{
 "exported_at": "2026-10-30T03:10:25.915489+00:00",
 "exported_by": {
  "app": "quantetta-a web",
  "code": {
   "git_commit": "",
   "dirty": false
  }
 },
 "recording_short": "M13Rec001",
 "header": {
  "short": "M13Rec001",
  "label": "Mouse heart, spiral wave and optogenetic termination",
  "facts": "64 \u00d7 55 px, 9,267 frames, 1 kHz, 133 \u00b5m/px, deposit checks: negative values, nan mask all frames, temporal smoothing, spatial smoothing",
  "run_short": "6d6015e6",
  "run_when": "2026-10-27 22:21 UTC",
  "params_version": 3,
  "commit": "13d8ceb",
  "dirty": false,
  "workers": null,
  "sig_short": "056f9e28",
  "run_status": "done",
  "protocol_name": "Mouse whole heart optical mapping (Luther lab)"
 },
 "parameters": "% Mouse whole heart optical mapping (Luther lab), v3, read-only\n% set by developer (not a domain scientist); provisional, REVIEW_NEEDED 16\nbaseline_frames  = 901;     % no baseline rule recorded for this run\npad_frames       = 500;     % each side, outside the window\nspatial_sigma    = 1.0;     % px, Gaussian, phase only\nspatial_truncate = 4.0;     % kernel radius, sigma\nlowpass          = [];      % none\npolarity         = -1;      % measured, skew of dV/dt\nrotor_threshold  = 0.9;     % turns, |winding| per plaquette\nrotor_erode_px   = 3;       % px from tissue edge ignored\nlink_px          = 4.0;     % tracking, max step per frame\nmax_gap          = 5;       % frames a track may vanish\nmin_cycles       = 1.0;     % own rotations, min_frames = 52\npair_dist_px     = 3.0;     % opposite-charge pairing\npaired_frac      = 0.5;     % max paired fraction of a track\nrender_step      = 4;       % movie only",
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   "analysed_range": [
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   "start": 0,
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   "cycle": "[not measured]",
   "expected": "present",
   "bounded": "LED on before frame 0 (DAQ) \u2192 termination step (image, \u00b117 frames)",
   "defined_by": "project lead (not a domain scientist), following the paper's design",
   "citation": {
    "ref": "10.1371/journal.pcbi.1011660",
    "quote": "t stimulus with LI = 3.44 \u03bcW/mm2 and PL = 5 s. Fig 2C shows a monophasic action potential (MAP) signal (in black) before, during, and after illumination. It shows the sinus rhythm returns after 3190 ms of illumination. Fig 2D presents a closer look at the MAP signal of the heart during the last few rotations of arrhythmia and the first few action potentials of sinus rhythm. Fig 2E illustrates a"
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   "provisional": true
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   "name": "illuminated_after_termination",
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   "short": "after termination",
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   "analysed": "3,170\u20134,977",
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   "cycle": "[not measured]",
   "expected": "absent",
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   "defined_by": "project lead (not a domain scientist), following the paper's design",
   "citation": {
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    "quote": "t stimulus with LI = 3.44 \u03bcW/mm2 and PL = 5 s. Fig 2C shows a monophasic action potential (MAP) signal (in black) before, during, and after illumination. It shows the sinus rhythm returns after 3190 ms of illumination. Fig 2D presents a closer look at the MAP signal of the heart during the last few rotations of arrhythmia and the first few action potentials of sinus rhythm. Fig 2E illustrates a"
   },
   "provisional": true
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   "short": "light off",
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   "analysed_range": [
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   "cycle": "[not measured]",
   "expected": "absent",
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   "defined_by": "project lead (not a domain scientist), following the paper's design",
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    "ref": "10.1371/journal.pcbi.1011660",
    "quote": "t stimulus with LI = 3.44 \u03bcW/mm2 and PL = 5 s. Fig 2C shows a monophasic action potential (MAP) signal (in black) before, during, and after illumination. It shows the sinus rhythm returns after 3190 ms of illumination. Fig 2D presents a closer look at the MAP signal of the heart during the last few rotations of arrhythmia and the first few action potentials of sinus rhythm. Fig 2E illustrates a"
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    "illuminated_after_termination.singularity_frames_frac",
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   {
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    "low": 18.75,
    "high": 20.0,
    "unit": "Hz",
    "scope": "one optical mapping recording in the same study (spiral wave before and during illumination); not a population range",
    "metric": "dominant_freq_hz",
    "source": {
     "ref": "10.1371/journal.pcbi.1011660",
     "quotes": [
      "rotational frequency of \u2248 20 Hz before illumination",
      "the frequency of the arrhythmia decreases to \u2248 18\\.75 Hz"
     ],
     "passages": [
      " is shown in Fig 3B. It shows that the arrhythmia consists of a single spiral wave with a stationary core dynamic and a rotational frequency of \u2248 20 Hz before illumination. During a single global optical pulse with a PL of 5000 ms and an LI of 3.21 \u03bcW/mm2, the frequency of the arrhythmia de",
      "ncy of \u2248 20 Hz before illumination. During a single global optical pulse with a PL of 5000 ms and an LI of 3.21 \u03bcW/mm2, the frequency of the arrhythmia decreases to \u2248 18.75 Hz. It is important to note that the frequency reverses its original value of \u2248 20 Hz when the light is turned off. Fig 3C"
     ]
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  "run_id": "6d6015e6-82f2-4762-97e2-5663d547c549",
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  "verdict": {
   "send_back": false,
   "critic_notes": "Verdict: report only stable descriptive findings and the provisional qualitative pattern, not unstable single values; physiology_ok is null because no stable ranged metric was available for pass/fail. Reportable items include stable absence of persistent rotors in light_off and illuminated_after_termination, stable maximum concurrent persistent-rotor count of 0 in those segments, stable dominant frequencies of 2.375 Hz in light_off and 2.214 Hz after termination, and a stable illuminated_arrhythmia singularity-frame fraction of 0.47902621722846445 with sensitivity range 0.3816479400749064\u20130.48801498127340825; the provisional persistent-rotor presence/absence rule holds using both the 52-frame measured-cycle threshold and the 50-frame paper-derived threshold from the 20.0 Hz context in DOI 10.1371/journal.pcbi.1011660. Not reportable as single values are light_off.singularity_frames_frac 0.0029023746701846965\u20130.02955145118733509, illuminated_arrhythmia.persistent_rotors 4.0\u201315.0, illuminated_arrhythmia.persistent_rotor_count_max 1.0\u20132.0, illuminated_arrhythmia.dominant_freq_hz 15.356\u201319.85 Hz, illuminated_after_termination.singularity_frames_frac 0.0005534034311012728\u20130.014941892639734366, and persistent_rotor_tracks 4.0\u201315.0. Needs review: pre-deposit processing/raw-data labeling, the provisional frame-3170 event interpretation, baseline/illumination artifact effects, and all provisional tool thresholds, ranges, stability threshold and criteria; the same-study frequency context is approximately 18.75\u201320.0 Hz, provisionally checked over 14.0625\u201325.0 Hz, in DOI 10.1371/journal.pcbi.1011660.",
   "review_items": [
    {
     "topic": "unstable:light_off.singularity_frames_frac",
     "detail": "Sensitivity range 0.0029023746701846965\u20130.02955145118733509 across the filter grid; do not report a single value until filter dependence is reviewed.",
     "severity": "warn",
     "reviewer_type": "analysis/domain reviewer"
    },
    {
     "topic": "unstable:illuminated_arrhythmia.persistent_rotors",
     "detail": "Sensitivity range 4.0\u201315.0 across filters and trackers; do not report a single count until tracking/filter dependence is reviewed.",
     "severity": "warn",
     "reviewer_type": "analysis/domain reviewer"
    },
    {
     "topic": "unstable:illuminated_arrhythmia.persistent_rotor_count_max",
     "detail": "Sensitivity range 1.0\u20132.0 across filters and trackers; do not report a single maximum concurrent count until tracking/filter dependence is reviewed.",
     "severity": "warn",
     "reviewer_type": "analysis/domain reviewer"
    },
    {
     "topic": "unstable:illuminated_arrhythmia.dominant_freq_hz",
     "detail": "Sensitivity range 15.356\u201319.85 Hz across baseline windows; do not report a single frequency until baseline-window dependence is reviewed against the same-study context in DOI 10.1371/journal.pcbi.1011660.",
     "severity": "warn",
     "reviewer_type": "domain reviewer"
    },
    {
     "topic": "unstable:illuminated_after_termination.singularity_frames_frac",
     "detail": "Sensitivity range 0.0005534034311012728\u20130.014941892639734366 across the filter grid; do not report a single value until filter dependence is reviewed.",
     "severity": "warn",
     "reviewer_type": "analysis/domain reviewer"
    },
    {
     "topic": "unstable:persistent_rotor_tracks",
     "detail": "Sensitivity range 4.0\u201315.0 across filters and trackers; do not report a single track count until tracking/filter dependence is reviewed.",
     "severity": "warn",
     "reviewer_type": "analysis/domain reviewer"
    },
    {
     "topic": "Pre-deposit processing / raw-data label",
     "detail": "README labels the recording as raw experimental data, but notebook documentation and measurements indicate masking, spatial smoothing, temporal smoothing, and normalization; avoid analyses that assume raw photon counts or independent pixel noise.",
     "severity": "warn",
     "reviewer_type": "data curator/domain reviewer"
    },
    {
     "topic": "Event interpretation at frame 3170",
     "detail": "Frame 3170 is a baseline_step only; illumination began before frame 0 and ended at frame 4977, so the stored spiral-termination label is provisional and should not be treated as direct light-onset evidence.",
     "severity": "warn",
     "reviewer_type": "domain reviewer"
    },
    {
     "topic": "Baseline and illumination artifact",
     "detail": "Blue stimulation light crosstalk, re-normalization by stimulation-light signal, slow baseline range, and a baseline step mean analyses using absolute baseline or amplitude must account for illumination/crosstalk/normalization effects.",
     "severity": "warn",
     "reviewer_type": "domain reviewer"
    },
    {
     "topic": "Provisional tool thresholds",
     "detail": "Event detection, processing flags, SNR, rhythm, reference-rate thresholds, ranges, stability threshold, and criteria are provisional and not yet reviewed by a domain scientist.",
     "severity": "info",
     "reviewer_type": "domain reviewer"
    }
   ],
