bluepyemodel.evaluation.modifiers

Functions for morphology modifications in evaluator.

Functions

get_synth_axon_hoc(params)
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.
replace_axon_legacy([sim, icell])	Replace axon used in legacy thalamus project
replace_axon_olfactory_bulb([sim, icell])	Replace axon used in olfactory bulb models.
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.
taper_function(distance, strength, ...[, scale])	Function to model tappered AIS.

isolate_axon(sim=None, icell=None)

Remove everything except the axon.

isolate_soma(sim=None, icell=None)

Remove everything except the soma.

remove_axon(sim=None, icell=None)

Remove the axon.

Removing the axonal branches breaks the code, so we set it to ZERO

remove_soma(sim=None, icell=None)

Remove the soma and connect dendrites together.

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.

replace_axon_legacy(sim=None, icell=None)

Replace axon used in legacy thalamus project

replace_axon_olfactory_bulb(sim=None, icell=None)

Replace axon used in olfactory bulb models.

replace_axon_with_taper(sim=None, icell=None)

Replace axon with tappered axon initial segment

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, strenght, taper_scale and terminal_diameter

• scale (floag) – scale parameter for each cell

taper_function(distance, strength, taper_scale, terminal_diameter, scale=1.0)

Function to model tappered AIS.