{
  "schemaVersion": 4,
  "key": "EV_IN_CELL_DETECTION",
  "meta": {
    "name": "EV in cell detection",
    "shortDescription": "EV in cell detection",
    "description": "Detects extracellular vesicles inside cells using median background subtraction, blurring, Li thresholding and watershed splitting. The class the objects get is the module's \"EVs in cells\" parameter.",
    "authors": [
      {
        "fullName": "Melanie Schuerz",
        "organization": "University of Salzburg"
      }
    ],
    "creationTime": "2026-10-20T17:24:51.268492007Z",
    "version": 2,
    "category": "Spot Detection",
    "tags": [
      "spot"
    ],
    "appVersion": "0.1.0"
  },
  "classes": [],
  "steps": [
    {
      "id": 1,
      "enabled": true,
      "command": {
        "type": "MEDIAN_SUBTRACT",
        "radius": 3.0
      }
    },
    {
      "id": 2,
      "enabled": true,
      "command": {
        "type": "BLUR",
        "kernelSize": 3
      }
    },
    {
      "id": 3,
      "enabled": true,
      "command": {
        "type": "THRESHOLD",
        "thresholds": [
          {
            "method": {
              "type": "LI"
            },
            "minThreshold": 0.0,
            "maxThreshold": 65535.0,
            "unit": "BIT",
            "segmentationClass": 3,
            "valueSource": "ACTUAL_IMAGE"
          }
        ]
      }
    },
    {
      "id": 4,
      "enabled": true,
      "command": {
        "type": "CONNECTED_COMPONENTS",
        "minSize": 0
      }
    },
    {
      "id": 5,
      "enabled": true,
      "command": {
        "type": "WATERSHED",
        "maximumFinderTolerance": 0.5,
        "smoothingSigma": 0.0,
        "minObjectSize": 0,
        "seedSource": "DISTANCE_MAP"
      }
    },
    {
      "id": 6,
      "enabled": true,
      "command": {
        "type": "EXTRACT_OBJECTS",
        "maxObjectsBeforeFail": 100000,
        "classMapping": [
          {
            "segmentationClass": 3,
            "objectClass": {
              "GLOBAL": 3
            }
          }
        ]
      }
    },
    {
      "id": 7,
      "enabled": true,
      "command": {
        "type": "CLASSIFY_OBJECTS",
        "originSegmentation": [],
        "inputClasses": [
          {
            "GLOBAL": 3
          }
        ],
        "matchHandling": "REMOVE_ALL_CLASSES_IF_NOT_MATCH",
        "outputClass": "UNSET",
        "overlappingWith": "UNSET",
        "minIntersectionArea": 0.0,
        "sizeUnit": "PIXELS",
        "minArea": 3.0,
        "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": true,
        "intensityFilters": []
      }
    }
  ],
  "parameters": [
    {
      "key": "evs_in_cells",
      "label": "EVs in cells",
      "description": "",
      "section": "Classes",
      "default": "3",
      "bindings": [
        {
          "step": 6,
          "param": "class_mapping.0.object_class"
        },
        {
          "step": 7,
          "param": "input_classes"
        }
      ]
    },
    {
      "key": "threshold_method",
      "label": "Threshold method",
      "description": "",
      "section": "Detection",
      "default": "Li",
      "bindings": [
        {
          "step": 3,
          "param": "thresholds.0.method"
        }
      ]
    },
    {
      "key": "min_threshold",
      "label": "Min threshold",
      "description": "",
      "section": "Detection",
      "default": 0,
      "bindings": [
        {
          "step": 3,
          "param": "thresholds.0.min_threshold"
        }
      ]
    },
    {
      "key": "min_area",
      "label": "Min area",
      "description": "",
      "section": "Filter",
      "default": 3,
      "bindings": [
        {
          "step": 7,
          "param": "min_area"
        }
      ]
    },
    {
      "key": "max_area",
      "label": "Max area",
      "description": "",
      "section": "Filter",
      "default": 2147483600,
      "bindings": [
        {
          "step": 7,
          "param": "max_area"
        }
      ]
    },
    {
      "key": "size_unit",
      "label": "Size unit",
      "description": "",
      "section": "Filter",
      "default": "px",
      "bindings": [
        {
          "step": 7,
          "param": "size_unit"
        }
      ]
    }
  ],
  "uses": []
}