napari_prism.pl.preview_tma_segmentation#
- napari_prism.pl.preview_tma_segmentation(sdata, image_name, segmentation_channel, color_order, channel_merge_method='max', optional_nuclear_channel=None, reference_coordinate_system='global', auto_contrast=True)#
Displays a visual preview of the input data given to Cellpose for segmentation. This is useful for checking if the provided markers provide a good representation for nuclei, cell membranes, cytoplasms, etc.
- Parameters:
sdata (
SpatialData) – The SpatialData object containing the image.image_name (
str) – The name of the image to display.segmentation_channel (
str|list[str]) – The channel(s) to use for segmentation.color_order (
list[str]) – The order of colors for the RGB image.channel_merge_method (
Literal['max','mean','min','sum'] (default:'max')) – Method to merge channels. Options are “max”, “mean”, “min”, or “sum”.optional_nuclear_channel (
Optional[str] (default:None)) – Optional nuclear channel for segmentation.reference_coordinate_system (
str(default:'global')) – Coordinate system to use for rendering.auto_contrast (
bool(default:True)) – Whether to apply auto contrast to the image.
- Return type: