Project and data layout¶

Use toric_spines_sim.paths instead of ../../data/... (see Path helpers).

Project layout¶

toric_spines_sim/
  data/                 morphologies and pointsets used by sims
  notebooks/            tutorial walkthrough + misc demos
  scripts/              CLI for mesh → SWC → sink (and catalogue build)
  simulations/          per-spine experiments (edit params here)
  toric_spines_sim/     Python package (geometry, model, simulator, viz)
  tests/
  archive/              superseded scripts and old SWC names — do not run

Path	Role
`data/`	Meshes, skeletons, SWCs, synapse / neck coordinates, axon maps
`scripts/`	Supported pipeline CLIs (`skeletonize_meshes.py`, `fit_swc.py`, `append_sink.py`, …)
`toric_spines_sim/`	Library: SWC I/O, sink append, `TSModel`, `TSSimulator`, events, viz
`simulations/`	One folder per spine plus shared axon-study code
`notebooks/tutorial/`	Numbered walkthrough (one notebook per package concept: mesh → simulate → k-matrix / viz)
`notebooks/misc/`	Extra demos (spiny dendrite, neurosignature, raw Arbor primer)
`archive/`	Historical scripts and morphologies

Data layout¶

Put new model files in data/ using the TS{id} stem (e.g. TS1, TS48). Pixel files are EM voxels; micron files are the same geometry scaled by 0.005 µm/pixel (5 nm/pixel) at conversion time (--um-per-px on append_sink.py / active_zones_from_nff.py). Simulations should load micron SWCs and synpts.

Path	What belongs there
`data/mesh/`	Closed triangle meshes: `TS{id}.obj`. Full cell: `cell_wrapped_simplified.obj` (neckpoints)
`data/skeletons/`	Mean-curvature skeletons: `TS{id}.polylines.txt`
`data/swc/pixels/`	Fitted cables `TS{id}.swc` and sink models `TS{id}_wsink_r{R}um.swc`
`data/swc/microns/`	Same SWCs in µm — use these for simulation
`data/nff/`	Active-zone NFF markers `TS{id}_AZ.nff` (pixel coords)
`data/pointsets/pixels/`	Neckpoints `TS{id}_neckpoint.txt`, AZ XYZ `TS{id}_AZ.txt`
`data/pointsets/microns/`	Neckpoints plus synapse sites `TS{id}_synpts.txt`
`data/ts_axons/`	Axon→synapse maps `ts{id}_axons.txt` (1-based synapse indices)
`data/events/`	Demo event streams

Precomputed experiment morphologies already in data/ are data/swc/microns/TS{id}_wsink_r10um.swc (also r5um). Older TS*_s50_* / TS*_s200_* names live under archive/data/swc/.

To add a spine, drop TS{id}.obj in data/mesh/ (and optionally TS{id}_AZ.nff in data/nff/), then run the morphology pipeline. From IMOD: From IMOD to mesh. Existing meshes: TS1, TS2, TS3, TS4, TS21, TS24, TS48, TS67, TS76.