pynwb.file module¶
-
class
pynwb.file.
LabMetaData
(name)[source]¶ Bases:
pynwb.core.NWBContainer
Parameters: name ( str
) – name of metadata-
namespace
= 'core'¶
-
neurodata_type
= 'LabMetaData'¶
-
-
class
pynwb.file.
Subject
(age=None, description=None, genotype=None, sex=None, species=None, subject_id=None, weight=None, date_of_birth=None)[source]¶ Bases:
pynwb.core.NWBContainer
Parameters: - age (
str
) – the age of the subject - description (
str
) – a description of the subject - genotype (
str
) – the genotype of the subject - sex (
str
) – the sex of the subject - species (
str
) – the species of the subject - subject_id (
str
) – a unique identifier for the subject - weight (
str
) – the weight of the subject - date_of_birth (
datetime
) – datetime of date of birth. May be supplied instead of age.
-
age
¶ the age of the subject
-
description
¶ a description of the subject
-
genotype
¶ the genotype of the subject
-
sex
¶ the sex of the subject
-
species
¶ the species of the subject
-
subject_id
¶ a unique identifier for the subject
-
weight
¶ the weight of the subject
-
date_of_birth
¶ datetime of date of birth. May be supplied instead of age.
-
namespace
= 'core'¶
-
neurodata_type
= 'Subject'¶
- age (
-
class
pynwb.file.
NWBFile
(session_description, identifier, session_start_time, file_create_date=None, timestamps_reference_time=None, experimenter=None, experiment_description=None, session_id=None, institution=None, keywords=None, notes=None, pharmacology=None, protocol=None, related_publications=None, slices=None, source_script=None, source_script_file_name=None, data_collection=None, surgery=None, virus=None, stimulus_notes=None, lab=None, acquisition=None, analysis=None, stimulus=None, stimulus_template=None, epochs=None, epoch_tags=set(), trials=None, invalid_times=None, intervals=None, units=None, processing=None, lab_meta_data=None, electrodes=None, electrode_groups=None, ic_electrodes=None, sweep_table=None, imaging_planes=None, ogen_sites=None, devices=None, subject=None, scratch=None, icephys_electrodes=None)[source]¶ Bases:
pynwb.core.MultiContainerInterface
A representation of an NWB file.
Parameters: - session_description (
str
) – a description of the session where this data was generated - identifier (
str
) – a unique text identifier for the file - session_start_time (
datetime
) – the start date and time of the recording session - file_create_date (
ndarray
orlist
ortuple
orDataset
orHDMFDataset
orAbstractDataChunkIterator
ordatetime
) – the date and time the file was created and subsequent modifications made - timestamps_reference_time (
datetime
) – date and time corresponding to time zero of all timestamps; defaults to value of session_start_time - experimenter (
tuple
orlist
orstr
) – name of person who performed experiment - experiment_description (
str
) – general description of the experiment - session_id (
str
) – lab-specific ID for the session - institution (
str
) – institution(s) where experiment is performed - keywords (
ndarray
orlist
ortuple
orDataset
orHDMFDataset
orAbstractDataChunkIterator
) – Terms to search over - notes (
str
) – Notes about the experiment. - pharmacology (
str
) – Description of drugs used, including how and when they were administered. Anesthesia(s), painkiller(s), etc., plus dosage, concentration, etc. - protocol (
str
) – Experimental protocol, if applicable. E.g., include IACUC protocol - related_publications (
tuple
orlist
orstr
) – Publication information.PMID, DOI, URL, etc. If multiple, concatenate together and describe which is which. such as PMID, DOI, URL, etc - slices (
str
) – Description of slices, including information about preparation thickness, orientation, temperature and bath solution - source_script (
str
) – Script file used to create this NWB file. - source_script_file_name (
str
) – Name of the source_script file - data_collection (
str
) – Notes about data collection and analysis. - surgery (
str
) – Narrative description about surgery/surgeries, including date(s) and who performed surgery. - virus (
str
