bluepyopt.ephys.morphologies

Morphology classes

class bluepyopt.ephys.morphologies.Morphology(name='', comment='')

Bases: bluepyopt.ephys.base.BaseEPhys

Morphology class

class bluepyopt.ephys.morphologies.NrnFileMorphology(morphology_path, do_replace_axon=False, do_set_nseg=True, comment='', replace_axon_hoc=None, nseg_frequency=40, morph_modifiers=None, morph_modifiers_hoc=None)

Bases: bluepyopt.ephys.morphologies.Morphology, bluepyopt.ephys.serializer.DictMixin

Morphology loaded from a file

Constructor

Parameters:

• morphology_path (str) – location of the file describing the morphology
• do_replace_axon (bool) – Does the axon need to be replaced by an AIS stub with default function ?
• replace_axon_hoc (str) – String replacement for the ‘replace_axon’ command in hoc Must include ‘proc replace_axon(){ … } If None,the default replace_axon is used
• nseg_frequency (float) – frequency of nseg
• do_set_nseg (bool) – if True, it will use nseg_frequency
• morph_modifiers (list) – list of functions to modify the icell with (sim, icell) as arguments
• morph_modifiers_hoc (list) – list of hoc strings corresponding to morph_modifiers

destroy(sim=None)

Destroy morphology instantiation

instantiate(sim=None, icell=None)

Load morphology

static replace_axon(sim=None, icell=None)

Replace axon

set_nseg(icell)

Set the nseg of every section