M13Rec001, run faeb5ebc
Status done, stage done; requested by project lead; worker worker; started 2026-10-27 23:05 UTC, finished 2026-10-27 23:11 UTC, 338 s; signature cf0c8a27
Stages
| Stage | Started | Seconds |
|---|---|---|
| [no stage log; run predates stage timing] | ||
Log
| Time | Agent | Action | Detail |
|---|---|---|---|
| 23:05:39 | runs | run started | {"checked_by": "openai:gpt-5.5", "protocol_params_version": 3, "recording_id": "55cb4aa3-6502-45a6-a14c-85cb676fe8c3", "run_id": "faeb5ebc-ee96-4994-96b0-025811d9374b"} |
| 23:11:17 | runs | signature written | {"criteria": "provisional", "holds": {"persistent_rotors": true, "persistent_rotors_fraction_superseded": false, "singularities": true}, "run_id": "faeb5ebc-ee96-4994-96b0-025811d9374b", "signature_id": "cf0c8a27-002b-40af-809c-72bd47871da0"} |
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 |
|---|---|---|
| Pre-deposit processing / raw-data label | warn | 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. |
| Event interpretation at frame 3170 | warn | The frame-3170 boundary is an interpreted fluorescence/rhythm event rather than measured light onset; segment interpretation is provisional. |
| Baseline and illumination artifact | info | Illumination crosstalk, normalization to stimulation-light signal, slow fluorescence change, and a fluorescence step affect absolute fluorescence and amplitude interpretation. |
| baseline-window rule | info | The coded rule passes with baseline_frames 901, slowest_cycle_frames 415, required_min_frames 830, and ratio 2.171. |
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.
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 202e66c5
A: this run, code b1be824 (uncommitted changes), None workers. B: run 202e66c5, 2026-10-27 23:02 UTC, code b1be824 (uncommitted changes), None workers. 10 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[16].values.anomalies[3] | baseline-window rule | Baseline-window rule |
| pipeline.check.anomalies[0].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. | The deposited movie should not be treated as raw camera counts: depositor documentation and measurements indicate masking, temporal smoothing, spatial smoothing, and normalization. The fixed pipeline may still be run, but its Gaussian phase smoothing is added on top of prior filtering of unknown effective total, and any interpretation requiring independent pixel noise or raw photon-count amplitudes would be misleading. |
| pipeline.check.anomalies[1].effect_on_analysis | The frame-3170 boundary is an interpreted fluorescence/rhythm event rather than measured light onset; segment interpretation is provisional. | The segment boundary at frame 3170 is based on a provisional termination/baseline-step interpretation, not a directly measured light onset. The fixed segment definitions can be analysed as defined, but results should be described relative to the provisional boundary and not as an illumination-on transition. |
| pipeline.check.anomalies[2].effect_on_analysis | Illumination crosstalk, normalization to stimulation-light signal, slow fluorescence change, and a fluorescence step affect absolute fluorescence and amplitude interpretation. | Blue-light crosstalk, re-normalization by stimulation-light signal, a large slow baseline range, and a baseline step can affect absolute baseline and amplitude. The fixed phase/rotor pipeline can proceed, but baseline- or amplitude-dependent interpretations need caution. |
| pipeline.check.anomalies[2].severity | info | warn |
| pipeline.check.anomalies[3].effect_on_analysis | The coded rule passes with baseline_frames 901, slowest_cycle_frames 415, required_min_frames 830, and ratio 2.171. | The coded rule reports ok: the 901-frame baseline is at least 2 times the slowest segment cycle from the MAP-channel DAQ log, so this rule does not hold the run. |
| pipeline.check.anomalies[3].topic | baseline-window rule | Baseline-window rule |
| pipeline.check.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. | Using the provisional parameter set version 3, with provisional segment definitions and provisional criteria, the recording was checked under the Mouse whole heart optical mapping (Luther lab) protocol with 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 × 55, frame rate 1000 Hz from the publication, and pixel size 133 µm from the publication. The analysed window is frames 500–8767; the provisional segments are illuminated_arrhythmia, frames 0–3170; illuminated_after_termination, frames 3170–4977; and light_off, frames 4977–9267. |
| pipeline.check.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. | The protocol is the intended mouse whole-heart optical-mapping protocol for this public reference recording, and the recording facts do not conflict with the protocol: the frame rate is 1000 Hz from the publication, the pixel size is 133 µm from the publication, and the 64 × 55 deposited movie is consistent with a cropped version of the 64 × 64 camera acquisition. The fixed version-3 parameters are therefore applicable as provisional pipeline settings, and the coded baseline-window rule passes for the slowest segment. The main limitations are not protocol mismatches but interpretation caveats: the deposited data are already masked, smoothed, and normalized; frame 3170 is a provisional termination/baseline-step boundary rather than light onset; and illumination/crosstalk/normalization affect baseline and amplitude. |
| 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. | Using the provisional parameter set version 3, with provisional segment definitions and provisional criteria, the recording was checked under the Mouse whole heart optical mapping (Luther lab) protocol with 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 × 55, frame rate 1000 Hz from the publication, and pixel size 133 µm from the publication. The analysed window is frames 500–8767; the provisional segments are illuminated_arrhythmia, frames 0–3170; illuminated_after_termination, frames 3170–4977; and light_off, frames 4977–9267. |