{
 "exported_at": "2026-10-30T03:11:22.625483+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": "0b805159",
  "run_when": "2026-10-27 22:13 UTC",
  "params_version": 2,
  "commit": "752b95b",
  "dirty": true,
  "workers": null,
  "sig_short": "080dd569",
  "run_status": "done",
  "protocol_name": "Mouse whole heart optical mapping (Luther lab)"
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 "parameters": "% Mouse whole heart optical mapping (Luther lab), v2, read-only\n% set by developer (not a domain scientist); provisional, REVIEW_NEEDED 16\nbaseline_frames  = 641;     % no baseline rule recorded for this run\npad_frames       = 400;     % 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 = 64\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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   "end": 3170,
   "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"
   },
   "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": {
    "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"
   },
   "provisional": true
  },
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   "short": "light off",
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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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       {
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       {
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       {
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        "start": 2206,
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        "rotation_period_frames": 22.91
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       {
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       {
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        "rotation_period_frames": 26.07
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       {
        "end": 2510,
        "core": [
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        "start": 2489,
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        "rotation_period_frames": 20.56
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      ],
      "persistent_rotor_frames_frac": 0.25415162454873647
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     "illuminated_after_termination": {
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      "singularity_count_max": 1,
      "singularity_count_mean": 0.0016602102933038186,
      "singularity_frames_frac": 0.0016602102933038186,
      "persistent_rotor_count_max": 0,
      "persistent_rotor_durations": [],
      "persistent_rotor_frames_frac": 0.0
     }
    },
    "is_run_setting": false,
    "persistent_rotor_tracks": 17
   }
  ]
 },
 "critic": {
  "code": {
   "dirty": false,
   "git_commit": "13d8ceb123e64ab2c7eaba9fbf51605361856f11"
  },
  "agent": "critic",
  "model": "openai:gpt-5.5",
  "checks": {
   "checks": {
    "persistent_rotor_tracks": {
     "unit": "count",
     "range": null,
     "metric": "persistent_rotor_tracks",
     "stable": false,
     "status": "unstable_not_reportable",
     "segment": null,
     "spread_frac": 1.083,
     "value_at_run_setting": 13,
     "range_across_settings": [
      4.0,
      17.0
     ]
    },
    "light_off.dominant_freq_hz": {
     "unit": "Hz",
     "range": null,
     "metric": "dominant_freq_hz",
     "stable": false,
     "status": "unstable_not_reportable",
     "segment": "light_off",
     "spread_frac": 1.111,
     "value_at_run_setting": 2.314,
     "range_across_settings": [
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      4.884
     ]
    },
    "light_off.persistent_rotors": {
     "unit": "count",
     "range": null,
     "metric": "persistent_rotors",
     "stable": true,
     "status": "no_cited_range",
     "segment": "light_off",
     "spread_frac": 0.0,
     "value_at_run_setting": 0,
     "range_across_settings": [
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     ]
    },
    "light_off.singularity_frames_frac": {
     "unit": "fraction of frames",
     "range": null,
     "metric": "singularity_frames_frac",
     "stable": false,
     "status": "unstable_not_reportable",
     "segment": "light_off",
     "spread_frac": 5.116,
     "value_at_run_setting": 0.003084832904884319,
     "range_across_settings": [
      0.002827763496143959,
      0.031105398457583547
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    },
    "light_off.persistent_rotor_count_max": {
     "unit": "count",
     "range": null,
     "metric": "persistent_rotor_count_max",
     "stable": true,
     "status": "no_cited_range",
     "segment": "light_off",
     "spread_frac": 0.0,
     "value_at_run_setting": 0,
     "range_across_settings": [
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      0.0
     ]
    },
    "illuminated_arrhythmia.dominant_freq_hz": {
     "unit": "Hz",
     "range": {
      "id": "mouse_spiral_rotation_hz",
      "ref": "10.1371/journal.pcbi.1011660",
      "cited_low": 18.75,
      "cited_high": 20.0,
      "checked_low": 14.0625,
      "checked_high": 25.0
     },
     "metric": "dominant_freq_hz",
     "stable": true,
     "status": "within_range",
     "segment": "illuminated_arrhythmia",
     "spread_frac": 0.0,
     "value_at_run_setting": 15.523,
     "range_across_settings": [
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      15.523
     ]
    },
    "illuminated_arrhythmia.persistent_rotors": {
     "unit": "count",
     "range": null,
     "metric": "persistent_rotors",
     "stable": false,
     "status": "unstable_not_reportable",
     "segment": "illuminated_arrhythmia",
     "spread_frac": 1.083,
     "value_at_run_setting": 13,
     "range_across_settings": [
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      17.0
     ]
    },
    "illuminated_after_termination.dominant_freq_hz": {
     "unit": "Hz",
     "range": null,
     "metric": "dominant_freq_hz",
     "stable": true,
     "status": "no_cited_range",
     "segment": "illuminated_after_termination",
     "spread_frac": 0.0,
     "value_at_run_setting": 2.214,
     "range_across_settings": [
      2.214,
      2.214
     ]
    },
    "illuminated_arrhythmia.singularity_frames_frac": {
     "unit": "fraction of frames",
     "range": null,
     "metric": "singularity_frames_frac",
     "stable": true,
     "status": "no_cited_range",
     "segment": "illuminated_arrhythmia",
     "spread_frac": 0.232,
     "value_at_run_setting": 0.4888086642599278,
     "range_across_settings": [
