{
 "exported_at": "2026-10-30T03:11:22.317563+00:00",
 "exported_by": {
  "app": "quantetta-a web",
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   "git_commit": "",
   "dirty": false
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 "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": "faeb5ebc",
  "run_when": "2026-10-27 23:05 UTC",
  "params_version": 3,
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  "workers": null,
  "sig_short": "cf0c8a27",
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  "protocol_name": "Mouse whole heart optical mapping (Luther lab)"
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 "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;     % >= 2 x slowest cycle (415, MAP): ok\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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    "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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 "critic": {
  "code": {
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    "illuminated_after_termination.singularity_frames_frac",
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  "ranges": [
   {
    "id": "mouse_spiral_rotation_hz",
    "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"
     ]
    },
    "status": "provisional",
    "tissue": "whole_heart",
    "species": "mouse",
    "applies_to": {
     "segment_expected_persistent_rotors": "present"
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    "checked_low": 14.0625,
    "checked_high": 25.0,
    "tolerance_frac": 0.25
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  ],
  "run_id": "faeb5ebc-ee96-4994-96b0-025811d9374b",
  "status": "provisional",
  "verdict": {
   "send_back": false,
   "critic_notes": "Verdict: report only stable descriptive findings and provisional presence/absence criteria, not unstable scalar values; physiology_ok is indeterminate because the only ranged check, illuminated-arrhythmia dominant frequency, is unstable over 15.356\u201319.85 Hz rather than reportable as a single value, although DOI 10.1371/journal.pcbi.1011660 provides same-study mouse context of approximately 20 Hz before illumination and approximately 18.75 Hz during illumination, with a 20.0 Hz rotation corresponding to 50 frames. Reportable items include stable absence of persistent rotors in light_off and illuminated_after_termination, stable persistent-rotor presence during illuminated_arrhythmia under the provisional rule, stable illuminated_arrhythmia singularity-frame fraction at 0.47902621722846445, stable light_off dominant frequency at 2.375 Hz, and stable illuminated_after_termination dominant frequency at 2.214 Hz, all with no cited physiology range except the unstable frequency context. Unstable and not reportable as single values are light_off.singularity_frames_frac over 0.0029023746701846965\u20130.02955145118733509, illuminated_arrhythmia.persistent_rotors over 4.0\u201315.0, illuminated_arrhythmia.persistent_rotor_count_max over 1.0\u20132.0, illuminated_arrhythmia.dominant_freq_hz over 15.356\u201319.85 Hz, illuminated_after_termination.singularity_frames_frac over 0.0005534034311012728\u20130.014941892639734366, and persistent_rotor_tracks over 4.0\u201315.0. Needs review: the deposited-data processing/raw label, frame-3170 event interpretation, baseline and illumination artifact, and all provisional tool thresholds; the ranges, the stability threshold, and the criteria are provisional.",
   "review_items": [
    {
     "topic": "unstable:light_off.singularity_frames_frac",
     "detail": "Filter sensitivity is high for the light-off singularity-frame fraction; do not report a single value, and review the range 0.0029023746701846965\u20130.02955145118733509 fraction of frames.",
     "severity": "warn",
     "reviewer_type": "domain scientist / analysis methods"
    },
    {
     "topic": "unstable:illuminated_arrhythmia.persistent_rotors",
