M13Rec001, run b646e930
Status done, stage done; requested by project lead; worker [not recorded]; started 2026-10-27 02:14 UTC, finished 2026-10-27 02:16 UTC, 85 s; signature 5a77e263
Stages
| Stage | Started | Seconds |
|---|---|---|
| [no stage log; run predates stage timing] | ||
Log
| Time | Agent | Action | Detail |
|---|---|---|---|
| 02:14:39 | runs | run started | {"recording_id": "55cb4aa3-6502-45a6-a14c-85cb676fe8c3", "run_id": "b646e930-aa7c-4a86-a318-5d87d5e841d4"} |
| 02:16:04 | runs | signature written | {"run_id": "b646e930-aa7c-4a86-a318-5d87d5e841d4", "sensitivity_holds": true, "signature_id": "5a77e263-e6fc-4de3-b912-b7b67a440297"} |
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Pipeline check
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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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