masked_data_RG_80nM, Rat heart, ventricular fibrillation
128 × 80 px, 3,800 frames, 1 kHz, 112.5 µm/px, deposit checks: unit range, non integer, nan mask partial, temporal smoothing, spatial smoothing
Run 5ae47ba0, 2026-10-27 22:09 UTC, protocol parameters v1, code 752b95b (uncommitted changes), None workers, signature 4535f454, run view 5ae47ba0, 9 signatures of this recording
Not reportable: range check not passed, code uncommitted changes, parameters unsigned, reviewer sign-off pending; 15 rules open
Properties
| Deposit | 10.5281/zenodo.18319102, https://zenodo.org/records/18319102 |
| Publication | 10.1093/cvr/cvaa141 |
| Licence | CC-BY-4.0 (as stated: cc-by-4.0) |
| Authors | Verstraeten, Bjorn; Lootens, Sebastiaan |
| File | public/masked_data_RG_80nM.mat, mat, 293,204,250 bytes |
| sha256 | 9e30977de373f78d1b5d236bd100e46bb79c72152d3a7516b9c03c4849391076 |
| Frame rate | 1000 Hz, deposit metadata 10.5281/zenodo.18319102 |
| Pixel size | 112.5 µm, deposit metadata 10.5281/zenodo.18319102, midpoint of the stated 100-125 um; conduction velocities carry a +/-11% range from this alone |
| Polarity | upright, measured |
| Segments source | developer (no comparison defined) |
| Protocol | Rat whole heart optical mapping (Zenodo 18319102), rat, whole heart; parameters v1 set by developer (not a domain scientist): version 1: the library defaults as of commit 363372b; provisional, see protocol_params.py |
| Run | 5ae47ba0-d7dc-4745-bd8b-91bfea5c6009 |
| Started, finished | 2026-10-27 22:09 UTC, 2026-10-27 22:11 UTC |
| Code | 752b95b01dde60f86eb71b47343448c7af4551c1 (uncommitted changes) |
| Workers | [not recorded] |
| Steps | load, deposit_checks, baseline_correct, polarity, spatial_filter(phase only), hilbert_phase, phase_singularities, track_and_pair, beats_apd_cv, sensitivity, render |
| Signature | 4535f454-5118-4ddc-aec3-51102954d005, 2026-10-27 22:11 UTC |
| Movie | runs/5ae47ba0-d7dc-4745-bd8b-91bfea5c6009/movie.mp4 |
| Lossless frames | [not stored] |
Parameters
% Rat whole heart optical mapping (Zenodo 18319102), v1, read-only % set by developer (not a domain scientist); provisional, REVIEW_NEEDED 16 baseline_frames = 121; % no baseline rule recorded for this run pad_frames = 200; % each side, outside the window spatial_sigma = 1.0; % px, Gaussian, phase only spatial_truncate = 4.0; % kernel radius, sigma lowpass = []; % none polarity = 1; % measured, skew of dV/dt rotor_threshold = 0.9; % turns, |winding| per plaquette rotor_erode_px = 3; % px from tissue edge ignored link_px = 4.0; % tracking, max step per frame max_gap = 5; % frames a track may vanish min_cycles = 1.0; % own rotations, min_frames = 25 pair_dist_px = 3.0; % opposite-charge pairing paired_frac = 0.5; % max paired fraction of a track render_step = 4; % movie only
Segments
| Segment | Defined | Analysed | Cycle, frames | Expected Rotors | Bounded By |
|---|---|---|---|---|---|
| Ventricular fibrillation (whole recording) | 0–3,800 | 200–3,600 | [not measured] | not stated | recording start → recording end |
Frames at 3,800 total, 1.0 ms per frame. Cycle from the MAP channel of the DAQ log (median interval) when one exists, else from per-pixel dominant frequency. Boundaries, expectations and the segment design are provisional (developer (no comparison defined)).
