bluecellulab.cell.section_tools

NEURON section helpers for BlueCelluLab.

Functions

currents_vars(section)	Return recordable currents (with units) at a given section.
mechs_vars(section[, include_point_mechs])	Return mechanism-scoped variables at a given section.
section_to_variable_recording_str(section, ...)	Build an evaluable NEURON pointer string for add_recording.

bluecellulab.cell.section_tools.currents_vars(section)[source]

Return recordable currents (with units) at a given section.

• Ionic currents from the ions block (e.g. ina, ik, ica), in mA/cm².

• Mechanism currents for variables i or ihcn, reported as <var>_<mech> (e.g. i_pas, ihcn_Ih), in mA/cm².

Parameters:

section – NEURON Section object.

Returns:

str, “kind”: str}.

Return type:

dict mapping variable names to {“units”

bluecellulab.cell.section_tools.mechs_vars(section, include_point_mechs=False)[source]

Return mechanism-scoped variables at a given section.

Parameters:

• section – NEURON Section object.

• include_point_mechs (bool) – Whether to include point processes.

Return type:

dict

bluecellulab.cell.section_tools.section_to_variable_recording_str(section, segx, variable)[source]

Build an evaluable NEURON pointer string for add_recording.

Accepts:

• top-level vars: “v”, “ina”, “ik”, …

• mechanism-scoped vars: “kca.gkca”, “na3.m”, “na3.h”, …

Returns examples:

neuron.h.soma[0](0.5)._ref_v neuron.h.soma[0](0.5)._ref_ina neuron.h.soma[0](0.5).kca._ref_gkca neuron.h.dend[3](0.7).na3._ref_m

Parameters:

• segx (float)

• variable (str)

Return type:

str