PySection2¶

class singlecell_input_mapper.udvary2022.cell.PySection2(name=None, cell=None, label=None)¶

Bases: object

Convenience class around NEURON’s Section class.

Provides an interface with existing methods in ISF for cell parsing and mapping synapses without any additional NEURON [7] dependencies.

Parameters:¶

name : str¶

Name of the section. Default: None.

cell : str¶

Name of the cell. Default: None.

label : str¶

Label of the section. Default: None.

Attributes:¶

name¶

Name of the section.

Type:¶

str

label¶

Label of the section (e.g. “Soma”, “Dendrite”, “ApicalDendrite” …).

Type:¶

str

parent¶

Parent section.

Type:¶

PySection2

parentx¶

Relative position along the parent section (0-1). Usually, sections are split up on branch points, making parentx equal to 1.0, but this is not always the case (e.g. when the section has a similar diameter beyond the branch point).

Type:¶

float

bounds¶

Bounding box around the section.

Type:¶

tuple

nrOfPts¶

Number of traced 3D coordinates.

Type:¶

int

pts¶

List of traced 3D coordinates.

Type:¶

list

relPts¶

List of relative position of 3D points along the section.

Type:¶

list

diamList¶

List of diameters at traced 3D coordinates.

Type:¶

list

L¶

Length of the section.

Type:¶

float

Methods:¶

set_3d_geometry(pts, diams)	Invokes NEURON [7] 3D geometry setup
_compute_bounds()	Compute the bounding box of the section.
_compute_relative_pts()	Compute the relative position of 3D points along the section.
_compute_length()	Calculate the length of the section.