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 e21e4827, 2026-10-27 23:37 UTC, protocol parameters v3, code 905d5be (uncommitted changes), 9 workers, signature a609cf0a, run view e21e4827, 13 signatures of this recording
Not reportable: range check not passed, code uncommitted changes, 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 | e21e4827-a6ed-4197-9e87-98959ab51755 |
| Started, finished | 2026-10-27 23:37 UTC, 2026-10-27 23:42 UTC |
| Code | 905d5bebbb29da7ad46cd5045db14330695037c3 (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 | a609cf0a-fd5e-4922-b909-9f81812f9726, 2026-10-27 23:42 UTC |
| Movie | runs/e21e4827-a6ed-4197-9e87-98959ab51755/movie.mp4 |
| Lossless frames | runs/e21e4827-a6ed-4197-9e87-98959ab51755/frames/voltage.npy, runs/e21e4827-a6ed-4197-9e87-98959ab51755/frames/phase.npy, runs/e21e4827-a6ed-4197-9e87-98959ab51755/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
Recording Mouse heart, spiral wave and optogenetic termination (M13Rec001) (doi:10.5281/zenodo.10228296; 64x55 px, 9267 frames, 1000 Hz) was analysed over frames 500-8767. Deposit shows signs of prior processing (provisional): negative values, non integer, nan mask all frames, temporal smoothing, spatial smoothing. Each pixel was baseline-corrected by subtracting a 901-frame centered moving average; NaN pixels were set to zero. Dye polarity (inverted) was taken from the sign of the median per-pixel skew of dV/dt. For phase only, each frame was spatially filtered with a Gaussian (sigma 1.0 px, truncated at 4.0 sigma); no temporal low-pass was applied. Phase was the angle of the Hilbert transform with 500 frames of padding on each side. Phase singularities were plaquettes with |winding| > 0.9 turns at least 3 px inside the tissue edge; they were tracked across frames (same charge, <= 4.0 px per frame, gaps <= 5 frames), and a persistent rotor was a track lasting >= 52 frames (1 cycle(s) of the fastest segment) within 3.0 px of an opposite-charge singularity in no more than 50% of its frames. Acquisition log (LED trigger channel, provisional interpretation): illumination on over frames 500-4977 of the analysed frames 500-8767. Segments (provisional, project lead (not a domain scientist), following the paper's design): illumination with arrhythmia frames 500-3170 (expected persistent rotors: present); illumination after termination frames 3170-4977 (expected persistent rotors: absent); light off frames 4977-8767 (expected persistent rotors: absent). Sensitivity: baseline 2712, 1356, 678, 901 frames x sigma 0.5, 1.0, 2.0 px, and tracker variants. singularities: across filters holds (provisional). persistent rotors: across filters holds (provisional); across trackers holds (provisional). persistent rotors fraction superseded: across filters does not hold (provisional); across trackers does not hold (provisional). All thresholds and criteria are provisional pending review by a domain scientist.
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. Reportable as provisional descriptive findings: singularity presence during illuminated arrhythmia is stable, persistent-rotor presence during illuminated arrhythmia and absence in light_off and illuminated_after_termination are stable, and stable descriptive values with no cited ranges include light_off persistent rotors 0, light_off persistent_rotor_count_max 0, light_off dominant_freq_hz 2.375 Hz, illuminated_after_termination persistent rotors 0, illuminated_after_termination persistent_rotor_count_max 0, and illuminated_after_termination dominant_freq_hz 2.214 Hz; 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; the persistent-rotor threshold result agrees for 52 frames and for the paper-context 50 frames derived from the cited 20.0 Hz rotation period, with context from DOI 10.1371/journal.pcbi.1011660, while review is still needed for the processed-data label, frame 3170 event interpretation, illumination/baseline artifacts, and provisional thresholds; the cited 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 |
| 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 | Range across settings is 0.0029023746701846965–0.02955145118733509, so this fraction should not be reported as a single value. | warn | domain scientist / analysis lead |
| unstable:illuminated_arrhythmia.persistent_rotors | Range across filters and trackers is 4.0–15.0; report robust presence only, not the exact count. | warn | domain scientist / analysis lead |
| unstable:illuminated_arrhythmia.persistent_rotor_count_max | Range across settings is 1.0–2.0, so the maximum concurrent count is not a stable single value. | warn | domain scientist / analysis lead |
| unstable:illuminated_arrhythmia.dominant_freq_hz | Range across baseline windows is 15.356–19.85 Hz; although DOI 10.1371/journal.pcbi.1011660 gives context of approximately 20 Hz and approximately 18.75 Hz for the study, this metric is not reportable as a single value here. | warn | domain scientist / analysis lead |
| unstable:illuminated_after_termination.singularity_frames_frac | Range across settings is 0.0005534034311012728–0.014941892639734366, so this fraction should not be reported as a single value. | warn | domain scientist / analysis lead |
| unstable:persistent_rotor_tracks | Range across filters and trackers is 4.0–15.0, so the exact track count is unstable and not reportable. | warn | domain scientist / analysis lead |
| Pre-deposit processing / raw-data label | The README labels M13Rec001 as raw experimental data, but notebook documentation and prior-processing flags indicate masking, spatial smoothing, temporal smoothing, and normalization; do not treat this as raw camera photon-count data. | warn | data curator / imaging analyst |
| Event interpretation at frame 3170 | Frame 3170 is an image baseline_step only; illumination began before frame 0 and ended at frame 4977, so frame 3170 should not be treated as light onset, and the spiral-termination label remains provisional. | warn | domain scientist |
| Baseline and illumination artifact | The publication reports blue-light crosstalk and re-normalization, and this recording has a large slow baseline range and a baseline step; amplitude or baseline-dependent analyses need artifact-aware review. | warn | optical mapping expert |
| 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 | 905d5bebbb29da7ad46cd5045db14330695037c3 (uncommitted changes) |
| Stored arrays | runs/e21e4827-a6ed-4197-9e87-98959ab51755/frames/voltage.npy, runs/e21e4827-a6ed-4197-9e87-98959ab51755/frames/phase.npy, runs/e21e4827-a6ed-4197-9e87-98959ab51755/frames/maps.npz |