plugin.json

{
  "name": "Nyxus",
  "version": "0.11.0",
  "containerId": "polusai/nyxus:0.11.0",
  "title": "Nyxus feature extraction",
  "description": "Nyxus feature extractor",
  "author": "friskluft + hsidky",
  "institution": "Axle Informatics",
  "repository": "https://github.com/PolusAI/nyxus",
  "website": "https://github.com/PolusAI/nyxus",
  "citation": "",
  "inputs": [
    {
      "name": "segDir",
      "description": "Labeled image collection",
      "type": "collection",
      "options": null,
      "required": true
    },
    {
      "name": "intDir",
      "description": "Intensity image collection",
      "type": "collection",
      "options": null,
      "required": true
    },
    {
      "name": "filePattern",
      "description": "Regular expression to filter file names. Examples: (1) all the files - .* (2) files ending in c0.ome.tif - .*c0\\.ome\\.tif",
      "type": "string",
      "options": null,
      "required": true
    },
    {
      "name": "pixelDistance",
      "description": "Pixel distance to calculate the neighbors touching cells",
      "type": "integer",
      "options": null,
      "required": false
    },
    {
      "name": "features",
      "description": "Select features for extraction",
      "type": "array",
      "options": {
        "items": {
          "type": "string",
          "title": "Select feature",
          "oneOf": [
            {
              "description": "All",
              "enum": [
                "*ALL*"
              ]
            },
            {
              "description": "ALL_INTENSITY",
              "enum": [
                "*ALL_INTENSITY*"
              ]
            },
            {
              "description": "ALL_MORPHOLOGY",
              "enum": [
                "*ALL_MORPHOLOGY*"
              ]
            },
            {
              "description": "BASIC_MORPHOLOGY (BBOX_YMIN, BBOX_XMIN, BBOX_HEIGHT, BBOX_WIDTH, AREA_PIXELS_COUNT, CENTROID_X, CENTROID_Y)",
              "enum": [
                "*BASIC_MORPHOLOGY*"
              ]
            },
            {
              "description": "ALL_GLCM",
              "enum": [
                "*ALL_GLCM*"
              ]
            },
            {
              "description": "ALL_GLRLM",
              "enum": [
                "*ALL_GLRLM*"
              ]
            },
            {
              "description": "ALL_GLSZM",
              "enum": [
                "*ALL_GLSZM*"
              ]
            },
            {
              "description": "ALL_GLDM",
              "enum": [
                "*ALL_GLDM*"
              ]
            },
            {
              "description": "ALL_NGTDM",
              "enum": [
                "*ALL_NGTDM*"
              ]
            },
            {
              "description": "MEAN",
              "enum": [
                "MEAN"
              ]
            },
            {
              "description": "MEDIAN",
              "enum": [
                "MEDIAN"
              ]
            },
            {
              "description": "MIN",
              "enum": [
                "MIN"
              ]
            },
            {
              "description": "MAX",
              "enum": [
                "MAX"
              ]
            },
            {
              "description": "RANGE",
              "enum": [
                "RANGE"
              ]
            },
            {
              "description": "STANDARD_DEVIATION",
              "enum": [
                "STANDARD_DEVIATION"
              ]
            },
            {
              "description": "SKEWNESS",
              "enum": [
                "SKEWNESS"
              ]
            },
            {
              "description": "KURTOSIS",
              "enum": [
                "KURTOSIS"
              ]
            },
            {
              "description": "MEAN_ABSOLUTE_DEVIATION",
              "enum": [
                "MEAN_ABSOLUTE_DEVIATION"
              ]
            },
            {
              "description": "ENERGY",
              "enum": [
                "ENERGY"
              ]
            },
            {
              "description": "ROOT_MEAN_SQUARED",
              "enum": [
                "ROOT_MEAN_SQUARED"
              ]
            },
            {
              "description": "ENTROPY",
              "enum": [
                "ENTROPY"
