| --- |
| language: |
| - en |
| - zh |
| tags: |
| - neuroscience |
| - connectomics |
| - reproducibility |
| --- |
| # NeuronMimic reusable data (updated 2026-11-01) |
|
|
| This dataset contains full KC anatomy handoffs, earlier compact source-bound tables, |
| and a deterministic passive cable fixture for reproducing NeuronMimic baselines. It deliberately does |
| not contain restricted raw MaleCNS/FlyWire connectome downloads or any claim of |
| biological validation. |
|
|
| The current structure/dynamics requirement matrix is maintained in the parent |
| BioFly project at `artifacts/wu_20261030_science_gate/WU_REQUIREMENTS_STATUS_20261030.md`. |
|
|
|
|
| ## Full KC structure package |
|
|
| [`structure_handoff_v1/`](structure_handoff_v1/README.md) adds complete KC-scope |
| skeleton/contact data: FlyWire5,177 cells/1,881,678 incident synapses and MaleCNS |
| v1.0 4,064 cells/4,027,967 incident synapses. Both pre/post coordinates, source |
| annotations and versioned group memberships are retained. FlyWire also includes |
| contact-to-branch mappings and whole-brain soma/region context. MaleCNS supplies |
| original v1.0 coarse SWC, detector confidence and site-level transmitter predictions. |
| This does not include whole-brain EM volumes or non-KC partner skeletons. |
|
|
| Query/export code is an addition to the existing |
| [NeuronMimic repository](https://github.com/ydchen0806/neuronmimic/blob/master/docs/STRUCTURE_HANDOFF.md). |
| Read COORDINATES.json before overlaying any points. Groups remain structural |
| candidates or official type groups, not confirmed biological functional units. |
|
|
| ## Latest: P1D-v3 / bilateral geometry |
|
|
| - `p1d_v3/`: original focused left-ap1 experiment, regional-tree tables, frozen |
| 18-cell historical identities, weak-edge controls, failed matched routing, |
| MaleCNS/BANC source QC and all negative results. Full rerun requires original |
| BioFly raw inputs; the source-mode scripts are archived on GitHub. |
| - `p1d_v3_bilateral/`: left148/right133 complete ap1 cohorts, all directed pairs, |
| exact soma-block assignments, design matrices, model weights, predictions, |
| seed/fold contrasts, source hashes and figures. Supports a tested standalone |
| model refit/evaluation from these inputs. Raw geometry extraction is not rerun. |
| - [Replay instructions and scientific scope](https://github.com/ydchen0806/neuronmimic/blob/master/docs/P1D_REPRODUCE.md). |
| - [Source code snapshot](https://github.com/ydchen0806/neuronmimic/tree/master/research/p1d_source_snapshot). |
|
|
| Regional tree proximity improved predictions in all10 soma-block folds and both |
| cross-side directions. This is retrospective evidence within one FlyWire animal, |
| not external replication or functional validation. Stable8 remains8/965; no new |
| functional unit is validated. The 18-cell candidate's matched controls failed; |
| its nested label increment interval includes zero. Every unfavorable result is retained. |
|
|
| Later MaleCNS QC found all31,355 annotation-missing endpoints in the same-release |
| original neurotransmitter table. The annotation gap persists; a version mismatch |
| was not established. Historical P0/P1 receipts are unchanged. BANC root_888 is the |
| frozen snapshot key; current root aliases and unknown side labels remain explicit. |
| |
| `SHA256SUMS.json` covers released files; all FlyWire/root IDs are strings in model |
| input/output tables. Source-data/model inference evidence labels remain separate |
| from the synthetic NeuronMimic Teacher results. No new dynamics were run here. |
| |
| ## Contents |
| |
| - `physics_teacher/`: historical fixture archive. Its old evaluation metrics are |
| **INVALIDATED**; use `p0_corrected_20261030/fixture_v2/` instead. |
| - `malecns/`: historical normalized source-bound aggregate tables. Endpoint annotation |
| joins are **BLOCKED**: 31,355 edge endpoint IDs do not match even the full source id |
| column. These tables are not a validated complete CNS or simulation-ready network. |
| - `flywire_kc_atlas/`: compact all-5,177-cell structural profiles and the |
| source-bound 20-unit entry registry. This is single-connectome structural |
| evidence, not independent biological replication. |
| - `provenance/`: protocol and source manifests. |
|
|
| ## Links |
|
|
| - Code: https://github.com/ydchen0806/neuronmimic |
| - Parent analysis repository: https://github.com/ydchen0806/bio_fly_cyber_lateralization |
| - Dataset: https://huggingface.co/datasets/cyd0806/neuronmimic-data |
| |
| The GitHub repository documents the code and the exact analysis boundaries; |
| this dataset provides the compact inputs and receipts. Raw data remain at their |
| original public repositories and are not mirrored here. |
| |
| ## Status and limits |
| |
| `FIXTURE_TEST_ONLY` is synthetic/passive-cable testing. `VERIFIED_REAL_DATA` |
| means the local source table was hashed and schema-checked. `BLOCKED_MISSING_DATA` |
| means the data required for a real multi-compartment biological calibration are |
| not present, especially contact coordinates, branch IDs, conductance values, |
| and held-out physiological recordings. |
| |
| |
| ## Corrected P0 release |
| |
| Use `p0_corrected_20261030/fixture_v2/` for reproducible Teacher data, four model baselines, and corrected results. Historical metric files are invalidated; see `HISTORICAL_METRICS_INVALIDATED.md`. All cable experiments are FIXTURE_TEST_ONLY. Code and scientific metric tests: https://github.com/ydchen0806/neuronmimic . Known-equation PhysicsOnly is more accurate than the trained Students; no biological or speed-accuracy advantage is established. |
|
|
| ## P1-v2.2 geometry and structure release |
|
|
| `p1_v2_fine_types/` contains the 5,177-cell identity registry, CM/SU crosswalk, |
| all directed pair split assignments, contact-free tree descriptors, six genuine spatial |
| fusion ablations, full-parent child membership, model predictions, figures and audit receipts. |
| See its P1_REPORT.md for conclusions and limits. The 18-cell left-ap1 residual subset |
| is exploratory, not a validated functional unit. Original stable8 remains unchanged. |
| |
| Reproduction instructions: https://github.com/ydchen0806/neuronmimic/blob/master/docs/P1_REPRODUCE.md . |
| The full soma distance matrix is exactly regenerated by the script rather than downloaded. |
| Raw-source audits and geometry extraction are not rerun by the compact replay; their |
| original hashes and receipts are provided. Do not treat imported audit receipts as a fresh audit. |
| Upstream data retain their original source terms; this release does not grant a new license |
| for the original connectomes. No independent physiology or wet-lab calibration data are included. |
|
|