   "tracker_note": "Strict, default, and loose tracking all give the same provisional rule verdict: persistent rotors present in the illuminated-arrhythmia segment and absent in light-off and illuminated-after-termination segments. The tracker rule therefore agrees, although the illuminated-arrhythmia count varies within the broader sensitivity range of 4.0\u201315.0 and the count itself is not reportable as a single value.",
   "physiology_ok": null,
   "metric_judgments": [
    {
     "note": "Unstable across the filter grid, so this fraction is not reportable; refer only to its sensitivity range of 0.0029023746701846965\u20130.02955145118733509 fraction of frames and review filter dependence before using it.",
     "metric": "light_off.singularity_frames_frac",
     "status": "unstable_not_reportable"
    },
    {
     "note": "Stable absence of persistent rotors in the light-off segment, but there is no cited physiology range for this count, so it can be reported descriptively rather than as physiologically validated.",
     "metric": "light_off.persistent_rotors",
     "status": "no_cited_range"
    },
    {
     "note": "Stable maximum concurrent persistent-rotor count of 0 in the light-off segment, with no cited range; report only as a descriptive analysis result.",
     "metric": "light_off.persistent_rotor_count_max",
     "status": "no_cited_range"
    },
    {
     "note": "Stable dominant frequency of 2.375 Hz in the light-off segment, but no cited range is available for this segment/context, so do not use it for physiology pass/fail.",
     "metric": "light_off.dominant_freq_hz",
     "status": "no_cited_range"
    },
    {
     "note": "Stable singularity-frame fraction of 0.47902621722846445 at the run setting, with sensitivity range 0.3816479400749064\u20130.48801498127340825, supporting descriptive reporting of frequent phase singularities during the illuminated arrhythmia; no cited range is available.",
     "metric": "illuminated_arrhythmia.singularity_frames_frac",
     "status": "no_cited_range"
    },
    {
     "note": "Unstable across filters and tracker settings, so the count is not reportable; refer only to its sensitivity range of 4.0\u201315.0 persistent rotors and review tracking/filter dependence.",
     "metric": "illuminated_arrhythmia.persistent_rotors",
     "status": "unstable_not_reportable"
    },
    {
     "note": "Unstable across filters and tracker settings, so the maximum concurrent count is not reportable; refer only to its sensitivity range of 1.0\u20132.0 and review tracking/filter dependence.",
     "metric": "illuminated_arrhythmia.persistent_rotor_count_max",
     "status": "unstable_not_reportable"
    },
    {
     "note": "Unstable across baseline windows, so the dominant frequency is not reportable as a single value; its sensitivity range is 15.356\u201319.85 Hz. The only cited comparator is a same-study optical-mapping context of approximately 18.75\u201320.0 Hz, checked provisionally over 14.0625\u201325.0 Hz, from DOI 10.1371/journal.pcbi.1011660.",
     "metric": "illuminated_arrhythmia.dominant_freq_hz",
     "status": "unstable_not_reportable"
    },
    {
     "note": "Unstable across the filter grid, so this fraction is not reportable; refer only to its sensitivity range of 0.0005534034311012728\u20130.014941892639734366 fraction of frames and review filter dependence.",
     "metric": "illuminated_after_termination.singularity_frames_frac",
     "status": "unstable_not_reportable"
    },
    {
     "note": "Stable absence of persistent rotors after termination, but no cited physiology range is available; report descriptively only.",
     "metric": "illuminated_after_termination.persistent_rotors",
     "status": "no_cited_range"
    },
    {
     "note": "Stable maximum concurrent persistent-rotor count of 0 after termination, with no cited range; report descriptively only.",
     "metric": "illuminated_after_termination.persistent_rotor_count_max",
     "status": "no_cited_range"
    },
    {
     "note": "Stable dominant frequency of 2.214 Hz after termination, but no cited range is available for this segment/context, so do not use it for physiology pass/fail.",
     "metric": "illuminated_after_termination.dominant_freq_hz",
     "status": "no_cited_range"
    },
    {
     "note": "Unstable across filters and tracker settings, so the overall persistent-rotor track count is not reportable; refer only to its sensitivity range of 4.0\u201315.0 tracks and review tracking/filter dependence.",
     "metric": "persistent_rotor_tracks",
     "status": "unstable_not_reportable"
    }
   ],
   "send_back_reason": null,
   "persistence_threshold_note": "The persistent-rotor rule holds provisionally using the measured-cycle threshold of 52 frames and also using the paper-derived 50-frame rotation period from 20.0 Hz at 1000 frames/s; both variants hold across filters and trackers and agree. The paper-derived threshold cites DOI 10.1371/journal.pcbi.1011660."
  },
  "passages": {
   "mouse_spiral_rotation_period": {
    "ref": "10.1371/journal.pcbi.1011660",
    "note": "At 1000 frames/s, 20 Hz is a 50-frame rotation; the illuminated value of 18.75 Hz would be 53 frames.",
    "quotes": [
     "rotational frequency of \u2248 20 Hz before illumination"
    ],
    "status": "provisional",
    "passages": [
     " is shown in Fig 3B. It shows that the arrhythmia consists of a single spiral wave with a stationary core dynamic and a rotational frequency of \u2248 20 Hz before illumination. During a single global optical pulse with a PL of 5000 ms and an LI of 3.21 \u03bcW/mm2, the frequency of the arrhythmia de"
    ],
    "applies_to": {
     "species": "mouse"
    },
    "rotation_hz": 20.0
   }
  },
  "trackers": {
   "note": "disagreement is reported as a review item, not folded into the pass/fail",
   "agree": true,
   "trackers": [
    {
     "link_px": 2.0,
     "max_gap": 1,
     "tracker": "strict",
     "is_run_setting": false,
     "persistent_rotor_rule": "holds (provisional)",
     "persistent_rotors_by_segment": {
      "light_off": 0,
      "illuminated_arrhythmia": 5,
      "illuminated_after_termination": 0
     }
    },
    {
     "link_px": 4.0,
     "max_gap": 5,
     "tracker": "default",
     "is_run_setting": true,
     "persistent_rotor_rule": "holds (provisional)",
     "persistent_rotors_by_segment": {
      "light_off": 0,
      "illuminated_arrhythmia": 13,
      "illuminated_after_termination": 0
     }
    },
    {
     "link_px": 6.0,
     "max_gap": 10,
     "tracker": "loose",
     "is_run_setting": false,
     "persistent_rotor_rule": "holds (provisional)",
     "persistent_rotors_by_segment": {
      "light_off": 0,
      "illuminated_arrhythmia": 15,
      "illuminated_after_termination": 0
     }
    }
   ]
  },
  "stability": {
   "persistent_rotor_tracks": {
    "max": 15.0,
    "min": 4.0,
    "median": 12.0,
    "stable": false,
    "settings": 15,
    "spread_frac": 0.917,
    "values_grid": [
     5,
     5,
     4,
     12,
     11,
     12,
     13,
     13,
     15,
     12,
     13,
     12
    ],
    "varied_over": "filter grid + trackers",
    "values_trackers": [
     5,
     13,
     15
    ]
   },
   "light_off.dominant_freq_hz": {
    "max": 2.375,
    "min": 2.375,
    "median": 2.375,
    "stable": true,
    "settings": 4,
    "spread_frac": 0.0,
    "varied_over": "baseline windows",
    "values_by_baseline": {
     "678": 2.375,
     "901": 2.375,
     "1356": 2.375,
     "2712": 2.375
    }
   },
   "light_off.persistent_rotors": {
    "max": 0.0,
    "min": 0.0,
    "median": 0.0,
    "stable": true,
    "settings": 15,
    "spread_frac": 0.0,
    "values_grid": [
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     0,
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    "varied_over": "filter grid + trackers",
    "values_trackers": [
     0,
     0,
     0
    ]
   },
   "light_off.singularity_frames_frac": {
    "max": 0.02955145118733509,
    "min": 0.0029023746701846965,
    "median": 0.008575197889182058,
    "stable": false,
    "settings": 12,
    "spread_frac": 3.108,
    "values_grid": [
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     0.008179419525065963,
     0.00712401055408971,
     0.0036939313984168864,
     0.0036939313984168864,
     0.0029023746701846965,
     0.013192612137203167,
     0.012137203166226913,
     0.008443271767810026
    ],
    "varied_over": "filter grid"
   },
   "light_off.persistent_rotor_present": {
    "stable": true,
    "values_grid": [
     false,
     false,
     false,
     false,
     false,
     false,
     false,
     false,
     false,
     false,
     false,
     false
    ],
    "varied_over": "filter grid + trackers",
    "values_trackers": [
     false,
     false,
     false
    ],
    "stable_across_filters": true,
    "stable_across_trackers": true
   },
   "light_off.persistent_rotor_count_max": {
    "max": 0.0,
    "min": 0.0,
    "median": 0.0,
    "stable": true,
    "settings": 15,
    "spread_frac": 0.0,
    "values_grid": [
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     0
    ],
    "varied_over": "filter grid + trackers",
    "values_trackers": [
     0,
     0,
     0
    ]
   },
   "illuminated_arrhythmia.dominant_freq_hz": {
    "max": 19.85,
    "min": 15.356,
    "median": 17.2285,
    "stable": false,
    "settings": 4,
    "spread_frac": 0.261,
    "varied_over": "baseline windows",
    "values_by_baseline": {
     "678": 19.85,
     "901": 19.101,
     "1356": 15.356,
     "2712": 15.356
    }
   },
   "illuminated_arrhythmia.persistent_rotors": {
    "max": 15.0,
    "min": 4.0,
    "median": 12.0,
    "stable": false,
    "settings": 15,
    "spread_frac": 0.917,
    "values_grid": [
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     12
    ],
    "varied_over": "filter grid + trackers",
    "values_trackers": [
     5,
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     15
    ]
   },
   "illuminated_after_termination.dominant_freq_hz": {
    "max": 2.214,
    "min": 2.214,
    "median": 2.214,
    "stable": true,
    "settings": 4,
    "spread_frac": 0.0,
    "varied_over": "baseline windows",
    "values_by_baseline": {
     "678": 2.214,
     "901": 2.214,
     "1356": 2.214,
     "2712": 2.214
    }
   },
   "illuminated_arrhythmia.singularity_frames_frac": {
    "max": 0.48801498127340825,
    "min": 0.3816479400749064,
    "median": 0.47191011235955055,
    "stable": true,
    "settings": 12,
    "spread_frac": 0.225,
    "values_grid": [
     0.40898876404494383,
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     0.4797752808988764,
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     0.45767790262172287,
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     0.4846441947565543,
     0.4681647940074906,
     0.4842696629213483,
     0.47902621722846445,
     0.4606741573033708
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    "varied_over": "filter grid"
   },
   "illuminated_after_termination.persistent_rotors": {
    "max": 0.0,
    "min": 0.0,
    "median": 0.0,
    "stable": true,
    "settings": 15,
    "spread_frac": 0.0,
    "values_grid": [
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    "varied_over": "filter grid + trackers",
    "values_trackers": [
