example.config

// Input/output Parameters
params.input_path = "input"
params.output_path = "output"

// Workflow control parameters
params.fill_gaps			= true		// Set to false to skip MindaGap Gap Filling
params.deduplicate			= true		// Set to false to skip MindaGap transcript deduplication
params.do_zip				= true		// Set to false to skip making ImageJ ROIs (faster)
params.segmentation_tool	= "mesmer"	// Use Mesmer (mesmer) or Cellpose (cellpose) for segmentation

// MindaGap transcript deduplication parameters
params.tile_size		= 2144	// Tile size (distance between gridlines)
params.window_size		= 30	// Window arround gridlines to search for duplicates
params.max_freq			= 400  // Maximum transcript count to calculate X/Y shifts (better to discard very common genes)
params.min_mode			= 10	// Minumum occurances of ~XYZ_shift to consider it valid

// Cellpose Segmentation Parameters
params.model_name = "cyto"
params.probability_threshold = 1
params.cell_diameter = 70

// Mesmer Segmentation Parameters
params.maxima_threshold          = 0.075	// Decrease for over segmentation. Default(0.075)
params.maxima_smooth             = 0		// Smoothing radius for maxima. Default(0)
params.interior_threshold        = 0.2		// Decrease to identify more cells. Default(0.2)
params.interior_smooth           = 2		// Smoothing radius for cell detection. Default(2)
params.small_objects_threshold   = 15		// Minimum object size. Default(15)
params.fill_holes_threshold      = 15		// Max Size for hole filling. Default(15)
params.radius                    = 2		// Undocuented in Mesmer. Default(2)