              ]
            },
            {
              "description": "MODE",
              "enum": [
                "MODE"
              ]
            },
            {
              "description": "UNIFORMITY",
              "enum": [
                "UNIFORMITY"
              ]
            },
            {
              "description": "P10",
              "enum": [
                "P10"
              ]
            },
            {
              "description": "P25",
              "enum": [
                "P25"
              ]
            },
            {
              "description": "P75",
              "enum": [
                "P75"
              ]
            },
            {
              "description": "P90",
              "enum": [
                "P90"
              ]
            },
            {
              "description": "INTERQUARTILE_RANGE",
              "enum": [
                "INTERQUARTILE_RANGE"
              ]
            },
            {
              "description": "ROBUST_MEAN_ABSOLUTE_DEVIATION",
              "enum": [
                "ROBUST_MEAN_ABSOLUTE_DEVIATION"
              ]
            },
            {
              "description": "WEIGHTED_CENTROID_Y",
              "enum": [
                "WEIGHTED_CENTROID_Y"
              ]
            },
            { "description": "WEIGHTED_CENTROID_X", "enum": ["WEIGHTED_CENTROID_X"] },
            { "description": "AREA_PIXELS_COUNT", "enum": ["AREA_PIXELS_COUNT"] },
            { "description": "AREA_UM2", "enum": ["AREA_UM2"] },
            {
              "description": "CENTROID_X",
              "enum": [
                "CENTROID_X"
              ]
            },
            {
              "description": "CENTROID_Y",
              "enum": [
                "CENTROID_Y"
              ]
            },
            {
              "description": "BBOX_YMIN",
              "enum": [
                "BBOX_YMIN"
              ]
            },
            {
              "description": "BBOX_XMIN",
              "enum": [
                "BBOX_XMIN"
              ]
            },
            {
              "description": "BBOX_HEIGHT",
              "enum": [
                "BBOX_HEIGHT"
              ]
            },
            {
              "description": "BBOX_WIDTH",
              "enum": [
                "BBOX_WIDTH"
              ]
            },
            {
              "description": "MAJOR_AXIS_LENGTH",
              "enum": [
                "MAJOR_AXIS_LENGTH"
              ]
            },
            {
              "description": "MINOR_AXIS_LENGTH",
              "enum": [
                "MINOR_AXIS_LENGTH"
              ]
            },
            {
              "description": "ECCENTRICITY",
              "enum": [
                "ECCENTRICITY"
              ]
            },
            {
              "description": "ORIENTATION",
              "enum": [
                "ORIENTATION"
              ]
            },
            {
              "description": "NUM_NEIGHBORS",
              "enum": [
                "NUM_NEIGHBORS"
              ]
            },
            {
              "description": "EXTENT",
              "enum": [
                "EXTENT"
              ]
            },
            {
              "description": "ASPECT_RATIO",
              "enum": [
                "ASPECT_RATIO"
              ]
            },
            {
              "description": "CONVEX_HULL_AREA",
              "enum": [
                "CONVEX_HULL_AREA"
              ]
            },
            {
              "description": "SOLIDITY",
              "enum": [
                "SOLIDITY"
              ]
            },
            {
              "description": "PERIMETER",
              "enum": [
                "PERIMETER"
              ]
            },
            {
              "description": "CIRCULARITY",
              "enum": [
                "CIRCULARITY"
              ]
            },
            {
              "description": "EXTREMA_P1_X",
              "enum": [
                "EXTREMA_P1_X"
              ]
            },
            {
              "description": "EXTREMA_P1_Y",
              "enum": [
                "EXTREMA_P1_Y"
              ]
            },
            {
              "description": "EXTREMA_P2_X",
              "enum": [
                "EXTREMA_P2_X"
              ]
