{
 "exported_at": "2026-10-30T03:09:23.418252+00:00",
 "exported_by": {
  "app": "quantetta-a web",
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   "git_commit": "",
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 "recording_short": "M13Rec001",
 "header": {
  "short": "M13Rec001",
  "label": "Mouse heart, spiral wave and optogenetic termination",
  "facts": "64 \u00d7 55 px, 9,267 frames, 1 kHz, 133 \u00b5m/px, deposit checks: negative values, nan mask all frames, temporal smoothing, spatial smoothing",
  "run_short": "202e66c5",
  "run_when": "2026-10-27 23:02 UTC",
  "params_version": 3,
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  "workers": null,
  "sig_short": "6ed9c8e5",
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  "protocol_name": "Mouse whole heart optical mapping (Luther lab)"
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   {
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    "low": 18.75,
    "high": 20.0,
    "unit": "Hz",
    "scope": "one optical mapping recording in the same study (spiral wave before and during illumination); not a population range",
    "metric": "dominant_freq_hz",
    "source": {
     "ref": "10.1371/journal.pcbi.1011660",
     "quotes": [
      "rotational frequency of \u2248 20 Hz before illumination",
      "the frequency of the arrhythmia decreases to \u2248 18\\.75 Hz"
     ],
     "passages": [
      " is shown in Fig 3B. It shows that the arrhythmia consists of a single spiral wave with a stationary core dynamic and a rotational frequency of \u2248 20 Hz before illumination. During a single global optical pulse with a PL of 5000 ms and an LI of 3.21 \u03bcW/mm2, the frequency of the arrhythmia de",
      "ncy of \u2248 20 Hz before illumination. During a single global optical pulse with a PL of 5000 ms and an LI of 3.21 \u03bcW/mm2, the frequency of the arrhythmia decreases to \u2248 18.75 Hz. It is important to note that the frequency reverses its original value of \u2248 20 Hz when the light is turned off. Fig 3C"
     ]
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    "status": "provisional",
    "tissue": "whole_heart",
    "species": "mouse",
    "applies_to": {
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  "run_id": "202e66c5-944f-4d65-bbb1-a060487247e1",
  "status": "provisional",
  "verdict": {
   "send_back": false,
   "critic_notes": "Verdict: the signature has no stable metric outside a cited range, but the only ranged check, illuminated_arrhythmia.dominant_freq_hz, is unstable and therefore not reportable as a single value; physiology_ok is null. Reportable items are limited to provisional algorithmic findings: singularity presence in illuminated_arrhythmia is stable over 0.3816479400749064\u20130.48801498127340825 fraction of frames, persistent-rotor presence in illuminated_arrhythmia holds across filters and trackers, and absence of persistent rotors is stable at 0 in light_off and illuminated_after_termination. Unstable items are light_off.singularity_frames_frac 0.0029023746701846965\u20130.02955145118733509, illuminated_arrhythmia.persistent_rotors 4.0\u201315.0, illuminated_arrhythmia.persistent_rotor_count_max 1.0\u20132.0, illuminated_arrhythmia.dominant_freq_hz 15.356\u201319.85, illuminated_after_termination.singularity_frames_frac 0.0005534034311012728\u20130.014941892639734366, and persistent_rotor_tracks 4.0\u201315.0. Persistence-threshold criteria agree at 52 frames and 50 frames; the cited mouse spiral-wave context reports approximately 20 Hz before illumination and approximately 18.75 Hz during illumination (DOI 10.1371/journal.pcbi.1011660). Review is needed for pre-deposit processing/raw-data labeling, frame-3170 interpretation, baseline and illumination artifact, and all provisional thresholds; the ranges, stability threshold, and criteria are provisional.",
   "review_items": [
    {
     "topic": "unstable:light_off.singularity_frames_frac",
     "detail": "Filter-grid dependence is large: 0.0029023746701846965\u20130.02955145118733509 fraction of frames, so the light-off singularity fraction is not reportable as a single value.",
     "severity": "warn",
     "reviewer_type": "domain scientist / signal-processing reviewer"
    },
    {
     "topic": "unstable:illuminated_arrhythmia.persistent_rotors",
     "detail": "The persistent-rotor count varies across filter and tracker settings from 4.0 to 15.0; keep only the qualitative presence/rule result until tracking sensitivity is reviewed.",
     "severity": "warn",
     "reviewer_type": "domain scientist / tracking reviewer"
    },
    {
     "topic": "unstable:illuminated_arrhythmia.persistent_rotor_count_max",
     "detail": "The maximum simultaneous persistent-rotor count varies from 1.0 to 2.0, so it is not reportable as a single value.",
     "severity": "warn",
     "reviewer_type": "domain scientist / tracking reviewer"
    },
    {
     "topic": "unstable:illuminated_arrhythmia.dominant_freq_hz",
     "detail": "Dominant frequency depends on baseline-window choice, 15.356\u201319.85 Hz, despite cited context of approximately 20 Hz and 18.75 Hz for this study; resolve baseline-window dependence before reporting a value.",
     "severity": "warn",
     "reviewer_type": "domain scientist / electrophysiology reviewer"
    },
    {
     "topic": "unstable:illuminated_after_termination.singularity_frames_frac",
     "detail": "Filter-grid dependence is large: 0.0005534034311012728\u20130.014941892639734366 fraction of frames, so the post-termination singularity fraction is not reportable as a single value.",
     "severity": "warn",
     "reviewer_type": "domain scientist / signal-processing reviewer"
    },
    {
     "topic": "unstable:persistent_rotor_tracks",
     "detail": "Total persistent-rotor tracks vary from 4.0 to 15.0 across filter and tracker settings, so the total track count is not reportable as a single value.",
     "severity": "warn",
     "reviewer_type": "domain scientist / tracking reviewer"
    },
    {
     "topic": "Pre-deposit processing / raw-data label",
     "detail": "The README labels M13Rec001 as raw experimental data, but the notebook documents masking, spatial smoothing, temporal smoothing, and normalization with Python Analyser; prior_processing measurements support processed data. Analyses requiring raw photon counts or independent pixel noise would be misleading if this is treated as raw camera data.",
     "severity": "warn",
     "reviewer_type": "data provenance reviewer"
    },
    {
     "topic": "Event interpretation at frame 3170",
     "detail": "The image event at frame 3170 is a baseline_step only. The DAQ shows illumination began before frame 0 and ended at frame 4977, so treating frame 3170 as light onset would be wrong. The stored spiral-termination label is provisional and based on timing relative to the paper, not a direct measurement.",
     "severity": "warn",
     "reviewer_type": "domain scientist"
    },
    {
     "topic": "Baseline and illumination artifact",
     "detail": "The publication reports blue stimulation light crosstalk causing an increase in fluorescence baseline and re-normalization by division to the recorded stimulation light signal; the recording also has a large slow baseline range and a baseline step. Analyses using absolute baseline or amplitude should account for illumination/crosstalk/normalization effects.",
     "severity": "warn",
     "reviewer_type": "optical-mapping reviewer"
    },
    {
     "topic": "Provisional tool thresholds",
     "detail": "Event detection, processing flags, SNR, rhythm, and reference-rate thresholds are provisional and not yet reviewed by a domain scientist; conclusions depending on them should be checked for critical analyses.",
     "severity": "info",
     "reviewer_type": "domain scientist"
    }
   ],
   "tracker_note": "Strict, default, and loose trackers all give the same provisional rule verdict, holds, with persistent rotors only in illuminated_arrhythmia; the counts differ across tracker variants: 5, 13, and 15 in illuminated_arrhythmia, with 0 in light_off and 0 in illuminated_after_termination.",
   "physiology_ok": null,
   "metric_judgments": [
    {
     "note": "Unstable across the filter grid, so this fraction should not be reported as a single value; describe only its range across settings, 0.0029023746701846965\u20130.02955145118733509 fraction of frames, and review the filter dependence before using it quantitatively.",
     "metric": "light_off.singularity_frames_frac",
     "status": "unstable_not_reportable"
    },
    {
     "note": "Stable at 0 across the filter grid and trackers, but there is no cited physiological range for this count, so it can be reported only as an algorithmic observation, not as a range-validated physiological measurement.",
     "metric": "light_off.persistent_rotors",
     "status": "no_cited_range"
    },
    {
     "note": "Stable at 0 across the filter grid and trackers, but there is no cited physiological range for this maximum count, so it can be reported only as an algorithmic observation.",
     "metric": "light_off.persistent_rotor_count_max",
     "status": "no_cited_range"
    },
    {
     "note": "Stable at 2.375 Hz across the tested baseline windows, but no cited range is available for this light-off segment in the provided checks, so do not treat it as physiology-range validated.",
     "metric": "light_off.dominant_freq_hz",
     "status": "no_cited_range"
    },
    {
     "note": "Stable across the filter grid at 0.3816479400749064\u20130.48801498127340825 fraction of frames, and the singularity-present criterion holds provisionally, but no cited physiological range is available for this fraction.",
     "metric": "illuminated_arrhythmia.singularity_frames_frac",
     "status": "no_cited_range"
    },
    {
     "note": "Unstable across the filter grid and tracker settings, so this count should not be reported as a single value; report only the qualitative persistent-rotor presence, which holds provisionally, and the range across settings, 4.0\u201315.0 counts, if needed for review.",
     "metric": "illuminated_arrhythmia.persistent_rotors",
     "status": "unstable_not_reportable"
    },
    {
     "note": "Unstable across the filter grid and tracker settings, so this maximum count should not be reported as a single value; use only the range across settings, 1.0\u20132.0 counts, for review.",
     "metric": "illuminated_arrhythmia.persistent_rotor_count_max",
     "status": "unstable_not_reportable"
    },
    {
     "note": "Unstable across baseline windows, so this frequency should not be reported as a single value; its range across settings is 15.356\u201319.85 Hz. The cited context for this mouse spiral recording reports approximately 20 Hz before illumination and approximately 18.75 Hz during illumination (DOI 10.1371/journal.pcbi.1011660), but this measured frequency is not reportable until baseline-window dependence is resolved.",
     "metric": "illuminated_arrhythmia.dominant_freq_hz",
     "status": "unstable_not_reportable"
    },
    {
     "note": "Unstable across the filter grid, so this fraction should not be reported as a single value; use only the range across settings, 0.0005534034311012728\u20130.014941892639734366 fraction of frames, for review.",
     "metric": "illuminated_after_termination.singularity_frames_frac",
     "status": "unstable_not_reportable"
    },
    {
     "note": "Stable at 0 across the filter grid and trackers, but there is no cited physiological range for this count, so it can be reported only as an algorithmic observation.",
     "metric": "illuminated_after_termination.persistent_rotors",
     "status": "no_cited_range"
    },
    {
     "note": "Stable at 0 across the filter grid and trackers, but there is no cited physiological range for this maximum count, so it can be reported only as an algorithmic observation.",
     "metric": "illuminated_after_termination.persistent_rotor_count_max",
     "status": "no_cited_range"
    },
    {
     "note": "Stable at 2.214 Hz across the tested baseline windows, but no cited range is available for this post-termination illuminated segment in the provided checks, so do not treat it as physiology-range validated.",
     "metric": "illuminated_after_termination.dominant_freq_hz",
     "status": "no_cited_range"
    },
    {
     "note": "Unstable across the filter grid and tracker settings, so the total persistent-rotor track count should not be reported as a single value; use only the range across settings, 4.0\u201315.0 counts, for review while retaining the qualitative rule verdict.",
     "metric": "persistent_rotor_tracks",
     "status": "unstable_not_reportable"
    }
   ],
   "send_back_reason": null,
   "persistence_threshold_note": "The persistent-rotor rule agrees under both thresholds: using the measured-cycle threshold of 52 frames and the cited 20.0 Hz paper rotation threshold of 50 frames, the rule holds across filters and trackers. The cited rotation-period context is DOI 10.1371/journal.pcbi.1011660; the paper notes approximately 20 Hz, i.e. 50 frames at 1000 frames/s, and the tool notes 18.75 Hz would be 53 frames."