     "detail": "Persistent-rotor counts during illuminated arrhythmia vary over 4.0\u201315.0 across filter and tracker settings; report presence/absence only under the provisional rule and review the count before use.",
     "severity": "warn",
     "reviewer_type": "domain scientist / analysis methods"
    },
    {
     "topic": "unstable:illuminated_arrhythmia.persistent_rotor_count_max",
     "detail": "Maximum concurrent persistent-rotor count during illuminated arrhythmia varies over 1.0\u20132.0; do not report a single maximum without review.",
     "severity": "warn",
     "reviewer_type": "domain scientist / analysis methods"
    },
    {
     "topic": "unstable:illuminated_arrhythmia.dominant_freq_hz",
     "detail": "Dominant frequency varies over 15.356\u201319.85 Hz across baseline windows; because this overlaps same-study context but is unstable, it should be reviewed before reporting.",
     "severity": "warn",
     "reviewer_type": "domain scientist / analysis methods"
    },
    {
     "topic": "unstable:illuminated_after_termination.singularity_frames_frac",
     "detail": "Post-termination illuminated singularity-frame fraction varies over 0.0005534034311012728\u20130.014941892639734366; do not report a single value without review.",
     "severity": "warn",
     "reviewer_type": "domain scientist / analysis methods"
    },
    {
     "topic": "unstable:persistent_rotor_tracks",
     "detail": "Total persistent-rotor tracks vary over 4.0\u201315.0 across filter and tracker settings; the track count is not reportable as a single value.",
     "severity": "warn",
     "reviewer_type": "domain scientist / analysis methods"
    },
    {
     "topic": "Pre-deposit processing / raw-data label",
     "detail": "The recording is labeled raw in the README, but documentation and prior-processing flags indicate masking, spatial smoothing, temporal smoothing, and normalization; analyses requiring raw photon counts or independent pixel noise should not treat it as raw camera data.",
     "severity": "warn",
     "reviewer_type": "data curator / methods reviewer"
    },
    {
     "topic": "Event interpretation at frame 3170",
     "detail": "Frame 3170 is a baseline_step image event, not light onset; illumination began before frame 0 and ended at frame 4977, so the stored spiral-termination interpretation is provisional.",
     "severity": "warn",
     "reviewer_type": "domain scientist"
    },
    {
     "topic": "Baseline and illumination artifact",
     "detail": "The publication reports blue-light crosstalk and re-normalization by recorded stimulation light signal, and this recording has a large slow baseline range and a baseline step; absolute baseline or amplitude analyses need artifact handling.",
     "severity": "warn",
     "reviewer_type": "methods reviewer"
    },
    {
     "topic": "Provisional tool thresholds",
     "detail": "Event detection, processing flags, SNR, rhythm, and reference-rate thresholds are provisional and not yet reviewed by a domain scientist.",
     "severity": "info",
     "reviewer_type": "domain scientist / methods reviewer"
    }
   ],
   "tracker_note": "Strict, default, and loose trackers found 5, 13, and 15 persistent rotors in the illuminated-arrhythmia segment and 0 in both the light-off and illuminated-after-termination segments; despite different counts, the provisional persistent-rotor presence/absence rule holds for all tracker variants, so the tracker rule verdicts agree.",
   "physiology_ok": null,
   "metric_judgments": [
    {
     "note": "Unstable across the filter grid, so the light-off singularity-frame fraction is not reportable as a single value; review only the sensitivity range 0.0029023746701846965\u20130.02955145118733509 fraction of frames.",
     "metric": "light_off.singularity_frames_frac",
     "status": "unstable_not_reportable"
    },
    {
     "note": "Stable at 0 persistent rotors, so this absence can be reported descriptively, but there is no cited physiology range for judging it.",
     "metric": "light_off.persistent_rotors",
