mouseventricle06062018_A_FLEC_1uM_Paced, Mouse Whole Heart Optical Mapping Data: Mouse Whole Heart.zip/Mouse Whole Heart/06062018 A/mouseventricle06062018 A_FLEC 1uM Paced
51 × 51 px, 5,000 frames, 1 kHz, 156 µm/px
Run 1d65814d, 2026-10-28 19:22 UTC, protocol parameters v3, code 4533745, 4 workers, signature daa60525, run view 1d65814d
Not reportable: range check not passed, code clean, parameters unsigned, reviewer sign-off pending; 16 rules open
Properties
| Deposit | 10.6084/m9.figshare.17158742.v1 |
| Publication | 10.1038/s41597-022-01253-1 |
| Licence | CC0 (as stated: CC0) |
| Authors | Ming Lei |
| File | uploads/public/5a7107e9/Mouse_Whole_Heart.zip/Mouse_Whole_Heart/06062018_A/mouseventricle06062018_A_FLEC_1uM_Paced.mat, mat, 24,803,475 bytes |
| sha256 | 1ab7a0072312341c56240fbd22c16132ce5908f5655c90c06c8677696b6f6195 |
| Frame rate | 1000.0 Hz, admission 10.1038/s41597-022-01253-1 |
| Pixel size | 156.0 µm, admission 10.1038/s41597-022-01253-1 |
| Polarity | inverted (depolarization downward), measured |
| Segments source | admission (project lead); no comparison defined |
| 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 | 1d65814d-f982-424e-ae62-1ed747dc6cf7 |
| Started, finished | 2026-10-28 19:22 UTC, 2026-10-28 19:25 UTC |
| Code | 4533745bb9cdd7aab7940336430ca22779950c4f |
| Workers | 4 |
| Steps | load, deposit_checks, baseline_correct, polarity, spatial_filter(phase only), hilbert_phase, phase_singularities, track_and_pair, beats_apd_cv, sensitivity, render |
| Signature | daa60525-79d0-40ac-80a8-d131bab1047a, 2026-10-28 19:25 UTC |
| Movie | runs/1d65814d-f982-424e-ae62-1ed747dc6cf7/movie.mp4 |
| Lossless frames | runs/1d65814d-f982-424e-ae62-1ed747dc6cf7/frames/voltage.npy, runs/1d65814d-f982-424e-ae62-1ed747dc6cf7/frames/phase.npy, runs/1d65814d-f982-424e-ae62-1ed747dc6cf7/frames/maps.npz; shape 4000 × 51 × 51, <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 (7, images): 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 = 108 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 |
|---|---|---|---|---|---|
| Whole recording | 0–5,000 | 500–4,500 | 7 (98% of pixels) | not stated | recording start → recording end |
Frames at 5,000 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 (admission (project lead); no comparison defined).
Metrics
| Metric | Unit | Whole recording | Physiological Range |
|---|---|---|---|
| Rhythm | |||
| Dominant frequency | Hz | 9.250 | none cited |
| Rotors | |||
| Persistent rotors | count | 0–13 | none cited |
| Max concurrent persistent rotors | count | 0–2 | none cited |
| Frames with a singularity | fraction | 0.021–0.670 | none cited |
| Beats, where a global rhythm exists | |||
| Beats | count | 38 | none cited |
| Global amplitude ratio | ratio | 0.78 | gate ≥ 0.30 provisional |
| APD50 | ms | 15 | none cited |
| APD90 | ms | 40 | none cited |
| Conduction velocity | cm/s | 2.6 | 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: 9.250 Hz.
| 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 provisional parameter set version 3 for protocol f65d786f-f194-4be2-88b8-10d3dd25d674, the fixed parameters are 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 5000 frames of 51 x 51 MAT data, with frame rate 1000.0 Hz from admission/paper_methods for 10.1038/s41597-022-01253-1 and pixel size 156.0 µm from the same source. The analysed window is frames 500 to 4500. The provisional segment definition is whole_recording, labelled whole recording, spanning frames 0 to 5000, defined at admission with no events detected or logged; the parameter set, segment definitions, and criteria are provisional.
