Recordings / M13Rec001 / Run
M13Rec001, run c0c30a22
Status done, stage done; requested by project lead; worker [not recorded]; started 2026-10-27 23:30 UTC, finished 2026-10-27 23:35 UTC, 324 s; signature b456870e
Stages
| Stage | Started | Seconds |
|---|---|---|
| [no stage log; run predates stage timing] | ||
Log
| Time | Agent | Action | Detail |
|---|---|---|---|
| 23:30:28 | runs | run started | {"checked_by": "no agent", "protocol_params_version": 3, "recording_id": "55cb4aa3-6502-45a6-a14c-85cb676fe8c3", "run_id": "c0c30a22-bf69-424a-8a7c-76e8fbac530d"} |
| 23:35:52 | runs | signature written | {"criteria": "provisional", "holds": {"persistent_rotors": true, "persistent_rotors_fraction_superseded": false, "singularities": true}, "run_id": "c0c30a22-bf69-424a-8a7c-76e8fbac530d", "signature_id": "b456870e-cc99-40a9-aff1-55e4133116c4"} |
Entries from the audit log for this run; new rows and stage changes arrive by realtime while the run is open (connecting).
Pipeline check
[no pipeline check stored for this run]
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 |
|---|---|---|---|---|
| persistent rotor tracks | all | 13 count | none cited | unstable not reportable |
| dominant freq (Hz) | light off | 2.375 Hz | none cited | no cited range |
| persistent rotors | light off | 0 count | none cited | no cited range |
| singularity frames fraction | light off | 0.01214 fraction of frames | none cited | unstable not reportable |
| persistent rotor count max | light off | 0 count | none cited | no cited range |
| dominant freq (Hz) | illuminated arrhythmia | 19.1 Hz | 18.75–20, checked 14.0625–25, 10.1371/journal.pcbi.1011660 | unstable not reportable |
| persistent rotors | illuminated arrhythmia | 13 count | none cited | unstable not reportable |
| dominant freq (Hz) | illuminated after termination | 2.214 Hz | none cited | no cited range |
| singularity frames fraction | illuminated arrhythmia | 0.479 fraction of frames | none cited | no cited range |
| persistent rotors | illuminated after termination | 0 count | none cited | no cited range |
| persistent rotor count max | illuminated arrhythmia | 2 count | none cited | unstable not reportable |
| singularity frames fraction | illuminated after termination | 0.01494 fraction of frames | none cited | unstable not reportable |
| persistent rotor count max | illuminated after termination | 0 count | none cited | no cited range |
Compare with run faeb5ebc
A: this run, code 905d5be, None workers. B: run faeb5ebc, 2026-10-27 23:05 UTC, code b1be824 (uncommitted changes), None workers. 28 stored values differ.
| File | A | B | Same | How |
|---|---|---|---|---|
| frames/voltage | [none] | [none] | [not comparable] | recorded sha256 |
| frames/phase | [none] | [none] | [not comparable] | recorded sha256 |
| frames/maps | [none] | [none] | [not comparable] | recorded sha256 |
| maps/activation.png | f0433d3a9771 | f0433d3a9771 | yes | sha256 of the stored file |
| maps/dominant_frequency.png | 9004a90ee80c | 9004a90ee80c | yes | sha256 of the stored file |
| movie.mp4 | 6519517 | 6519517 | yes | size in bytes only; frames not compared |
| Stored Value | A | B |
|---|---|---|
| criteria_status.rules | length 19 | length 20 |
| criteria_status.rules[16].description | Cited physiological ranges (single-study values widened by a 25% tolerance), applied to segments by their expected rhythm; used by the critic and for frame-rate sanity checks | The pipeline agent's hold/proceed decision from protocol mismatches and inspector anomalies; it chooses no parameter |
| criteria_status.rules[16].expert | cardiac electrophysiologist per species | optical mapping analyst |
| criteria_status.rules[16].location | worker/voltage/physiology.py (RANGES, TOLERANCE_FRAC) | worker/agents/pipeline.py (INSTRUCTIONS, validator) |
| criteria_status.rules[16].values.anomalies | [absent] | ['Pre-deposit processing / raw-data label', 'Event interpretation at frame 3170', 'Baseline and illumination artifact', 'baseline-window rule'] |
| criteria_status.rules[16].values.mismatches | [absent] | [] |
| criteria_status.rules[16].values.model | [absent] | openai:gpt-5.5 |
