SignatureRun
Recordings / masked_data_RG_80nM / Run

masked_data_RG_80nM, run 99a6c948

Status done, stage done; requested by project lead; worker [not recorded]; started 2026-10-27 20:34 UTC, finished 2026-10-27 20:37 UTC, 177 s; signature 14055c81

Stages

StageStartedSeconds
[no stage log; run predates stage timing]

Log

TimeAgentActionDetail
20:34:08runsrun started{"planned_by": "openai:gpt-5.5", "recording_id": "73e4ebe2-6b09-4582-a1d6-ded901b7d124", "run_id": "99a6c948-270e-4ae3-9ba6-e8688472fd6c"}
20:37:04runssignature written{"criteria": "provisional", "holds": null, "run_id": "99a6c948-270e-4ae3-9ba6-e8688472fd6c", "signature_id": "14055c81-389d-464e-9eb6-b567c936de03"}

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 a preprocessed ex vivo Langendorff rat whole-heart VF optical-mapping recording under 80 nM rotigaptide, recorded at 1000 Hz according to the deposit; that agrees with the value already on record. The 128 × 80 deposited image size matches both the deposit and the linked paper, and the paper also reports 1000 frames/s. The data have documented preprocessing before deposit, including background subtraction, 3 × 3 spatial binning, 100 Hz low-pass filtering, drift removal, and normalization, so analyses should not treat them as raw camera counts. Measured polarity is consistently non-inverted even though RH237 normally dims on depolarization, so use measured polarity for orientation. No acquisition-log or detected event annotations are available for this recording.

MeasurementValueMethod, Caveat
SNR, median (p10–p90)18.8 (13.9–25.9)assumes white noise; on temporally smoothed deposits noise is underestimated and SNR inflated
Mask coverage50.9%, 5216 of 10240 pxdepositor NaN mask (frame 0)
Polarityblocks 7, inverted False, blocks agreeing 7, median dvdt skew 0.08132843673229218sign of median per-pixel skew of dV/dt, baseline-corrected (121 frames)
Drift / bleachingbaseline change -0.0108, vs beat amplitude -0.0979, slow range 0.162, trend, Spearman -0.356running median (381 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 processingunit range, non integer, nan mask partial, temporal smoothing, spatial smoothingdeposit checks
Dominant cycle by block, frames0–1000: 29.4, 1000–2000: 28.6, 2000–3000: 28.6, 3000–3800: 25.0
ConcernSeverityDetail
preprocessed depositwarnThe deposit is not raw camera data: it is documented as background-subtracted, spatially binned, low-pass filtered, drift-removed, and the publication says normalized. Analyses requiring raw fluorescence/counts or unfiltered noise statistics would be misleading.
polarity transformed relative to dyewarnRH237 normally dims on depolarization, but measured polarity is non-inverted with 7/7 blocks agreeing. The depositor appears to have flipped or transformed the sign; the pipeline should orient from the measured polarity, so this is not expected to make activation analysis wrong if handled.
SNR depends on preprocessinginfoMedian SNR is high, but documented temporal filtering and detected temporal smoothing can inflate the SNR estimate by reducing apparent frame-to-frame noise.
reference thresholds provisionalinfoNo frame-rate inference was needed because the deposit states 1 kHz. Any conclusions from automated processing flags and provisional rhythm/reference-rate tools should be treated as not yet domain-scientist reviewed.

Inspector report 2026-10-27 20:27 UTC, model openai:gpt-5.5, provisional. Median per-pixel SNR over tissue is 18.818067017408147, with p10 = 13.893293967898506 and p90 = 25.936276941781777 over 3000 frames. The SNR tool cautions that temporal smoothing underestimates noise and inflates SNR; that caveat applies because low-pass filtering is documented and temporal smoothing was detected. The tissue mask contains 5216 pixels out of 10240 total pixels, coverage 0.509375. The mask source is a depositor NaN mask in frame 0; frame 0 has 5024 NaN pixels. No stored events were returned, no acquisition log is present, and no detected light transitions or image baseline-step events were returned. Therefore there are no event frames to interpret for this recording. If events are later added, image-only baseline steps should be treated only as fluorescence changes unless a log shows a light transition at the same frame. The tissue-mean slow baseline, measured with a 381-frame running median, changes from 0.4981755316257477 to 0.48741528391838074, a change of -0.010760247707366943, equal to -0.09788043294092134 of the p5–p95 beat amplitude. Slow baseline range is 0.1622154712677002 and Spearman trend is -0.3557674750723145. Because the deposit documents drift removal and normalization, residual bleaching cannot be separated from preprocessing effects here.

