{
  "schemaVersion": 4,
  "key": "YEAST_CELLS_BRIGHTFIELD",
  "meta": {
    "name": "Yeast cells brightfield",
    "shortDescription": "Yeast cells brightfield",
    "description": "Segments yeast cells from a brightfield image using contrast enhancement, Gaussian blur, Canny edge detection, manual thresholding and a Voronoi tessellation around detected cell centers. The class the cells get is the module's \"Yeast cells\" parameter. The Hough-transform cell-center detection of the original pipeline is approximated by Connected Components on the thresholded edges; the detected objects (the component's own class \"Cell centers\") are used as Voronoi centers.",
    "authors": [
      {
        "fullName": "Melanie Schuerz",
        "organization": "University of Salzburg"
      }
    ],
    "creationTime": "2026-06-11T00:00:00Z",
    "version": 1,
    "category": "",
    "tags": [],
    "appVersion": "0.1.0"
  },
  "classes": [
    {
      "id": 1,
      "color": "#bfbfbf",
      "name": "Cell centers",
      "notes": ""
    }
  ],
  "steps": [
    {
      "id": 1,
      "enabled": true,
      "command": {
        "type": "INTENSITY_TRANSFORMATION",
        "mode": "MANUAL",
        "contrast": 0.8,
        "brightness": 0.0
      }
    },
    {
      "id": 2,
      "enabled": true,
      "command": {
        "type": "GAUSSIAN_BLUR",
        "kernelSize": 5,
        "sigma": 1.0
      }
    },
    {
      "id": 3,
      "enabled": true,
      "command": {
        "type": "EDGE_DETECTION_CANNY",
        "kernelSize": 3,
        "thresholdMin": 0.019607844,
        "thresholdMax": 0.23529412
      }
    },
    {
      "id": 4,
      "enabled": true,
      "command": {
        "type": "THRESHOLD",
        "thresholds": [
          {
            "method": {
              "type": "MANUAL"
            },
            "minThreshold": 4000.0,
            "maxThreshold": 65535.0,
            "unit": "BIT",
            "segmentationClass": 1,
            "valueSource": "ACTUAL_IMAGE"
          }
        ]
      }
    },
    {
      "id": 5,
      "enabled": true,
      "command": {
        "type": "CONNECTED_COMPONENTS",
        "minSize": 0
      }
    },
    {
      "id": 6,
      "enabled": true,
      "command": {
        "type": "EXTRACT_OBJECTS",
        "maxObjectsBeforeFail": 100000,
        "classMapping": [
          {
            "segmentationClass": 1,
            "objectClass": {
              "LOCAL": 1
            }
          }
        ]
      }
    },
    {
      "id": 7,
      "enabled": true,
      "command": {
        "type": "VORONOI",
        "centers": {
          "LOCAL": 1
        },
        "centerFilterClasses": [],
        "mask": "UNSET",
        "maskFilterClasses": [],
        "outputClass": {
          "GLOBAL": 4
        },
        "unit": "PIXELS",
        "maxRadius": 30.0,
        "excludeAreasAtTheEdges": false,
        "excludeAreasWithNoCenter": false
      }
    }
  ],
  "parameters": [
    {
      "key": "yeast_cells",
      "label": "Yeast cells",
      "description": "",
      "section": "Classes",
      "default": "4",
      "bindings": [
        {
          "step": 7,
          "param": "output_class"
        }
      ]
    },
    {
      "key": "edge_threshold",
      "label": "Edge threshold",
      "description": "",
      "section": "Detection",
      "default": 4000,
      "bindings": [
        {
          "step": 4,
          "param": "thresholds.0.min_threshold"
        }
      ]
    },
    {
      "key": "max_cell_radius",
      "label": "Max cell radius",
      "description": "",
      "section": "Detection",
      "default": 30,
      "bindings": [
        {
          "step": 7,
          "param": "max_radius"
        }
      ]
    },
    {
      "key": "radius_unit",
      "label": "Radius unit",
      "description": "",
      "section": "Detection",
      "default": "px",
      "bindings": [
        {
          "step": 7,
          "param": "unit"
        }
      ]
    }
  ],
  "uses": []
}