  },
  "passages": {
   "mouse_spiral_rotation_period": {
    "ref": "10.1371/journal.pcbi.1011660",
    "note": "At 1000 frames/s, 20 Hz is a 50-frame rotation; the illuminated value of 18.75 Hz would be 53 frames.",
    "quotes": [
     "rotational frequency of \u2248 20 Hz before illumination"
    ],
    "status": "provisional",
    "passages": [
     " is shown in Fig 3B. It shows that the arrhythmia consists of a single spiral wave with a stationary core dynamic and a rotational frequency of \u2248 20 Hz before illumination. During a single global optical pulse with a PL of 5000 ms and an LI of 3.21 \u03bcW/mm2, the frequency of the arrhythmia de"
    ],
    "applies_to": {
     "species": "mouse"
    },
    "rotation_hz": 20.0
   }
  },
  "trackers": {
   "note": "disagreement is reported as a review item, not folded into the pass/fail",
   "agree": true,
   "trackers": [
    {
     "link_px": 2.0,
     "max_gap": 1,
     "tracker": "strict",
     "is_run_setting": false,
     "persistent_rotor_rule": "holds (provisional)",
     "persistent_rotors_by_segment": {
      "light_off": 0,
      "illuminated_arrhythmia": 5,
      "illuminated_after_termination": 0
     }
    },
    {
     "link_px": 4.0,
     "max_gap": 5,
     "tracker": "default",
     "is_run_setting": true,
     "persistent_rotor_rule": "holds (provisional)",
     "persistent_rotors_by_segment": {
      "light_off": 0,
      "illuminated_arrhythmia": 13,
      "illuminated_after_termination": 0
     }
    },
    {
     "link_px": 6.0,
     "max_gap": 10,
     "tracker": "loose",
     "is_run_setting": false,
     "persistent_rotor_rule": "holds (provisional)",
     "persistent_rotors_by_segment": {
      "light_off": 0,
      "illuminated_arrhythmia": 15,
      "illuminated_after_termination": 0
     }
    }
   ]
  },
  "stability": {
   "persistent_rotor_tracks": {
    "max": 15.0,
    "min": 4.0,
    "median": 12.0,
    "stable": false,
    "settings": 15,
    "spread_frac": 0.917,
    "values_grid": [
     5,
     5,
     4,
     12,
     11,
     12,
     13,
     13,
     15,
     12,
     13,
     12
    ],
    "varied_over": "filter grid + trackers",
    "values_trackers": [
     5,
     13,
     15
    ]
   },
   "light_off.dominant_freq_hz": {
    "max": 2.375,
    "min": 2.375,
    "median": 2.375,
    "stable": true,
    "settings": 4,
    "spread_frac": 0.0,
    "varied_over": "baseline windows",
    "values_by_baseline": {
     "678": 2.375,
     "901": 2.375,
     "1356": 2.375,
     "2712": 2.375
    }
   },
   "light_off.persistent_rotors": {
    "max": 0.0,
    "min": 0.0,
    "median": 0.0,
    "stable": true,
    "settings": 15,
    "spread_frac": 0.0,
    "values_grid": [
     0,
     0,
     0,
     0,
     0,
     0,
     0,
     0,
     0,
     0,
     0,
     0
    ],
    "varied_over": "filter grid + trackers",
    "values_trackers": [
     0,
     0,
     0
    ]
   },
   "light_off.singularity_frames_frac": {
    "max": 0.02955145118733509,
    "min": 0.0029023746701846965,
    "median": 0.008575197889182058,
    "stable": false,
    "settings": 12,
    "spread_frac": 3.108,
    "values_grid": [
     0.02928759894459103,
     0.02955145118733509,
     0.02691292875989446,
     0.008707124010554089,
     0.008179419525065963,
     0.00712401055408971,
     0.0036939313984168864,
     0.0036939313984168864,
     0.0029023746701846965,
     0.013192612137203167,
     0.012137203166226913,
     0.008443271767810026
    ],
    "varied_over": "filter grid"
   },
   "light_off.persistent_rotor_present": {
    "stable": true,
    "values_grid": [
     false,
     false,
     false,
     false,
     false,
     false,
     false,
     false,
     false,
     false,
     false,
     false
    ],
    "varied_over": "filter grid + trackers",
    "values_trackers": [
     false,
     false,
     false
    ],
    "stable_across_filters": true,
    "stable_across_trackers": true
   },
   "light_off.persistent_rotor_count_max": {
    "max": 0.0,
    "min": 0.0,
    "median": 0.0,
    "stable": true,
    "settings": 15,
    "spread_frac": 0.0,
    "values_grid": [
     0,
     0,
     0,
     0,
     0,
     0,
     0,
     0,
     0,
     0,
     0,
     0
    ],
    "varied_over": "filter grid + trackers",
    "values_trackers": [
     0,
     0,
     0
    ]
   },
   "illuminated_arrhythmia.dominant_freq_hz": {
    "max": 19.85,
    "min": 15.356,
    "median": 17.2285,
    "stable": false,
    "settings": 4,
    "spread_frac": 0.261,
    "varied_over": "baseline windows",
    "values_by_baseline": {
     "678": 19.85,
     "901": 19.101,
     "1356": 15.356,
     "2712": 15.356
    }
   },
   "illuminated_arrhythmia.persistent_rotors": {
    "max": 15.0,
    "min": 4.0,
    "median": 12.0,
    "stable": false,
    "settings": 15,
    "spread_frac": 0.917,
    "values_grid": [
     5,
     5,
     4,
     12,
     11,
     12,
     13,
     13,
     15,
     12,
     13,
     12
    ],
    "varied_over": "filter grid + trackers",
    "values_trackers": [
     5,
     13,
     15
    ]
   },
   "illuminated_after_termination.dominant_freq_hz": {
    "max": 2.214,
    "min": 2.214,
    "median": 2.214,
    "stable": true,
    "settings": 4,
    "spread_frac": 0.0,
    "varied_over": "baseline windows",
    "values_by_baseline": {
     "678": 2.214,
     "901": 2.214,
     "1356": 2.214,
     "2712": 2.214
    }
   },
   "illuminated_arrhythmia.singularity_frames_frac": {
    "max": 0.48801498127340825,
    "min": 0.3816479400749064,
    "median": 0.47191011235955055,
    "stable": true,
    "settings": 12,
    "spread_frac": 0.225,
    "values_grid": [
     0.40898876404494383,
     0.40299625468164796,
     0.3816479400749064,
     0.4797752808988764,
     0.4756554307116105,
     0.45767790262172287,
     0.48801498127340825,
     0.4846441947565543,
     0.4681647940074906,
     0.4842696629213483,
     0.47902621722846445,
     0.4606741573033708
    ],
    "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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     0,
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    ],
    "varied_over": "filter grid + trackers",
    "values_trackers": [
     0,
     0,
     0
    ]
   },
   "illuminated_arrhythmia.persistent_rotor_present": {
    "stable": true,
    "values_grid": [
     true,
     true,
     true,
     true,
     true,
     true,
     true,
     true,
     true,
     true,
     true,
     true
    ],
    "varied_over": "filter grid + trackers",
    "values_trackers": [
     true,
     true,
     true
    ],
    "stable_across_filters": true,
    "stable_across_trackers": true
   },
   "illuminated_arrhythmia.persistent_rotor_count_max": {
    "max": 2.0,
    "min": 1.0,
    "median": 2.0,
    "stable": false,
    "settings": 15,
    "spread_frac": 0.5,
    "values_grid": [
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     2,
     2,
     2,
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    ],
    "varied_over": "filter grid + trackers",
    "values_trackers": [
     1,
     2,
     2
    ]
   },
   "illuminated_after_termination.singularity_frames_frac": {
    "max": 0.014941892639734366,
    "min": 0.0005534034311012728,
    "median": 0.005534034311012729,
    "stable": false,
    "settings": 12,
    "spread_frac": 2.6,
    "values_grid": [
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     0.002767017155506364,
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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,
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     false,
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    ],
    "varied_over": "filter grid + trackers",
    "values_trackers": [
     false,
     false,
     false
    ],
    "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,
     0,
     0
    ]
   }
  },
  "reviewed_at": "2026-10-27T23:09:22.379993+00:00",
  "recording_id": "55cb4aa3-6502-45a6-a14c-85cb676fe8c3",
  "signature_id": "6ed9c8e5-4bef-4549-b04f-f5014db32b5b",
  "prompt_version": "critic-v1",
  "criteria_status": {
   "note": null,
   "rules": [
    {
     "id": "physiology_reference_rates",
     "expert": "cardiac electrophysiologist per species",
     "status": "provisional",
     "values": {
      "ranges": [
       "mouse_spiral_rotation_hz"
      ],
      "tolerance_frac": 0.25,
      "segment_rhythm_rule": "expected persistent rotors 'present' -> spiral arrhythmia"
     },
     "decision": null,
     "location": "worker/voltage/physiology.py (RANGES, TOLERANCE_FRAC)",
     "reviewed": false,
     "reviewer": null,
     "description": "Cited physiological ranges (single-study values widened by a 25% tolerance), applied to segments by their expected rhythm; used by the critic and for frame-rate sanity checks",
     "reviewed_at": null
    },
    {
     "id": "stability_rule",
     "expert": "biostatistician + optical mapping analyst",
     "status": "provisional",
     "values": {
      "unstable": [
       "light_off.singularity_frames_frac",
       "illuminated_arrhythmia.persistent_rotors",
       "illuminated_arrhythmia.persistent_rotor_count_max",
       "illuminated_arrhythmia.dominant_freq_hz",
       "illuminated_after_termination.singularity_frames_frac",
       "persistent_rotor_tracks"
      ],
      "stable_frac": 0.25
     },
     "decision": null,
     "location": "worker/agents/critic.py (STABLE_FRAC, stability)",
     "reviewed": false,
     "reviewer": null,
     "description": "A metric is reportable only if its spread across all sensitivity settings is <= 25% of its median (zero spread when all values are 0); otherwise 'unstable, not reportable'",
     "reviewed_at": null
    },
    {
     "id": "persistence_threshold_variants",
     "expert": "computational cardiac electrophysiologist (phase mapping)",
     "status": "provisional",
