Document WormTrack-Verify alpha scope and pinned source inventory

Development pilot in the existing dataset repository. Source-specific licensing; all 118 WormID assets and 36 tracking acquisitions mapped. Full release gates remain open. No existing data is deleted.

README.md

@@ -1,3 +1,145 @@
 ---
-license: mit
+pretty_name: WormTrack-Verify (development pilot)
+license: other
+license_name: source-specific-data-licenses
+license_link: https://huggingface.co/datasets/pytc/trackingBench/blob/main/docs/LICENSING.md
+language:
+- en
+tags:
+- biology
+- microscopy
+- cell-tracking
+- c-elegans
+- verification
+- 3d
+size_categories:
+- 100K<n<1M
+configs:
+- config_name: recordings
+  data_files:
+  - split: development
+    path: data/recordings/**/*.parquet
+- config_name: detections
+  data_files:
+  - split: development
+    path: data/detections/**/*.parquet
+- config_name: tracks
+  data_files:
+  - split: development
+    path: data/tracks/**/*.parquet
+- config_name: posture
+  data_files:
+  - split: development
+    path: data/posture/**/*.parquet
+- config_name: anatomy
+  data_files:
+  - split: development
+    path: data/anatomy/**/*.parquet
+- config_name: perturbations
+  data_files:
+  - split: development
+    path: data/perturbations/**/*.parquet
+- config_name: verification
+  data_files:
+  - split: development
+    path: data/verification/**/*.parquet
 ---
+
+# WormTrack-Verify — v0.1.0-alpha.1
+
+A public **development pilot** for testing anatomical verification of anonymous neuron trajectories in *C. elegans*. This is usable data and executable evaluation machinery. **The full initial benchmark and release gates A/B/C are not complete.** There is no frozen held-out test set in this release.
+
+## Motivation and scientific hypothesis
+
+Tracking errors contaminate neural activity measurements. Eutely supports persistent neuronal populations in adult hermaphrodites; it does not imply 302 visible detections or immutable positions. The hypothesis is that an independently estimated, restricted deformation model can predict neuronal positions with uncertainty sufficiently smaller than local inter-neuron spacing to expose identity errors. Four planar eigenworm modes do not establish a four-dimensional model of 3D internal tissue motion. The benchmark must allow this hypothesis to fail.
+
+## Inventory and actual included material
+
+| Component | Observed count / status |
+|---|---|
+| Recording-level registry | 264 |
+| Original WormID source assets | 118 |
+| ASCENT human-corrected observations | 105599 |
+| ASCENT anonymous tracks | 96 |
+| Hosted imaging excerpts | 44 volumes across four recordings |
+| Reference point clouds | 2 |
+| Independent behavior summaries | 6,400 samples; one SF acquisition |
+| Measured centerlines / eigenworm coefficients | 0; unavailable |
+| Frozen train/validation/test | Not released; development only |
+
+The five standardized tracking tables cover ASCENT, ZephIR, a NeRVE-derived recording redistributed in ZephIR, Targettrack, and a 16-frame WormID EY excerpt. Only ASCENT is currently eligible for the trusted tracking and corruption pilot. ZephIR scorer codes and Targettrack mask provenance are retained; unresolved annotations are **unknown**, not ground truth. The archive also contains a mouse experiment, which is excluded.
+
+All 36 WormID tracking acquisitions and 38 excluded SF recordings are mapped at inventory level. NP/HL structural recordings are not presented as dynamic tracking. [Assembly report](docs/ASSEMBLY_REPORT.md) distinguishes inventoried assets, inspected data, validated tables, and trusted correspondence labels. [Source audit](docs/SOURCE_AUDIT.md) records blocked resources.
+
+## Tracking versus verification
+
+`tracking_gt` isolates association on fixed source-supported objects and preserves the original WormID reference-frame protocol for future reproduction. `anatomical_verification` tests labeled identity corruptions. `anatomical_consistency` contains consistency diagnostics with incomplete labels. These protocols are distinct from train/validation/test partitions.
+
+The pilot provides two untrained oracle association baselines (Euclidean nearest neighbor and Hungarian assignment), six controlled error types, clean controls, and a fixed-reference-distance consistency baseline. Its threshold is a declared **5 micrometers**, chosen as a development demonstration, not calibrated to a guaranteed false-acceptance target. Reported results are descriptive development diagnostics. No full-image tracking, HOTA/IDF1, independent deformation fitting, or cross-laboratory generalization claim is made.
+
+## Data formats and coordinates
+
+Structured data are recording-partitioned Parquet. Original annotation HDF5 files and a small original structural NWB are retained where allowed. Imaging pilots use lossless chunked HDF5 with one CZYX dataset per hosted frame; source intensities are unnormalized. The logical volume axis order is TCZYX. This HDF5 representation is not advertised as OME-Zarr/NGFF.
+
+Point coordinates are named XYZ. Native voxel coordinates and transforms are preserved. Physical fields are null when calibration is unavailable. ASCENT spacing is (0.243, 0.243, 1.5) micrometers in XYZ, from the source record. WormID spacing comes from the inspected NWB. ZephIR normalized coordinates are converted through the source pixel-center convention; 17 out-of-bounds observations remain present with `validity=false`. Targettrack centroids remain in its source-processed image coordinates with an unresolved transform direction.
+
+## Ground-truth provenance
+