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    ]
   },
   "illuminated_arrhythmia.persistent_rotor_present": {
    "stable": true,
    "values_grid": [
     true,
     true,
     true,
     true,
     true,
     true,
     true,
     true,
     true,
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     true,
     true
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    "varied_over": "filter grid + trackers",
    "values_trackers": [
     true,
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     true
    ],
    "stable_across_filters": true,
    "stable_across_trackers": true
   },
   "illuminated_arrhythmia.persistent_rotor_count_max": {
    "max": 2.0,
    "min": 1.0,
    "median": 2.0,
    "stable": false,
    "settings": 15,
    "spread_frac": 0.5,
    "values_grid": [
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    "varied_over": "filter grid + trackers",
    "values_trackers": [
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   },
   "illuminated_after_termination.singularity_frames_frac": {
    "max": 0.014941892639734366,
    "min": 0.0005534034311012728,
    "median": 0.005534034311012729,
    "stable": false,
    "settings": 12,
    "spread_frac": 2.6,
    "values_grid": [
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    "varied_over": "filter grid"
   },
   "illuminated_after_termination.persistent_rotor_present": {
    "stable": true,
    "values_grid": [
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    "varied_over": "filter grid + trackers",
    "values_trackers": [
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    "stable_across_filters": true,
    "stable_across_trackers": true
   },
   "illuminated_after_termination.persistent_rotor_count_max": {
    "max": 0.0,
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    "spread_frac": 0.0,
    "values_grid": [
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    "varied_over": "filter grid + trackers",
    "values_trackers": [
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   }
  },
  "reviewed_at": "2026-10-27T22:28:01.907909+00:00",
  "recording_id": "55cb4aa3-6502-45a6-a14c-85cb676fe8c3",
  "signature_id": "056f9e28-85a3-4436-aea7-6df0842b39e3",
  "prompt_version": "critic-v1",
  "criteria_status": {
   "note": null,
   "rules": [
    {
     "id": "physiology_reference_rates",
     "expert": "cardiac electrophysiologist per species",
     "status": "provisional",
     "values": {
      "ranges": [
       "mouse_spiral_rotation_hz"
      ],
      "tolerance_frac": 0.25,
      "segment_rhythm_rule": "expected persistent rotors 'present' -> spiral arrhythmia"
     },
     "decision": null,
     "location": "worker/voltage/physiology.py (RANGES, TOLERANCE_FRAC)",
     "reviewed": false,
     "reviewer": null,
     "description": "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",
     "reviewed_at": null
    },
    {
     "id": "stability_rule",
     "expert": "biostatistician + optical mapping analyst",
     "status": "provisional",
     "values": {
      "unstable": [
       "light_off.singularity_frames_frac",
       "illuminated_arrhythmia.persistent_rotors",
       "illuminated_arrhythmia.persistent_rotor_count_max",
       "illuminated_arrhythmia.dominant_freq_hz",
       "illuminated_after_termination.singularity_frames_frac",
       "persistent_rotor_tracks"
      ],
      "stable_frac": 0.25
     },
     "decision": null,
     "location": "worker/agents/critic.py (STABLE_FRAC, stability)",
     "reviewed": false,
     "reviewer": null,
     "description": "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'",
     "reviewed_at": null
    },
    {
     "id": "persistence_threshold_variants",
     "expert": "computational cardiac electrophysiologist (phase mapping)",
     "status": "provisional",
     "values": {
      "measured_cycle": 52,
      "paper_rotation": 50
     },
     "decision": null,
     "location": "worker/agents/critic.py (persistence_variants)",
     "reviewed": false,
     "reviewer": null,
     "description": "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",
     "reviewed_at": null
    },
    {
     "id": "persistent_rotor_criterion",
     "expert": "cardiac electrophysiologist",
     "status": "provisional",
     "values": {
      "max_absent": 0,
      "min_present": 1
     },
     "decision": null,
     "location": "worker/voltage/sensitivity.py (MIN_ROTORS_PRESENT, MAX_ROTORS_ABSENT)",
     "reviewed": false,
     "reviewer": null,
     "description": "Persistent-rotor finding holds if every 'present' segment has >= 1 persistent rotor and every 'absent' segment has none, at every setting",
     "reviewed_at": null
    },
    {
     "id": "sensitivity_grid",
     "expert": "optical mapping analyst",
     "status": "provisional",
     "values": {
      "spatial_sigma": {
       "light": 0.5,
       "default": 1.0,
       "heavier": 2.0
      },
      "baseline_frames": {
       "run": 901,
       "3x_cycle": 1356,
       "6x_cycle": 2712,
       "1.5x_cycle": 678
      },
      "baseline_scaling": {
       "multiples": {
        "3x_cycle": 3.0,
        "6x_cycle": 6.0,
        "1.5x_cycle": 1.5
       },
       "reference_segment": "illuminated_after_termination",
       "segment_cycles_frames": {
        "light_off": 421,
        "illuminated_arrhythmia": 52,
        "illuminated_after_termination": 452
       },
       "reference_cycle_frames": 452,
       "window_over_cycle_per_segment": {
        "run": {
         "light_off": 2.14,
         "illuminated_arrhythmia": 17.33,
         "illuminated_after_termination": 1.99
        },
        "3x_cycle": {
         "light_off": 3.22,
         "illuminated_arrhythmia": 26.08,
         "illuminated_after_termination": 3.0
        },
        "6x_cycle": {
         "light_off": 6.44,
         "illuminated_arrhythmia": 52.15,
         "illuminated_after_termination": 6.0
        },
        "1.5x_cycle": {
         "light_off": 1.61,
         "illuminated_arrhythmia": 13.04,
         "illuminated_after_termination": 1.5
        }
       }
      },
      "tracker(link_px, max_gap)": {
       "loose": [
        6.0,
        10
       ],
       "strict": [
        2.0,
        1
       ],
       "default": [
        4.0,
        5
       ]
      }
     },
     "decision": null,
     "location": "worker/voltage/sensitivity.py (SIGMAS, BASELINE_MULTIPLES, baseline_levels)",
     "reviewed": false,
     "reviewer": null,
     "description": "Filter levels tested: spatial sigma and baseline window values",
     "reviewed_at": null
    }
   ],
   "status": "provisional",
   "all_reviewed": false,
   "superseded_by_run": null
  },
  "persistence_variants": {
   "agree": true,
   "measured_cycle": {
    "basis": "one dominant cycle of the fastest segment at the run setting",
    "applicable": true,
    "min_frames": 52,
    "segment_counts_grid": {
     "light_off": [
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      0,
      0,
      0,
      0,
      0,
      0,
      0,
      0,
      0,
      0,
      0
     ],
     "illuminated_arrhythmia": [
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      5,
      4,
      12,
      11,
      12,
      13,
      13,
      15,
      12,
      13,
      12
     ],
     "illuminated_after_termination": [
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      0,
      0,
      0,
      0,
      0,
      0,
      0,
      0,
      0,
      0,
      0
     ]
    },
    "holds_across_filters": true,
    "label_across_filters": "holds (provisional)",
    "holds_across_trackers": true,
    "label_across_trackers": "holds (provisional)",
    "segment_lifetimes_run": {
     "light_off": [],
     "illuminated_arrhythmia": [
      40,
      34,
      57,
      106,
      37,
      57,
      41,
      34,
      62,
      21,
      37,
      32,
      23
     ],
     "illuminated_after_termination": []
    }
   },
   "paper_rotation": {
    "ref": "10.1371/journal.pcbi.1011660",
    "basis": "1000 frames/s / 20 Hz, cited",
    "passage": " is shown in Fig 3B. It shows that the arrhythmia consists of a single spiral wave with a stationary core dynamic and a rotational frequency of \u2248 20 Hz before illumination. During a single global optical pulse with a PL of 5000 ms and an LI of 3.21 \u03bcW/mm2, the frequency of the arrhythmia de",
    "applicable": true,
    "min_frames": 50,
    "rotation_hz": 20.0,
    "segment_counts_grid": {
     "light_off": [
      0,
      0,
      0,
      0,
      0,
      0,
      0,
      0,
      0,
      0,
      0,
      0
     ],
     "illuminated_arrhythmia": [
      5,
      5,
      4,
      12,
      11,
      12,
      13,
      13,
      15,
      12,
      13,
      12
     ],
     "illuminated_after_termination": [
      0,
      0,
      0,
      0,
      0,
      0,
      0,
      0,
      0,
      0,
      0,
      0
     ]
    },
    "holds_across_filters": true,
    "label_across_filters": "holds (provisional)",
    "holds_across_trackers": true,
    "label_across_trackers": "holds (provisional)",
    "segment_lifetimes_run": {
     "light_off": [],
     "illuminated_arrhythmia": [
      40,
      34,
      57,
      106,
      37,
      57,
      41,
      34,
      62,
      21,
      37,
      32,
      23
     ],
     "illuminated_after_termination": []
    }
   }
  },
  "required_review_topics": [
   "unstable:light_off.singularity_frames_frac",
   "unstable:illuminated_arrhythmia.persistent_rotors",
   "unstable:illuminated_arrhythmia.persistent_rotor_count_max",
   "unstable:illuminated_arrhythmia.dominant_freq_hz",
   "unstable:illuminated_after_termination.singularity_frames_frac",
   "unstable:persistent_rotor_tracks"
  ]
 },
 "criteria": [
  {
   "criterion": "Singularities present where the design expects them, absent elsewhere",
   "rule": "each 'present' segment: frac >= 0.1 and >= 2.0 x max frac over 'absent' segments, at every setting",
   "result": "holds at 12 filter settings",
   "superseded": false,
   "provisional": true
  },
  {
   "criterion": "Persistent rotors present where the design expects them, absent elsewhere",
   "rule": "each 'present' segment: count >= 1; each 'absent' segment: count <= 0, at every setting",
   "result": "holds at 12 filter settings and 3 trackers",
   "superseded": false,
   "provisional": true
  },
  {
   "criterion": "Persistence threshold, paper context",
   "rule": "lifetime \u2265 52 frames (measured cycle) and \u2265 50 frames (cited 20 Hz)",
   "result": "agree",
   "provisional": true
  }
 ],
 "report": {
  "methods": "For this run, the provisional parameter set and criteria are protocol f65d786f-f194-4be2-88b8-10d3dd25d674 version 3 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 frame rate is 1000 Hz from the publication, and the pixel size is 133 \u00b5m from the publication. The analysed window is frames 500 to 8767. The provisional segment definitions are illuminated_arrhythmia, frames 0 to 3170; illuminated_after_termination, frames 3170 to 4977; and light_off, frames 4977 to 9267.",
  "rules": [
   {
    "id": "protocol_parameter_set",
    "description": "Each protocol's fixed, versioned analysis parameters (version 1 = developer defaults); no run or agent may deviate",
    "expert": "optical mapping analyst",
