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:

name (str) – name of this SweepTable
description (str) – Description of this SweepTable
id (ndarray or list or tuple or Dataset or HDMFDataset or AbstractDataChunkIterator or DataIO 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 HDMFDataset or AbstractDataChunkIterator) – the ordered names of the columns in this table. columns must also be provided.

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.