{
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  "run_when": "2026-10-27 23:46 UTC",
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       {
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       {
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       {
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       },
       {
        "end": 3411,
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       {
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       {
        "end": 3453,
        "core": [
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       {
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        "start": 3414,
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       },
       {
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        "core": [
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        "start": 3420,
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        "rotation_period_frames": 25.12
       },
       {
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        "core": [
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        "start": 3423,
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        "rotation_period_frames": 27.16
       },
       {
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        "core": [
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        "start": 3445,
        "charge": -1,
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        "lifetime_cycles": 1.88,
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        "frames_in_segment": 47,
        "rotation_period_frames": 24.25
       },
       {
        "end": 3516,
        "core": [
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        "start": 3465,
        "charge": -1,
        "rotations": 2.11,
        "lifetime_cycles": 2.08,
        "lifetime_frames": 52,
        "frames_in_segment": 52,
        "rotation_period_frames": 24.64
       },
       {
        "end": 3512,
        "core": [
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        "start": 3467,
        "charge": 1,
        "rotations": 1.378,
        "lifetime_cycles": 1.84,
        "lifetime_frames": 46,
        "frames_in_segment": 46,
        "rotation_period_frames": 33.38
       },
       {
        "end": 3498,
        "core": [
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        "start": 3474,
        "charge": 1,
        "rotations": 1.063,
        "lifetime_cycles": 1.0,
        "lifetime_frames": 25,
        "frames_in_segment": 25,
        "rotation_period_frames": 23.52
       },
       {
        "end": 3533,
        "core": [
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        "start": 3479,
        "charge": -1,
        "rotations": 1.992,
        "lifetime_cycles": 2.2,
        "lifetime_frames": 55,
        "frames_in_segment": 55,
        "rotation_period_frames": 27.62
       },
       {
        "end": 3521,
        "core": [
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        "start": 3488,
        "charge": 1,
        "rotations": 1.106,
        "lifetime_cycles": 1.36,
        "lifetime_frames": 34,
        "frames_in_segment": 34,
        "rotation_period_frames": 30.75
       },
       {
        "end": 3597,
        "core": [
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        "start": 3490,
        "charge": 1,
        "rotations": 4.277,
        "lifetime_cycles": 4.32,
        "lifetime_frames": 108,
        "frames_in_segment": 108,
        "rotation_period_frames": 25.25
       },
       {
        "end": 3599,
        "core": [
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        "start": 3492,
        "charge": -1,
        "rotations": 4.175,
        "lifetime_cycles": 4.32,
        "lifetime_frames": 108,
        "frames_in_segment": 108,
        "rotation_period_frames": 25.87
       },
       {
        "end": 3581,
        "core": [
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        "start": 3492,
        "charge": -1,
        "rotations": 2.927,
        "lifetime_cycles": 3.6,
        "lifetime_frames": 90,
        "frames_in_segment": 90,
        "rotation_period_frames": 30.75
       },
       {
        "end": 3550,
        "core": [
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        "start": 3503,
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        "frames_in_segment": 48,
        "rotation_period_frames": 26.58
       },
       {
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        "core": [
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        "start": 3509,
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       },
       {
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        "core": [
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        "rotation_period_frames": 25.86
