SignatureRun

M13Rec001, run d59dab8d

Status done, stage done; requested by project lead; worker [not recorded]; started 2026-10-27 21:11 UTC, finished 2026-10-27 21:16 UTC, 339 s; signature 2e9d5ea7

Stages

StageStartedSeconds
[no stage log; run predates stage timing]

Log

TimeAgentActionDetail
21:11:01runsrun started{"planned_by": "openai:gpt-5.5", "recording_id": "55cb4aa3-6502-45a6-a14c-85cb676fe8c3", "run_id": "d59dab8d-e40f-48f9-a571-37f2348df594"}
21:16:40runssignature written{"criteria": "provisional", "holds": {"persistent_rotors": false, "persistent_rotors_fraction_superseded": false, "singularities": true}, "run_id": "d59dab8d-e40f-48f9-a571-37f2348df594", "signature_id": "2e9d5ea7-cdd9-4952-9308-bbaf2cf035d7"}

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.

MeasurementValueMethod, 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 coverage66.2%, 2332 of 3520 pxdepositor NaN mask (frame 0)
Polarityblocks 18, inverted True, blocks agreeing 18, median dvdt skew -4.419912338256836sign of median per-pixel skew of dV/dt, baseline-corrected (121 frames)
Drift / bleachingbaseline change -1.61, vs beat amplitude -1.12, slow range 3.33, trend, Spearman -0.489running 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 processingnegative values, nan mask all frames, temporal smoothing, spatial smoothingdeposit checks
Dominant cycle by block, frames0–1000: 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
ConcernSeverityDetail
Pre-deposit processing / raw-data labelwarnThe 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 3170warnThe 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 artifactwarnThe 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 thresholdsinfoEvent 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.
EventFrameSourceMethod
illumination on0 ± 11acquisition logmidpoint threshold on DAQ channel 'led_trigger', mapped to frames via camera triggers
illumination off4977 ± 11acquisition logmidpoint threshold on DAQ channel 'led_trigger', mapped to frames via camera triggers
baseline step3170 ± 17imageconsensus 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

MetricSegmentValue at Run SettingCited RangeStatus
persistent rotor tracksall4 countnone citedunstable not reportable
dominant freq (Hz)light off7.335 Hznone citedunstable not reportable
persistent rotorslight off0 countnone citedno cited range
singularity frames fractionlight off0.06235 fraction of framesnone citedunstable not reportable
persistent rotor count maxlight off0 countnone citedno cited range
dominant freq (Hz)illuminated arrhythmia15.49 Hz18.75–20, checked 14.0625–25, 10.1371/journal.pcbi.1011660within range
persistent rotorsilluminated arrhythmia4 countnone citedunstable not reportable
dominant freq (Hz)illuminated after termination7.194 Hznone citedunstable not reportable
singularity frames fractionilluminated arrhythmia0.5195 fraction of framesnone citedno cited range
persistent rotorsilluminated after termination0 countnone citedno cited range
persistent rotor count maxilluminated arrhythmia1 countnone citedunstable not reportable
singularity frames fractionilluminated after termination0.04483 fraction of framesnone citedunstable not reportable
persistent rotor count maxilluminated after termination0 countnone citedno cited range

Compare with run 590e35c0

A: this run, code 9b8a172, None workers. B: run 590e35c0, 2026-10-27 20:28 UTC, code 586a5b6, None workers. 727 stored values differ.

