bluepyefe package

Submodules

bluepyefe.extra module

Extra e-features functions

bluepyefe.extra.main()[source]

Main

bluepyefe.extra.spikerate_drop(peaktimes, nstart=1, nend=2)[source]

Spike rate drop feature

bluepyefe.extra.spikerate_slope(peaktimes)[source]

Spike rate slope feature

bluepyefe.extra.spikerate_tau_fit(peaktimes, nstart=1, nend=2)[source]

Spike rate tau fit feature

bluepyefe.extra.spikerate_tau_jj(peaktimes)[source]

Spike rate tau feature

bluepyefe.extra.spikerate_tau_log(peaktimes)[source]

Spike rate tau log feature

bluepyefe.extra.spikerate_tau_slope(peaktimes)[source]

Spike rate tau slope feature

bluepyefe.extractor module

Extractor class

class bluepyefe.extractor.Extractor(mainname='PC', config={})[source]

Bases: object

Extractor class

Constructor

Args:
mainname (str): name of the cell type. Used to create the output directory config (dict): metadata containing the protocols and cells for which to extract the efeatures.
analyse_threshold()[source]

Get the spiking threshold and holding current for all cells. Save them in hypamp_threshold.json

boxcoxcell(a, nanopt='nanmean_cell', lm_vec=array([-3., -2.85, -2.7, -2.55, -2.4, -2.25, -2.1, -1.95, -1.8, -1.65, -1.5, -1.35, -1.2, -1.05, -0.9, -0.75, -0.6, -0.45, -0.3, -0.15, 0., 0.15, 0.3, 0.45, 0.6, 0.75, 0.9, 1.05, 1.2, 1.35, 1.5, 1.65, 1.8, 1.95, 2.1, 2.25, 2.4, 2.55, 2.7, 2.85, 3. ]))[source]
create_dataset()[source]

Read the trace files and add them to the dictionnary self.dataset

create_feature_config(directory, dataset, version=None)[source]

Save the efeatures and protocols for each protocol/target combo in json file

create_metadataset()[source]

Fill a dictionary with metadata for every file to be processed If no metadata file is present, default values are inserted

extract_features(threshold=-20)[source]

Extract features from the traces

feature_config_all(version=None)[source]
feature_config_cells(version=None)[source]
get_threshold(amp, numspikes)[source]

Get the spiking threshold of a cell by taking the smallest current amplitude for which it fires

mean_features()[source]

Compute the mean for each features for each target

newmean(a)[source]
newmeancell(a)[source]
newstd(a)[source]
newstdcell(a)[source]
plt_features()[source]

Plot the features

plt_features_dist()[source]

Plot the distribution of features

plt_traces()[source]

Plot traces

process_file(**kwargs)[source]

Get data from a trace file

bluepyefe.plottools module

Plotting tools

bluepyefe.plottools.adjust_spines(ax, spines, color='k', d_out=10, d_down=[])[source]
bluepyefe.plottools.light_palette(color, n_colors=6, reverse=False, lumlight=0.8, light=None)[source]
bluepyefe.plottools.tiled_figure(figname='', frames=1, columns=2, figs={}, axs=None, orientation='page', width_ratios=None, height_ratios=None, top=0.97, bottom=0.05, left=0.07, right=0.97, hspace=0.6, wspace=0.2, dirname='')[source]

Module contents

Init script