     "status": "no_cited_range"
    },
    {
     "note": "Stable at a maximum concurrent persistent-rotor count of 0, so this absence can be reported descriptively, but there is no cited physiology range for judging it.",
     "metric": "light_off.persistent_rotor_count_max",
     "status": "no_cited_range"
    },
    {
     "note": "Stable at 2.375 Hz, but no cited range is available for this light-off segment; report only as a measured segment frequency, not as physiologically validated.",
     "metric": "light_off.dominant_freq_hz",
     "status": "no_cited_range"
    },
    {
     "note": "Stable at 0.47902621722846445 fraction of frames, supporting singularity presence during illuminated arrhythmia under the provisional criterion, but no cited physiology range is available.",
     "metric": "illuminated_arrhythmia.singularity_frames_frac",
     "status": "no_cited_range"
    },
    {
     "note": "The persistent-rotor count is unstable across filter and tracker settings, so the count is not reportable as a single value; review only the sensitivity range 4.0\u201315.0 rotors. The mouse context in DOI 10.1371/journal.pcbi.1011660 describes a single spiral-wave example, so this automated count range needs domain review rather than direct physiological interpretation.",
     "metric": "illuminated_arrhythmia.persistent_rotors",
     "status": "unstable_not_reportable"
    },
    {
     "note": "The maximum concurrent persistent-rotor count is unstable across filter and tracker settings, so it is not reportable as a single value; review only the sensitivity range 1.0\u20132.0.",
     "metric": "illuminated_arrhythmia.persistent_rotor_count_max",
     "status": "unstable_not_reportable"
    },
    {
     "note": "Dominant frequency is unstable across baseline windows, so it is not reportable as a single value; review only the sensitivity range 15.356\u201319.85 Hz. The relevant same-study mouse spiral-wave context cites approximately 20 Hz before illumination and approximately 18.75 Hz during illumination in DOI 10.1371/journal.pcbi.1011660.",
     "metric": "illuminated_arrhythmia.dominant_freq_hz",
     "status": "unstable_not_reportable"
    },
    {
     "note": "Unstable across the filter grid, so the post-termination illuminated singularity-frame fraction is not reportable as a single value; review only the sensitivity range 0.0005534034311012728\u20130.014941892639734366 fraction of frames.",
     "metric": "illuminated_after_termination.singularity_frames_frac",
     "status": "unstable_not_reportable"
    },
    {
     "note": "Stable at 0 persistent rotors, so this absence can be reported descriptively, but there is no cited physiology range for judging it.",
     "metric": "illuminated_after_termination.persistent_rotors",
     "status": "no_cited_range"
    },
    {
     "note": "Stable at a maximum concurrent persistent-rotor count of 0, so this absence can be reported descriptively, but there is no cited physiology range for judging it.",
     "metric": "illuminated_after_termination.persistent_rotor_count_max",
     "status": "no_cited_range"
    },
    {
     "note": "Stable at 2.214 Hz, but no cited range is available for this illuminated-after-termination segment; report only as a measured segment frequency, not as physiologically validated.",
     "metric": "illuminated_after_termination.dominant_freq_hz",
     "status": "no_cited_range"
    },
    {
     "note": "The total persistent-rotor track count is unstable across filter and tracker settings, so it is not reportable as a single value; review only the sensitivity range 4.0\u201315.0 tracks.",
     "metric": "persistent_rotor_tracks",
     "status": "unstable_not_reportable"
    }
   ],
   "send_back_reason": null,
   "persistence_threshold_note": "The persistent-rotor rule holds using both thresholds: the measured-cycle threshold is 52 frames and the cited paper-rotation threshold is 50 frames at 20.0 Hz; both variants hold across filters and trackers, and the verdicts agree."