) – Information about virus(es) used in experiments, including virus ID, source, date made, injection location, volume, etc. - stimulus_notes (
str
) – Notes about stimuli, such as how and where presented. - lab (
str
) – lab where experiment was performed - acquisition (
list
ortuple
) – Raw TimeSeries objects belonging to this NWBFile - analysis (
list
ortuple
) – result of analysis - stimulus (
list
ortuple
) – Stimulus TimeSeries objects belonging to this NWBFile - stimulus_template (
list
ortuple
) – Stimulus template TimeSeries objects belonging to this NWBFile - epochs (
TimeIntervals
) – Epoch objects belonging to this NWBFile - epoch_tags (
tuple
orlist
orset
) – A sorted list of tags used across all epochs - trials (
TimeIntervals
) – A table containing trial data - invalid_times (
TimeIntervals
) – A table containing times to be omitted from analysis - intervals (
list
ortuple
) – any TimeIntervals tables storing time intervals - units (
Units
) – A table containing unit metadata - processing (
list
ortuple
) – ProcessingModule objects belonging to this NWBFile - lab_meta_data (
list
ortuple
) – an extension that contains lab-specific meta-data - electrodes (
DynamicTable
) – the ElectrodeTable that belongs to this NWBFile - electrode_groups (
Iterable
) – the ElectrodeGroups that belong to this NWBFile - ic_electrodes (
list
ortuple
) – DEPRECATED use icephys_electrodes parameter instead. IntracellularElectrodes that belong to this NWBFile - sweep_table (
SweepTable
) – the SweepTable that belong to this NWBFile - imaging_planes (
list
ortuple
) – ImagingPlanes that belong to this NWBFile - ogen_sites (
list
ortuple
) – OptogeneticStimulusSites that belong to this NWBFile - devices (
list
ortuple
) – Device objects belonging to this NWBFile - subject (
Subject
) – subject metadata - scratch (
list
ortuple
) – scratch data - icephys_electrodes (
list
ortuple
) – IntracellularElectrodes that belong to this NWBFile.
-
objects
¶
-
modules
¶
-
ec_electrode_groups
¶
-
ec_electrodes
¶
-
ic_electrodes
¶
-
add_ic_electrode
(*args, **kwargs)[source]¶ This method is deprecated and will be removed in future versions. Please use
add_icephys_electrode
instead
-
create_ic_electrode
(*args, **kwargs)[source]¶ This method is deprecated and will be removed in future versions. Please use
create_icephys_electrode
instead
-
get_ic_electrode
(*args, **kwargs)[source]¶ This method is deprecated and will be removed in future versions. Please use
get_icephys_electrode
instead
-
add_epoch_column
(name, description, data=[], table=False, index=False, vocab=False)[source]¶ - Add a column to the electrode table.
- See
add_column
for more details
Parameters: - name (
str
) – the name of this VectorData - description (
str
) – a description for this column - data (
ndarray
orlist
ortuple
orDataset
orHDMFDataset
orAbstractDataChunkIterator
orDataIO
) – a dataset where the first dimension is a concatenation of multiple vectors - table (
bool
or DynamicTable) – whether or not this is a table region or the table the region applies to - index (
bool
orVectorIndex
orndarray
orlist
ortuple
orDataset
orHDMFDataset
orAbstractDataChunkIterator
) – whether or not this column should be indexed - vocab (
bool
orndarray
orlist
ortuple
orDataset
orHDMFDataset
orAbstractDataChunkIterator
) – whether or not this column contains data from a controlled vocabulary or the controlled vocabulary
-
add_epoch_metadata_column
(*args, **kwargs)[source]¶ This method is deprecated and will be removed in future versions. Please use
add_epoch_column
instead
-
add_epoch
(start_time, stop_time, tags=None, timeseries=None)[source]¶ - Creates a new Epoch object. Epochs are used to track intervals
- in an experiment, such as exposure to a certain type of stimuli (an interval where orientation gratings are shown, or of sparse noise) or a different paradigm (a rat exploring an enclosure versus sleeping between explorations)
Parameters:
-
add_electrode_column
(name, description, data=[], table=False, index=False, vocab=False)[source]¶ - Add a column to the electrode table.
