mouseventricle06062018_A_Cool_SR, run 59f54d2a
Status done, stage done; requested by project lead; worker local worker; started 2026-10-28 19:02 UTC, finished 2026-10-28 19:06 UTC, 247 s; signature b65bf0ab
Stages
| Stage | Started | Seconds |
|---|---|---|
| claimed | 19:01:52 | 0.7 |
| pipeline_check | 19:01:53 | 30.5 |
| baseline_rule | 19:02:24 | 1.0 |
| deposit_checks | 19:02:25 | 0.3 |
| analysis | 19:02:25 | 11.2 |
| render | 19:02:36 | 184.5 |
| persist | 19:05:41 | 0.7 |
| critic | 19:05:41 | 48.9 |
| done | 19:06:30 | 0.2 |
Log
| Time | Agent | Action | Detail |
|---|---|---|---|
| 17:55:27 | 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_Cool SR.mat", "paper": "10.1038/s41597-022-01253-1", "recording_id": "ca67ef56-963e-4640-ab6d-c71eda5fa96b", "run_id": "59f54d2a-663b-4591-befa-75a5fcb08c8e", "shape": [5000, 51, 51]} |
| 17:55:34 | 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": "59f54d2a-663b-4591-befa-75a5fcb08c8e", "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"} |
| 19:02:24 | runs | run started | {"checked_by": "openai:gpt-5.5", "protocol_params_version": 3, "recording_id": "ca67ef56-963e-4640-ab6d-c71eda5fa96b", "run_id": "59f54d2a-663b-4591-befa-75a5fcb08c8e"} |
| 19:05:41 | runs | signature written | {"criteria": "provisional", "holds": null, "run_id": "59f54d2a-663b-4591-befa-75a5fcb08c8e", "signature_id": "b65bf0ab-0e52-4c93-8182-b8211c4efb27"} |
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 |
|---|---|---|---|---|
| no mismatches | ||||
| Anomaly | Severity | Effect on the Fixed Pipeline |
|---|---|---|
| Frame rate not documented | info | The inspector could not document the frame rate from the sources available to it and inferred a low-confidence range, but the admitted recording facts give 1000.0 Hz from the paper methods; the fixed frame-based pipeline can therefore use the admitted frame rate for timing statements. |
| Rhythm assumption is provisional | warn | The inspector's physiology-based frame-rate inference depended on provisional mouse spiral-rotation rates; because an admitted 1000.0 Hz frame rate is available, this does not set the acquisition timing for the pipeline, but it remains a caution against using the inference as evidence about physiology. |
| Tissue/chamber metadata conflict | warn | The protocol is for mouse whole-heart optical mapping, while the inspector reports an overview label of atrium and a path containing mouseventricle; this does not change the fixed analysis parameters, but chamber-specific interpretation should not be made unless the metadata conflict is resolved. |
| Publication/deposit text unavailable | warn | The inspector could not verify preprocessing, dye identity, or acquisition details from deposit/publication text; the admitted recording facts nevertheless provide the frame rate and pixel size from the paper methods, so the remaining effect is uncertainty about undocumented acquisition or preprocessing details. |
| Baseline-window rule | info | The coded baseline-window rule passed for this recording; by policy this rule is reported only as information and is not escalated. |
The fixed protocol is broadly appropriate for this recording because the admitted facts identify a 5000-frame, 51 × 51 mouse optical-mapping recording from the Mouse Whole Heart data set, with a documented 1000.0 Hz sampling rate and 156.0 µm pixel size from the paper methods, and there are no recording facts that contradict the protocol parameters. The main limitations are interpretive rather than parameter-breaking: the inspector reports chamber metadata conflict, unavailable publication/deposit text in its own source checks, full-frame masking, strong slow baseline drift, and inverted deposited polarity. These issues should be disclosed, but they do not require changing the fixed frame-based protocol parameters or holding the run as long as results are not overinterpreted by chamber or undocumented preprocessing assumptions.