  },
  "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": [
     0,
     0,
     0,
     0,
     0,
     0,
     0,
     0,
     0,
     0,
     0,
     0
    ],
    "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": [
     0.02928759894459103,
     0.02955145118733509,
     0.02691292875989446,
     0.008707124010554089,
     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": [
     0,
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     0,
     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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     13,
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    ],
    "varied_over": "filter grid + trackers",
    "values_trackers": [
     5,
     13,
     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,
     0.40299625468164796,
     0.3816479400749064,
     0.4797752808988764,
     0.4756554307116105,
     0.45767790262172287,
     0.48801498127340825,
     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": [
     0,
     0,
     0
    ]
   },
   "illuminated_arrhythmia.persistent_rotor_present": {
    "stable": true,
    "values_grid": [
     true,
     true,
     true,
     true,
     true,
     true,
     true,
     true,
     true,
     true,
     true,
     true
    ],
    "varied_over": "filter grid + trackers",
    "values_trackers": [
     true,
     true,
     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": [
     1,
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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": [
     false,
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     false,
     false,
     false,
     false,
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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,
    "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": [
     0,
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   }
  },
  "reviewed_at": "2026-10-27T23:12:22.113336+00:00",
  "recording_id": "55cb4aa3-6502-45a6-a14c-85cb676fe8c3",
  "signature_id": "cf0c8a27-002b-40af-809c-72bd47871da0",
  "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": [
      5,
      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": "Using provisional parameter set version 3 for protocol f65d786f-f194-4be2-88b8-10d3dd25d674, the fixed parameters were baseline_frames=901, spatial_sigma=1.0, spatial_truncate=4.0, pad_frames=500, rotor_threshold=0.9, rotor_erode_px=3, link_px=4.0, max_gap=5, min_cycles=1.0, pair_dist_px=3.0, paired_frac=0.5, and render_step=4. The recording has 9267 frames in npy format with image size 64 by 55, frame rate 1000 Hz from publication 10.1371/journal.pcbi.1011660 with DAQ consistency, and pixel size 133 \u00b5m from the same publication. The analysed window was frames 500 to 8767, with provisional segment definitions and criteria: 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": "baseline_window_rule",
    "description": "A run proceeds only if the protocol's baseline window is >= 2x the slowest segment's cycle, the cycle from the MAP channel when a DAQ log exists, else from per-pixel dominant frequency on linearly detrended pixels; otherwise the run is held by code",
    "expert": "optical mapping analyst",
    "status": "provisional",
    "location": "worker/voltage/baseline_rule.py (FACTOR, evaluate)",
    "values": {
     "ok": true,
     "factor": 2.0,
     "source": "MAP channel (DAQ log)",
     "required_min_frames": 830,
     "slowest_cycle_frames": 415
    }
   },
   {
    "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",
      "baseline-window rule"
     ],
     "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": "Filter sensitivity is high for the light-off singularity-frame fraction; do not report a single value, and review the range 0.0029023746701846965\u20130.02955145118733509 fraction of frames.",
    "severity": "warn",
    "reviewer": "domain scientist / analysis methods"
   },
   {
    "topic": "unstable:illuminated_arrhythmia.persistent_rotors",
    "detail": "Persistent-rotor counts during illuminated arrhythmia vary over 4.0\u201315.0 across filter and tracker settings; report presence/absence only under the provisional rule and review the count before use.",
    "severity": "warn",
    "reviewer": "domain scientist / analysis methods"
   },
   {
    "topic": "unstable:illuminated_arrhythmia.persistent_rotor_count_max",
    "detail": "Maximum concurrent persistent-rotor count during illuminated arrhythmia varies over 1.0\u20132.0; do not report a single maximum without review.",
    "severity": "warn",
    "reviewer": "domain scientist / analysis methods"
   },
   {
    "topic": "unstable:illuminated_arrhythmia.dominant_freq_hz",
    "detail": "Dominant frequency varies over 15.356\u201319.85 Hz across baseline windows; because this overlaps same-study context but is unstable, it should be reviewed before reporting.",
    "severity": "warn",
    "reviewer": "domain scientist / analysis methods"
   },
   {
    "topic": "unstable:illuminated_after_termination.singularity_frames_frac",