- See
add_column
for more details
Parameters: - name (
str
) – the name of this VectorData - description (
str
) – a description for this column - data (
ndarray
orlist
ortuple
orDataset
orHDMFDataset
orAbstractDataChunkIterator
orDataIO
) – a dataset where the first dimension is a concatenation of multiple vectors - table (
bool
or DynamicTable) – whether or not this is a table region or the table the region applies to - index (
bool
orVectorIndex
orndarray
orlist
ortuple
orDataset
orHDMFDataset
orAbstractDataChunkIterator
) – whether or not this column should be indexed - vocab (
bool
orndarray
orlist
ortuple
orDataset
orHDMFDataset
orAbstractDataChunkIterator
) – whether or not this column contains data from a controlled vocabulary or the controlled vocabulary
-
add_electrode
(x, y, z, imp, location, filtering, group, id=None, rel_x=None, rel_y=None, rel_z=None, reference=None)[source]¶ - Add an electrode to the electrodes table.
See
add_row
for more details.Required fields are x, y, z, imp, location, filtering, group and any columns that have been added (through calls to add_electrode_columns).
Parameters: - x (float) – the x coordinate of the position (+x is posterior)
- y (float) – the y coordinate of the position (+y is inferior)
- z (float) – the z coordinate of the position (+z is right)
- imp (float) – the impedance of the electrode, in ohms
- location (
str
) – the location of electrode within the subject e.g. brain region - filtering (
str
) – description of hardware filtering, including the filter name and frequency cutoffs - group (
ElectrodeGroup
) – the ElectrodeGroup object to add to this NWBFile - id (
int
) – a unique identifier for the electrode - rel_x (float) – the x coordinate within the electrode group
- rel_y (float) – the y coordinate within the electrode group
- rel_z (float) – the z coordinate within the electrode group
- reference (
str
) – Description of the reference used for this electrode.
-
add_unit_column
(name, description, data=[], table=False, index=False, vocab=False)[source]¶ - Add a column to the unit table.
- See
add_column
for more details
Parameters: - name (
str
) – the name of this VectorData - description (
str
) – a description for this column - data (
ndarray
orlist
ortuple
orDataset
orHDMFDataset
orAbstractDataChunkIterator
orDataIO
) – a dataset where the first dimension is a concatenation of multiple vectors - table (
bool
or DynamicTable) – whether or not this is a table region or the table the region applies to - index (
bool
orVectorIndex
orndarray
orlist
ortuple
orDataset
orHDMFDataset
orAbstractDataChunkIterator
) – whether or not this column should be indexed - vocab (
bool
orndarray
orlist
ortuple
orDataset
orHDMFDataset
orAbstractDataChunkIterator
) – whether or not this column contains data from a controlled vocabulary or the controlled vocabulary
-
add_unit
(spike_times=None, obs_intervals=None, electrodes=None, electrode_group=None, waveform_mean=None, waveform_sd=None, id=None)[source]¶ - Add a unit to the unit table.
- See
add_row
for more details.
Parameters: - spike_times (
ndarray
orlist
ortuple
orDataset
orHDMFDataset
orAbstractDataChunkIterator
) – the spike times for each unit - obs_intervals (
ndarray
orlist
ortuple
orDataset
orHDMFDataset
orAbstractDataChunkIterator
) – the observation intervals (valid times) for each unit. All spike_times for a given unit should fall within these intervals. [[start1, end1], [start2, end2], …] - electrodes (
ndarray
orlist
ortuple
orDataset
orHDMFDataset
orAbstractDataChunkIterator
) – the electrodes that each unit came from - electrode_group (ElectrodeGroup) – the electrode group that each unit came from
- waveform_mean (
ndarray
orlist
ortuple
orDataset
orHDMFDataset
orAbstractDataChunkIterator
) – the spike waveform mean for each unit. Shape is (time,) or (time, electrodes) - waveform_sd (
ndarray
orlist
ortuple
orDataset
orHDMFDataset
orAbstractDataChunkIterator
) – the spike waveform standard deviation for each unit. Shape is (time,) or (time, electrodes) - id (
int
) – the id for each unit
-
add_trial_column
(name, description, data=[], table=False, index=False, vocab=False)[source]¶ - Add a column to the trial table.
