lazyslide.pl.tissue

tissue(wsi, tissue_id=None, tissue_key='tissues', title=None, show_contours=True, show_id=True, mark_origin=True, scalebar=True, in_bounds=True, zoom=None, img_bytes_limit=2000000000.0, display_aware=True, oversample=1.5, target_dpi=None, ax=None, ncols=4, wspace=0.5, hspace=0.5, return_figure=False)

Display the tissue image.

Parameters:

wsiWSIData

The whole-slide image object.

tissue_idint or ‘all’, default: None

The tissue id (piece) to extract.

tissue_keystr, default: “tissue”

The tissue key.

titlestr or array of str, default: None

The title of the plot.

show_contoursbool, default: True

Show the tissue contours.

mark_originbool, default: True

Show the origin.

show_idbool, default: True

Show the tissue id.

scalebarbool, default: True

Show the scalebar.

in_boundsbool, default: True

Show the tissue in bounds.

zoom(xmin, xmax, ymin, ymax), default: None

A zoom view for the current viewport. If in range [0, 1], will be interpreted as a fraction of the image size. If > 1, will be interpreted as the absolute size in pixels.

img_bytes_limitint, default: 2e9

A safety ceiling on the bytes of the image to read. The level is primarily chosen from the displayed size (see display_aware).

display_awarebool, default: True

Choose the image pyramid level from the displayed figure size at render time, avoiding reading a high-resolution image into a small figure.

oversamplefloat, default: 1.5

Read this many times more pixels than the axes occupies, for crispness.

target_dpifloat, optional

Override the figure DPI when sizing the image. Set to the export DPI (e.g. target_dpi=300 for savefig(dpi=300)) for high-DPI output.

axmatplotlib.axes.Axes, default: None

The axes to plot on.

Examples

>>> import lazyslide as zs
>>> wsi = zs.datasets.gtex_artery()
>>> zs.pl.tissue(wsi, tissue_id="all")