mouseventricle06062018_A_FLEC_1uM_Paced, run 1d65814d
Status done, stage done; requested by project lead; worker local worker; started 2026-10-28 19:22 UTC, finished 2026-10-28 19:25 UTC, 228 s; signature daa60525
Stages
| Stage | Started | Seconds |
|---|---|---|
| claimed | 19:21:16 | 0.6 |
| pipeline_check | 19:21:17 | 49.2 |
| baseline_rule | 19:22:06 | 0.8 |
| deposit_checks | 19:22:07 | 0.3 |
| analysis | 19:22:07 | 8.7 |
| render | 19:22:16 | 191.0 |
| persist | 19:25:27 | 0.7 |
| critic | 19:25:27 | 26.2 |
| done | 19:25:53 | 0.2 |
Log
| Time | Agent | Action | Detail |
|---|---|---|---|
| 17:55:42 | admission | recording registered | {"by": "project lead", "candidate_id": "5a7107e9-5221-4ea8-bfb1-1d63afde37d5", "deposit": "10.6084/m9.figshare.17158742.v1", "member": "Mouse Whole Heart.zip/Mouse Whole Heart/06062018 A/mouseventricle06062018 A_FLEC 1uM Paced.mat", "paper": "10.1038/s41597-022-01253-1", "recording_id": "f84bc560-2a52-46d8-8ca3-e654c30d8fdf", "run_id": "1d65814d-f982-424e-ae62-1ed747dc6cf7", "shape": [5000, 51, 51]} |
| 17:55:56 | runner | run failed | {"error": "HTTPError(\u0027503 Server Error: for url: https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=DOI%3A10.1038%2Fs41597-022-01253-1\u0026format=json\u0026resultType=lite\u0027)", "run_id": "1d65814d-f982-424e-ae62-1ed747dc6cf7", "trace": ".venv/lib/python3.12/site-packages/anyio/_backends/_asyncio.py\", line 1100, in run\n result = context.run(func, *args)\n ^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/Users/xx/Documents/Code/quantetta-a/.venv/lib/python3.12/site-packages/pydantic_ai/_utils.py\", line 186, in call_with_sync_agent_guard\n return func(*args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^\n File \"/Users/xx/Documents/Code/quantetta-a/worker/agents/inspector.py\", line 127, in publication_methods\n return _cached(ctx, \"publication\", run)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/Users/xx/Documents/Code/quantetta-a/worker/agents/inspector.py\", line 96, in _cached\n ctx.deps.results[name] = fn()\n ^^^^\n File \"/Users/xx/Documents/Code/quantetta-a/worker/agents/inspector.py\", line 125, in run\n p = publication.fetch(doi)\n ^^^^^^^^^^^^^^^^^^^^^^\n File \"/Users/xx/Documents/Code/quantetta-a/worker/voltage/publication.py\", line 48, in fetch\n got = _xml(doi)\n ^^^^^^^^^\n File \"/Users/xx/Documents/Code/quantetta-a/worker/voltage/publication.py\", line 28, in _xml\n r.raise_for_status()\n File \"/Users/xx/Documents/Code/quantetta-a/.venv/lib/python3.12/site-packages/requests/models.py\", line 1167, in raise_for_status\n raise HTTPError(http_error_msg, response=self)\nrequests.exceptions.HTTPError: 503 Server Error: for url: https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=DOI%3A10.1038%2Fs41597-022-01253-1\u0026format=json\u0026resultType=lite\n"} |
| 19:22:06 | runs | run started | {"checked_by": "openai:gpt-5.5", "protocol_params_version": 3, "recording_id": "f84bc560-2a52-46d8-8ca3-e654c30d8fdf", "run_id": "1d65814d-f982-424e-ae62-1ed747dc6cf7"} |
| 19:25:27 | runs | signature written | {"criteria": "provisional", "holds": null, "run_id": "1d65814d-f982-424e-ae62-1ed747dc6cf7", "signature_id": "daa60525-79d0-40ac-80a8-d131bab1047a"} |
Entries from the audit log for this run; new rows and stage changes arrive by realtime while the run is open (connecting).
Pipeline check
Proceed: True; parameters v3.
| Field | Protocol | Recording | Severity | Detail |
|---|---|---|---|---|
| tissue | whole_heart | recording row identified as atrium by the inspector; path label contains 'mouseventricle' while the deposit label is Mouse Whole Heart | warn | The protocol is a mouse whole-heart optical-mapping protocol, but the available tissue annotations are internally inconsistent. This does not by itself make the fixed frame-based parameters wrong, but it limits tissue-specific interpretation and interacts with the full-frame mask warning. |
| Anomaly | Severity | Effect on the Fixed Pipeline |
|---|---|---|
| Frame rate unavailable | warn | The inspector could not independently recover a frame rate, which would block conversion of the paced dominant cycle to time. The recording_facts source, however, supplies 1000.0 Hz from admission/paper_methods, so the fixed analysis can proceed using that source; timing statements should cite that source. |
| Accessible depositor documentation unavailable | warn | Depositor README/notebook statements and documented preprocessing could not be verified by the inspector. Automated prior-processing checks did not flag smoothing or other pre-deposit processing, but absence of processing is not independently documented. |
| Tissue annotation/mask | warn | The mask covers the full 51 x 51 frame using nonzero temporal standard deviation only. If the frame contains background, the fixed pipeline would analyze it as tissue, affecting spatial, phase, and rotor measurements; the inconsistent atrium/ventricle/whole-heart labels also limit anatomical interpretation. |
| Baseline drift/bleaching | warn | The slow baseline changes by nearly one beat amplitude, so detrending and the fixed 901-frame baseline correction materially affect amplitude-based measurements; phase-based outputs may still be usable but remain dependent on baseline handling. |
| Baseline-window rule | info | The coded baseline rule reports ok: baseline_frames 901, factor 2.0, slowest_segment whole_recording, slowest_cycle_frames 7, required_min_frames 14, ratio 128.714. Per instruction this rule is reported only as informational and does not hold the run. |
The protocol is broadly applicable because this is a mouse optical-mapping recording in the Luther-lab whole-heart reference dataset, and the recording_facts source provides the needed acquisition scale: 1000.0 Hz and 156.0 µm/pixel. The fixed version-3 parameters are frame-based and the coded baseline-window rule passes; the segment-level dominant cycle is 108.1 frames over the analysed window, giving baseline_over_cycle 8.33 under the 901-frame baseline. The run should nevertheless be treated as provisional because tissue labels are inconsistent, the full frame is treated as tissue, depositor documentation was not accessible for independent preprocessing verification, and the recording has substantial slow baseline drift/bleaching.