            },
            {
              "description": "EXTREMA_P2_Y",
              "enum": [
                "EXTREMA_P2_Y"
              ]
            },
            {
              "description": "EXTREMA_P3_X",
              "enum": [
                "EXTREMA_P3_X"
              ]
            },
            {
              "description": "EXTREMA_P3_Y",
              "enum": [
                "EXTREMA_P3_Y"
              ]
            },
            {
              "description": "EXTREMA_P4_X",
              "enum": [
                "EXTREMA_P4_X"
              ]
            },
            {
              "description": "EXTREMA_P4_Y",
              "enum": [
                "EXTREMA_P4_Y"
              ]
            },
            {
              "description": "EXTREMA_P5_X",
              "enum": [
                "EXTREMA_P5_X"
              ]
            },
            {
              "description": "EXTREMA_P5_Y",
              "enum": [
                "EXTREMA_P5_Y"
              ]
            },
            {
              "description": "EXTREMA_P6_X",
              "enum": [
                "EXTREMA_P6_X"
              ]
            },
            {
              "description": "EXTREMA_P6_Y",
              "enum": [
                "EXTREMA_P6_Y"
              ]
            },
            {
              "description": "EXTREMA_P7_X",
              "enum": [
                "EXTREMA_P7_X"
              ]
            },
            {
              "description": "EXTREMA_P7_Y",
              "enum": [
                "EXTREMA_P7_Y"
              ]
            },
            {
              "description": "EXTREMA_P8_X",
              "enum": [
                "EXTREMA_P8_X"
              ]
            },
            {
              "description": "EXTREMA_P8_Y",
              "enum": [
                "EXTREMA_P8_Y"
              ]
            },
            {
              "description": "MIN_FERET_ANGLE",
              "enum": [
                "MIN_FERET_ANGLE"
              ]
            },
            {
              "description": "MAX_FERET_ANGLE",
              "enum": [
                "MAX_FERET_ANGLE"
              ]
            },
            {
              "description": "STAT_FERET_DIAM_MIN",
              "enum": [
                "STAT_FERET_DIAM_MIN"
              ]
            },
            {
              "description": "STAT_FERET_DIAM_MAX",
              "enum": [
                "STAT_FERET_DIAM_MAX"
              ]
            },
            {
              "description": "STAT_FERET_DIAM_MEAN",
              "enum": [
                "STAT_FERET_DIAM_MEAN"
              ]
            },
            {
              "description": "STAT_FERET_DIAM_MEDIAN",
              "enum": [
                "STAT_FERET_DIAM_MEDIAN"
              ]
            },
            {
              "description": "STAT_FERET_DIAM_STDDEV",
              "enum": [
                "STAT_FERET_DIAM_STDDEV"
              ]
            },
            {
              "description": "STAT_FERET_DIAM_MODE",
              "enum": [
                "STAT_FERET_DIAM_MODE"
              ]
            },
            {
              "description": "STAT_MARTIN_DIAM_MIN",
              "enum": [
                "STAT_MARTIN_DIAM_MIN"
              ]
            },
            {
              "description": "STAT_MARTIN_DIAM_MAX",
              "enum": [
                "STAT_MARTIN_DIAM_MAX"
              ]
            },
            {
              "description": "STAT_MARTIN_DIAM_MEAN",
              "enum": [
                "STAT_MARTIN_DIAM_MEAN"
              ]
            },
            {
              "description": "STAT_MARTIN_DIAM_MEDIAN",
              "enum": [
                "STAT_MARTIN_DIAM_MEDIAN"
              ]
            },
            {
              "description": "STAT_MARTIN_DIAM_STDDEV",
              "enum": [
                "STAT_MARTIN_DIAM_STDDEV"
              ]
            },
            {
              "description": "STAT_MARTIN_DIAM_MODE",
              "enum": [
                "STAT_MARTIN_DIAM_MODE"
              ]
            },
            {
              "description": "STAT_NASSENSTEIN_DIAM_MIN",
              "enum": [
                "STAT_NASSENSTEIN_DIAM_MIN"
              ]
            },
            {
              "description": "STAT_NASSENSTEIN_DIAM_MAX",
              "enum": [