    "status": "provisional",
    "location": "worker/voltage/protocol_params.py (developer_defaults, set_params)",
    "values": {
     "set_by": "developer (not a domain scientist)",
     "protocol": "Mouse whole heart optical mapping (Luther lab)",
     "protocol_id": "f65d786f-f194-4be2-88b8-10d3dd25d674",
     "params_version": 3
    }
   },
   {
    "id": "filter_defaults",
    "description": "Default baseline window (frames) and spatial Gaussian sigma/truncate for phase",
    "expert": "optical mapping analyst (cardiac electrophysiology)",
    "status": "provisional",
    "location": "worker/voltage/preprocess.py (Params)",
    "values": {
     "lowpass": null,
     "spatial_sigma": 1.0,
     "baseline_frames": 901,
     "spatial_truncate": 4.0
    }
   },
   {
    "id": "tissue_mask",
    "description": "Tissue = not NaN in frame 0 and nonzero temporal std",
    "expert": "optical mapping analyst",
    "status": "provisional",
    "location": "worker/voltage/io.py (tissue_mask)",
    "values": {
     "rule": "not NaN in frame 0 and nonzero std",
     "tissue_pixels": 2332
    }
   },
   {
    "id": "polarity",
    "description": "Dye polarity from sign of median per-pixel skew of dV/dt",
    "expert": "optical mapping analyst / voltage dye chemist",
    "status": "provisional",
    "location": "worker/voltage/preprocess.py (polarity)",
    "values": {
     "method": "median skew of dV/dt",
     "result": -1
    }
   },
   {
    "id": "singularity_detection",
    "description": "Phase singularity = |winding| > threshold turns, >= erode px from tissue edge",
    "expert": "computational cardiac electrophysiologist (phase mapping)",
    "status": "provisional",
    "location": "worker/voltage/preprocess.py (Params.rotor_threshold, rotor_erode_px)",
    "values": {
     "rotor_erode_px": 3,
     "rotor_threshold": 0.9
    }
   },
   {
    "id": "rotor_persistence",
    "description": "Track linking distance/gap and minimum lifetime for a persistent rotor",
    "expert": "computational cardiac electrophysiologist (phase mapping)",
    "status": "provisional",
    "location": "worker/voltage/rotors.py (TrackParams)",
    "values": {
     "link_px": 4.0,
     "max_gap": 5,
     "min_cycles": 1.0,
     "min_frames": 52
    }
   },
   {
    "id": "chirality_pairing",
    "description": "Opposite-charge singularities within pair distance are a pair; tracks paired most of their life are excluded from rotors",
    "expert": "computational cardiac electrophysiologist (phase mapping)",
    "status": "provisional",
    "location": "worker/voltage/rotors.py (TrackParams.pair_dist_px, paired_frac)",
    "values": {
     "paired_frac": 0.5,
     "pair_dist_px": 3.0
    }
   },
   {
    "id": "sensitivity_grid",
    "description": "Filter levels tested: spatial sigma and baseline window values",
    "expert": "optical mapping analyst",
    "status": "provisional",
    "location": "worker/voltage/sensitivity.py (SIGMAS, BASELINE_MULTIPLES, baseline_levels)",
    "values": {
     "sigmas": {
      "light": 0.5,
      "default": 1.0,
      "heavier": 2.0
     },
     "trackers": {
      "loose": [
       6.0,
       10
      ],
      "strict": [
       2.0,
       1
      ],
      "default": [
       4.0,
       5
      ]
     },
     "baselines": {
      "run": 901,
      "3x_cycle": 1356,
      "6x_cycle": 2712,
      "1.5x_cycle": 678
     }
    }
   },
   {
    "id": "analysis_window",
    "description": "Frames analysed: whole recording minus one filter pad at each end (unless the plan narrows it)",
    "expert": "cardiac electrophysiologist familiar with the dataset",
    "status": "provisional",
    "location": "worker/voltage/runs.py (default_window)",
    "values": {
     "f0": 500,
     "f1": 8767
    }
   },
   {
    "id": "prior_processing_flags",
    "description": "Thresholds for flagging depositor processing (normalization, masking, temporal/spatial smoothing)",
    "expert": "imaging scientist (camera acquisition and noise)",
    "status": "provisional",
    "location": "worker/voltage/inspect.py (prior_processing)",
    "values": {
     "flags": [
      "negative_values",
      "non_integer",
      "nan_mask_all_frames",
      "temporal_smoothing",
      "spatial_smoothing"
     ],
     "thresholds": {
      "int_frac": 0.5,
      "neg_frac": 0.01,
      "dv_autocorr": 0.5,
      "neighbour_corr": 0.8
     }
    }
   },
   {
    "id": "baseline_step_detection",
    "description": "Baseline step = consensus upward step in tissue-mean raw baseline (cause not inferred; first misread as light onset, contradicted by the DAQ)",
    "expert": "optical mapping experimentalist",
    "status": "provisional",
    "location": "worker/voltage/events.py (detect_baseline_step)",
    "values": {
     "frames": [
      3170
     ]
    }
   },
   {
    "id": "daq_interpretation",
    "description": "DAQ channel names from depositor notebook; frames = first N triggers of closest burst; midpoint thresholds",
    "expert": "experimentalist who recorded the data (or the depositor)",
    "status": "provisional",
    "location": "worker/voltage/daq.py",
    "values": {
     "events": [
      "illumination_on@0",
      "arrhythmia_termination@3153",
      "illumination_off@4977"
     ]
    }
   },
   {
    "id": "segment_definitions",
    "description": "Mouse segments bounded by DAQ light events and the baseline step, interpreted as spiral termination under illumination (project lead, from Hussaini et al. 2023)",
    "expert": "cardiac electrophysiologist (ideally the depositing authors)",
    "status": "provisional",
    "location": "worker/voltage/annotations.py (MOUSE_SEGMENTS)",
    "values": {
     "light_off": [
      4977,
      9267
     ],
     "illuminated_arrhythmia": [
      0,
      3170
     ],
     "illuminated_after_termination": [
      3170,
      4977
     ]
    }
   },
   {
    "id": "rotor_finding_criterion",
    "description": "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)",
    "expert": "cardiac electrophysiologist + biostatistician",
    "status": "provisional",
    "location": "worker/voltage/sensitivity.py (MIN_FRAC, MIN_RATIO)",
    "values": {
     "min_frac": 0.1,
     "min_ratio": 2.0
    }
   },
   {
    "id": "persistent_rotor_criterion",
    "description": "Persistent-rotor finding holds if every 'present' segment has >= 1 persistent rotor and every 'absent' segment has none, at every setting",
    "expert": "cardiac electrophysiologist",
    "status": "provisional",
    "location": "worker/voltage/sensitivity.py (MIN_ROTORS_PRESENT, MAX_ROTORS_ABSENT)",
    "values": {
     "expect": {
      "light_off": "absent",
      "illuminated_arrhythmia": "present",
      "illuminated_after_termination": "absent"
     },
     "max_absent": 0,
     "min_present": 1,
     "spanning_rotor": "counts in every segment it overlaps",
     "min_lifetime_frames": 52
    }
   },
   {
    "id": "pipeline_check",
    "description": "The pipeline agent's hold/proceed decision from protocol mismatches and inspector anomalies; it chooses no parameter",
    "expert": "optical mapping analyst",
    "status": "provisional",
    "location": "worker/agents/pipeline.py (INSTRUCTIONS, validator)",
    "values": {
     "model": "openai:gpt-5.5",
     "proceed": true,
     "anomalies": [
      "Pre-deposit processing / raw-data label",
      "Event interpretation at frame 3170",
      "Baseline and illumination artifact"
     ],
     "mismatches": []
    }
   },
   {
    "id": "physiology_reference_rates",
    "description": "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",
    "expert": "cardiac electrophysiologist per species",
    "status": "provisional",
    "location": "worker/voltage/physiology.py (RANGES, TOLERANCE_FRAC)",
    "values": {
     "ranges": [
      "mouse_spiral_rotation_hz"
     ],
     "tolerance_frac": 0.25,
     "segment_rhythm_rule": "expected persistent rotors 'present' -> spiral arrhythmia"
    }
   },
   {
    "id": "stability_rule",
    "description": "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'",
    "expert": "biostatistician + optical mapping analyst",
    "status": "provisional",
    "location": "worker/agents/critic.py (STABLE_FRAC, stability)",
    "values": {
     "unstable": [
      "light_off.singularity_frames_frac",
      "illuminated_arrhythmia.persistent_rotors",
      "illuminated_arrhythmia.persistent_rotor_count_max",
      "illuminated_arrhythmia.dominant_freq_hz",
      "illuminated_after_termination.singularity_frames_frac",
      "persistent_rotor_tracks"
     ],
     "stable_frac": 0.25
    }
   },
   {
    "id": "persistence_threshold_variants",
    "description": "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",
    "expert": "computational cardiac electrophysiologist (phase mapping)",
    "status": "provisional",
    "location": "worker/agents/critic.py (persistence_variants)",
    "values": {
     "measured_cycle": 52,
     "paper_rotation": 50
    }
   }
  ],
  "review_items": [
   {
    "topic": "unstable:light_off.singularity_frames_frac",
    "detail": "Sensitivity range 0.0029023746701846965\u20130.02955145118733509 across the filter grid; do not report a single value until filter dependence is reviewed.",
    "severity": "warn",
    "reviewer": "analysis/domain reviewer"
   },
   {
    "topic": "unstable:illuminated_arrhythmia.persistent_rotors",
    "detail": "Sensitivity range 4.0\u201315.0 across filters and trackers; do not report a single count until tracking/filter dependence is reviewed.",
    "severity": "warn",
    "reviewer": "analysis/domain reviewer"
   },
   {
    "topic": "unstable:illuminated_arrhythmia.persistent_rotor_count_max",
    "detail": "Sensitivity range 1.0\u20132.0 across filters and trackers; do not report a single maximum concurrent count until tracking/filter dependence is reviewed.",
    "severity": "warn",
    "reviewer": "analysis/domain reviewer"
   },
   {
    "topic": "unstable:illuminated_arrhythmia.dominant_freq_hz",
    "detail": "Sensitivity range 15.356\u201319.85 Hz across baseline windows; do not report a single frequency until baseline-window dependence is reviewed against the same-study context in DOI 10.1371/journal.pcbi.1011660.",
    "severity": "warn",
    "reviewer": "domain reviewer"
   },
   {
    "topic": "unstable:illuminated_after_termination.singularity_frames_frac",
    "detail": "Sensitivity range 0.0005534034311012728\u20130.014941892639734366 across the filter grid; do not report a single value until filter dependence is reviewed.",
    "severity": "warn",
    "reviewer": "analysis/domain reviewer"
   },
   {
    "topic": "unstable:persistent_rotor_tracks",
    "detail": "Sensitivity range 4.0\u201315.0 across filters and trackers; do not report a single track count until tracking/filter dependence is reviewed.",
    "severity": "warn",
    "reviewer": "analysis/domain reviewer"
   },
   {
    "topic": "Pre-deposit processing / raw-data label",
    "detail": "README labels the recording as raw experimental data, but notebook documentation and measurements indicate masking, spatial smoothing, temporal smoothing, and normalization; avoid analyses that assume raw photon counts or independent pixel noise.",
    "severity": "warn",
    "reviewer": "data curator/domain reviewer"
   },
