Aida3Dpreprocessing/workflow.example.json at main · 3DxN/Aida3Dpreprocessing · GitHub

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{
  "imaris_xml": "rawdata/012523_303_1_63X_stitchable.xml",
  "output_dir": "data",
  "hne": {
    "hne_res_level": 1,
    "nuclear_channel": 3,
    "cyto_channel": 4,
    "fixed_z_position": 11,
    "z_anisotropy": 2.0
  },
  "segmentation": {
    "out_dir": "data/CellposeSegmentations",
    "cellpose_model": "cyto",
    "cellpose_diameter": 30.0,
    "batch_size": 2,
    "anisotropy": 0.0,
    "use_gpu": false,
    "gpu_device": "0"
  },
  "analysis": {
    "classes": [
      "control",
      "treated"
    ],
    "segmentation_path": [
      "data/CellposeSegmentations",
      "data/CellposeSegmentations"
    ],
    "raw_image_path": [
      "data/raw",
      "data/raw"
    ],
    "xml_files_path": [
      "data/raw/012523_303_1_63X_stitchable.xml",
      "data/raw/012523_303_1_63X_stitchable.xml"
    ],
    "gh2ax_threshold": [
      1300,
      1300
    ],
    "cd8_threshold": [
      750,
      1000
    ],
    "gh2ax_pixel_count_threshold": 100,
    "radii": [
      32,
      48,
      64,
      128
    ],
    "n_pseudo_classes": 5,
    "cd8_dapi_box_overlap_threshold": 0.2
  },
  "plot": {
    "plot_output_format": "pdf",
    "classes": [
      "control",
      "treated"
    ],
    "num_pseudo_classes": 5
  }
}