       },
       {
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        "core": [
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        "rotation_period_frames": 30.02
       },
       {
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        "core": [
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       },
       {
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        "lifetime_frames": 60,
        "frames_in_segment": 60,
        "rotation_period_frames": 40.06
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      ],
      "persistent_rotor_frames_frac": 1.0
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    },
    "is_run_setting": false,
    "persistent_rotor_tracks": 450
   }
  ]
 },
 "critic": {
  "code": {
   "dirty": true,
   "git_commit": "905d5bebbb29da7ad46cd5045db14330695037c3"
  },
  "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": 0.858,
     "value_at_run_setting": 303,
     "range_across_settings": [
      204.0,
      464.0
     ]
    },
    "whole_recording.dominant_freq_hz": {
     "unit": "Hz",
     "range": null,
     "metric": "dominant_freq_hz",
     "stable": true,
     "status": "no_cited_range",
     "segment": "whole_recording",
     "spread_frac": 0.0,
     "value_at_run_setting": 40.294,
     "range_across_settings": [
      40.294,
      40.294
     ]
    },
    "whole_recording.persistent_rotors": {
     "unit": "count",
     "range": null,
     "metric": "persistent_rotors",
     "stable": false,
     "status": "unstable_not_reportable",
     "segment": "whole_recording",
     "spread_frac": 0.858,
     "value_at_run_setting": 303,
     "range_across_settings": [
      204.0,
      464.0
     ]
    },
    "whole_recording.singularity_frames_frac": {
     "unit": "fraction of frames",
     "range": null,
     "metric": "singularity_frames_frac",
     "stable": true,
     "status": "no_cited_range",
     "segment": "whole_recording",
     "spread_frac": 0.0,
     "value_at_run_setting": 1.0,
     "range_across_settings": [
      1.0,
      1.0
     ]
    },
    "whole_recording.persistent_rotor_count_max": {
     "unit": "count",
     "range": null,
     "metric": "persistent_rotor_count_max",
     "stable": false,
     "status": "unstable_not_reportable",
     "segment": "whole_recording",
     "spread_frac": 0.8,
     "value_at_run_setting": 15,
     "range_across_settings": [
      9.0,
      21.0
     ]
    }
   },
   "unstable": [
    "whole_recording.persistent_rotors",
    "whole_recording.persistent_rotor_count_max",
    "persistent_rotor_tracks"
   ],
   "physiology_ok": null,
   "ranged_checks": []
  },
  "ranges": [],
  "run_id": "82fe7343-d416-4536-b39e-19b7eca30443",
  "status": "provisional",
  "verdict": {
   "send_back": false,
   "critic_notes": "Verdict: this signature has no physiology-range pass/fail verdict because the checked stable metrics have no cited ranges, and the provisional ranges, stability threshold and criteria are provisional. Reportable as descriptive outputs are singularity_frames_frac at 1.0 fraction of frames and dominant_freq_hz at 40.294 Hz; the persistent-rotor counts are unstable and not reportable as single values, with whole_recording.persistent_rotors and persistent_rotor_tracks spanning 204.0\u2013464.0 and whole_recording.persistent_rotor_count_max spanning 9.0\u201321.0 across settings. Persistent-rotor interpretation needs methods review because a cited analysis of the same rat deposit warns that naive phase-singularity detections may include false positives at conduction blocks (DOI 10.1371/journal.pcbi.1013963); additionally, the strict/default/loose trackers found 250/303/450 counts, and the recording is preprocessed rather than raw camera data, with transformed measured polarity and preprocessing-dependent SNR noted by inspection.",
   "review_items": [
    {
     "topic": "unstable:whole_recording.persistent_rotors",
     "detail": "The persistent-rotor count varies over 204.0\u2013464.0 across the filter grid and tracker variants, exceeding the provisional stability threshold and making the single count not reportable.",
     "severity": "warn",
     "reviewer_type": "domain scientist / methods reviewer"
    },
    {
     "topic": "unstable:whole_recording.persistent_rotor_count_max",
     "detail": "The maximum simultaneous persistent-rotor count varies over 9.0\u201321.0 across the filter grid and tracker variants, exceeding the provisional stability threshold and making the single count not reportable.",
     "severity": "warn",
     "reviewer_type": "domain scientist / methods reviewer"
    },
    {
     "topic": "unstable:persistent_rotor_tracks",
     "detail": "The persistent-rotor track count varies over 204.0\u2013464.0 across the filter grid and tracker variants, exceeding the provisional stability threshold and making the single track count not reportable.",
