sparrow.pl.plot_image

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sparrow.pl.plot_image#

sparrow.pl.plot_image(sdata, img_layer='raw_image', channel=None, z_slice=None, crd=None, to_coordinate_system='global', output=None, **kwargs)#

Plot an image based on given parameters.

Parameters:

  • sdata (SpatialData) – Data containing spatial information for plotting.

  • img_layer (str (default: 'raw_image')) – Image layer to be plotted. Default is “raw_image”.

  • channel (Union[int, str, Iterable[int | str], None] (default: None)) – Channel(s) to be displayed from the image.

  • z_slice (Optional[float] (default: None)) – The z_slice to visualize in case of 3D (c,z,y,x) image.

  • crd (Optional[tuple[int, int, int, int]] (default: None)) – The coordinates for the region of interest in the format (xmin, xmax, ymin, ymax). If None, the entire image is considered, by default None.

  • to_coordinate_system (str (default: 'global')) – Coordinate system to plot.

  • output (Union[str, Path, None] (default: None)) – Path to save the plot. If not provided, plot will be displayed.

  • **kwargs (dict[str, Any]) – Additional arguments to be passed to the sp.pl.plot_shapes function.

Return type:

None

See also

sparrow.pl.plot_shapes

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