spatialgraph_to_cell¶

single_cell_parser.cell_parser.CellParser.spatialgraph_to_cell(parameters=None, axon=False, scaleFunc=None, force_connect_soma_halfway=True)¶

Create a Cell object from the Morphology.

Reads a Morphology file and sets up PySections and Cell object.

Parameters:¶

axon : bool¶

Whether or not to add a custom axon initial segment (AIS) instead of the one in the morphology file. If True, an AIS is created according to the methods described in Hay et al. [10].

force_connect_soma_halfway : bool¶

Force direct descendants of the soma to connect to the soma at \(x=0.5\). Sections that connect to soma at \(x=0\) mess up the calculation of \(R_a\). In addition, this flag is useful for consistency for those morphologies where the soma geometry is ill-defined, or to preserve continuity between .swc and .hoc in those cases where .hoc defines connectivity between soma and child sections in ways that .swc can’t define (i.e. continuous coordinate that lands in-between points) Default is True.

See also

_create_ais_Hay2013() for how a custom AIS is created.

Deprecated since version 0.1.0: The scaleFunc argument is deprecated and will be removed in a future version. To ensure simulation reproducability, scaleFunc should be specified in the parameters, as described in cell_modify_funs

Deprecated since version 0.1.0: The parameters keyword is optional for this method. It was previously used to check for spines. Instead of passing parameters as a keyword, the Cell parameters file is used to apply biophysical mechanisms during set_up_biophysics().