TP.yaml

Params:
  format: .mat                 # .mat, .tif, .czi
  pixel_size:                   # unit: micron
    x: 0.11
    y: 0.11
  roi:
    roi_size: [31,31]           # vector of 2 or 3 element, roi size in [y, x] or [z, y, x]
    gauss_sigma: [12,12]          # blur kernel size, corresponding to dimensions defined in roi_size
    max_kernel: [13,13]           # maximum filter kernel size, corresponding to dimensions defined in roi_size
  
  insitu:               
    frame_range: []     # set the frames to be loaded, only for .tif format

  option:   
    imaging:                       
      emission_wavelength: 0.67    # unit: micron
      RI: 
        imm: 1.518
        med: 1.33
        cov: 1.518
      NA: 1.45
    insitu:
      zernike_index: [12]           # for initial pupil, a vector of any size, if [], search for optimal zernike term
      zernike_coeff: [-2]         # for initial pupil, value corresponding to the zernike index 
      partition_size: [31,100]     # number of z segments, maximum number of emitter per segment
      z_range: 4.0                 # unit: micron, z range of insitu psf model