merquaco.pixel_classification.generate_ventricle_mask

merquaco.pixel_classification.generate_ventricle_mask(ventricle_genes_image_path: str | Path, dapi_mask_path: str | Path, transcripts_mask_path: str | Path, ilastik_program_path: str | Path, pixel_classification_model_path: str | Path, object_classification_model_path: str | Path, transcripts: DataFrame, ventricle_genes: list = ['Crb2', 'Glis3Inhbb', 'Naaa', 'Cd24a', 'Dsg2', 'Hdc', 'Shroom3', 'Vit', 'Rgs12', 'Trp73']) → ndarray

Creates and saves binary ventricle marker genes mask from transcripts dataframe and ventricle gene list

Parameters:

  • ventricle_genes_image_path (str or Path) – Path to ventricle genes image

  • dapi_mask_path (str or Path) – Path to binary DAPI mask

  • transcripts_mask_path (str or Path) – Path to binary transcripts mask

  • 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 dataframe

  • ventricle_genes (list, optional) –

    List of ventricle marker genes. Default is [“Crb2”, “Glis3”, “Inhbb”,

    ”Naaa”, “Cd24a”, “Dsg2”, “Hdc”, “Shroom3”, “Vit”, “Rgs12”, “Trp73”]

Returns:

ventricle_mask – Ventricle mask

Return type:

np.ndarray