single_cell_parser ❭ cell ❭ PySection

PySection¶

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

Wrapper around nrn.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.