Metrics
| Metric | Unit | Ventricular fibrillation (whole recording) | Physiological Range |
|---|---|---|---|
| Rhythm | |||
| Dominant frequency | Hz | 40.294 | none cited |
| Rotors | |||
| Persistent rotors | count | 204–464 | none cited |
| Max concurrent persistent rotors | count | 9–21 | none cited |
| Frames with a singularity | fraction | 1.000 | none cited |
| Beats, where a global rhythm exists | |||
| Beats | count | 0 | none cited |
| Global amplitude ratio | ratio | 0.28 | gate ≥ 0.30 provisional |
| APD50 | ms | no global beat | none cited |
| APD90 | ms | no global beat | none cited |
| Conduction velocity | cm/s | no global beat | none cited |
Values at the run setting. Red: range across the sensitivity grid (12 baseline × sigma settings, 3 trackers) where the spread exceeds 25 % of the median; not reportable as a value. Beat metrics are not varied over the grid. Dominant frequency over the whole analysed window: 40.294 Hz. No global upstroke found (no beat-wise activation map, CV or APD for this segment).
| Criterion | Rule | Result |
|---|---|---|
| Design expectations | none stated for this recording's segments | no criterion to test; counts are descriptive provisional |
Report
The PDF carries the parameters as run, segments, metrics, criteria, reportable values, every provisional rule, the review items, the opening frame as camera, voltage and phase with the parameter footer, and the provenance block. The JSON carries the same plus the full stored metrics, sensitivity and critic records.
Methods
Using provisional parameter set version 1 for protocol a0059cf5-fbde-4942-a18f-399ebe70e9ff, the analysis would use baseline_frames = 121, spatial_sigma = 1.0, spatial_truncate = 4.0, pad_frames = 200, 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 frame rate is 1000 Hz from deposit_metadata, and the pixel size is 112.5 µm from deposit_metadata. The analysed frames are 200 to 3600. The provisional segment definition is whole_recording, labelled ventricular fibrillation (whole recording), with start_frame = 0 and end_frame = 3800, defined as the whole recording with no events detected or logged; the parameter set, segment definitions, and criteria are provisional.
Reportable values
| Metric | Segment | Value | Unit | Status |
|---|---|---|---|---|
| persistent rotor tracks | all | 204–464 | count | unstable, not reportable |
| dominant freq (Hz) | whole recording | 40.29 | Hz | no cited range |
| persistent rotors | whole recording | 204–464 | count | unstable, not reportable |
| singularity frames fraction | whole recording | 1 | fraction of frames | no cited range |
| persistent rotor count max | whole recording | 9–21 | count | unstable, not reportable |
physiology_ok: not decided (no cited range passed or failed); send back: False. Verdict: physiology_ok is not decidable because there are no cited ranges for the stable descriptive metrics and the rotor-count metrics are unstable; reportable items are singularity_frames_frac as a descriptive value stable over 1.0 to 1.0 and dominant_freq_hz as a descriptive value stable over 40.294 to 40.294 Hz, while whole_recording.persistent_rotors and persistent_rotor_tracks are unstable over 204.0 to 464.0 and whole_recording.persistent_rotor_count_max is unstable over 9.0 to 21.0 and should not be reported as numeric signature metrics. The strict, default, and loose trackers found 250, 303, and 450 persistent rotors, respectively, so tracker sensitivity needs review even though the tracker agreement flag is true; the persistent-threshold variants are not applicable because there were no segment expectations. The deposit preprocessing and polarity transformation need reviewer awareness, and rotor-count interpretation should account for the same-rat context warning that naive phase-singularity detectors can produce false rotational drivers at conduction blocks (DOI 10.1371/journal.pcbi.1013963). The ranges, the stability threshold of 0.25 x median, and the criteria are provisional.
