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Package tour

The library lives in toric_spines_sim/. Full signatures and docstrings are in the API reference.

  • geometry/ — SWC I/O, cycle breaks, mesh→skeleton→SWC, sink append, dendrite helpers
  • model/ — TSModel, synapses, gap junctions, TSRecipe, check_catalogue
  • simulation/ — parameters, TSSimulator, inputs, SimulationResults
  • events/ — event generators / rate curves
  • viz/ — Plotly / Dash / animation helpers
  • kmatrix.py, report.py — pairwise integration analysis / PDF reporting
  • paths.py — repo-root data paths (get_swc_path, …)

Temperature is Kelvin (in vitro ~297 K; barn owl in vivo ~313 K). Capacitance is µF/cm²; leak is S/cm²; axial resistivity is Ω·cm. See Software for ICx in-vitro / in-vivo banks.

Path helpers

from toric_spines_sim.paths import (
    get_swc_path,
    get_pointset_path,
    get_mesh_path,
    get_skeleton_path,
    get_simulation_path,
    DATA_DIR,
)

swc_file = get_swc_path("TS1_wsink_r10um.swc", units="microns")
pointset = get_pointset_path("TS1_synpts.txt", units="microns")
mesh = get_mesh_path("TS1.obj")
skeleton = get_skeleton_path("TS1.polylines.txt")
output_file = get_simulation_path("ts1", "axons", "results")