- See
add_column
for more details
Parameters: - name (
str
) – the name of this VectorData - description (
str
) – a description for this column - data (
ndarray
orlist
ortuple
orDataset
orHDMFDataset
orAbstractDataChunkIterator
orDataIO
) – a dataset where the first dimension is a concatenation of multiple vectors - table (
bool
or DynamicTable) – whether or not this is a table region or the table the region applies to - index (
bool
orVectorIndex
orndarray
orlist
ortuple
orDataset
orHDMFDataset
orAbstractDataChunkIterator
) – whether or not this column should be indexed - vocab (
bool
orndarray
orlist
ortuple
orDataset
orHDMFDataset
orAbstractDataChunkIterator
) – whether or not this column contains data from a controlled vocabulary or the controlled vocabulary
-
add_trial
(start_time, stop_time, tags=None, timeseries=None)[source]¶ - Add a trial to the trial table.
See
add_interval
for more details.Required fields are start_time, stop_time, and any columns that have been added (through calls to add_trial_columns).
Parameters:
-
add_invalid_times_column
(name, description, data=[], table=False, index=False, vocab=False)[source]¶ - Add a column to the trial table.
- See
add_column
for more details
Parameters: - name (
str
) – the name of this VectorData - description (
str
) – a description for this column - data (
ndarray
orlist
ortuple
orDataset
orHDMFDataset
orAbstractDataChunkIterator
orDataIO
) – a dataset where the first dimension is a concatenation of multiple vectors - table (
bool
or DynamicTable) – whether or not this is a table region or the table the region applies to - index (
bool
orVectorIndex
orndarray
orlist
ortuple
orDataset
orHDMFDataset
orAbstractDataChunkIterator
) – whether or not this column should be indexed - vocab (
bool
orndarray
orlist
ortuple
orDataset
orHDMFDataset
orAbstractDataChunkIterator
) – whether or not this column contains data from a controlled vocabulary or the controlled vocabulary
-
add_invalid_time_interval
(**kwargs)[source]¶ Add a trial to the trial table. See
add_row
for more details.Required fields are start_time, stop_time, and any columns that have been added (through calls to add_invalid_times_columns).
-
set_electrode_table
(electrode_table)[source]¶ Set the electrode table of this NWBFile to an existing ElectrodeTable
Parameters: electrode_table ( DynamicTable
) – the ElectrodeTable for this file
-
add_acquisition
(nwbdata)[source]¶ Parameters: nwbdata ( NWBDataInterface
orDynamicTable
) – None
-
add_stimulus
(timeseries)[source]¶ Parameters: timeseries ( TimeSeries
) – None
-
add_stimulus_template
(timeseries)[source]¶ Parameters: timeseries ( TimeSeries
) – None
-
add_scratch
(data, name=None, notes=None, table_description='')[source]¶ Add data to the scratch space
Parameters: - data (
ndarray
orlist
ortuple
orDataFrame
orDynamicTable
orNWBContainer
orScratchData
) – None - name (
str
) – None - notes (
str
) – None - table_description (
str
) – None
- data (
-
acquisition
¶ a dictionary containing the NWBDataInterface or DynamicTable in this NWBFile
-
add_analysis
(analysis)¶ Add a NWBContainer to this NWBFile
Parameters: analysis ( list
ortuple
ordict
orNWBContainer
orDynamicTable
) – the NWBContainer or DynamicTable to add
-
add_device
(devices)¶ Add a Device to this NWBFile
Parameters: devices ( list
ortuple
ordict
orDevice
) – the Device to add
-
add_electrode_group
(electrode_groups)¶ Add an ElectrodeGroup to this NWBFile
Parameters: electrode_groups ( list
ortuple
ordict
orElectrodeGroup
) – the ElectrodeGroup to add
-
add_icephys_electrode