     "severity": "warn",
     "reviewer_type": "domain scientist / methods reviewer"
    },
    {
     "topic": "preprocessed deposit",
     "detail": "The deposit is not raw camera data and is documented as background-subtracted, spatially binned, low-pass filtered, drift-removed, and normalized; analyses requiring raw fluorescence/counts or unfiltered noise statistics would be misleading.",
     "severity": "warn",
     "reviewer_type": "data provenance reviewer"
    },
    {
     "topic": "polarity transformed relative to dye",
     "detail": "RH237 normally dims on depolarization, but measured polarity is non-inverted with 7/7 blocks agreeing; using measured polarity for orientation should avoid activation-analysis errors, but this transformation should be documented.",
     "severity": "warn",
     "reviewer_type": "methods reviewer"
    },
    {
     "topic": "SNR depends on preprocessing",
     "detail": "Median SNR is high, but documented temporal filtering and detected temporal smoothing can inflate SNR by reducing apparent frame-to-frame noise.",
     "severity": "info",
     "reviewer_type": "methods reviewer"
    },
    {
     "topic": "reference thresholds provisional",
     "detail": "No frame-rate inference was needed because the deposit states 1 kHz, but automated processing flags and provisional rhythm/reference-rate tools are not yet domain-scientist reviewed.",
     "severity": "info",
     "reviewer_type": "domain scientist"
    },
    {
     "topic": "naive phase singularity false positives",
     "detail": "A cited analysis of the same rat deposit reports that naive phase-singularity approaches can create spurious rotational-driver detections at functional conduction blocks, so rotor counts and tracks should be interpreted cautiously.",
     "severity": "warn",
     "reviewer_type": "domain scientist / methods reviewer"
    },
    {
     "topic": "tracker sensitivity",
     "detail": "Strict, default, and loose trackers find 250, 303, and 450 persistent rotors respectively; the rule verdicts agree, but the count sensitivity reinforces that the rotor counts should not be reported as single values.",
     "severity": "warn",
     "reviewer_type": "methods reviewer"
    }
   ],
   "tracker_note": "The tracker variants produced different counts for the whole recording: strict 250, default 303, and loose 450 persistent rotors, while the rule verdicts agree; this tracker sensitivity should be reviewed but is not by itself a reason to call the finding false.",
   "physiology_ok": null,
   "metric_judgments": [
    {
     "note": "Stable across settings at 1.0 fraction of frames, but there is no cited physiology range for this check, so it can be reported only as a descriptive analysis output, not as evidence that the signature is within or outside a reference range.",
     "metric": "whole_recording.singularity_frames_frac",
     "status": "no_cited_range"
    },
    {
     "note": "Persistent-rotor count is unstable across sensitivity and tracker settings, spanning 204.0\u2013464.0, so this count is not reportable as a single value. Because the cited context for this rat deposit warns that naive phase-singularity detections can include false positives at conduction blocks, this finding needs method review before interpreting rotors as genuine drivers (DOI 10.1371/journal.pcbi.1013963).",
     "metric": "whole_recording.persistent_rotors",
     "status": "unstable_not_reportable"
    },
    {
     "note": "The maximum simultaneous persistent-rotor count is unstable across sensitivity and tracker settings, spanning 9.0\u201321.0, so it is not reportable as a single value and should be reviewed before use.",
     "metric": "whole_recording.persistent_rotor_count_max",
     "status": "unstable_not_reportable"
    },
    {
     "note": "Dominant frequency is stable at 40.294 Hz across the tested baseline windows, but there is no cited physiology range for this check, so it can be reported descriptively only.",
     "metric": "whole_recording.dominant_freq_hz",
     "status": "no_cited_range"
    },
    {
     "note": "Persistent-rotor tracks are unstable across sensitivity and tracker settings, spanning 204.0\u2013464.0, so the track count is not reportable as a single value. The same-deposit context cautions that naive phase-singularity counts may include false positives at conduction blocks, so rotor-track interpretation needs review (DOI 10.1371/journal.pcbi.1013963).",
     "metric": "persistent_rotor_tracks",
     "status": "unstable_not_reportable"
    }
   ],
   "send_back_reason": null,
   "persistence_threshold_note": "Not applicable: both the measured-cycle and cited-paper-rotation persistence variants report no segment expectations, so there is no persistence threshold to test and no agreement verdict."
