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'¶
- name (
-
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
orlist
ortuple
orDataset
orHDMFDataset
orAbstractDataChunkIterator
orDataIO
orTimeSeries
) – 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
orlist
ortuple
orDataset
orHDMFDataset
orAbstractDataChunkIterator
orDataIO
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.
-
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'¶
- name (
-
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
orlist
ortuple
orDataset
orHDMFDataset
orAbstractDataChunkIterator
orDataIO
orTimeSeries
) – 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
orlist
ortuple
orDataset
orHDMFDataset
orAbstractDataChunkIterator
orDataIO
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'¶
- name (
-
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
orlist
ortuple
orDataset
orHDMFDataset
orAbstractDataChunkIterator
orDataIO
orTimeSeries
) – 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
orlist
ortuple
orDataset
orHDMFDataset
orAbstractDataChunkIterator
orDataIO
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'¶
- name (
-
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
orlist
ortuple
orDataset
orHDMFDataset
orAbstractDataChunkIterator
orDataIO
orTimeSeries
) – 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
orlist
ortuple
orDataset
orHDMFDataset
orAbstractDataChunkIterator
orDataIO
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'¶
- name (
-
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
orlist
ortuple
orDataset
orHDMFDataset
orAbstractDataChunkIterator
orDataIO
orTimeSeries
) – 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
orlist
ortuple
orDataset
orHDMFDataset
orAbstractDataChunkIterator
orDataIO
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'¶
- name (
-
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
orlist
ortuple
orDataset
orHDMFDataset
orAbstractDataChunkIterator
orDataIO
orTimeSeries
) – 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
orlist
ortuple
orDataset
orHDMFDataset
orAbstractDataChunkIterator
orDataIO
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'¶
- name (
-
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
orlist
ortuple
orDataset
orHDMFDataset
orAbstractDataChunkIterator
orDataIO
orElementIdentifiers
) – the identifiers for this table - columns (
tuple
orlist
) – the columns in this table - colnames (
ndarray
orlist
ortuple
orDataset
orHDMFDataset
orAbstractDataChunkIterator
) – 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
-
namespace
= 'core'¶
-
neurodata_type
= 'SweepTable'¶
- name (