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 6d6015e6, 2026-10-27 22:21 UTC, protocol parameters v3, code 13d8ceb, None workers, signature 056f9e28, run view 6d6015e6, 13 signatures of this recording
Not reportable: range check not passed, code clean, parameters unsigned, reviewer sign-off pending; 19 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 | 6d6015e6-82f2-4762-97e2-5663d547c549 |
| Started, finished | 2026-10-27 22:21 UTC, 2026-10-27 22:26 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 | 056f9e28-85a3-4436-aea7-6df0842b39e3, 2026-10-27 22:26 UTC |
| Movie | runs/6d6015e6-82f2-4762-97e2-5663d547c549/movie.mp4 |
| Lossless frames | [not stored] |
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; % no baseline rule recorded for this run 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 | [not measured] | present | LED on before frame 0 (DAQ) → termination step (image, ±17 frames) |
| Illumination after termination | 3,170–4,977 | 3,170–4,977 | [not measured] | absent | termination step (image, ±17 frames) → illumination off (DAQ, ±11 frames) |
| Light off | 4,977–9,267 | 4,977–8,767 | [not measured] | 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 this run, the provisional parameter set and criteria are protocol f65d786f-f194-4be2-88b8-10d3dd25d674 version 3 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, and the pixel size is 133 µm from the publication. The analysed window is frames 500 to 8767. The provisional segment definitions are illuminated_arrhythmia, frames 0 to 3170; illuminated_after_termination, frames 3170 to 4977; and light_off, frames 4977 to 9267.
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 stable descriptive findings and the provisional qualitative pattern, not unstable single values; physiology_ok is null because no stable ranged metric was available for pass/fail. Reportable items include stable absence of persistent rotors in light_off and illuminated_after_termination, stable maximum concurrent persistent-rotor count of 0 in those segments, stable dominant frequencies of 2.375 Hz in light_off and 2.214 Hz after termination, and a stable illuminated_arrhythmia singularity-frame fraction of 0.47902621722846445 with sensitivity range 0.3816479400749064–0.48801498127340825; the provisional persistent-rotor presence/absence rule holds using both the 52-frame measured-cycle threshold and the 50-frame paper-derived threshold from the 20.0 Hz context in DOI 10.1371/journal.pcbi.1011660. Not reportable as single values are light_off.singularity_frames_frac 0.0029023746701846965–0.02955145118733509, illuminated_arrhythmia.persistent_rotors 4.0–15.0, illuminated_arrhythmia.persistent_rotor_count_max 1.0–2.0, illuminated_arrhythmia.dominant_freq_hz 15.356–19.85 Hz, illuminated_after_termination.singularity_frames_frac 0.0005534034311012728–0.014941892639734366, and persistent_rotor_tracks 4.0–15.0. Needs review: pre-deposit processing/raw-data labeling, the provisional frame-3170 event interpretation, baseline/illumination artifact effects, and all provisional tool thresholds, ranges, stability threshold and criteria; the same-study frequency context is approximately 18.75–20.0 Hz, provisionally checked over 14.0625–25.0 Hz, in DOI 10.1371/journal.pcbi.1011660.
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 |
| 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 | Sensitivity range 0.0029023746701846965–0.02955145118733509 across the filter grid; do not report a single value until filter dependence is reviewed. | warn | analysis/domain reviewer |
| unstable:illuminated_arrhythmia.persistent_rotors | Sensitivity range 4.0–15.0 across filters and trackers; do not report a single count until tracking/filter dependence is reviewed. | warn | analysis/domain reviewer |
| unstable:illuminated_arrhythmia.persistent_rotor_count_max | Sensitivity range 1.0–2.0 across filters and trackers; do not report a single maximum concurrent count until tracking/filter dependence is reviewed. | warn | analysis/domain reviewer |
| unstable:illuminated_arrhythmia.dominant_freq_hz | Sensitivity range 15.356–19.85 Hz across baseline windows; do not report a single frequency until baseline-window dependence is reviewed against the same-study context in DOI 10.1371/journal.pcbi.1011660. | warn | domain reviewer |
| unstable:illuminated_after_termination.singularity_frames_frac | Sensitivity range 0.0005534034311012728–0.014941892639734366 across the filter grid; do not report a single value until filter dependence is reviewed. | warn | analysis/domain reviewer |
| unstable:persistent_rotor_tracks | Sensitivity range 4.0–15.0 across filters and trackers; do not report a single track count until tracking/filter dependence is reviewed. | warn | analysis/domain reviewer |
| Pre-deposit processing / raw-data label | README labels the recording as raw experimental data, but notebook documentation and measurements indicate masking, spatial smoothing, temporal smoothing, and normalization; avoid analyses that assume raw photon counts or independent pixel noise. | warn | data curator/domain 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 label is provisional and should not be treated as direct light-onset evidence. | warn | domain reviewer |
| Baseline and illumination artifact | Blue stimulation light crosstalk, re-normalization by stimulation-light signal, slow baseline range, and a baseline step mean analyses using absolute baseline or amplitude must account for illumination/crosstalk/normalization effects. | warn | domain reviewer |
| Provisional tool thresholds | Event detection, processing flags, SNR, rhythm, reference-rate thresholds, ranges, stability threshold, and criteria are provisional and not yet reviewed by a domain scientist. | info | domain reviewer |
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 | 13d8ceb123e64ab2c7eaba9fbf51605361856f11 |
| Stored arrays | [not stored] |