diameter_synthesis.build_diameters

Build neurite diameters from a pre-generated model.

Functions

build(neuron, neurite_types, model_params, ...)

Builder function for generating diameters of a neuron from the a diameter models.

diametrize_axon(morphology[, main_diameter, ...])

Diametrize axon in place without learning from reconstructed axons.
diameter_synthesis.build_diameters.build(neuron, neurite_types, model_params, diam_params, random_generator=numpy.random)

Builder function for generating diameters of a neuron from the a diameter models.

Parameters:

  • neuron (morphio.mut.Morphology) – neuron to diametrize.

  • neurite_types (list[str] or str or list[SectionType] or SectionType) – the neurite type(s) to consider.

  • model_params (dict) – model parameters.

  • diam_params (dict) – general configuration parameters.

  • random_generator (numpy.random.Generator) – the random number generator to use.

diameter_synthesis.build_diameters.diametrize_axon(morphology, main_diameter=1.0, collateral_diameter=0.1, main_taper=-0.0005, axon_point_isec=None, ais_length=60, rng=numpy.random)

Diametrize axon in place without learning from reconstructed axons.

The main axon branch (from soma to axon point) will have a tapered diameter, and the colaterals a constant diameter.

If an axon point is not provided, and main_diameter > collateral_diameter, the diameters will decrease with taper and bifurcations, with hardcoded parameters sibling_ratio = 0.5 and diameter_power_relation = 0.5.

Parameters:

  • morphology (morphio.mut.Morphology) – morphology to diametrize.

  • main_diameter (float) – diameter of main axon branch (from soma to axon_point_isec).

  • collateral_diameter (float) – diameter of collateral branches.

  • main_taper (float) – taper rate of main branch (set to 0 for no taper, should be negative).

  • axon_point_isec (int) – morphio section id of axon point (see morph_tool.axon_point module).

  • ais_length (float) – length of ais for which we keep original diameters.

  • rng (numpy.random.Generator) – the random number generator to use.