(icephys_electrodes)¶ Add an IntracellularElectrode to this NWBFile
Parameters: icephys_electrodes ( list
ortuple
ordict
orIntracellularElectrode
) – the IntracellularElectrode to add
-
add_imaging_plane
(imaging_planes)¶ Add an ImagingPlane to this NWBFile
Parameters: imaging_planes ( list
ortuple
ordict
orImagingPlane
) – the ImagingPlane to add
-
add_lab_meta_data
(lab_meta_data)¶ Add a LabMetaData to this NWBFile
Parameters: lab_meta_data ( list
ortuple
ordict
orLabMetaData
) – the LabMetaData to add
-
add_ogen_site
(ogen_sites)¶ Add an OptogeneticStimulusSite to this NWBFile
Parameters: ogen_sites ( list
ortuple
ordict
orOptogeneticStimulusSite
) – the OptogeneticStimulusSite to add
-
add_processing_module
(processing)¶ Add a ProcessingModule to this NWBFile
Parameters: processing ( list
ortuple
ordict
orProcessingModule
) – the ProcessingModule to add
-
add_time_intervals
(intervals)¶ Add a TimeIntervals to this NWBFile
Parameters: intervals ( list
ortuple
ordict
orTimeIntervals
) – the TimeIntervals to add
-
analysis
¶ a dictionary containing the NWBContainer or DynamicTable in this NWBFile
-
create_device
(name, description=None, manufacturer=None)¶ Create a Device and add it to this NWBFile
Parameters: Returns: the Device object that was created
Return type:
-
create_electrode_group
(name, description, location, device, position=None)¶ Create an ElectrodeGroup and add it to this NWBFile
Parameters: - name (
str
) – the name of this electrode - description (
str
) – description of this electrode group - location (
str
) – description of location of this electrode group - device (
Device
) – the device that was used to record from this electrode group - position (
ndarray
orlist
ortuple
orDataset
orHDMFDataset
orAbstractDataChunkIterator
) – stereotaxic position of this electrode group (x, y, z)
Returns: the ElectrodeGroup object that was created
Return type: - name (
-
create_icephys_electrode
(name, device, description, slice=None, seal=None, location=None, resistance=None, filtering=None, initial_access_resistance=None)¶ Create an IntracellularElectrode and add it to this NWBFile
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.
Returns: the IntracellularElectrode object that was created
Return type: - name (
-
create_imaging_plane
(name, optical_channel, description, device, excitation_lambda, indicator, location, imaging_rate=None, manifold=None, conversion=1.0, unit='meters', reference_frame=None, origin_coords=None, origin_coords_unit='meters', grid_spacing=None, grid_spacing_unit='meters')¶ Create an ImagingPlane and add it to this NWBFile
Parameters: - name (
str
) – the name of this container - optical_channel (
list
orOpticalChannel
) – One of possibly many groups storing channel-specific data. - description (
str
) – Description of this ImagingPlane. - device (
Device
) – the device that was used to record - excitation_lambda (float) – Excitation wavelength in nm.
- indicator (
str
) – Calcium indicator - location (
str
) – Location of image plane. - imaging_rate (float) – Rate images are acquired, in Hz. If the corresponding TimeSeries is present, the rate should be stored there instead.
- manifold (
ndarray
orlist
ortuple
orDataset
orHDMFDataset
orAbstractDataChunkIterator
) – DEPRECATED: Physical position of each pixel. size=(“height”, “width”, “xyz”). Deprecated in favor of origin_coords and grid_spacing. - conversion (float) – DEPRECATED: Multiplier to get from stored values to specified unit (e.g., 1e-3 for millimeters) Deprecated in favor of origin_coords and grid_spacing.