     "values": {
      "measured_cycle": 52,
      "paper_rotation": 50
     },
     "decision": null,
     "location": "worker/agents/critic.py (persistence_variants)",
     "reviewed": false,
     "reviewer": null,
     "description": "The persistent-rotor rule is run at two lifetimes, one measured cycle of the fastest segment and the paper's cited rotation period; both verdicts stored, disagreement flagged",
     "reviewed_at": null
    },
    {
     "id": "persistent_rotor_criterion",
     "expert": "cardiac electrophysiologist",
     "status": "provisional",
     "values": {
      "max_absent": 0,
      "min_present": 1
     },
     "decision": null,
     "location": "worker/voltage/sensitivity.py (MIN_ROTORS_PRESENT, MAX_ROTORS_ABSENT)",
     "reviewed": false,
     "reviewer": null,
     "description": "Persistent-rotor finding holds if every 'present' segment has >= 1 persistent rotor and every 'absent' segment has none, at every setting",
     "reviewed_at": null
    },
    {
     "id": "sensitivity_grid",
     "expert": "optical mapping analyst",
     "status": "provisional",
     "values": {
      "spatial_sigma": {
       "light": 0.5,
       "default": 1.0,
       "heavier": 2.0
      },
      "baseline_frames": {
       "run": 901,
       "3x_cycle": 1356,
       "6x_cycle": 2712,
       "1.5x_cycle": 678
      },
      "baseline_scaling": {
       "multiples": {
        "3x_cycle": 3.0,
        "6x_cycle": 6.0,
        "1.5x_cycle": 1.5
       },
       "reference_segment": "illuminated_after_termination",
       "segment_cycles_frames": {
        "light_off": 421,
        "illuminated_arrhythmia": 52,
        "illuminated_after_termination": 452
       },
       "reference_cycle_frames": 452,
       "window_over_cycle_per_segment": {
        "run": {
         "light_off": 2.14,
         "illuminated_arrhythmia": 17.33,
         "illuminated_after_termination": 1.99
        },
        "3x_cycle": {
         "light_off": 3.22,
         "illuminated_arrhythmia": 26.08,
         "illuminated_after_termination": 3.0
        },
        "6x_cycle": {
         "light_off": 6.44,
         "illuminated_arrhythmia": 52.15,
         "illuminated_after_termination": 6.0
        },
        "1.5x_cycle": {
         "light_off": 1.61,
         "illuminated_arrhythmia": 13.04,
         "illuminated_after_termination": 1.5
        }
       }
      },
      "tracker(link_px, max_gap)": {
       "loose": [
        6.0,
        10
       ],
       "strict": [
        2.0,
        1
       ],
       "default": [
        4.0,
        5
       ]
      }
     },
     "decision": null,
     "location": "worker/voltage/sensitivity.py (SIGMAS, BASELINE_MULTIPLES, baseline_levels)",
     "reviewed": false,
     "reviewer": null,
     "description": "Filter levels tested: spatial sigma and baseline window values",
     "reviewed_at": null
    }
   ],
   "status": "provisional",
   "all_reviewed": false,
   "superseded_by_run": null
  },
  "persistence_variants": {
   "agree": true,
   "measured_cycle": {
    "basis": "one dominant cycle of the fastest segment at the run setting",
    "applicable": true,
    "min_frames": 52,
    "segment_counts_grid": {
     "light_off": [
      0,
      0,
      0,
      0,
      0,
      0,
      0,
      0,
      0,
      0,
      0,
      0
     ],
     "illuminated_arrhythmia": [
      5,
      5,
      4,
      12,
      11,
      12,
      13,
      13,
      15,
      12,
      13,
      12
     ],
     "illuminated_after_termination": [
      0,
      0,
      0,
      0,
      0,
      0,
      0,
      0,
      0,
      0,
      0,
      0
     ]
    },
    "holds_across_filters": true,
    "label_across_filters": "holds (provisional)",
    "holds_across_trackers": true,
    "label_across_trackers": "holds (provisional)",
    "segment_lifetimes_run": {
     "light_off": [],
     "illuminated_arrhythmia": [
      40,
      34,
      57,
      106,
      37,
      57,
      41,
      34,
      62,
      21,
      37,
      32,
      23
     ],
     "illuminated_after_termination": []
    }
   },
   "paper_rotation": {
    "ref": "10.1371/journal.pcbi.1011660",
    "basis": "1000 frames/s / 20 Hz, cited",
    "passage": " is shown in Fig 3B. It shows that the arrhythmia consists of a single spiral wave with a stationary core dynamic and a rotational frequency of \u2248 20 Hz before illumination. During a single global optical pulse with a PL of 5000 ms and an LI of 3.21 \u03bcW/mm2, the frequency of the arrhythmia de",
    "applicable": true,
    "min_frames": 50,
    "rotation_hz": 20.0,
    "segment_counts_grid": {
     "light_off": [
      0,
      0,
      0,
      0,
      0,
      0,
      0,
      0,
      0,
      0,
      0,
      0
     ],
     "illuminated_arrhythmia": [
      5,
      5,
      4,
      12,
      11,
      12,
      13,
      13,
      15,
      12,
      13,
      12
     ],
     "illuminated_after_termination": [
      0,
      0,
      0,
      0,
      0,
      0,
      0,
      0,
      0,
      0,
      0,
      0
     ]
    },
    "holds_across_filters": true,
    "label_across_filters": "holds (provisional)",
    "holds_across_trackers": true,
    "label_across_trackers": "holds (provisional)",
    "segment_lifetimes_run": {
     "light_off": [],
     "illuminated_arrhythmia": [
      40,
      34,
      57,
      106,
      37,
      57,
      41,
      34,
      62,
      21,
      37,
      32,
      23
     ],
     "illuminated_after_termination": []
    }
   }
  },
  "required_review_topics": [
   "unstable:light_off.singularity_frames_frac",
   "unstable:illuminated_arrhythmia.persistent_rotors",
   "unstable:illuminated_arrhythmia.persistent_rotor_count_max",
   "unstable:illuminated_arrhythmia.dominant_freq_hz",
   "unstable:illuminated_after_termination.singularity_frames_frac",
   "unstable:persistent_rotor_tracks"
  ]
 },
 "criteria": [
  {
   "criterion": "Singularities present where the design expects them, absent elsewhere",
   "rule": "each 'present' segment: frac >= 0.1 and >= 2.0 x max frac over 'absent' segments, at every setting",
   "result": "holds at 12 filter settings",
   "superseded": false,
   "provisional": true
  },
  {
   "criterion": "Persistent rotors present where the design expects them, absent elsewhere",
   "rule": "each 'present' segment: count >= 1; each 'absent' segment: count <= 0, at every setting",
   "result": "holds at 12 filter settings and 3 trackers",
   "superseded": false,
   "provisional": true
  },
  {
   "criterion": "Persistence threshold, paper context",
   "rule": "lifetime \u2265 52 frames (measured cycle) and \u2265 50 frames (cited 20 Hz)",
   "result": "agree",
   "provisional": true
  }
 ],
 "report": {
  "methods": "Using the provisional parameter set version 3, with provisional segment definitions and provisional criteria, the recording was checked under the Mouse whole heart optical mapping (Luther lab) protocol with baseline_frames = 901, spatial_sigma = 1.0, spatial_truncate = 4.0, pad_frames = 500, rotor_threshold = 0.9, rotor_erode_px = 3, link_px = 4.0, max_gap = 5, min_cycles = 1.0, pair_dist_px = 3.0, paired_frac = 0.5, and render_step = 4. The recording has 9267 frames in npy format with image size 64 \u00d7 55, frame rate 1000 Hz from the publication, and pixel size 133 \u00b5m from the publication. The analysed window is frames 500\u20138767; the provisional segments are illuminated_arrhythmia, frames 0\u20133170; illuminated_after_termination, frames 3170\u20134977; and light_off, frames 4977\u20139267.",
  "rules": [
   {
    "id": "protocol_parameter_set",
    "description": "Each protocol's fixed, versioned analysis parameters (version 1 = developer defaults); no run or agent may deviate",
    "expert": "optical mapping analyst",
    "status": "provisional",
    "location": "worker/voltage/protocol_params.py (developer_defaults, set_params)",
    "values": {
     "set_by": "developer (not a domain scientist)",
     "protocol": "Mouse whole heart optical mapping (Luther lab)",
     "protocol_id": "f65d786f-f194-4be2-88b8-10d3dd25d674",
     "params_version": 3
    }
   },
   {
    "id": "baseline_window_rule",
    "description": "A run proceeds only if the protocol's baseline window is >= 2x the slowest segment's cycle, the cycle from the MAP channel when a DAQ log exists, else from per-pixel dominant frequency on linearly detrended pixels; otherwise the run is held by code",
    "expert": "optical mapping analyst",
    "status": "provisional",
    "location": "worker/voltage/baseline_rule.py (FACTOR, evaluate)",
    "values": {
     "ok": true,
     "factor": 2.0,
     "source": "MAP channel (DAQ log)",
     "required_min_frames": 830,
     "slowest_cycle_frames": 415
    }
   },
   {
    "id": "filter_defaults",
    "description": "Default baseline window (frames) and spatial Gaussian sigma/truncate for phase",
    "expert": "optical mapping analyst (cardiac electrophysiology)",
    "status": "provisional",
    "location": "worker/voltage/preprocess.py (Params)",
    "values": {
     "lowpass": null,
     "spatial_sigma": 1.0,
     "baseline_frames": 901,
     "spatial_truncate": 4.0
    }
   },
   {
    "id": "tissue_mask",
    "description": "Tissue = not NaN in frame 0 and nonzero temporal std",
    "expert": "optical mapping analyst",
    "status": "provisional",
    "location": "worker/voltage/io.py (tissue_mask)",
    "values": {
     "rule": "not NaN in frame 0 and nonzero std",
     "tissue_pixels": 2332
    }
   },
   {
    "id": "polarity",
    "description": "Dye polarity from sign of median per-pixel skew of dV/dt",
    "expert": "optical mapping analyst / voltage dye chemist",
    "status": "provisional",
    "location": "worker/voltage/preprocess.py (polarity)",
    "values": {
     "method": "median skew of dV/dt",