+ASCENT tracks were initialized with ZephIR and manually proofread/corrected by the source authors. This is **human-corrected algorithm output**, not independent de novo dense annotation. Source predictions live separately under `evaluation/source_predictions/` because their detections differ from oracle objects. Anonymous track IDs are sufficient; neuronal names are optional and are not used by the verifier.
+
+The WormID EY inspected source has 962 image frames and 961 segmentation frames. Only the available observations are published. No coordinate clamping, identity interpolation, or missing annotation fabrication is performed.
+
+## Anatomy and posture
+
+ASCENT's proofread first frame and a same-animal NeuroPAL structural cloud are included. Neither is a universal anatomical atlas. Unknown reference uncertainty is null. SF measured behavior summaries retain source timestamps and empty/unknown units. They are not centerlines, body coordinates, or a validated 3D deformation map. The client raises an explicit missing-component error for unsupported posture or imaging frames.
+
+## Splits and duplicates
+
+All included examples are assigned to `development`; train/validation/test are empty and no test performance is claimed. Original WormID fold values are preserved verbatim as a reproduction reference, not interpreted as this benchmark's partitions. The original split CSV has 120 rows and 118 unique filenames; two repeated structural entries are preserved in that reference table.
+
+Shared DANDI subject identifiers, particularly SK1 and DANDI 001623, are flagged as possible overlaps. Common animals/acquisitions and derivatives must stay together; unresolved overlap cannot be used to establish split disjointness. The NeRVE excerpt in ZephIR is not counted as an additional independent source acquisition. Test labels, when frozen in a later release, cannot calibrate corruptions or verification thresholds.
+
+## Access examples
+
+```python
+from datasets import load_dataset
+# Pin a commit SHA or the alpha tag after publication.
+registry = load_dataset("pytc/trackingBench", "recordings", revision="v0.1.0-alpha.1")
+tracks = load_dataset("pytc/trackingBench", "tracks", revision="v0.1.0-alpha.1", streaming=True)
+corruptions = load_dataset("pytc/trackingBench", "perturbations", revision="v0.1.0-alpha.1", streaming=True)
+print(next(iter(tracks["development"])))
+```
+
+The named configurations are `recordings`, `detections`, `tracks`, `posture`, `anatomy`, `perturbations`, and `verification`. The `posture` configuration currently contains **behavior summaries**, with explicit `component_type`, and zero measured centerlines. Loading tables does not download microscopy volumes. The recording registry includes inventory-only acquisitions; `hosted_tracks` and `hosted_volume` distinguish available components.
+
+For the bundled selective Python client, install this repository's small code subset:
+
+```python
+from huggingface_hub import snapshot_download
+import subprocess, sys
+code = snapshot_download("pytc/trackingBench", repo_type="dataset", revision="v0.1.0-alpha.1",
+                         allow_patterns=["src/**", "pyproject.toml", "README.md", "requirements.lock.txt"])
+subprocess.check_call([sys.executable, "-m", "pip", "install", code])
+from cell_tracking.data.wormtrack_verify import BenchmarkClient
+client = BenchmarkClient(revision="v0.1.0-alpha.1")
+annotations = client.load_tracks("ascent-opterra")
+volume = client.load_volume("ascent-opterra", frame=0)  # Small hosted excerpt only; CZYX.
+```
+
+Use [the executable pilot](examples/pilot.py) to reproduce the corruption and metric demonstration. Files larger than the client's 128 MiB budget require an explicit increased budget; no function silently downloads the benchmark or a multi-GB original movie. Original assets resolve through immutable DANDI asset IDs and versioned Zenodo records in `metadata/upstream_assets.json`. External assets are not Hub-hosted movies.
+
+## Licensing and attribution
+
+The original empty repository displayed MIT. That does not license third-party data. Included DANDI and Zenodo data are CC BY 4.0 per their release metadata. Benchmark helper code is MIT; source data retain their own licenses and attribution. Resources with unresolved redistribution rights remain references only. See [per-source licensing](docs/LICENSING.md), [catalog](docs/DATASET_CATALOG.md), and [citations](docs/CITATIONS.md).
+
+## Limitations and biases
+
+This pilot has only one trusted proofread tracking specimen, no measured centerlines, no independently calibrated deformation uncertainty, and no held-out evaluation. Unknown scorer codes are not promoted to manual ground truth. Fixed-reference residuals include legitimate tissue motion and are permutation-sensitive only because reference correspondences remain fixed. A static unordered point cloud cannot detect identity swaps. Acceptance by a geometric heuristic is not proof of biological identity.
+
+Coverage and selective risk use the full declared observation population; rejecting everything yields zero coverage. Sources differ in optics, visibility, annotation construction, and acquisition restrictions. The 302-neuron assumption is not universal across sex/stage and is never used to force observed counts.
+
+## Release history
+
+- `v0.1.0-alpha.1`: development pilot; source inventory, five standardized tracking tables, imaging excerpts, two reference clouds, measured behavior summaries, controlled corruptions, and reference baseline outputs. Full initial release gates remain open.
+
+Each release has a SHA256 assembly manifest, an upstream asset manifest, dependency pins, and machine-readable validation results. No model weights or externally pretrained models are used by these pilot baselines.

