What this is
A code-grounded 3D anatomy of the C. elegans Tier4 whole-cell electrical substrate — the Brian2 model that puts CeNGEN-scaled ion channels, ligand-gated receptors, pumps, transporters, gap junctions, and single-pool ion dynamics onto 300 cells at their real morphological positions.
The design principle is honesty about completeness. Every structure is rendered with a status read straight from the assemble path:
- ON — integrated and active on the default assemble path
- default-OFF — integrated but a build flag is needed to flip it on
- ORPHANED — module exists / registers but is not on the assemble path
- NOT INTEGRATED — known-missing structure, diagnosed by audit
Nothing is illustrative unless it is explicitly flagged as such. The voltage colour and Ca²⁺ glow are driven by a real Brian2 trajectory emitted from the model, not hand-authored.
How to read it
Two views share one data bundle:
- Hero cell — AVA at full molecular detail: per-segment morphology (soma / axon / dendrite) plus its channel, receptor, and pump complement with per-channel gbar (CeNGEN TPM × γ × C_global).
- Network — 300 cells at their real µm soma positions, wired by the actual connectome (chemical + gap-junction edges), coloured live by the substrate’s own voltage trajectory.
The completeness panel on the right is the audit, rendered: status chips
filter the inventory, and every structure carries its file:line provenance.
Known-missing structure
Three structures are deliberately marked NOT INTEGRATED and cited to the
substrate audits (docs/SUBSTRATE_LIMITER_AUDIT_2026-06-19.md,
docs/K_PARTITION_DISCRIMINATOR_VERDICT.md):
- Spatial glial K-siphon — current glia is a K sink only, with no return path to the cell interior.
- Multi-compartment cleft ↔ reservoir with a grounded K_in source (the local-nkcc route was ruled out).
- Grounded γ_NCA — a regenerative inward N-shape with a first-principles conductance rather than a stability-floor placeholder.
These are the foundation gaps the substrate work is converging on, shown in red rather than hidden.