- unit (
str
) – DEPRECATED: Base unit that coordinates are stored in (e.g., Meters). Deprecated in favor of origin_coords_unit and grid_spacing_unit. - reference_frame (
str
) – Describes position and reference frame of manifold based on position of first element in manifold. - origin_coords (
ndarray
orlist
ortuple
orDataset
orHDMFDataset
orAbstractDataChunkIterator
) – Physical location of the first element of the imaging plane (0, 0) for 2-D data or (0, 0, 0) for 3-D data. See also reference_frame for what the physical location is relative to (e.g., bregma). - origin_coords_unit (
str
) – Measurement units for origin_coords. The default value is ‘meters’. - grid_spacing (
ndarray
orlist
ortuple
orDataset
orHDMFDataset
orAbstractDataChunkIterator
) – Space between pixels in (x, y) or voxels in (x, y, z) directions, in the specified unit. Assumes imaging plane is a regular grid. See also reference_frame to interpret the grid. - grid_spacing_unit (
str
) – Measurement units for grid_spacing. The default value is ‘meters’.
Returns: the ImagingPlane object that was created
Return type: - name (
-
create_lab_meta_data
(name)¶ Create a LabMetaData and add it to this NWBFile
Parameters: name ( str
) – name of metadataReturns: the LabMetaData object that was created Return type: LabMetaData
-
create_ogen_site
(name, device, description, excitation_lambda, location)¶ Create an OptogeneticStimulusSite and add it to this NWBFile
Parameters: Returns: the OptogeneticStimulusSite object that was created
Return type:
-
create_processing_module
(name, description, data_interfaces=None)¶ Create a ProcessingModule and add it to this NWBFile
Parameters: Returns: the ProcessingModule object that was created
Return type:
-
create_time_intervals
(name, description='experimental intervals', id=None, columns=None, colnames=None)¶ Create a TimeIntervals and add it to this NWBFile
Parameters: - name (
str
) – name of this TimeIntervals - description (
str
) – Description of this TimeIntervals - 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.
Returns: the TimeIntervals object that was created
Return type: - name (
-
data_collection
¶ Notes about data collection and analysis.
-
devices
¶ a dictionary containing the Device in this NWBFile
-
electrode_groups
¶ a dictionary containing the ElectrodeGroup in this NWBFile
-
electrodes
¶ the ElectrodeTable that belongs to this NWBFile
A sorted list of tags used across all epochs
-
epochs
¶ Epoch objects belonging to this NWBFile
-
experiment_description
¶ general description of the experiment
-
experimenter
¶ name of person who performed experiment
-
file_create_date
¶ the date and time the file was created and subsequent modifications made
-
get_acquisition
(name=None)¶ Get a NWBDataInterface from this NWBFile
Parameters: name ( str
) – the name of the NWBDataInterface or DynamicTableReturns: the NWBDataInterface or DynamicTable with the given name Return type: (<class ‘pynwb.core.NWBDataInterface’>, <class ‘hdmf.common.table.DynamicTable’>)
-
get_analysis
(name=None)¶ Get a NWBContainer from this NWBFile
Parameters: name ( str
) – the name of the NWBContainer or DynamicTableReturns: the NWBContainer or DynamicTable with the given name Return type: (<class ‘pynwb.core.NWBContainer’>, <class ‘hdmf.common.table.DynamicTable’>)
-
get_device
(name=None)¶ Get a Device from this NWBFile
Parameters: name ( str
) – the name of the DeviceReturns: the Device with the given name Return type: Device
-
get_electrode_group
(name=None)¶ Get an ElectrodeGroup from this NWBFile
Parameters: name ( str
) – the name of the ElectrodeGroupReturns: the ElectrodeGroup with the given name Return type: ElectrodeGroup
-
get_icephys_electrode
(name=None)¶ Get an IntracellularElectrode from this NWBFile
Parameters: name ( str
) – the name of the IntracellularElectrodeReturns: the IntracellularElectrode with the given name Return type: IntracellularElectrode
-
get_imaging_plane
(name=None)¶ Get an ImagingPlane from this NWBFile
Parameters: name ( str
) – the name of the ImagingPlaneReturns: the ImagingPlane with the given name Return type: ImagingPlane
-
get_lab_meta_data
(name=None)¶ Get a LabMetaData from this NWBFile
Parameters: name ( str
) – the name of the LabMetaDataReturns: the LabMetaData with the given name Return type: LabMetaData
-
get_ogen_site
(name=None)¶ Get an OptogeneticStimulusSite from this NWBFile
Parameters: name ( str
) – the name of the OptogeneticStimulusSiteReturns: the OptogeneticStimulusSite with the given name Return type: OptogeneticStimulusSite
-
get_processing_module
(name=None)¶ Get a ProcessingModule from this NWBFile
Parameters: name ( str
) – the name of the ProcessingModuleReturns: the ProcessingModule with the given name Return type: ProcessingModule
-
