CellParser¶

class single_cell_parser.cell_parser.CellParser(fn='')¶

Bases: object

Configure a Cell object from a Morphology file.

This class is used to read a Morphology file and set up a Cell object for single cell simulations. It segmentizes the morphology accroding to Hines and Carnevale [7], and sets the Cell object’s membrane properties, mechanisms, and ion properties based on a Cell parameters file.

Parameters:¶

fn : str¶

Path to Morphology file.

Attributes:¶

path¶

Path to the morphology file

Type:¶

str

hoc_path¶

Path to the .hoc morphology file (if the morphology is in the .hoc format)

Type:¶

str

swc_path¶

Path to the .swc morphology file (if the morphology is in the .swc format)

Type:¶

str

membraneParams¶

Membrane parameters

Type:¶

dict

cell_modify_functions_applied¶

Whether or not cell modify functions have already been applied. See: apply_cell_modify_functions()

Type:¶

bool

cell¶

Cell object.

Type:¶

Cell

Methods:¶

spatialgraph_to_cell(parameters, axon, scaleFunc, force_connect_soma_halfway)	Create a Cell object from the Morphology.
set_up_biophysics(parameters, full)	Initialize membrane properties.
apply_cell_modify_functions(parameters)	Apply cell modify functions to the cell object.
get_cell()	Returns cell if it is set up for simulations.
insert_membrane_properties(label, props)	Inserts membrane properties into all structures named as label.
insert_range_mechanisms(label, mechs)	Inserts range mechanisms into all structures named as label.
update_range_mechanisms(label, updateMechName, mechs)	Updates range mechanism updateMechName in all structures named as label.
_insert_ion_properties(label, ionParam)	Inserts ion properties into all structures named as label
_add_spines(label, spineParam)	Adds passive spines to the membrane.
_add_spines_ar(label, spineParam)	Adds passive spines to anomalously rectifying membrane [8].
insert_passive_membrane(label)	Set up a passive membrane with default values.
insert_hh_membrane(label)	Set up a Hodgkin-Huxley membrane with default values.
determine_nseg(f, full, max_seg_length)	Determine the number of segments for each section according to the d-lambda rule.
_create_ais()	Create axon hillock and AIS according to Mainen et al. [9]
_create_ais_Hay2013()	Create axon hillock and AIS according to Hay et al. [10]