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 2aec1b88, 2026-10-28 18:59 UTC, protocol parameters v3, code 0aee293 (uncommitted changes), 4 workers, signature 0187eb93, run view 2aec1b88, 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 | 2aec1b88-1bc3-430f-9d57-a9ddcf39928c |
| Started, finished | 2026-10-28 18:59 UTC, 2026-10-28 19:01 UTC |
| Code | 0aee29346248785f557664cd859ddeb50fecd3d5 (uncommitted changes) |
| 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 | 0187eb93-2c8b-4500-b11c-9d0062c96d4a, 2026-10-28 19:00 UTC |
| Movie | runs/2aec1b88-1bc3-430f-9d57-a9ddcf39928c/movie.mp4 |
| Lossless frames | runs/2aec1b88-1bc3-430f-9d57-a9ddcf39928c/frames/voltage.npy, runs/2aec1b88-1bc3-430f-9d57-a9ddcf39928c/frames/phase.npy, runs/2aec1b88-1bc3-430f-9d57-a9ddcf39928c/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 (22, 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 = 150 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 | 22 (10% 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 | 6.532 | none cited |
| Rotors | |||
| Persistent rotors | count | 0–3 | none cited |
| Max concurrent persistent rotors | count | 0–1 | none cited |
| Frames with a singularity | fraction | 0.182–0.746 | none cited |
| Beats, where a global rhythm exists | |||
| Beats | count | 8 | none cited |
| Global amplitude ratio | ratio | 0.75 | gate ≥ 0.30 provisional |
| APD50 | ms | 23 | none cited |
| APD90 | ms | 58 | 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: 6.532 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 provisional fixed criteria use 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 size 100x100; the frame rate used is 977.0 Hz from the recording-row admission source citing 10.1371/journal.pone.0259174, and the pixel size is not provided. The analysed frames are 500 to 1547 for the whole-recording analysis window, and the provisional segment definition is whole_recording from frame 0 to frame 2047, defined at admission with no detected or logged events.
Reportable values
| Metric | Segment | Value | Unit | Status |
|---|---|---|---|---|
| persistent rotor tracks | all | 0–3 | count | unstable, not reportable |
| dominant freq (Hz) | whole recording | 6.532 | Hz | no cited range |
| persistent rotors | whole recording | 0–3 | count | unstable, not reportable |
| singularity frames fraction | whole recording | 0.182–0.746 | fraction of frames | unstable, not reportable |
| persistent rotor count max | whole recording | 0–1 | count | unstable, not reportable |
physiology_ok: not decided (no cited range passed or failed); send back: True. Send back this signature as not reportable as it stands: the whole_recording singularity-frame fraction is unstable across 0.18242597898758356 to 0.7459407831900668, persistent_rotors across 0.0 to 3.0, persistent_rotor_count_max across 0.0 to 1.0, and persistent_rotor_tracks across 0.0 to 3.0, all under the provisional stability threshold of (max - min) <= 0.25 x median and provisional criteria; the only stable metric is dominant_freq_hz at 6.532 Hz across baseline-window settings, but it has no cited acceptance range for this paced control context, and the available mouse spiral-wave context instead describes approximately 18.75 to 20.0 Hz rotation in another study (DOI 10.1371/journal.pcbi.1011660). Persistent-rotor threshold tests are not applicable because there are no segment expectations, while tracker sensitivity needs review because strict/default tracking is at the lower end of the unstable rotor range and loose tracking is at the upper end; also review the frame-rate provenance for the MiCAM-labelled file using the 977.0 Hz admission value, possible pre-deposit sign or conditioning, all-negative integer values, the unsuitable rhythm-detector short-cycle result relative to the expected pacing period, and the non-biological mask; all ranges, the stability threshold, and 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 | The singularity-frame fraction is unstable across the filter grid, ranging from 0.18242597898758356 to 0.7459407831900668; do not report a definitive value without resolving parameter sensitivity. | block | analysis_qc |
| unstable:whole_recording.persistent_rotors | Across sensitivity settings the range is 0.0 to 3.0; do not report persistent_rotors as a definitive result without resolving tracking and filtering sensitivity. | block | analysis_qc |
| unstable:whole_recording.persistent_rotor_count_max | Across sensitivity settings the range is 0.0 to 1.0; do not report persistent_rotor_count_max as a definitive result without sensitivity review. | block | analysis_qc |
| unstable:persistent_rotor_tracks | Across sensitivity settings the range is 0.0 to 3.0; track-level persistence is not reportable as a definitive result. | block | analysis_qc |
| tracker_variant_count_disagreement | Strict/default tracking sits at the lower end of the unstable rotor range, while loose tracking sits at the upper end; review this as tracker sensitivity, not as proof that rotors are absent or present. | warn | analysis_qc |
| Frame-rate provenance for a MiCAM file | Use the admission value of 977.0 Hz as the working frame rate, but review provenance because the cited paper quote aligns with the custom iDS system while this deposited file is labelled MiCAM, and the Zenodo metadata does not state the MiCAM frame rate. | warn | data_provenance |
| Pre-deposit sign/conditioning | The signal is consistently non-inverted even though Di-4-ANEPPS usually dims on depolarization, suggesting sign flip or other transformation before deposit/export; downstream orientation from the measurement makes this a warning rather than a block. | warn | data_provenance |
| Unexplained all-negative data values | All values are negative integers and are flagged as processed_before_deposit; the linked paper documents possible filtering/averaging workflows, but no deposit README explains this file-level transformation. | warn | data_provenance |
| Rhythm detector not suitable for the expected paced period here | Do not use the rhythm detector's short-cycle result to infer physiology or frame rate here, because the expected pacing period lies beyond the rhythm tool's baseline-correction window. | info | analysis_qc |
| Mask is not a heart segmentation | The current analysis mask is based on nonzero temporal standard deviation, not a biological tissue segmentation; spatial map interpretation needs a tissue-only mask. | warn | analysis_qc |
Data and code availability
| Recording | 10.5281/zenodo.5557829, cc-by-4.0, Rybashlykov Dmitry |
| Publication | 10.1371/journal.pone.0259174 |
| Analysis code | 0aee29346248785f557664cd859ddeb50fecd3d5 (uncommitted changes) |
| Stored arrays | runs/2aec1b88-1bc3-430f-9d57-a9ddcf39928c/frames/voltage.npy, runs/2aec1b88-1bc3-430f-9d57-a9ddcf39928c/frames/phase.npy, runs/2aec1b88-1bc3-430f-9d57-a9ddcf39928c/frames/maps.npz |