| criteria_status.rules[16].values.proceed | [absent] | True |
| criteria_status.rules[16].values.ranges | ['mouse_spiral_rotation_hz'] | [absent] |
| criteria_status.rules[16].values.segment_rhythm_rule | expected persistent rotors 'present' -> spiral arrhythmia | [absent] |
| criteria_status.rules[16].values.tolerance_frac | 0.25 | [absent] |
| criteria_status.rules[17].description | A metric is reportable only if its spread across all sensitivity settings is <= 25% of its median (zero spread when all values are 0); otherwise 'unstable, not reportable' | Cited physiological ranges (single-study values widened by a 25% tolerance), applied to segments by their expected rhythm; used by the critic and for frame-rate sanity checks |
| criteria_status.rules[17].expert | biostatistician + optical mapping analyst | cardiac electrophysiologist per species |
| criteria_status.rules[17].location | worker/agents/critic.py (STABLE_FRAC, stability) | worker/voltage/physiology.py (RANGES, TOLERANCE_FRAC) |
| criteria_status.rules[17].values.ranges | [absent] | ['mouse_spiral_rotation_hz'] |
| criteria_status.rules[17].values.segment_rhythm_rule | [absent] | expected persistent rotors 'present' -> spiral arrhythmia |
| criteria_status.rules[17].values.stable_frac | 0.25 | [absent] |
| criteria_status.rules[17].values.tolerance_frac | [absent] | 0.25 |
| criteria_status.rules[17].values.unstable | ['light_off.singularity_frames_frac', 'illuminated_arrhythmia.persistent_rotors', 'illuminated_arrhythmia.persistent_rotor_count_max', 'illuminated_arrhythmia.dominant_freq_hz', 'illuminated_after_termination.singularity_frames_frac', 'persistent_rotor_tracks'] | [absent] |
| criteria_status.rules[18].description | The persistent-rotor rule is run at two lifetimes, one measured cycle of the fastest segment and the paper's cited rotation period; both verdicts stored, disagreement flagged | A metric is reportable only if its spread across all sensitivity settings is <= 25% of its median (zero spread when all values are 0); otherwise 'unstable, not reportable' |
| criteria_status.rules[18].expert | computational cardiac electrophysiologist (phase mapping) | biostatistician + optical mapping analyst |
| criteria_status.rules[18].location | worker/agents/critic.py (persistence_variants) | worker/agents/critic.py (STABLE_FRAC, stability) |
| criteria_status.rules[18].values.measured_cycle | 52 | [absent] |
| criteria_status.rules[18].values.paper_rotation | 50 | [absent] |
| criteria_status.rules[18].values.stable_frac | [absent] | 0.25 |
| criteria_status.rules[18].values.unstable | [absent] | ['light_off.singularity_frames_frac', 'illuminated_arrhythmia.persistent_rotors', 'illuminated_arrhythmia.persistent_rotor_count_max', 'illuminated_arrhythmia.dominant_freq_hz', 'illuminated_after_termination.singularity_frames_frac', 'persistent_rotor_tracks'] |
| pipeline.check | None | {'model': 'openai:gpt-5.5', 'proceed': True, 'anomalies': [{'topic': 'Pre-deposit processing / raw-data label', 'severity': 'warn', 'effect_on_analysis': "The recording should not be treated as raw camera counts; masking, temporal smoothing, spatial smoothing, and normalization affect noise assumptions and add unknown filtering before the protocol's Gaussian phase smoothing."}, {'topic': 'Event interpretation at frame 3170', 'severity': 'warn', 'effect_on_analysis': 'The frame-3170 boundary is an interpreted fluorescence/rhythm event rather than measured light onset; segment interpretation is provisional.'}, {'topic': 'Baseline and illumination artifact', 'severity': 'info', 'effect_on_analysis': 'Illumination crosstalk, normalization to stimulation-light signal, slow fluorescence change, and a fluorescence step affect absolute fluorescence and amplitude interpretation.'}, {'topic': 'baseline-window rule', 'severity': 'info', 'effect_on_analysis': 'The coded rule passes with baseline_frames 901, slowest_cycle_frames 415, required_min_frames 830, and ratio 2.171.'