navis.interfaces.neuron.comp.CompartmentModel¶
- class navis.interfaces.neuron.comp.CompartmentModel(x, res=10)[source]¶
Compartment model representing a single neuron in NEURON.
- Parameters:
x (navis.TreeNeuron) – Neuron to generate model for. Has to be in microns!
res (int) – Approximate length [um] of segments. This guarantees that no section has any segment that is longer than res but for small branches (i.e. “sections”) the segments might be smaller. Lower
res
= more detailed simulation.
Initialize Neuron.
Methods
__init__
(x[, res])Initialize Neuron.
add_current_record
(where[, label])Add current recording to model.
add_spike_detector
(where[, threshold, label])Add a spike detector at given node(s).
add_synaptic_current
(where[, start, tau, ...])Add synaptic current(s) (AlphaSynapse) to model.
add_synaptic_input
(where[, start, spike_no, ...])Add synaptic input to model.
add_voltage_record
(where[, label])Add voltage recording to model.
clear
()Attempt to remove model from NEURON space.
Clear records.
Clear stimuli.
clear_synapses
()Clear synapses.
connect
(pre, where[, syn_tau1, syn_tau2, ...])Connect object to model.
get_node_section
(node_ids)Return section(s) for given node(s).
get_node_segment
(node_ids)Return segment(s) for given node(s).
inject_current_pulse
(where[, start, ...])Add current injection (IClamp) stimulation to model.
insert
(mechanism[, subset])Insert biophysical mechanism for model.
plot_results
([axes])Plot results.
plot_structure
()Visualize structure in 3D using matplotlib.
run_simulation
([duration, v_init])Run the simulation.
uninsert
(mechanism[, subset])Remove biophysical mechanism from model.
Attributes
Ra
Axial resistance [Ohm * cm] of all sections.
cm
Membran capacity [micro Farads / cm^2] of all sections.
label
Name/label of the neuron.
n_records
Number of records (across all types) active on this model.
n_sections
Number of sections in this model.
n_stimuli
Number of stimuli active on this model.
nodes
Node table of the skeleton.
records
Return mapping of node ID(s) to recordings.
sections
List of sections making up this model.
stimuli
Return mapping of node ID(s) to stimuli.
synapses
Return mapping of node ID(s) to synapses.
t
The global time.