Reportable values
| Metric | Segment | Value | Unit | Status |
|---|---|---|---|---|
| persistent rotor tracks | all | 0–13 | count | unstable, not reportable |
| dominant freq (Hz) | whole recording | 9.25 | Hz | no cited range |
| persistent rotors | whole recording | 0–13 | count | unstable, not reportable |
| singularity frames fraction | whole recording | 0.021–0.67 | fraction of frames | unstable, not reportable |
| persistent rotor count max | whole recording | 0–2 | count | unstable, not reportable |
physiology_ok: not decided (no cited range passed or failed); send back: False. Provisional review: the only stable metric is dominant_freq_hz at 9.25 Hz, but it has no applicable cited range for this paced mouse whole-heart recording; the mouse spiral-wave context from DOI 10.1371/journal.pcbi.1011660 gives ≈20 Hz and ≈18.75 Hz, corresponding at 1000 frames/s to 50 and 53 frames, but that is not a population range for this file. The rotor-related outputs are unstable and not reportable: singularity_frames_frac spans 0.021 to 0.6705, persistent_rotors spans 0.0 to 13.0, persistent_rotor_count_max spans 0.0 to 2.0, and persistent_rotor_tracks spans 0.0 to 13.0 across the tested settings. The persistent-rotor threshold variants are not applicable because there are no segment expectations; strict/default/loose trackers found 0, 4, and 13 persistent rotors, so tracking sensitivity needs review rather than serving as proof that the finding is false. Before reporting, review the inspector block on frame-rate provenance, unavailable depositor documentation, tissue annotation/mask, physiology-reference limitations, and baseline drift/bleaching; all 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_info, otsu_threshold, largest_component) | Tissue mask from, in order: (1) NaN in frame 0 when the recording has any NaN; (2) a mask or background-image variable shipped in the file whose shape matches the frame (binary as is, an intensity image thresholded with Otsu); (3) Otsu's threshold on the mean image, the class with more temporal signal as tissue, largest connected component kept; source, coverage and threshold recorded | 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.singularity_frames_frac | Varies from 0.021 to 0.6705 across the filter grid, exceeding the provisional stability rule. | warn | analysis |
| unstable:whole_recording.persistent_rotors | Varies from 0.0 to 13.0 across filter and tracker settings, so persistent-rotor count is not reportable. | warn | analysis |
| unstable:whole_recording.persistent_rotor_count_max | Varies from 0.0 to 2.0 across filter and tracker settings, so the maximum simultaneous count is not reportable. | warn | analysis |
| unstable:persistent_rotor_tracks | Varies from 0.0 to 13.0 across filter and tracker settings, so track count is not reportable. | warn | analysis |
| Frame rate unavailable | Inspector reports that no frame-rate source was available from upload/admission, accessible deposit metadata, publication text, or acquisition log, so time conversion for paced data needs review despite the analysis overview listing 1000.0 Hz. | block | data curator |
| Accessible depositor documentation unavailable | Figshare deposit documentation could not be read by the metadata tool, so preprocessing steps and protocol statements were not independently verified. | warn | data curator |
| Tissue annotation/mask | Recording metadata and path labeling conflict on atrium versus mouseventricle, and the analysis mask covers the full 51 x 51 frame based only on nonzero temporal standard deviation. | warn | imaging reviewer |
| Physiology-reference limitations | The only provisional reference rate is mouse spiral rotation at 14.0625 to 25.0 Hz from a different context, while this filename indicates paced recording. | info | physiology reviewer |
| Baseline drift/bleaching | Inspector reports slow baseline change nearly one beat amplitude, so detrending and baseline handling may materially affect amplitude-based and rotor-related measurements. | warn | signal-processing reviewer |
| tracker sensitivity | Strict/default/loose tracker settings returned 0/4/13 persistent rotors; treat as a tracking-sensitivity review item rather than a false-positive verdict by itself. | warn | analysis |
Data and code availability
| Recording | 10.6084/m9.figshare.17158742.v1, CC0, Ming Lei |
| Publication | 10.1038/s41597-022-01253-1 |
| Analysis code | 4533745bb9cdd7aab7940336430ca22779950c4f |
| Stored arrays | runs/1d65814d-f982-424e-ae62-1ed747dc6cf7/frames/voltage.npy, runs/1d65814d-f982-424e-ae62-1ed747dc6cf7/frames/phase.npy, runs/1d65814d-f982-424e-ae62-1ed747dc6cf7/frames/maps.npz |