connectome_manipulator.connectome_manipulation.manipulation.conn_wiring.ConnectomeWiring

Special case of connectome manipulation class for wiring a connectome:

Special operation of connectome wiring, which generates an empty connectome from scratch, or simply adds connections to an existing connectome. The manipulation can be applied through the apply() method.

IMPORTANT: This is a highly optimized operation for wiring huge connectomes by pathways (i.e., for each pair of pre-/post-synaptic hemisphere/region/m-type). However, only specific properties like source/target node, afferent synapse positions, synapse type (INH: 0, EXC: 100), and delay (optional) will be generated. For general purpose wiring, please use the connectome_manipulator.connectome_manipulation.manipulation.conn_rewiring.ConnectomeRewiring() operation!

connectome_manipulator.connectome_manipulation.manipulation.conn_wiring.ConnectomeWiring.apply(self, split_ids, sel_src=None, sel_dest=None, pos_map_file=None, amount_pct=100.0, morph_ext='swc', prob_model_spec=None, nsynconn_model_spec=None, delay_model_spec=None, pathway_specs=None, **kwargs)

Applies a wiring (generation) of structural connections between pairs of neurons based on a given connectivity model.

Parameters:

  • split_ids (list-like) – List of neuron IDs that are part of the current data split; will be automatically provided by the manipulator framework

  • sel_src (str/list-like/dict) – Source (pre-synaptic) neuron selection

  • sel_dest (str/list-like/dict) – Target (post-synaptic) neuron selection

  • pos_map_file (str/list-like) – Optional position mapping file pointing to a position mapping model (.json) or voxel data map (.nrrd); one or two files for source/target node populations may be provided

  • amount_pct (float) – Percentage of randomly sampled target (post-synaptic) neurons that will be wired

  • morph_ext (str) – Morphology file extension, e.g., “swc”, “asc”, “h5”

  • prob_model_spec (dict) – Connection probability model specification; a file can be specified by {"file": "path/file.json"}

  • nsynconn_model_spec (dict) – Model specifications for #synapses/connection; a file can be specified by {"file": "path/file.json"}

  • delay_model_spec (dict) – Delay model specification; a file can be specified by {"file": "path/file.json"}

  • pathway_specs (dict) – Optional model specifications for efficiently setting model coefficients by pathway; will be automatically provided by the manipulator framework in case a .parquet file (containing a coefficient table for all pathways) is specified under “model_pathways” in the manipulation configuration file; only works with specific types of models

  • **kwargs – Additional keyword arguments - Not used

Note

Only structural synapse properties will be set: pre-/postsynaptic neuron IDs, synapse positions, type, axonal delays