sparrow.pl.plot_labels

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sparrow.pl.plot_labels#

sparrow.pl.plot_labels(sdata, labels_layer='segmentation_mask', z_slice=None, crd=None, to_coordinate_system='global', output=None, **kwargs)#

Plot a labels layer (masks) based on given parameters.

Parameters:

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

  • labels_layer (str (default: 'segmentation_mask')) – Labels layer to be plotted. Default is “segmentation_mask”.

  • z_slice (float | None (default: None)) – The z_slice to visualize in case of 3D (c,z,y,x) labels.

  • crd (tuple[int, int, int, int] | None (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 (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 sparrow.pl.plot_shapes() function.

Return type:

None

See also

sparrow.pl.plot_shapes, sparrow.pl.plot

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