  },
  "passages": {
   "false_phase_singularities": {
    "ref": "10.1371/journal.pcbi.1013963",
    "note": "This paper analyses the same rat deposit and argues that phase-singularity counts on such data include false positives at conduction blocks; our singularity detector is of the naive kind it describes.",
    "quotes": [
     "the naive approach implicitly assumes a continuous phase, causing wavefront endpoints attached to functional conduction blocks to appear as spurious rotational drivers",
     "We analyzed one case with maximally increased gap junction coupling \\(80 nM rotigaptide\\) to test our methods on stable rotors"
    ],
    "status": "provisional",
    "passages": [
     "suggesting they reflect the presence of a defect rather than genuine rotational activity. For the optical mapping data, the naive approach implicitly assumes a continuous phase, causing wavefront endpoints attached to functional conduction blocks to appear as spurious rotational drivers. Our method shifts the paradigm from rotation around singular points to rotation around two-dimensional phase defects, ",
     "yzed in [16] (See Fig 4). The data was obtained from [35], where details of heart preparation and ethics are described. We analyzed one case with maximally increased gap junction coupling (80 nM rotigaptide) to test our methods on stable rotors. 10.1371/journal.pcbi.1013963.g004Fig 4Ventricular fibrillation optical map.Snapshot of an optical intensity map of ven"
    ],
    "applies_to": {
     "species": "rat",
     "metric_prefix": "persistent_rotors"
    }
   }
  },
  "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_rotors_by_segment": {
      "whole_recording": 250
     }
    },
    {
     "link_px": 4.0,
     "max_gap": 5,
     "tracker": "default",
     "is_run_setting": true,
     "persistent_rotors_by_segment": {
      "whole_recording": 303
     }
    },
    {
     "link_px": 6.0,
     "max_gap": 10,
     "tracker": "loose",
     "is_run_setting": false,
     "persistent_rotors_by_segment": {
      "whole_recording": 450
     }
    }
   ]
  },
  "stability": {
   "persistent_rotor_tracks": {
    "max": 464.0,
    "min": 204.0,
    "median": 303.0,
    "stable": false,
    "settings": 15,
    "spread_frac": 0.858,
    "values_grid": [
     337,
     282,
     204,
     462,
     380,
     249,
     464,
     358,
     238,
     384,
     303,
     213
    ],
    "varied_over": "filter grid + trackers",
    "values_trackers": [
     250,
     303,
     450
    ]
   },
   "whole_recording.dominant_freq_hz": {
    "max": 40.294,
    "min": 40.294,
    "median": 40.294,
    "stable": true,
    "settings": 4,
    "spread_frac": 0.0,
    "varied_over": "baseline windows",
    "values_by_baseline": {
     "38": 40.294,
     "75": 40.294,
     "121": 40.294,
     "150": 40.294
    }
   },
   "whole_recording.persistent_rotors": {
    "max": 464.0,
    "min": 204.0,
    "median": 303.0,
    "stable": false,
    "settings": 15,
    "spread_frac": 0.858,
    "values_grid": [
     337,
     282,
     204,
     462,
     380,
     249,
     464,
     358,
     238,
     384,
     303,
     213
    ],
    "varied_over": "filter grid + trackers",
    "values_trackers": [
     250,
     303,
     450
    ]
   },
   "whole_recording.singularity_frames_frac": {
    "max": 1.0,
    "min": 1.0,
    "median": 1.0,
    "stable": true,
    "settings": 12,
    "spread_frac": 0.0,
    "values_grid": [
     1.0,
     1.0,
     1.0,
     1.0,
     1.0,
     1.0,
     1.0,
     1.0,
     1.0,
     1.0,
     1.0,
     1.0
    ],
    "varied_over": "filter grid"
   },
   "whole_recording.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
   },
   "whole_recording.persistent_rotor_count_max": {
    "max": 21.0,
    "min": 9.0,
    "median": 15.0,
    "stable": false,
    "settings": 15,
    "spread_frac": 0.8,
    "values_grid": [
     13,
     12,
     9,
     17,
     17,
     13,
     20,
     15,
     11,
     16,
     15,
     10
    ],
    "varied_over": "filter grid + trackers",
    "values_trackers": [
     9,
     15,
     21
    ]
   }
  },
  "reviewed_at": "2026-10-27T23:49:12.019950+00:00",