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      0.4942238267148014
     ]
    },
    "illuminated_after_termination.persistent_rotors": {
     "unit": "count",
     "range": null,
     "metric": "persistent_rotors",
     "stable": true,
     "status": "no_cited_range",
     "segment": "illuminated_after_termination",
     "spread_frac": 0.0,
     "value_at_run_setting": 0,
     "range_across_settings": [
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      0.0
     ]
    },
    "illuminated_arrhythmia.persistent_rotor_count_max": {
     "unit": "count",
     "range": null,
     "metric": "persistent_rotor_count_max",
     "stable": false,
     "status": "unstable_not_reportable",
     "segment": "illuminated_arrhythmia",
     "spread_frac": 0.5,
     "value_at_run_setting": 2,
     "range_across_settings": [
      1.0,
      2.0
     ]
    },
    "illuminated_after_termination.singularity_frames_frac": {
     "unit": "fraction of frames",
     "range": null,
     "metric": "singularity_frames_frac",
     "stable": false,
     "status": "unstable_not_reportable",
     "segment": "illuminated_after_termination",
     "spread_frac": 2.182,
     "value_at_run_setting": 0.0016602102933038186,
     "range_across_settings": [
      0.0005534034311012728,
      0.007194244604316547
     ]
    },
    "illuminated_after_termination.persistent_rotor_count_max": {
     "unit": "count",
     "range": null,
     "metric": "persistent_rotor_count_max",
     "stable": true,
     "status": "no_cited_range",
     "segment": "illuminated_after_termination",
     "spread_frac": 0.0,
     "value_at_run_setting": 0,
     "range_across_settings": [
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      0.0
     ]
    }
   },
   "unstable": [
    "light_off.singularity_frames_frac",
    "light_off.dominant_freq_hz",
    "illuminated_arrhythmia.persistent_rotors",
    "illuminated_arrhythmia.persistent_rotor_count_max",
    "illuminated_after_termination.singularity_frames_frac",
    "persistent_rotor_tracks"
   ],
   "physiology_ok": true,
   "ranged_checks": [
    "illuminated_arrhythmia.dominant_freq_hz"
   ]
  },
  "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"
    },
    "checked_low": 14.0625,
    "checked_high": 25.0,
    "tolerance_frac": 0.25
   }
  ],
  "run_id": "0b805159-6ca0-4616-995e-14b1e224b0be",
  "status": "provisional",
  "verdict": {
   "send_back": false,
   "critic_notes": "Verdict: report only stable/descriptive findings and the stable in-range illuminated-arrhythmia dominant frequency; physiology_ok is true because the only ranged check, illuminated_arrhythmia.dominant_freq_hz, is stable at 15.523 Hz and within the checked 14.0625\u201325.0 Hz contextual range derived from the cited mouse spiral-wave passages reporting approximately 20.0 Hz and 18.75 Hz (DOI 10.1371/journal.pcbi.1011660). Do not report single values for unstable metrics: light_off.singularity_frames_frac 0.002827763496143959\u20130.031105398457583547, light_off.dominant_freq_hz 2.314\u20134.884 Hz, illuminated_arrhythmia.persistent_rotors 4.0\u201317.0, illuminated_arrhythmia.persistent_rotor_count_max 1.0\u20132.0, illuminated_after_termination.singularity_frames_frac 0.0005534034311012728\u20130.007194244604316547, and persistent_rotor_tracks 4.0\u201317.0. Persistent-rotor presence holds provisionally with the 64-frame measured-cycle criterion and the 50-frame paper-rotation criterion, and strict/default/loose trackers agree on the rule verdict despite varying counts. Review the pre-deposit processing/raw-data label, the frame-3170 event interpretation, and baseline/illumination artifact before using this for critical analysis; the ranges, the stability threshold, and the criteria are provisional.",
   "review_items": [
    {
     "topic": "unstable:light_off.singularity_frames_frac",
     "detail": "Filter-grid sensitivity gives 0.002827763496143959\u20130.031105398457583547; do not report a single light-off singularity-frames fraction.",
     "severity": "warn",
     "reviewer_type": "analysis"
    },
    {
     "topic": "unstable:light_off.dominant_freq_hz",
     "detail": "Baseline-window sensitivity gives 2.314\u20134.884 Hz; do not report a single light-off dominant frequency.",
     "severity": "warn",
     "reviewer_type": "analysis"
    },
    {
     "topic": "unstable:illuminated_arrhythmia.persistent_rotors",
     "detail": "Filter and tracker sensitivity gives 4.0\u201317.0 persistent rotors; report presence only, not a single count.",
     "severity": "warn",
     "reviewer_type": "analysis"
    },
    {
     "topic": "unstable:illuminated_arrhythmia.persistent_rotor_count_max",
     "detail": "Filter and tracker sensitivity gives 1.0\u20132.0 maximum simultaneous persistent rotors; do not report a single maximum count.",
     "severity": "warn",
     "reviewer_type": "analysis"
    },
    {
     "topic": "unstable:illuminated_after_termination.singularity_frames_frac",
     "detail": "Filter-grid sensitivity gives 0.0005534034311012728\u20130.007194244604316547; do not report a single post-termination singularity-frames fraction.",
     "severity": "warn",
     "reviewer_type": "analysis"
    },
    {
     "topic": "unstable:persistent_rotor_tracks",
     "detail": "Aggregate persistent-rotor tracks vary from 4.0 to 17.0 across filters and trackers; do not report a single track count.",
     "severity": "warn",
     "reviewer_type": "analysis"
    },
    {
     "topic": "Pre-deposit processing / raw-data label",
     "detail": "The recording is labeled as raw experimental data in the README, but documentation and measurements indicate masking, spatial smoothing, temporal smoothing, and normalization; analyses that require raw photon counts or independent pixel noise should not treat this as raw camera data.",
     "severity": "warn",
     "reviewer_type": "data_inspector"
    },
    {
     "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 frame 3170 should not be treated as light onset. The termination label is provisional.",
     "severity": "warn",
     "reviewer_type": "data_inspector"
    },
    {
     "topic": "Baseline and illumination artifact",
     "detail": "The paper reports stimulation-light crosstalk and re-normalization; this recording also has a large slow baseline range and a baseline step, so absolute baseline or amplitude analyses require artifact review.",
     "severity": "warn",
     "reviewer_type": "data_inspector"
    },
    {
     "topic": "Provisional tool thresholds",
