ovrlpy.cell_integrity_from_masks
================================

.. py:function:: ovrlpy.cell_integrity_from_masks(ovrlp, segmentation_masks, cell_ids)

   Collect VSI per cell using segmentation masks.

   Get the signal strength and VSI values for each cell using their segmentation masks.
   The segmentation masks will be rasterized and all pixels corresponding to a cell mapped to
   extract VSI and signal strength values.
   This requires the :py:attr:`ovrlpy.Ovrlp.origin` and :py:attr:`ovrlpy.Ovrlp.gridsize`
   to be set (which is done automatically if processing the transcripts with
   :py:func:`ovrlpy.Ovrlp.process_coordinates`).

   :param ovrlp:
   :type ovrlp: ovrlpy.Ovrlp
   :param segmentation_masks: List of segmentation masks as `shapely` Geometries (e.g., :py:class:`shapely.Polygon`).
   :type segmentation_masks: collections.abc.Sequence[shapely.geometry.base.BaseGeometry]
   :param cell_ids: List of the cell IDs or labels. Must be in the same order as the segmentation masks.
   :type cell_ids: collections.abc.Sequence

   :returns: DataFrame containing all pixels and their corresponding signal strength and VSI
             values per cell.
   :rtype: polars.DataFrame