anatomy/README.md

@@ -0,0 +1 @@
+Reference point-cloud Parquet tables live in data/anatomy; no licensed population atlas has been redistributed.

docs/ASSEMBLY_REPORT.md

@@ -0,0 +1,19 @@
+# Assembly report — 0.1.0-alpha.1
+
+Generated from inspected assets, not publication counts.
+
+| Recording | Valid observations | Observed frames | Track IDs | Provenance |
+|---|---:|---:|---:|---|
+| ascent-opterra | 105599 | 1100 | 96 | {'human_corrected': 105599} |
+| zephir-zm9624 | 188663 | 1060 | 178 | {'unknown': 188663} |
+| nerve-al-w1-via-zephir | 121344 | 1536 | 79 | {'unknown': 119019, 'algorithm_prediction': 2325} |
+| targettrack-epfl10 | 1951 | 147 | 15 | {'unknown': 1951} |
+| dandi-000541-sub-20190924-01 | 2896 | 16 | 181 | {'unknown': 2896} |
+
+Registry: 264 source recordings; original WormID: 118 assets. These are not independent-animal counts. Imaging excerpts: 44 frames; references: 2 clouds; measured centerlines: 0. Exact verified observation/checkpoint coverage: ASCENT 105,599 human-corrected observations over 1,100 frames, 96 tracks. Other labels are not promoted to verified checkpoints.
+
+Release gates: {"A": "partial: full non-DANDI inventories pending", "B": "partial: independent moving-worm GT and centerline pending", "C": "not_passed: all P0 ingestion and held-out evaluation pending"}
+
+No full initial release gate is claimed. No test results, source-wide GT completeness, or cross-laboratory anatomical verification are claimed. Pilot diagnostic outputs and two oracle baseline predictions are in `evaluation/`.
+
+Source snapshots and asset digests pin upstream versions. Local workspace used `/tmp/wormtrack-verify-assembly` because the project filesystem quota rejected writes; public loading does not depend on that workspace.

docs/BENCHMARK_SPEC.md

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+# Benchmark specification — development alpha
+
+Mission: tracking verification with anonymous persistent identities, independent anatomical evidence, explicit uncertainty, and the possibility of falsifying the deformation hypothesis. Auto-identification, calcium inference, and new tracking architectures are outside this assembly.
+
+Protocols: `tracking_gt`, `anatomical_verification`, `anatomical_consistency`. All current usable examples are development data, with empty train/validation/test partitions. Original WormID folds are preservation/reproduction metadata only. Future frozen partitions must be at physical-animal/provenance-group level and quarantine unresolved overlaps. Fit normalization, motion bounds and thresholds on training/calibration animals only. Never tune using hidden test labels.
+
+Oracle association uses fixed source detections. The pilot permits one recording-wide identity alignment through maximum overlap; never independent per-frame rematching. `correct_observation_rate` is globally aligned correct observed detections divided by all trusted reference observations. Missing predictions count against the fixed denominator. `identity_switches` counts changes in predicted identity along an observed reference trajectory. `fragmentations` counts identity runs or reappearance after missing predictions beyond the first run. These diagnostics are explicitly defined here, not canonical HOTA/IDF1 substitutes. Extra predicted observations are counted separately. Raw-image tracking is not evaluated in this alpha.
+
+Corruptions: one declared development seed 20261007; first anchor frame remains clean; start frame 300; single-frame swap, persistent swap, swap-and-recovery, nearby swap, fragmentation, and dropout. Recovery/nearby interval ends at 700; other persistent intervals end with the recording. Generic pairs use the declared random seed; the nearby-swap pair is chosen by nearest physical reference separation, on development data only. Preserve all original coordinates/detections/images; swaps change identity assignments, fragmentation creates a new ID, dropout toggles observation validity. Per-row error labels compare against the anchor identity, whereas the global-alignment association diagnostic optimizes one full-trajectory naming. Clean control rows are included and explicitly tagged.
+
+The pilot fixed-reference-distance verifier measures displacement in micrometers from the trusted same-animal first frame. It uses no candidate-specific refitting and assigns unsupported fragment identities to abstention. It also penalizes real tissue motion and is therefore a consistency diagnostic, not an independent deformation certificate. Threshold = 5 um declared as a demonstration; it is not a calibrated false-acceptance guarantee.
+
+Observation-level error AUROC/AUPRC use scikit-learn; prevalence is reported. Certified coverage = accepted observations / full fixed population. Selective risk = accepted labeled errors / all accepted observations (undefined if nothing accepted). False-certification rate = accepted labeled errors / all labeled errors (undefined without errors). Correct certified coverage = accepted correct observations / full population. Acceptance requires a finite score <= threshold. Risk-coverage ties enter together; unsupported observations retain their denominator and abstain. No independent-frame confidence intervals or pooled generalization estimates are reported for one specimen.
+
+Deferred full-benchmark work: source-provided dense/sparse GT audit across moving worms, physical uncertainty calibration, independent centerline/roll evidence, deformation prediction versus local spacing, additional corruption modes (smooth drift, duplicate identities and long-gap reassociation), canonical HOTA/IDF1 adapters with reference parity, cross-animal/lab/deformation splits, confidence intervals by experimental unit, and calibrated feasible-matching uniqueness. Eutely does not resolve swaps; unordered anatomy is permutation invariant; smooth registration fitted to candidate tracks cannot certify itself.