     "detail": "Event detection, processing flags, SNR, rhythm, and reference-rate thresholds have not yet been reviewed by a domain scientist.",
     "severity": "info",
     "reviewer_type": "data_inspector"
    }
   ],
   "tracker_note": "Strict, default, and loose trackers all support the provisional persistent-rotor rule: light_off 0, illuminated_arrhythmia 4/13/17, illuminated_after_termination 0. The trackers agree on the rule verdict even though the illuminated_arrhythmia count varies, so the presence pattern is reportable but the count is unstable.",
   "physiology_ok": true,
   "metric_judgments": [
    {
     "note": "Unstable across the filter grid, so this fraction is not reportable as a single value; only the sensitivity range 0.002827763496143959\u20130.031105398457583547 should be used for review.",
     "metric": "light_off.singularity_frames_frac",
     "status": "unstable_not_reportable"
    },
    {
     "note": "Stable at 0 persistent rotors, but there is no cited physiological range for this count, so it can be reported only descriptively, not as physiology range-validated.",
     "metric": "light_off.persistent_rotors",
     "status": "no_cited_range"
    },
    {
     "note": "Stable at 0 maximum simultaneous persistent rotors, but no cited range is available, so this is descriptive only.",
     "metric": "light_off.persistent_rotor_count_max",
     "status": "no_cited_range"
    },
    {
     "note": "Unstable across baseline windows, so the light-off dominant frequency is not reportable as a single value; review only the range 2.314\u20134.884 Hz.",
     "metric": "light_off.dominant_freq_hz",
     "status": "unstable_not_reportable"
    },
    {
     "note": "Stable across the filter grid, but no cited physiological range is available for this fraction, so it may be reported descriptively with the range 0.38339350180505416\u20130.4942238267148014 rather than as range-validated physiology.",
     "metric": "illuminated_arrhythmia.singularity_frames_frac",
     "status": "no_cited_range"
    },
    {
     "note": "Unstable across filters and trackers, so the count is not reportable as a single value; use only the range 4.0\u201317.0 for review.",
     "metric": "illuminated_arrhythmia.persistent_rotors",
     "status": "unstable_not_reportable"
    },
    {
     "note": "Unstable across filters and trackers, so maximum simultaneous persistent-rotor count is not reportable as a single value; use only the range 1.0\u20132.0 for review.",
     "metric": "illuminated_arrhythmia.persistent_rotor_count_max",
     "status": "unstable_not_reportable"
    },
    {
     "note": "Stable at 15.523 Hz and within the checked 14.0625\u201325.0 Hz range derived from the cited mouse spiral-wave context; the underlying paper reports approximately 20.0 Hz before illumination and 18.75 Hz during illumination (DOI 10.1371/journal.pcbi.1011660), so this is reportable with the caveat that the range is contextual, not a population range.",
     "metric": "illuminated_arrhythmia.dominant_freq_hz",
     "status": "within_range"
    },
    {
     "note": "Unstable across the filter grid, so this fraction is not reportable as a single value; review only the range 0.0005534034311012728\u20130.007194244604316547.",
     "metric": "illuminated_after_termination.singularity_frames_frac",
     "status": "unstable_not_reportable"
    },
    {
     "note": "Stable at 0 persistent rotors, but no cited physiological range is available, so it can be reported only descriptively.",
     "metric": "illuminated_after_termination.persistent_rotors",
     "status": "no_cited_range"
    },
    {
     "note": "Stable at 0 maximum simultaneous persistent rotors, but no cited range is available, so it can be reported only descriptively.",
     "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 post-termination segment, so it can be reported descriptively only.",
     "metric": "illuminated_after_termination.dominant_freq_hz",
     "status": "no_cited_range"
    },
    {
     "note": "Unstable across filters and trackers, so the aggregate track count is not reportable as a single value; use only the range 4.0\u201317.0 for review.",
     "metric": "persistent_rotor_tracks",
     "status": "unstable_not_reportable"
    }
   ],
   "send_back_reason": null,
   "persistence_threshold_note": "Persistent-rotor presence holds provisionally using both thresholds: the measured-cycle rule uses min_frames 64, and the paper-rotation rule uses min_frames 50 from 1000 frames/s and 20.0 Hz. The two persistence variants 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": 4,
      "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": 17,
      "illuminated_after_termination": 0
     }
    }
   ]
  },
  "stability": {
   "persistent_rotor_tracks": {
    "max": 17.0,
    "min": 4.0,
    "median": 12.0,
    "stable": false,
    "settings": 15,
    "spread_frac": 1.083,
    "values_grid": [
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     13,
     13,
     15,
     12,
     13,
     14
    ],
    "varied_over": "filter grid + trackers",
    "values_trackers": [
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     13,
     17
    ]
   },
   "light_off.dominant_freq_hz": {
    "max": 4.884,
    "min": 2.314,
    "median": 2.314,
    "stable": false,
    "settings": 4,
    "spread_frac": 1.111,
    "varied_over": "baseline windows",
    "values_by_baseline": {
     "641": 2.314,
     "678": 2.314,
     "1356": 2.314,
     "2712": 4.884
    }
   },
   "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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     0,
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    ],
    "varied_over": "filter grid + trackers",
    "values_trackers": [
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     0,
     0
    ]
   },
   "light_off.singularity_frames_frac": {
    "max": 0.031105398457583547,
    "min": 0.002827763496143959,
    "median": 0.005526992287917738,
    "stable": false,
    "settings": 12,
    "spread_frac": 5.116,
    "values_grid": [
     0.030848329048843187,
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     0.02853470437017995,
     0.008997429305912597,
     0.008483290488431876,
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     0.0035989717223650387,
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     0.003084832904884319,
     0.003084832904884319
    ],
    "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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    ],
