single_cell_parser ❭ cell_parser ❭ CellParser ❭ set_up_biophysics

CellParser.set_up_biophysics¶

single_cell_parser.cell_parser.CellParser.set_up_biophysics(parameters, full=False)¶

Initialize membrane properties.

Default method for determining the compartment sizes for NEURON simulation, initializing membrane properties, and mechanisms. Properties are constants that are defined for an entire structure. Mechanisms have specific densities (not always uniform), and can be transient. Poperties are added to the section by executing the NEURON command sec.<property>=<value>.

• Properties:

  • \(C_m\) (see insert_membrane_properties())

  • \(R_a\) (see insert_membrane_properties())

  • ion properties (see _insert_ion_properties())

• Mechanisms:

  • range mechanisms (see insert_range_mechanisms())

The workflow is as follows:

1. Add membrane properties to all structures (see insert_membrane_properties()).

2. Determine the number of segments for each structure (see determine_nseg()).

3. Add range mechanisms to all structures (see insert_range_mechanisms()).

4. Add ion properties to all structures (see _insert_ion_properties()), if the ion keyword is present in the Cell parameters file.

5. Add spines, if the spines keyword is present in the Cell parameters file.

   5.1 Add passive spines if pas is present in the range mechanisms (see _add_spines()). 5.2 Add passive spines to anomalously rectifying membrane if ar is present in the range mechanisms (see _add_spines_ar()).

Parameters:¶

• parameters (ParameterSet) – Neuron biophysical parameters, read from a Cell parameters file.

• full (bool) – Whether or not to use full spatial discretization.