scallops.segmentation.cellpose.segment_cells_cellpose

scallops.segmentation.cellpose.segment_cells_cellpose(image, nuclei_channel=0, cyto_channel=None, diameter=None, chunks=None, **kwargs)

Segment cells using cellpose.

Parameters:

  • image (DataArray) – Input image with dimensions (t, c, z, y, x).

  • nuclei_channel (int) – Index of nuclei channel (typically DAPI).

  • cyto_channel (int | list[int] | None) – Index or list of indices for cyto channel(s). If not provided, all channels except for the nuclei channel are used.

  • diameter (float | None) – The diameter parameter for cellpose.

  • chunks (tuple[int, int] | None) – Chunk size to perform segmentation using overlapping chunks.

  • kwargs (Any) – Additional arguments to pass to model.eval.

Returns:

Cell labels.

Return type:

ndarray | Array