    "varied_over": "filter grid + trackers",
    "values_trackers": [
     0,
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   },
   "illuminated_arrhythmia.dominant_freq_hz": {
    "max": 15.523,
    "min": 15.523,
    "median": 15.523,
    "stable": true,
    "settings": 4,
    "spread_frac": 0.0,
    "varied_over": "baseline windows",
    "values_by_baseline": {
     "641": 15.523,
     "678": 15.523,
     "1356": 15.523,
     "2712": 15.523
    }
   },
   "illuminated_arrhythmia.persistent_rotors": {
    "max": 17.0,
    "min": 4.0,
    "median": 12.0,
    "stable": false,
    "settings": 15,
    "spread_frac": 1.083,
    "values_grid": [
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     11,
     12,
     13,
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     13,
     14
    ],
    "varied_over": "filter grid + trackers",
    "values_trackers": [
     4,
     13,
     17
    ]
   },
   "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": {
     "641": 2.214,
     "678": 2.214,
     "1356": 2.214,
     "2712": 2.214
    }
   },
   "illuminated_arrhythmia.singularity_frames_frac": {
    "max": 0.4942238267148014,
    "min": 0.38339350180505416,
    "median": 0.478158844765343,
    "stable": true,
    "settings": 12,
    "spread_frac": 0.232,
    "values_grid": [
     0.4108303249097473,
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     0.4888086642599278,
     0.4707581227436823
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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": [
     1,
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     2,
     2,
     2,
     2,
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     2,
     2,
     2
    ],
    "varied_over": "filter grid + trackers",
    "values_trackers": [
     1,
     2,
     2
    ]
   },
   "illuminated_after_termination.singularity_frames_frac": {
    "max": 0.007194244604316547,
    "min": 0.0005534034311012728,
    "median": 0.0030437188710570008,
    "stable": false,
    "settings": 12,
    "spread_frac": 2.182,
    "values_grid": [
     0.007194244604316547,
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    ],
    "varied_over": "filter grid"
   },
   "illuminated_after_termination.persistent_rotor_present": {
    "stable": true,
    "values_grid": [
     false,
     false,
     false,
     false,
     false,
     false,
     false,
     false,
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    "varied_over": "filter grid + trackers",
    "values_trackers": [
     false,
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     false
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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": "2026-10-27T22:20:49.082511+00:00",
  "recording_id": "55cb4aa3-6502-45a6-a14c-85cb676fe8c3",
  "signature_id": "080dd569-7f7f-42c9-9083-593437cf3245",
  "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",
       "light_off.dominant_freq_hz",
       "illuminated_arrhythmia.persistent_rotors",
       "illuminated_arrhythmia.persistent_rotor_count_max",
       "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": 64,
      "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": 641,
       "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": 432,
        "illuminated_arrhythmia": 64,
        "illuminated_after_termination": 452
       },
       "reference_cycle_frames": 452,
       "window_over_cycle_per_segment": {
        "run": {
         "light_off": 1.48,
         "illuminated_arrhythmia": 10.02,
         "illuminated_after_termination": 1.42
        },
        "3x_cycle": {
         "light_off": 3.14,
         "illuminated_arrhythmia": 21.19,
         "illuminated_after_termination": 3.0
        },
        "6x_cycle": {
         "light_off": 6.28,
         "illuminated_arrhythmia": 42.38,
         "illuminated_after_termination": 6.0
        },
        "1.5x_cycle": {
         "light_off": 1.57,
         "illuminated_arrhythmia": 10.59,
         "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": 64,
    "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,
      14
     ],
     "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": [
      39,
      34,
      57,
      36,
      103,
      37,
      57,
      41,
      34,
      62,
      37,
      57,
      30
     ],
     "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,
      14
     ],
     "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": [
      39,
      34,
      57,
      36,
      103,
      37,
      57,
      41,
      34,
      62,
      37,
      57,
      30
     ],
     "illuminated_after_termination": []
    }
   }
  },
  "required_review_topics": [
   "unstable:light_off.singularity_frames_frac",
   "unstable:light_off.dominant_freq_hz",
   "unstable:illuminated_arrhythmia.persistent_rotors",
   "unstable:illuminated_arrhythmia.persistent_rotor_count_max",
   "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 64 frames (measured cycle) and \u2265 50 frames (cited 20 Hz)",
   "result": "agree",
   "provisional": true
  }
 ],
 "report": {
  "methods": "Using the provisional parameter set version 2 for protocol f65d786f-f194-4be2-88b8-10d3dd25d674, the fixed parameters were baseline_frames=641, spatial_sigma=1.0, spatial_truncate=4.0, pad_frames=400, 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 was 1000 Hz from the publication source recorded for this movie, and the pixel size was 133 um from the publication source. The analysed window was frames 400 to 8867, with provisional segment definitions and provisional criteria: illuminated_arrhythmia from frames 0 to 3170, illuminated_after_termination from frames 3170 to 4977, and light_off from frames 4977 to 9267; within the analysed window these correspond to analysed frames 400 to 3170, 3170 to 4977, and 4977 to 8867.",
  "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": 2
    }
   },
   {
    "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": 641,
     "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": 64
    }
   },
   {
    "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": 641,
      "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": 400,
     "f1": 8867
    }
   },
   {
    "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": 64
    }
   },
   {
    "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 versus post-termination rhythm"
     ],
     "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",
      "light_off.dominant_freq_hz",
