config.json

{
  "imgFolder": "data",
  "segmentation": "segmentation3D",
  "3D": 1,
  "render": 0,
  "marching_cubes": 0,
  "small_RAM_mode": 0,
  "segmentation3D": {
    "smoothing": 1,
    "core_threshold": 3.0,
    "core_vessel_1": 1,
    "gamma_1": 5,
    "sigma_1": 1.0,
    "cutoff_method_1": "threshold_triangle",
    "core_vessel_2": 1,
    "gamma_2": 5,
    "sigma_2": 2.0,
    "cutoff_method_2": "threshold_li",
    "post_closing": 5,
    "post_thinning": 1,
    "thin": 1,
    "min_thickness": 1,
    "post_cleaning": 100
  },
  "segmentation2D": {
    "denoise": 1,
    "back_sub": 1,
    "frangi": {
      "sigma_min": 0.01,
      "sigma_max": 1,
      "sigma_steps": 0.01,
      "alpha": 0.5,
      "beta": 0.5,
      "gamma": 100
    },
    "threshold": {
      "ball_radius": 1,
      "artifact_size": 5,
      "block_size": 17,
      "value": 0
    }
  },
  "franginet": {
    "model": "models/guided/model.ckpt",
    "mode": "guided",
    "normalization": false,
    "average": true,
    "mode_img": "OneCubeBatch",
    "gpus": "0",
    "batch_size": "1"
  },
  "graphAnalysis": {
    "pixel_dimensions": "2.0,1.015625,1.015625",
    "pruning_scale": 1.5,
    "length_limit": 3,
    "diameter_scale": 2,
    "branching_threshold": 0.25,
    "extended_output": 1,
    "experimental_flag": 0,
    "remove_border_end_pts": 1,
    "remove_end_pts_from_small_filaments": 1,
    "seg_interpolate": 0,
    "spline_degree": 3,
    "cut_neighbor_brpt_segs": 1
  },
  "rendering": {
    "save_raw": 1,
    "save_glb": 1,
    "background_transparent": 1,
    "render_device": "GPU",
    "render_distance": 500000,
    "image_resolution_x": 1920,
    "image_resolution_y": 1080,
    "image_compression": 0.0
  },
  "rendering_binary": {
    "mesh_r": 0.528,
    "mesh_g": 0.002,
    "mesh_b": 0.0013,
    "mesh_roughness": 0.65,
    "mesh_metallic": 0.0,
    "mesh_sheen": 0.0,
    "mesh_specular": 0.0
  },
  "rendering_skeleton": {
    "mesh_r": 0.01,
    "mesh_g": 0.06,
    "mesh_b": 0.528,
    "mesh_roughness": 0.408,
    "mesh_metallic": 0.267,
    "mesh_sheen": 0.0,
    "mesh_specular": 0.308
  }
}