Morphology

These functions are used to reconstruct a neuronal structure imaged using a custom AOD microscope.

pyneurotrace.morphology.treePostProcessing(nodeIDs, nodeXYZ, traceIDs, data, rootID, tree)

Processes the tree structure, adding locations, calculating branches, and reordering nodes by branch.

Parameters:

  • nodeIDs (array) – List of node IDs.

  • nodeXYZ (array) – Array of node locations (XYZ coordinates).

  • traceIDs (array) – List of trace IDs.

  • data (array) – Data array containing raw traces.

  • rootID (int) – ID of the root node.

  • tree (dict) – Dictionary representing the tree structure.

Returns:

  • nodeIDs (array) – Processed list of node IDs.

  • nodeXYZ (array) – Processed array of node locations (XYZ coordinates).

  • finalTraceIDs (array) – Processed list of trace IDs.

  • finalTraceBranches (array) – List of trace branches.

  • data (array) – Processed data array containing raw traces.

  • branchIDs (array) – List of branch IDs.

  • branchIDMap (dict) – Dictionary mapping node IDs to branch IDs.

pyneurotrace.morphology.buildBranchIDMap(nodeID, nodes, splitAtBranch=False)

Builds a map of branch IDs for the given tree structure.

Parameters:

  • nodeID (int) – ID of the starting node.

  • nodes (dict) – Dictionary representing the tree structure.

  • splitAtBranch (bool, optional) – Flag indicating whether to split at branches. Default is False.

Returns:

branchIDMap – Dictionary mapping node IDs to branch IDs.

Return type:

dict

pyneurotrace.morphology.treeToFiloTipAndBase(nodeIDs, nodeXYZ, tree, rootID, filoDist=5.0)

Maps nodes to filopodia tips and bases based on the specified distance.

Parameters:

  • nodeIDs (array) – List of node IDs.

  • nodeXYZ (array) – Array of node locations (XYZ coordinates).

  • tree (dict) – Dictionary representing the tree structure.

  • rootID (int) – ID of the root node.

  • filoDist (float, optional) – Distance threshold for identifying filopodia tips and bases. Default is 5.0.

Returns:

mapping – Dictionary mapping node IDs to branch IDs, indicating filopodia tips and bases.

Return type:

dict