      "illuminated_arrhythmia.persistent_rotors",
      "illuminated_arrhythmia.persistent_rotor_count_max",
      "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": 64,
     "paper_rotation": 50
    }
   }
  ],
  "review_items": [
   {
    "topic": "unstable:light_off.singularity_frames_frac",
    "detail": "Filter-grid sensitivity gives 0.002827763496143959\u20130.031105398457583547; do not report a single light-off singularity-frames fraction.",
    "severity": "warn",
    "reviewer": "analysis"
   },
   {
    "topic": "unstable:light_off.dominant_freq_hz",
    "detail": "Baseline-window sensitivity gives 2.314\u20134.884 Hz; do not report a single light-off dominant frequency.",
    "severity": "warn",
    "reviewer": "analysis"
   },
   {
    "topic": "unstable:illuminated_arrhythmia.persistent_rotors",
    "detail": "Filter and tracker sensitivity gives 4.0\u201317.0 persistent rotors; report presence only, not a single count.",
    "severity": "warn",
    "reviewer": "analysis"
   },
   {
    "topic": "unstable:illuminated_arrhythmia.persistent_rotor_count_max",
    "detail": "Filter and tracker sensitivity gives 1.0\u20132.0 maximum simultaneous persistent rotors; do not report a single maximum count.",
    "severity": "warn",
    "reviewer": "analysis"
   },
   {
    "topic": "unstable:illuminated_after_termination.singularity_frames_frac",
    "detail": "Filter-grid sensitivity gives 0.0005534034311012728\u20130.007194244604316547; do not report a single post-termination singularity-frames fraction.",
    "severity": "warn",
    "reviewer": "analysis"
   },
   {
    "topic": "unstable:persistent_rotor_tracks",
    "detail": "Aggregate persistent-rotor tracks vary from 4.0 to 17.0 across filters and trackers; do not report a single track count.",
    "severity": "warn",
    "reviewer": "analysis"
   },
   {
    "topic": "Pre-deposit processing / raw-data label",
    "detail": "The recording is labeled as raw experimental data in the README, but documentation and measurements indicate masking, spatial smoothing, temporal smoothing, and normalization; analyses that require raw photon counts or independent pixel noise should not treat this as raw camera data.",
    "severity": "warn",
    "reviewer": "data_inspector"
   },
   {
    "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 frame 3170 should not be treated as light onset. The termination label is provisional.",
    "severity": "warn",
    "reviewer": "data_inspector"
   },
   {
    "topic": "Baseline and illumination artifact",
    "detail": "The paper reports stimulation-light crosstalk and re-normalization; this recording also has a large slow baseline range and a baseline step, so absolute baseline or amplitude analyses require artifact review.",
    "severity": "warn",
    "reviewer": "data_inspector"
   },
   {
    "topic": "Provisional tool thresholds",
    "detail": "Event detection, processing flags, SNR, rhythm, and reference-rate thresholds have not yet been reviewed by a domain scientist.",
    "severity": "info",
    "reviewer": "data_inspector"
   }
  ],
  "reportable": [
   {
    "metric": "persistent rotor tracks",
    "segment": "all",
    "value": "4\u201317",
    "unit": "count",
    "status": "unstable, not reportable"
   },
   {
    "metric": "dominant freq (Hz)",
    "segment": "light off",
    "value": "2.31\u20134.88",
    "unit": "Hz",
    "status": "unstable, not reportable"
   },
   {
    "metric": "persistent rotors",
    "segment": "light off",
    "value": "0",
    "unit": "count",
    "status": "no cited range"
   },
   {
    "metric": "singularity frames fraction",
    "segment": "light off",
    "value": "0.00283\u20130.0311",
    "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": "15.52",
    "unit": "Hz",
    "status": "within range"
   },
   {
    "metric": "persistent rotors",
    "segment": "illuminated arrhythmia",
    "value": "4\u201317",
    "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": "0.4888",
    "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\u20130.00719",
    "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": true,
   "send_back": false,
   "notes": "Verdict: report only stable/descriptive findings and the stable in-range illuminated-arrhythmia dominant frequency; physiology_ok is true because the only ranged check, illuminated_arrhythmia.dominant_freq_hz, is stable at 15.523 Hz and within the checked 14.0625\u201325.0 Hz contextual range derived from the cited mouse spiral-wave passages reporting approximately 20.0 Hz and 18.75 Hz (DOI 10.1371/journal.pcbi.1011660). Do not report single values for unstable metrics: light_off.singularity_frames_frac 0.002827763496143959\u20130.031105398457583547, light_off.dominant_freq_hz 2.314\u20134.884 Hz, illuminated_arrhythmia.persistent_rotors 4.0\u201317.0, illuminated_arrhythmia.persistent_rotor_count_max 1.0\u20132.0, illuminated_after_termination.singularity_frames_frac 0.0005534034311012728\u20130.007194244604316547, and persistent_rotor_tracks 4.0\u201317.0. Persistent-rotor presence holds provisionally with the 64-frame measured-cycle criterion and the 50-frame paper-rotation criterion, and strict/default/loose trackers agree on the rule verdict despite varying counts. Review the pre-deposit processing/raw-data label, the frame-3170 event interpretation, and baseline/illumination artifact before using this for critical analysis; 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": "0b805159-6ca0-4616-995e-14b1e224b0be",
    "status": "done",
    "started_at": "2026-10-27T22:13:23.355061+00:00",
    "finished_at": "2026-10-27T22:19:36.177173+00:00",
    "code": {
     "dirty": true,
     "git_commit": "752b95b01dde60f86eb71b47343448c7af4551c1"
    },
    "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": 400,
      "paired_frac": 0.5,
      "render_step": 4,
      "pair_dist_px": 3.0,
      "spatial_sigma": 1.0,
      "rotor_erode_px": 3,
      "baseline_frames": 641,
      "rotor_threshold": 0.9,
      "spatial_truncate": 4.0
     },
     "version": 2,
     "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: masking, temporal smoothing, spatial smoothing, and normalization were documented and measured. The protocol's Gaussian phase smoothing is therefore added on top of prior spatial filtering of unknown total, noise/SNR assumptions are not independent raw-pixel noise, and amplitude or photon-count interpretations would be misleading; phase/rotor analysis may proceed with this caveat."