docs/CITATIONS.md

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+# Source citations and immutable releases
+
+All source authors retain attribution. Complete author lists are in the linked official release metadata; this file does not invent missing bibliographic fields.
+
+- WormID/WormND benchmark: https://github.com/focolab/WormND/tree/0c74e9ddffee138cfc6330ab65c0e690e8e199dd and https://doi.org/10.1101/2025.01.06.631621 . Cohort-specific DANDI releases and attribution are in `metadata/sources.json` and `metadata/dandi_asset_provenance.json`.
+- Han et al., ASCENT: https://doi.org/10.1101/2025.07.23.666425 ; data https://doi.org/10.5281/zenodo.17561700 .
+- Torkashvand, Ryu, Venkatachalam: ZephIR data https://doi.org/10.5281/zenodo.10818810 ; code https://github.com/venkatachalamlab/ZephIR/tree/2842342b039c3aed8dab3b96b3ac0708e950e5b7 .
+- Nguyen et al. (2017), Automatically tracking neurons in a moving and deforming brain: https://doi.org/10.1371/journal.pcbi.1005517 ; original data https://doi.org/10.21227/H2901H .
+- Park et al., Targettrack: https://doi.org/10.1038/s41592-023-02096-3 ; data https://doi.org/10.5281/zenodo.10008744 .
+- Wu et al., CeNDeR: https://doi.org/10.1371/journal.pcbi.1010594 ; https://github.com/Wenlab/CeNDeR ; https://osf.io/v2b5n/ .
+- BrainAlignNet / ANTSUN 2.0: https://doi.org/10.7910/DVN/8UE0H9 ; metadata access incomplete, precise publication citation verify.
+- DANDI 001623 and 000981: pinned versions and official attribution in `metadata/sources.json` and `metadata/dandi_asset_provenance.json`.
+- Skuhersky anatomical atlas: https://github.com/bluevex/elegans-atlas/tree/65967d8abc38027ca69cdac18024052d168b8575 ; https://doi.org/10.1101/2021.06.09.447813 .
+- NeuroPAL, Yemini et al.: https://doi.org/10.1016/j.cell.2020.12.012 ; https://github.com/openworm/NeuroPAL/tree/85783437bea1112c1e4b1cacaac3e5337e7ce4a4 .
+- Statistical atlas: https://github.com/amin-nejat/stat-atlas/tree/29652ab83b6ff870b71a5969e25328fa8e488c90 ; precise paper citation verify.
+- OpenWorm Movement Database: https://movement.openworm.org/ ; access unavailable in audit.
+- Stephens, Johnson-Kerner, Bialek, Ryu (2008), Dimensionality and Dynamics in the Behavior of C. elegans: https://doi.org/10.1371/journal.pcbi.1000028 .

docs/DATASET_CATALOG.md

@@ -0,0 +1,24 @@
+# Dataset catalog (observed release metadata)
+
+| Source | Priority | Pinned version | Status | License | Bytes inventoried |
+|---|---|---|---|---|---|
+| [EY](https://dandiarchive.org/dandiset/000541/0.241009.1457) | P0 | 0.241009.1457 | inventoried_assets_not_bulk_ingested | ['spdx:CC-BY-4.0'] | 30525162874 |
+| [KK](https://dandiarchive.org/dandiset/000692/0.240402.2118) | P0 | 0.240402.2118 | inventoried_assets_not_bulk_ingested | ['spdx:CC-BY-4.0'] | 80537036658 |
+| [SK1](https://dandiarchive.org/dandiset/000565/0.241009.1504) | P0 | 0.241009.1504 | inventoried_assets_not_bulk_ingested | ['spdx:CC-BY-4.0'] | 46250221065 |
+| [SK2](https://dandiarchive.org/dandiset/000472/0.241009.1502) | P0 | 0.241009.1502 | inventoried_assets_not_bulk_ingested | ['spdx:CC-BY-4.0'] | 18442605394 |
+| [SF](https://dandiarchive.org/dandiset/000776/0.241009.1509) | P0 | 0.241009.1509 | inventoried_assets_not_bulk_ingested | ['spdx:CC-BY-4.0'] | 1011743300552 |
+| [NP](https://dandiarchive.org/dandiset/000715/0.241009.1514) | P0 | 0.241009.1514 | inventoried_assets_not_bulk_ingested | ['spdx:CC-BY-4.0'] | 835049434 |
+| [HL](https://dandiarchive.org/dandiset/000714/0.241009.1516) | P0 | 0.241009.1516 | inventoried_assets_not_bulk_ingested | ['spdx:CC-BY-4.0'] | 478075700 |
+| [Dunn](https://dandiarchive.org/dandiset/001623/0.251015.0312) | P1 | 0.251015.0312 | inventoried_assets_not_bulk_ingested | ['spdx:CC-BY-4.0'] | 774224141637 |
+| [Chemosensory](https://dandiarchive.org/dandiset/000981/0.260910.1747) | P1 | 0.260910.1747 | inventoried_assets_not_bulk_ingested | ['spdx:CC-BY-4.0'] | 82267067651 |
+| [ASCENT](https://zenodo.org/records/17561700) | P1 | 10.5281/zenodo.17561700 | pilot_assets_and_tables | cc-by-4.0 | 6253241706 |
+| [ZephIR](https://zenodo.org/records/10818810) | P0 | 10.5281/zenodo.10818810 | pilot_assets_and_tables | cc-by-4.0 | 14869755504 |
+| [Targettrack](https://zenodo.org/records/10008744) | P1 | 10.5281/zenodo.10008744 | pilot_assets_and_tables | cc-by-4.0 | 24089089928 |
+| [NeRVE original release](https://doi.org/10.21227/H2901H) | P0 | verify | one_annotation_recording_via_ZephIR; original_inventory_pending | verify | unknown |
+| [CeNDeR C1-C3](https://osf.io/v2b5n/) | P0 | verify | blocked_data_license_unstated; OSF_storage_empty; linked_Google_Drive_API_404 | verify | unknown |
+| [BrainAlignNet / ANTSUN 2.0](https://doi.org/10.7910/DVN/8UE0H9) | P1 | verify | Dataverse_API_unavailable; license_and_overlap_pending | verify | unknown |
+| [Skuhersky 3D anatomical atlas](https://github.com/bluevex/elegans-atlas) | P2 | verify | data_license_unresolved; external_reference_only | verify | unknown |
+| [NeuroPAL canonical positions](https://github.com/openworm/NeuroPAL) | P2 | verify | shared_Skuhersky_CSV; data_license_unresolved | verify | unknown |
+| [Statistical anatomical atlas](https://github.com/amin-nejat/stat-atlas) | P2 | verify | data_license_unresolved; external_reference_only | verify | unknown |
+| [OpenWorm Movement Database](https://movement.openworm.org/) | P2 | verify | DNS_resolution_failed; license_and_assets_unresolved | verify | unknown |
+| [Stephens et al. 2008](https://doi.org/10.1371/journal.pcbi.1000028) | P2 | verify | paper_audited; reusable_basis_asset_not_ingested | verify | unknown |

