CellParser.spatialgraph_to_cell¶

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

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

Reads cell morphology from Amira hoc file and sets up PySections and Cell object.

Parameters:¶

axon : bool¶: Whether or not to add an axon initial segment (AIS). AIS creation is according to Hay et al. [10].

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().

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