Range checks

MetricSegmentValue at Run SettingCited RangeStatus
persistent rotor tracksall513 countnone citedunstable not reportable
dominant freq (Hz)whole recording40.59 Hznone citedno cited range
persistent rotorswhole recording513 countnone citedunstable not reportable
singularity frames fractionwhole recording1 fraction of framesnone citedno cited range
persistent rotor count maxwhole recording16 countnone citedunstable not reportable

Compare with run f6b6ff59

A: this run, code 586a5b6, None workers. B: run f6b6ff59, 2026-10-27 20:06 UTC, code 701ee65, None workers. 1025 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.mp4122831446820976nosize in bytes only; frames not compared
Stored ValueAB
metrics.amplitude_p990.325816154479980470.32620033621788025
metrics.dominant_freq40.5882352941176450.033999999999999996
metrics.dominant_freq_unitHzcycles/frame
metrics.min_rotor_frames2529
metrics.paired_singularity_frac0.63654027646699610.32411012714930565
metrics.persistent_rotor_count_max1613
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metrics.singularity_count_max10644
metrics.singularity_count_mean47.6814705882352919.347333333333335
metrics.tracks218963709
filter_params.render.step42
filter_params.spatial_sigma0.01.0
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filter_params.window.f136001700
filter_params.window.frame_rate_hz1000[absent]
filter_params.window.frame_rate_source{'ref': '10.5281/zenodo.18319102', 'kind': 'deposit_metadata', 'quote': 'Emitted fluorescence was recorded with high-resolution CMOS cameras at a sampling rate of 1 kHz, with a spatial resolution of 128 × 80 pixels and a pixel size of approximately 100–125 µm.'}[absent]
filter_params.window.segment_cycles_frames.whole_recording25[absent]
filter_params.window.segment_cycles_frames.window[absent]29
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filter_params.window.split_event[absent]None
sensitivity.fixed.expectNone[absent]
sensitivity.fixed.min_rotor_frames2529
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sensitivity.fixed.segments.window[absent][200, 1700]
sensitivity.fixed.window[1]36001700
sensitivity.gridlength 12length 9
sensitivity.grid[0].is_run_settingFalse[absent]
sensitivity.grid[0].persistent_rotor_tracks492149
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sensitivity.grid[1].is_run_settingFalse[absent]
sensitivity.grid[1].persistent_rotor_tracks349126
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sensitivity.grid[2].is_run_settingFalse[absent]
sensitivity.grid[2].persistent_rotor_tracks23689
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sensitivity.grid[3].baselinelightdefault
sensitivity.grid[3].baseline_frames241121
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sensitivity.grid[3].sigmarunlight
sensitivity.grid[3].spatial_sigma0.00.5
sensitivity.grid[4].is_run_settingFalse[absent]
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sensitivity.grid[4].sigmalightdefault
sensitivity.grid[4].spatial_sigma0.51.0
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sensitivity.grid[5].sigmadefaultheavier
sensitivity.grid[5].spatial_sigma1.02.0
sensitivity.grid[6].baselinedefaultheavier
sensitivity.grid[6].baseline_frames12181
sensitivity.grid[6].is_run_settingFalse[absent]
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sensitivity.grid[6].sigmaheavierlight
sensitivity.grid[6].spatial_sigma2.00.5
sensitivity.grid[7].baselinedefaultheavier
sensitivity.grid[7].baseline_frames12181
sensitivity.grid[7].is_run_settingTrue[absent]
sensitivity.grid[7].persistent_rotor_tracks513156
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sensitivity.grid[7].sigmarundefault
sensitivity.grid[7].spatial_sigma0.01.0
