M13Rec001, run e8e250de
Status deferred, stage deferred; requested by project lead; worker [not recorded]; started [not recorded], finished [not recorded]
Stages
| Stage | Started | Seconds |
|---|---|---|
| [no stage log; run predates stage timing] | ||
Log
| Time | Agent | Action | Detail |
|---|---|---|---|
| 01:10:14 | runner | run failed | {"error": "ChecksumMismatch(\u0027public/M13Rec001_complete.npy: sha256 e3b0c44298fc... != recorded 3f8f2e1b8f77...; cached copy removed\u0027)", "run_id": "e8e250de-fe1c-4811-bf43-775d2fd01820", "trace": "_sync_in_worker_thread(\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/site-packages/anyio/_backends/_asyncio.py\", line 2706, in run_sync_in_worker_thread\n return await future\n ^^^^^^^^^^^^\n File \"/usr/local/lib/python3.12/site-packages/anyio/_backends/_asyncio.py\", line 1100, in run\n result = context.run(func, *args)\n ^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/usr/local/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 \"/app/worker/agents/pipeline.py\", line 170, in rhythm_by_segment\n return _cached(ctx, \"rhythm\", run)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/app/worker/agents/pipeline.py\", line 74, in _cached\n ctx.deps.results[name] = fn()\n ^^^^\n File \"/app/worker/agents/pipeline.py\", line 156, in run\n _, raw, mask, _info = io.load_recording_masked(row[\"id\"])\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File \"/app/worker/voltage/io.py\", line 288, in load_recording_masked\n path = download(row)\n ^^^^^^^^^^^^^\n File \"/app/worker/voltage/io.py\", line 254, in download\n raise ChecksumMismatch(f\"{path}: sha256 {got[:12]}... != recorded {row[\u0027sha256\u0027][:12]}...; cached copy removed\")\nworker.voltage.io.ChecksumMismatch: public/M13Rec001_complete.npy: sha256 e3b0c44298fc... != recorded 3f8f2e1b8f77...; cached copy removed\n"} |
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: False, held: The fixed baseline window is shorter than the provisional ~1.5-cycle criterion in the slower post-termination rhythm segments, so the fixed pipeline may attenuate the rhythm under the current parameter set.; parameters v2.
| Field | Protocol | Recording | Severity | Detail |
|---|---|---|---|---|
| no mismatches | ||||
| Anomaly | Severity | Effect on the Fixed Pipeline |
|---|---|---|
| Pre-deposit processing / raw-data label | warn | The deposited movie should not be treated as raw camera counts: masking, temporal smoothing, spatial smoothing, and normalization were documented and measured. The protocol's Gaussian phase smoothing would be applied on top of prior spatial filtering of unknown total strength, and noise/SNR or pixel-independence assumptions would be misleading. |
| Event interpretation at frame 3170 | warn | The segment boundary at frame 3170 is an interpreted baseline/rhythm-change event, not light onset. Segment-wise analysis may be appropriate only with the provisional definition that illumination was already on and that frame 3170 marks interpreted spiral termination; analyses treating it as stimulation onset would be wrong. |
| Baseline and illumination artifact | warn | Slow baseline change, a baseline step, blue-light crosstalk, and re-normalization can affect amplitude and absolute-baseline measurements. Phase or rotor analyses using the fixed baseline removal may still run only if the baseline window is otherwise valid, but amplitude-related interpretations need caution. |
| Baseline window versus dominant cycle | block | With baseline_frames = 641, the post-termination segments have baseline_over_cycle values below the provisional ~1.5-cycle criterion, so the fixed high-pass baseline step may attenuate the slower rhythm and the protocol parameters are not appropriate as-is. |
The recording matches the protocol identity: it is a mouse whole-heart optical mapping recording, and the 1000 Hz frame rate from the publication agrees with the recording facts and the protocol parameter note. However, the version 2 fixed baseline window of 641 frames was intended to be about 1.5 cycles for the post-termination rhythm, while the measured dominant cycles in the slower segments make the baseline window 1.42 and 1.48 cycles; the rhythm tool cautions that a baseline window shorter than about 1.5 cycles attenuates that rhythm. Because the service does not change protocol parameters during this check, the run should be held until the provisional parameter set or criterion is reviewed. The reader should also be told that the deposit is processed rather than raw, that frame 3170 is not light onset, and that illumination/crosstalk/normalization affect baseline and amplitude.