docs/DATA_CARD.md

@@ -0,0 +1,99 @@
+
+# WormTrack-Verify — v0.1.0-alpha.1
+
+A public **development pilot** for testing anatomical verification of anonymous neuron trajectories in *C. elegans*. This is usable data and executable evaluation machinery. **The full initial benchmark and release gates A/B/C are not complete.** There is no frozen held-out test set in this release.
+
+## Motivation and scientific hypothesis
+
+Tracking errors contaminate neural activity measurements. Eutely supports persistent neuronal populations in adult hermaphrodites; it does not imply 302 visible detections or immutable positions. The hypothesis is that an independently estimated, restricted deformation model can predict neuronal positions with uncertainty sufficiently smaller than local inter-neuron spacing to expose identity errors. Four planar eigenworm modes do not establish a four-dimensional model of 3D internal tissue motion. The benchmark must allow this hypothesis to fail.
+
+## Inventory and actual included material
+
+| Component | Observed count / status |
+|---|---|
+| Recording-level registry | 264 |
+| Original WormID source assets | 118 |
+| ASCENT human-corrected observations | 105599 |
+| ASCENT anonymous tracks | 96 |
+| Hosted imaging excerpts | 44 volumes across four recordings |
+| Reference point clouds | 2 |
+| Independent behavior summaries | 6,400 samples; one SF acquisition |
+| Measured centerlines / eigenworm coefficients | 0; unavailable |
+| Frozen train/validation/test | Not released; development only |
+
+The five standardized tracking tables cover ASCENT, ZephIR, a NeRVE-derived recording redistributed in ZephIR, Targettrack, and a 16-frame WormID EY excerpt. Only ASCENT is currently eligible for the trusted tracking and corruption pilot. ZephIR scorer codes and Targettrack mask provenance are retained; unresolved annotations are **unknown**, not ground truth. The archive also contains a mouse experiment, which is excluded.
+
+All 36 WormID tracking acquisitions and 38 excluded SF recordings are mapped at inventory level. NP/HL structural recordings are not presented as dynamic tracking. [Assembly report](docs/ASSEMBLY_REPORT.md) distinguishes inventoried assets, inspected data, validated tables, and trusted correspondence labels. [Source audit](docs/SOURCE_AUDIT.md) records blocked resources.
+
+## Tracking versus verification
+
+`tracking_gt` isolates association on fixed source-supported objects and preserves the original WormID reference-frame protocol for future reproduction. `anatomical_verification` tests labeled identity corruptions. `anatomical_consistency` contains consistency diagnostics with incomplete labels. These protocols are distinct from train/validation/test partitions.
+
+The pilot provides two untrained oracle association baselines (Euclidean nearest neighbor and Hungarian assignment), six controlled error types, clean controls, and a fixed-reference-distance consistency baseline. Its threshold is a declared **5 micrometers**, chosen as a development demonstration, not calibrated to a guaranteed false-acceptance target. Reported results are descriptive development diagnostics. No full-image tracking, HOTA/IDF1, independent deformation fitting, or cross-laboratory generalization claim is made.
+
+## Data formats and coordinates
+
+Structured data are recording-partitioned Parquet. Original annotation HDF5 files and a small original structural NWB are retained where allowed. Imaging pilots use lossless chunked HDF5 with one CZYX dataset per hosted frame; source intensities are unnormalized. The logical volume axis order is TCZYX. This HDF5 representation is not advertised as OME-Zarr/NGFF.
+
+Point coordinates are named XYZ. Native voxel coordinates and transforms are preserved. Physical fields are null when calibration is unavailable. ASCENT spacing is (0.243, 0.243, 1.5) micrometers in XYZ, from the source record. WormID spacing comes from the inspected NWB. ZephIR normalized coordinates are converted through the source pixel-center convention; 17 out-of-bounds observations remain present with `validity=false`. Targettrack centroids remain in its source-processed image coordinates with an unresolved transform direction.
+
+## Ground-truth provenance
+
+ASCENT tracks were initialized with ZephIR and manually proofread/corrected by the source authors. This is **human-corrected algorithm output**, not independent de novo dense annotation. Source predictions live separately under `evaluation/source_predictions/` because their detections differ from oracle objects. Anonymous track IDs are sufficient; neuronal names are optional and are not used by the verifier.
+
+The WormID EY inspected source has 962 image frames and 961 segmentation frames. Only the available observations are published. No coordinate clamping, identity interpolation, or missing annotation fabrication is performed.
+
+## Anatomy and posture
+