      },
      {
       "topic": "Event interpretation at frame 3170",
       "severity": "warn",
       "effect_on_analysis": "Frame 3170 should be used only as the provisional segment boundary supplied to the run, not as measured light onset. DAQ and photodiode evidence indicate illumination was already present before frame 0 and ended at frame 4977, so any segment-level interpretation depending on frame 3170 as light onset would be wrong; the numerical pipeline itself can use the boundary as a provisional event boundary."
      },
      {
       "topic": "Baseline and illumination artifact",
       "severity": "warn",
       "effect_on_analysis": "Blue-light crosstalk, normalization by the stimulation-light signal, a large slow baseline range, and a baseline step mean absolute baseline and amplitude measurements are not reliable as raw fluorescence physiology. The fixed high-pass/baseline procedure and rotor criteria may still be applied, but baseline-dependent interpretation should be cautious."
      },
      {
       "topic": "Baseline window versus post-termination rhythm",
       "severity": "warn",
       "effect_on_analysis": "With the fixed baseline_frames value, the measured post-termination segment rhythms put the baseline window at about the provisional lower limit stated by the rhythm tool. This may modestly attenuate slow post-termination rhythm components, but it is not a block because the frame rate is the intended 1000 Hz and this version of the protocol was set for this recording."
      }
     ],
     "rationale": "The recording may be analysed under protocol version 2 as it stands. The recording is the intended mouse whole-heart public reference recording, and the 1000 Hz frame rate from the publication agrees with the protocol note underlying the fixed 641-frame baseline window; no species, tissue, frame-rate, pixel-size, or image-size mismatch requires a hold. The important limitations are interpretive rather than eligibility-blocking: the deposit is processed rather than raw, the frame-3170 event is a provisional termination/baseline-change boundary rather than light onset, illumination/crosstalk/normalization affect baseline and amplitude, and the post-termination rhythm is close to the baseline-window caveat threshold. These warnings should accompany any results, but they do not make the fixed parameters inapplicable.",
     "mismatches": [],
     "hold_reason": null,
     "protocol_id": "f65d786f-f194-4be2-88b8-10d3dd25d674",
     "methods_text": "Using the provisional parameter set version 2 for protocol f65d786f-f194-4be2-88b8-10d3dd25d674, the fixed parameters were baseline_frames=641, spatial_sigma=1.0, spatial_truncate=4.0, pad_frames=400, 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 was 1000 Hz from the publication source recorded for this movie, and the pixel size was 133 um from the publication source. The analysed window was frames 400 to 8867, with provisional segment definitions and provisional criteria: illuminated_arrhythmia from frames 0 to 3170, illuminated_after_termination from frames 3170 to 4977, and light_off from frames 4977 to 9267; within the analysed window these correspond to analysed frames 400 to 3170, 3170 to 4977, and 4977 to 8867.",
     "recording_id": "55cb4aa3-6502-45a6-a14c-85cb676fe8c3",
     "params_version": 2,
     "prompt_version": "pipeline-v2"
    }
   },
   "signature": {
    "id": "080dd569-7f7f-42c9-9083-593437cf3245",
    "created_at": "2026-10-27T22:19:36.139923+00:00",
    "movie_path": "runs/0b805159-6ca0-4616-995e-14b1e224b0be/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": 400,
      "f1": 8867,
      "segments": [
       {
        "name": "illuminated_arrhythmia",
        "label": "illumination with arrhythmia",
        "defined": [
         0,
         3170
        ],
        "analysed": [
         400,
         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": [
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        ],
        "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"
       },
       {
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        "defined": [
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         9267
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         4977,
         8867
        ],
        "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 400-4977 of the analysed frames 400-8867.",
      "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": 432,
       "illuminated_arrhythmia": 64,
       "illuminated_after_termination": 452
      }
     },
     "lowpass": null,
     "polarity": -1,
     "tracking": {
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      "max_gap": 5,
      "min_cycles": 1.0,
      "min_frames": 64,
      "paired_frac": 0.5,
      "pair_dist_px": 3.0
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     "pad_frames": 400,
     "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": 641,
     "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"
    },
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     "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",
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       "location": "worker/voltage/protocol_params.py (developer_defaults, set_params)",
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       "reviewer": null,
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       "reviewed_at": null
      },
      {
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       "expert": "optical mapping analyst (cardiac electrophysiology)",
       "status": "provisional",
       "values": {
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       },
       "decision": null,
       "location": "worker/voltage/preprocess.py (Params)",
       "reviewed": false,
       "reviewer": null,
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       "reviewed_at": null
      },
      {
       "id": "tissue_mask",
       "expert": "optical mapping analyst",
       "status": "provisional",
       "values": {
        "rule": "not NaN in frame 0 and nonzero std",
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       "location": "worker/voltage/io.py (tissue_mask)",
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       "reviewer": null,
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       "values": {
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       "location": "worker/voltage/preprocess.py (polarity)",
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       "reviewer": null,
       "description": "Dye polarity from sign of median per-pixel skew of dV/dt",
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      },
      {
       "id": "singularity_detection",
       "expert": "computational cardiac electrophysiologist (phase mapping)",
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       "values": {
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        "rotor_threshold": 0.9
       },
       "decision": null,
       "location": "worker/voltage/preprocess.py (Params.rotor_threshold, rotor_erode_px)",
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       "reviewer": null,
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      {
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       "location": "worker/voltage/rotors.py (TrackParams.pair_dist_px, paired_frac)",
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        "trackers": {
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         "1.5x_cycle": 678
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       },
       "decision": null,
       "location": "worker/voltage/sensitivity.py (SIGMAS, BASELINE_MULTIPLES, baseline_levels)",
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       "reviewer": null,
       "description": "Filter levels tested: spatial sigma and baseline window values",
       "reviewed_at": null
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      {
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        "f1": 8867
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       "decision": null,
       "location": "worker/voltage/runs.py (default_window)",
