emodel_generalisation.model.modifiers

Functions for morphology modifications in evaluator.

Functions

get_replace_axon_hoc(params)	Get replace_axon hoc string.
get_synth_modifiers(combo[, morph_modifiers])	Insert synth_axon to start of morph_modifiers if AIS info in combo, else use replace_axon_with_taper.
isolate_axon([sim, icell])	Remove everything except the axon.
isolate_soma([sim, icell])	Remove everything except the soma.
remove_axon([sim, icell])	Remove the axon.
remove_soma([sim, icell])	Remove the soma and connect dendrites together at the axon.
replace_axon_hillock([sim, icell, ...])	Replace axon with tappered axon initial segment.
replace_axon_justAIS([sim, icell, diam, ...])	Adapted from original replace_axon_with_taper, but no taper.
replace_axon_with_taper([sim, icell])	Replace axon with tappered axon initial segment
synth_axon([sim, icell, params, scale])	Replace axon with tappered axon initial segment.
synth_soma([sim, icell, params, scale])	Synthesize a simple soma with given scale and parameters.
taper_function(distance, strength, ...[, ...])	Function to model tappered AIS.

emodel_generalisation.model.modifiers.get_replace_axon_hoc(params)

Get replace_axon hoc string.

emodel_generalisation.model.modifiers.get_synth_modifiers(combo, morph_modifiers=None)

Insert synth_axon to start of morph_modifiers if AIS info in combo, else use replace_axon_with_taper.

emodel_generalisation.model.modifiers.isolate_axon(sim=None, icell=None)

Remove everything except the axon.

emodel_generalisation.model.modifiers.isolate_soma(sim=None, icell=None)

Remove everything except the soma.

emodel_generalisation.model.modifiers.remove_axon(sim=None, icell=None)

Remove the axon.

emodel_generalisation.model.modifiers.remove_soma(sim=None, icell=None)

Remove the soma and connect dendrites together at the axon.

For this to work, we leave the soma connected to the axon, and with diameter 1e-6. BluePyOp requires a soma for parameter scaling, and NEURON fails is the soma size is =0.

emodel_generalisation.model.modifiers.replace_axon_hillock(sim=None, icell=None, length_ais=46, delta=5, taper_scale=1, taper_strength=0, myelin_diameter=1, nseg_frequency=1)

Replace axon with tappered axon initial segment. :param sim and icell: neuron related arguments :param length: length of ais :param delta: distance of ais to soma (length of hillock) :param taper: taper rater of hillock + ais :param myelin_diameter: diameter of myelin, approximately end of ais (if taper is not too large) :param nseg_frequency: nseg freq as in bpopt of hillock + ais

emodel_generalisation.model.modifiers.replace_axon_justAIS(sim=None, icell=None, diam=1.0, L_target=45)

Adapted from original replace_axon_with_taper, but no taper.

Also named as version used for optimisation for backward compatibility: /gpfs/bbp.cscs.ch/project/proj130/singlecell/optimisation/morph_modifiers.py

emodel_generalisation.model.modifiers.replace_axon_with_taper(sim=None, icell=None)

Replace axon with tappered axon initial segment

emodel_generalisation.model.modifiers.synth_axon(sim=None, icell=None, params=None, scale=1.0)

Replace axon with tappered axon initial segment.

Parameters:

• icell (sim and) – neuron related arguments

• params (list) – fixed parameter for an emodel, should be length, strength, taper_scale and terminal_diameter

• scale (float) – scale parameter for each cell

emodel_generalisation.model.modifiers.synth_soma(sim=None, icell=None, params=None, scale=1.0)

Synthesize a simple soma with given scale and parameters.

emodel_generalisation.model.modifiers.taper_function(distance, strength, taper_scale, terminal_diameter, scale=1.0, dist_max=None)

Function to model tappered AIS.