single_cell_parser ❭ cell_parser ❭ CellParser

CellParser¶

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

Configure a Cell object from a NEURON hoc file.

This class is used to read a hoc 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.

See also

This is not the same class as singlecell_input_mapper.singlecell_input_mapper.cell.CellParser. This class provides biophysical details, such as segmentation, channel mechanisms, and membrane properties.

Parameters:¶: hocFilename (str) – Path to .hoc file.
Attributes:¶

hoc_path¶

Path to hoc file

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)	Create a `Cell` object from an AMIRA spatial graph in .hoc format.
`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]