Inspector
This is an ex vivo optogenetic mouse whole-heart optical mapping recording associated with spiral-wave termination experiments. Use 1000 Hz: the linked paper states 64 × 64 camera acquisition at 1 kHz, and the deposit’s 64 × 55 frame size is consistent with a cropped version; this agrees with the frame rate already on record. The deposited movie is not truly raw camera output: depositor documentation and measurements indicate masking, temporal/spatial smoothing, and normalization. Polarity is robustly inverted, so depolarization appears as a downward deflection. Illumination was already on before frame 0 and turned off at frame 4977; the frame-3170 image step should be treated as a fluorescence baseline/rhythm-change event with provisional interpretation as spiral termination, not as light onset.
| Measurement | Value | Method, Caveat |
|---|---|---|
| SNR, median (p10–p90) | 32.5 (26.9–44.9) | assumes white noise; on temporally smoothed deposits noise is underestimated and SNR inflated |
| Mask coverage | 66.2%, 2332 of 3520 px | depositor NaN mask (frame 0) |
| Polarity | blocks 18, inverted True, blocks agreeing 18, median dvdt skew -4.419912338256836 | sign of median per-pixel skew of dV/dt, baseline-corrected (121 frames) |
| Drift / bleaching | baseline change -1.61, vs beat amplitude -1.12, slow range 3.33, trend, Spearman -0.489 | running median (927 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 |
| Prior processing | negative values, nan mask all frames, temporal smoothing, spatial smoothing | deposit checks |
| Dominant cycle by block, frames | 0–1000: 66.7, 1000–2000: 66.7, 2000–3000: 52.6, 3000–4000: 83.3, 4000–5000: 100.0, 5000–6000: 142.9, 6000–7000: 100.0, 7000–8000: 142.9, 8000–9000: 83.3 |
| Concern | Severity | Detail |
|---|---|---|
| Pre-deposit processing / raw-data label | warn | The README labels M13Rec001 as raw experimental data, but the notebook documents masking, spatial smoothing, temporal smoothing, and normalization with Python Analyser; prior_processing measurements support processed data. Analyses requiring raw photon counts or independent pixel noise would be misleading if this is treated as raw camera data. |
| Event interpretation at frame 3170 | warn | The image event at frame 3170 is a baseline_step only. The DAQ shows illumination began before frame 0 and ended at frame 4977, so treating frame 3170 as light onset would be wrong. The stored spiral-termination label is a provisional interpretation from timing relative to the paper, not a direct measurement. |
| Baseline and illumination artifact | warn | The publication reports blue stimulation light crosstalk causing an increase in fluorescence baseline and re-normalization by division to the recorded stimulation light signal; the recording also has a large slow baseline range and a baseline step. Analyses using absolute baseline or amplitude should account for illumination/crosstalk/normalization effects. |
| Provisional tool thresholds | info | Event detection, processing flags, SNR, rhythm, and reference-rate thresholds are provisional and not yet reviewed by a domain scientist; conclusions depending on them should be checked for critical analyses. |
| Event | Frame | Source | Method |
|---|---|---|---|
| illumination on | 0 ± 11 | acquisition log | midpoint threshold on DAQ channel 'led_trigger', mapped to frames via camera triggers |
| illumination off | 4977 ± 11 | acquisition log | midpoint threshold on DAQ channel 'led_trigger', mapped to frames via camera triggers |
| baseline step | 3170 ± 17 | image | consensus upward step in running-median baseline of tissue-mean raw signal |
Inspector report 2026-10-27 20:27 UTC, model openai:gpt-5.5, provisional. Per-pixel SNR is high by the provisional metric: median = 32.506531024253725, p10 = 26.87502130582481, p90 = 44.884363625066875 over 3000 frames. Because the deposit is documented and measured as temporally smoothed, the tool caveat applies: white-noise assumptions can underestimate noise and inflate SNR. The depositor NaN mask in frame 0 contains 2332 tissue pixels out of 3520 total pixels, coverage = 0.6625, with 1188 NaN pixels. Acquisition log detects illumination already on at the first deposited frame: led_trigger transition occurred before_first_frame, 23.0 frames before frame 0, reported as illumination_on at frame 0 with uncertainty 11 frames; photodiode agrees. Acquisition log detects illumination_off at frame 4977 with uncertainty 11 frames; photodiode agrees. Image analysis detects a baseline_step at frame 3170 with uncertainty 17 frames: this measurement only shows the tissue-mean fluorescence baseline changed, not illumination onset. A stored project-lead interpretation, citing Hussaini et al. 2023 Fig 2C, labels the frame-3170 step as “spiral termination under illumination”; the source caveat says the paper does not name M13Rec001 and the termination assignment is inferred from timing, so it should be treated as provisional interpretation, not a direct measurement. The stored image-based “illumination_on” at frame 3170 is contradicted by the DAQ led_trigger and photodiode, which show light already on from before frame 0 until frame 4977. The tissue-mean slow baseline changes substantially: baseline_start = 1.439404845237732, baseline_end = -0.17559432983398438, baseline_change = -1.6149991750717163, which is -1.1213198412261043 times the beat amplitude; slow_baseline_range = 3.3284222781658173 and monotonic_trend_spearman = -0.4894475048599732. The tool cautions that steps from events, rhythm change, depositor normalization, or drift removal affect the baseline, so bleaching cannot be separated here.
Range checks
| Metric | Segment | Value at Run Setting | Cited Range | Status |
|---|---|---|---|---|
| [no critic verdict for this run] | ||||
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