   {
    "topic": "Event interpretation at frame 3170",
    "detail": "Frame 3170 is a baseline_step only; illumination began before frame 0 and ended at frame 4977, so the stored spiral-termination label is provisional and should not be treated as direct light-onset evidence.",
    "severity": "warn",
    "reviewer": "domain reviewer"
   },
   {
    "topic": "Baseline and illumination artifact",
    "detail": "Blue stimulation light crosstalk, re-normalization by stimulation-light signal, slow baseline range, and a baseline step mean analyses using absolute baseline or amplitude must account for illumination/crosstalk/normalization effects.",
    "severity": "warn",
    "reviewer": "domain reviewer"
   },
   {
    "topic": "Provisional tool thresholds",
    "detail": "Event detection, processing flags, SNR, rhythm, reference-rate thresholds, ranges, stability threshold, and criteria are provisional and not yet reviewed by a domain scientist.",
    "severity": "info",
    "reviewer": "domain reviewer"
   }
  ],
  "reportable": [
   {
    "metric": "persistent rotor tracks",
    "segment": "all",
    "value": "4\u201315",
    "unit": "count",
    "status": "unstable, not reportable"
   },
   {
    "metric": "dominant freq (Hz)",
    "segment": "light off",
    "value": "2.375",
    "unit": "Hz",
    "status": "no cited range"
   },
   {
    "metric": "persistent rotors",
    "segment": "light off",
    "value": "0",
    "unit": "count",
    "status": "no cited range"
   },
   {
    "metric": "singularity frames fraction",
    "segment": "light off",
    "value": "0.0029\u20130.0296",
    "unit": "fraction of frames",
    "status": "unstable, not reportable"
   },
   {
    "metric": "persistent rotor count max",
    "segment": "light off",
    "value": "0",
    "unit": "count",
    "status": "no cited range"
   },
   {
    "metric": "dominant freq (Hz)",
    "segment": "illuminated arrhythmia",
    "value": "15.4\u201319.9",
    "unit": "Hz",
    "status": "unstable, not reportable"
   },
   {
    "metric": "persistent rotors",
    "segment": "illuminated arrhythmia",
    "value": "4\u201315",
    "unit": "count",
    "status": "unstable, not reportable"
   },
   {
    "metric": "dominant freq (Hz)",
    "segment": "illuminated after termination",
    "value": "2.214",
    "unit": "Hz",
    "status": "no cited range"
   },
   {
    "metric": "singularity frames fraction",
    "segment": "illuminated arrhythmia",
    "value": "0.479",
    "unit": "fraction of frames",
    "status": "no cited range"
   },
   {
    "metric": "persistent rotors",
    "segment": "illuminated after termination",
    "value": "0",
    "unit": "count",
    "status": "no cited range"
   },
   {
    "metric": "persistent rotor count max",
    "segment": "illuminated arrhythmia",
    "value": "1\u20132",
    "unit": "count",
    "status": "unstable, not reportable"
   },
   {
    "metric": "singularity frames fraction",
    "segment": "illuminated after termination",
    "value": "0.000553\u20130.0149",
    "unit": "fraction of frames",
    "status": "unstable, not reportable"
   },
   {
    "metric": "persistent rotor count max",
    "segment": "illuminated after termination",
    "value": "0",
    "unit": "count",
    "status": "no cited range"
   }
  ],
  "verdict": {
   "physiology_ok": null,
   "send_back": false,
   "notes": "Verdict: report only stable descriptive findings and the provisional qualitative pattern, not unstable single values; physiology_ok is null because no stable ranged metric was available for pass/fail. Reportable items include stable absence of persistent rotors in light_off and illuminated_after_termination, stable maximum concurrent persistent-rotor count of 0 in those segments, stable dominant frequencies of 2.375 Hz in light_off and 2.214 Hz after termination, and a stable illuminated_arrhythmia singularity-frame fraction of 0.47902621722846445 with sensitivity range 0.3816479400749064\u20130.48801498127340825; the provisional persistent-rotor presence/absence rule holds using both the 52-frame measured-cycle threshold and the 50-frame paper-derived threshold from the 20.0 Hz context in DOI 10.1371/journal.pcbi.1011660. Not reportable as single values are light_off.singularity_frames_frac 0.0029023746701846965\u20130.02955145118733509, illuminated_arrhythmia.persistent_rotors 4.0\u201315.0, illuminated_arrhythmia.persistent_rotor_count_max 1.0\u20132.0, illuminated_arrhythmia.dominant_freq_hz 15.356\u201319.85 Hz, illuminated_after_termination.singularity_frames_frac 0.0005534034311012728\u20130.014941892639734366, and persistent_rotor_tracks 4.0\u201315.0. Needs review: pre-deposit processing/raw-data labeling, the provisional frame-3170 event interpretation, baseline/illumination artifact effects, and all provisional tool thresholds, ranges, stability threshold and criteria; the same-study frequency context is approximately 18.75\u201320.0 Hz, provisionally checked over 14.0625\u201325.0 Hz, in DOI 10.1371/journal.pcbi.1011660."
  },
  "provenance": {
   "recording": {
    "id": "55cb4aa3-6502-45a6-a14c-85cb676fe8c3",
    "label": "Mouse heart, spiral wave and optogenetic termination (M13Rec001)",
    "source": "public",
    "source_ref": "10.5281/zenodo.10228296",
    "publication_ref": "10.1371/journal.pcbi.1011660",
    "storage_path": "public/M13Rec001_complete.npy",
    "format": "npy",
    "sha256": "3f8f2e1b8f776633089b33ccd4bf3fccb4f13140b71991f1dcd0e0a12bb48cbc",
    "size_bytes": 260958848,
    "license": "CC-BY-4.0",
    "attribution": "Hussaini, Sayedeh; Luther, Stefan; L\u00e4dke, Sarah L.",
    "rights_source": {
     "ref": "10.5281/zenodo.10228296",
     "url": "https://zenodo.org/records/10228296",
     "kind": "deposit_metadata",
     "creators": [
      "Hussaini, Sayedeh",
      "Luther, Stefan",
      "L\u00e4dke, Sarah L."
     ],
     "license_as_stated": "cc-by-4.0"
    },
    "frame_rate_hz": 1000,
    "frame_rate_source": {
     "ref": "10.1371/journal.pcbi.1011660",
     "kind": "publication",
     "note": "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.",
     "quote": " 775 \u00b1 70nm bandpass filter (FF01\u2013775/140-25, Semrock) and finally by the camera (EMCCD, Cascade 128+, Photometrics) with a spatial resolution of 64 \u00d7 64 pixels (133 \u03bcm per pixel) at 1 kHz. Optical Mapping recordings were acquired with software MultiRecorder and analysed with software PythonAnalyser (both developed by Research Group Biomedical Physics). Electrical s",
     "section": "Materials and methods: Optical mapping experiments on ventricular arrhythmia and its termination in the intact mouse heart"
    },
    "pixel_size_um": 133,
    "pixel_size_source": {
     "ref": "10.1371/journal.pcbi.1011660",
     "kind": "publication",
     "note": "paper states 64 x 64 px at 133 um; the deposit is 64 x 55 (cropped, not rebinned)",
     "quote": "rst collected by a 775 \u00b1 70nm bandpass filter (FF01\u2013775/140-25, Semrock) and finally by the camera (EMCCD, Cascade 128+, Photometrics) with a spatial resolution of 64 \u00d7 64 pixels (133 \u03bcm per pixel) at 1 kHz. Optical Mapping recordings were acquired with software MultiRecorder and analysed with software PythonAnalyser (both developed by Research Group Biomedical Physics). El"
    },
    "frames": 9267,
    "height": 64,
    "width": 55,
    "inverted": true
   },
   "protocol": {
    "id": "f65d786f-f194-4be2-88b8-10d3dd25d674",
    "name": "Mouse whole heart optical mapping (Luther lab)",
    "species": "mouse",
    "tissue": "whole_heart",
    "params_version": 3,
    "params_set_by": "developer (not a domain scientist)",
    "params_note": "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": {
    "id": "6d6015e6-82f2-4762-97e2-5663d547c549",
    "status": "done",
    "started_at": "2026-10-27T22:21:41.750259+00:00",
    "finished_at": "2026-10-27T22:26:59.721801+00:00",
    "code": {
     "dirty": false,
     "git_commit": "13d8ceb123e64ab2c7eaba9fbf51605361856f11"
    },
    "workers": null,
    "steps": [
     "load",
     "deposit_checks",
     "baseline_correct",
     "polarity",
     "spatial_filter(phase only)",
     "hilbert_phase",
     "phase_singularities",
     "track_and_pair",
     "beats_apd_cv",
     "sensitivity",
     "render"
    ],
    "protocol_params": {
     "params": {
      "link_px": 4.0,
      "max_gap": 5,
      "min_cycles": 1.0,
      "pad_frames": 500,
      "paired_frac": 0.5,
      "render_step": 4,
      "pair_dist_px": 3.0,
      "spatial_sigma": 1.0,
      "rotor_erode_px": 3,
      "baseline_frames": 901,
      "rotor_threshold": 0.9,
      "spatial_truncate": 4.0
     },
     "version": 3,
     "protocol_id": "f65d786f-f194-4be2-88b8-10d3dd25d674"
    },
    "baseline_rule": null,
    "deposit_checks": {
     "flags": [
      {
       "flag": "negative_values",
       "value": 0.3231635934819897,
       "suggests": "baseline-subtracted or normalized; raw fluorescence counts are non-negative",
       "threshold": 0.01
      },
      {
       "flag": "non_integer",
       "value": 0.0,
       "suggests": "not raw camera counts (camera output is integer); weak alone",
       "threshold": 0.5
      },
      {
       "flag": "nan_mask_all_frames",
       "value": 1188,
       "suggests": "tissue masked by depositor; the mask is theirs"
      },
      {
       "flag": "temporal_smoothing",
       "value": 0.9120054707808141,
       "suggests": "temporally low-pass filtered (white shot noise gives dV lag-1 autocorr near -0.5)",
       "threshold": 0.5
      },
      {
       "flag": "spatial_smoothing",
       "value": 0.9957938301611564,
       "suggests": "spatially filtered or binned (shot noise is independent between pixels)",
       "threshold": 0.8
      }
     ],
     "status": "provisional",
     "measures": {
      "max": 4.49806547164917,
      "min": -6.050762176513672,
      "frames_used": 2000,
      "integer_frac": 0.0,
      "negative_frac": 0.3231635934819897,
      "frames_with_nan": 9267,
      "dv_lag1_autocorr_median": 0.9120054707808141,
      "neighbour_dv_corr_median": 0.9957938301611564
     },
     "processed_before_deposit": true
    },
    "pipeline_check": {
     "model": "openai:gpt-5.5",
     "proceed": true,
     "anomalies": [
      {
       "topic": "Pre-deposit processing / raw-data label",
       "severity": "warn",
       "effect_on_analysis": "The deposited movie should not be treated as raw camera counts: documentation and measurements indicate masking, temporal smoothing, spatial smoothing, and normalization before deposit. The fixed pipeline can still be run, but the protocol spatial_sigma = 1.0 Gaussian for phase is applied on top of prior spatial smoothing, so the total filtering is unknown; noise- or amplitude-dependent interpretations, including SNR and fine spatial structure, should be treated cautiously."
      },
      {
       "topic": "Event interpretation at frame 3170",
       "severity": "warn",
       "effect_on_analysis": "The segment boundary at frame 3170 is usable only as a provisional fluorescence baseline/rhythm-change or inferred termination boundary. DAQ and photodiode evidence indicate illumination was already on before frame 0 and turned off at frame 4977, so analyses must not interpret frame 3170 as light onset."