  "recording_id": "73e4ebe2-6b09-4582-a1d6-ded901b7d124",
  "signature_id": "3b8cc8b6-ef45-4633-9365-0217c5c54720",
  "prompt_version": "critic-v1",
  "criteria_status": {
   "note": null,
   "rules": [
    {
     "id": "physiology_reference_rates",
     "expert": "cardiac electrophysiologist per species",
     "status": "provisional",
     "values": {
      "ranges": [],
      "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": [
       "whole_recording.persistent_rotors",
       "whole_recording.persistent_rotor_count_max",
       "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": 25,
      "paper_rotation": null
     },
     "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": 121,
       "3x_cycle": 75,
       "6x_cycle": 150,
       "1.5x_cycle": 38
      },
      "baseline_scaling": {
       "multiples": {
        "3x_cycle": 3.0,
        "6x_cycle": 6.0,
        "1.5x_cycle": 1.5
       },
       "reference_segment": "whole_recording",
       "segment_cycles_frames": {
        "whole_recording": 25
       },
       "reference_cycle_frames": 25,
       "window_over_cycle_per_segment": {
        "run": {
         "whole_recording": 4.84
        },
        "3x_cycle": {
         "whole_recording": 3.0
        },
        "6x_cycle": {
         "whole_recording": 6.0
        },
        "1.5x_cycle": {
         "whole_recording": 1.52
        }
       }
      },
      "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": null,
   "measured_cycle": {
    "basis": "one dominant cycle of the fastest segment at the run setting",
    "reason": "no segment expectations, so the rule has nothing to test",
    "applicable": false,
    "min_frames": 25
   },
   "paper_rotation": {
    "reason": "no segment expectations",
    "applicable": false
   }
  },
  "required_review_topics": [
   "unstable:whole_recording.persistent_rotors",
   "unstable:whole_recording.persistent_rotor_count_max",
   "unstable:persistent_rotor_tracks"
  ]
 },
 "criteria": [
  {
   "criterion": "Design expectations",
   "rule": "none stated for this recording's segments",
   "result": "no criterion to test; counts are descriptive",
   "provisional": true
  }
 ],
 "report": {
  "methods": "Recording Rat heart, ventricular fibrillation (RG 80 nM) (doi:10.5281/zenodo.18319102; 128x80 px, 3800 frames, 1000 Hz) was analysed over frames 200-3600. Deposit shows signs of prior processing (provisional): unit range, non integer, nan mask partial, temporal smoothing, spatial smoothing. Each pixel was baseline-corrected by subtracting a 121-frame centered moving average; NaN pixels were set to zero. Dye polarity (upright) was taken from the sign of the median per-pixel skew of dV/dt. For phase only, each frame was spatially filtered with a Gaussian (sigma 1.0 px, truncated at 4.0 sigma); no temporal low-pass was applied. Phase was the angle of the Hilbert transform with 200 frames of padding on each side. Phase singularities were plaquettes with |winding| > 0.9 turns at least 3 px inside the tissue edge; they were tracked across frames (same charge, <= 4.0 px per frame, gaps <= 5 frames), and a persistent rotor was a track lasting >= 25 frames (1 cycle(s) of the fastest segment) within 3.0 px of an opposite-charge singularity in no more than 50% of its frames. Sensitivity: baseline 150, 75, 38, 121 frames x sigma 0.5, 1.0, 2.0 px, and tracker variants. All thresholds and criteria are provisional pending review by a domain scientist.",
  "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": "Rat whole heart optical mapping (Zenodo 18319102)",
     "protocol_id": "a0059cf5-fbde-4942-a18f-399ebe70e9ff",
     "params_version": 1
    }
   },
   {
    "id": "baseline_window_rule",
    "description": "A run proceeds only if the protocol's baseline window is >= 2x the slowest segment's cycle, the cycle from the MAP channel when a DAQ log exists, else from per-pixel dominant frequency on linearly detrended pixels; otherwise the run is held by code",
    "expert": "optical mapping analyst",
    "status": "provisional",
    "location": "worker/voltage/baseline_rule.py (FACTOR, evaluate)",