     "result": -1
    }
   },
   {
    "id": "singularity_detection",
    "description": "Phase singularity = |winding| > threshold turns, >= erode px from tissue edge",
    "expert": "computational cardiac electrophysiologist (phase mapping)",
    "status": "provisional",
    "location": "worker/voltage/preprocess.py (Params.rotor_threshold, rotor_erode_px)",
    "values": {
     "rotor_erode_px": 3,
     "rotor_threshold": 0.9
    }
   },
   {
    "id": "rotor_persistence",
    "description": "Track linking distance/gap and minimum lifetime for a persistent rotor",
    "expert": "computational cardiac electrophysiologist (phase mapping)",
    "status": "provisional",
    "location": "worker/voltage/rotors.py (TrackParams)",
    "values": {
     "link_px": 4.0,
     "max_gap": 5,
     "min_cycles": 1.0,
     "min_frames": 52
    }
   },
   {
    "id": "chirality_pairing",
    "description": "Opposite-charge singularities within pair distance are a pair; tracks paired most of their life are excluded from rotors",
    "expert": "computational cardiac electrophysiologist (phase mapping)",
    "status": "provisional",
    "location": "worker/voltage/rotors.py (TrackParams.pair_dist_px, paired_frac)",
    "values": {
     "paired_frac": 0.5,
     "pair_dist_px": 3.0
    }
   },
   {
    "id": "sensitivity_grid",
    "description": "Filter levels tested: spatial sigma and baseline window values",
    "expert": "optical mapping analyst",
    "status": "provisional",
    "location": "worker/voltage/sensitivity.py (SIGMAS, BASELINE_MULTIPLES, baseline_levels)",
    "values": {
     "sigmas": {
      "light": 0.5,
      "default": 1.0,
      "heavier": 2.0
     },
     "trackers": {
      "loose": [
       6.0,
       10
      ],
      "strict": [
       2.0,
       1
      ],
      "default": [
       4.0,
       5
      ]
     },
     "baselines": {
      "run": 901,
      "3x_cycle": 1356,
      "6x_cycle": 2712,
      "1.5x_cycle": 678
     }
    }
   },
   {
    "id": "analysis_window",
    "description": "Frames analysed: whole recording minus one filter pad at each end (unless the plan narrows it)",
    "expert": "cardiac electrophysiologist familiar with the dataset",
    "status": "provisional",
    "location": "worker/voltage/runs.py (default_window)",
    "values": {
     "f0": 500,
     "f1": 8767
    }
   },
   {
    "id": "prior_processing_flags",
    "description": "Thresholds for flagging depositor processing (normalization, masking, temporal/spatial smoothing)",
    "expert": "imaging scientist (camera acquisition and noise)",
    "status": "provisional",
    "location": "worker/voltage/inspect.py (prior_processing)",
    "values": {
     "flags": [
      "negative_values",
      "non_integer",
      "nan_mask_all_frames",
      "temporal_smoothing",
      "spatial_smoothing"
     ],
     "thresholds": {
      "int_frac": 0.5,
      "neg_frac": 0.01,
      "dv_autocorr": 0.5,
      "neighbour_corr": 0.8
     }
    }
   },
   {
    "id": "baseline_step_detection",
    "description": "Baseline step = consensus upward step in tissue-mean raw baseline (cause not inferred; first misread as light onset, contradicted by the DAQ)",
    "expert": "optical mapping experimentalist",
    "status": "provisional",
    "location": "worker/voltage/events.py (detect_baseline_step)",
    "values": {
     "frames": [
      3170
     ]
    }
   },
   {
    "id": "daq_interpretation",
    "description": "DAQ channel names from depositor notebook; frames = first N triggers of closest burst; midpoint thresholds",
    "expert": "experimentalist who recorded the data (or the depositor)",
    "status": "provisional",
    "location": "worker/voltage/daq.py",
    "values": {
     "events": [
      "illumination_on@0",
      "arrhythmia_termination@3153",
      "illumination_off@4977"
     ]
    }
   },
   {
    "id": "segment_definitions",
    "description": "Mouse segments bounded by DAQ light events and the baseline step, interpreted as spiral termination under illumination (project lead, from Hussaini et al. 2023)",
    "expert": "cardiac electrophysiologist (ideally the depositing authors)",
    "status": "provisional",
    "location": "worker/voltage/annotations.py (MOUSE_SEGMENTS)",
    "values": {
     "light_off": [
      4977,
      9267
     ],
     "illuminated_arrhythmia": [
      0,
      3170
     ],
     "illuminated_after_termination": [
      3170,
      4977
     ]
    }
   },
   {
    "id": "rotor_finding_criterion",
    "description": "Singularity before/after finding holds if frac(before) >= min_frac and >= min_ratio x frac(after) at every setting (also kept, superseded, for persistent rotors)",
    "expert": "cardiac electrophysiologist + biostatistician",
    "status": "provisional",
    "location": "worker/voltage/sensitivity.py (MIN_FRAC, MIN_RATIO)",
    "values": {
     "min_frac": 0.1,
     "min_ratio": 2.0
    }
   },
   {
    "id": "persistent_rotor_criterion",
    "description": "Persistent-rotor finding holds if every 'present' segment has >= 1 persistent rotor and every 'absent' segment has none, at every setting",
    "expert": "cardiac electrophysiologist",
    "status": "provisional",
    "location": "worker/voltage/sensitivity.py (MIN_ROTORS_PRESENT, MAX_ROTORS_ABSENT)",
    "values": {
     "expect": {
      "light_off": "absent",
      "illuminated_arrhythmia": "present",
      "illuminated_after_termination": "absent"
     },
     "max_absent": 0,
     "min_present": 1,
     "spanning_rotor": "counts in every segment it overlaps",
     "min_lifetime_frames": 52
    }
   },
   {
    "id": "pipeline_check",
    "description": "The pipeline agent's hold/proceed decision from protocol mismatches and inspector anomalies; it chooses no parameter",
    "expert": "optical mapping analyst",
    "status": "provisional",
    "location": "worker/agents/pipeline.py (INSTRUCTIONS, validator)",
    "values": {
     "model": "openai:gpt-5.5",
     "proceed": true,
     "anomalies": [
      "Pre-deposit processing / raw-data label",
      "Event interpretation at frame 3170",
      "Baseline and illumination artifact",
      "Baseline-window rule"
     ],
     "mismatches": []
    }
   },
   {
    "id": "physiology_reference_rates",
    "description": "Cited physiological ranges (single-study values widened by a 25% tolerance), applied to segments by their expected rhythm; used by the critic and for frame-rate sanity checks",
    "expert": "cardiac electrophysiologist per species",
    "status": "provisional",
    "location": "worker/voltage/physiology.py (RANGES, TOLERANCE_FRAC)",
    "values": {
     "ranges": [
      "mouse_spiral_rotation_hz"
     ],
     "tolerance_frac": 0.25,
     "segment_rhythm_rule": "expected persistent rotors 'present' -> spiral arrhythmia"
    }
   },
   {
    "id": "stability_rule",
    "description": "A metric is reportable only if its spread across all sensitivity settings is <= 25% of its median (zero spread when all values are 0); otherwise 'unstable, not reportable'",
    "expert": "biostatistician + optical mapping analyst",
    "status": "provisional",
    "location": "worker/agents/critic.py (STABLE_FRAC, stability)",
    "values": {
     "unstable": [
      "light_off.singularity_frames_frac",
      "illuminated_arrhythmia.persistent_rotors",
      "illuminated_arrhythmia.persistent_rotor_count_max",
      "illuminated_arrhythmia.dominant_freq_hz",
      "illuminated_after_termination.singularity_frames_frac",
      "persistent_rotor_tracks"
     ],
     "stable_frac": 0.25
    }
   },
   {
    "id": "persistence_threshold_variants",
    "description": "The persistent-rotor rule is run at two lifetimes, one measured cycle of the fastest segment and the paper's cited rotation period; both verdicts stored, disagreement flagged",
    "expert": "computational cardiac electrophysiologist (phase mapping)",
    "status": "provisional",
    "location": "worker/agents/critic.py (persistence_variants)",
    "values": {
     "measured_cycle": 52,
     "paper_rotation": 50
    }
   }
  ],
  "review_items": [
   {
    "topic": "unstable:light_off.singularity_frames_frac",
    "detail": "Filter-grid dependence is large: 0.0029023746701846965\u20130.02955145118733509 fraction of frames, so the light-off singularity fraction is not reportable as a single value.",
    "severity": "warn",
    "reviewer": "domain scientist / signal-processing reviewer"
   },
   {
    "topic": "unstable:illuminated_arrhythmia.persistent_rotors",
    "detail": "The persistent-rotor count varies across filter and tracker settings from 4.0 to 15.0; keep only the qualitative presence/rule result until tracking sensitivity is reviewed.",
    "severity": "warn",
    "reviewer": "domain scientist / tracking reviewer"
   },
   {
    "topic": "unstable:illuminated_arrhythmia.persistent_rotor_count_max",
    "detail": "The maximum simultaneous persistent-rotor count varies from 1.0 to 2.0, so it is not reportable as a single value.",
    "severity": "warn",
    "reviewer": "domain scientist / tracking reviewer"
   },
   {
    "topic": "unstable:illuminated_arrhythmia.dominant_freq_hz",
    "detail": "Dominant frequency depends on baseline-window choice, 15.356\u201319.85 Hz, despite cited context of approximately 20 Hz and 18.75 Hz for this study; resolve baseline-window dependence before reporting a value.",
    "severity": "warn",
    "reviewer": "domain scientist / electrophysiology reviewer"
   },
   {
    "topic": "unstable:illuminated_after_termination.singularity_frames_frac",
    "detail": "Filter-grid dependence is large: 0.0005534034311012728\u20130.014941892639734366 fraction of frames, so the post-termination singularity fraction is not reportable as a single value.",
    "severity": "warn",
    "reviewer": "domain scientist / signal-processing reviewer"
   },
