different PatchClampSeries together via the sweep_table
  • unit (str) – The base unit of measurement (must be ‘volts’)
bias_current

Amp

Type:Unit
bridge_balance

Ohm

Type:Unit
capacitance_compensation

Farad

Type:Unit
namespace = 'core'
neurodata_type = 'CurrentClampSeries'
class pynwb.icephys.IZeroClampSeries(name, data, electrode, gain, stimulus_description='NA', resolution=-1.0, conversion=1.0, timestamps=None, starting_time=None, rate=None, comments='no comments', description='no description', control=None, control_description=None, sweep_number=None, unit='volts')[source]

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
  • data (ndarray or list or tuple or Dataset or HDMFDataset or AbstractDataChunkIterator or DataIO or TimeSeries) – The data values. The first dimension must be time.
  • electrode (IntracellularElectrode) – IntracellularElectrode group that describes the electrode that was used to apply or record this data.
  • gain (float) – Units: Volt/Volt
  • stimulus_description (str) – the stimulus name/protocol
  • resolution (str or float) – The smallest meaningful difference (in specified unit) between values in data
  • conversion (str or float) – Scalar to multiply each element in data to convert it to the specified unit
  • timestamps (ndarray or list or tuple or Dataset or HDMFDataset or AbstractDataChunkIterator or DataIO 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
  • sweep_number (int or uint32 or uint64) – Sweep number, allows for grouping different PatchClampSeries together via the sweep_table
  • unit (str) – The base unit of measurement (must be ‘volts’)
namespace = 'core'
neurodata_type = 'IZeroClampSeries'
class pynwb.icephys.CurrentClampStimulusSeries(name, data, electrode, gain, stimulus_description='NA', resolution=-1.0, conversion=1.0, timestamps=None, starting_time=None, rate=None, comments='no comments', description='no description', control=None, control_description=None, sweep_number=None, unit='amperes')[source]

Bases: pynwb.icephys.PatchClampSeries

Alias 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
  • data (ndarray or list or tuple or Dataset or HDMFDataset or AbstractDataChunkIterator or DataIO or TimeSeries) – The data values. The first dimension must be time.
  • 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 (str or float) – The smallest meaningful difference (in specified unit) between values in data
  • conversion (str or float) – Scalar to multiply each element in data to convert it to the specified unit
  • timestamps (ndarray or list or tuple or Dataset or HDMFDataset or AbstractDataChunkIterator or DataIO 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
  • sweep_number (int or uint32 or uint64) – Sweep number, allows for grouping different PatchClampSeries together via the sweep_table
  • unit (str) – The base unit of measurement (must be ‘amperes’)
namespace = 'core'
neurodata_type = 'CurrentClampStimulusSeries'
class pynwb.icephys.VoltageClampSeries(name, data, electrode, gain, stimulus_description='NA', capacitance_fast=None, capacitance_slow=None, resistance_comp_bandwidth=None, resistance_comp_correction=None, resistance_comp_prediction=None, whole_cell_capacitance_comp=None, whole_cell_series_resistance_comp=None, resolution=-1.0, conversion=1.0, timestamps=None, starting_time=None, rate=None, comments='no comments', description='no description', control=None, control_description=None, sweep_number=None, unit='amperes')[source]

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
  • data (ndarray or list or tuple or Dataset or HDMFDataset or AbstractDataChunkIterator or DataIO or TimeSeries) – The data values. The first dimension must be time.
  • electrode (IntracellularElectrode) – IntracellularElectrode group that describes the electrode that was used to apply or record this data.
  • gain (float) – Units: Volt/Amp
  • stimulus_description (str) – the stimulus name/protocol
  • capacitance_fast (float) – Unit: Farad
  • capacitance_slow (float) – Unit: Farad
  • resistance_comp_bandwidth (float) – Unit: Hz
  • resistance_comp_correction (float) – Unit: percent
  • resistance_comp_prediction (float) – Unit: percent
  • whole_cell_capacitance_comp (float) – Unit: Farad
  • whole_cell_series_resistance_comp (float) – Unit: Ohm
  • resolution (str or float) – The smallest meaningful difference (in specified unit) between values in data
  • conversion (str or float) – Scalar to multiply each element in data to convert it to the specified unit
  • timestamps (ndarray or list or tuple or Dataset or HDMFDataset or AbstractDataChunkIterator or DataIO 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
  • sweep_number (int or uint32 or uint64) – Sweep number, allows for grouping different PatchClampSeries together via the sweep_table
  • unit (str) – The base unit of measurement (must be ‘amperes’)
capacitance_fast

Farad

Type:Unit
capacitance_slow

Farad

Type:Unit
resistance_comp_bandwidth

Hz

Type:Unit
resistance_comp_correction

percent

Type:Unit
resistance_comp_prediction

percent

Type:Unit
whole_cell_capacitance_comp

Farad

Type:Unit
whole_cell_series_resistance_comp

Ohm

Type:Unit
namespace = 'core'
neurodata_type = 'VoltageClampSeries'
class pynwb.icephys.VoltageClampStimulusSeries(name, data, electrode, gain, stimulus_description='NA', resolution=-1.0, conversion=1.0, timestamps=None, starting_time=None, rate=None, comments='no comments', description='no description', control=None, control_description=None, sweep_number=None, unit='volts')[source]

Bases: pynwb.icephys.PatchClampSeries

Alias 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
  • data (ndarray or list or tuple or Dataset or HDMFDataset or AbstractDataChunkIterator or DataIO or TimeSeries) – The data values. The first dimension must be time.
  • 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 (str or float) – The smallest meaningful difference (in specified unit) between values in data
  • conversion (str or float) – Scalar to multiply each element in data to convert it to the specified unit
  • timestamps (ndarray or list or tuple or Dataset or HDMFDataset or AbstractDataChunkIterator or DataIO 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
  • sweep_number (int or uint32 or uint64) – Sweep number, allows for grouping different PatchClampSeries together via the sweep_table
  • unit (str) – The base unit of measurement (must be ‘volts’)
namespace = 'core'
neurodata_type = 'VoltageClampStimulusSeries'
class pynwb.icephys.SweepTable(name='sweep_table', description='A sweep table groups different PatchClampSeries together.', id=None, columns=None, colnames=None)[source]

Bases: hdmf.common.table.DynamicTable

A SweepTable allows to group PatchClampSeries together which stem from the same sweep. A sweep is a group of PatchClampSeries which have the same starting point in time.

Parameters:
add_entry(pcs)[source]

Add the passed PatchClampSeries to the sweep table.

Parameters:pcs (PatchClampSeries) – PatchClampSeries to add to the table must have a valid sweep_number
get_series(sweep_number)[source]

Return a list of PatchClampSeries for the given sweep number.

namespace = 'core'
neurodata_type = 'SweepTable'
pynwb.icephys.ensure_unit(self, name, current_unit, unit, nwb_version)[source]

A helper to ensure correct unit used.

Issues a warning with details if current_unit is to be ignored, and unit to be used instead.