rt106SpecificAdaptorDefinitions.json

{
  "name" : "whole-cell-segmentation",
  "version" : "v1_0_0",
  "queue" : "whole-cell-segmentation--v1_0_0",
  "parameters" : {
    "slide" : {
      "label" : "Slide Name",
      "description" : "The slide being analyzed.",
      "type" : "string",
      "default" : ""
    },
    "region" : {
      "label" : "Region",
      "description" : "The region being analyzed.",
      "type" : "string",
      "default" : ""
    },
    "branch" : {
      "label" : "Analysis Container",
      "description" : "Tag for analysis results.",
      "type" : "string",
      "default" : "templateAnalysis"
    },
    "channel" : {
      "label" : "Cell Channel",
      "description" : "Channel to use for whole-cell segmentation.",
      "type" : "string",
      "default" : ""
    },
    "force" : {
      "label" : "Force",
      "description" : "Whether to force an overwrite",
      "type" : "boolean",
      "default" : false
    },
    "dapi_channel" : {
      "label" : "Nuclei Channel",
      "description" : "Nuclei channel to use for whole-cell segmentation.",
      "type" : "string",
      "default" : "DAPI"
    },
    "minLevel" : {
      "label" : "Min Level",
      "description" : "",
      "type" : "number",
      "default" : 4
    },
    "maxLevel" : {
      "label" : "Max Level",
      "description" : "",
      "type" : "number",
      "default" : 5
    },
    "smoothingSigma" : {
      "label" : "Smoothing Sigma",
      "description" : "",
      "type" : "number",
      "default" : 1
    },
    "maxCytoplasmThickness" : {
      "label" : "Max Cytoplasm Thickness",
      "description" : "",
      "type" : "number",
      "default" : 3
    },
    "cellSegSensitivity" : {
      "label" : "Cell Segmentation Sensitivity",
      "description" : "",
      "type" : "number",
      "default" : 2
    },
    "required" : ["slide", "region", "branch", "force", "dapi_channel", "minLevel", "maxLevel", "smoothingSigma", "maxCytoplasmThickness"]
  },
  "results" : {
    "nucleiImage" : {
      "label" : "Nuclei Image",
      "description" : "Input URI to nucleus-stained image",
      "type" : "pathologyImage",
      "value" : "slide/region/source/DAPI"
    },
    "cellImage" : {
      "label" : "Cell Image",
      "description" : "Input URI to image stained for a cell (cytoplasm) marker",
      "type" : "pathologyImage",
      "value" : "slide/region/source/channel"
    },
    "nucleiMap" : {
      "label" : "Nuclei Label Map",
      "description" : "Label map showing nuclei regions",
      "type" : "pathologyImage",
      "value" : "slide/region/branch/NucSeg"
    },
    "cellMap" : {
      "label" : "Cell Label Map",
      "description" : "Label map showing cellular regions",
      "type" : "pathologyImage",
      "value" : "slide/region/branch/CellSeg"
    }
  },
  "result_display" : {
    "grid" : {
      "shape" : [1,1],
      "columns" : [1.0],
      "rows" : [1.0]
    },
    "cells" : [
      {
        "column" : 0,
        "row" : 0,
        "cellType" : "pathologyImage",
        "source" : "result",
        "parameter" : "nucleiImage"
      },
      {
        "column": 0,
        "row": 0,
        "cellType": "pathologyImage",
        "source": "result",
        "parameter": "nucleiMap",
        "imageProcessing" : "toBinaryImage",
        "properties" : {
          "color" : "rgb(255,51,51)"
        },
        "controls": {
          "opacity": "Mask Opacity: ",
          "color": "Mask Color: "
        }
      }
    ]
  },
  "api" : {
    "context" : "none"
  },
  "doc" : {
    "short" : "A short bit of documentation",
    "full" : "Full documentation"
  },
  "classification" : "segmentation/cell"
}