neurots.astrocyte.grower

NeuroTS class: Grower object that contains the grower functionality.

Classes

AstrocyteGrower(input_parameters, ...[, ...])

The specific grower for astrocytes.

class neurots.astrocyte.grower.AstrocyteGrower(input_parameters, input_distributions, context, skip_preprocessing=True, external_diametrizer=None, rng_or_seed=numpy.random)

Bases: NeuronGrower

The specific grower for astrocytes.

A Grower object is a container for an Astrocyte, encoded in the (groups, points) structure, as a morphIO Morphology object. A set of input distributions that store the data consumed by the algorithms and the user-selected parameters are also stored.

_add_active_neurite(initial_soma_point, parameters, distributions)

Create a TreeGrower with the input data and add it to the active neurites.

_create_process_trunks(tree_type, parameters, distributions)

Creates the starts of the processes for the astrocyte.

Parameters:
  • tree_type (str) –

  • parameters (dict) –

  • distributions (distributions) –

Notes

Astrocytic perivascular type corresponds to the neuronal axon, while perisynaptic type to basal or apical type.

_grow_trunks()

Grow the trunks.

Generates the initial points of each tree, which depend on the selected tree types and the soma surface. All the trees start growing from the surface of the soma. The outgrowth direction is either specified in the input parameters, as parameters[‘type’][‘orientation’] or it is randomly chosen according to the biological distribution of trunks on the soma surface if ‘orientation’ is None.

_orientations_to_points(oris, n_trees, distr)

Return soma points from directions.

Checks the type of orientation input and returns the soma points generated by the corresponding selection.

Currently accepted orientations include the following options:
  • list of 3D points: select the orientation externally

  • None: creates a list of orientations according to the biological distributions.

  • ‘from_space’: generates orientations depending on spatial input (not implemented yet).

_post_grow()

After the cell has grown ensure that endfeet targets have been reached.

validate_distribs()

Astrocyte distribution validation.

validate_params()

Astrocyte parameter validation.

neurots.astrocyte.grower._ensure_endfeet_are_reached(cell, targets)

Ensure Endfeet points are reached.

If there are any targets left active, i.e. not reached, the closest section to each one of them will be grown to reach it. This is the last resort to ensure that endfeet targets will be reached no matter what. However, a warning will be emitted.

neurots.astrocyte.grower._number_of_trees(tree_type, oris, distributions, random_generator=numpy.random)

Sample the number of trees depending on the tree type if no predef orientations.