   {
    "topic": "unstable:persistent_rotor_tracks",
    "detail": "Total persistent-rotor tracks vary from 4.0 to 15.0 across filter and tracker settings, so the total track count is not reportable as a single value.",
    "severity": "warn",
    "reviewer": "domain scientist / tracking reviewer"
   },
   {
    "topic": "Pre-deposit processing / raw-data label",
    "detail": "The README labels M13Rec001 as raw experimental data, but the notebook documents masking, spatial smoothing, temporal smoothing, and normalization with Python Analyser; prior_processing measurements support processed data. Analyses requiring raw photon counts or independent pixel noise would be misleading if this is treated as raw camera data.",
    "severity": "warn",
    "reviewer": "data provenance reviewer"
   },
   {
    "topic": "Event interpretation at frame 3170",
    "detail": "The image event at frame 3170 is a baseline_step only. The DAQ shows illumination began before frame 0 and ended at frame 4977, so treating frame 3170 as light onset would be wrong. The stored spiral-termination label is provisional and based on timing relative to the paper, not a direct measurement.",
    "severity": "warn",
    "reviewer": "domain scientist"
   },
   {
    "topic": "Baseline and illumination artifact",
    "detail": "The publication reports blue stimulation light crosstalk causing an increase in fluorescence baseline and re-normalization by division to the recorded stimulation light signal; the recording also has a large slow baseline range and a baseline step. Analyses using absolute baseline or amplitude should account for illumination/crosstalk/normalization effects.",
    "severity": "warn",
    "reviewer": "optical-mapping reviewer"
   },
   {
    "topic": "Provisional tool thresholds",
    "detail": "Event detection, processing flags, SNR, rhythm, and reference-rate thresholds are provisional and not yet reviewed by a domain scientist; conclusions depending on them should be checked for critical analyses.",
    "severity": "info",
    "reviewer": "domain scientist"
   }
  ],
  "reportable": [
   {
    "metric": "persistent rotor tracks",
    "segment": "all",
    "value": "4\u201315",
    "unit": "count",
    "status": "unstable, not reportable"
   },
   {
    "metric": "dominant freq (Hz)",
    "segment": "light off",
    "value": "2.375",
    "unit": "Hz",
    "status": "no cited range"
   },
   {
    "metric": "persistent rotors",
    "segment": "light off",
    "value": "0",
    "unit": "count",
    "status": "no cited range"
   },
   {
    "metric": "singularity frames fraction",
    "segment": "light off",
    "value": "0.0029\u20130.0296",
    "unit": "fraction of frames",
    "status": "unstable, not reportable"
   },
   {
    "metric": "persistent rotor count max",
    "segment": "light off",
    "value": "0",
    "unit": "count",
    "status": "no cited range"
   },
   {
    "metric": "dominant freq (Hz)",
    "segment": "illuminated arrhythmia",
    "value": "15.4\u201319.9",
    "unit": "Hz",
    "status": "unstable, not reportable"
   },
   {
    "metric": "persistent rotors",
    "segment": "illuminated arrhythmia",
    "value": "4\u201315",
    "unit": "count",
    "status": "unstable, not reportable"
   },
   {
    "metric": "dominant freq (Hz)",
    "segment": "illuminated after termination",
    "value": "2.214",
    "unit": "Hz",
    "status": "no cited range"
   },
   {
    "metric": "singularity frames fraction",
    "segment": "illuminated arrhythmia",
    "value": "0.479",
    "unit": "fraction of frames",
    "status": "no cited range"
   },
   {
    "metric": "persistent rotors",
    "segment": "illuminated after termination",
    "value": "0",
    "unit": "count",
    "status": "no cited range"
   },
   {
    "metric": "persistent rotor count max",
    "segment": "illuminated arrhythmia",
    "value": "1\u20132",
    "unit": "count",
    "status": "unstable, not reportable"
   },
   {
    "metric": "singularity frames fraction",
    "segment": "illuminated after termination",
    "value": "0.000553\u20130.0149",
    "unit": "fraction of frames",
    "status": "unstable, not reportable"
   },
   {
    "metric": "persistent rotor count max",
    "segment": "illuminated after termination",
    "value": "0",
    "unit": "count",
    "status": "no cited range"
   }
  ],
  "verdict": {
   "physiology_ok": null,
   "send_back": false,
   "notes": "Verdict: the signature has no stable metric outside a cited range, but the only ranged check, illuminated_arrhythmia.dominant_freq_hz, is unstable and therefore not reportable as a single value; physiology_ok is null. Reportable items are limited to provisional algorithmic findings: singularity presence in illuminated_arrhythmia is stable over 0.3816479400749064\u20130.48801498127340825 fraction of frames, persistent-rotor presence in illuminated_arrhythmia holds across filters and trackers, and absence of persistent rotors is stable at 0 in light_off and illuminated_after_termination. Unstable items are light_off.singularity_frames_frac 0.0029023746701846965\u20130.02955145118733509, illuminated_arrhythmia.persistent_rotors 4.0\u201315.0, illuminated_arrhythmia.persistent_rotor_count_max 1.0\u20132.0, illuminated_arrhythmia.dominant_freq_hz 15.356\u201319.85, illuminated_after_termination.singularity_frames_frac 0.0005534034311012728\u20130.014941892639734366, and persistent_rotor_tracks 4.0\u201315.0. Persistence-threshold criteria agree at 52 frames and 50 frames; the cited mouse spiral-wave context reports approximately 20 Hz before illumination and approximately 18.75 Hz during illumination (DOI 10.1371/journal.pcbi.1011660). Review is needed for pre-deposit processing/raw-data labeling, frame-3170 interpretation, baseline and illumination artifact, and all provisional thresholds; the ranges, stability threshold, and 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": "202e66c5-944f-4d65-bbb1-a060487247e1",
    "status": "done",
    "started_at": "2026-10-27T23:02:29.97199+00:00",
    "finished_at": "2026-10-27T23:08:06.753472+00:00",
    "code": {
     "dirty": true,
     "git_commit": "b1be82429ddde2ad90ee88afacaae98a173e4403"
    },
    "workers": null,
    "steps": [
     "load",
     "deposit_checks",
     "baseline_correct",
     "polarity",
     "spatial_filter(phase only)",
     "hilbert_phase",
     "phase_singularities",
     "track_and_pair",
     "beats_apd_cv",
     "sensitivity",
     "render"
    ],
    "protocol_params": {
     "params": {
      "link_px": 4.0,
      "max_gap": 5,
      "min_cycles": 1.0,
      "pad_frames": 500,
      "paired_frac": 0.5,
      "render_step": 4,
      "pair_dist_px": 3.0,
      "spatial_sigma": 1.0,
      "rotor_erode_px": 3,
      "baseline_frames": 901,
      "rotor_threshold": 0.9,
      "spatial_truncate": 4.0
     },
     "version": 3,
     "protocol_id": "f65d786f-f194-4be2-88b8-10d3dd25d674"
    },
    "baseline_rule": {
     "ok": true,
     "ratio": 2.171,
     "cycles": {
      "light_off": {
       "cycle_frames": 411,
       "n_activations": 10,
       "polarity_used": -1,
       "median_interval_ms": 410.9
      },
      "illuminated_arrhythmia": {
       "cycle_frames": 52,
       "n_activations": 53,
       "polarity_used": -1,
       "median_interval_ms": 52.25
      },
      "illuminated_after_termination": {
       "cycle_frames": 415,
       "n_activations": 4,
       "polarity_used": -1,
       "median_interval_ms": 415.0
      }
     },
     "factor": 2.0,
     "reason": null,
     "source": "MAP channel (DAQ log)",
     "status": "provisional",
     "daq_file": "0111210010.txt",
     "baseline_frames": 901,
     "slowest_segment": "illuminated_after_termination",
     "required_min_frames": 830,
     "slowest_cycle_frames": 415
    },
    "deposit_checks": {
     "flags": [
      {
       "flag": "negative_values",
       "value": 0.3231635934819897,
       "suggests": "baseline-subtracted or normalized; raw fluorescence counts are non-negative",
       "threshold": 0.01
      },
      {
       "flag": "non_integer",
       "value": 0.0,
       "suggests": "not raw camera counts (camera output is integer); weak alone",
       "threshold": 0.5
      },
      {
       "flag": "nan_mask_all_frames",
       "value": 1188,
       "suggests": "tissue masked by depositor; the mask is theirs"
      },
      {
       "flag": "temporal_smoothing",
       "value": 0.9120054707808141,
       "suggests": "temporally low-pass filtered (white shot noise gives dV lag-1 autocorr near -0.5)",
       "threshold": 0.5
      },
      {
       "flag": "spatial_smoothing",
       "value": 0.9957938301611564,
       "suggests": "spatially filtered or binned (shot noise is independent between pixels)",
       "threshold": 0.8
      }
     ],
     "status": "provisional",
     "measures": {
      "max": 4.49806547164917,
      "min": -6.050762176513672,
      "frames_used": 2000,
      "integer_frac": 0.0,
      "negative_frac": 0.3231635934819897,
      "frames_with_nan": 9267,
      "dv_lag1_autocorr_median": 0.9120054707808141,
      "neighbour_dv_corr_median": 0.9957938301611564
     },
     "processed_before_deposit": true
    },
    "pipeline_check": {
     "model": "openai:gpt-5.5",
     "proceed": true,
     "anomalies": [
      {
       "topic": "Pre-deposit processing / raw-data label",
       "severity": "warn",
       "effect_on_analysis": "The deposited movie should not be treated as raw camera counts: depositor documentation and measurements indicate masking, temporal smoothing, spatial smoothing, and normalization. The fixed pipeline may still be run, but its Gaussian phase smoothing is added on top of prior filtering of unknown effective total, and any interpretation requiring independent pixel noise or raw photon-count amplitudes would be misleading."
