pysted.utils.generate_synaptic_fibers

pysted.utils.generate_synaptic_fibers(image_shape, main_nodes, n_sec_fibers, n_synapses, min_fiber_dist=3, min_synapse_dist=1, sec_fiber_len=(10, 20), synapse_scale=(5, 5), seed=None)

This function wraps up the generation of fibers with secondary branches and synapses in a stand-alone function

TODO: - Add variable number of synapses, distances, - Add “position identifiers” to the synapses so I can easily make them flash after

Parameters:

  • image_shape – The shape of the ROI in which we want to spawn stuff

  • main_nodes –

    ???

  • n_sec_fibers – The interval for the number of secondary fibers branching from the main fiber (tuple)

  • n_synapses – The interval for the number of synapses (tuple)

  • min_fiber_dist – The minimum distance separating the secondary fibers

  • min_synapse_dist – The minimum distance separating the synapses

  • sec_fiber_len – The interval for the lengths of the secondary fibers

  • synapse_scale – The interval for the size of the synapses

  • seed – Random number generator seed

Returns:

An array containing the disposition of molecules corresponding to the generated shape and a list containing all the synapses (Polygon objects)