dataset.yml

# Must be in the same ordering as actual channel
# 'INST' mean each int value denotes different inst mask
# 'TYPE' mean each int value denotes different semantic class

# assuming each dataset only has 1 img_dir, where 
# each img may have one or many annotations

gland:
  img_dir: 'dataset/MTL_sample/original_data/Gland/Images/'
  img_ext: '.png' # can also be a list of extension
  msk_dir: 'dataset/MTL_sample/original_data/Gland/Tissue/' # only extract patches within tissue area
  msk_ext: '.png'
  split_info: 'dataset/MTL_sample/original_data/info_gland.csv'
  nr_splits: 3
  ann_info: # Ann_Type : Ann_Dir, Ann_Ext
    Gland:
      ann_dir: 'dataset/MTL_sample/original_data/Gland/Labels/'
      ann_ext: '.mat'
      channel_code: ['INST', 'TYPE']
  viz_info:
    line_width: 12
    inst_colour: [255, 255, 0, 0]
    type_colour: {
      0: [0, 0, 0, 0], 
      1: [255, 255, 0, 0], 
      2: [177, 52, 235, 0]
    }
    type_names:
      ['nolabel', 'gland', 'surface-epi']

lumen:
  img_dir: 'dataset/MTL_sample/original_data/Lumen/Images/'
  img_ext: '.png' # can also be a list of extension
  msk_dir: 'dataset/MTL_sample/original_data/Gland/Tissue/' # only extract patches within tissue area
  msk_ext: '.png'
  split_info: 'dataset/MTL_sample/original_data/info_lumen.csv'
  nr_splits: 3
  ann_info: # Ann_Type : Ann_Dir, Ann_Ext
    Lumen:
      ann_dir: 'dataset/MTL_sample/original_data/Lumen/Labels/'
      ann_ext: '.mat'
      channel_code: ['INST']
  viz_info:
    line_width: 12
    inst_colour: [255, 0, 255, 0]
    type_colour: {
      0: [0, 0, 0, 0], 
      1: [131, 235, 52, 0], 
    }
    type_names:
      ['nolabel', 'lumen']

nuclei:
  img_dir: 'dataset/MTL_sample/original_data/Nuclei/Images/'
  img_ext: '.png' # can also be a list of extension
  msk_dir: 'dataset/MTL_sample/original_data/Nuclei/Tissue/' # only extract patches within tissue area
  msk_ext: '.png'
  split_info: 'dataset/MTL_sample/original_data/info_nuclei.csv'
  nr_splits: 3
  ann_info: 
    Nuclei:
      ann_dir: 'dataset/MTL_sample/original_data/Nuclei/Labels/'
      ann_ext: '.mat'
      channel_code: ['INST', 'TYPE']
  viz_info:
    line_width: 3
    inst_colour: [0, 255, 0, 1]
    type_colour: {
      0: [0, 0, 0, 1],
      1: [0, 0, 255, 1],
      2: [0, 255, 0, 1],
      3: [255, 0, 255, 1],
      4: [176, 244, 230, 1],
      5: [0, 191, 255, 1],
      6: [255, 165, 0, 1]
    }
    type_names:
      ['nolabel', 'neutrophil', 'epithelial', 'lymphocyte', 'plasma', 'eosinophil', 'connective']

tissue-type:
  img_dir: "dataset/MTL_sample/original_data/Tissue-Type"
  img_ext: ".png"
  split_info: 'dataset/MTL_sample/original_data/info_tissue-type.csv'
  nr_splits: 3
  type_names:
    ["background", "abnormal_epi", "normal_epi", "inflammatory", "muscle", "stroma", "debris", "mucous", "adipose"]