}], 'rationale': 'The fixed protocol is appropriate to run as a provisional analysis because the recording matches the intended mouse whole-heart optical mapping reference data and no recording fact mismatch makes the frame-based parameters wrong. The frame rate is 1000 Hz from the publication with DAQ consistency, and the coded baseline rule passes for the version 3 baseline of 901 frames. Interpretation is qualified by prior processing, the provisional frame-3170 event boundary, and illumination/normalization effects on fluorescence amplitude.', 'mismatches': [], 'hold_reason': None, 'protocol_id': 'f65d786f-f194-4be2-88b8-10d3dd25d674', 'methods_text': 'Using provisional parameter set version 3 for protocol f65d786f-f194-4be2-88b8-10d3dd25d674, the fixed parameters were baseline_frames=901, spatial_sigma=1.0, spatial_truncate=4.0, pad_frames=500, rotor_threshold=0.9, rotor_erode_px=3, link_px=4.0, max_gap=5, min_cycles=1.0, pair_dist_px=3.0, paired_frac=0.5, and render_step=4. The recording has 9267 frames in npy format with image size 64 by 55, frame rate 1000 Hz from publication 10.1371/journal.pcbi.1011660 with DAQ consistency, and pixel size 133 µm from the same publication. The analysed window was frames 500 to 8767, with provisional segment definitions and criteria: illuminated_arrhythmia frames 0 to 3170, illuminated_after_termination frames 3170 to 4977, and light_off frames 4977 to 9267.', 'params_version': 3, 'prompt_version': 'pipeline-v2'} |
| methods_text | Recording Mouse heart, spiral wave and optogenetic termination (M13Rec001) (doi:10.5281/zenodo.10228296; 64x55 px, 9267 frames, 1000 Hz) was analysed over frames 500-8767. Deposit shows signs of prior processing (provisional): negative values, non integer, nan mask all frames, temporal smoothing, spatial smoothing. Each pixel was baseline-corrected by subtracting a 901-frame centered moving average; NaN pixels were set to zero. Dye polarity (inverted) was taken from the sign of the median per-pixel skew of dV/dt. For phase only, each frame was spatially filtered with a Gaussian (sigma 1.0 px, truncated at 4.0 sigma); no temporal low-pass was applied. Phase was the angle of the Hilbert transform with 500 frames of padding on each side. Phase singularities were plaquettes with |winding| > 0.9 turns at least 3 px inside the tissue edge; they were tracked across frames (same charge, <= 4.0 px per frame, gaps <= 5 frames), and a persistent rotor was a track lasting >= 52 frames (1 cycle(s) of the fastest segment) within 3.0 px of an opposite-charge singularity in no more than 50% of its frames. Acquisition log (LED trigger channel, provisional interpretation): illumination on over frames 500-4977 of the analysed frames 500-8767. Segments (provisional, project lead (not a domain scientist), following the paper's design): illumination with arrhythmia frames 500-3170 (expected persistent rotors: present); illumination after termination frames 3170-4977 (expected persistent rotors: absent); light off frames 4977-8767 (expected persistent rotors: absent). Sensitivity: baseline 2712, 1356, 678, 901 frames x sigma 0.5, 1.0, 2.0 px, and tracker variants. singularities: across filters holds (provisional). persistent rotors: across filters holds (provisional); across trackers holds (provisional). persistent rotors fraction superseded: across filters does not hold (provisional); across trackers does not hold (provisional). All thresholds and criteria are provisional pending review by a domain scientist. | Using provisional parameter set version 3 for protocol f65d786f-f194-4be2-88b8-10d3dd25d674, the fixed parameters were baseline_frames=901, spatial_sigma=1.0, spatial_truncate=4.0, pad_frames=500, rotor_threshold=0.9, rotor_erode_px=3, link_px=4.0, max_gap=5, min_cycles=1.0, pair_dist_px=3.0, paired_frac=0.5, and render_step=4. The recording has 9267 frames in npy format with image size 64 by 55, frame rate 1000 Hz from publication 10.1371/journal.pcbi.1011660 with DAQ consistency, and pixel size 133 µm from the same publication. The analysed window was frames 500 to 8767, with provisional segment definitions and criteria: illuminated_arrhythmia frames 0 to 3170, illuminated_after_termination frames 3170 to 4977, and light_off frames 4977 to 9267. |