      },
      {
       "topic": "Event interpretation at frame 3170",
       "severity": "warn",
       "effect_on_analysis": "The segment boundary at frame 3170 is based on a provisional termination/baseline-step interpretation, not a directly measured light onset. The fixed segment definitions can be analysed as defined, but results should be described relative to the provisional boundary and not as an illumination-on transition."
      },
      {
       "topic": "Baseline and illumination artifact",
       "severity": "warn",
       "effect_on_analysis": "Blue-light crosstalk, re-normalization by stimulation-light signal, a large slow baseline range, and a baseline step can affect absolute baseline and amplitude. The fixed phase/rotor pipeline can proceed, but baseline- or amplitude-dependent interpretations need caution."
      },
      {
       "topic": "Baseline-window rule",
       "severity": "info",
       "effect_on_analysis": "The coded rule reports ok: the 901-frame baseline is at least 2 times the slowest segment cycle from the MAP-channel DAQ log, so this rule does not hold the run."
      }
     ],
     "rationale": "The protocol is the intended mouse whole-heart optical-mapping protocol for this public reference recording, and the recording facts do not conflict with the protocol: the frame rate is 1000 Hz from the publication, the pixel size is 133 \u00b5m from the publication, and the 64 \u00d7 55 deposited movie is consistent with a cropped version of the 64 \u00d7 64 camera acquisition. The fixed version-3 parameters are therefore applicable as provisional pipeline settings, and the coded baseline-window rule passes for the slowest segment. The main limitations are not protocol mismatches but interpretation caveats: the deposited data are already masked, smoothed, and normalized; frame 3170 is a provisional termination/baseline-step boundary rather than light onset; and illumination/crosstalk/normalization affect baseline and amplitude.",
     "mismatches": [],
     "hold_reason": null,
     "protocol_id": "f65d786f-f194-4be2-88b8-10d3dd25d674",
     "methods_text": "Using the provisional parameter set version 3, with provisional segment definitions and provisional criteria, the recording was checked under the Mouse whole heart optical mapping (Luther lab) protocol with baseline_frames = 901, spatial_sigma = 1.0, spatial_truncate = 4.0, pad_frames = 500, rotor_threshold = 0.9, rotor_erode_px = 3, link_px = 4.0, max_gap = 5, min_cycles = 1.0, pair_dist_px = 3.0, paired_frac = 0.5, and render_step = 4. The recording has 9267 frames in npy format with image size 64 \u00d7 55, frame rate 1000 Hz from the publication, and pixel size 133 \u00b5m from the publication. The analysed window is frames 500\u20138767; the provisional segments are illuminated_arrhythmia, frames 0\u20133170; illuminated_after_termination, frames 3170\u20134977; and light_off, frames 4977\u20139267.",
     "recording_id": "55cb4aa3-6502-45a6-a14c-85cb676fe8c3",
     "params_version": 3,
     "prompt_version": "pipeline-v2"
    }
   },
   "signature": {
    "id": "6ed9c8e5-4bef-4549-b04f-f5014db32b5b",
    "created_at": "2026-10-27T23:08:06.969496+00:00",
    "movie_path": "runs/202e66c5-944f-4d65-bbb1-a060487247e1/movie.mp4",
    "frames": {},
    "filter_params": {
     "mask": "not NaN in frame 0 and nonzero temporal std",
     "render": {
      "step": 4,
      "palettes": {
       "phase": "twilight",
       "camera": "gray",
       "voltage": "gray"
      },
      "interpolation": "nearest"
     },
     "window": {
      "f0": 500,
      "f1": 8767,
      "segments": [
       {
        "name": "illuminated_arrhythmia",
        "label": "illumination with arrhythmia",
        "defined": [
         0,
         3170
        ],
        "analysed": [
         500,
         3170
        ],
        "citation": {
         "ref": "10.1371/journal.pcbi.1011660",
         "quote": "t stimulus with LI = 3.44 \u03bcW/mm2 and PL = 5 s. Fig 2C shows a monophasic action potential (MAP) signal (in black) before, during, and after illumination. It shows the sinus rhythm returns after 3190 ms of illumination. Fig 2D presents a closer look at the MAP signal of the heart during the last few rotations of arrhythmia and the first few action potentials of sinus rhythm. Fig 2E illustrates a"
        },
        "defined_by": "project lead (not a domain scientist), following the paper's design",
        "segment_id": "f6ca0bce-f7e9-437d-84b6-1bb1b24f80ba",
        "end_event_id": "46c59a51-1a01-4aed-8021-db9a63720a1d",
        "start_event_id": null,
        "expected_persistent_rotors": "present"
       },
       {
        "name": "illuminated_after_termination",
        "label": "illumination after termination",
        "defined": [
         3170,
         4977
        ],
        "analysed": [
         3170,
         4977
        ],
        "citation": {
         "ref": "10.1371/journal.pcbi.1011660",
         "quote": "t stimulus with LI = 3.44 \u03bcW/mm2 and PL = 5 s. Fig 2C shows a monophasic action potential (MAP) signal (in black) before, during, and after illumination. It shows the sinus rhythm returns after 3190 ms of illumination. Fig 2D presents a closer look at the MAP signal of the heart during the last few rotations of arrhythmia and the first few action potentials of sinus rhythm. Fig 2E illustrates a"
        },
        "defined_by": "project lead (not a domain scientist), following the paper's design",
        "segment_id": "c1444c59-1863-45aa-b6f3-2208392bf55a",
        "end_event_id": "db2ad5f3-9b96-4ec1-9ccd-9c82c3425609",
        "start_event_id": "46c59a51-1a01-4aed-8021-db9a63720a1d",
        "expected_persistent_rotors": "absent"
       },
       {
        "name": "light_off",
        "label": "light off",
        "defined": [
         4977,
         9267
        ],
        "analysed": [
         4977,
         8767
        ],
        "citation": {
         "ref": "10.1371/journal.pcbi.1011660",
         "quote": "t stimulus with LI = 3.44 \u03bcW/mm2 and PL = 5 s. Fig 2C shows a monophasic action potential (MAP) signal (in black) before, during, and after illumination. It shows the sinus rhythm returns after 3190 ms of illumination. Fig 2D presents a closer look at the MAP signal of the heart during the last few rotations of arrhythmia and the first few action potentials of sinus rhythm. Fig 2E illustrates a"
        },
        "defined_by": "project lead (not a domain scientist), following the paper's design",
        "segment_id": "4eeedfd6-84c2-40d3-8a4a-8758716d02d9",
        "end_event_id": null,
        "start_event_id": "db2ad5f3-9b96-4ec1-9ccd-9c82c3425609",
        "expected_persistent_rotors": "absent"
       }
      ],
      "illumination": "Acquisition log (LED trigger channel, provisional interpretation): illumination on over frames 500-4977 of the analysed frames 500-8767.",
      "frame_rate_hz": 1000.0,
      "frame_rate_source": {
       "ref": "10.1371/journal.pcbi.1011660",
       "kind": "publication",
       "note": "Camera frames are 64 x 64 in the paper; the deposit is 64 x 55 (cropped). Consistent with the DAQ: 10 samples per frame and a 5 s light pulse spanning 50,001 samples imply a 10 kHz DAQ.",
       "quote": " 775 \u00b1 70nm bandpass filter (FF01\u2013775/140-25, Semrock) and finally by the camera (EMCCD, Cascade 128+, Photometrics) with a spatial resolution of 64 \u00d7 64 pixels (133 \u03bcm per pixel) at 1 kHz. Optical Mapping recordings were acquired with software MultiRecorder and analysed with software PythonAnalyser (both developed by Research Group Biomedical Physics). Electrical s",
       "section": "Materials and methods: Optical mapping experiments on ventricular arrhythmia and its termination in the intact mouse heart"
      },
      "segment_cycles_frames": {
       "light_off": 421,
       "illuminated_arrhythmia": 52,
       "illuminated_after_termination": 452
      }
     },
     "lowpass": null,
     "polarity": -1,
     "tracking": {
      "link_px": 4.0,
      "max_gap": 5,
      "min_cycles": 1.0,
      "min_frames": 52,
      "paired_frac": 0.5,
      "pair_dist_px": 3.0
     },
     "pad_frames": 500,
     "phase_method": "angle of scipy.signal.hilbert along time, on spatially filtered signal",
     "spatial_sigma": 1.0,
     "rotor_erode_px": 3,
     "spatial_method": "scipy.ndimage.gaussian_filter per frame, mode=reflect; NaN set to 0 before filtering, non-tissue zeroed after",
     "baseline_frames": 901,
     "baseline_method": "scipy.ndimage.uniform_filter1d, mode=reflect, subtracted per pixel",
     "polarity_method": "sign of median per-pixel skew of dV/dt on baseline-corrected signal",
     "rotor_threshold": 0.9,
     "spatial_truncate": 4.0,
     "spatial_applies_to": "phase/activation only; displayed voltage is baseline-corrected only"
    },
    "criteria_status": {
     "note": null,
     "rules": [
      {
       "id": "protocol_parameter_set",
       "expert": "optical mapping analyst",
       "status": "provisional",
       "values": {
        "set_by": "developer (not a domain scientist)",
        "protocol": "Mouse whole heart optical mapping (Luther lab)",
        "protocol_id": "f65d786f-f194-4be2-88b8-10d3dd25d674",
        "params_version": 3
       },
       "decision": null,
       "location": "worker/voltage/protocol_params.py (developer_defaults, set_params)",
       "reviewed": false,
       "reviewer": null,
       "description": "Each protocol's fixed, versioned analysis parameters (version 1 = developer defaults); no run or agent may deviate",
       "reviewed_at": null
      },
      {
       "id": "baseline_window_rule",
       "expert": "optical mapping analyst",
       "status": "provisional",
       "values": {
        "ok": true,
        "factor": 2.0,
        "source": "MAP channel (DAQ log)",
        "required_min_frames": 830,
        "slowest_cycle_frames": 415
       },