Inspector
This is a 5000-frame, 51 × 51 mouse whole-heart optical mapping recording associated with Hussaini et al. The frame rate is 1000.0 Hz from the recording admission record, quoting the linked paper, and the paper’s 51 × 51 murine whole-heart image size matches the file. The signal polarity is consistently inverted by measurement, as expected for raw rh-237 fluorescence that dims on depolarization. No depositor-documented pre-deposit processing was available or detected, and no events/acquisition logs were found. The main analysis issues are substantial slow baseline decline and a detected 76.9-frame rhythm that should be used instead of assuming the paper’s generic 110 ms pacing condition for this specific file.
| Measurement | Value | Method, Caveat |
|---|---|---|
| SNR, median (p10–p90) | 6.0 (5.0–6.7) | assumes white noise; on temporally smoothed deposits noise is underestimated and SNR inflated |
| Mask coverage | 76.6%, 1993 of 2601 px | otsu_mean_image |
| Polarity | blocks 10, inverted True, blocks agreeing 10, median dvdt skew -0.1170167475938797 | sign of median per-pixel skew of dV/dt, baseline-corrected (121 frames) |
| Drift / bleaching | baseline change -702, vs beat amplitude -1.94, slow range 1.4e+03, trend, Spearman -0.999 | 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: 76.9, 1000–2000: 76.9, 2000–3000: 76.9, 3000–4000: 76.9, 4000–5000: 76.9 |
| Concern | Severity | Detail |
|---|---|---|
| Deposit metadata unavailable | info | The deposit_metadata tool cannot read this Figshare DOI and returned: “only Zenodo DOIs are supported,” so depositor README/notebook text could not be checked for file-specific statements or processing notes. |
| No acquisition log | info | The acquisition_log tool found no logs, so illumination timing and camera/DAQ timing cannot be independently checked beyond the admission/paper frame-rate source. |
| Baseline drift/bleaching | warn | The slow tissue-mean baseline falls by -702.1455078125 intensity units, about -1.9355984146871341 times the beat amplitude; analyses should apply baseline correction/detrending rather than using raw fluorescence levels directly. |
| Rhythm differs from generic paper pacing description | warn | The rhythm tool finds a dominant cycle of 76.9 frames in every 1000-frame block. At the admitted 1000.0 Hz frame rate, that corresponds to 76.9 ms, while the paper’s general murine whole-heart method states pacing at a PCL of 110 ms; do not assume this file is the 110 ms paced condition solely from the paper method. |
| Provisional tool thresholds | info | Masking, polarity, SNR, drift, and rhythm measurements come from automated tools with provisional thresholds/methods not yet domain-scientist reviewed; conclusions based only on these measurements should be treated accordingly. |
Inspector report 2026-10-28 19:16 UTC, model openai:gpt-5.5, provisional. Per-pixel SNR over tissue has median 6.010530622011562, p10 4.958654710455078, and p90 6.719206839761184, calculated from 3000 frames. The SNR method assumes white noise; on temporally smoothed deposits noise can be underestimated, but the prior-processing tool did not flag temporal smoothing. The tissue mask contains 1993 of 2601 pixels, covering 0.766243752402922 of the frame. It comes from an Otsu threshold of 18097.535643577576 on the mean image, using the brighter/more temporally active class and largest connected component; there were 0 NaN pixels in frame 0. No acquisition log is present in the deposit, and the stored/detected event tools returned no events for this recording. Therefore there are no logged light transitions or image baseline-step events to interpret for this file. The tissue-mean slow baseline decreases from 27058.6123046875 to 26356.466796875, a change of -702.1455078125 raw intensity units. This is -1.9355984146871341 times the p5–p95 beat amplitude (362.75371093750005), with a slow-baseline range of 1401.728515625 and strongly monotone negative trend (Spearman -0.9987563956397382). The tool cautions that bleaching cannot be separated here from possible events or depositor normalization/drift removal, although no events or prior processing were detected.
Range checks
| Metric | Segment | Value at Run Setting | Cited Range | Status |
|---|---|---|---|---|
| persistent rotor tracks | all | 6 count | none cited | unstable not reportable |
| dominant freq (Hz) | whole recording | 6.5 Hz | none cited | no cited range |
| persistent rotors | whole recording | 6 count | none cited | unstable not reportable |
| singularity frames fraction | whole recording | 0.163 fraction of frames | none cited | unstable not reportable |
| persistent rotor count max | whole recording | 2 count | none cited | unstable not reportable |