    "values": {
     "ok": true,
     "factor": 2.0,
     "source": "per-pixel dominant frequency (images)",
     "required_min_frames": 52,
     "slowest_cycle_frames": 26
    }
   },
   {
    "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": 121,
     "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": 5216
    }
   },
   {
    "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": 25
    }
   },
   {
    "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": 121,
      "3x_cycle": 75,
      "6x_cycle": 150,
      "1.5x_cycle": 38
     }
    }
   },
   {
    "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": 200,
     "f1": 3600
    }
   },
   {
    "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": [
      "unit_range",
      "non_integer",
      "nan_mask_partial",
      "temporal_smoothing",
      "spatial_smoothing"
     ],
     "thresholds": {
      "int_frac": 0.5,
      "neg_frac": 0.01,
      "dv_autocorr": 0.5,
      "neighbour_corr": 0.8
     }
    }
   },
   {
    "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": [],
     "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": [
      "whole_recording.persistent_rotors",
      "whole_recording.persistent_rotor_count_max",
      "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": 25,
     "paper_rotation": null
    }
   },
   {
    "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": {
     "max_absent": 0,
     "min_present": 1
    }
   }
  ],
  "review_items": [
   {
    "topic": "unstable:whole_recording.persistent_rotors",
    "detail": "The persistent-rotor count varies over 204.0\u2013464.0 across the filter grid and tracker variants, exceeding the provisional stability threshold and making the single count not reportable.",
    "severity": "warn",
    "reviewer": "domain scientist / methods reviewer"
   },
   {
    "topic": "unstable:whole_recording.persistent_rotor_count_max",
    "detail": "The maximum simultaneous persistent-rotor count varies over 9.0\u201321.0 across the filter grid and tracker variants, exceeding the provisional stability threshold and making the single count not reportable.",
    "severity": "warn",
    "reviewer": "domain scientist / methods reviewer"
   },
   {
    "topic": "unstable:persistent_rotor_tracks",
    "detail": "The persistent-rotor track count varies over 204.0\u2013464.0 across the filter grid and tracker variants, exceeding the provisional stability threshold and making the single track count not reportable.",
    "severity": "warn",
    "reviewer": "domain scientist / methods reviewer"
   },
   {
    "topic": "preprocessed deposit",
    "detail": "The deposit is not raw camera data and is documented as background-subtracted, spatially binned, low-pass filtered, drift-removed, and normalized; analyses requiring raw fluorescence/counts or unfiltered noise statistics would be misleading.",
    "severity": "warn",
    "reviewer": "data provenance reviewer"
   },
   {
    "topic": "polarity transformed relative to dye",
    "detail": "RH237 normally dims on depolarization, but measured polarity is non-inverted with 7/7 blocks agreeing; using measured polarity for orientation should avoid activation-analysis errors, but this transformation should be documented.",
    "severity": "warn",
    "reviewer": "methods reviewer"
   },
   {
    "topic": "SNR depends on preprocessing",
    "detail": "Median SNR is high, but documented temporal filtering and detected temporal smoothing can inflate SNR by reducing apparent frame-to-frame noise.",
    "severity": "info",
    "reviewer": "methods reviewer"
   },
   {
    "topic": "reference thresholds provisional",
    "detail": "No frame-rate inference was needed because the deposit states 1 kHz, but automated processing flags and provisional rhythm/reference-rate tools are not yet domain-scientist reviewed.",
    "severity": "info",
    "reviewer": "domain scientist"
   },
   {
    "topic": "naive phase singularity false positives",
    "detail": "A cited analysis of the same rat deposit reports that naive phase-singularity approaches can create spurious rotational-driver detections at functional conduction blocks, so rotor counts and tracks should be interpreted cautiously.",
