{
  "schemaVersion": 2,
  "meta": {
    "name": "Example Colocalization",
    "shortDescription": "Ported from CellProfiler ExampleColocalization pipeline",
    "description": "Two-channel spot colocalization (Cy3-like / Cy5-like nucleosome staining). Ported from the CellProfiler ExampleColocalization.cppipe example. Channel 0 = OrigStain1 (files *_N_R), Channel 1 = OrigStain2 (files *_N_G), merged into one 2-channel TIFF per site via Fiji. Object counts run ~10-15% off CP and coloc% ~5pt high, mainly because evanalyzer's watershed declumping (prominence-based) splits touching spots differently than CP's fixed-radius local-maxima method, and evanalyzer's illumination correction averages over blocks before fitting (more robust to bright spots) instead of fitting the raw pixels directly like CP does.",
    "authors": ["Jeff Reifenberger","Brad Berstein's"],
    "authorOrganization": "Massachusetts General Hospital",
    "creationTime": "2026-08-23T00:00:00Z",
    "category": "Colocalization",
    "tags": [
      "colocalization",
      "spots",
      "2-channel",
      "cellprofiler"
    ],
    "appVersion": "0.1.0"
  },
  "classification": {
    "classes": [
      {
        "id": {
          "VALID": 0
        },
        "color": "#97978f",
        "name": "Background",
        "notes": ""
      },
      {
        "id": {
          "VALID": 1
        },
        "color": "#FF3333",
        "name": "ch1@spot",
        "notes": "Objects1 in CP pipeline (Stain1 / *_N_R channel)"
      },
      {
        "id": {
          "VALID": 2
        },
        "color": "#33CC33",
        "name": "ch2@spot",
        "notes": "Objects2 in CP pipeline (Stain2 / *_N_G channel)"
      },
      {
        "id": {
          "VALID": 3
        },
        "color": "#9933FF",
        "name": "ch1-ch2@coloc",
        "notes": "Overlap area between ch1@spot and ch2@spot"
      }
    ]
  },
  "plate": {
    "groupingMode": "NO_GROUPING",
    "groupingRegex": "",
    "plateCols": 1,
    "plateRows": 1,
    "wellCols": 4,
    "wellRows": 4,
    "wellImageOrder": [
      1,
      2,
      3,
      4,
      5,
      6,
      7,
      8,
      9,
      10,
      11,
      12,
      13,
      14,
      15,
      16
    ]
  },
  "pipelines": [
    {
      "id": 1,
      "name": "ch1 spots",
      "imageSource": {
        "channel": 0
      },
      "enabled": true,
      "steps": [
        {
          "enabled": true,
          "command": {
            "type": "ILLUMINATION_CORRECTION",
            "applyMethod": "DIVIDE",
            "blockSize": 60,
            "method": "REGULAR",
            "rescale": false,
            "smoothing": {
              "type": "FIT_POLYNOMIAL"
            }
          }
        },
        {
          "enabled": true,
          "command": {
            "type": "BLUR",
            "kernelSize": 3
          }
        },
        {
          "enabled": true,
          "command": {
            "type": "THRESHOLD",
            "thresholds": [
              {
                "method": {
                  "type": "OTSU",
                  "classes": {
                    "type": "THREE",
                    "middleClass": "BACKGROUND"
                  }
                },
                "minThreshold": 100.0,
                "maxThreshold": 65535.0,
                "unit": "BIT",
                "objectClassId": 1,
                "valueSource": "ACTUAL_IMAGE"
              }
            ]
          }
        },
        {
          "enabled": true,
          "command": {
            "type": "WATERSHED",
            "maximumFinderTolerance": 0.5,
            "smoothingSigma": 0.0,
            "minObjectSize": 0
          }
        },
        {
          "enabled": true,
          "command": {
            "type": "CONNECTED_COMPONENTS"
          }
        },
        {
          "enabled": true,
          "command": {
            "type": "EXTRACT_OBJECTS",
            "maxObjectsBeforeFail": 100000
          }
        },
        {
          "enabled": true,
          "command": {
            "type": "CLASSIFY_OBJECTS",
            "originSegmentation": [],
            "inputClasses": [
              {
                "VALID": 1
              }
            ],
            "matchHandling": "REMOVE_ALL_CLASSES_IF_NOT_MATCH",
            "outputClass": "UNSET",
            "overlappingWith": "UNSET",
            "minIntersectionArea": 0.0,
            "sizeUnit": "PIXELS",
            "minArea": 9.0,
            "maxArea": 177.0,
            "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
          }
        }
      ]
    },
    {
      "id": 2,
      "name": "ch2 spots",
      "imageSource": {
        "channel": 1
      },
      "enabled": true,
      "steps": [
        {
          "enabled": true,
          "command": {
            "type": "ILLUMINATION_CORRECTION",
            "applyMethod": "DIVIDE",
            "blockSize": 60,
            "method": "REGULAR",
            "rescale": false,
            "smoothing": {
              "type": "FIT_POLYNOMIAL"
            }
          }
        },
        {
          "enabled": true,
          "command": {
            "type": "BLUR",
            "kernelSize": 3
          }
        },
        {
          "enabled": true,
          "command": {
            "type": "THRESHOLD",
            "thresholds": [
              {
                "method": {
                  "type": "OTSU",
                  "classes": {
                    "type": "THREE",
                    "middleClass": "BACKGROUND"
                  }
                },
                "minThreshold": 100.0,
                "maxThreshold": 65535.0,
                "unit": "BIT",
                "objectClassId": 2,
                "valueSource": "ACTUAL_IMAGE"
              }
            ]
          }
        },
        {
          "enabled": true,
          "command": {
            "type": "WATERSHED",
            "maximumFinderTolerance": 0.5,
            "smoothingSigma": 0.0,
            "minObjectSize": 0
          }
        },
        {
          "enabled": true,
          "command": {
            "type": "CONNECTED_COMPONENTS"
          }
        },
        {
          "enabled": true,
          "command": {
            "type": "EXTRACT_OBJECTS",
            "maxObjectsBeforeFail": 100000
          }
        },
        {
          "enabled": true,
          "command": {
            "type": "CLASSIFY_OBJECTS",
            "originSegmentation": [],
            "inputClasses": [
              {
                "VALID": 2
              }
            ],
            "matchHandling": "REMOVE_ALL_CLASSES_IF_NOT_MATCH",
            "outputClass": "UNSET",
            "overlappingWith": "UNSET",
            "minIntersectionArea": 0.0,
            "sizeUnit": "PIXELS",
            "minArea": 10.0,
            "maxArea": 177.0,
            "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
          }
        }
      ]
    },
    {
      "id": 3,
      "name": "Coloc",
      "imageSource": "SCRATCHPAD",
      "enabled": true,
      "steps": [
        {
          "enabled": true,
          "command": {
            "type": "COLOCALIZATION",
            "classesToColoc": [
              {
                "VALID": 1
              },
              {
                "VALID": 2
              }
            ],
            "filterClasses": [],
            "classForOverlappingAreas": {
              "VALID": 3
            },
            "multiplicity": "ONE_TO_ONE",
            "sizeUnit": "PIXELS",
            "minColocArea": 0.0
          }
        }
      ]
    }
  ]
}