       "decision": null,
       "location": "worker/voltage/baseline_rule.py (FACTOR, evaluate)",
       "reviewed": false,
       "reviewer": null,
       "description": "A run proceeds only if the protocol's baseline window is >= 2x the slowest segment's cycle, the cycle from the MAP channel when a DAQ log exists, else from per-pixel dominant frequency on linearly detrended pixels; otherwise the run is held by code",
       "reviewed_at": null
      },
      {
       "id": "filter_defaults",
       "expert": "optical mapping analyst (cardiac electrophysiology)",
       "status": "provisional",
       "values": {
        "lowpass": null,
        "spatial_sigma": 1.0,
        "baseline_frames": 901,
        "spatial_truncate": 4.0
       },
       "decision": null,
       "location": "worker/voltage/preprocess.py (Params)",
       "reviewed": false,
       "reviewer": null,
       "description": "Default baseline window (frames) and spatial Gaussian sigma/truncate for phase",
       "reviewed_at": null
      },
      {
       "id": "tissue_mask",
       "expert": "optical mapping analyst",
       "status": "provisional",
       "values": {
        "rule": "not NaN in frame 0 and nonzero std",
        "tissue_pixels": 2332
       },
       "decision": null,
       "location": "worker/voltage/io.py (tissue_mask)",
       "reviewed": false,
       "reviewer": null,
       "description": "Tissue = not NaN in frame 0 and nonzero temporal std",
       "reviewed_at": null
      },
      {
       "id": "polarity",
       "expert": "optical mapping analyst / voltage dye chemist",
       "status": "provisional",
       "values": {
        "method": "median skew of dV/dt",
        "result": -1
       },
       "decision": null,
       "location": "worker/voltage/preprocess.py (polarity)",
       "reviewed": false,
       "reviewer": null,
       "description": "Dye polarity from sign of median per-pixel skew of dV/dt",
       "reviewed_at": null
      },
      {
       "id": "singularity_detection",
       "expert": "computational cardiac electrophysiologist (phase mapping)",
       "status": "provisional",
       "values": {
        "rotor_erode_px": 3,
        "rotor_threshold": 0.9
       },
       "decision": null,
       "location": "worker/voltage/preprocess.py (Params.rotor_threshold, rotor_erode_px)",
       "reviewed": false,
       "reviewer": null,
       "description": "Phase singularity = |winding| > threshold turns, >= erode px from tissue edge",
       "reviewed_at": null
      },
      {
       "id": "rotor_persistence",
       "expert": "computational cardiac electrophysiologist (phase mapping)",
       "status": "provisional",
       "values": {
        "link_px": 4.0,
        "max_gap": 5,
        "min_cycles": 1.0,
        "min_frames": 52
       },
       "decision": null,
       "location": "worker/voltage/rotors.py (TrackParams)",
       "reviewed": false,
       "reviewer": null,
       "description": "Track linking distance/gap and minimum lifetime for a persistent rotor",
       "reviewed_at": null
      },
      {
       "id": "chirality_pairing",
       "expert": "computational cardiac electrophysiologist (phase mapping)",
       "status": "provisional",
       "values": {
        "paired_frac": 0.5,
        "pair_dist_px": 3.0
       },
       "decision": null,
       "location": "worker/voltage/rotors.py (TrackParams.pair_dist_px, paired_frac)",
       "reviewed": false,
       "reviewer": null,
       "description": "Opposite-charge singularities within pair distance are a pair; tracks paired most of their life are excluded from rotors",
       "reviewed_at": null
      },
      {
       "id": "sensitivity_grid",
       "expert": "optical mapping analyst",
       "status": "provisional",
       "values": {
        "sigmas": {
         "light": 0.5,
         "default": 1.0,
         "heavier": 2.0
        },
        "trackers": {
         "loose": [
          6.0,
          10
         ],
         "strict": [
          2.0,
          1
         ],
         "default": [
          4.0,
          5
         ]
        },
        "baselines": {
         "run": 901,
         "3x_cycle": 1356,
         "6x_cycle": 2712,
         "1.5x_cycle": 678
        }
       },
       "decision": null,
       "location": "worker/voltage/sensitivity.py (SIGMAS, BASELINE_MULTIPLES, baseline_levels)",
       "reviewed": false,
       "reviewer": null,
       "description": "Filter levels tested: spatial sigma and baseline window values",
       "reviewed_at": null
      },
      {
       "id": "analysis_window",
       "expert": "cardiac electrophysiologist familiar with the dataset",
       "status": "provisional",
       "values": {
        "f0": 500,
        "f1": 8767
       },
       "decision": null,
       "location": "worker/voltage/runs.py (default_window)",
       "reviewed": false,
       "reviewer": null,
       "description": "Frames analysed: whole recording minus one filter pad at each end (unless the plan narrows it)",
       "reviewed_at": null
      },
      {
       "id": "prior_processing_flags",
       "expert": "imaging scientist (camera acquisition and noise)",
       "status": "provisional",
       "values": {
        "flags": [
         "negative_values",
         "non_integer",
         "nan_mask_all_frames",
         "temporal_smoothing",
         "spatial_smoothing"
        ],
        "thresholds": {
         "int_frac": 0.5,
         "neg_frac": 0.01,
         "dv_autocorr": 0.5,
         "neighbour_corr": 0.8
        }
       },
       "decision": null,
       "location": "worker/voltage/inspect.py (prior_processing)",
       "reviewed": false,
       "reviewer": null,
       "description": "Thresholds for flagging depositor processing (normalization, masking, temporal/spatial smoothing)",
       "reviewed_at": null
      },
      {
       "id": "baseline_step_detection",
       "expert": "optical mapping experimentalist",
       "status": "provisional",
       "values": {
        "frames": [
         3170
        ]
       },
       "decision": null,
       "location": "worker/voltage/events.py (detect_baseline_step)",
       "reviewed": false,
       "reviewer": null,
       "description": "Baseline step = consensus upward step in tissue-mean raw baseline (cause not inferred; first misread as light onset, contradicted by the DAQ)",
       "reviewed_at": null
      },
      {
       "id": "daq_interpretation",
       "expert": "experimentalist who recorded the data (or the depositor)",
       "status": "provisional",
       "values": {
        "events": [
         "illumination_on@0",
         "arrhythmia_termination@3153",
         "illumination_off@4977"
        ]
       },
       "decision": null,
       "location": "worker/voltage/daq.py",
       "reviewed": false,
       "reviewer": null,
       "description": "DAQ channel names from depositor notebook; frames = first N triggers of closest burst; midpoint thresholds",
       "reviewed_at": null
      },
      {
       "id": "segment_definitions",
       "expert": "cardiac electrophysiologist (ideally the depositing authors)",
       "status": "provisional",
       "values": {
        "light_off": [
         4977,
         9267
        ],
        "illuminated_arrhythmia": [
         0,
         3170
        ],
        "illuminated_after_termination": [
         3170,
         4977
        ]
       },
       "decision": null,
       "location": "worker/voltage/annotations.py (MOUSE_SEGMENTS)",
       "reviewed": false,
       "reviewer": null,
       "description": "Mouse segments bounded by DAQ light events and the baseline step, interpreted as spiral termination under illumination (project lead, from Hussaini et al. 2023)",
       "reviewed_at": null
      },
      {
       "id": "rotor_finding_criterion",
       "expert": "cardiac electrophysiologist + biostatistician",
       "status": "provisional",
       "values": {
        "min_frac": 0.1,
        "min_ratio": 2.0
       },
       "decision": null,
       "location": "worker/voltage/sensitivity.py (MIN_FRAC, MIN_RATIO)",
       "reviewed": false,
       "reviewer": null,
       "description": "Singularity before/after finding holds if frac(before) >= min_frac and >= min_ratio x frac(after) at every setting (also kept, superseded, for persistent rotors)",
       "reviewed_at": null
      },
      {
       "id": "persistent_rotor_criterion",
       "expert": "cardiac electrophysiologist",
       "status": "provisional",
       "values": {
        "expect": {
         "light_off": "absent",
         "illuminated_arrhythmia": "present",
         "illuminated_after_termination": "absent"
        },
        "max_absent": 0,
        "min_present": 1,
        "spanning_rotor": "counts in every segment it overlaps",
        "min_lifetime_frames": 52
       },
       "decision": null,
       "location": "worker/voltage/sensitivity.py (MIN_ROTORS_PRESENT, MAX_ROTORS_ABSENT)",
       "reviewed": false,
       "reviewer": null,
       "description": "Persistent-rotor finding holds if every 'present' segment has >= 1 persistent rotor and every 'absent' segment has none, at every setting",
       "reviewed_at": null
      },
      {
       "id": "pipeline_check",
       "expert": "optical mapping analyst",
       "status": "provisional",
       "values": {
        "model": "openai:gpt-5.5",
        "proceed": true,
        "anomalies": [
         "Pre-deposit processing / raw-data label",
         "Event interpretation at frame 3170",
         "Baseline and illumination artifact",
         "Baseline-window rule"
        ],
        "mismatches": []
       },
       "decision": null,
       "location": "worker/agents/pipeline.py (INSTRUCTIONS, validator)",
       "reviewed": false,
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      {
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        "tolerance_frac": 0.25,
