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 struct defined in the Rcpp backend of the DACx package. They are essentially labeled lists whose fields are described by the parameters below. 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,
  tau_fast = 1,
  tau_slow = 60,
  tau_Vs = 100,
  I_slow = 0.01,
  U_Vs = 0.05,
  max_spike_rate = 0.1,
  transmission_velocity = 30000,
  spine_density = 0,
  axon_target = "dendrite_shaft",
  I_spike = 1000,
  spike_potential = 35,
  resting_potential = -70,
  threshold = -55,
  leak_conductance = 10,
  axon_branch_count = 10L,
  dendrite_branch_count = 10L,
  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.
tau_fast: Time constant (ms) of the fast sodium (Na+) current (positive current, time to flow in). Default is 1.0.
tau_slow: Time constant (ms) of the slow calcium (Ca2+) current (negative current, time to pump out). Default is 60.0.
tau_Vs: Time constant (ms) for restoring presynaptic vesicles, i.e., recovery from short-term depression (STD). Default is 100.0.
I_slow: Slow-current molecule (e.g., Ca2+) influx as concentration per spike (concentration/spike). Default is 0.01.
U_Vs: Utilization ratio (concentration/spike) of vesicles per spike. Default is 0.05.
max_spike_rate: Constant (spikes/ms) controlling estimation of spike rate and its maximum value. Default is 0.1.
transmission_velocity: Transmission velocity (in microns/ms) along axon, for each neuron type. Default value is 30e3.
spine_density: Scale controlling percentage of dendrite nodes with spines: zero means none, one means all. Default is 0.0.
axon_target: Character string giving target of axon projections, one of: "spine", "dendrite_shaft", "soma", or "axon_shaft". Default is "dendrite_shaft".
I_spike: Spike current, in pA; absolute value plus a little bit used as dHdv_bound. Default value is 1e3 (i.e., 1 nA).
spike_potential: Peak potential during a spike, in mV. Default value is 35.0.
resting_potential: Resting potential, in mV; absolute value plus a little bit used as v_bound. Default value is -70.0.
threshold: Spike threshold, in mV. Default value is -55.0.
leak_conductance: Conductance controlling the leak current, I_leak = leak_conductance * (resting_potential - v), in nS. Default value is 10.0.
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 is "none".

Value

Nothing.