FileABSameHow
frames/voltage[none][none][not comparable]recorded sha256
frames/phase[none][none][not comparable]recorded sha256
frames/maps[none][none][not comparable]recorded sha256
movie.mp478868727523541nosize in bytes only; frames not compared
Stored ValueAB
metrics.amplitude_p992.5024089813232422.7878506183624268
metrics.dominant_freq7.3305514830269534.849441750310138
metrics.paired_singularity_frac0.058068872383524640.08071748878923767
metrics.persistent_rotor_durationslength 4length 3
metrics.persistent_rotor_durations[0].frames_in_segment7675
metrics.persistent_rotor_durations[0].lifetime_cycles1.171.15
metrics.persistent_rotor_durations[0].lifetime_frames7675
metrics.persistent_rotor_durations[0].start333334
metrics.persistent_rotor_durations[1].end767735
metrics.persistent_rotor_durations[1].frames_in_segment9765
metrics.persistent_rotor_durations[1].lifetime_cycles1.491.0
metrics.persistent_rotor_durations[1].lifetime_frames9765
metrics.persistent_rotor_durations[2].end12161212
metrics.persistent_rotor_durations[2].frames_in_segment108103
metrics.persistent_rotor_durations[2].lifetime_cycles1.661.58
metrics.persistent_rotor_durations[2].lifetime_frames108103
metrics.persistent_rotor_durations[2].start11091110
metrics.persistent_rotor_frames_frac0.042629976316679820.027404984775008457
metrics.persistent_rotor_lifetimeslength 4length 3
metrics.persistent_rotor_lifetimes[0]108103
metrics.persistent_rotor_lifetimes[1]9775
metrics.persistent_rotor_lifetimes[2]9765
metrics.persistent_rotor_tracks43
metrics.persistent_rotors43
metrics.segments.illuminated_after_termination.singularity_count_max119
metrics.segments.illuminated_after_termination.singularity_count_mean0.098505810736026560.11566131710016603
metrics.segments.illuminated_arrhythmia.persistent_rotor_durationslength 4length 3
metrics.segments.illuminated_arrhythmia.persistent_rotor_durations[0].frames_in_segment7675
metrics.segments.illuminated_arrhythmia.persistent_rotor_durations[0].lifetime_cycles1.171.15
metrics.segments.illuminated_arrhythmia.persistent_rotor_durations[0].lifetime_frames7675
metrics.segments.illuminated_arrhythmia.persistent_rotor_durations[0].start333334
metrics.segments.illuminated_arrhythmia.persistent_rotor_durations[1].end767735
metrics.segments.illuminated_arrhythmia.persistent_rotor_durations[1].frames_in_segment9765
metrics.segments.illuminated_arrhythmia.persistent_rotor_durations[1].lifetime_cycles1.491.0
metrics.segments.illuminated_arrhythmia.persistent_rotor_durations[1].lifetime_frames9765
metrics.segments.illuminated_arrhythmia.persistent_rotor_durations[2].end12161212
metrics.segments.illuminated_arrhythmia.persistent_rotor_durations[2].frames_in_segment108103
metrics.segments.illuminated_arrhythmia.persistent_rotor_durations[2].lifetime_cycles1.661.58
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metrics.segments.illuminated_arrhythmia.singularity_count_mean0.76969696969696970.7380471380471381
metrics.segments.illuminated_arrhythmia.singularity_frames_frac0.51952861952861950.49966329966329964
metrics.segments.light_off.singularity_count_max1213
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metrics.singularity_count_max1213
metrics.singularity_count_mean0.33404759219578210.32694259614300214
metrics.singularity_frames_frac0.21190932671704070.20232322093154392
metrics.tracks751816
filter_params.baseline_frames151241
filter_params.window.segment_cycles_frames.illuminated_after_termination139201
filter_params.window.segment_cycles_frames.light_off136204
sensitivity.gridlength 16length 12
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sensitivity.varied.baseline_scaling{'multiples': {'3x_cycle': 3.0, '6x_cycle': 6.0, '1.5x_cycle': 1.5}, 'reference_segment': 'illuminated_after_termination', 'segment_cycles_frames': {'light_off': 136, 'illuminated_arrhythmia': 65, 'illuminated_after_termination': 139}, 'reference_cycle_frames': 139, 'window_over_cycle_per_segment': {'run': {'light_off': 1.11, 'illuminated_arrhythmia': 2.32, 'illuminated_after_termination': 1.09}, '3x_cycle': {'light_off': 3.07, 'illuminated_arrhythmia': 6.42, 'illuminated_after_termination': 3.0}, '6x_cycle': {'light_off': 6.13, 'illuminated_arrhythmia': 12.83, 'illuminated_after_termination': 6.0}, '1.5x_cycle': {'light_off': 1.53, 'illuminated_arrhythmia': 3.2, 'illuminated_after_termination': 1.5}}}[absent]