        "segment_rhythm_rule": "expected persistent rotors 'present' -> spiral arrhythmia"
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       "decision": null,
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       "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",
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      {
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       "expert": "biostatistician + optical mapping analyst",
       "status": "provisional",
       "values": {
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      "quote": "t stimulus with LI = 3.44 \u03bcW/mm2 and PL = 5 s. Fig 2C shows a monophasic action potential (MAP) signal (in black) before, during, and after illumination. It shows the sinus rhythm returns after 3190 ms of illumination. Fig 2D presents a closer look at the MAP signal of the heart during the last few rotations of arrhythmia and the first few action potentials of sinus rhythm. Fig 2E illustrates a"
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      "quote": "t stimulus with LI = 3.44 \u03bcW/mm2 and PL = 5 s. Fig 2C shows a monophasic action potential (MAP) signal (in black) before, during, and after illumination. It shows the sinus rhythm returns after 3190 ms of illumination. Fig 2D presents a closer look at the MAP signal of the heart during the last few rotations of arrhythmia and the first few action potentials of sinus rhythm. Fig 2E illustrates a"
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     "citation": {
      "ref": "10.1371/journal.pcbi.1011660",
      "quote": "t stimulus with LI = 3.44 \u03bcW/mm2 and PL = 5 s. Fig 2C shows a monophasic action potential (MAP) signal (in black) before, during, and after illumination. It shows the sinus rhythm returns after 3190 ms of illumination. Fig 2D presents a closer look at the MAP signal of the heart during the last few rotations of arrhythmia and the first few action potentials of sinus rhythm. Fig 2E illustrates a"
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     "method": "consensus upward step in running-median baseline of tissue-mean raw signal"
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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."
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    "license_as_stated": "cc-by-4.0"
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   "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)."
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  "run": {
   "id": "202e66c5-944f-4d65-bbb1-a060487247e1",
   "status": "done",
   "started_at": "2026-10-27T23:02:29.97199+00:00",
   "finished_at": "2026-10-27T23:08:06.753472+00:00",
   "code": {
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   "steps": [
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    "baseline_correct",
    "polarity",
    "spatial_filter(phase only)",
    "hilbert_phase",
    "phase_singularities",
    "track_and_pair",
    "beats_apd_cv",
    "sensitivity",
    "render"
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   "protocol_params": {
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     "max_gap": 5,
     "min_cycles": 1.0,
     "pad_frames": 500,
     "paired_frac": 0.5,
     "render_step": 4,
     "pair_dist_px": 3.0,
     "spatial_sigma": 1.0,
     "rotor_erode_px": 3,
     "baseline_frames": 901,
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    "version": 3,
    "protocol_id": "f65d786f-f194-4be2-88b8-10d3dd25d674"
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   "baseline_rule": {
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      "n_activations": 10,
      "polarity_used": -1,
      "median_interval_ms": 410.9
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     "illuminated_arrhythmia": {
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      "n_activations": 53,
      "polarity_used": -1,
      "median_interval_ms": 52.25
     },
     "illuminated_after_termination": {
      "cycle_frames": 415,
      "n_activations": 4,
      "polarity_used": -1,
      "median_interval_ms": 415.0
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    "factor": 2.0,
    "reason": null,
    "source": "MAP channel (DAQ log)",
    "status": "provisional",
    "daq_file": "0111210010.txt",
    "baseline_frames": 901,
    "slowest_segment": "illuminated_after_termination",
    "required_min_frames": 830,
    "slowest_cycle_frames": 415
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   "deposit_checks": {
    "flags": [
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      "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": {
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     "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
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    "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: depositor documentation and measurements indicate masking, temporal smoothing, spatial smoothing, and normalization. The fixed pipeline may still be run, but its Gaussian phase smoothing is added on top of prior filtering of unknown effective total, and any interpretation requiring independent pixel noise or raw photon-count amplitudes would be misleading."
     },
     {
      "topic": "Event interpretation at frame 3170",
      "severity": "warn",
      "effect_on_analysis": "The segment boundary at frame 3170 is based on a provisional termination/baseline-step interpretation, not a directly measured light onset. The fixed segment definitions can be analysed as defined, but results should be described relative to the provisional boundary and not as an illumination-on transition."
     },
     {
      "topic": "Baseline and illumination artifact",
      "severity": "warn",
      "effect_on_analysis": "Blue-light crosstalk, re-normalization by stimulation-light signal, a large slow baseline range, and a baseline step can affect absolute baseline and amplitude. The fixed phase/rotor pipeline can proceed, but baseline- or amplitude-dependent interpretations need caution."
     },
     {
      "topic": "Baseline-window rule",
      "severity": "info",
      "effect_on_analysis": "The coded rule reports ok: the 901-frame baseline is at least 2 times the slowest segment cycle from the MAP-channel DAQ log, so this rule does not hold the run."
     }
    ],
    "rationale": "The protocol is the intended mouse whole-heart optical-mapping protocol for this public reference recording, and the recording facts do not conflict with the protocol: the frame rate is 1000 Hz from the publication, the pixel size is 133 \u00b5m from the publication, and the 64 \u00d7 55 deposited movie is consistent with a cropped version of the 64 \u00d7 64 camera acquisition. The fixed version-3 parameters are therefore applicable as provisional pipeline settings, and the coded baseline-window rule passes for the slowest segment. The main limitations are not protocol mismatches but interpretation caveats: the deposited data are already masked, smoothed, and normalized; frame 3170 is a provisional termination/baseline-step boundary rather than light onset; and illumination/crosstalk/normalization affect baseline and amplitude.",
    "mismatches": [],
    "hold_reason": null,
    "protocol_id": "f65d786f-f194-4be2-88b8-10d3dd25d674",
    "methods_text": "Using the provisional parameter set version 3, with provisional segment definitions and provisional criteria, the recording was checked under the Mouse whole heart optical mapping (Luther lab) protocol with baseline_frames = 901, spatial_sigma = 1.0, spatial_truncate = 4.0, pad_frames = 500, rotor_threshold = 0.9, rotor_erode_px = 3, link_px = 4.0, max_gap = 5, min_cycles = 1.0, pair_dist_px = 3.0, paired_frac = 0.5, and render_step = 4. The recording has 9267 frames in npy format with image size 64 \u00d7 55, frame rate 1000 Hz from the publication, and pixel size 133 \u00b5m from the publication. The analysed window is frames 500\u20138767; the provisional segments are illuminated_arrhythmia, frames 0\u20133170; illuminated_after_termination, frames 3170\u20134977; and light_off, frames 4977\u20139267.",
    "recording_id": "55cb4aa3-6502-45a6-a14c-85cb676fe8c3",
    "params_version": 3,
    "prompt_version": "pipeline-v2"
   }
  },
  "signature": {
   "id": "6ed9c8e5-4bef-4549-b04f-f5014db32b5b",
   "created_at": "2026-10-27T23:08:06.969496+00:00",
   "movie_path": "runs/202e66c5-944f-4d65-bbb1-a060487247e1/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": {
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     "f1": 8767,
     "segments": [
      {
       "name": "illuminated_arrhythmia",
       "label": "illumination with arrhythmia",
       "defined": [
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        3170
       ],
       "analysed": [
        500,
        3170
       ],
       "citation": {
        "ref": "10.1371/journal.pcbi.1011660",
        "quote": "t stimulus with LI = 3.44 \u03bcW/mm2 and PL = 5 s. Fig 2C shows a monophasic action potential (MAP) signal (in black) before, during, and after illumination. It shows the sinus rhythm returns after 3190 ms of illumination. Fig 2D presents a closer look at the MAP signal of the heart during the last few rotations of arrhythmia and the first few action potentials of sinus rhythm. Fig 2E illustrates a"
       },
       "defined_by": "project lead (not a domain scientist), following the paper's design",
       "segment_id": "f6ca0bce-f7e9-437d-84b6-1bb1b24f80ba",
       "end_event_id": "46c59a51-1a01-4aed-8021-db9a63720a1d",
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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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        "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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      "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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}