    "detail": "Post-termination illuminated singularity-frame fraction varies over 0.0005534034311012728\u20130.014941892639734366; do not report a single value without review.",
    "severity": "warn",
    "reviewer": "domain scientist / analysis methods"
   },
   {
    "topic": "unstable:persistent_rotor_tracks",
    "detail": "Total persistent-rotor tracks vary over 4.0\u201315.0 across filter and tracker settings; the track count is not reportable as a single value.",
    "severity": "warn",
    "reviewer": "domain scientist / analysis methods"
   },
   {
    "topic": "Pre-deposit processing / raw-data label",
    "detail": "The recording is labeled raw in the README, but documentation and prior-processing flags indicate masking, spatial smoothing, temporal smoothing, and normalization; analyses requiring raw photon counts or independent pixel noise should not treat it as raw camera data.",
    "severity": "warn",
    "reviewer": "data curator / methods reviewer"
   },
   {
    "topic": "Event interpretation at frame 3170",
    "detail": "Frame 3170 is a baseline_step image event, not light onset; illumination began before frame 0 and ended at frame 4977, so the stored spiral-termination interpretation is provisional.",
    "severity": "warn",
    "reviewer": "domain scientist"
   },
   {
    "topic": "Baseline and illumination artifact",
    "detail": "The publication reports blue-light crosstalk and re-normalization by recorded stimulation light signal, and this recording has a large slow baseline range and a baseline step; absolute baseline or amplitude analyses need artifact handling.",
    "severity": "warn",
    "reviewer": "methods reviewer"
   },
   {
    "topic": "Provisional tool thresholds",
    "detail": "Event detection, processing flags, SNR, rhythm, and reference-rate thresholds are provisional and not yet reviewed by a domain scientist.",
    "severity": "info",
    "reviewer": "domain scientist / methods 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 provisional presence/absence criteria, not unstable scalar values; physiology_ok is indeterminate because the only ranged check, illuminated-arrhythmia dominant frequency, is unstable over 15.356\u201319.85 Hz rather than reportable as a single value, although DOI 10.1371/journal.pcbi.1011660 provides same-study mouse context of approximately 20 Hz before illumination and approximately 18.75 Hz during illumination, with a 20.0 Hz rotation corresponding to 50 frames. Reportable items include stable absence of persistent rotors in light_off and illuminated_after_termination, stable persistent-rotor presence during illuminated_arrhythmia under the provisional rule, stable illuminated_arrhythmia singularity-frame fraction at 0.47902621722846445, stable light_off dominant frequency at 2.375 Hz, and stable illuminated_after_termination dominant frequency at 2.214 Hz, all with no cited physiology range except the unstable frequency context. Unstable and not reportable as single values are light_off.singularity_frames_frac over 0.0029023746701846965\u20130.02955145118733509, illuminated_arrhythmia.persistent_rotors over 4.0\u201315.0, illuminated_arrhythmia.persistent_rotor_count_max over 1.0\u20132.0, illuminated_arrhythmia.dominant_freq_hz over 15.356\u201319.85 Hz, illuminated_after_termination.singularity_frames_frac over 0.0005534034311012728\u20130.014941892639734366, and persistent_rotor_tracks over 4.0\u201315.0. Needs review: the deposited-data processing/raw label, frame-3170 event interpretation, baseline and illumination artifact, and all provisional tool thresholds; the ranges, the stability threshold, and the criteria are provisional."
  },
  "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": "faeb5ebc-ee96-4994-96b0-025811d9374b",
    "status": "done",
    "started_at": "2026-10-27T23:05:39.363118+00:00",
    "finished_at": "2026-10-27T23:11:17.349504+00:00",
    "code": {
     "dirty": true,
     "git_commit": "b1be82429ddde2ad90ee88afacaae98a173e4403"
    },
    "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": {
     "ok": true,
     "ratio": 2.171,
     "cycles": {
      "light_off": {
       "cycle_frames": 411,
       "n_activations": 10,
       "polarity_used": -1,
       "median_interval_ms": 410.9
      },
      "illuminated_arrhythmia": {
       "cycle_frames": 52,
       "n_activations": 53,
       "polarity_used": -1,
       "median_interval_ms": 52.25
      },
      "illuminated_after_termination": {
       "cycle_frames": 415,
       "n_activations": 4,
       "polarity_used": -1,
       "median_interval_ms": 415.0
      }
     },
     "factor": 2.0,
     "reason": null,
     "source": "MAP channel (DAQ log)",
     "status": "provisional",
     "daq_file": "0111210010.txt",
     "baseline_frames": 901,
     "slowest_segment": "illuminated_after_termination",
     "required_min_frames": 830,
     "slowest_cycle_frames": 415
    },
    "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 recording should not be treated as raw camera counts; masking, temporal smoothing, spatial smoothing, and normalization affect noise assumptions and add unknown filtering before the protocol's Gaussian phase smoothing."