                "STAT_NASSENSTEIN_DIAM_MAX"
              ]
            },
            {
              "description": "STAT_NASSENSTEIN_DIAM_MEAN",
              "enum": [
                "STAT_NASSENSTEIN_DIAM_MEAN"
              ]
            },
            {
              "description": "STAT_NASSENSTEIN_DIAM_MEDIAN",
              "enum": [
                "STAT_NASSENSTEIN_DIAM_MEDIAN"
              ]
            },
            {
              "description": "STAT_NASSENSTEIN_DIAM_STDDEV",
              "enum": [
                "STAT_NASSENSTEIN_DIAM_STDDEV"
              ]
            },
            {
              "description": "STAT_NASSENSTEIN_DIAM_MODE",
              "enum": [
                "STAT_NASSENSTEIN_DIAM_MODE"
              ]
            },
            {
              "description": "EULER_NUMBER",
              "enum": [
                "EULER_NUMBER"
              ]
            },
            {
              "description": "POLYGONALITY_AVE",
              "enum": [
                "POLYGONALITY_AVE"
              ]
            },
            {
              "description": "HEXAGONALITY_AVE",
              "enum": [
                "HEXAGONALITY_AVE"
              ]
            },
            {
              "description": "HEXAGONALITY_STDDEV",
              "enum": [
                "HEXAGONALITY_STDDEV"
              ]
            },
            {
              "description": "DIAMETER_MIN_ENCLOSING_CIRCLE",
              "enum": [
                "DIAMETER_MIN_ENCLOSING_CIRCLE"
              ]
            },
            {
              "description": "DIAMETER_CIRCUMSCRIBING_CIRCLE",
              "enum": [
                "DIAMETER_CIRCUMSCRIBING_CIRCLE"
              ]
            },
            {
              "description": "DIAMETER_INSCRIBING_CIRCLE",
              "enum": [
                "DIAMETER_INSCRIBING_CIRCLE"
              ]
            },
            {
              "description": "GEODETIC_LENGTH",
              "enum": [
                "GEODETIC_LENGTH"
              ]
            },
            {
              "description": "THICKNESS",
              "enum": [
                "THICKNESS"
              ]
            },
            {
              "description": "GLRLM_SRE",
              "enum": [
                "GLRLM_SRE"
              ]
            },
            {
              "description": "GLRLM_LRE",
              "enum": [
                "GLRLM_LRE"
              ]
            },
            {
              "description": "GLRLM_GLN",
              "enum": [
                "GLRLM_GLN"
              ]
            },
            {
              "description": "GLRLM_GLNN",
              "enum": [
                "GLRLM_GLNN"
              ]
            },
            {
              "description": "GLRLM_RLN",
              "enum": [
                "GLRLM_RLN"
              ]
            },
            {
              "description": "GLRLM_RLNN",
              "enum": [
                "GLRLM_RLNN"
              ]
            },
            {
              "description": "GLRLM_RP",
              "enum": [
                "GLRLM_RP"
              ]
            },
            {
              "description": "GLRLM_GLV",
              "enum": [
                "GLRLM_GLV"
              ]
            },
            {
              "description": "GLRLM_RV",
              "enum": [
                "GLRLM_RV"
              ]
            },
            {
              "description": "GLRLM_RE",
              "enum": [
                "GLRLM_RE"
              ]
            },
            {
              "description": "GLRLM_LGLRE",
              "enum": [
                "GLRLM_LGLRE"
              ]
            },
            {
              "description": "GLRLM_HGLRE",
              "enum": [
                "GLRLM_HGLRE"
              ]
            },
            {
              "description": "GLRLM_SRLGLE",
              "enum": [
                "GLRLM_SRLGLE"
              ]
            },
            {
              "description": "GLRLM_SRHGLE",
              "enum": [
                "GLRLM_SRHGLE"
              ]
            },
            {
              "description": "GLRLM_LRLGLE",
              "enum": [
                "GLRLM_LRLGLE"
              ]
            },
            {
              "description": "GLRLM_LRHGLE",
              "enum": [
