PySection¶

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

Bases: nrn

Wrapper around Section providing additional functionality for geometry and mechanisms.

NEURON sections are a collection of points and their diameter of the form secname If no section name is known, they are printed as __nrnsec_0x------------, where the dashed code represents the memory pointer. Each section consists of nseg segments of equal length. Each segment is represented by secname(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¶

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.