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WIPP-annotations2masks-plugin

This plugin converts image annotations extracted from a JSON file generated by WIPP using web deep zoom toolkit (WDZT) and creates a mask image based on unique color, shape, or text

Command line interface parameters

Implemented in class: MaskFromAnnotations, method: CMDlaunch

  • @param inputJSONFileFolder - input folder with JSON files
  • @param uniqueType - integer defining whether the masks are created based on label (1), color (2) or shape (3)
  • @param combineAllUnique - boolean flag whether to create one mask with all unique types of color/label/shape (value = true) or one mask per of color/label/shape unique type (value = false)

Note: if the spatial annotations for two different colors/labels/shapes overlap spatially then combineAllUnique=true leads to a pixel assignment based on the order of annotations

  • @param inputRawFileFolder - input folder with raw TIFF files

  • @param outFileFolder - output folder for the generated masks

  • @return boolean depending on the success

Note: The method assumes that the JSON files and RawImageFiles in their appropriate folders have matching names except for their suffixes.