hnn_core.Cell¶

class hnn_core.Cell(name, pos, sections, synapses, topology, sect_loc, gid=None)[source]¶

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’.
topologylist of list: The topology of cell sections. Each element is a list of 4 items in the format [parent_sec, parent_loc, child_sec, child_loc] where parent_sec and parent_loc are float between 0 and 1 specifying the location in the section to connect and parent_sec and child_sec are names of the connecting 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.

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).
rec_vh.Vector(): Recording of somatic voltage. Must be enabled by running simulate_dipole(net, record_vsoma=True)
rec_idict: Contains recording of somatic currents indexed by synapse type. (keys are soma_gabaa, soma_gabab etc.) Must be enabled by running simulate_dipole(net, record_isoma=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.

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.
`parconnect_from_src`(gid_presyn, nc_dict, …)	Parallel receptor-centric connect FROM presyn TO this cell,
`plot_morphology`([ax, cell_types, show])	Plot the cell morphology.
`record_soma`([record_vsoma, record_isoma])	Record current and voltage at soma.
`setup_source_netcon`(threshold)	Created for _PC.cell and specifies SOURCES of spikes.
`syn_create`(secloc, e, tau1, tau2)	Create an h.Exp2Syn synapse.

build(sec_name_apical=None)[source]¶

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.

create_tonic_bias(amplitude, t0, tstop, loc=0.5)[source]¶

Create tonic bias at the soma.

Parameters

parconnect_from_src(gid_presyn, nc_dict, postsyn, inplane_distance)[source]¶

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

plot_morphology(ax=None, cell_types=None, show=True)[source]¶

Plot the cell morphology.

Parameters

Returns

record_soma(record_vsoma=False, record_isoma=False)[source]¶

Record current and voltage at soma.

Parameters

setup_source_netcon(threshold)[source]¶

Created for _PC.cell and specifies SOURCES of spikes.

Parameters

syn_create(secloc, e, tau1, tau2)[source]¶

Create an h.Exp2Syn synapse.

Parameters

Returns