M13Rec001, Mouse heart, spiral wave and optogenetic termination
64 × 55 px, 9,267 frames, 1 kHz, 133 µm/px, deposit checks: negative values, nan mask all frames, temporal smoothing, spatial smoothing
Run 339921d8, 2026-10-28 18:40 UTC, protocol parameters v3, code 008c2dc (uncommitted changes), 9 workers, signature 9b40a32d, run view 339921d8, 13 signatures of this recording
Not reportable: range check not passed, code uncommitted changes, parameters unsigned, reviewer sign-off pending; 20 rules open
Properties
| Deposit | 10.5281/zenodo.10228296, https://zenodo.org/records/10228296 |
| Publication | 10.1371/journal.pcbi.1011660 |
| Licence | CC-BY-4.0 (as stated: cc-by-4.0) |
| Authors | Hussaini, Sayedeh; Luther, Stefan; Lädke, Sarah L. |
| File | public/M13Rec001_complete.npy, npy, 260,958,848 bytes |
| sha256 | 3f8f2e1b8f776633089b33ccd4bf3fccb4f13140b71991f1dcd0e0a12bb48cbc |
| Frame rate | 1000 Hz, publication 10.1371/journal.pcbi.1011660, Camera frames are 64 x 64 in the paper; the deposit is 64 x 55 (cropped). Consistent with the DAQ: 10 samples per frame and a 5 s light pulse spanning 50,001 samples imply a 10 kHz DAQ. |
| Pixel size | 133 µm, publication 10.1371/journal.pcbi.1011660, paper states 64 x 64 px at 133 um; the deposit is 64 x 55 (cropped, not rebinned) |
| Polarity | inverted (depolarization downward), measured |
| Segments source | project lead (not a domain scientist), following the paper's design, 10.1371/journal.pcbi.1011660 |
| Protocol | Mouse whole heart optical mapping (Luther lab), mouse, whole heart; parameters v3 set by developer (not a domain scientist): version 3: baseline 901 frames = 2.1 x the 433-frame (2.31 Hz) post-termination cycle resolved under v2; v2's 641 frames was 1.48 cycles, on the 1.5-cycle line, and the pipeline check held one run and passed another on the same inputs. pad 500 >= half the window. Provisional (REVIEW_NEEDED item 16). |
| Run | 339921d8-9255-4d78-9789-6816dd8b409c |
| Started, finished | 2026-10-28 18:40 UTC, 2026-10-28 18:48 UTC |
| Code | 008c2dc076bcebf9e7fa01a05e8b7c4b5a713b37 (uncommitted changes) |
| Workers | 9 |
| Steps | load, deposit_checks, baseline_correct, polarity, spatial_filter(phase only), hilbert_phase, phase_singularities, track_and_pair, beats_apd_cv, sensitivity, render |
| Signature | 9b40a32d-d6e2-4d0d-9976-9137ed881bea, 2026-10-28 18:47 UTC |
| Movie | runs/339921d8-9255-4d78-9789-6816dd8b409c/movie.mp4 |
| Lossless frames | runs/339921d8-9255-4d78-9789-6816dd8b409c/frames/voltage.npy, runs/339921d8-9255-4d78-9789-6816dd8b409c/frames/phase.npy, runs/339921d8-9255-4d78-9789-6816dd8b409c/frames/maps.npz; shape 8267 × 64 × 55, <f4 |
Parameters
% Mouse whole heart optical mapping (Luther lab), v3, read-only % set by developer (not a domain scientist); provisional, REVIEW_NEEDED 16 baseline_frames = 901; % >= 2 x slowest cycle (415, MAP): ok pad_frames = 500; % 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 = 52 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 |
|---|---|---|---|---|---|
| Illumination with arrhythmia | 0–3,170 | 500–3,170 | 52 (n = 53) | present | LED on before frame 0 (DAQ) → termination step (image, ±17 frames) |
| Illumination after termination | 3,170–4,977 | 3,170–4,977 | 415 (n = 4) | absent | termination step (image, ±17 frames) → illumination off (DAQ, ±11 frames) |
| Light off | 4,977–9,267 | 4,977–8,767 | 411 (n = 10) | absent | illumination off (DAQ, ±11 frames) → recording end |
Frames at 9,267 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 (project lead (not a domain scientist), following the paper's design, 10.1371/journal.pcbi.1011660).
