4pi.yaml

Params:
  format: .mat                  # .mat, .tif, .czi
  stage_mov_dir: reverse         # normal, reverse: normal direction is where stage move towards the object when taking a z-stack bead data
  pixel_size:                   # unit: micron
    x: 0.129
    y: 0.129
  roi:
    roi_size: [21,21]           # vector of 2 or 3 element, roi size in [y, x] or [z, y, x]
    gauss_sigma: [2,2]          # blur kernel size, corresponding to dimensions defined in roi_size
    max_kernel: [3,3]           # maximum filter kernel size, corresponding to dimensions defined in roi_size

  fpi:                           # parameters only for 4pi systems
    modulation_period: 0.26      # unit: micron
  insitu:               
    frame_range: []     # set the frames to be loaded, only for .tif format

  option:   
    imaging:                       
      emission_wavelength: 0.6    # unit: micron
      RI: 
        imm: 1.406
        med: 1.406
        cov: 1.516
      NA: 1.35
    fpi:
      link_zernikecoeff: true
      phase_dm: [2,0,-2]           # unit: radian
      sampleheight: 2
      var_sampleheight: false
      phase_delay_dir: descend     # phase delay between four channels, 'descend' or 'ascend'
    insitu:
      zernike_index: [5]           # for initial pupil, a vector of any size, if [], search for optimal zernike term
      zernike_coeff: [-0.5]         # for initial pupil, value corresponding to the zernike index 
      partition_size: [11,400]     # number of z segments, maximum number of emitter per segment
      z_range: 1.2                 # unit: micron, z range of insitu psf model