    "severity": "warn",
    "reviewer": "domain scientist / methods reviewer"
   },
   {
    "topic": "tracker sensitivity",
    "detail": "Strict, default, and loose trackers find 250, 303, and 450 persistent rotors respectively; the rule verdicts agree, but the count sensitivity reinforces that the rotor counts should not be reported as single values.",
    "severity": "warn",
    "reviewer": "methods reviewer"
   }
  ],
  "reportable": [
   {
    "metric": "persistent rotor tracks",
    "segment": "all",
    "value": "204\u2013464",
    "unit": "count",
    "status": "unstable, not reportable"
   },
   {
    "metric": "dominant freq (Hz)",
    "segment": "whole recording",
    "value": "40.29",
    "unit": "Hz",
    "status": "no cited range"
   },
   {
    "metric": "persistent rotors",
    "segment": "whole recording",
    "value": "204\u2013464",
    "unit": "count",
    "status": "unstable, not reportable"
   },
   {
    "metric": "singularity frames fraction",
    "segment": "whole recording",
    "value": "1",
    "unit": "fraction of frames",
    "status": "no cited range"
   },
   {
    "metric": "persistent rotor count max",
    "segment": "whole recording",
    "value": "9\u201321",
    "unit": "count",
    "status": "unstable, not reportable"
   }
  ],
  "verdict": {
   "physiology_ok": null,
   "send_back": false,
   "notes": "Verdict: this signature has no physiology-range pass/fail verdict because the checked stable metrics have no cited ranges, and the provisional ranges, stability threshold and criteria are provisional. Reportable as descriptive outputs are singularity_frames_frac at 1.0 fraction of frames and dominant_freq_hz at 40.294 Hz; the persistent-rotor counts are unstable and not reportable as single values, with whole_recording.persistent_rotors and persistent_rotor_tracks spanning 204.0\u2013464.0 and whole_recording.persistent_rotor_count_max spanning 9.0\u201321.0 across settings. Persistent-rotor interpretation needs methods review because a cited analysis of the same rat deposit warns that naive phase-singularity detections may include false positives at conduction blocks (DOI 10.1371/journal.pcbi.1013963); additionally, the strict/default/loose trackers found 250/303/450 counts, and the recording is preprocessed rather than raw camera data, with transformed measured polarity and preprocessing-dependent SNR noted by inspection."
  },
  "provenance": {
   "recording": {
    "id": "73e4ebe2-6b09-4582-a1d6-ded901b7d124",
    "label": "Rat heart, ventricular fibrillation (RG 80 nM)",
    "source": "public",
    "source_ref": "10.5281/zenodo.18319102",
    "publication_ref": "10.1093/cvr/cvaa141",
    "storage_path": "public/masked_data_RG_80nM.mat",
    "format": "mat",
    "sha256": "9e30977de373f78d1b5d236bd100e46bb79c72152d3a7516b9c03c4849391076",
    "size_bytes": 293204250,
    "license": "CC-BY-4.0",
    "attribution": "Verstraeten, Bjorn; Lootens, Sebastiaan",
    "rights_source": {
     "ref": "10.5281/zenodo.18319102",
     "url": "https://zenodo.org/records/18319102",
     "kind": "deposit_metadata",
     "creators": [
      "Verstraeten, Bjorn",
      "Lootens, Sebastiaan"
     ],
     "license_as_stated": "cc-by-4.0"
    },
    "frame_rate_hz": 1000,
    "frame_rate_source": {
     "ref": "10.5281/zenodo.18319102",
     "kind": "deposit_metadata",
     "quote": "Emitted fluorescence was recorded with high-resolution CMOS cameras at a sampling rate of 1 kHz, with a spatial resolution of 128 \u00d7 80 pixels and a pixel size of approximately 100\u2013125 \u00b5m."
    },
    "pixel_size_um": 112.5,
    "pixel_size_source": {
     "ref": "10.5281/zenodo.18319102",
     "kind": "deposit_metadata",
     "note": "midpoint of the stated 100-125 um; conduction velocities carry a +/-11% range from this alone",
     "quote": "Emitted fluorescence was recorded with high-resolution CMOS cameras at a sampling rate of 1 kHz, with a spatial resolution of 128 \u00d7 80 pixels and a pixel size of approximately 100\u2013125 \u00b5m."
