{
  "schemaVersion": 4,
  "meta": {
    "name": "Example Track Objects",
    "shortDescription": "Ported from CellProfiler ExampleTrackObjects pipeline",
    "description": "Drosophila embryo GFP-histone time-lapse: segment embryos per frame and track them. Ported from the CellProfiler ExampleTrackObjects.cppipe example. Input: images/SequenceN.tif, one gray 21-frame time stack per sequence, built with Fiji from the RGB frames as (R+G+B)/3 (= CP ColorToGray 'Combine', equal weights); each sequence is its own image, which replaces CP's per-folder grouping. Embryos = CP IdentifyPrimaryObjects: Gaussian sigma 1 (CP threshold smoothing scale 1.3488), 2-class Otsu computed on the raw image (lower bound 0.01), fill holes, intensity-seeded watershed with CP's automatic declumping values (seed smoothing sigma 7.14, maxima suppression 16.7 px; CP's low-resolution speed-up is not reproduced), minimum equivalent diameter 25 px (area >= 491 px), border objects discarded. Tracking: SIMPLE_TRACKER (nearest neighbour, max 50 px) instead of CP's Overlap method. Result vs CP: objects 63/120/115 vs 65/119/109 per sequence, every CP object matched within 15 px in Seq1/Seq3 and 116/119 in Seq2, median per-object area ratio 0.99-1.00. Tracks: Seq1 3 vs 4 (CP's extra one is a one-frame object), Seq3 7 vs 7; Seq2 10 vs 6 because CP's Overlap gives both daughters of a dividing embryo the parent's label, whereas nearest-neighbour tracking continues the parent in one daughter and starts a new track for the other, plus one frame (t=4) where two touching embryos are merged. Track data: `evanalyzer cli export csv --group-by track --class Embryos` gives a time course per track (area, shape, intensity per frame); the per-object export has T and Track ID columns. CP's per-track motion measurements (Displacement, IntegratedDistance, Linearity) are not computed by evanalyzer; they can be derived from the centroids in `export parquet` and then agree with CP for tracks without a division (e.g. Seq3 displacement 35.8/43.2/51.8/59.1 px CP vs 34.7/42.8/50.5/59.1 px eva).",
    "authors": [
      {
        "fullName": "Victoria Foe",
        "organization": ""
      },
      {
        "fullName": "G. Odell",
        "organization": ""
      },
      {
        "fullName": "Rob Saint",
        "organization": ""
      }
    ],
    "creationTime": "2026-10-21T00:00:00Z",
    "category": "Tracking",
    "tags": [
      "tracking",
      "time-lapse",
      "drosophila",
      "cellprofiler"
    ],
    "appVersion": "0.1.0"
  },
  "classification": {
    "classes": [
      {
        "id": 0,
        "color": "#97978f",
        "name": "Background",
        "notes": ""
      },
      {
        "id": 1,
        "color": "#3357ff",
        "name": "Embryos",
        "notes": "Embryos in CP pipeline (IdentifyPrimaryObjects on the gray histone image), tracked over time"
      }
    ]
  },
  "plate": {
    "groupingMode": "AUTO",
    "groupingRegex": "",
    "plateSize": "AUTO",
    "wellLayout": {
      "FIXED": {
        "rows": 1,
        "cols": 1
      }
    },
    "wellImageOrder": [
      1
    ]
  },
  "pipelines": [
    {
      "id": 1,
      "name": "Embryos",
      "description": null,
      "imageSource": {
        "channel": 0
      },
      "enabled": true,
      "steps": [
        {
          "id": 1,
          "enabled": true,
          "command": {
            "type": "GAUSSIAN_BLUR",
            "kernelSize": 7,
            "sigma": 1.0
          }
        },
        {
          "id": 2,
          "enabled": true,
          "command": {
            "type": "THRESHOLD",
            "thresholds": [
              {
                "method": {
                  "type": "OTSU",
                  "classes": {
                    "type": "TWO"
                  }
                },
                "minThreshold": 2.55,
                "maxThreshold": 65535.0,
                "unit": "BIT",
                "segmentationClass": 1,
                "valueSource": "RAW_IMAGE"
              }
            ]
          }
        },
        {
          "id": 3,
          "enabled": true,
          "command": {
            "type": "FILL_HOLES"
          }
        },
        {
          "id": 4,
          "enabled": true,
          "command": {
            "type": "CONNECTED_COMPONENTS",
            "minSize": 1
          }
        },
        {
          "id": 5,
          "enabled": true,
          "command": {
            "type": "WATERSHED",
            "maximumFinderTolerance": 16.7,
            "smoothingSigma": 7.14,
            "minObjectSize": 0,
            "seedSource": "INTENSITY"
          }
        },
        {
          "id": 6,
          "enabled": true,
          "command": {
            "type": "FILL_OBJECT_HOLES"
          }
        },
        {
          "id": 7,
          "enabled": true,
          "command": {
            "type": "EXTRACT_OBJECTS",
            "maxObjectsBeforeFail": 100000,
            "classMapping": [
              {
                "segmentationClass": 1,
                "objectClass": {
                  "GLOBAL": 1
                }
              }
            ]
          }
        },
        {
          "id": 8,
          "enabled": true,
          "command": {
            "type": "CLASSIFY_OBJECTS",
            "originSegmentation": [],
            "inputClasses": [
              {
                "GLOBAL": 1
              }
            ],
            "matchHandling": "REMOVE_ALL_CLASSES_IF_NOT_MATCH",
            "outputClass": "UNSET",
            "overlappingWith": "UNSET",
            "minIntersectionArea": 0.0,
            "sizeUnit": "PIXELS",
            "minArea": 491.0,
            "maxArea": 2147483600.0,
            "minCircularity": 0.0,
            "maxCircularity": 1.0,
            "minSolidity": 0.0,
            "maxSolidity": 1.0,
            "minAspectRatio": 0.0,
            "maxAspectRatio": 2147483600.0,
            "minEccentricity": 0.0,
            "maxEccentricity": 1.0,
            "minFeret": 0.0,
            "maxFeret": 2147483600.0,
            "allowEdgeTouching": false,
            "intensityFilters": []
          }
        }
      ]
    },
    {
      "id": 2,
      "name": "Track embryos",
      "description": null,
      "imageSource": "SCRATCHPAD",
      "enabled": true,
      "steps": [
        {
          "id": 1,
          "enabled": true,
          "command": {
            "type": "SIMPLE_TRACKER",
            "objectClass": {
              "GLOBAL": 1
            },
            "unit": "PIXELS",
            "maxDistance": 50.0
          }
        }
      ]
    }
  ],
  "modules": []
}