Add new cell type — add.cell.type • DACx

This function adds a user-defined cell type to the current session. It's just a wrapper for the Rcpp-exported add_cell_type function. Technically, cell_type is a struc defined in the Rcpp backend of the neurons package. They are essentially labeled lists with the following entries: type_name, valence, temporal_modulation_bias, temporal_modulation_timeconstant, temporal_modulation_amplitude, transmission_velocity, v_bound, dHdv_bound, I_spike, coupling_scaling_factor, spike_potential, resting_potential, and threshold. Each session stores cell types in the Rcpp backend in an unordered_map with string labels. All parameters come with biologically realistic (and mathematically workable) default values, except for type_name and valence.

Usage

add.cell.type(
  type_name,
  valence,
  temporal_modulation_bias = 0.001,
  temporal_modulation_timeconstant = 1,
  temporal_modulation_amplitude = 0.005,
  transmission_velocity = 30000,
  spine_density = 0,
  axon_target = "dendrite_shaft",
  v_bound = 85,
  dHdv_bound = 1.05e-06,
  I_spike = 1e-06,
  spike_potential = 35,
  resting_potential = -70,
  threshold = -55,
  axon_branch_count = 10,
  dendrite_branch_count = 10,
  branch_independence = 0.5,
  branch_spread = 0.5,
  apical_target_layer = "none"
)

Arguments

type_name: Character string giving name of the cell type, e.g. "pyramidal", "PV", "SST", etc.
valence: Valence of each neuron type, +1 for excitatory, -1 for inhibitory
temporal_modulation_bias: Temporal modulation time (in ms) bias for each neuron type. Default value is 1e-3.
temporal_modulation_timeconstant: Temporal modulation time (in ms) step for each neuron type. Default value is 1e0.
temporal_modulation_amplitude: Temporal modulation time (in ms) cutoff for each neuron type. Default value is 5e-3.
transmission_velocity: Transmission velocity (in microns/ms) for each neuron type. Default value is 30e3.
spine_density: Scale between 0 and 1; 0 = no spines, 1 = every node along dendrite is a spine. Default is 0.0.
axon_target: Character string giving target of axon projections for each neuron type, one of: "spine", "dendrite_shaft", "soma", or "axon_shaft". Default is "dendrite_shaft".
v_bound: Potential bound, such that -v_bound <= v_traces <= v_bound, in unit_potential (mV), for each neuron in the network, based on its type. Default value is 85.0.
dHdv_bound: Bound on derivative of metabolic energy wrt potential, such that dHdv_bound > abs(dHdv), in mA, for each neuron in the network, based on its type. Default value is 1.05e-6.
I_spike: Spike current, in mA. Default value is 1e-6 (i.e., 1 nA).
spike_potential: Magnitude of each spike, in mV. Default value is 35.0.
resting_potential: Resting potential, in mV. Default value is -70.0.
threshold: Spike threshold, in mV. Default value is -55.0.
axon_branch_count: Expected number of axon branches. Default is 10.
dendrite_branch_count: Expected number of dendrite branches. Default is 10.
branch_independence: Scale between 0 and 1; 0 = all branches connect to soma from single segment, 1 = all branches connect directly to soma. Default is 0.5.
branch_spread: Scale between 0 and 1; 0 = no tendency to extend away from soma, 1 = straight line away from soma. Default is 0.5.
apical_target_layer: Character string giving target layer for apical dendrites. Default: "none".

Value

Nothing.