sensitivity.grid[8].is_run_settingFalse[absent]
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sensitivity.grid[8].sigmalightheavier
sensitivity.grid[8].spatial_sigma0.52.0
sensitivity.trackers[0].is_run_settingFalse[absent]
sensitivity.trackers[0].persistent_rotor_tracks310108
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sensitivity.trackers[1].is_run_settingTrue[absent]
sensitivity.trackers[1].persistent_rotor_tracks513138
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sensitivity.trackers[2].is_run_settingFalse[absent]
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sensitivity.varied.spatial_sigma.run0.0[absent]
criteria_status.ruleslength 10length 9
criteria_status.rules[0].values.spatial_sigma0.01.0
criteria_status.rules[4].values.min_frames2529
criteria_status.rules[6].values.sigmas.run0.0[absent]
criteria_status.rules[7].descriptionFrames analysed: whole recording minus one filter pad at each end (unless the plan narrows it)Frame window analysed per seed recording
criteria_status.rules[7].locationworker/voltage/runs.py (default_window)worker/voltage/runs.py (SEED_RUNS)
criteria_status.rules[7].values.f136001700
reportable{'persistent_rotor_tracks': {'unit': 'count', 'status': 'unstable, not reportable', 'settings': 'sensitivity grid + trackers', 'range_across_settings': [236.0, 738.0]}, 'whole_recording.dominant_freq_hz': {'unit': 'Hz', 'value': 40.588, 'checked': 'no_cited_range'}, 'whole_recording.persistent_rotors': {'unit': 'count', 'status': 'unstable, not reportable', 'settings': 'sensitivity grid + trackers', 'range_across_settings': [236.0, 738.0]}, 'whole_recording.singularity_frames_frac': {'unit': 'fraction of frames', 'value': 1.0, 'checked': 'no_cited_range'}, 'whole_recording.persistent_rotor_count_max': {'unit': 'count', 'status': 'unstable, not reportable', 'settings': 'sensitivity grid + trackers', 'range_across_settings': [10.0, 27.0]}}None
rotor_count1613
critic.checks{'checks': {'persistent_rotor_tracks': {'unit': 'count', 'range': None, 'metric': 'persistent_rotor_tracks', 'stable': False, 'status': 'unstable_not_reportable', 'segment': None, 'spread_frac': 1.02, 'value_at_run_setting': 513, 'range_across_settings': [236.0, 738.0]}, 'whole_recording.dominant_freq_hz': {'unit': 'Hz', 'range': None, 'metric': 'dominant_freq_hz', 'stable': True, 'status': 'no_cited_range', 'segment': 'whole_recording', 'spread_frac': 0.0, 'value_at_run_setting': 40.588, 'range_across_settings': [40.588, 40.588]}, 'whole_recording.persistent_rotors': {'unit': 'count', 'range': None, 'metric': 'persistent_rotors', 'stable': False, 'status': 'unstable_not_reportable', 'segment': 'whole_recording', 'spread_frac': 1.02, 'value_at_run_setting': 513, 'range_across_settings': [236.0, 738.0]}, 'whole_recording.singularity_frames_frac': {'unit': 'fraction of frames', 'range': None, 'metric': 'singularity_frames_frac', 'stable': True, 'status': 'no_cited_range', 'segment': 'whole_recording', 'spread_frac': 0.0, 'value_at_run_setting': 1.0, 'range_across_settings': [1.0, 1.0]}, 'whole_recording.persistent_rotor_count_max': {'unit': 'count', 'range': None, 'metric': 'persistent_rotor_count_max', 'stable': False, 'status': 'unstable_not_reportable', 'segment': 'whole_recording', 'spread_frac': 1.062, 'value_at_run_setting': 16, 'range_across_settings': [10.0, 27.0]}}, 'unstable': ['whole_recording.persistent_rotors', 'whole_recording.persistent_rotor_count_max', 'persistent_rotor_tracks'], 'physiology_ok': None, 'ranged_checks': []}None
