bluepyefe.cell¶

Cell class

Classes

Contains the metadata related to a cell as well as the electrophysiological recordings once they are read

class Cell(name)[source]¶

Bases: object

Contains the metadata related to a cell as well as the electrophysiological recordings once they are read

Constructor

compute_relative_amp()[source]¶: Compute the relative current amplitude for all the recordings as a percentage of the rheobase.

extract_efeatures(protocol_name, efeatures, efeature_names=None, efel_settings=None)[source]¶

Extract the efeatures for the recordings matching the protocol name.

Parameters:

protocol_name (str) – name of the protocol for which to extract the efeatures.
efeatures (list of str) – name of the efeatures to extract from the recordings.
efeature_names (list of str) – Optional. Given name for the features. Can and should be used if the same feature is to be extracted several time on different sections of the same recording.

get_protocol_names()[source]¶: List of all the protocols available for the present cell.

get_recordings_by_protocol_name(protocol_name)[source]¶

List of all the recordings available for the present cell for a given protocol.

Parameters:: protocol_name (str) – name of the protocol for which to get the recordings.

get_recordings_id_by_protocol_name(protocol_name)[source]¶

List of the indexes of the recordings available for the present cell for a given protocol.

Parameters:: protocol_name (str) – name of the protocol for which to get the recordings.

plot_all_recordings(output_dir=None, show=False)[source]¶

Plot all the recordings of the cell.

Parameters:

output_dir (str) – path to the output directory to which to save the figures.
show (bool) – should the figures be displayed in addition to being saved.

plot_recordings(protocol_name, output_dir=None, show=False)[source]¶

Plot all the recordings matching a protocol name

Parameters:

protocol_name (str) – name of the protocol for which to plot the recordings.
output_dir (str) – path to the output directory to which to save the figures.
show (bool) – should the figures be displayed in addition to being saved.

read_recordings(protocol_data, protocol_name, recording_reader=None, efel_settings=None)[source]¶

For each member of a list of recordings metadata, instantiate a Recording object and populate it by reading the matching data file.

Parameters:

protocol_data (list of dict) – list of metadata for the recordings considered.
protocol_name (str) – name of the protocol for which to get the recordings.
recording_reader (callable or None) – method that will be used to read the files containing the recordings. If None, the function used will be chosen automatically based on the extension of the file.
efel_settings (dict) – eFEL settings in the form {setting_name: setting_value}.

reader(config_data, recording_reader=None)[source]¶

Define the reader method used to read the ephys data for the present recording and returns the data contained in the file.

Parameters:

config_data (dict) – metadata for the recording considered.
recording_reader (callable or None) – method that will be used to read the files containing the recordings. If None, the function used will be chosen automatically based on the extension of the file.