      },
      {
       "topic": "Baseline and illumination artifact",
       "severity": "warn",
       "effect_on_analysis": "Blue-light crosstalk, re-normalization to the stimulation-light signal, a large slow baseline range, and a baseline step can bias absolute fluorescence baseline and amplitude measures. The fixed high-pass baseline window and phase analysis may proceed, but baseline/amplitude results and event-related changes need caveats."
      }
     ],
     "rationale": "The recording fits the mouse whole-heart Luther-lab protocol as available: the species and tissue agree, the publication-supported frame rate is 1000 Hz, and the 64 \u00d7 55 deposited image is consistent with a cropped version of the 64 \u00d7 64 camera acquisition described in the paper rather than a protocol conflict. The protocol has no fixed indicator, frame-rate, pixel-size, or image-size value that is contradicted by the recording facts. With the fixed version 3 baseline_frames = 901, the baseline window spans more than the caveated minimum cycle coverage in each segment at the measured dominant rhythms, so the frame-based temporal parameters are not made inappropriate by this recording. The main limitations are not blocking mismatches but warnings: prior smoothing/normalization, provisional event interpretation at frame 3170, and illumination-related baseline artifacts affect interpretation of filtered, amplitude, and event-aligned outputs.",
     "mismatches": [],
     "hold_reason": null,
     "protocol_id": "f65d786f-f194-4be2-88b8-10d3dd25d674",
     "methods_text": "For this run, the provisional parameter set and criteria are protocol f65d786f-f194-4be2-88b8-10d3dd25d674 version 3 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 frame rate is 1000 Hz from the publication, and the pixel size is 133 \u00b5m from the publication. The analysed window is frames 500 to 8767. The provisional segment definitions are illuminated_arrhythmia, frames 0 to 3170; illuminated_after_termination, frames 3170 to 4977; and light_off, frames 4977 to 9267.",
     "recording_id": "55cb4aa3-6502-45a6-a14c-85cb676fe8c3",
     "params_version": 3,
     "prompt_version": "pipeline-v2"
    }
   },
   "signature": {
    "id": "056f9e28-85a3-4436-aea7-6df0842b39e3",
    "created_at": "2026-10-27T22:26:59.842083+00:00",
    "movie_path": "runs/6d6015e6-82f2-4762-97e2-5663d547c549/movie.mp4",
    "frames": {},
    "filter_params": {
     "mask": "not NaN in frame 0 and nonzero temporal std",
     "render": {
      "step": 4,
      "palettes": {
       "phase": "twilight",
       "camera": "gray",
       "voltage": "gray"
      },
      "interpolation": "nearest"
     },
     "window": {
      "f0": 500,
      "f1": 8767,
      "segments": [
       {
        "name": "illuminated_arrhythmia",
        "label": "illumination with arrhythmia",
        "defined": [
         0,
         3170
        ],
        "analysed": [
         500,
         3170
        ],
        "citation": {
         "ref": "10.1371/journal.pcbi.1011660",
         "quote": "t stimulus with LI = 3.44 \u03bcW/mm2 and PL = 5 s. Fig 2C shows a monophasic action potential (MAP) signal (in black) before, during, and after illumination. It shows the sinus rhythm returns after 3190 ms of illumination. Fig 2D presents a closer look at the MAP signal of the heart during the last few rotations of arrhythmia and the first few action potentials of sinus rhythm. Fig 2E illustrates a"
        },
        "defined_by": "project lead (not a domain scientist), following the paper's design",
        "segment_id": "f6ca0bce-f7e9-437d-84b6-1bb1b24f80ba",
        "end_event_id": "46c59a51-1a01-4aed-8021-db9a63720a1d",
        "start_event_id": null,
        "expected_persistent_rotors": "present"
       },
       {
        "name": "illuminated_after_termination",
        "label": "illumination after termination",
        "defined": [
         3170,
         4977
        ],
        "analysed": [
         3170,
         4977
        ],
        "citation": {
         "ref": "10.1371/journal.pcbi.1011660",
         "quote": "t stimulus with LI = 3.44 \u03bcW/mm2 and PL = 5 s. Fig 2C shows a monophasic action potential (MAP) signal (in black) before, during, and after illumination. It shows the sinus rhythm returns after 3190 ms of illumination. Fig 2D presents a closer look at the MAP signal of the heart during the last few rotations of arrhythmia and the first few action potentials of sinus rhythm. Fig 2E illustrates a"
        },
        "defined_by": "project lead (not a domain scientist), following the paper's design",
        "segment_id": "c1444c59-1863-45aa-b6f3-2208392bf55a",
        "end_event_id": "db2ad5f3-9b96-4ec1-9ccd-9c82c3425609",
        "start_event_id": "46c59a51-1a01-4aed-8021-db9a63720a1d",
        "expected_persistent_rotors": "absent"
       },
       {
        "name": "light_off",
        "label": "light off",
        "defined": [
         4977,
         9267
        ],
        "analysed": [
         4977,
         8767
        ],
        "citation": {
         "ref": "10.1371/journal.pcbi.1011660",
         "quote": "t stimulus with LI = 3.44 \u03bcW/mm2 and PL = 5 s. Fig 2C shows a monophasic action potential (MAP) signal (in black) before, during, and after illumination. It shows the sinus rhythm returns after 3190 ms of illumination. Fig 2D presents a closer look at the MAP signal of the heart during the last few rotations of arrhythmia and the first few action potentials of sinus rhythm. Fig 2E illustrates a"
        },
        "defined_by": "project lead (not a domain scientist), following the paper's design",
        "segment_id": "4eeedfd6-84c2-40d3-8a4a-8758716d02d9",
        "end_event_id": null,
        "start_event_id": "db2ad5f3-9b96-4ec1-9ccd-9c82c3425609",
        "expected_persistent_rotors": "absent"
       }
      ],
      "illumination": "Acquisition log (LED trigger channel, provisional interpretation): illumination on over frames 500-4977 of the analysed frames 500-8767.",
      "frame_rate_hz": 1000.0,
      "frame_rate_source": {
       "ref": "10.1371/journal.pcbi.1011660",
       "kind": "publication",
       "note": "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.",
       "quote": " 775 \u00b1 70nm bandpass filter (FF01\u2013775/140-25, Semrock) and finally by the camera (EMCCD, Cascade 128+, Photometrics) with a spatial resolution of 64 \u00d7 64 pixels (133 \u03bcm per pixel) at 1 kHz. Optical Mapping recordings were acquired with software MultiRecorder and analysed with software PythonAnalyser (both developed by Research Group Biomedical Physics). Electrical s",
       "section": "Materials and methods: Optical mapping experiments on ventricular arrhythmia and its termination in the intact mouse heart"
      },
      "segment_cycles_frames": {
       "light_off": 421,
       "illuminated_arrhythmia": 52,
       "illuminated_after_termination": 452
      }
     },
     "lowpass": null,
     "polarity": -1,
     "tracking": {
      "link_px": 4.0,
      "max_gap": 5,
      "min_cycles": 1.0,
      "min_frames": 52,
      "paired_frac": 0.5,
      "pair_dist_px": 3.0
     },
     "pad_frames": 500,
     "phase_method": "angle of scipy.signal.hilbert along time, on spatially filtered signal",
     "spatial_sigma": 1.0,
     "rotor_erode_px": 3,
     "spatial_method": "scipy.ndimage.gaussian_filter per frame, mode=reflect; NaN set to 0 before filtering, non-tissue zeroed after",
     "baseline_frames": 901,
     "baseline_method": "scipy.ndimage.uniform_filter1d, mode=reflect, subtracted per pixel",
     "polarity_method": "sign of median per-pixel skew of dV/dt on baseline-corrected signal",
     "rotor_threshold": 0.9,
     "spatial_truncate": 4.0,
     "spatial_applies_to": "phase/activation only; displayed voltage is baseline-corrected only"
    },
    "criteria_status": {
     "note": null,
     "rules": [
      {
       "id": "protocol_parameter_set",
       "expert": "optical mapping analyst",
       "status": "provisional",
       "values": {
        "set_by": "developer (not a domain scientist)",
        "protocol": "Mouse whole heart optical mapping (Luther lab)",
        "protocol_id": "f65d786f-f194-4be2-88b8-10d3dd25d674",
        "params_version": 3
       },
       "decision": null,
       "location": "worker/voltage/protocol_params.py (developer_defaults, set_params)",
       "reviewed": false,
       "reviewer": null,
       "description": "Each protocol's fixed, versioned analysis parameters (version 1 = developer defaults); no run or agent may deviate",
       "reviewed_at": null
      },
      {
       "id": "filter_defaults",
       "expert": "optical mapping analyst (cardiac electrophysiology)",
       "status": "provisional",
       "values": {
        "lowpass": null,
        "spatial_sigma": 1.0,
        "baseline_frames": 901,
        "spatial_truncate": 4.0
       },
       "decision": null,
       "location": "worker/voltage/preprocess.py (Params)",
       "reviewed": false,
       "reviewer": null,
       "description": "Default baseline window (frames) and spatial Gaussian sigma/truncate for phase",
       "reviewed_at": null
      },
      {
       "id": "tissue_mask",
       "expert": "optical mapping analyst",
       "status": "provisional",
       "values": {
        "rule": "not NaN in frame 0 and nonzero std",
        "tissue_pixels": 2332
       },
       "decision": null,
       "location": "worker/voltage/io.py (tissue_mask)",
       "reviewed": false,
       "reviewer": null,
       "description": "Tissue = not NaN in frame 0 and nonzero temporal std",
       "reviewed_at": null
      },
      {
       "id": "polarity",
       "expert": "optical mapping analyst / voltage dye chemist",
       "status": "provisional",
       "values": {
        "method": "median skew of dV/dt",
        "result": -1
       },
       "decision": null,
       "location": "worker/voltage/preprocess.py (polarity)",
       "reviewed": false,
       "reviewer": null,
       "description": "Dye polarity from sign of median per-pixel skew of dV/dt",
       "reviewed_at": null
      },
      {
       "id": "singularity_detection",
       "expert": "computational cardiac electrophysiologist (phase mapping)",
       "status": "provisional",
       "values": {
        "rotor_erode_px": 3,
        "rotor_threshold": 0.9
       },
       "decision": null,
       "location": "worker/voltage/preprocess.py (Params.rotor_threshold, rotor_erode_px)",
       "reviewed": false,
       "reviewer": null,
       "description": "Phase singularity = |winding| > threshold turns, >= erode px from tissue edge",
       "reviewed_at": null
      },
      {
       "id": "rotor_persistence",
       "expert": "computational cardiac electrophysiologist (phase mapping)",
       "status": "provisional",
       "values": {
        "link_px": 4.0,
        "max_gap": 5,
        "min_cycles": 1.0,
        "min_frames": 52
       },
       "decision": null,
       "location": "worker/voltage/rotors.py (TrackParams)",
       "reviewed": false,
       "reviewer": null,
       "description": "Track linking distance/gap and minimum lifetime for a persistent rotor",
       "reviewed_at": null
      },
      {
       "id": "chirality_pairing",
       "expert": "computational cardiac electrophysiologist (phase mapping)",
       "status": "provisional",
       "values": {
        "paired_frac": 0.5,
        "pair_dist_px": 3.0
       },
       "decision": null,
       "location": "worker/voltage/rotors.py (TrackParams.pair_dist_px, paired_frac)",
       "reviewed": false,
       "reviewer": null,
       "description": "Opposite-charge singularities within pair distance are a pair; tracks paired most of their life are excluded from rotors",
