btrack_cell_config.json

{
  "TrackerConfig":
    {
      "MotionModel":
        {
          "name": "cell_motion",
          "dt": 1.0,
          "measurements": 3,
          "states": 6,
          "accuracy": 7.5,
          "prob_not_assign": 0.1,
          "max_lost": 5,
          "A": {
            "matrix": [1,0,0,1,0,0,
                       0,1,0,0,1,0,
                       0,0,1,0,0,1,
                       0,0,0,1,0,0,
                       0,0,0,0,1,0,
                       0,0,0,0,0,1]
          },
          "H": {
            "matrix": [1,0,0,0,0,0,
                       0,1,0,0,0,0,
                       0,0,1,0,0,0]
          },
          "P": {
            "sigma": 150.0,
            "matrix": [0.1,0,0,0,0,0,
                       0,0.1,0,0,0,0,
                       0,0,0.1,0,0,0,
                       0,0,0,1,0,0,
                       0,0,0,0,1,0,
                       0,0,0,0,0,1]
          },
          "G": {
            "sigma": 15.0,
            "matrix": [0.5,0.5,0.5,1,1,1]

          },
          "R": {
            "sigma": 5.0,
            "matrix": [1,0,0,
                       0,1,0,
                       0,0,1]
          }
        },
      "ObjectModel":
        {},
      "HypothesisModel":
        {
          "name": "cell_hypothesis",
          "hypotheses": ["P_FP", "P_init", "P_term", "P_link", "P_branch", "P_dead"],
          "lambda_time": 5.0,
          "lambda_dist": 3.0,
          "lambda_link": 10.0,
          "lambda_branch": 50.0,
          "eta": 1e-10,
          "theta_dist": 20.0,
          "theta_time": 5.0,
          "dist_thresh": 40,
          "time_thresh": 2,
          "apop_thresh": 5,
          "segmentation_miss_rate": 0.1,
          "apoptosis_rate": 0.001,
          "relax": true
        }
    }
}