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Glossary

SWC. File format for cable morphologies (spec). Each row is index tag x y z r parent. A strict SWC describes an arborescence (acyclic rooted directed tree).

Cable model. A 3D graph of neuronal (or subneuronal) morphology: vertices have XYZ and radius; edges are frusta. Not synonymous with SWC — a cable model need not be rooted, directed, or acyclic. This project writes cables as SWC plus header directives (# CYCLE_BREAK, # MULTI_NECK) so loops can be restored in Arbor as gap junctions.

Skeleton. A 1D curve network in 3D, stored as polylines (data/skeletons/TS{id}.polylines.txt). Convertible to an undirected graph. Input to mascaf.

Triangle mesh. Here, a triangle mesh, usually Wavefront OBJ. For MCFS it should be a single component and watertight (no holes in the surface, no duplicate vertices/edges/faces, no self-intersections). It may contain topological holes (genus > 0) — that is the point of toric spines.

MorphologyGraph / basis. mascaf terms for the central graph of a cable without radii: a downsampled skeleton that will become SWC nodes and edges. Basis optimization refines that graph before radius fitting.

Morphology vs geometry vs topology (as used here):

  • Morphology — the biologically relevant cable in the simulation
  • Geometry — meshes, skeletons, 3D graphs (MCFS is a geometric algorithm)
  • Topology — closed surfaces and their holes → genus

Sink. A cylindrical cable appended at the spine neck (SWC tags 5 / 6) so the isolated spine can leak into a stand-in for the rest of the cell.

Neckpoint. A point near the center of the cut surface where the spine was separated from the dendrite. Used as the sink attachment. Computed by comparing the isolated mesh to cell_wrapped_simplified.obj (scripts/compute_neckpoints.py).

Active zone (AZ) / synpts. Synapse coordinates. NFF exports from IMOD become TS{id}_AZ.txt; projected, micron-scaled sites used in simulation are TS{id}_synpts.txt.

SSN. Space-specific neuron in barn-owl ICx (external nucleus of the inferior colliculus) — the cell class that bears toric spines.

Neurosignature. Framework that embeds a multi-channel event-in / multi-channel signal-out operator \(F\) in a descriptor space \(\mathcal{Z}\) under an input ensemble \(\theta\). The current \(W\) compares internal activity to a downstream output (residuals, residual energy, transfer efficiency); users can add descriptors. See Neurosignature.