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 faeb5ebc, 2026-10-27 23:05 UTC, protocol parameters v3, code b1be824 (uncommitted changes), None workers, signature cf0c8a27, run view faeb5ebc, 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 | faeb5ebc-ee96-4994-96b0-025811d9374b |
| Started, finished | 2026-10-27 23:05 UTC, 2026-10-27 23:11 UTC |
| Code | b1be82429ddde2ad90ee88afacaae98a173e4403 (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 | cf0c8a27-002b-40af-809c-72bd47871da0, 2026-10-27 23:11 UTC |
| Movie | runs/faeb5ebc-ee96-4994-96b0-025811d9374b/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; % >= 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
Using provisional parameter set version 3 for protocol f65d786f-f194-4be2-88b8-10d3dd25d674, the fixed parameters were 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 recording has 9267 frames in npy format with image size 64 by 55, frame rate 1000 Hz from publication 10.1371/journal.pcbi.1011660 with DAQ consistency, and pixel size 133 µm from the same publication. The analysed window was frames 500 to 8767, with provisional segment definitions and criteria: 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 provisional presence/absence criteria, not unstable scalar values; physiology_ok is indeterminate because the only ranged check, illuminated-arrhythmia dominant frequency, is unstable over 15.356–19.85 Hz rather than reportable as a single value, although DOI 10.1371/journal.pcbi.1011660 provides same-study mouse context of approximately 20 Hz before illumination and approximately 18.75 Hz during illumination, with a 20.0 Hz rotation corresponding to 50 frames. Reportable items include stable absence of persistent rotors in light_off and illuminated_after_termination, stable persistent-rotor presence during illuminated_arrhythmia under the provisional rule, stable illuminated_arrhythmia singularity-frame fraction at 0.47902621722846445, stable light_off dominant frequency at 2.375 Hz, and stable illuminated_after_termination dominant frequency at 2.214 Hz, all with no cited physiology range except the unstable frequency context. Unstable and 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. Needs review: the deposited-data processing/raw label, frame-3170 event interpretation, baseline and illumination artifact, and all provisional tool thresholds; 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 | Filter sensitivity is high for the light-off singularity-frame fraction; do not report a single value, and review the range 0.0029023746701846965–0.02955145118733509 fraction of frames. | warn | domain scientist / analysis methods |
| unstable:illuminated_arrhythmia.persistent_rotors | Persistent-rotor counts during illuminated arrhythmia vary over 4.0–15.0 across filter and tracker settings; report presence/absence only under the provisional rule and review the count before use. | warn | domain scientist / analysis methods |
| unstable:illuminated_arrhythmia.persistent_rotor_count_max | Maximum concurrent persistent-rotor count during illuminated arrhythmia varies over 1.0–2.0; do not report a single maximum without review. | warn | domain scientist / analysis methods |
| unstable:illuminated_arrhythmia.dominant_freq_hz | Dominant frequency varies over 15.356–19.85 Hz across baseline windows; because this overlaps same-study context but is unstable, it should be reviewed before reporting. | warn | domain scientist / analysis methods |
| unstable:illuminated_after_termination.singularity_frames_frac | Post-termination illuminated singularity-frame fraction varies over 0.0005534034311012728–0.014941892639734366; do not report a single value without review. | warn | domain scientist / analysis methods |
| unstable:persistent_rotor_tracks | Total persistent-rotor tracks vary over 4.0–15.0 across filter and tracker settings; the track count is not reportable as a single value. | warn | domain scientist / analysis methods |
| Pre-deposit processing / raw-data label | The recording is labeled raw in the README, but documentation and prior-processing flags indicate masking, spatial smoothing, temporal smoothing, and normalization; analyses requiring raw photon counts or independent pixel noise should not treat it as raw camera data. | warn | data curator / methods reviewer |
| Event interpretation at frame 3170 | Frame 3170 is a baseline_step image event, not light onset; illumination began before frame 0 and ended at frame 4977, so the stored spiral-termination interpretation is provisional. | warn | domain scientist |
| Baseline and illumination artifact | The publication reports blue-light crosstalk and re-normalization by recorded stimulation light signal, and this recording has a large slow baseline range and a baseline step; absolute baseline or amplitude analyses need artifact handling. | warn | methods reviewer |
| Provisional tool thresholds | Event detection, processing flags, SNR, rhythm, and reference-rate thresholds are provisional and not yet reviewed by a domain scientist. | info | domain scientist / methods 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 | b1be82429ddde2ad90ee88afacaae98a173e4403 (uncommitted changes) |
| Stored arrays | [not stored] |