merquaco.pixel_classification.generate_dapi_mask

merquaco.pixel_classification.generate_dapi_mask(dapi_image_path: str | Path, ilastik_program_path: str | Path, pixel_classification_model_path: str | Path, object_classification_model_path: str | Path, high_res_dapi_image_path: str | Path = '') → ndarray

Generate binary DAPI mask from compressde DAPI image or high-res DAPI output image

Parameters:

  • dapi_image_path (str or Path) – Path to compressed DAPI image

  • ilastik_program_path (str or Path) – Path to ilastik program

  • pixel_classification_model_path (str or Path) – Path to pixel classification model

  • object_classification_model_path (str or Path) – Path to object classification model

  • high_res_dapi_image (str or Path, optional) – Path to high-resolution DAPI image. Default is ‘’.

Returns:

dapi_mask – DAPI mask array

Return type:

np.ndarray

Raises:

ValueError – If neither high_res_dapi_image_path or dapi_image_path exist