Inspector
This is a 5000-frame, 51 x 51 mouse whole-heart optical-mapping MAT recording labeled as FLEC 1 uM paced, with no frame rate available from the recording row, accessible deposit metadata, publication text, or acquisition log. The deposited signal is inverted by measurement: depolarization corresponds to downward deflections, consistently across all 10 blocks. No pre-deposit processing was detected by the automated prior_processing checks, but depositor documentation could not be accessed, so this is not independently documented. The full frame is currently treated as tissue, and the slow baseline drifts downward by nearly one beat amplitude, so masking and baseline correction should be handled carefully before analysis.
| Measurement | Value | Method, Caveat |
|---|---|---|
| SNR, median (p10–p90) | 6.6 (3.4–7.4) | assumes white noise; on temporally smoothed deposits noise is underestimated and SNR inflated |
| Mask coverage | 100.0%, 2601 of 2601 px | nonzero temporal std only (no NaN mask in deposit) |
| Polarity | blocks 10, inverted True, blocks agreeing 10, median dvdt skew -0.03058957401663065 | sign of median per-pixel skew of dV/dt, baseline-corrected (121 frames) |
| Drift / bleaching | baseline change -330, vs beat amplitude -0.951, slow range 827, trend, Spearman -0.978 | running median (501 frames) of the tissue-mean raw signal; steps from events (light, rhythm change) and depositor normalization or drift removal change or erase the baseline; bleaching cannot be separated from them here |
| Dominant cycle by block, frames | 0–1000: 111.1, 1000–2000: 111.1, 2000–3000: 111.1, 3000–4000: 111.1, 4000–5000: 111.1 |
| Concern | Severity | Detail |
|---|---|---|
| Frame rate unavailable | block | No frame rate was recorded on upload/admission; deposit metadata was unavailable; publication full-text fetch failed; and no acquisition log exists. The 111.1-frame dominant cycle cannot be converted to time for paced data without a pacing frequency or frame-rate source. |
| Accessible depositor documentation unavailable | warn | The deposit_metadata tool supports only Zenodo DOIs and could not read the Figshare deposit, so documented preprocessing steps and dye/protocol statements from README/notebooks could not be verified. |
| Tissue annotation/mask | warn | The recording row identifies tissue as atrium, while the path label contains 'mouseventricle'. The analysis mask covers the entire 51 x 51 frame based only on nonzero temporal standard deviation, so any background included in the frame would be analyzed as tissue unless a better mask is supplied. |
| Physiology-reference limitations | info | The only available provisional reference rate was mouse spiral rotation (14.0625 to 25.0 Hz), but the filename indicates paced recording. Conclusions depending on provisional reference rates should be treated as unreviewed. |
| Baseline drift/bleaching | warn | The slow baseline change is nearly one beat amplitude over the recording; detrending/baseline handling will materially affect amplitude-based measurements. |
Inspector report 2026-10-28 18:38 UTC, model openai:gpt-5.5, provisional. Median per-pixel SNR over tissue was 6.579690968744715 (p10 3.4102512969676595, p90 7.396162695361042) over 3000 frames. The SNR method assumes white noise; temporal smoothing would inflate SNR, although prior_processing did not flag smoothing. The mask covers 2601/2601 pixels (coverage 1.0). It was derived from nonzero temporal standard deviation only, with no NaN mask in the deposit and 0 NaN pixels in frame 0, so the full 51 x 51 frame is treated as tissue. No acquisition-log light transitions were available because no acquisition log was found. The detected-events tool reported no baseline-step events, and there are no stored event interpretations for this recording. The tissue-mean slow baseline fell from 19214.2392578125 to 18884.130859375, a change of -330.1083984375, which is -0.9512053874934153 times the p5-p95 beat amplitude (347.0421875). The slow baseline range was 827.09765625 with a strongly decreasing Spearman trend of -0.9783918222198467. The tool notes that bleaching cannot be separated here from event steps or depositor processing.
Range checks
| Metric | Segment | Value at Run Setting | Cited Range | Status |
|---|---|---|---|---|
| persistent rotor tracks | all | 4 count | none cited | unstable not reportable |
| dominant freq (Hz) | whole recording | 9.25 Hz | none cited | no cited range |
| persistent rotors | whole recording | 4 count | none cited | unstable not reportable |
| singularity frames fraction | whole recording | 0.1447 fraction of frames | none cited | unstable not reportable |
| persistent rotor count max | whole recording | 2 count | none cited | unstable not reportable |