--- 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.