merquaco.pixel_classification.create_ventricle_genes_image

merquaco.pixel_classification.create_ventricle_genes_image(ventricle_genes_image_path: str | Path, dapi_mask_path: str | Path, transcripts_mask_path: str | Path, transcripts: DataFrame, ventricle_genes: list = ['Crb2', 'Glis3', 'Inhbb', 'Naaa', 'Cd24a', 'Dsg2', 'Hdc', 'Shroom3', 'Vit', 'Rgs12', 'Trp73'], threshold: int = 2) → ndarray

Creates and saves image of ventricle genes superimposed on DAPI image

Parameters:

• ventricle_genes_image_path (str or Path) – Path at which to save the ventricle genes image

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

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

• transcripts (pd.DataFrame) – Transcripts table

• ventricle_genes (list, optional) –

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

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

• threshold (int, optional) – Threshold to binarize ventricle gene density image. Default is 2.

Returns:

dapi_ventricles – Ventricle genes image overlayed on DAPI mask

Return type:

np.ndarray