config.yaml

convert-input:
  sep: "_"
  channels: 1
  z_slice: null
  lazy: false
  subtract_background: null
  subtract_func: "mean"
  rescale: null
  in_memory: false
  loc: "data"
  chunks: "infer"
  compression: null
  overwrite: false

motion-correction:
  working_directory: null
  loc: ""
  max_shifts: [ 50, 50 ]
  niter_rig: 3
  splits_rig: 14
  num_splits_to_process_rig: null
  strides: [ 48, 48 ]
  overlaps: [ 24, 24 ]
  pw_rigid: false
  splits_els: 14
  num_splits_to_process_els: null
  upsample_factor_grid: 4
  max_deviation_rigid: 3
  nonneg_movie: true
  gsig_filt: [ 20, 20 ]
  loc_out: "mc"
  chunks: null
  compression: null
  overwrite: false

train-denoiser:
  validation_files: null
  loc: null
  batch_size: 16
  batch_size_val: 4
  epochs: 10
  patience: 3
  min_delta: 0.001
  input_size: [ 256, 256 ]
  train_rotation: [ 1, 2, 3 ]
  train_flip: [ 0, 1 ]
  pre_post_frames: 5
  gap_frames: 0
  normalize: global
  padding: null
  max_per_file: 8
  max_per_val_file: 3
  learning_rate: 0.001
  decay_rate: 0.99
  decay_steps: 250
  n_stacks: 2
  kernel: 32
  batch_normalize: false
  loss: annealed_loss
  pretrained_weights: null
  save_path: null
  use_cpu: true
  in_memory: false

denoise:
  batch_size: 8
  input_size: [ 256, 256 ]
  pre_post_frame: 5
  gap_frames: 0
  z_select: null
  overlap: 10
  padding: edge
  normalize: global
  loc: "mc/ast"
  in_memory: false
  logging_level: 20  # INFO level
  out_loc: "dn/ast"
  dtype: "same"
  chunk_size: null
  rescale: true

subtract-delta:
  output_path: null
  loc_in: ""
  method: "background"
  processing_chunks: "infer"
  save_chunks: "infer"
  overwrite_first_frame: true
  lazy: true
  loc_out: "dff"
  compression: null
  overwrite: false

detect-events:
  area_threshold: 10
  comb_type: '&'
  debug: false
  exclude_border: 3
  fill_holes: true
  fill_holes_first: true
  loc: dff/ch0
  holes_connectivity: 1
  holes_depth: 1
  logging_level: 20
  min_size: 10
  object_connectivity: 1
  objects_depth: 1
  output_path: infer
  overwrite: false
  remove_objects: true
  smooth_radius: 2
  smooth_sigma: 3
  spatial_min_ratio: 1
  spatial_z_depth: 1
  split_events: false
  temporal_prominence: 10
  temporal_rel_height: 0.9
  temporal_width: 3
  temporal_wlen: 60
  use_smoothing: false
  use_spatial: true
  use_temporal: true

detect-events:
  loc: null
  threshold: null
  exclude_border: 0
  use_smoothing: true
  smooth_radius: 2
  smooth_sigma: 2
  use_spatial: true
  spatial_min_ratio: 1
  spatial_z_depth: 1
  use_temporal: true
  temporal_prominence: 10
  temporal_width: 3
  temporal_rel_height: 0.9
  temporal_wlen: 60
  temporal_plateau_size: null
  comb_type: "&"
  fill_holes: true
  area_threshold: 10
  holes_connectivity: 1
  holes_depth: 1
  remove_objects: true
  min_size: 20
  object_connectivity: 1
  objects_depth: 1
  fill_holes_first: true
  lazy: true
  adjust_for_noise: false
  subset: null
  split_events: false
  debug: false
  parallel: true
  output_path: null
  overwrite: false