merquaco.pixel_classification.generate_transcripts_mask

merquaco.pixel_classification.generate_transcripts_mask(transcripts_image_path: str | Path, ilastik_program_path: str | Path, pixel_classification_model_path: str | Path, object_classification_model_path: str | Path, transcripts: DataFrame = None) → ndarray

Return transcripts mask, either from image path (if exists), or by generating from transcripts table

Parameters:

• transcripts_image_path (str or Path) – Path to trancsripts 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

• transcripts (pd.DataFrame) – Transcripts table

Returns:

transcripts_mask – Transcripts mask array

Return type:

np.ndarray

Raises:

ValueError – If transcripts_image_path does not exist and transcripts is none