lazyslide.pl.annotations

annotations(wsi, key, color=None, label=None, show_image=True, mark_origin=True, scalebar=True, in_bounds=True, img_bytes_limit=2000000000.0, tissue_key='tissues', tissue_id=None, zoom=None, fill=True, linewidth=0.5, palette=None, alpha=0.9, legend_kws=None, legend=True, title=None, ncols=4, wspace=0.5, hspace=0.5, ax=None, backend=None)

Display the annotation .

Parameters:

wsiWSIData

The whole-slide image object.

keystr

The annotation key.

colorstr, optional

The column or feature name to use for coloring the annotations.

labelstr, optional

The column or feature name to use for labeling the annotations.

show_imagebool, default: True

Whether to display the underlying tissue image.

mark_originbool, default: True

Whether to mark the origin on the plot.

scalebarbool, default: True

Whether to show a scalebar.

in_boundsbool, default: True

Whether to restrict annotations to the image bounds.

img_bytes_limitint, default: 2e9

The maximum number of bytes for the image.

tissue_keystr, default: “tissue”

The key for tissue segmentation.

tissue_idint or ‘all’, optional

The tissue id(s) to display annotations for.

zoomtuple, optional

(xmin, xmax, ymin, ymax) for zooming into a region.

fillbool, default: True

Whether to fill the annotation polygons.

linewidthfloat, default: 0.5

The line width of the annotation polygons.

palettestr, optional

The color palette to use.

alphafloat, default: 0.5

The transparency of the annotation polygons.

legend_kwsdict, optional

Additional keyword arguments for the legend.

legendbool, default: True

Whether to display a legend.

titlestr or list of str, optional

The title(s) for the plot(s).

ncolsint, default: 4

Number of columns for subplot arrangement.

wspacefloat, default: 0.5

Width space between subplots.

hspacefloat, default: 0.5

Height space between subplots.

axmatplotlib.axes.Axes, optional

The axes to plot on.

backendstr, {‘matplotlib’, ‘datashader’}

The backend to use for plotting. Will automatically use datashader when there are too many polygons.

Returns:

None or matplotlib.figure.Figure

The figure if multiple axes are created and return_figure is True, otherwise None.

Examples

>>> import lazyslide as zs
>>> wsi = zs.datasets.sample()
>>> zs.pl.annotations(wsi, key="annotations", tissue_id="all")