neurorosettes.neurons#
This module deals with the neuron structure and functions
Module Contents#
Classes#
Class to represent a neuron as a combination of a cell body and neurites. |
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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.