      },
      {
       "topic": "Event interpretation at frame 3170",
       "severity": "warn",
       "effect_on_analysis": "The frame-3170 boundary is an interpreted fluorescence/rhythm event rather than measured light onset; segment interpretation is provisional."
      },
      {
       "topic": "Baseline and illumination artifact",
       "severity": "info",
       "effect_on_analysis": "Illumination crosstalk, normalization to stimulation-light signal, slow fluorescence change, and a fluorescence step affect absolute fluorescence and amplitude interpretation."
      },
      {
       "topic": "baseline-window rule",
       "severity": "info",
       "effect_on_analysis": "The coded rule passes with baseline_frames 901, slowest_cycle_frames 415, required_min_frames 830, and ratio 2.171."
      }
     ],
     "rationale": "The fixed protocol is appropriate to run as a provisional analysis because the recording matches the intended mouse whole-heart optical mapping reference data and no recording fact mismatch makes the frame-based parameters wrong. The frame rate is 1000 Hz from the publication with DAQ consistency, and the coded baseline rule passes for the version 3 baseline of 901 frames. Interpretation is qualified by prior processing, the provisional frame-3170 event boundary, and illumination/normalization effects on fluorescence amplitude.",
     "mismatches": [],
     "hold_reason": null,
     "protocol_id": "f65d786f-f194-4be2-88b8-10d3dd25d674",
     "methods_text": "Using provisional parameter set version 3 for protocol f65d786f-f194-4be2-88b8-10d3dd25d674, the fixed parameters were baseline_frames=901, spatial_sigma=1.0, spatial_truncate=4.0, pad_frames=500, rotor_threshold=0.9, rotor_erode_px=3, link_px=4.0, max_gap=5, min_cycles=1.0, pair_dist_px=3.0, paired_frac=0.5, and render_step=4. The recording has 9267 frames in npy format with image size 64 by 55, frame rate 1000 Hz from publication 10.1371/journal.pcbi.1011660 with DAQ consistency, and pixel size 133 \u00b5m from the same publication. The analysed window was frames 500 to 8767, with provisional segment definitions and criteria: 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": "cf0c8a27-002b-40af-809c-72bd47871da0",
    "created_at": "2026-10-27T23:11:17.346398+00:00",
    "movie_path": "runs/faeb5ebc-ee96-4994-96b0-025811d9374b/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": "baseline_window_rule",
       "expert": "optical mapping analyst",
       "status": "provisional",
       "values": {
        "ok": true,
        "factor": 2.0,
        "source": "MAP channel (DAQ log)",
        "required_min_frames": 830,
        "slowest_cycle_frames": 415
       },
       "decision": null,
       "location": "worker/voltage/baseline_rule.py (FACTOR, evaluate)",
       "reviewed": false,
       "reviewer": null,
       "description": "A run proceeds only if the protocol's baseline window is >= 2x the slowest segment's cycle, the cycle from the MAP channel when a DAQ log exists, else from per-pixel dominant frequency on linearly detrended pixels; otherwise the run is held by code",
       "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",
         "baseline-window rule"
        ],
        "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",
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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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      "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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      "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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   "label": "Mouse heart, spiral wave and optogenetic termination (M13Rec001)",
   "source": "public",
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   "license": "CC-BY-4.0",
   "attribution": "Hussaini, Sayedeh; Luther, Stefan; L\u00e4dke, Sarah L.",
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    "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"
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   "name": "Mouse whole heart optical mapping (Luther lab)",
   "species": "mouse",
   "tissue": "whole_heart",
   "params_version": 3,
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   "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)."
