merquaco.pixel_classification.classify_pixels

merquaco.pixel_classification.classify_pixels(transcripts_mask_input: ndarray | str | Path, detachment_mask_input: ndarray | str | Path, ventricle_mask_input: ndarray | str | Path = None, damage_mask_input: ndarray | str | Path = None, full_classification_out_file: str | Path = None) → ndarray

Combine all masks and classify each pixel as either damage, tissue, detachment, ventricle, or off-tissue

Parameters:

  • transcripts_mask_input (np.ndarray, str or Path) – Transcripts mask

  • detachment_mask_input (np.ndarray, str or Path) – Detachment mask

  • ventricle_mask_input (np.ndarray, str or Path) – Ventricle mask

  • damage_mask_input (np.ndarray, str or Path) – Damage mask

  • full_classification_out_file (str or Path) – Path at which to save full pixel classification

Returns:

pixel_classification – Full pixel classification array

Return type:

np.ndarray

Raises:

ValueError – If only one of ventricle_mask_input and damage_mask_input are not provided