                "GLRLM_LRHGLE"
              ]
            },
            {
              "description": "GLSZM_SAE",
              "enum": [
                "GLSZM_SAE"
              ]
            },
            {
              "description": "GLSZM_LAE",
              "enum": [
                "GLSZM_LAE"
              ]
            },
            {
              "description": "GLSZM_GLN",
              "enum": [
                "GLSZM_GLN"
              ]
            },
            {
              "description": "GLSZM_GLNN",
              "enum": [
                "GLSZM_GLNN"
              ]
            },
            {
              "description": "GLSZM_SZN",
              "enum": [
                "GLSZM_SZN"
              ]
            },
            {
              "description": "GLSZM_SZNN",
              "enum": [
                "GLSZM_SZNN"
              ]
            },
            {
              "description": "GLSZM_ZP",
              "enum": [
                "GLSZM_ZP"
              ]
            },
            {
              "description": "GLSZM_GLV",
              "enum": [
                "GLSZM_GLV"
              ]
            },
            {
              "description": "GLSZM_ZV",
              "enum": [
                "GLSZM_ZV"
              ]
            },
            {
              "description": "GLSZM_ZE",
              "enum": [
                "GLSZM_ZE"
              ]
            },
            {
              "description": "GLSZM_LGLZE",
              "enum": [
                "GLSZM_LGLZE"
              ]
            },
            {
              "description": "GLSZM_HGLZE",
              "enum": [
                "GLSZM_HGLZE"
              ]
            },
            {
              "description": "GLSZM_SALGLE",
              "enum": [
                "GLSZM_SALGLE"
              ]
            },
            {
              "description": "GLSZM_SAHGLE",
              "enum": [
                "GLSZM_SAHGLE"
              ]
            },
            {
              "description": "GLSZM_LALGLE",
              "enum": [
                "GLSZM_LALGLE"
              ]
            },
            {
              "description": "GLSZM_LAHGLE",
              "enum": [
                "GLSZM_LAHGLE"
              ]
            },
            {
              "description": "GLDM_SDE",
              "enum": [
                "GLDM_SDE"
              ]
            },
            {
              "description": "GLDM_LDE",
              "enum": [
                "GLDM_LDE"
              ]
            },
            {
              "description": "GLDM_GLN",
              "enum": [
                "GLDM_GLN"
              ]
            },
            {
              "description": "GLDM_DN",
              "enum": [
                "GLDM_DN"
              ]
            },
            {
              "description": "GLDM_DNN",
              "enum": [
                "GLDM_DNN"
              ]
            },
            {
              "description": "GLDM_GLV",
              "enum": [
                "GLDM_GLV"
              ]
            },
            {
              "description": "GLDM_DV",
              "enum": [
                "GLDM_DV"
              ]
            },
            {
              "description": "GLDM_DE",
              "enum": [
                "GLDM_DE"
              ]
            },
            {
              "description": "GLDM_LGLE",
              "enum": [
                "GLDM_LGLE"
              ]
            },
            {
              "description": "GLDM_HGLE",
              "enum": [
                "GLDM_HGLE"
              ]
            },
            {
              "description": "GLDM_SDLGLE",
              "enum": [
                "GLDM_SDLGLE"
              ]
            },
            {
              "description": "GLDM_SDHGLE",
              "enum": [
                "GLDM_SDHGLE"
              ]
            },
            {
              "description": "GLDM_LDLGLE",
              "enum": [
                "GLDM_LDLGLE"
              ]
            },
            {
              "description": "GLDM_LDHGLE",
              "enum": [
                "GLDM_LDHGLE"
              ]
            },
            {
              "description": "NGTDM_COARSENESS",
              "enum": [
                "NGTDM_COARSENESS"
              ]
            },