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criteria_status.rules[6].locationworker/voltage/sensitivity.py (SIGMAS, BASELINE_MULTIPLES, baseline_levels)worker/voltage/sensitivity.py (SIGMAS, BASELINES)
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criteria_status.rules[14].values.deviations[0].chosen151241
criteria_status.rules[14].values.deviations[0].reasonAt default filters, the light_off segment has a dominant cycle length of 136.3 frames, and the parameter menu states that a baseline window shorter than a cycle distorts it; choosing 151 frames keeps the window longer than the slowest segment cycle while remaining relatively local around the reported frame-3170 baseline step and frame-4977 illumination-off event.The rhythm estimate at default filtering reports dominant cycle lengths of 64.6, 100.4, and 136.3 frames for the three segments, and the rhythm tool cautions that cycles longer than the baseline window are attenuated; the menu also notes that a baseline window shorter than a cycle distorts it. A 241-frame window is within the allowed bounds and longer than the longest segment cycle.
criteria_status.rules[14].values.deviations[1].reasonThe inspector reports that the deposited movie was already spatially smoothed before deposit, with measured neighbour_dv_corr_median = 0.9957938301611564 and documentation stating spatial smoothing; therefore an additional phase-only Gaussian blur is omitted.The inspector reports that the deposited movie is already spatially smoothed according to depositor documentation and measured neighbour-difference correlation, so adding the default phase-only Gaussian blur would apply an extra spatial filter to already processed data.
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critic.trackers.trackers[1].persistent_rotors_by_segment.illuminated_arrhythmia43
critic.trackers.trackers[2].persistent_rotors_by_segment.illuminated_arrhythmia43
pipeline.params.baseline_frames151241
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pipeline.params.window.segment_cycles_frames.light_off136204
methods_textUsing provisional defaults, bounds, segment definitions and criteria that have not yet been reviewed by a domain scientist, recording 55cb4aa3-6502-45a6-a14c-85cb676fe8c3 was loaded and checked as a processed optical-mapping deposit; the frame rate was 1000 Hz from the publication source cited by the inspector report. The whole recording was analysed with window = null, with the pipeline pads applied by the analysis code, covering the provisional segments illuminated_arrhythmia frames 0–3170, illuminated_after_termination frames 3170–4977, and light_off frames 4977–9267. Signals were baseline-corrected with a centered moving-average window of 151 frames, inverted-polarity handling was applied, no phase-only spatial Gaussian filter was applied because spatial_sigma = 0, Hilbert phase was computed, phase singularities were detected with rotor_threshold = 0.9 turns and rotor_erode_px = 3 px, singularities were tracked and paired with link_px = 4.0 px, max_gap = 5 frames, pair_dist_px = 3.0 px and paired_frac = 0.5, the fixed sensitivity grid plus these chosen values was run, and rendering used render_step = 4.The recording will be loaded and checked as processed deposit data, then analysed over the whole available window after filter padding, with analysed frames 200–9067 from a 9267-frame, 64 × 55 recording at 1000 Hz from the publication-based frame-rate source. The provisional segments, defaults, bounds, thresholds and criteria are not yet reviewed by a domain scientist; the provisional segments are illuminated_arrhythmia frames 0–3170, illuminated_after_termination frames 3170–4977, and light_off frames 4977–9267. Baseline correction will use a centered moving-average window of 241 frames, polarity will be handled as inverted, no phase-only spatial Gaussian filter will be applied because spatial_sigma is 0, Hilbert phase will be computed, phase singularities will be counted at |winding| threshold 0.9 turns while excluding plaquettes within rotor_erode_px 3 of the tissue edge, singularities will be tracked and paired with link_px 4, max_gap 5, pair_dist_px 3, and paired_frac 0.5, the fixed sensitivity grid plus these chosen values will be run, and rendering will show every 4th frame.
Statusdone
Stagedone
Heartbeat–
Log2 entries