Provisional rules
| Rule, Location | Description | Expert | Status |
|---|---|---|---|
| protocol_parameter_set worker/voltage/protocol_params.py (developer_defaults, set_params) | Each protocol's fixed, versioned analysis parameters (version 1 = developer defaults); no run or agent may deviate | optical mapping analyst | provisional |
| filter_defaults worker/voltage/preprocess.py (Params) | Default baseline window (frames) and spatial Gaussian sigma/truncate for phase | optical mapping analyst (cardiac electrophysiology) | provisional |
| tissue_mask worker/voltage/io.py (tissue_mask) | Tissue = not NaN in frame 0 and nonzero temporal std | optical mapping analyst | provisional |
| polarity worker/voltage/preprocess.py (polarity) | Dye polarity from sign of median per-pixel skew of dV/dt | optical mapping analyst / voltage dye chemist | provisional |
| singularity_detection worker/voltage/preprocess.py (Params.rotor_threshold, rotor_erode_px) | Phase singularity = |winding| > threshold turns, >= erode px from tissue edge | computational cardiac electrophysiologist (phase mapping) | provisional |
| rotor_persistence worker/voltage/rotors.py (TrackParams) | Track linking distance/gap and minimum lifetime for a persistent rotor | computational cardiac electrophysiologist (phase mapping) | provisional |
| chirality_pairing worker/voltage/rotors.py (TrackParams.pair_dist_px, paired_frac) | Opposite-charge singularities within pair distance are a pair; tracks paired most of their life are excluded from rotors | computational cardiac electrophysiologist (phase mapping) | provisional |
| sensitivity_grid worker/voltage/sensitivity.py (SIGMAS, BASELINE_MULTIPLES, baseline_levels) | Filter levels tested: spatial sigma and baseline window values | optical mapping analyst | provisional |
| analysis_window worker/voltage/runs.py (default_window) | Frames analysed: whole recording minus one filter pad at each end (unless the plan narrows it) | cardiac electrophysiologist familiar with the dataset | provisional |
| prior_processing_flags worker/voltage/inspect.py (prior_processing) | Thresholds for flagging depositor processing (normalization, masking, temporal/spatial smoothing) | imaging scientist (camera acquisition and noise) | provisional |
| pipeline_check worker/agents/pipeline.py (INSTRUCTIONS, validator) | The pipeline agent's hold/proceed decision from protocol mismatches and inspector anomalies; it chooses no parameter | optical mapping analyst | provisional |
| physiology_reference_rates worker/voltage/physiology.py (RANGES, TOLERANCE_FRAC) | 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 | cardiac electrophysiologist per species | provisional |
| stability_rule worker/agents/critic.py (STABLE_FRAC, stability) | 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' | biostatistician + optical mapping analyst | provisional |
| persistence_threshold_variants worker/agents/critic.py (persistence_variants) | 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 | computational cardiac electrophysiologist (phase mapping) | provisional |
| persistent_rotor_criterion worker/voltage/sensitivity.py (MIN_ROTORS_PRESENT, MAX_ROTORS_ABSENT) | Persistent-rotor finding holds if every 'present' segment has >= 1 persistent rotor and every 'absent' segment has none, at every setting | cardiac electrophysiologist | provisional |
Review items
| Topic | Detail | Severity | Reviewer |
|---|---|---|---|
| unstable:whole_recording.persistent_rotors | The whole-recording persistent-rotor count ranged from 204.0 to 464.0 across filter grid and tracker settings, exceeding the provisional stability criterion and making the numeric count not reportable. | warn | automated stability critic |
| unstable:whole_recording.persistent_rotor_count_max | The whole-recording maximum simultaneous persistent-rotor count ranged from 9.0 to 21.0 across filter grid and tracker settings, exceeding the provisional stability criterion and making the numeric maximum not reportable. | warn | automated stability critic |
| unstable:persistent_rotor_tracks | Persistent rotor tracks ranged from 204.0 to 464.0 across filter grid and tracker settings, exceeding the provisional stability criterion and making the numeric track count not reportable. | warn | automated stability critic |
| preprocessed deposit | The deposit is documented as background-subtracted, spatially binned, low-pass filtered, drift-removed, and normalized, so analyses requiring raw fluorescence/counts or unfiltered noise statistics would be misleading. | warn | recording inspector |
| polarity transformed relative to dye | RH237 normally dims on depolarization, but measured polarity is non-inverted with 7/7 blocks agreeing; the pipeline should orient from measured polarity. | warn | recording inspector |
| SNR depends on preprocessing | Median SNR may be inflated because documented temporal filtering and detected temporal smoothing can reduce apparent frame-to-frame noise. | info | recording inspector |
| reference thresholds provisional | No frame-rate inference was needed because the deposit states 1 kHz, but conclusions from automated processing flags and provisional rhythm/reference-rate tools should be treated as not yet domain-scientist reviewed. | info | recording inspector |
Data and code availability
| Recording | 10.5281/zenodo.18319102, CC-BY-4.0, Verstraeten, Bjorn; Lootens, Sebastiaan |
| Publication | 10.1093/cvr/cvaa141 |
| Analysis code | 752b95b01dde60f86eb71b47343448c7af4551c1 (uncommitted changes) |
| Stored arrays | [not stored] |