    },
    "frames": 3800,
    "height": 128,
    "width": 80,
    "inverted": false
   },
   "protocol": {
    "id": "a0059cf5-fbde-4942-a18f-399ebe70e9ff",
    "name": "Rat whole heart optical mapping (Zenodo 18319102)",
    "species": "rat",
    "tissue": "whole_heart",
    "params_version": 1,
    "params_set_by": "developer (not a domain scientist)",
    "params_note": "version 1: the library defaults as of commit 363372b; provisional, see protocol_params.py"
   },
   "run": {
    "id": "82fe7343-d416-4536-b39e-19b7eca30443",
    "status": "done",
    "started_at": "2026-10-27T23:46:44.310458+00:00",
    "finished_at": "2026-10-27T23:48:45.548478+00:00",
    "code": {
     "dirty": true,
     "git_commit": "905d5bebbb29da7ad46cd5045db14330695037c3"
    },
    "workers": 9,
    "steps": [
     "load",
     "deposit_checks",
     "baseline_correct",
     "polarity",
     "spatial_filter(phase only)",
     "hilbert_phase",
     "phase_singularities",
     "track_and_pair",
     "beats_apd_cv",
     "sensitivity",
     "render"
    ],
    "protocol_params": {
     "params": {
      "link_px": 4.0,
      "max_gap": 5,
      "min_cycles": 1.0,
      "pad_frames": 200,
      "paired_frac": 0.5,
      "render_step": 4,
      "pair_dist_px": 3.0,
      "spatial_sigma": 1.0,
      "rotor_erode_px": 3,
      "baseline_frames": 121,
      "rotor_threshold": 0.9,
      "spatial_truncate": 4.0
     },
     "version": 1,
     "protocol_id": "a0059cf5-fbde-4942-a18f-399ebe70e9ff"
    },
    "baseline_rule": {
     "ok": true,
     "ratio": 4.654,
     "cycles": {
      "whole_recording": {
       "n_frames": 3800,
       "cycle_frames": 26,
       "pixels_agreeing_frac": 0.8585122699386503,
       "pixels_with_rhythm_frac": 1.0,
       "interval_quartiles_frames": [
        25.0,
        26.0,
        29.0
       ]
      }
     },
     "factor": 2.0,
     "reason": null,
     "source": "per-pixel dominant frequency (images)",
     "status": "provisional",
     "baseline_frames": 121,
     "slowest_segment": "whole_recording",
     "required_min_frames": 52,
     "slowest_cycle_frames": 26
    },
    "deposit_checks": {
     "flags": [
      {
       "flag": "unit_range",
       "value": [
        0.0,
        1.0
       ],
       "suggests": "min-max normalized",
       "threshold": "[0, 1] spanned"
      },
      {
       "flag": "non_integer",
       "value": 0.0003442292944785276,
       "suggests": "not raw camera counts (camera output is integer); weak alone",
       "threshold": 0.5
      },
      {
       "flag": "nan_mask_partial",
       "value": [
        0
       ],
       "suggests": "mask encoded in a few frames only; other frames carry non-tissue values"
      },
      {
       "flag": "temporal_smoothing",
       "value": 0.959237783400513,
       "suggests": "temporally low-pass filtered (white shot noise gives dV lag-1 autocorr near -0.5)",
       "threshold": 0.5
      },
      {
       "flag": "spatial_smoothing",
       "value": 0.9479694003115444,
       "suggests": "spatially filtered or binned (shot noise is independent between pixels)",
       "threshold": 0.8
      }
     ],
     "status": "provisional",
     "measures": {
      "max": 1.0,
      "min": 0.0,
      "frames_used": 2000,
      "integer_frac": 0.0003442292944785276,
      "negative_frac": 0.0,
      "frames_with_nan": 1,
      "dv_lag1_autocorr_median": 0.959237783400513,
      "neighbour_dv_corr_median": 0.9479694003115444
     },
     "processed_before_deposit": true
    },
    "pipeline_check": null
   },
   "signature": {
    "id": "3b8cc8b6-ef45-4633-9365-0217c5c54720",
    "created_at": "2026-10-27T23:48:45.169738+00:00",
    "movie_path": "runs/82fe7343-d416-4536-b39e-19b7eca30443/movie.mp4",
    "frames": {
     "f0": 200,
     "f1": 3600,
     "maps": "runs/82fe7343-d416-4536-b39e-19b7eca30443/frames/maps.npz",
     "dtype": "<f4",
     "phase": "runs/82fe7343-d416-4536-b39e-19b7eca30443/frames/phase.npy",
     "shape": [
      3400,
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  ],
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 }
}