neurorosettes.neurons#

This module deals with the neuron structure and functions

Module Contents#

Classes#

Neuron

Class to represent a neuron as a combination of a cell body and neurites.

NeuronFactory

Helper class to create instances of neurons based on defined properties.
class neurorosettes.neurons.Neuron(position, outgrowth_axis, factory, clocks, max_number_of_neurites=4, differentiation_grade=0)[source]#

Class to represent a neuron as a combination of a cell body and neurites.

Parameters:

  • position (numpy.ndarray) – The center position of the neuron’s cell body.

  • outgrowth_axis (numpy.ndarray) – The direction of growth of the neuron’s neurites.

  • factory (neurorosettes.subcellular.ObjectFactory) – The factory object to be used to create new neuron components.

  • clocks (neurorosettes.clocks.CellClocks) – The rates of the neuron’s biological processes.

  • max_number_of_neurites (int) – The total number of neurites a neuron can have before proliferation is blocked.

  • differentiation_grade (int) – The starting differentiation stage of the neurite, represented by the initial number of neurites.

property cell_radius#

The radius of the neuron’s cell body.

property ready_for_division#

If the neuron is ready to proliferate.

property ready_for_differentiation#

If the neuron is ready to differentiate.

property ready_to_die#

If the neuron is ready to die.

set_outgrowth_axis(coordinates)[source]#

Sets the axis that neurites will follow when new neurites are created.

Prameters#

outgrowth_axis

The direction of growth of the neuron’s neurites.

Parameters:

coordinates (numpy.ndarray) –

Return type:

None

get_neurite_position_on_cell_surface()[source]#

Returns the coordinates on the cell surface where the first neurite should be placed

Return type:

numpy.ndarray

place_neurite_on_cell_surface(neurite)[source]#

Places the neurite base on the cell surface according to the cell-distal vector.

Parameters:

neurite (neurorosettes.subcellular.Neurite) – The neurite to be placed on the cell body’s surface.

Return type:

None

create_first_neurite(factory)[source]#

Creates a neurite attached to the soma cell

Parameters:

factory (neurorosettes.subcellular.ObjectFactory) – The factory object to be used to create new neuron components.

Return type:

None

create_secondary_neurite(factory)[source]#

Creates a neurite attached to the most recent neurite.

Parameters:

factory (neurorosettes.subcellular.ObjectFactory) – The factory object to be used to create new neuron components.

Return type:

None

class neurorosettes.neurons.NeuronFactory[source]#

Helper class to create instances of neurons based on defined properties.

max_number_of_neurites: int#

The maximum number of neurites that a neuron can have.

objects_factory: neurorosettes.subcellular.ObjectFactory#

The ObjectFactory used to create new object instances.

clocks_factory: neurorosettes.clocks.ClocksFactory#

The ClocksFactory used to create new clock instances.

create_neuron(coordinates, outgrowth_axis)[source]#

Returns a Neuron object placed in the given coordinates.

Parameters:

  • coordinates (numpy.ndarray) –

  • outgrowth_axis (numpy.ndarray) –

Return type:

Neuron