config.yaml.example

# Example configuration file for organoid analysis pipeline
# This file can be used with --config flag, or parameters can be overridden via command-line

# Markers to analyze
# Each marker is a dictionary with:
#   - name: Marker name (for output column naming)
#   - channel: Channel index (0-indexed) in the image
#   - location: Either "cell" or "membrane" - where to measure the marker
markers:
  - name: "Occludin_RFP"
    channel: 0
    location: "membrane"
  - name: "Claudin_FITC"
    channel: 1
    location: "membrane"
  - name: "Occludin_RFP"
    channel: 0
    location: "cell"

# Output directories
# Results will be saved to: results_folder / experiment_id / {well_id}_per_cell_results.csv
results_folder: "results"

# Cellpose label cache directories (created under image directory if relative)
# Two directories for cell (cytoplasm) and nuclei labels; same layout as BP notebook
cellpose_cell_labels: "cellpose_cell_labels"
cellpose_nuclei_labels: "cellpose_nuclei_labels"

# Image downsampling factor
# Use 2 or 4 for downsampling in XY (None for no downsampling)
# This reduces processing time but may affect accuracy
slicing_factor_xy: null

# Cellpose segmentation parameters
cellpose_params:
  # Cell diameter in pixels (XY)
  diameter: 20
  
  # Flow threshold (lower = more cells detected)
  flow_threshold: 0.4
  
  # Cell probability threshold (lower = more cells detected)
  cellprob_threshold: 0.0
  
  # Minimum cell size in pixels
  min_size: 15
  
  # Cellpose model type (e.g., "cyto3", "cyto2", "nuclei")
  model_type: "cyto3"

# GPU and logging options
# Set to false to skip GPU availability check (useful for HPC environments)
check_gpu: true

# Enable Cellpose logger setup (produces verbose output)
enable_logger_setup: false

# Optional: Input directory path (not needed if using --image argument)
# directory_path: null