hnn_core.L5Pyr

class hnn_core.L5Pyr(pos=None, override_params=None, gid=None)

Layer 5 Pyramidal class.

Parameters
postuple

Coordinates of cell soma in xyz-space

override_paramsdict or None (optional)

Parameters specific to L2 pyramidal neurons to override the default set

gidint or None (optional)

Each cell in a network is uniquely identified by it’s “global ID”: GID. The GID is an integer from 0 to n_cells, or None if the cell is not yet attached to a network. Once the GID is set, it cannot be changed.

Attributes
namestr

The name of the cell

list_dendlist of str

List of dendrites.

dendsdict

The dendrites. The key is the name of the dendrite and the value is an instance of h.Section.

synapsesdict

The synapses that the cell can use for connections.

__repr__()

Return repr(self).

create_dends(p_dend_props)

Create dendrites.

create_soma()

Create soma and set geometry.

create_tonic_bias(amplitude, t0, T, loc=0.5)

Create tonic bias at the soma.

Parameters
amplitudefloat

The amplitude of the input.

t0float

The start time of tonic input (in ms).

Tfloat

The end time of tonic input (in ms).

locfloat (0 to 1)

The location of the input in the soma section.

get_sections()

Get sections in a cell.

insert_dipole(yscale)

Insert dipole into each section of this cell.

Parameters
yscaledict

Dictionary of length scales to calculate dipole without 3d shape.

move_to_pos()

Move cell to position.

parconnect_from_src(gid_presyn, nc_dict, postsyn)
Parallel receptor-centric connect FROM presyn TO this cell,

based on GID.

Parameters
gid_presynint

The cell ID of the presynaptic neuron

nc_dictdict

Dictionary with keys: pos_src, A_weight, A_delay, lamtha Defines the connection parameters

postsyninstance of h.Exp2Syn

The postsynaptic cell object.

Returns
ncinstance of h.NetCon

A network connection object.

record_soma(record_vsoma=False, record_isoma=False)

Record current and voltage at soma.

Parameters
record_vsomabool

Option to record somatic voltages from cells

record_isomabool

Option to record somatic currents from cells

secs()

The geometry of the default sections in the Neuron.

set_biophysics(p_all)

Set the biophysics for the default Pyramidal cell.

set_geometry(p_dend)

Define shape of the neuron and connect sections.

Parameters
p_denddict | None

Nested dictionary. The outer dictionary has keys with names of dendrites and the inner dictionary specifies the geometry of these sections.

  • L: length of a section in microns

  • diam: diameter of a section in microns

  • cm: membrane capacitance in micro-Farads

  • Ra: axial resistivity in ohm-cm

setup_source_netcon(threshold)

Created for _PC.cell and specifies SOURCES of spikes.

Parameters
thresholdfloat

The voltage threshold for action potential.

shape_soma()

Define 3D shape of soma.

Warning

needed for gui representation of cell DO NOT need to call h.define_shape() explicitly!

syn_create(secloc, e, tau1, tau2)

Create an h.Exp2Syn synapse.

Parameters
seclocinstance of nrn.Segment

The section location. E.g., soma(0.5).

e: float

Reverse potential (in mV)

tau1: float

Rise time (in ms)

tau2: float

Decay time (in ms)

Returns
syninstance of h.Exp2Syn

A two state kinetic scheme synapse.