critic.stability{'persistent_rotor_tracks': {'max': 738.0, 'min': 236.0, 'median': 492.0, 'stable': False, 'settings': 15, 'spread_frac': 1.02, 'values_grid': [492, 349, 236, 495, 499, 396, 254, 513, 504, 430, 262, 558], 'varied_over': 'filter grid + trackers', 'values_trackers': [310, 513, 738]}, 'whole_recording.dominant_freq_hz': {'max': 40.588, 'min': 40.588, 'median': 40.588, 'stable': True, 'settings': 3, 'spread_frac': 0.0, 'varied_over': 'baseline windows', 'values_by_baseline': {'81': 40.588, '121': 40.588, '241': 40.588}}, 'whole_recording.persistent_rotors': {'max': 738.0, 'min': 236.0, 'median': 492.0, 'stable': False, 'settings': 15, 'spread_frac': 1.02, 'values_grid': [492, 349, 236, 495, 499, 396, 254, 513, 504, 430, 262, 558], 'varied_over': 'filter grid + trackers', 'values_trackers': [310, 513, 738]}, 'whole_recording.singularity_frames_frac': {'max': 1.0, 'min': 1.0, 'median': 1.0, 'stable': True, 'settings': 12, 'spread_frac': 0.0, 'values_grid': [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0], 'varied_over': 'filter grid'}, 'whole_recording.persistent_rotor_present': {'stable': True, 'values_grid': [True, True, True, True, True, True, True, True, True, True, True, True], 'varied_over': 'filter grid + trackers', 'values_trackers': [True, True, True], 'stable_across_filters': True, 'stable_across_trackers': True}, 'whole_recording.persistent_rotor_count_max': {'max': 27.0, 'min': 10.0, 'median': 16.0, 'stable': False, 'settings': 15, 'spread_frac': 1.062, 'values_grid': [14, 14, 10, 15, 18, 17, 12, 16, 17, 20, 11, 17], 'varied_over': 'filter grid + trackers', 'values_trackers': [11, 16, 27]}}None
critic.persistence_variants{'agree': None, 'measured_cycle': {'basis': 'one dominant cycle of the fastest segment at the run setting', 'reason': 'no segment expectations, so the rule has nothing to test', 'applicable': False, 'min_frames': 25}, 'paper_rotation': {'reason': 'no segment expectations', 'applicable': False}}None
critic.trackers{'note': 'disagreement is reported as a review item, not folded into the pass/fail', 'agree': True, 'trackers': [{'link_px': 2.0, 'max_gap': 1, 'tracker': 'strict', 'is_run_setting': False, 'persistent_rotors_by_segment': {'whole_recording': 310}}, {'link_px': 4.0, 'max_gap': 5, 'tracker': 'default', 'is_run_setting': True, 'persistent_rotors_by_segment': {'whole_recording': 513}}, {'link_px': 6.0, 'max_gap': 10, 'tracker': 'loose', 'is_run_setting': False, 'persistent_rotors_by_segment': {'whole_recording': 738}}]}None
critic.required_review_topics['unstable:whole_recording.persistent_rotors', 'unstable:whole_recording.persistent_rotor_count_max', 'unstable:persistent_rotor_tracks']None
critic.ranges[]None
critic.passages{'false_phase_singularities': {'ref': '10.1371/journal.pcbi.1013963', 'note': 'This paper analyses the same rat deposit and argues that phase-singularity counts on such data include false positives at conduction blocks; our singularity detector is of the naive kind it describes.', 'quotes': ['the naive approach implicitly assumes a continuous phase, causing wavefront endpoints attached to functional conduction blocks to appear as spurious rotational drivers', 'We analyzed one case with maximally increased gap junction coupling \\(80 nM rotigaptide\\) to test our methods on stable rotors'], 'status': 'provisional', 'passages': ['suggesting they reflect the presence of a defect rather than genuine rotational activity. For the optical mapping data, the naive approach implicitly assumes a continuous phase, causing wavefront endpoints attached to functional conduction blocks to appear as spurious rotational drivers. Our method shifts the paradigm from rotation around singular points to rotation around two-dimensional phase defects, ', 'yzed in [16] (See Fig 4). The data was obtained from [35], where details of heart preparation and ethics are described. We analyzed one case with maximally increased gap junction coupling (80 nM rotigaptide) to test our methods on stable rotors. 10.1371/journal.pcbi.1013963.g004Fig 4Ventricular fibrillation optical map.Snapshot of an optical intensity map of ven'], 'applies_to': {'species': 'rat', 'metric_prefix': 'persistent_rotors'}}}None
