mouse_2609_150ms_control_MiCAM, Open-Source Low-Cost Cardiac Optical Mapping System: mouse_2609_150ms_control_MiCAM
100 × 100 px, 2,047 frames, 0.977 kHz, pixel size not stated, deposit checks: negative values
Run 6e21b7f8, 2026-10-28 18:15 UTC, protocol parameters v3, code 008c2dc (uncommitted changes), 9 workers, signature 804ddd67, run view 6e21b7f8, 2 signatures of this recording
Not reportable: range check not passed, code uncommitted changes, 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_MiCAM.mat, mat, 30,452,226 bytes |
| sha256 | 6f7fd1ea3f1f2610645c5d235dd4bc189bcdf58c1a038c8f8e68e2233948253e |
| 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 | 6e21b7f8-7cd1-499c-8e8f-ab37b36c7113 |
| Started, finished | 2026-10-28 18:15 UTC, 2026-10-28 18:18 UTC |
| Code | 008c2dc076bcebf9e7fa01a05e8b7c4b5a713b37 (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 | 804ddd67-f7b9-45c6-a823-bef795065584, 2026-10-28 18:17 UTC |
| Movie | runs/6e21b7f8-7cd1-499c-8e8f-ab37b36c7113/movie.mp4 |
| Lossless frames | runs/6e21b7f8-7cd1-499c-8e8f-ab37b36c7113/frames/voltage.npy, runs/6e21b7f8-7cd1-499c-8e8f-ab37b36c7113/frames/phase.npy, runs/6e21b7f8-7cd1-499c-8e8f-ab37b36c7113/frames/maps.npz; shape 1047 × 100 × 100, <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 = 17 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 | 0–2,047 | 500–1,547 | 7 (86% of pixels) | not stated | recording start → recording end |
Frames at 2,047 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 | 55.989–107.311 | none cited |
| Rotors | |||
| Persistent rotors | count | 1–5,211 | none cited |
| Max concurrent persistent rotors | count | 1–124 | none cited |
| Frames with a singularity | fraction | 1.000 | none cited |
| Beats, where a global rhythm exists | |||
| Beats | count | 63 | none cited |
| Global amplitude ratio | ratio | 2.00 | gate ≥ 0.30 provisional |
| APD50 | ms | 4 | none cited |
| APD90 | ms | 5 | none cited |
| Conduction velocity | cm/s | [not computed] | 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: 55.989 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 protocol f65d786f-f194-4be2-88b8-10d3dd25d674 with provisional parameter set version 3, the fixed analysis 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 2047 frames of 100 by 100 pixels in mat format; the frame rate used was 977.0 Hz from the recording-row admission entry citing 10.1371/journal.pone.0259174, and the pixel size was not available. The analysed window used for rhythm reporting was frames 500 to 1547, and the provisional segment definition was one whole_recording segment spanning frames 0 to 2047; the parameter set, segment definitions, and criteria are provisional.
Reportable values
| Metric | Segment | Value | Unit | Status |
|---|---|---|---|---|
| persistent rotor tracks | all | 1–5.21e+03 | count | unstable, not reportable |
| dominant freq (Hz) | whole recording | 56–107 | Hz | unstable, not reportable |
| persistent rotors | whole recording | 1–5.21e+03 | count | unstable, not reportable |
| singularity frames fraction | whole recording | 1 | fraction of frames | no cited range |
| persistent rotor count max | whole recording | 1–124 | count | unstable, not reportable |
physiology_ok: not decided (no cited range passed or failed); send back: False. Verdict: no physiology pass/fail can be computed because no stable ranged checks are available; the provisional ranges, stability threshold, and criteria should be treated as provisional. What is reportable is the stable whole-recording singularity-frames fraction, range 1.0 to 1.0, only as an observed output without a cited physiological range. What is not reportable as single values is persistent rotors, range 1.0 to 5211.0; maximum concurrent persistent-rotor count, range 1.0 to 124.0; dominant frequency, range 55.989 to 107.311 Hz; and persistent rotor tracks, range 1.0 to 5211.0. A same-species mouse spiral-wave context passage is available, but dominant-frequency comparison should wait because this metric is unstable (DOI 10.1371/journal.pcbi.1011660). Review the tracker count sensitivity, with strict/default/loose counts of 327, 1118, and 94, and the inspector concerns about 977.0 Hz MiCAM frame-rate provenance, likely pre-deposit sign or conditioning, all-negative integer data values, rhythm-detector unsuitability for the expected paced period, and the non-biological mask.
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 |
| 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 | Persistent-rotor count varies across the range 1.0 to 5211.0 across filter and tracker settings, exceeding the provisional stability rule. | warn | analysis |
| unstable:whole_recording.persistent_rotor_count_max | Maximum concurrent persistent-rotor count varies across the range 1.0 to 124.0 across filter and tracker settings, exceeding the provisional stability rule. | warn | analysis |
| unstable:whole_recording.dominant_freq_hz | Dominant frequency varies across the range 55.989 to 107.311 Hz across baseline windows, exceeding the provisional stability rule. | warn | analysis |
| unstable:persistent_rotor_tracks | Persistent rotor tracks vary across the range 1.0 to 5211.0 across filter and tracker settings, exceeding the provisional stability rule. | warn | analysis |
| tracker_count_sensitivity | Tracker variants produced different counts: strict 327, default 1118, and loose 94, so count magnitude needs tracking-parameter review even though rule-level agreement is true. | warn | analysis |
| Frame-rate provenance for a MiCAM file | Use 977.0 Hz as the working frame rate, but the cited paper quote is for the custom system whereas this file is labelled MiCAM; Zenodo metadata does not state the MiCAM frame rate. | warn | inspector |
| Pre-deposit sign/conditioning | Measured polarity is consistently non-inverted despite Di-4-ANEPPS normally dimming on depolarization, suggesting a sign flip or conditioning before deposit or export. | warn | inspector |
| Unexplained all-negative data values | All values are negative integers and are flagged as processed_before_deposit; the linked paper documents possible workflows, but the deposit README does not explain this file-level transformation. | warn | inspector |
| Rhythm detector not suitable for the expected paced period here | The rhythm tool result should not be used for physiology or frame-rate inference here because the expected paced period lies beyond the rhythm tool's baseline-window suitability. | info | inspector |
| Mask is not a heart segmentation | The mask is based only on nonzero temporal standard deviation and covers almost the entire image; tissue-only spatial interpretation needs a biological mask. | warn | inspector |
Data and code availability
| Recording | 10.5281/zenodo.5557829, cc-by-4.0, Rybashlykov Dmitry |
| Publication | 10.1371/journal.pone.0259174 |
| Analysis code | 008c2dc076bcebf9e7fa01a05e8b7c4b5a713b37 (uncommitted changes) |
| Stored arrays | runs/6e21b7f8-7cd1-499c-8e8f-ab37b36c7113/frames/voltage.npy, runs/6e21b7f8-7cd1-499c-8e8f-ab37b36c7113/frames/phase.npy, runs/6e21b7f8-7cd1-499c-8e8f-ab37b36c7113/frames/maps.npz |