+ASCENT's proofread first frame and a same-animal NeuroPAL structural cloud are included. Neither is a universal anatomical atlas. Unknown reference uncertainty is null. SF measured behavior summaries retain source timestamps and empty/unknown units. They are not centerlines, body coordinates, or a validated 3D deformation map. The client raises an explicit missing-component error for unsupported posture or imaging frames.
+
+## Splits and duplicates
+
+All included examples are assigned to `development`; train/validation/test are empty and no test performance is claimed. Original WormID fold values are preserved verbatim as a reproduction reference, not interpreted as this benchmark's partitions. The original split CSV has 120 rows and 118 unique filenames; two repeated structural entries are preserved in that reference table.
+
+Shared DANDI subject identifiers, particularly SK1 and DANDI 001623, are flagged as possible overlaps. Common animals/acquisitions and derivatives must stay together; unresolved overlap cannot be used to establish split disjointness. The NeRVE excerpt in ZephIR is not counted as an additional independent source acquisition. Test labels, when frozen in a later release, cannot calibrate corruptions or verification thresholds.
+
+## Access examples
+
+```python
+from datasets import load_dataset
+# Pin a commit SHA or the alpha tag after publication.
+registry = load_dataset("pytc/trackingBench", "recordings", revision="v0.1.0-alpha.1")
+tracks = load_dataset("pytc/trackingBench", "tracks", revision="v0.1.0-alpha.1", streaming=True)
+corruptions = load_dataset("pytc/trackingBench", "perturbations", revision="v0.1.0-alpha.1", streaming=True)
+print(next(iter(tracks["development"])))
+```
+
+The named configurations are `recordings`, `detections`, `tracks`, `posture`, `anatomy`, `perturbations`, and `verification`. The `posture` configuration currently contains **behavior summaries**, with explicit `component_type`, and zero measured centerlines. Loading tables does not download microscopy volumes. The recording registry includes inventory-only acquisitions; `hosted_tracks` and `hosted_volume` distinguish available components.
+
+For the bundled selective Python client, install this repository's small code subset:
+
+```python
+from huggingface_hub import snapshot_download
+import subprocess, sys
+code = snapshot_download("pytc/trackingBench", repo_type="dataset", revision="v0.1.0-alpha.1",
+                         allow_patterns=["src/**", "pyproject.toml", "README.md", "requirements.lock.txt"])
+subprocess.check_call([sys.executable, "-m", "pip", "install", code])
+from cell_tracking.data.wormtrack_verify import BenchmarkClient
+client = BenchmarkClient(revision="v0.1.0-alpha.1")
+annotations = client.load_tracks("ascent-opterra")
+volume = client.load_volume("ascent-opterra", frame=0)  # Small hosted excerpt only; CZYX.
+```
+
+Use [the executable pilot](examples/pilot.py) to reproduce the corruption and metric demonstration. Files larger than the client's 128 MiB budget require an explicit increased budget; no function silently downloads the benchmark or a multi-GB original movie. Original assets resolve through immutable DANDI asset IDs and versioned Zenodo records in `metadata/upstream_assets.json`. External assets are not Hub-hosted movies.
+
+## Licensing and attribution
+
+The original empty repository displayed MIT. That does not license third-party data. Included DANDI and Zenodo data are CC BY 4.0 per their release metadata. Benchmark helper code is MIT; source data retain their own licenses and attribution. Resources with unresolved redistribution rights remain references only. See [per-source licensing](docs/LICENSING.md), [catalog](docs/DATASET_CATALOG.md), and [citations](docs/CITATIONS.md).
+
+## Limitations and biases
+
+This pilot has only one trusted proofread tracking specimen, no measured centerlines, no independently calibrated deformation uncertainty, and no held-out evaluation. Unknown scorer codes are not promoted to manual ground truth. Fixed-reference residuals include legitimate tissue motion and are permutation-sensitive only because reference correspondences remain fixed. A static unordered point cloud cannot detect identity swaps. Acceptance by a geometric heuristic is not proof of biological identity.
+
+Coverage and selective risk use the full declared observation population; rejecting everything yields zero coverage. Sources differ in optics, visibility, annotation construction, and acquisition restrictions. The 302-neuron assumption is not universal across sex/stage and is never used to force observed counts.
+
+## Release history
+
+- `v0.1.0-alpha.1`: development pilot; source inventory, five standardized tracking tables, imaging excerpts, two reference clouds, measured behavior summaries, controlled corruptions, and reference baseline outputs. Full initial release gates remain open.
+
+Each release has a SHA256 assembly manifest, an upstream asset manifest, dependency pins, and machine-readable validation results. No model weights or externally pretrained models are used by these pilot baselines.