get_stimulus
(name=None)¶ Get a TimeSeries from this NWBFile
Parameters: name ( str
) – the name of the TimeSeriesReturns: the TimeSeries with the given name Return type: TimeSeries
-
get_stimulus_template
(name=None)¶ Get a TimeSeries from this NWBFile
Parameters: name ( str
) – the name of the TimeSeriesReturns: the TimeSeries with the given name Return type: TimeSeries
-
get_time_intervals
(name=None)¶ Get a TimeIntervals from this NWBFile
Parameters: name ( str
) – the name of the TimeIntervalsReturns: the TimeIntervals with the given name Return type: TimeIntervals
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icephys_electrodes
¶ a dictionary containing the IntracellularElectrode in this NWBFile
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identifier
¶ a unique text identifier for the file
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imaging_planes
¶ a dictionary containing the ImagingPlane in this NWBFile
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institution
¶ institution(s) where experiment is performed
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intervals
¶ a dictionary containing the TimeIntervals in this NWBFile
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invalid_times
¶ A table containing times to be omitted from analysis
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keywords
¶ Terms to search over
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lab
¶ lab where experiment was performed
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lab_meta_data
¶ a dictionary containing the LabMetaData in this NWBFile
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namespace
= 'core'¶
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neurodata_type
= 'NWBFile'¶
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notes
¶ Notes about the experiment.
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ogen_sites
¶ a dictionary containing the OptogeneticStimulusSite in this NWBFile
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pharmacology
¶ Description of drugs used, including how and when they were administered. Anesthesia(s), painkiller(s), etc., plus dosage, concentration, etc.
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processing
¶ a dictionary containing the ProcessingModule in this NWBFile
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protocol
¶ Experimental protocol, if applicable. E.g., include IACUC protocol
Publication information.PMID, DOI, URL, etc. If multiple, concatenate together and describe which is which. such as PMID, DOI, URL, etc
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scratch
¶ a dictionary containing the DynamicTable, NWBContainer, or ScratchData in this NWBFile
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session_description
¶ a description of the session where this data was generated
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session_id
¶ lab-specific ID for the session
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session_start_time
¶ the start date and time of the recording session
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slices
¶ Description of slices, including information about preparation thickness, orientation, temperature and bath solution
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source_script
¶ Script file used to create this NWB file.
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source_script_file_name
¶ Name of the source_script file
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stimulus
¶ a dictionary containing the TimeSeries in this NWBFile
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stimulus_notes
¶ Notes about stimuli, such as how and where presented.
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stimulus_template
¶ a dictionary containing the TimeSeries in this NWBFile
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subject
¶ subject metadata
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surgery
¶ Narrative description about surgery/surgeries, including date(s) and who performed surgery.
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sweep_table
¶ the SweepTable that belong to this NWBFile
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timestamps_reference_time
¶ date and time corresponding to time zero of all timestamps; defaults to value of session_start_time
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trials
¶ A table containing trial data
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units
¶ A table containing unit metadata
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virus
¶ Information about virus(es) used in experiments, including virus ID, source, date made, injection location, volume, etc.
- session_description (