h5sc

Functions to work with scPortrait’s standardized single-cell data format.

scportrait.tools.h5sc.get_image_with_cellid(adata, cell_id: list[int] | int, select_channel: int | list[int] | None = None) → ndarray

Get single cell images from the cells with the provided cell IDs. Images are returned in the order of the cell IDs.

Parameters:

• adata – An AnnData object with obsm[“single_cell_images”] containing a memory-backed array of the single-cell images.

• cell_id – The cell ID of the cell to retrieve the image for.

• select_channel – The channel to select from the image. If None, all channels are returned.

Returns:

The image(s) of the cell with the passed Cell IDs.