Modify existing cell type or add new cell type based on existing cell type

This function modifies parameters of an existing cell type in the current session. Parameters can be updated selectively. If a parameter is not specified (or is specified as NULL), the existing value will be kept. Will either generate a new cell type from an existing one, or modify an existing one, depending on whether new_type_name is specified.

Usage

modify.cell.type(
  old_type_name,
  new_type_name = NULL,
  tau_fast = NULL,
  tau_slow = NULL,
  tau_Vs = NULL,
  dCdr = NULL,
  dVdr = NULL,
  max_spike_rate = NULL,
  g_leak = NULL,
  spike_velocity = NULL,
  spine_density = NULL,
  axon_target = NULL,
  I_spike = NULL,
  dHdv_bound = NULL,
  v_spike = NULL,
  tau_spike = NULL,
  v_threshold = NULL,
  v_eq = NULL,
  v_rest = NULL,
  v_bound = NULL,
  g_syn = NULL,
  tau_syn = NULL,
  axon_branch_count = NULL,
  dendrite_branch_count = NULL,
  branch_independence = NULL,
  branch_spread = NULL,
  apical_target_layer = NULL
)

Arguments

old_type_name: Character string giving name of the cell type from which to start, e.g. "pyramidal", "PV", "SST", etc.
new_type_name: Character string giving name to label new cell type created from old_type_name. If NULL, old_type_name is modified directly and no new cell type is created.
tau_fast: Time constant (ms) of the fast sodium (Na+) current (Na+ influx is inward, i.e. negative under the outward-positive convention; time to flow in).
tau_slow: Time constant (ms) of the slow calcium (Ca2+) current (Ca2+ influx is inward, i.e. negative under the outward-positive convention; time to pump out).
tau_Vs: Time constant (ms) for restoring presynaptic vesicles, i.e., recovery from short-term depression (STD).
dCdr: Slow-current molecule (Ca2+) influx as concentration per spike (concentration/spike).
dVdr: Utilization ratio (concentration/spike) of vesicles per spike.
max_spike_rate: Constant (spikes/ms) controlling estimation of spike rate and its maximum value.
g_leak: Conductance controlling the leak current, I_leak = g_leak * (v - v_rest) (outward-positive), in nS.
spike_velocity: Transmission velocity (in microns/ms) along axon, for each neuron type.
spine_density: Scale controlling percentage of dendrite nodes with spines: zero means none, one means all.
axon_target: Character string giving target of axon projections, one of: "spine", "dendrite_shaft", "soma", or "axon_shaft".
I_spike: Spike current, in pA.
dHdv_bound: Scale factor giving the bound on derivative of metabolic energy wrt potential, such that dHdv_bound * I_spike > abs(dHdv), for each neuron in the network, based on its type.
v_spike: Peak potential during a spike, in mV.
tau_spike: Time spike activates synapse, in ms.
v_threshold: Spike threshold, in mV.
v_eq: Induced potential (mV) at which no current naturally flows across this cell type's membrane, given the neurotransmitter released by each possible presynaptic cell type (e.g., 0 mV for an excitatory presynaptic cell, -70 mV for an inhibitory presynaptic cell). Accepts the same formats as g_syn.
v_rest: Resting potential, in mV; absolute value plus a little bit used as v_bound.
v_bound: Multiplier on the absolute value of v_rest giving the membrane potential barrier (mirrors dHdv_bound). Increase to allow hyperpolarization below rest.
g_syn: Conductance (nS) of this cell type's synapses, treating this cell type as postsynaptic and indexing by the type of each possible presynaptic cell. Can be a single number (applied uniformly to every presynaptic type), a numeric vector ordered as in print.known.celltypes(), or a named list keyed by presynaptic type name, e.g. list(pyramidal = 0.xx, PV = 0.yy).
tau_syn: Decay time constant (ms) of the postsynaptic current evoked by the neurotransmitter of each possible presynaptic cell type (e.g., faster for AMPA, slower for GABA_A). A larger value makes the current outlast the presynaptic spike; 0 recovers an instantaneous (boxcar) current. Accepts the same formats as g_syn.
axon_branch_count: Expected number of axon branches.
dendrite_branch_count: Expected number of dendrite branches.
branch_independence: Scale between 0 and 1; 0 = all branches connect to soma from single segment, 1 = all branches connect directly to soma.
branch_spread: Scale between 0 and 1; 0 = no tendency to extend away from soma, 1 = straight line away from soma.
apical_target_layer: Character string giving target layer for apical dendrites.

Value

Nothing.