pynwb.icephys module

class pynwb.icephys.IntracellularElectrode(name, device, 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
  • 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, 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, sweep_number=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
  • data (ndarray or list or tuple or Dataset or AbstractDataChunkIterator or FORMDataset or DataIO 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 FORMDataset 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 uint64) – Sweep number, allows for grouping different PatchClampSeries together via the sweep_table
  • 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

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, 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, sweep_number=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
  • data (ndarray or list or tuple or Dataset or AbstractDataChunkIterator or FORMDataset or DataIO 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 FORMDataset or DataIO 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
  • sweep_number (int or uint64) – Sweep number, allows for grouping different PatchClampSeries together via the sweep_table
  • 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, 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, sweep_number=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
  • data (ndarray or list or tuple or Dataset or AbstractDataChunkIterator or FORMDataset or DataIO 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 FORMDataset 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 uint64) – Sweep number, allows for grouping different PatchClampSeries together via the sweep_table
  • parent (NWBContainer) – The parent NWBContainer for this NWBContainer
namespace = 'core'
neurodata_type = 'IZeroClampSeries'
class pynwb.icephys.CurrentClampStimulusSeries(name, 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, sweep_number=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
  • data (ndarray or list or tuple or Dataset or AbstractDataChunkIterator or FORMDataset or DataIO 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 FORMDataset 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 uint64) – Sweep number, allows for grouping different PatchClampSeries together via the sweep_table
  • parent (NWBContainer) – The parent NWBContainer for this NWBContainer
namespace = 'core'
neurodata_type = 'CurrentClampStimulusSeries'
class pynwb.icephys.VoltageClampSeries(name, 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, sweep_number=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
  • data (ndarray or list or tuple or Dataset or AbstractDataChunkIterator or FORMDataset or DataIO 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 FORMDataset 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 uint64) – Sweep number, allows for grouping different PatchClampSeries together via the sweep_table
  • 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, 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, sweep_number=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
  • data (ndarray or list or tuple or Dataset or AbstractDataChunkIterator or FORMDataset or DataIO 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 FORMDataset 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 uint64) – Sweep number, allows for grouping different PatchClampSeries together via the sweep_table
  • parent (NWBContainer) – The parent NWBContainer for this NWBContainer
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)

Bases: pynwb.core.DynamicTable

A SweepTable allows to group PatchClampSeries together which stem from the same sweep.

Parameters:
  • name (str) – name of this SweepTable
  • description (str) – Description of this SweepTable
  • id (ndarray or list or tuple or Dataset or AbstractDataChunkIterator or FORMDataset or ElementIdentifiers) – the identifiers for this table
  • columns (tuple or list) – the columns in this table
  • colnames (ndarray or list or tuple or Dataset or AbstractDataChunkIterator or FORMDataset) – the names of the columns in this table
add_entry(pcs)

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)

Return a list of PatchClampSeries for the given sweep number.

namespace = 'core'
neurodata_type = 'SweepTable'