critic.verdict.send_backFalseNone
critic.verdict.metric_statuseslength 5length 0
pipeline.params.render.step42
pipeline.params.spatial_sigma0.01.0
pipeline.params.tracking.min_frames2529
pipeline.params.window.f136001700
pipeline.params.window.frame_rate_hz1000[absent]
pipeline.params.window.frame_rate_source{'ref': '10.5281/zenodo.18319102', 'kind': 'deposit_metadata', 'quote': 'Emitted fluorescence was recorded with high-resolution CMOS cameras at a sampling rate of 1 kHz, with a spatial resolution of 128 × 80 pixels and a pixel size of approximately 100–125 µm.'}[absent]
pipeline.params.window.segment_cycles_frames.whole_recording25[absent]
pipeline.params.window.segment_cycles_frames.window[absent]29
pipeline.params.window.segments[{'name': 'whole_recording', 'label': 'ventricular fibrillation (whole recording)', 'defined': [0, 3800], 'analysed': [200, 3600], 'citation': None, 'defined_by': 'developer (no comparison defined)', 'segment_id': 'c2bb42bc-7898-4c1b-8808-99cb68b94504', 'end_event_id': None, 'start_event_id': None, 'expected_persistent_rotors': None}]{'window': [200, 1700]}
pipeline.params.window.split_event[absent]None
pipeline.stepslength 9length 11
pipeline.steps[2]baseline_correctdetect_events
pipeline.steps[3]polaritybaseline_correct
pipeline.steps[4]hilbert_phasepolarity
pipeline.steps[5]phase_singularitiesspatial_filter(phase only)
pipeline.steps[6]track_and_pairhilbert_phase
pipeline.steps[7]sensitivityphase_singularities
pipeline.steps[8]rendertrack_and_pair
methods_textUsing provisional defaults, bounds, segment definitions, and criteria that have not yet been reviewed by a domain scientist, the recording was loaded and deposit checks were performed, then baseline correction was applied with a centered moving-average window of 121 frames, polarity was oriented from the measured non-inverted polarity, Hilbert phase was computed without a phase-only Gaussian spatial filter because spatial_sigma was 0, phase singularities were detected with rotor_threshold 0.9 turns while ignoring plaquettes within rotor_erode_px 3 pixels of the tissue edge, singularities were tracked and paired with link_px 4, max_gap 5, pair_dist_px 3, and paired_frac 0.5, the fixed sensitivity check was run with the chosen values included, and rendering used render_step 4. The frame rate was 1000 Hz from the deposit metadata; the analysis window was null, meaning the whole recording minus the fixed 200-frame filter pads, corresponding to analysed frames 200 to 3600, and the segment was whole_recording from frame 0 to frame 3800.Recording Rat heart, ventricular fibrillation (RG 80 nM) (doi:10.5281/zenodo.18319102; 128x80 px, 3800 frames, frame rate not stated) was analysed over frames 200-1700. Deposit shows signs of prior processing (provisional): unit range, non integer, nan mask partial, temporal smoothing, spatial smoothing. Each pixel was baseline-corrected by subtracting a 121-frame centered moving average; NaN pixels were set to zero. Dye polarity (upright) 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, computed with 200 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 >= 29 frames (one cycle of the fastest segment) that was within 3.0 px of an opposite-charge singularity in no more than 50% of its frames. Sensitivity: baseline 241, 121, 81 frames x sigma 0.5, 1.0, 2.0 px, and tracker variants. All thresholds and criteria are provisional pending review by a domain scientist.
Statusdone
Stagedone
Heartbeat–
Log2 entries