docs/LICENSING.md

@@ -0,0 +1,9 @@
+# Per-source redistribution audit
+
+Included DANDI releases list `spdx:CC-BY-4.0`; included Zenodo records 17561700, 10818810, and 10008744 list `cc-by-4.0`. Original source versions, filenames, checksums, and citations accompany derived tables and excerpts. Conversion, axis permutations, centroid extraction, and controlled identity errors are benchmark modifications, not original source annotations.
+
+NeRVE-derived annotations are obtained from the CC-BY-4.0 ZephIR release and identified as the original Nguyen et al. recording. This does not establish the license of every original IEEE-hosted NeRVE asset.
+
+CeNDeR's GitHub MIT license covers its code; the OSF data project has no stated data license. CeNDeR imagery/annotations are not redistributed. The Skuhersky, NeuroPAL canonical-position, and statistical-atlas repositories have no independently verified data license in this audit; they are linked only. BrainAlignNet and OpenWorm access/licensing remain unresolved. Eigenworm paper access does not automatically establish licensing for an arbitrary downloadable basis.
+
+Benchmark helper code is MIT, provided in `LICENSE-code.txt`. Data are not uniformly MIT. CC BY 4.0: https://creativecommons.org/licenses/by/4.0/ . The assembly excludes assets with unresolved data redistribution permissions.

docs/SCHEMAS.md

@@ -0,0 +1,13 @@
+# Schema and coordinate version 0.1.0-alpha.1
+
+Recording registry: one row per source asset/recording, not a guaranteed unique physical animal. Stable `recording_id`, `source_dataset`, source version/asset/path/checksum, lab/animal/session IDs, license, QC and hosted-component flags are required. Nullable biological fields stay unknown until directly inspected. JSON strings encode optional TCZYX shapes, XYZ voxel spacings, channel arrays, and source digest mappings.
+
+Tracking: one row per observation; scope is recording + label_set + frame_index. Detection IDs and track assignments are unique in each valid scope. Native XYZ voxel fields remain present. Physical XYZ micrometers are nullable. `annotation_type`, raw scorer provenance, validity, and coordinate system distinguish trusted annotations, predictions, and unresolved provenance. Missing source observations are not interpolated; dropped perturbation observations remain rows with validity false.
+
+ZephIR: normalized point coordinates map to continuous voxel centers as `normalized * axis_size - 0.5`, inverse of the native GUI's `(index + 0.5)/shape`. Original normalized values remain present. Out-of-bounds rows are preserved and flagged. Native imagery and annotations remain inspectable.
+
+Targettrack: original frame CXYZ is permuted to CZYX. Mask centers are computed in native XYZ, separately from the unresolved original-to-processed affine direction. This is derived localization from a mask, with unknown annotation quality. No micron spacing is guessed.
+
+Anatomy: same-animal reference origin is explicit; uncertainty is null where unknown. Population atlases are not substituted for temporal truth. SF behavior summaries preserve original timestamps, signal paths and empty source units; they cannot be interpreted as centerlines or synchronized 3D body transport without further audit.
+
+Schemas are in `schemas/`, full Parquet types in `schemas/arrow_schemas.json`, and integrity results in `evaluation/validation.json`. Large structured tables are recording-partitioned. The standard library client never bulk downloads volumes.

docs/SOURCE_AUDIT.md

@@ -0,0 +1,11 @@
+# Source audit
+
+The audit pins nine published DANDI versions, inventories 260 immutable NWB assets, and maps all 118 original WormID assets plus the exact 36 tracking acquisitions (EY 21, KK 9, SK1 4, SK2 2). SF's 38 records remain weakly labeled, and NP/HL remain structural. The original split file has two repeated structural rows. Raw image shape is checked on acquired or range-read pilot assets, not inferred solely from publications.
+
+The ZephIR ZIP central directory was range-read before acquisition. Only small worm annotation files and one 125 MB compressed image member were acquired; the mouse recording and all macOS metadata are excluded. Per-member extraction checks ZIP CRC, while the full 14.9 GB archive MD5 is only an upstream reference and is **not verified locally**. Targettrack's 164 MB volumetric archive and ASCENT CSV files pass source MD5 checks. Derived/selected image assets have their own SHA256 checksums; selective NWB/HDF5 reads do not verify the full source file checksum.
+
+Shared DANDI subject identifiers produce potential overlap groups. DANDI 001623 overlaps identifiers from SK1, so independent specimen counts cannot be inferred by summing registry rows. NeRVE-in-ZephIR is a derivative of an existing acquisition. Skuhersky and NeuroPAL canonical CSVs appear identical in published Git trees; they are references only and not counted as two anatomical datasets.
+
+Known blocks: CeNDeR OSF native storage lists no files, linked Google Drive API returns 404, and OSF data license is unstated. BrainAlignNet Dataverse API did not return usable metadata. OpenWorm movement hostname fails DNS. NeRVE original IEEE page resolves but its full recording inventory and download terms are not completed. Reusable population atlas licensing and an eigenworm basis remain unresolved. None of these blocked sources is silently replaced with synthetic data.
+
+A total source storage inventory is an upper bound that includes duplicates. The original SF corpus alone exceeds 1 TB. This alpha release selectively acquires small source files and range reads and publishes a compact subset (exact hosted bytes in the assembly manifest; total HTTP transfer bytes were not measured), avoiding duplicated multi-terabyte movies. Extended full acquisition and hosting require a deduplicated transfer budget. No scheduler jobs or immutable experiment worktrees are modified.

