mouse_2609_150ms_control_iDS, Open-Source Low-Cost Cardiac Optical Mapping System: mouse_2609_150ms_control_iDS
200 × 200 px, 1,954 frames, 0.977 kHz, pixel size not stated, deposit checks: negative values
Run ee804172, 2026-10-28 20:47 UTC, protocol parameters v3, code 0d2391b, 4 workers, signature 4091a5ca, run view ee804172, 2 signatures of this recording
Not reportable: range check not passed, code clean, parameters unsigned, reviewer sign-off pending; 16 rules open
Properties
| Deposit | 10.5281/zenodo.5557829 |
| Publication | 10.1371/journal.pone.0259174 |
| Licence | cc-by-4.0 (as stated: cc-by-4.0) |
| Authors | Rybashlykov Dmitry |
| File | uploads/public/7764050e/mouse_2609_150ms_control_iDS.mat, mat, 114,024,466 bytes |
| sha256 | f9f4309fb395aa43ccae96f6e85724a7a739a98c295ff45598a6417b01605709 |
| Frame rate | 977.0 Hz, admission 10.1371/journal.pone.0259174 |
| Pixel size | None µm |
| Polarity | upright, 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 | ee804172-2876-47fb-94df-d522ea5c6e03 |
| Started, finished | 2026-10-28 20:47 UTC, 2026-10-28 20:51 UTC |
| Code | 0d2391b04113d316716bce2e2f9ee6ec6728d5d3 |
| 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 | 4091a5ca-4825-4b42-bced-67d6ecc7a015, 2026-10-28 20:50 UTC |
| Movie | runs/ee804172-2876-47fb-94df-d522ea5c6e03/movie.mp4 |
| Lossless frames | runs/ee804172-2876-47fb-94df-d522ea5c6e03/frames/voltage.npy, runs/ee804172-2876-47fb-94df-d522ea5c6e03/frames/phase.npy, runs/ee804172-2876-47fb-94df-d522ea5c6e03/frames/maps.npz; shape 954 × 200 × 200, <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; % 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 = 136 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 | 0–1,954 | 500–1,454 | [not measured] | not stated | recording start → recording end |
Frames at 1,954 total, 1.024 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 | 7.169 | none cited |
| Rotors | |||
| Persistent rotors | count | 9–609 | none cited |
| Max concurrent persistent rotors | count | 1–75 | none cited |
| Frames with a singularity | fraction | 1.000 | none cited |
| Beats, where a global rhythm exists | |||
| Beats | count | 0 | none cited |
| Global amplitude ratio | ratio | 0.28 | gate ≥ 0.30 provisional |
| APD50 | ms | no global beat | none cited |
| APD90 | ms | no global beat | none cited |
| Conduction velocity | cm/s | no global beat | 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: 7.169 Hz. No global upstroke found (no beat-wise activation map, CV or APD for this segment).
| 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 provisional fixed criteria were applied 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 recording has 1954 frames of 200 x 200 pixels in mat format; the frame rate is 977.0 Hz from the recording-row admission citing the paper methods quote that recordings were 200x200 pixels at 977 frames per second, and the pixel size is not available. The analysed frames are 500 to 1454, and the provisional segment definition is one whole_recording segment, labelled whole recording, from start_frame=0 to end_frame=1954, defined at admission with no detected or logged events.
Reportable values
| Metric | Segment | Value | Unit | Status |
|---|---|---|---|---|
| persistent rotor tracks | all | 9–609 | count | unstable, not reportable |
| dominant freq (Hz) | whole recording | 7.169 | Hz | no cited range |
| persistent rotors | whole recording | 9–609 | count | unstable, not reportable |
| singularity frames fraction | whole recording | 1 | fraction of frames | no cited range |
| persistent rotor count max | whole recording | 1–75 | count | unstable, not reportable |
physiology_ok: not decided (no cited range passed or failed); send back: False. Verdict: no cited-range physiology pass/fail can be assigned, and the ranges, the stability threshold of 0.25 x median, and the criteria are provisional; reportable descriptive outputs are singularity_frames_frac with range 0.9444444444444444 to 1.0 fraction of frames and dominant_freq_hz with range 6.145 to 7.169 Hz, while whole_recording.persistent_rotors and persistent_rotor_tracks are unstable at 9.0 to 609.0 and whole_recording.persistent_rotor_count_max is unstable at 1.0 to 75.0, so those counts are not reportable as single values; review the undocumented all-negative deposited values, low-confidence polarity, whole-frame mask, provisional SNR/processing thresholds, and tracker sensitivity of 80, 308, and 64 rotors, with mouse spiral-wave context from 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 |
| 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.persistent_rotors | The metric varies from 9.0 to 609.0 across filter grid and tracker settings and is not reportable as a single count. | warn | analysis |
| unstable:whole_recording.persistent_rotor_count_max | The metric varies from 1.0 to 75.0 across filter grid and tracker settings and is not reportable as a single maximum count. | warn | analysis |
| unstable:persistent_rotor_tracks | The metric varies from 9.0 to 609.0 across filter grid and tracker settings and is not reportable as a single track count. | warn | analysis |
| Undocumented pre-deposit transformation | The deposited file appears transformed before deposit based on all-negative integer values, and the deposit metadata and paper text do not explain that transformation. | warn | data_inspector |
| Polarity confidence | Measured polarity is not inverted, but confidence is low; use pipeline measurement-based orientation rather than assuming raw Di-4-ANEPPS fluorescence polarity. | warn | data_inspector |
| Whole-frame mask | No depositor mask exists and the generated mask may include background as tissue; replace or check the mask before spatial interpretation. | warn | data_inspector |
| SNR and processing thresholds are provisional | SNR and the flags used to infer prior processing come from provisional tool thresholds and methods, and temporal smoothing may inflate SNR. | info | data_inspector |
| tracker count sensitivity | Strict, default, and loose tracker settings returned 80, 308, and 64 persistent rotors, while the rule verdict agrees; this should be reviewed as sensitivity rather than taken as proof the qualitative finding is false. | warn | analysis |
Data and code availability
| Recording | 10.5281/zenodo.5557829, cc-by-4.0, Rybashlykov Dmitry |
| Publication | 10.1371/journal.pone.0259174 |
| Analysis code | 0d2391b04113d316716bce2e2f9ee6ec6728d5d3 |
| Stored arrays | runs/ee804172-2876-47fb-94df-d522ea5c6e03/frames/voltage.npy, runs/ee804172-2876-47fb-94df-d522ea5c6e03/frames/phase.npy, runs/ee804172-2876-47fb-94df-d522ea5c6e03/frames/maps.npz |