       "reviewed_at": null
      },
      {
       "id": "sensitivity_grid",
       "expert": "optical mapping analyst",
       "status": "provisional",
       "values": {
        "sigmas": {
         "light": 0.5,
         "default": 1.0,
         "heavier": 2.0
        },
        "trackers": {
         "loose": [
          6.0,
          10
         ],
         "strict": [
          2.0,
          1
         ],
         "default": [
          4.0,
          5
         ]
        },
        "baselines": {
         "run": 901,
         "3x_cycle": 1356,
         "6x_cycle": 2712,
         "1.5x_cycle": 678
        }
       },
       "decision": null,
       "location": "worker/voltage/sensitivity.py (SIGMAS, BASELINE_MULTIPLES, baseline_levels)",
       "reviewed": false,
       "reviewer": null,
       "description": "Filter levels tested: spatial sigma and baseline window values",
       "reviewed_at": null
      },
      {
       "id": "analysis_window",
       "expert": "cardiac electrophysiologist familiar with the dataset",
       "status": "provisional",
       "values": {
        "f0": 500,
        "f1": 8767
       },
       "decision": null,
       "location": "worker/voltage/runs.py (default_window)",
       "reviewed": false,
       "reviewer": null,
       "description": "Frames analysed: whole recording minus one filter pad at each end (unless the plan narrows it)",
       "reviewed_at": null
      },
      {
       "id": "prior_processing_flags",
       "expert": "imaging scientist (camera acquisition and noise)",
       "status": "provisional",
       "values": {
        "flags": [
         "negative_values",
         "non_integer",
         "nan_mask_all_frames",
         "temporal_smoothing",
         "spatial_smoothing"
        ],
        "thresholds": {
         "int_frac": 0.5,
         "neg_frac": 0.01,
         "dv_autocorr": 0.5,
         "neighbour_corr": 0.8
        }
       },
       "decision": null,
       "location": "worker/voltage/inspect.py (prior_processing)",
       "reviewed": false,
       "reviewer": null,
       "description": "Thresholds for flagging depositor processing (normalization, masking, temporal/spatial smoothing)",
       "reviewed_at": null
      },
      {
       "id": "baseline_step_detection",
       "expert": "optical mapping experimentalist",
       "status": "provisional",
       "values": {
        "frames": [
         3170
        ]
       },
       "decision": null,
       "location": "worker/voltage/events.py (detect_baseline_step)",
       "reviewed": false,
       "reviewer": null,
       "description": "Baseline step = consensus upward step in tissue-mean raw baseline (cause not inferred; first misread as light onset, contradicted by the DAQ)",
       "reviewed_at": null
      },
      {
       "id": "daq_interpretation",
       "expert": "experimentalist who recorded the data (or the depositor)",
       "status": "provisional",
       "values": {
        "events": [
         "illumination_on@0",
         "arrhythmia_termination@3153",
         "illumination_off@4977"
        ]
       },
       "decision": null,
       "location": "worker/voltage/daq.py",
       "reviewed": false,
       "reviewer": null,
       "description": "DAQ channel names from depositor notebook; frames = first N triggers of closest burst; midpoint thresholds",
       "reviewed_at": null
      },
      {
       "id": "segment_definitions",
       "expert": "cardiac electrophysiologist (ideally the depositing authors)",
       "status": "provisional",
       "values": {
        "light_off": [
         4977,
         9267
        ],
        "illuminated_arrhythmia": [
         0,
         3170
        ],
        "illuminated_after_termination": [
         3170,
         4977
        ]
       },
       "decision": null,
       "location": "worker/voltage/annotations.py (MOUSE_SEGMENTS)",
       "reviewed": false,
       "reviewer": null,
       "description": "Mouse segments bounded by DAQ light events and the baseline step, interpreted as spiral termination under illumination (project lead, from Hussaini et al. 2023)",
       "reviewed_at": null
      },
      {
       "id": "rotor_finding_criterion",
       "expert": "cardiac electrophysiologist + biostatistician",
       "status": "provisional",
       "values": {
        "min_frac": 0.1,
        "min_ratio": 2.0
       },
       "decision": null,
       "location": "worker/voltage/sensitivity.py (MIN_FRAC, MIN_RATIO)",
       "reviewed": false,
       "reviewer": null,
       "description": "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)",
       "reviewed_at": null
      },
      {
       "id": "persistent_rotor_criterion",
       "expert": "cardiac electrophysiologist",
       "status": "provisional",
       "values": {
        "expect": {
         "light_off": "absent",
         "illuminated_arrhythmia": "present",
         "illuminated_after_termination": "absent"
        },
        "max_absent": 0,
        "min_present": 1,
        "spanning_rotor": "counts in every segment it overlaps",
        "min_lifetime_frames": 52
       },
       "decision": null,
       "location": "worker/voltage/sensitivity.py (MIN_ROTORS_PRESENT, MAX_ROTORS_ABSENT)",
       "reviewed": false,
       "reviewer": null,
       "description": "Persistent-rotor finding holds if every 'present' segment has >= 1 persistent rotor and every 'absent' segment has none, at every setting",
       "reviewed_at": null
      },
      {
       "id": "pipeline_check",
       "expert": "optical mapping analyst",
       "status": "provisional",
       "values": {
        "model": "openai:gpt-5.5",
        "proceed": true,
        "anomalies": [
         "Pre-deposit processing / raw-data label",
         "Event interpretation at frame 3170",
         "Baseline and illumination artifact"
        ],
        "mismatches": []
       },
       "decision": null,
       "location": "worker/agents/pipeline.py (INSTRUCTIONS, validator)",
       "reviewed": false,
       "reviewer": null,
       "description": "The pipeline agent's hold/proceed decision from protocol mismatches and inspector anomalies; it chooses no parameter",
       "reviewed_at": null
      },
      {
       "id": "physiology_reference_rates",
       "expert": "cardiac electrophysiologist per species",
       "status": "provisional",
       "values": {
        "ranges": [
         "mouse_spiral_rotation_hz"
        ],
        "tolerance_frac": 0.25,
        "segment_rhythm_rule": "expected persistent rotors 'present' -> spiral arrhythmia"
       },
       "decision": null,
       "location": "worker/voltage/physiology.py (RANGES, TOLERANCE_FRAC)",
       "reviewed": false,
       "reviewer": null,
       "description": "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",
       "reviewed_at": null
      },
      {
       "id": "stability_rule",
       "expert": "biostatistician + optical mapping analyst",
       "status": "provisional",
       "values": {
        "unstable": [
         "light_off.singularity_frames_frac",
         "illuminated_arrhythmia.persistent_rotors",
         "illuminated_arrhythmia.persistent_rotor_count_max",
         "illuminated_arrhythmia.dominant_freq_hz",
         "illuminated_after_termination.singularity_frames_frac",
         "persistent_rotor_tracks"
        ],
        "stable_frac": 0.25
       },
       "decision": null,
       "location": "worker/agents/critic.py (STABLE_FRAC, stability)",
       "reviewed": false,
       "reviewer": null,
       "description": "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'",
       "reviewed_at": null
      },
      {
       "id": "persistence_threshold_variants",
       "expert": "computational cardiac electrophysiologist (phase mapping)",
       "status": "provisional",
       "values": {
        "measured_cycle": 52,
        "paper_rotation": 50
       },
       "decision": null,
       "location": "worker/agents/critic.py (persistence_variants)",
       "reviewed": false,
       "reviewer": null,
       "description": "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",
       "reviewed_at": null
      }
     ],
     "status": "provisional",
     "all_reviewed": false,
     "superseded_by_run": null
    }
   },
   "segments": [
    {
     "id": "f6ca0bce-f7e9-437d-84b6-1bb1b24f80ba",
     "position": 1,
     "name": "illuminated_arrhythmia",
     "label": "illumination with arrhythmia",
     "start_frame": 0,
     "end_frame": 3170,
     "expected_persistent_rotors": "present",
     "definition": "from recording start to spiral termination (interpreted; under illumination)",
     "defined_by": "project lead (not a domain scientist), following the paper's design",
     "citation": {
      "ref": "10.1371/journal.pcbi.1011660",
      "quote": "t stimulus with LI = 3.44 \u03bcW/mm2 and PL = 5 s. Fig 2C shows a monophasic action potential (MAP) signal (in black) before, during, and after illumination. It shows the sinus rhythm returns after 3190 ms of illumination. Fig 2D presents a closer look at the MAP signal of the heart during the last few rotations of arrhythmia and the first few action potentials of sinus rhythm. Fig 2E illustrates a"
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     "citation": {
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      "quote": "t stimulus with LI = 3.44 \u03bcW/mm2 and PL = 5 s. Fig 2C shows a monophasic action potential (MAP) signal (in black) before, during, and after illumination. It shows the sinus rhythm returns after 3190 ms of illumination. Fig 2D presents a closer look at the MAP signal of the heart during the last few rotations of arrhythmia and the first few action potentials of sinus rhythm. Fig 2E illustrates a"
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     "citation": {
      "ref": "10.1371/journal.pcbi.1011660",
      "quote": "t stimulus with LI = 3.44 \u03bcW/mm2 and PL = 5 s. Fig 2C shows a monophasic action potential (MAP) signal (in black) before, during, and after illumination. It shows the sinus rhythm returns after 3190 ms of illumination. Fig 2D presents a closer look at the MAP signal of the heart during the last few rotations of arrhythmia and the first few action potentials of sinus rhythm. Fig 2E illustrates a"
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    {
     "id": "46c59a51-1a01-4aed-8021-db9a63720a1d",
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     "label": "spiral termination (interpreted; under illumination)",
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     "status": "detected",
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     "method": "consensus upward step in running-median baseline of tissue-mean raw signal"
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    {
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 "provenance": {
  "recording": {
   "id": "55cb4aa3-6502-45a6-a14c-85cb676fe8c3",
   "label": "Mouse heart, spiral wave and optogenetic termination (M13Rec001)",
   "source": "public",
   "source_ref": "10.5281/zenodo.10228296",
   "publication_ref": "10.1371/journal.pcbi.1011660",
   "storage_path": "public/M13Rec001_complete.npy",
   "format": "npy",
   "sha256": "3f8f2e1b8f776633089b33ccd4bf3fccb4f13140b71991f1dcd0e0a12bb48cbc",
   "size_bytes": 260958848,
   "license": "CC-BY-4.0",
   "attribution": "Hussaini, Sayedeh; Luther, Stefan; L\u00e4dke, Sarah L.",
   "rights_source": {
    "ref": "10.5281/zenodo.10228296",
    "url": "https://zenodo.org/records/10228296",
    "kind": "deposit_metadata",
    "creators": [
     "Hussaini, Sayedeh",
     "Luther, Stefan",
     "L\u00e4dke, Sarah L."