            {
              "description": "NGTDM_CONTRAST",
              "enum": [
                "NGTDM_CONTRAST"
              ]
            },
            {
              "description": "NGTDM_BUSYNESS",
              "enum": [
                "NGTDM_BUSYNESS"
              ]
            },
            {
              "description": "NGTDM_COMPLEXITY",
              "enum": [
                "NGTDM_COMPLEXITY"
              ]
            },
            {
              "description": "NGTDM_STRENGTH",
              "enum": [
                "NGTDM_STRENGTH"
              ]
            },
            {
              "description": "HU_M1",
              "enum": [
                "HU_M1"
              ]
            },
            {
              "description": "HU_M2",
              "enum": [
                "HU_M2"
              ]
            },
            {
              "description": "HU_M3",
              "enum": [
                "HU_M3"
              ]
            },
            {
              "description": "HU_M4",
              "enum": [
                "HU_M4"
              ]
            },
            {
              "description": "HU_M5",
              "enum": [
                "HU_M5"
              ]
            },
            {
              "description": "HU_M6",
              "enum": [
                "HU_M6"
              ]
            },
            {
              "description": "HU_M7",
              "enum": [
                "HU_M7"
              ]
            },
            {
              "description": "ZERNIKE2D",
              "enum": [
                "ZERNIKE2D"
              ]
            },
            {
              "description": "Gabor",
              "enum": [
                "GABOR"
              ]
            }
          ],
          "default": "ALL_INTENSITY",
          "widget": "select",
          "minItems": 1,
          "uniqueItems": "true"
        },
        "required": "true"
      },
      "required": true
    },
    {
      "name": "outputType",
      "description": "outputType : singlecsv for saving values in one csv file, separatecsv to save values for each image in a separate csv file, arrowipc and parquet for saving in Apache Arrow IPC and Parquet file formats respectively",
      "type": "enum",
      "options": {
        "values": [
          "singlecsv",
          "separatecsv",
          "arrowipc",
          "parquet"
        ]
      },
      "required": true
    },
    {
      "name": "embeddedpixelsize",
      "description": "Use embedded pixel size",
      "type": "boolean",
      "options": null,
      "required": false
    },
    {
      "name": "pixelsPerCentimeter",
      "description": "Enter the number of pixels per centimeter",
      "type": "number",
      "options": null,
      "required": false
    }
  ],
  "outputs": [
    {
      "name": "outDir",
      "description": "Output collection",
      "type": "csvCollection",
      "options": null,
      "required": true
    }
  ],
  "ui": [
    {
      "key": "inputs.segDir",
      "title": "Label image collection",
      "description": "Labeled image collection"
    },
    {
      "key": "inputs.intDir",
      "title": "Intensity image collection",
      "description": "Intensity image collection"
    },
    {
      "key": "inputs.filePattern",
      "title": "File pattern",
      "description": "To match intensity and segmented image files",
	  "default": ".*"
    },
    {
      "key": "inputs.pixelDistance",
      "title": "Pixel Distance",
      "description": "Pixel distance to calculate the neighbors touching cells",
	  "default": "5"
    },
    {
      "key": "inputs.features",
      "title": "Features",
      "description": "Select features"
    },
    {
      "key": "inputs.outputType",
      "title": "Output file type",
      "description": "Save csv file separately for each image or one csv file for all images. Alternatively, output can be written as an Arrow IPC or Parquet file"
    },
    {
      "key": "inputs.embeddedpixelsize",
      "title": "Embedded pixel size",
      "description": "Use embedded pixel size",
      "default": true
    },
    {
      "key": "inputs.pixelsPerCentimeter",
      "title": "Pixels per centimeter",
      "description": "Enter the number of pixels per centimeter",
      "condition": "model.inputs.embeddedpixelsize==false"
    }
  ],
  "validators": null
}