triage_segs - jaybgager/tracertools GitHub Wiki

This function checks if a list of segment IDs pass through any of the known swamps for a given datastack.

[!NOTE] This function is experimental. Swamp map currently only exists for brain_and_nerve_cord as of 2026/10/06.

Arguments:

• datastack (string, mandatory)
  • the name of the CAVE datastack that contains the segments
• seg_ids (list of integers, mandatory)
  • the ids of the segments to check

Returns:

• results (3-item list, see description)
  • first item is a list of True/False values for each segment
  • second item is a list of intersection points as 3-shape numpy arrays if any exist and None values if they don't
  • third item is list of neuroglancer links with each segment's intersection points annotated if any exist

Example

Coming soon.

[!NOTE] Under the hood, this function first skeletonizes the segments and then checks if those skeletons intersect the swamp meshes. For this reason it's possible (though unlikely) to get false positives and/or false negatives if a segment's skeleton doesn't accurately represent its shape, as can happen occasionally for very blobby structures like mergers, glia, or cell bodies. This shouldn't be an issue for typical neuronal processes, which is what the function is designed for.