Metrics
| Metric | Unit | Illumination with arrhythmia | Illumination after termination | Light off | Physiological Range |
|---|---|---|---|---|---|
| Rhythm | |||||
| Dominant frequency | Hz | 15.356–19.850 | 2.214 | 2.375 | 18.75–20 Hz, one recording, 10.1371/journal.pcbi.1011660, ±25% provisional |
| Rotors | |||||
| Persistent rotors | count | 4–15 | 0 | 0 | none cited |
| Max concurrent persistent rotors | count | 1–2 | 0 | 0 | none cited |
| Frames with a singularity | fraction | 0.479 | 0.001–0.015 | 0.003–0.030 | none cited |
| Beats, where a global rhythm exists | |||||
| Beats | count | 57 | 4 | 9 | none cited |
| Global amplitude ratio | ratio | 0.72 | 0.95 | 0.95 | gate ≥ 0.30 provisional |
| APD50 | ms | 14 | 16 | 16 | none cited |
| APD90 | ms | 25 | 76 | 75 | none cited |
| Conduction velocity | cm/s | 31.3 | 58.5 | 60.0 | 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: 2.419 Hz.
| Criterion | Rule | Result |
|---|---|---|
| Singularities present where the design expects them, absent elsewhere | each 'present' segment: frac >= 0.1 and >= 2.0 x max frac over 'absent' segments, at every setting | holds at 12 filter settings provisional |
| Persistent rotors present where the design expects them, absent elsewhere | each 'present' segment: count >= 1; each 'absent' segment: count <= 0, at every setting | holds at 12 filter settings and 3 trackers provisional |
| Persistence threshold, paper context | lifetime ≥ 52 frames (measured cycle) and ≥ 50 frames (cited 20 Hz) | agree 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
For recording 55cb4aa3-6502-45a6-a14c-85cb676fe8c3 under protocol f65d786f-f194-4be2-88b8-10d3dd25d674, the provisional parameter set version 3 is used 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 frame rate is 1000 Hz from the publication, with DAQ consistency noted, and the pixel size is 133 µm from the publication. The recording has 9267 frames in a 64 by 55 npy movie; the analysed window is frames 500 to 8767. The provisional segment definitions are illuminated_arrhythmia from frames 0 to 3170, illuminated_after_termination from frames 3170 to 4977, and light_off from frames 4977 to 9267; the parameter set, the segment definitions and the criteria are provisional.
Reportable values
| Metric | Segment | Value | Unit | Status |
|---|---|---|---|---|
| persistent rotor tracks | all | 4–15 | count | unstable, not reportable |
| dominant freq (Hz) | light off | 2.375 | Hz | no cited range |
| persistent rotors | light off | 0 | count | no cited range |
| singularity frames fraction | light off | 0.0029–0.0296 | fraction of frames | unstable, not reportable |
| persistent rotor count max | light off | 0 | count | no cited range |
| dominant freq (Hz) | illuminated arrhythmia | 15.4–19.9 | Hz | unstable, not reportable |
| persistent rotors | illuminated arrhythmia | 4–15 | count | unstable, not reportable |
| dominant freq (Hz) | illuminated after termination | 2.214 | Hz | no cited range |
| singularity frames fraction | illuminated arrhythmia | 0.479 | fraction of frames | no cited range |
| persistent rotors | illuminated after termination | 0 | count | no cited range |
| persistent rotor count max | illuminated arrhythmia | 1–2 | count | unstable, not reportable |
| singularity frames fraction | illuminated after termination | 0.000553–0.0149 | fraction of frames | unstable, not reportable |
| persistent rotor count max | illuminated after termination | 0 | count | no cited range |
physiology_ok: not decided (no cited range passed or failed); send back: False. Verdict: report only sensitivity-stable qualitative/algorithmic findings and do not report unstable metrics as single values; physiology_ok is null because the only cited range check, illuminated_arrhythmia.dominant_freq_hz, is unstable rather than physiology-validated. Stable observations include 0 persistent rotors and 0 maximum persistent-rotor count in light_off and illuminated_after_termination, dominant frequencies of 2.375 Hz in light_off and 2.214 Hz in illuminated_after_termination, and illuminated_arrhythmia singularity_frames_frac over 0.3816479400749064–0.48801498127340825, all without cited physiological ranges; unstable, not reportable as single values, are light_off.singularity_frames_frac over 0.0029023746701846965–0.02955145118733509, illuminated_arrhythmia.persistent_rotors over 4.0–15.0, illuminated_arrhythmia.persistent_rotor_count_max over 1.0–2.0, illuminated_arrhythmia.dominant_freq_hz over 15.356–19.85 Hz, illuminated_after_termination.singularity_frames_frac over 0.0005534034311012728–0.014941892639734366, and persistent_rotor_tracks over 4.0–15.0. The persistent-rotor rule holds using both the 52-frame measured-cycle threshold and the 50-frame cited 20 Hz rotation-period threshold, which agree; the relevant same-study context reports approximately 20 Hz before illumination and approximately 18.75 Hz during illumination (DOI 10.1371/journal.pcbi.1011660). Review required: pre-deposit processing/raw-data label, frame-3170 event interpretation, baseline/illumination artifact, provisional tool thresholds, and tracker sensitivity; 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 |
