PySection¶

class single_cell_parser.cell.PySection(name=None, cell=None, label=None)¶

Wrapper around Section providing additional functionality for geometry and mechanisms.

NEURON sections are objects of the form __nrnsec_0x------------, where the dashed code represents the memory pointer. Each section consists of nseg segments of equal length. Each segment is represented by __nrnsec_0x------------(x), which looks similar to the section representation, but has an additional (x): a relative coordinate representing the center point of the segment.

Iterating the section will provide the individual segments. Each segment consists of one or more points. Accessing a segment’s biophysical properties can be done as seg.<param>.<param_name>.

Example:

>>> sec = cell.soma
>>> for seg in sec:
...    print(seg.NaTa_t.gNaTa_tbar)

Parameters:¶

name : str, optional¶

name of the section

cell : Cell, optional¶

reference to the cell object

label : str, optional¶

label of the section

Attributes:¶

label¶

label of the section (e.g. “Soma”, “Dendrite”, “Myelin”).

Type:¶

str

label_detailed¶

Detailed label of the section (e.g. “oblique”, “basal”, “trunk”). These are manually assigned or automatically generated by augment_cell_with_detailed_labels(). Used in scale_by_detailed_compartment().

Type:¶

str, optional

parent¶

reference to parent section.

Type:¶

PySection

parentx¶

connection point at parent section.

Type:¶

float

bounds¶

bounding box around 3D coordinates.

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 section.

Type:¶

list

diamList¶

list of diameters at traced 3D coordinates.

Type:¶

list

area¶

total area of all NEURON segments in this section.

Type:¶

float

segPts¶

list of segment centers (x coordinate). Useful for looping akin to the hoc function for(x). Excluding 0 and 1.

Type:¶

list

segx¶

list of x values corresponding to center of each segment.

Type:¶

list

segDiams¶

list of diameters of each segment. Used for visualization purposes only.

Type:¶

list

recVList¶

list of neuron Vectors recording voltage in each compartment.

Type:¶

list

recordVars¶

dict of range variables recorded.

Type:¶

dict

Methods:¶

set_3d_geometry(pts, diams)	Invokes NEURON 3D geometry setup.
set_segments(nrOfSegments)	Set spatial discretization.
get_seg_conductance(seg, var, param_name)	Get the conductance of a segment.
get_range_conductances(range_vars, density)	Get the transmembrane conductance of each range variable separately.
_compute_seg_diameters()	Computes the diameter of each segment in this section.
_compute_total_area()	Computes total area of all NEURON segments in this section
_compute_bounds()	Computes the bounding box around the 3D coordinates.
_compute_relative_pts()	Computes the relative position of 3D points along the section.
_compute_seg_pts()	Computes the 3D center points of each segment in this section.
_init_vm_recording()	Record the membrane voltage at every point in this section.
_re_init_vm_recording()	Reinitialize votage recordings
_re_init_range_var_recording()	Re-initialize the range mechanism recordings.
_init_range_var_recording(var, mech)	Initialize recording of a range mechanism.