demo_config.yaml

##################################################################################################
# This file defines the settings for the demo cell segmentation and tracking analysis pipeline.
##################################################################################################

---

# STEP 1: Cell segmentation related settings.
segmentation_settings:
  # Set to True if we want to run segmentation. If False, segmentation will be skipped.
  run_cellpose: True
  # The path of the directory that holds the input raw image files to be segmented.
  raw_data_dir: "./demo_data"
  # The path of the directory that masks will be written to.
  output_data_dir: "./demo_data/masks"
  # The file pattern to match against (e.g. all files in raw_data_dir matching "*.tif" will be included).
  file_pattern: "*.tif"
  # The cellpose model to use.
  cellpose_model: "cyto3"
  # An estimated average cell diameter, measured in pixels.
  cell_diameter_est: 140
  # Other settings.
  flow_threshold: 2.19
  min_size_mask: 40
  cell_prob_threshold: -1
  cell_body_channel: 0
  cell_nucleus_channel: 2

# STEP 2: Cell tracking related settings.
tracking_settings:
  # Set to True if we want to run tracking. If False, tracking will be skipped.
  run_trackastra: True
  # The path of the directory that holds the input raw image files to be tracked.
  raw_data_dir: "./demo_data/masks"
  # The path of the directory that tracks will be written to.
  output_data_dir: "./demo_data/tracks"
  # Whether to use a GFP filter.
  use_gfp_filter: True
  # Which model to use.
  trackastra_model: "greedy_nodiv"
  # The maximum distance in pixels the cells are expected to move. Keep low if mostly stationary.
  max_track_distance: 50

...