ovrlpy.cell_integrity_from_transcripts

ovrlpy.cell_integrity_from_transcripts(ovrlp, *, cell_id='cell_id', unassigned=-1)

Collect VSI per cell.

Get the signal strength and VSI values for each cell using the assignment of transcripts to cells. This requires a column in the ovrlpy.Ovrlp.transcripts DataFrame that maps transcripts to cell identifiers.

Parameters:

  • ovrlp (Ovrlp)

  • cell_id (str, optional) – Name of the column in the ovrlp.transcripts DataFame that stores the cell identifier.

  • unassigned – Value in the cell identifier column that indicates that a transcript is not assigned to any cell.

Returns:

DataFrame containing all pixels and their corresponding signal strength and VSI values per cell.

Return type:

polars.DataFrame