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 20dfde82, 2026-10-27 22:15 UTC, protocol parameters v1, code 13d8ceb, None workers, signature fb42c503, run view 20dfde82, 9 signatures of this recording
Not reportable: range check not passed, code clean, 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 | 20dfde82-4f4a-4a14-9732-14f64668db46 |
| Started, finished | 2026-10-27 22:15 UTC, 2026-10-27 22:19 UTC |
| Code | 13d8ceb123e64ab2c7eaba9fbf51605361856f11 |
| 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 | fb42c503-638b-471d-b7b2-834ee2023623, 2026-10-27 22:19 UTC |
| Movie | runs/20dfde82-4f4a-4a14-9732-14f64668db46/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 the provisional protocol parameter set and provisional criteria, version 1, the analysis uses 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 the deposit metadata midpoint of the stated range. The recording has 3800 frames, with the provisional segment definition whole_recording, labelled ventricular fibrillation (whole recording), spanning frames 0 to 3800; the analysed frames are 200 to 3600.
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: report only descriptive stable quantities for this provisional signature, not the rotor counts. The singularity-frame fraction is stable at 1.0 and dominant frequency is stable at 40.294 Hz, but neither has a cited physiological range, so physiology_ok is null rather than pass/fail. The persistent-rotor count is unstable over 204.0–464.0, the maximum concurrent persistent-rotor count is unstable over 9.0–21.0, and persistent-rotor tracks are unstable over 204.0–464.0, so those values are not reportable as single numbers; strict/default/loose tracking gave 250/303/450 persistent rotors while the tracker rule verdicts agree. The persistence-threshold rule is not applicable because there are no segment expectations or cited rotation period. Review is needed for the preprocessed deposit, transformed polarity relative to RH237, SNR dependence on preprocessing, and provisional reference thresholds; for the rotor metrics, also consider the published caution for this rat optical-mapping context that naive phase-singularity methods can yield false rotational drivers at conduction blocks (DOI 10.1371/journal.pcbi.1013963). The ranges, the stability threshold 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 count ranges from 204.0 to 464.0 across filter and tracker settings, exceeding the provisional stability criterion; do not report a single count without review. | block | domain scientist / signal-processing reviewer |
| unstable:whole_recording.persistent_rotor_count_max | The maximum concurrent count ranges from 9.0 to 21.0 across settings, exceeding the provisional stability criterion; do not report a single maximum count without review. | block | domain scientist / signal-processing reviewer |
| unstable:persistent_rotor_tracks | Track counts range from 204.0 to 464.0 across sensitivity settings; the cited rat-data context warns that naive phase-singularity approaches can create false rotational drivers at conduction blocks (DOI 10.1371/journal.pcbi.1013963). | block | domain scientist / signal-processing reviewer |
| preprocessed deposit | The deposit is not raw camera data and is documented as background-subtracted, spatially binned, low-pass filtered, drift-removed, and normalized; analyses requiring raw fluorescence/counts or unfiltered noise statistics would be misleading. | warn | data provenance reviewer |
| polarity transformed relative to dye | RH237 normally dims on depolarization, but measured polarity is non-inverted with 7/7 blocks agreeing; the depositor appears to have flipped or transformed sign, so the pipeline should orient from measured polarity. | warn | optical-mapping reviewer |
| SNR depends on preprocessing | Median SNR is high, but temporal filtering and detected temporal smoothing can inflate SNR by reducing apparent frame-to-frame noise. | info | signal-processing reviewer |
| reference thresholds provisional | No frame-rate inference was needed because the deposit states 1 kHz; automated processing flags and provisional rhythm/reference-rate tools are not yet domain-scientist reviewed. | info | domain scientist |
Data and code availability
| Recording | 10.5281/zenodo.18319102, CC-BY-4.0, Verstraeten, Bjorn; Lootens, Sebastiaan |
| Publication | 10.1093/cvr/cvaa141 |
| Analysis code | 13d8ceb123e64ab2c7eaba9fbf51605361856f11 |
| Stored arrays | [not stored] |