    ],
    "license_as_stated": "cc-by-4.0"
   },
   "frame_rate_hz": 1000,
   "frame_rate_source": {
    "ref": "10.1371/journal.pcbi.1011660",
    "kind": "publication",
    "note": "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.",
    "quote": " 775 \u00b1 70nm bandpass filter (FF01\u2013775/140-25, Semrock) and finally by the camera (EMCCD, Cascade 128+, Photometrics) with a spatial resolution of 64 \u00d7 64 pixels (133 \u03bcm per pixel) at 1 kHz. Optical Mapping recordings were acquired with software MultiRecorder and analysed with software PythonAnalyser (both developed by Research Group Biomedical Physics). Electrical s",
    "section": "Materials and methods: Optical mapping experiments on ventricular arrhythmia and its termination in the intact mouse heart"
   },
   "pixel_size_um": 133,
   "pixel_size_source": {
    "ref": "10.1371/journal.pcbi.1011660",
    "kind": "publication",
    "note": "paper states 64 x 64 px at 133 um; the deposit is 64 x 55 (cropped, not rebinned)",
    "quote": "rst collected by a 775 \u00b1 70nm bandpass filter (FF01\u2013775/140-25, Semrock) and finally by the camera (EMCCD, Cascade 128+, Photometrics) with a spatial resolution of 64 \u00d7 64 pixels (133 \u03bcm per pixel) at 1 kHz. Optical Mapping recordings were acquired with software MultiRecorder and analysed with software PythonAnalyser (both developed by Research Group Biomedical Physics). El"
   },
   "frames": 9267,
   "height": 64,
   "width": 55,
   "inverted": true
  },
  "protocol": {
   "id": "f65d786f-f194-4be2-88b8-10d3dd25d674",
   "name": "Mouse whole heart optical mapping (Luther lab)",
   "species": "mouse",
   "tissue": "whole_heart",
   "params_version": 3,
   "params_set_by": "developer (not a domain scientist)",
   "params_note": "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": {
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   "status": "done",
   "started_at": "2026-10-27T22:21:41.750259+00:00",
   "finished_at": "2026-10-27T22:26:59.721801+00:00",
   "code": {
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    "git_commit": "13d8ceb123e64ab2c7eaba9fbf51605361856f11"
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    "baseline_correct",
    "polarity",
    "spatial_filter(phase only)",
    "hilbert_phase",
    "phase_singularities",
    "track_and_pair",
    "beats_apd_cv",
    "sensitivity",
    "render"
   ],
   "protocol_params": {
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     "link_px": 4.0,
     "max_gap": 5,
     "min_cycles": 1.0,
     "pad_frames": 500,
     "paired_frac": 0.5,
     "render_step": 4,
     "pair_dist_px": 3.0,
     "spatial_sigma": 1.0,
     "rotor_erode_px": 3,
     "baseline_frames": 901,
     "rotor_threshold": 0.9,
     "spatial_truncate": 4.0
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    "version": 3,
    "protocol_id": "f65d786f-f194-4be2-88b8-10d3dd25d674"
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     {
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     {
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      "value": 1188,
      "suggests": "tissue masked by depositor; the mask is theirs"
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     {
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   "pipeline_check": {
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    "proceed": true,
    "anomalies": [
     {
      "topic": "Pre-deposit processing / raw-data label",
      "severity": "warn",
      "effect_on_analysis": "The deposited movie should not be treated as raw camera counts: documentation and measurements indicate masking, temporal smoothing, spatial smoothing, and normalization before deposit. The fixed pipeline can still be run, but the protocol spatial_sigma = 1.0 Gaussian for phase is applied on top of prior spatial smoothing, so the total filtering is unknown; noise- or amplitude-dependent interpretations, including SNR and fine spatial structure, should be treated cautiously."
     },
     {
      "topic": "Event interpretation at frame 3170",
      "severity": "warn",
      "effect_on_analysis": "The segment boundary at frame 3170 is usable only as a provisional fluorescence baseline/rhythm-change or inferred termination boundary. DAQ and photodiode evidence indicate illumination was already on before frame 0 and turned off at frame 4977, so analyses must not interpret frame 3170 as light onset."
     },
     {
      "topic": "Baseline and illumination artifact",
      "severity": "warn",
      "effect_on_analysis": "Blue-light crosstalk, re-normalization to the stimulation-light signal, a large slow baseline range, and a baseline step can bias absolute fluorescence baseline and amplitude measures. The fixed high-pass baseline window and phase analysis may proceed, but baseline/amplitude results and event-related changes need caveats."
     }
    ],
    "rationale": "The recording fits the mouse whole-heart Luther-lab protocol as available: the species and tissue agree, the publication-supported frame rate is 1000 Hz, and the 64 \u00d7 55 deposited image is consistent with a cropped version of the 64 \u00d7 64 camera acquisition described in the paper rather than a protocol conflict. The protocol has no fixed indicator, frame-rate, pixel-size, or image-size value that is contradicted by the recording facts. With the fixed version 3 baseline_frames = 901, the baseline window spans more than the caveated minimum cycle coverage in each segment at the measured dominant rhythms, so the frame-based temporal parameters are not made inappropriate by this recording. The main limitations are not blocking mismatches but warnings: prior smoothing/normalization, provisional event interpretation at frame 3170, and illumination-related baseline artifacts affect interpretation of filtered, amplitude, and event-aligned outputs.",
    "mismatches": [],
    "hold_reason": null,
    "protocol_id": "f65d786f-f194-4be2-88b8-10d3dd25d674",
    "methods_text": "For this run, the provisional parameter set and criteria are protocol f65d786f-f194-4be2-88b8-10d3dd25d674 version 3 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 frame rate is 1000 Hz from the publication, and the pixel size is 133 \u00b5m from the publication. The analysed window is frames 500 to 8767. The provisional segment definitions are illuminated_arrhythmia, frames 0 to 3170; illuminated_after_termination, frames 3170 to 4977; and light_off, frames 4977 to 9267.",
    "recording_id": "55cb4aa3-6502-45a6-a14c-85cb676fe8c3",
    "params_version": 3,
    "prompt_version": "pipeline-v2"
   }
  },
  "signature": {
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   "created_at": "2026-10-27T22:26:59.842083+00:00",
   "movie_path": "runs/6d6015e6-82f2-4762-97e2-5663d547c549/movie.mp4",
   "frames": {},
   "filter_params": {
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    "render": {
     "step": 4,
     "palettes": {
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      "camera": "gray",
      "voltage": "gray"
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     "interpolation": "nearest"
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    "window": {
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       "label": "illumination with arrhythmia",
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       "citation": {
        "ref": "10.1371/journal.pcbi.1011660",
        "quote": "t stimulus with LI = 3.44 \u03bcW/mm2 and PL = 5 s. Fig 2C shows a monophasic action potential (MAP) signal (in black) before, during, and after illumination. It shows the sinus rhythm returns after 3190 ms of illumination. Fig 2D presents a closer look at the MAP signal of the heart during the last few rotations of arrhythmia and the first few action potentials of sinus rhythm. Fig 2E illustrates a"
       },
       "defined_by": "project lead (not a domain scientist), following the paper's design",
       "segment_id": "f6ca0bce-f7e9-437d-84b6-1bb1b24f80ba",
       "end_event_id": "46c59a51-1a01-4aed-8021-db9a63720a1d",
       "start_event_id": null,
       "expected_persistent_rotors": "present"
      },
      {
       "name": "illuminated_after_termination",
       "label": "illumination after termination",
       "defined": [
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       "analysed": [
        3170,
        4977
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       "citation": {
        "ref": "10.1371/journal.pcbi.1011660",
        "quote": "t stimulus with LI = 3.44 \u03bcW/mm2 and PL = 5 s. Fig 2C shows a monophasic action potential (MAP) signal (in black) before, during, and after illumination. It shows the sinus rhythm returns after 3190 ms of illumination. Fig 2D presents a closer look at the MAP signal of the heart during the last few rotations of arrhythmia and the first few action potentials of sinus rhythm. Fig 2E illustrates a"
       },
       "defined_by": "project lead (not a domain scientist), following the paper's design",
       "segment_id": "c1444c59-1863-45aa-b6f3-2208392bf55a",
       "end_event_id": "db2ad5f3-9b96-4ec1-9ccd-9c82c3425609",
       "start_event_id": "46c59a51-1a01-4aed-8021-db9a63720a1d",
       "expected_persistent_rotors": "absent"
      },
      {
       "name": "light_off",
       "label": "light off",
       "defined": [
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       "analysed": [
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        8767
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       "citation": {
        "ref": "10.1371/journal.pcbi.1011660",
        "quote": "t stimulus with LI = 3.44 \u03bcW/mm2 and PL = 5 s. Fig 2C shows a monophasic action potential (MAP) signal (in black) before, during, and after illumination. It shows the sinus rhythm returns after 3190 ms of illumination. Fig 2D presents a closer look at the MAP signal of the heart during the last few rotations of arrhythmia and the first few action potentials of sinus rhythm. Fig 2E illustrates a"
       },
       "defined_by": "project lead (not a domain scientist), following the paper's design",
       "segment_id": "4eeedfd6-84c2-40d3-8a4a-8758716d02d9",
       "end_event_id": null,
       "start_event_id": "db2ad5f3-9b96-4ec1-9ccd-9c82c3425609",
       "expected_persistent_rotors": "absent"
      }
     ],
     "illumination": "Acquisition log (LED trigger channel, provisional interpretation): illumination on over frames 500-4977 of the analysed frames 500-8767.",
     "frame_rate_hz": 1000.0,
     "frame_rate_source": {
      "ref": "10.1371/journal.pcbi.1011660",
      "kind": "publication",
      "note": "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.",
      "quote": " 775 \u00b1 70nm bandpass filter (FF01\u2013775/140-25, Semrock) and finally by the camera (EMCCD, Cascade 128+, Photometrics) with a spatial resolution of 64 \u00d7 64 pixels (133 \u03bcm per pixel) at 1 kHz. Optical Mapping recordings were acquired with software MultiRecorder and analysed with software PythonAnalyser (both developed by Research Group Biomedical Physics). Electrical s",
      "section": "Materials and methods: Optical mapping experiments on ventricular arrhythmia and its termination in the intact mouse heart"
     },
     "segment_cycles_frames": {
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      "illuminated_arrhythmia": 52,
      "illuminated_after_termination": 452
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    "tracking": {
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     "min_cycles": 1.0,
     "min_frames": 52,
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    "pad_frames": 500,
    "phase_method": "angle of scipy.signal.hilbert along time, on spatially filtered signal",
    "spatial_sigma": 1.0,
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    "spatial_method": "scipy.ndimage.gaussian_filter per frame, mode=reflect; NaN set to 0 before filtering, non-tissue zeroed after",
    "baseline_frames": 901,
    "baseline_method": "scipy.ndimage.uniform_filter1d, mode=reflect, subtracted per pixel",
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}