scallops.segmentation.util.cyto_channel_summary

scallops.segmentation.util.cyto_channel_summary(image)

Takes minimum intensity over cycles, followed by mean intensity over channels if both are present. If more than one channel and only one cycle (t) is present, takes median over channels. Note that if your image contains DAPI and SBS channels, you need to select non-DAPI channels first:

>>> image.isel(
...     c=np.delete(np.arange(image.sizes["c"]), nuclei_channel)
... )

Parameters:

image (DataArray) – Image with dimensions (t, c, z, y, x)

Returns:

The cell mask

Return type:

DataArray