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       "reviewer": null,
       "description": "Frames analysed: whole recording minus one filter pad at each end (unless the plan narrows it)",
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      {
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       "values": {
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         "temporal_smoothing",
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        "thresholds": {
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         "dv_autocorr": 0.5,
         "neighbour_corr": 0.8
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       },
       "decision": null,
       "location": "worker/voltage/inspect.py (prior_processing)",
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       "reviewer": null,
       "description": "Thresholds for flagging depositor processing (normalization, masking, temporal/spatial smoothing)",
       "reviewed_at": null
      },
      {
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        ]
       },
       "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)",
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      },
      {
       "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)",
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       "values": {
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         9267
        ],
        "illuminated_arrhythmia": [
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        "illuminated_after_termination": [
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       },
       "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)",
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      },
      {
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       },
       "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)",
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      },
      {
       "id": "persistent_rotor_criterion",
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       "status": "provisional",
       "values": {
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         "illuminated_after_termination": "absent"
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        "max_absent": 0,
        "min_present": 1,
        "spanning_rotor": "counts in every segment it overlaps",
        "min_lifetime_frames": 64
       },
       "decision": null,
       "location": "worker/voltage/sensitivity.py (MIN_ROTORS_PRESENT, MAX_ROTORS_ABSENT)",
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       "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
      },
      {
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       "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 versus post-termination rhythm"
        ],
        "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": {
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         "light_off.dominant_freq_hz",
         "illuminated_arrhythmia.persistent_rotors",
         "illuminated_arrhythmia.persistent_rotor_count_max",
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         "persistent_rotor_tracks"
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        "stable_frac": 0.25
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       "location": "worker/agents/critic.py (STABLE_FRAC, stability)",
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       "reviewer": null,
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       "reviewed_at": null
      },
      {
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       "status": "provisional",
       "values": {
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       "decision": null,
       "location": "worker/agents/critic.py (persistence_variants)",
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       "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",
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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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     "expected_persistent_rotors": "absent",
     "definition": "from spiral termination (interpreted; under illumination) to illumination_off",
     "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"
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        "baseline_pre": -0.5335609912872314,
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        "interpretation": "mean fluorescence changed; cause not determined from the image",
        "beat_amplitude_p5_p95": 1.4402662966400377
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       "uncertainty_frames": 17
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     },
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    },
    {
     "id": "4eeedfd6-84c2-40d3-8a4a-8758716d02d9",
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     "label": "light off",
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     "expected_persistent_rotors": "absent",
     "definition": "from illumination_off to recording end",
     "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"
     },
     "evidence": {
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      "start": {
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     "source": "acquisition_log",
     "status": "detected",
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     "method": "midpoint threshold on DAQ channel 'led_trigger', mapped to frames via camera triggers"
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    {
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     "kind": "arrhythmia_termination",
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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"
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    {
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    },
    {
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     "status": "detected",
     "uncertainty_frames": 11,
     "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"
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    {
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     "kind": "illumination_on",
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     "label": null,
     "source": "image",
     "status": "contradicted",
     "uncertainty_frames": 17,
     "method": "consensus upward step in running-median baseline of tissue-mean raw signal"
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    {
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     "method": "midpoint threshold on DAQ channel 'led_trigger', mapped to frames via camera triggers"
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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": {
   "id": "0b805159-6ca0-4616-995e-14b1e224b0be",
   "status": "done",
   "started_at": "2026-10-27T22:13:23.355061+00:00",
   "finished_at": "2026-10-27T22:19:36.177173+00:00",
   "code": {
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    "git_commit": "752b95b01dde60f86eb71b47343448c7af4551c1"
   },
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   "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": 400,
     "paired_frac": 0.5,
     "render_step": 4,
     "pair_dist_px": 3.0,
     "spatial_sigma": 1.0,
     "rotor_erode_px": 3,
     "baseline_frames": 641,
     "rotor_threshold": 0.9,
     "spatial_truncate": 4.0
    },
    "version": 2,
    "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",
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     "negative_frac": 0.3231635934819897,
     "frames_with_nan": 9267,
     "dv_lag1_autocorr_median": 0.9120054707808141,
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    },
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   },
   "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: masking, temporal smoothing, spatial smoothing, and normalization were documented and measured. The protocol's Gaussian phase smoothing is therefore added on top of prior spatial filtering of unknown total, noise/SNR assumptions are not independent raw-pixel noise, and amplitude or photon-count interpretations would be misleading; phase/rotor analysis may proceed with this caveat."