metadata/assembly_counts.json

@@ -0,0 +1,64 @@
+{
+  "version": "0.1.0-alpha.1",
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+  "ingested": {
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+    },
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+        "algorithm_prediction": 2325
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+      "invalid_observations_preserved": 0
+    },
+    "targettrack-epfl10": {
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+      "frames": 147,
+      "tracks": 15,
+      "annotation_types": {
+        "unknown": 1951
+      },
+      "invalid_observations_preserved": 0
+    },
+    "dandi-000541-sub-20190924-01": {
+      "observations": 2896,
+      "frames": 16,
+      "tracks": 181,
+      "annotation_types": {
+        "unknown": 2896
+      },
+      "invalid_observations_preserved": 0
+    }
+  },
+  "source_inventory_entries": 20,
+  "pilot_imaging_frames": 44,
+  "anatomical_clouds": 2,
+  "measured_centerlines": 0,
+  "independent_behavior_summary_recordings": 1,
+  "release_gates": {
+    "A": "partial: full non-DANDI inventories pending",
+    "B": "partial: independent moving-worm GT and centerline pending",
+    "C": "not_passed: all P0 ingestion and held-out evaluation pending"
+  }
+}

metadata/assembly_manifest.json

@@ -0,0 +1,416 @@
+{
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+      "nullable": true
+    },
+    {
+      "name": "hosted_tracks",
+      "type": "bool",
+      "nullable": true
+    },
+    {
+      "name": "hosted_volume",
+      "type": "bool",
+      "nullable": true
+    },
+    {
+      "name": "wormid_tracking_subset",
+      "type": "bool",
+      "nullable": true
+    },
+    {
+      "name": "wormid_fold",
+      "type": "large_string",
+      "nullable": true
+    }
+  ]
+}

schemas/assembly_manifest.schema.json

@@ -0,0 +1,44 @@
+{
+  "$schema": "https://json-schema.org/draft/2020-12/schema",
+  "title": "WormTrackVerifyAssemblyManifest",
+  "type": "object",
+  "required": [
+    "version",
+    "files",
+    "upstream_manifest"
+  ],
+  "additionalProperties": false,
+  "properties": {
+    "version": {
+      "type": "string"
+    },
+    "upstream_manifest": {
+      "const": "metadata/upstream_assets.json"
+    },
+    "files": {
+      "type": "array",
+      "items": {
+        "type": "object",
+        "required": [
+          "path",
+          "bytes",
+          "sha256"
+        ],
+        "additionalProperties": false,
+        "properties": {
+          "path": {
+            "type": "string"
+          },
+          "bytes": {
+            "type": "integer",
+            "minimum": 0
+          },
+          "sha256": {
+            "type": "string",
+            "pattern": "^[0-9a-f]{64}$"
+          }
+        }
+      }
+    }
+  }
+}

schemas/track_observation.schema.json

@@ -0,0 +1,70 @@
+{
+  "$schema": "https://json-schema.org/draft/2020-12/schema",
+  "type": "object",
+  "required": [
+    "recording_id",
+    "frame_index",
+    "detection_id",
+    "track_id",
+    "x_voxel",
+    "y_voxel",
+    "z_voxel",
+    "annotation_type",
+    "validity"
+  ],
+  "properties": {
+    "recording_id": {
+      "type": "string"
+    },
+    "frame_index": {
+      "type": "integer",
+      "minimum": 0
+    },
+    "detection_id": {
+      "type": "string"
+    },
+    "track_id": {
+      "type": "string"
+    },
+    "x_voxel": {
+      "type": "number"
+    },
+    "y_voxel": {
+      "type": "number"
+    },
+    "z_voxel": {
+      "type": "number"
+    },
+    "x_um": {
+      "type": [
+        "number",
+        "null"
+      ]
+    },
+    "y_um": {
+      "type": [
+        "number",
+        "null"
+      ]
+    },
+    "z_um": {
+      "type": [
+        "number",
+        "null"
+      ]
+    },
+    "annotation_type": {
+      "enum": [
+        "human_corrected",
+        "manually_verified",
+        "verified_checkpoint",
+        "algorithm_prediction",
+        "unknown"
+      ]
+    },
+    "validity": {
+      "type": "boolean"
+    }
+  },
+  "additionalProperties": true
+}

splits/assignments.json

@@ -0,0 +1,40 @@
+{
+  "seed": 20261007,
+  "status": "development_only_no_frozen_test",
+  "protocols": {
+    "tracking_gt": {
+      "train": [],
+      "validation": [],
+      "test": [],
+      "development": [
+        "ascent-opterra"
+      ],
+      "quarantine": []
+    },
+    "anatomical_verification": {
+      "train": [],
+      "validation": [],
+      "test": [],
+      "development": [
+        "ascent-opterra"
+      ],
+      "quarantine": []
+    },
+    "anatomical_consistency": {
+      "train": [],
+      "validation": [],
+      "test": [],
+      "development": [
+        "ascent-opterra",
+        "dandi-000541-sub-20190924-01",
+        "dandi-000715-sub-56-YAaDV",
+        "dandi-000776-sub-2022-06-14-13-SWF702",
+        "nerve-al-w1-via-zephir",
+        "targettrack-epfl10",
+        "zephir-zm9624"
+      ],
+      "quarantine": []
+    }
+  },
+  "original_wormid_commit": "0c74e9ddffee138cfc6330ab65c0e690e8e199dd"
+}

splits/original_wormid_folds.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:17c84659e3853c6ce3b0adb87c04fe7970ff667cf91b2c3f8854fbd1b071361d
+size 12951