hnn_core.Cell

class hnn_core.Cell(name, pos, sections, synapses, sect_loc, cell_tree, gid=None)

Create a cell object.

Parameters:

namestr

The name of the cell.

postuple

The (x, y, z) coordinates.

sectionsdict of Section

Dictionary with keys as section name.

synapsesdict of dict

Keys are name of synaptic mechanism. Each synaptic mechanism has keys for parameters of the mechanism, e.g., ‘e’, ‘tau1’, ‘tau2’. sections.

sect_locdict of list

Can have keys ‘proximal’ or ‘distal’ each containing names of section locations that are proximal or distal.

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.

cell_treedict of list

Stores the tree representation of a cell. Root is the 0 end of ‘soma’. Nodes are a tuple (sec_name, node_pos) where sec_name is the name of the section and node_pos is the 0 end or 1 end. The data structure is the adjacency list representation of a tree. The keys of the dict are the parent nodes. The value is the list of nodes (children nodes) connected to the parent node.

Examples

>>> section_soma = Section(
        L=39,
        diam=20,
        cm=0.85,
        Ra=200.,
        end_pts=[[0, 0, 0], [0, 39., 0]]
    )

Attributes:

poslist of length 3

The position of the cell.

sectionsnested dict

The section parameters. The key is the name of the section and the value is a dictionary parametrizing the morphology of the section and the mechanisms inserted.

synapsesdict

The synapses that the cell can use for connections.

dipole_pplist of h.Dipole()

The Dipole objects (see dipole.mod).

vsecdict

Recording of section specific voltage. Must be enabled by running simulate_dipole(net, record_vsec=True) or simulate_dipole(net, record_vsoma=True)

isecdict

Contains recording of section specific currents indexed by synapse type (keys can be soma_gabaa, soma_gabab etc.). Must be enabled by running simulate_dipole(net, record_isec=True) or simulate_dipole(net, record_isoma=True)

cadict

Contains recording of section speicifc calcium concentration. Must be enabled by running simulate_dipole(net, record_ca=True).

tonic_biaseslist of h.IClamp

The current clamps inserted at each section of the cell for tonic biasing inputs.

gidint

GID of the cell in a network (or None if not yet assigned)

sect_locdict of list

Can have keys ‘proximal’ or ‘distal’ each containing names of section locations that are proximal or distal.

cell_treedict of list

Stores the tree representation of a cell. Root is the 0 end of ‘soma’. Nodes are a tuple (sec_name, node_pos) where sec_name is the name of the section and node_pos is the 0 end or 1 end. The data structure is the adjacency list representation of a tree. The keys of the dict are the parent nodes. The value is the list of nodes (children nodes) connected to the parent node.

Methods

build([sec_name_apical])	Build cell in Neuron and insert dipole if applicable.
copy()	Return copy of instance.
create_tonic_bias(amplitude, t0, tstop[, loc])	Create tonic bias at the soma.
define_shape(node)	Redefines end_pts according to section lengths.
distance_section(target_sec_name, curr_node)	Find distance between the current node and the target section.
modify_section(sec_name[, L, diam, cm, Ra])	Change attributes of section specified by sec_name
parconnect_from_src(gid_presyn, nc_dict, ...)	Parallel receptor-centric connect FROM presyn TO this cell,
plot_morphology([ax, color, pos, xlim, ...])	Plot the cell morphology.
record([record_vsec, record_isec, record_ca])	Record current and voltage from all sections
setup_source_netcon(threshold)	Created for _PC.cell and specifies SOURCES of spikes.
syn_create(secloc, e, tau1, tau2)	Create an h.Exp2Syn synapse.
to_dict()	Converts an object of Cell class to a dictionary.

__repr__()

Return repr(self).

build(sec_name_apical=None)

Build cell in Neuron and insert dipole if applicable.

Parameters:

sec_name_apicalstr | None

If not None, a dipole will be inserted in this cell in alignment with this section. The section should belong to the apical dendrite of a pyramidal neuron.

copy()

Return copy of instance.

create_tonic_bias(amplitude, t0, tstop, 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).

tstopfloat

The end time of tonic input (in ms).

locfloat (0 to 1)

The location of the input in the soma section.

define_shape(node)

Redefines end_pts according to section lengths.

Detects change in section lengths of the sections in the subtree of the input node.

Parameters:

nodetuple of size 2

The first element is the section name The second element is the node end used (0 or 1)

distance_section(target_sec_name, curr_node)

Find distance between the current node and the target section.

Parameters:

target_sec_namestring

Name of the target section

curr_nodetuple

Source node from where search begins. It is of the the form (sec_name, end_pt).

Returns:

distancefloat

Path distance between source node and mid of the target section.

modify_section(sec_name, L=None, diam=None, cm=None, Ra=None)

Change attributes of section specified by sec_name

Parameters:

sec_namestr

Name of section to be modified. Must be a key of Cell.sections

Lfloat | int | None

length of a section in microns. Default None.

diamfloat | int | None

diameter of a section in microns.

cmfloat | int | None

membrane capacitance in micro-Farads.

Rafloat | int | None

axial resistivity in ohm-cm.

Notes

Leaving default of None produces no change.

parconnect_from_src(gid_presyn, nc_dict, postsyn, inplane_distance)

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.

inplane_distancefloat

The in plane-distance (in um) between pyramidal cell somas in the square grid.

Returns:

ncinstance of h.NetCon

A network connection object.

plot_morphology(ax=None, color=None, pos=(0, 0, 0), xlim=(-250, 150), ylim=(-100, 100), zlim=(-100, 1200), show=True)

Plot the cell morphology.

Parameters:

axinstance of Axes3D

Matplotlib 3D axis

colorstr | dict | None

Color of cell. If str, entire cell plotted with color indicated by str. If dict, colors of individual sections can be specified. Must have a key for every section in cell as defined in the Cell.sections attribute.

| Ex: ``{‘apical_trunk’: ‘r’, ‘soma’: ‘b’, …}``

postuple of int or float | None

Position of cell soma. Must be a tuple of 3 elements for the (x, y, z) position of the soma in 3D space. Default: (0, 0, 0)

xlimtuple of int | tuple of float

x limits of plot window. Default (-250, 150)

ylimtuple of int | tuple of float

y limits of plot window. Default (-100, 100)

zlimtuple of int | tuple of float

z limits of plot window. Default (-100, 1200)

showbool

If True, show the plot

Returns:

axesinstance of Axes3D

The matplotlib 3D axis handle.

record(record_vsec=False, record_isec=False, record_ca=False)

Record current and voltage from all sections

Parameters:

record_vsec‘all’ | ‘soma’ | False

Option to record voltages from all sections (‘all’), or just the soma (‘soma’). Default: False.

record_isec‘all’ | ‘soma’ | False

Option to record voltages from all sections (‘all’), or just the soma (‘soma’). Default: False.

record_ca‘all’ | ‘soma’ | False

Option to record calcium concentration from all sections (‘all’), or just the soma (‘soma’). Default: False.

setup_source_netcon(threshold)

Created for _PC.cell and specifies SOURCES of spikes.

Parameters:

thresholdfloat

The voltage threshold for action potential.

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.

to_dict()

Converts an object of Cell class to a dictionary.

Returns:

dictionary form of an object of Cell class.