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    "anomalies": [
     {
      "topic": "Pre-deposit processing / raw-data label",
      "severity": "warn",
      "effect_on_analysis": "The recording should not be treated as raw camera counts; masking, temporal smoothing, spatial smoothing, and normalization affect noise assumptions and add unknown filtering before the protocol's Gaussian phase smoothing."
     },
     {
      "topic": "Event interpretation at frame 3170",
      "severity": "warn",
      "effect_on_analysis": "The frame-3170 boundary is an interpreted fluorescence/rhythm event rather than measured light onset; segment interpretation is provisional."
     },
     {
      "topic": "Baseline and illumination artifact",
      "severity": "info",
      "effect_on_analysis": "Illumination crosstalk, normalization to stimulation-light signal, slow fluorescence change, and a fluorescence step affect absolute fluorescence and amplitude interpretation."
     },
     {
      "topic": "baseline-window rule",
      "severity": "info",
      "effect_on_analysis": "The coded rule passes with baseline_frames 901, slowest_cycle_frames 415, required_min_frames 830, and ratio 2.171."
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    ],
    "rationale": "The fixed protocol is appropriate to run as a provisional analysis because the recording matches the intended mouse whole-heart optical mapping reference data and no recording fact mismatch makes the frame-based parameters wrong. The frame rate is 1000 Hz from the publication with DAQ consistency, and the coded baseline rule passes for the version 3 baseline of 901 frames. Interpretation is qualified by prior processing, the provisional frame-3170 event boundary, and illumination/normalization effects on fluorescence amplitude.",
    "mismatches": [],
    "hold_reason": null,
    "protocol_id": "f65d786f-f194-4be2-88b8-10d3dd25d674",
    "methods_text": "Using provisional parameter set version 3 for protocol f65d786f-f194-4be2-88b8-10d3dd25d674, the fixed parameters were baseline_frames=901, spatial_sigma=1.0, spatial_truncate=4.0, pad_frames=500, rotor_threshold=0.9, rotor_erode_px=3, link_px=4.0, max_gap=5, min_cycles=1.0, pair_dist_px=3.0, paired_frac=0.5, and render_step=4. The recording has 9267 frames in npy format with image size 64 by 55, frame rate 1000 Hz from publication 10.1371/journal.pcbi.1011660 with DAQ consistency, and pixel size 133 \u00b5m from the same publication. The analysed window was frames 500 to 8767, with provisional segment definitions and criteria: 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",
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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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    "method": "last activation on DAQ channel 'ecg' (MAP) followed by an interval > 2x the arrhythmic interval; mapped to frames via camera triggers"
   },
   {
    "id": "46c59a51-1a01-4aed-8021-db9a63720a1d",
    "kind": "baseline_step",
    "frame": 3170,
    "label": "spiral termination (interpreted; under illumination)",
    "source": "image",
    "status": "detected",
    "uncertainty_frames": 17,
    "method": "consensus upward step in running-median baseline of tissue-mean raw signal"
   },
   {
    "id": "42ba71e2-c2c4-4833-abc2-467506ec90a1",
    "kind": "illumination_on",
    "frame": 3170,
    "label": null,
    "source": "image",
    "status": "contradicted",
    "uncertainty_frames": 17,
    "method": "consensus upward step in running-median baseline of tissue-mean raw signal"
   },
   {
    "id": "db2ad5f3-9b96-4ec1-9ccd-9c82c3425609",
    "kind": "illumination_off",
    "frame": 4977,
    "label": null,
    "source": "acquisition_log",
    "status": "detected",
    "uncertainty_frames": 11,
    "method": "midpoint threshold on DAQ channel 'led_trigger', mapped to frames via camera triggers"
   }
  ]
 }
}