| baseline_window_rule worker/voltage/baseline_rule.py (FACTOR, evaluate) | A run proceeds only if the protocol's baseline window is >= 2x the slowest segment's cycle, the cycle from the MAP channel when a DAQ log exists, else from per-pixel dominant frequency on linearly detrended pixels; otherwise the run is held by code | 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 |
| baseline_step_detection worker/voltage/events.py (detect_baseline_step) | Baseline step = consensus upward step in tissue-mean raw baseline (cause not inferred; first misread as light onset, contradicted by the DAQ) | optical mapping experimentalist | provisional |
| daq_interpretation worker/voltage/daq.py | DAQ channel names from depositor notebook; frames = first N triggers of closest burst; midpoint thresholds | experimentalist who recorded the data (or the depositor) | provisional |
| segment_definitions worker/voltage/annotations.py (MOUSE_SEGMENTS) | Mouse segments bounded by DAQ light events and the baseline step, interpreted as spiral termination under illumination (project lead, from Hussaini et al. 2023) | cardiac electrophysiologist (ideally the depositing authors) | provisional |
| rotor_finding_criterion worker/voltage/sensitivity.py (MIN_FRAC, MIN_RATIO) | Singularity before/after finding holds if frac(before) >= min_frac and >= min_ratio x frac(after) at every setting (also kept, superseded, for persistent rotors) | cardiac electrophysiologist + biostatistician | 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 |
| 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 |
Review items
| Topic | Detail | Severity | Reviewer |
|---|---|---|---|
| unstable:light_off.singularity_frames_frac | This metric varies over 0.0029023746701846965–0.02955145118733509 across the filter grid and should not be reported as a single value. | warn | domain scientist / analysis lead |
| unstable:illuminated_arrhythmia.persistent_rotors | This metric varies over 4.0–15.0 across filter and tracker settings and should not be reported as a single count. | warn | domain scientist / analysis lead |
| unstable:illuminated_arrhythmia.persistent_rotor_count_max | This metric varies over 1.0–2.0 across filter and tracker settings and should not be reported as a single maximum concurrent count. | warn | domain scientist / analysis lead |
| unstable:illuminated_arrhythmia.dominant_freq_hz | This metric varies over 15.356–19.85 Hz across baseline-window settings; frequency interpretation should be reviewed against the same-study cited rotation context. | warn | domain scientist / electrophysiology reviewer |
| unstable:illuminated_after_termination.singularity_frames_frac | This metric varies over 0.0005534034311012728–0.014941892639734366 across the filter grid and should not be reported as a single value. | warn | domain scientist / analysis lead |
| unstable:persistent_rotor_tracks | This metric varies over 4.0–15.0 across filter and tracker settings and should not be reported as a single total track count. | warn | domain scientist / analysis lead |
| Pre-deposit processing / raw-data label | The recording is labeled as raw experimental data, but documentation and measurements indicate masking, spatial smoothing, temporal smoothing, and normalization; do not treat it as raw camera photon counts for analyses that require raw data or independent pixel noise. | warn | data provenance reviewer |
| Event interpretation at frame 3170 | Frame 3170 is a baseline_step only; illumination began before frame 0 and ended at frame 4977, so the stored spiral-termination interpretation is provisional and should not be treated as direct light onset evidence. | warn | domain scientist |
| Baseline and illumination artifact | The publication reports stimulation-light crosstalk and re-normalization; the recording also has a large slow baseline range and a baseline step, so absolute baseline or amplitude analyses need artifact review. | warn | optical mapping reviewer |
| Provisional tool thresholds | Event detection, processing flags, SNR, rhythm, reference-rate thresholds, stability threshold, and criteria are provisional and should be checked for critical uses. | info | domain scientist / methods reviewer |
| tracker sensitivity of rotor counts | The persistent-rotor rule agrees across strict, default, and loose trackers, but the illuminated-arrhythmia counts differ across trackers, so report the qualitative rule result rather than a single count. | warn | analysis lead |
Data and code availability
| Recording | 10.5281/zenodo.10228296, CC-BY-4.0, Hussaini, Sayedeh; Luther, Stefan; Lädke, Sarah L. |
| Publication | 10.1371/journal.pcbi.1011660 |
| Analysis code | 008c2dc076bcebf9e7fa01a05e8b7c4b5a713b37 (uncommitted changes) |
| Stored arrays | runs/339921d8-9255-4d78-9789-6816dd8b409c/frames/voltage.npy, runs/339921d8-9255-4d78-9789-6816dd8b409c/frames/phase.npy, runs/339921d8-9255-4d78-9789-6816dd8b409c/frames/maps.npz |