     },
     {
      "topic": "Event interpretation at frame 3170",
      "severity": "warn",
      "effect_on_analysis": "Frame 3170 should be used only as the provisional segment boundary supplied to the run, not as measured light onset. DAQ and photodiode evidence indicate illumination was already present before frame 0 and ended at frame 4977, so any segment-level interpretation depending on frame 3170 as light onset would be wrong; the numerical pipeline itself can use the boundary as a provisional event boundary."
     },
     {
      "topic": "Baseline and illumination artifact",
      "severity": "warn",
      "effect_on_analysis": "Blue-light crosstalk, normalization by the stimulation-light signal, a large slow baseline range, and a baseline step mean absolute baseline and amplitude measurements are not reliable as raw fluorescence physiology. The fixed high-pass/baseline procedure and rotor criteria may still be applied, but baseline-dependent interpretation should be cautious."
     },
     {
      "topic": "Baseline window versus post-termination rhythm",
      "severity": "warn",
      "effect_on_analysis": "With the fixed baseline_frames value, the measured post-termination segment rhythms put the baseline window at about the provisional lower limit stated by the rhythm tool. This may modestly attenuate slow post-termination rhythm components, but it is not a block because the frame rate is the intended 1000 Hz and this version of the protocol was set for this recording."
     }
    ],
    "rationale": "The recording may be analysed under protocol version 2 as it stands. The recording is the intended mouse whole-heart public reference recording, and the 1000 Hz frame rate from the publication agrees with the protocol note underlying the fixed 641-frame baseline window; no species, tissue, frame-rate, pixel-size, or image-size mismatch requires a hold. The important limitations are interpretive rather than eligibility-blocking: the deposit is processed rather than raw, the frame-3170 event is a provisional termination/baseline-change boundary rather than light onset, illumination/crosstalk/normalization affect baseline and amplitude, and the post-termination rhythm is close to the baseline-window caveat threshold. These warnings should accompany any results, but they do not make the fixed parameters inapplicable.",
    "mismatches": [],
    "hold_reason": null,
    "protocol_id": "f65d786f-f194-4be2-88b8-10d3dd25d674",
    "methods_text": "Using the provisional parameter set version 2 for protocol f65d786f-f194-4be2-88b8-10d3dd25d674, the fixed parameters were baseline_frames=641, spatial_sigma=1.0, spatial_truncate=4.0, pad_frames=400, 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 was 1000 Hz from the publication source recorded for this movie, and the pixel size was 133 um from the publication source. The analysed window was frames 400 to 8867, with provisional segment definitions and provisional criteria: illuminated_arrhythmia from frames 0 to 3170, illuminated_after_termination from frames 3170 to 4977, and light_off from frames 4977 to 9267; within the analysed window these correspond to analysed frames 400 to 3170, 3170 to 4977, and 4977 to 8867.",
    "recording_id": "55cb4aa3-6502-45a6-a14c-85cb676fe8c3",
    "params_version": 2,
    "prompt_version": "pipeline-v2"
   }
  },
  "signature": {
   "id": "080dd569-7f7f-42c9-9083-593437cf3245",
   "created_at": "2026-10-27T22:19:36.139923+00:00",
   "movie_path": "runs/0b805159-6ca0-4616-995e-14b1e224b0be/movie.mp4",
   "frames": {},
   "filter_params": {
    "mask": "not NaN in frame 0 and nonzero temporal std",
    "render": {
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     "palettes": {
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      "camera": "gray",
      "voltage": "gray"
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    "window": {
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       "analysed": [
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        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": [
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        4977
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       "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
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       "analysed": [
        4977,
        8867
       ],
       "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"
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     ],
     "illumination": "Acquisition log (LED trigger channel, provisional interpretation): illumination on over frames 400-4977 of the analysed frames 400-8867.",
     "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"
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      "illuminated_arrhythmia": 64,
      "illuminated_after_termination": 452
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    "tracking": {
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     "min_cycles": 1.0,
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    "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": 641,
    "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",
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    "spatial_applies_to": "phase/activation only; displayed voltage is baseline-corrected only"
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    "rules": [
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      "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",
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     },
     {
      "id": "filter_defaults",
      "expert": "optical mapping analyst (cardiac electrophysiology)",
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      "decision": null,
      "location": "worker/voltage/preprocess.py (Params)",
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      "description": "Default baseline window (frames) and spatial Gaussian sigma/truncate for phase",
      "reviewed_at": null
     },
     {
      "id": "tissue_mask",
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       "rule": "not NaN in frame 0 and nonzero std",
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      "decision": null,
      "location": "worker/voltage/io.py (tissue_mask)",
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      "reviewer": null,
      "description": "Tissue = not NaN in frame 0 and nonzero temporal std",
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     },
     {
      "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)",
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      "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": {
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       "min_cycles": 1.0,
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      },
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      "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": {
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      },
      "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": {
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        "heavier": 2.0
       },
       "trackers": {
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}