bubcount/params.py

from dataclasses import dataclass
from typing import Optional


@dataclass
class AnalysisParameters:
    # Microscope
    scale_um_per_pixel: float = 0.0825
    sample_volume_per_frame_uL: float = 0.00089

    # Size filtering
    min_diameter_um: float = 0.5
    max_diameter_um: float = 50.0

    # Histogram
    bin_size_um: float = 0.165

    # Gas dose calculation
    injection_volume_uL: float = 100.0

    # Cellpose
    pretrained_model: str = "cpsam"
    gpu: bool = True
    diameter: Optional[float] = None
    flow_threshold: float = 0.4
    cellprob_threshold: float = 0.0

    # Shape QC
    min_circularity: float = 0.5
    max_aspect_ratio: float = 2.0