API reference

This page presents the complete API documentation.

axon_synthesis	axon-synthesis package.
axon_synthesis.atlas	Helpers for atlas.
axon_synthesis.base_path_builder	Module to define a base class for relative paths storage and processing.
axon_synthesis.constants	Store some constant values.
axon_synthesis.typing	Module to define custom types used in axon-synthesis.
axon_synthesis.utils	Some utils for the AxonSynthesis package.
axon_synthesis.validation	Validation sub-package for axon synthesis.
axon_synthesis.validation.mimic	Validation workflow that mimics inputs morphologies.
axon_synthesis.validation.statistics	Compute and plot some statistics.
axon_synthesis.white_matter_recipe	Helpers for white matter recipe.
axon_synthesis.cli	Main entry point of the Command Line Interface for the axon_synthesis package.
axon_synthesis.cli.common	Common entries of the Command Line Interface.
axon_synthesis.cli.input_creation	Entries of the Command Line Interface dedicated to the input creation.
axon_synthesis.cli.synthesis	Entries of the Command Line Interface dedicated to synthesis.
axon_synthesis.cli.utils	Some utils for the CLI of axon-synthesis.
axon_synthesis.cli.validation	Entries of the Command Line Interface dedicated to the validation.
axon_synthesis.inputs	Define the class to store the inputs.
axon_synthesis.inputs.clustering	Cluster the terminal points of a morphology to define a main truk and a set of tufts.
axon_synthesis.inputs.clustering.extract_terminals	Extract the terminal points of a morphology so that a Steiner Tree can be computed on them.
axon_synthesis.inputs.clustering.from_barcodes	Clustering from barcodes.
axon_synthesis.inputs.clustering.from_brain_regions	Clustering from brain regions.
axon_synthesis.inputs.clustering.from_sphere_parents	Clustering from sphere parents.
axon_synthesis.inputs.clustering.from_spheres	Clustering from spheres.
axon_synthesis.inputs.clustering.plot	Some plot utils for clustering.
axon_synthesis.inputs.clustering.utils	Some utils for clustering.
axon_synthesis.inputs.create	Package to create inputs.
axon_synthesis.inputs.pop_neuron_numbers	Create number of neurons in each population.
axon_synthesis.inputs.trunk_properties	Compute the long-range trunk properties after clustering.
axon_synthesis.synthesis	Base of the synthesis modules.
axon_synthesis.synthesis.add_tufts	Add tufts to Steiner solutions.
axon_synthesis.synthesis.main_trunk	Tools to create the main trunk of an axon.
axon_synthesis.synthesis.main_trunk.create_graph	Create the edges between the terminals and the obstacles (if any).
axon_synthesis.synthesis.main_trunk.create_graph.plot	Some plot utils for create graph.
axon_synthesis.synthesis.main_trunk.create_graph.utils	Some utils for graph creation.
axon_synthesis.synthesis.main_trunk.post_process	Post-process the Steiner solutions.
axon_synthesis.synthesis.main_trunk.steiner_morphology	Create morphologies from the Steiner Tree solutions.
axon_synthesis.synthesis.main_trunk.steiner_tree	Compute the Steiner Tree.
axon_synthesis.synthesis.outputs	Define the class to store the synthesis outputs.
axon_synthesis.synthesis.plot	Some plot utils for create graph.
axon_synthesis.synthesis.source_points	Create the source points from the atlas.
axon_synthesis.synthesis.target_points	Find the target points of the input morphologies.
axon_synthesis.synthesis.tuft_properties	Update the properties of the tufts that will be generated later.